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Sample records for barrier-to-autointegration factor proteome

  1. NCBI nr-aa BLAST: CBRC-EEUR-01-0952 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-0952 ref|NP_003851.1| barrier to autointegration factor 1 [Homo sapien...s] ref|NP_892033.1| barrier to autointegration factor 1 [Bos taurus] ref|XP_854776.1| PREDICTED: similar to barrier to autointegratio...n factor 1 [Canis familiaris] ref|XP_001111817.1| PREDICTED: similar to barrier to autointegration...: similar to barrier to autointegration factor 1 isoform 2 [Macaca mulatta] ref|XP_001111884.1| PREDICTED: s...imilar to barrier to autointegration factor 1 isoform 3 [Macaca mulatta] ref|XP_001111924.1| PREDICTED: similar to barrier to autoint

  2. The SET complex acts as a barrier to autointegration of HIV-1.

    Directory of Open Access Journals (Sweden)

    Nan Yan

    2009-03-01

    Full Text Available Retroviruses and retrotransposons are vulnerable to a suicidal pathway known as autointegration, which occurs when the 3'-ends of the reverse transcript are activated by integrase and then attack sites within the viral DNA. Retroelements have diverse strategies for suppressing autointegration, but how HIV-1 protects itself from autointegration is not well-understood. Here we show that knocking down any of the components of the SET complex, an endoplasmic reticulum-associated complex that contains 3 DNases (the base excision repair endonuclease APE1, 5'-3' exonuclease TREX1, and endonuclease NM23-H1, inhibits HIV-1 and HIV-2/SIV, but not MLV or ASV, infection. Inhibition occurs at a step in the viral life cycle after reverse transcription but before chromosomal integration. Antibodies to SET complex proteins capture HIV-1 DNA in the cytoplasm, suggesting a direct interaction between the SET complex and the HIV preintegration complex. Cloning of HIV integration sites in cells with knocked down SET complex components revealed an increase in autointegration, which was verified using a novel semi-quantitative nested PCR assay to detect autointegrants. When SET complex proteins are knocked down, autointegration increases 2-3-fold and chromosomal integration correspondingly decreases approximately 3-fold. Therefore, the SET complex facilitates HIV-1 infection by preventing suicidal autointegration.

  3. InterProScan Result: FS907382 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available FS907382 FS907382_1_ORF2 1C0441A9D0DDEE80 SUPERFAMILY SSF47798 Barrier-to-autointegration... factor, BAF 1.3e-44 T IPR004122 Barrier- to-autointegration factor, BAF Molecular Function: DNA binding (GO:0003677) ...

  4. NCBI nr-aa BLAST: CBRC-EEUR-01-0952 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-0952 pdb|1CI4|A Chain A, The Crystal Structure Of Human Barrier-To-Autointegration... Factor (Baf) pdb|1CI4|B Chain B, The Crystal Structure Of Human Barrier-To-Autointegration Factor (Baf) 1CI4 3e-07 52% ...

  5. InterProScan Result: FS735919 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available FS735919 FS735919_4_ORF2 1C0441A9D0DDEE80 SUPERFAMILY SSF47798 Barrier-to-autointegration... factor, BAF 1.3e-44 T IPR004122 Barrier- to-autointegration factor, BAF Molecular Function: DNA binding (GO:0003677) ...

  6. NCBI nr-aa BLAST: CBRC-EEUR-01-0952 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-0952 ref|XP_935572.1| PREDICTED: similar to barrier to autointegration... factor 1 [Homo sapiens] ref|XP_946635.1| PREDICTED: similar to barrier to autointegration factor 1 [Homo sapiens] XP_935572.1 8e-07 69% ...

  7. TrSDB: a proteome database of transcription factors

    Science.gov (United States)

    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. PMID:14681387

  8. Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan O.; Prášil, Ilja T.; Renaut, Jenny

    2018-01-01

    HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic

  9. 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...... proteomics data. Two characteristics of legumes are the high seed protein level and the nitrogen fixing symbiosis. Thus, the majority of the proteomics studies in Lotus have been performed on seed/pod and nodule/root tissues in order to create proteome reference maps and to enable comparative analyses within...... Lotus tissues or toward similar tissues from other legume species. More recently, N-glycan structures and compositions have been determined from mature Lotus seeds using glycomics and glycoproteomics, and finally, phosphoproteomics has been employed...

  10. Proteome Stability as a Key Factor of Genome Integrity

    Directory of Open Access Journals (Sweden)

    Sentiljana Gumeni

    2017-09-01

    Full Text Available DNA damage is constantly produced by both endogenous and exogenous factors; DNA lesions then trigger the so-called DNA damaged response (DDR. This is a highly synchronized pathway that involves recognition, signaling and repair of the damage. Failure to eliminate DNA lesions is associated with genome instability, a driving force in tumorigenesis. Proteins carry out the vast majority of cellular functions and thus proteome quality control (PQC is critical for the maintenance of cellular functionality. PQC is assured by the proteostasis network (PN, which under conditions of proteome instability address the triage decision of protein fold, hold, or degrade. Key components of the PN are the protein synthesis modules, the molecular chaperones and the two main degradation machineries, namely the autophagy-lysosome and the ubiquitin-proteasome pathways; also, part of the PN are a number of stress-responsive cellular sensors including (among others heat shock factor 1 (Hsf1 and the nuclear factor erythroid 2-related factor 2 (Nrf2. Nevertheless, the lifestyle- and/or ageing-associated gradual accumulation of stressors results in increasingly damaged and unstable proteome due to accumulation of misfolded proteins and/or protein aggregates. This outcome may then increase genomic instability due to reduced fidelity in processes like DNA replication or repair leading to various age-related diseases including cancer. Herein, we review the role of proteostatic machineries in nuclear genome integrity and stability, as well as on DDR responses.

  11. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus.

    Science.gov (United States)

    Ray, Ann; Kinch, Lisa N; de Souza Santos, Marcela; Grishin, Nick V; Orth, Kim; Salomon, Dor

    2016-07-26

    Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells. The pan-genome of the genus Vibrio is a potential reservoir of unidentified toxins that can provide insight into how members of this genus have successfully risen as emerging pathogens worldwide. We focused on Vibrio proteolyticus, a marine bacterium that was previously implicated in virulence toward marine animals, and characterized its interaction with eukaryotic cells. We found that this bacterium causes actin cytoskeleton rearrangements and leads to cell death. Using a

  12. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

    Full Text Available Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.

  13. Proteomic identification of CIB1 as a potential diagnostic factor in ...

    Indian Academy of Sciences (India)

    Proteomic identification of CIB1 as a potential diagnostic factor in hepatocellular carcinoma. Tong Junrong Zhou Huancheng H E Feng Gao Yi Yang Xiaoqin Luo Zhengmao Zhang Hong Zeng Jianying Wang Yin Huang Yuanhang Zhang Jianlin Sun Longhua He Guolin. Articles Volume 36 Issue 4 September 2011 pp 659- ...

  14. A mammalian transcription factor-specific peptide repository for targeted proteomics.

    Science.gov (United States)

    Simicevic, Jovan; Moniatte, Marc; Hamelin, Romain; Ahrné, Erik; Deplancke, Bart

    2015-02-01

    Site-specific transcription factors (TFs) play an essential role in mammalian development and function as they are vital for the majority of cellular processes. Despite their biological importance, TF proteomic data is scarce in the literature, likely due to difficulties in detecting peptides as the abundance of TFs in cells tends to be low. In recent years, significant improvements in MS-based technologies in terms of sensitivity and specificity have increased the interest in developing quantitative methodologies specifically targeting relatively lowly abundant proteins such as TFs in mammalian models. Such efforts would be greatly aided by the availability of TF peptide-specific information as such data would not only enable improvements in speed and accuracy of protein identifications, but also ameliorate cross-comparisons of quantitative proteomics data and allow for a more efficient development of targeted proteomics assays. However, to date, no comprehensive TF proteotypic peptide database has been developed. To address this evident lack of TF peptide data in public repositories, we are generating a comprehensive, experimentally derived TF proteotypic peptide spectral library dataset based on in vitro protein expression. Our library currently contains peptide information for 89 TFs and this number is set to increase in the near future. All MS data have been deposited in the ProteomeXchange with identifier PXD001212 (http://proteomecentral.proteomexchange.org/dataset/PXD001212). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Identification of factors that function in Drosophila salivary gland cell death during development using proteomics

    Science.gov (United States)

    McPhee, C K; Balgley, B M; Nelson, C; Hill, J H; Batlevi, Y; Fang, X; Lee, C S; Baehrecke, E H

    2013-01-01

    Proteasome inhibitors induce cell death and are used in cancer therapy, but little is known about the relationship between proteasome impairment and cell death under normal physiological conditions. Here, we investigate the relationship between proteasome function and larval salivary gland cell death during development in Drosophila. Drosophila larval salivary gland cells undergo synchronized programmed cell death requiring both caspases and autophagy (Atg) genes during development. Here, we show that ubiquitin proteasome system (UPS) function is reduced during normal salivary gland cell death, and that ectopic proteasome impairment in salivary gland cells leads to early DNA fragmentation and salivary gland condensation in vivo. Shotgun proteomic analyses of purified dying salivary glands identified the UPS as the top category of proteins enriched, suggesting a possible compensatory induction of these factors to maintain proteolysis during cell death. We compared the proteome following ectopic proteasome impairment to the proteome during developmental cell death in salivary gland cells. Proteins that were enriched in both populations of cells were screened for their function in salivary gland degradation using RNAi knockdown. We identified several factors, including trol, a novel gene CG11880, and the cop9 signalsome component cop9 signalsome 6, as required for Drosophila larval salivary gland degradation. PMID:22935612

  16. Identification of factors that function in Drosophila salivary gland cell death during development using proteomics.

    Science.gov (United States)

    McPhee, C K; Balgley, B M; Nelson, C; Hill, J H; Batlevi, Y; Fang, X; Lee, C S; Baehrecke, E H

    2013-02-01

    Proteasome inhibitors induce cell death and are used in cancer therapy, but little is known about the relationship between proteasome impairment and cell death under normal physiological conditions. Here, we investigate the relationship between proteasome function and larval salivary gland cell death during development in Drosophila. Drosophila larval salivary gland cells undergo synchronized programmed cell death requiring both caspases and autophagy (Atg) genes during development. Here, we show that ubiquitin proteasome system (UPS) function is reduced during normal salivary gland cell death, and that ectopic proteasome impairment in salivary gland cells leads to early DNA fragmentation and salivary gland condensation in vivo. Shotgun proteomic analyses of purified dying salivary glands identified the UPS as the top category of proteins enriched, suggesting a possible compensatory induction of these factors to maintain proteolysis during cell death. We compared the proteome following ectopic proteasome impairment to the proteome during developmental cell death in salivary gland cells. Proteins that were enriched in both populations of cells were screened for their function in salivary gland degradation using RNAi knockdown. We identified several factors, including trol, a novel gene CG11880, and the cop9 signalsome component cop9 signalsome 6, as required for Drosophila larval salivary gland degradation.

  17. Proteome study of secreted prostatic factors affecting osteoblastic activity

    DEFF Research Database (Denmark)

    Andersen, H; Jensen, Ole Nørregaard; Eriksen, E F

    2003-01-01

    ranging from 5 to 30 kDa were analysed by matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS). One of these spots was identified as cyclophilin A. We examined whether cyclophilin A alone or in combination with insulin-like growth factor-I (IGF-I) had any effects...... on the proliferation or differentiation of hBMS cells. Cyclophilin A at 1, 10, and 100 nM and cyclophilin A at 10 nM combined with 10 ng/ml IGF decreased the proliferation of hBMS cells up to 49+/-30, 38+/-29, 50+/-8 and 60+/-16%, respectively [mean (treated/control)+/-standard error of the means (SEM)] of control...

  18. Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways and transcription factors

    DEFF Research Database (Denmark)

    Deshmukh, Atul S; Murgia, Marta; Nagaraja, Nagarjuna

    2015-01-01

    Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging due to highly abundant contractile proteins that interfere with detection of regulatory proteins. Using a state-of-the art mass...... spectrometric (MS) workflow and a strategy to map identifications from the C2C12 cell line model to tissues, we identified a total of 10,218 proteins, including skeletal muscle specific transcription factors like myod1 and myogenin and circadian clock proteins. We obtain absolute abundances for proteins...

  19. Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes.

    Directory of Open Access Journals (Sweden)

    Yun-Jong Park

    Full Text Available Severe xerostomia (dry mouth compromises the quality of life in patients with Sjögren's syndrome or radiation therapy for head and neck cancer. A clinical management of xerostomia is often unsatisfactory as most interventions are palliative with limited efficacy. Following up our previous study demonstrating that mouse BM-MSCs are capable of differentiating into salivary epithelial cells in a co-culture system, we further explored the molecular basis that governs the MSC reprogramming by utilizing high-throughput iTRAQ-2D-LC-MS/MS-based proteomics. Our data revealed the novel induction of pancreas-specific transcription factor 1a (PTF1α, muscle, intestine and stomach expression-1 (MIST-1, and achaete-scute complex homolog 3 (ASCL3 in 7 day co-cultured MSCs but not in control MSCs. More importantly, a common notion of pancreatic-specific expression of PTF1 α was challenged for the first time by our verification of PTF1 α expression in the mouse salivary glands. Furthermore, a molecular network simulation of our selected putative MSC reprogramming factors demonstrated evidence for their perspective roles in salivary gland development. In conclusion, quantitative proteomics with extensive data analyses narrowed down a set of MSC reprograming factors potentially contributing to salivary gland regeneration. Identification of their differential/synergistic impact on MSC conversion warrants further investigation.

  20. Clinical proteomics

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Frederiksen, Hanne; Johannsen, Trine Holm

    2018-01-01

    )-platforms already implemented in many clinical laboratories for routine quantitation of small molecules (i.e. uHPLC coupled to triple-quadrupole MS). Progress in targeted proteomics of circulating insulin-like growth factor 1 (IGF-I) have provided valuable insights about tryptic peptides, transitions, internal......Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS...... standards and calibrants. The present challenge is to examine if targeted proteomics of IGF-I can truly measure up to the routine performance that must be expected from a clinical testing platform....

  1. 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 a...

  2. Proteomic Assessment of the Relevant Factors Affecting Pork Meat Quality Associated with Muscles in Duroc Pigs

    Directory of Open Access Journals (Sweden)

    Jin Hyoung Cho

    2016-11-01

    Full Text Available Meat quality is a complex trait influenced by many factors, including genetics, nutrition, feeding environment, animal handling, and their interactions. To elucidate relevant factors affecting pork quality associated with oxidative stress and muscle development, we analyzed protein expression in high quality longissimus dorsi muscles (HQLD and low quality longissimus dorsi muscles (LQLD from Duroc pigs by liquid chromatographytandem mass spectrometry (LC-MS/MS–based proteomic analysis. Between HQLD (n = 20 and LQLD (n = 20 Duroc pigs, 24 differentially expressed proteins were identified by LC-MS/MS. A total of 10 and 14 proteins were highly expressed in HQLD and LQLD, respectively. The 24 proteins have putative functions in the following seven categories: catalytic activity (31%, ATPase activity (19%, oxidoreductase activity (13%, cytoskeletal protein binding (13%, actin binding (12%, calcium ion binding (6%, and structural constituent of muscle (6%. Silver-stained image analysis revealed significant differential expression of lactate dehydrogenase A (LDHA between HQLD and LQLD Duroc pigs. LDHA was subjected to in vitro study of myogenesis under oxidative stress conditions and LDH activity assay to verification its role in oxidative stress. No significant difference of mRNA expression level of LDHA was found between normal and oxidative stress condition. However, LDH activity was significantly higher under oxidative stress condition than at normal condition using in vitro model of myogenesis. The highly expressed LDHA was positively correlated with LQLD. Moreover, LDHA activity increased by oxidative stress was reduced by antioxidant resveratrol. This paper emphasizes the importance of differential expression patterns of proteins and their interaction for the development of meat quality traits. Our proteome data provides valuable information on important factors which might aid in the regulation of muscle development and the improvement of

  3. Lamins, laminopathies and disease mechanisms: Possible role for ...

    Indian Academy of Sciences (India)

    Abbreviations used: ATR, ATM-and-Rad3-related; BAF, barrier-to-autointegration factor; Cdk1, cyclin-dependent kinase 1; CMT, Charcot-Marie-. Tooth disorder; DCM, dilated cardiomyopathy; EMD, Emery-Dreifuss muscular dystrophy; FPLD, familial partial lipodystrophy; HGPS,. Hutchinson-Gilford progeria syndrome; HP1α ...

  4. Discovery of porcine maternal factors related to nuclear reprogramming and early embryo development by proteomic analysis.

    Science.gov (United States)

    Zhao, Qi; Guo, Zheng; Piao, Shanhua; Wang, Chunsheng; An, Tiezhu

    2015-01-01

    Differentiated cell nuclei can be reprogrammed to a pluripotent state in several ways, including incubation with oocyte extracts, transfer into enucleated oocytes, and induced pluripotent stem cell technology. Nuclear transfer-mediated reprogramming has been proven to be the most efficient method. Maternal factors stored in oocytes have critical roles on nuclear reprogramming and early embryo development, but remain elusive. In this study, we showed most of porcine oocytes became nuclear matured at 33 h of IVM and the rate had no significant difference with oocytes at 42 h of IVM (p > 0.05). Moreover, the cleavage and blastocyst rates of SCNT and PA embryos derived from 42O were significantly higher than that of 33O (p embryo development with higher cleavage and blastocyst rates comparing to 42O (p development potential difference between 33O and 42O, 18 differentially expressed proteins were identified by proteomic analysis, and randomly selected proteins were confirmed by Western blot. Bioinformatic analysis of these proteins revealed that 33O highly synthesized proteins related to fertilization, and 42O was rich in nuclear reprogramming factors. These results present a unique insight into maternal factors related to nuclear reprogramming and early embryo development.

  5. Sigma-1 receptor mediates cocaine-induced transcriptional regulation by recruiting chromatin-remodeling factors at the nuclear envelope.

    Science.gov (United States)

    Tsai, Shang-Yi A; Chuang, Jian-Ying; Tsai, Meng-Shan; Wang, Xiao-Fei; Xi, Zheng-Xiong; Hung, Jan-Jong; Chang, Wen-Chang; Bonci, Antonello; Su, Tsung-Ping

    2015-11-24

    The sigma-1 receptor (Sig-1R) chaperone at the endoplasmic reticulum (ER) plays important roles in cellular regulation. Here we found a new function of Sig-1R, in that it translocates from the ER to the nuclear envelope (NE) to recruit chromatin-remodeling molecules and regulate the gene transcription thereof. Sig-1Rs mainly reside at the ER-mitochondrion interface. However, on stimulation by agonists such as cocaine, Sig-1Rs translocate from ER to the NE, where Sig-1Rs bind NE protein emerin and recruit chromatin-remodeling molecules, including lamin A/C, barrier-to-autointegration factor (BAF), and histone deacetylase (HDAC), to form a complex with the gene repressor specific protein 3 (Sp3). Knockdown of Sig-1Rs attenuates the complex formation. Cocaine was found to suppress the gene expression of monoamine oxidase B (MAOB) in the brain of wild-type but not Sig-1R knockout mouse. A single dose of cocaine (20 mg/kg) in rats suppresses the level of MAOB at nuclear accumbens without affecting the level of dopamine transporter. Daily injections of cocaine in rats caused behavioral sensitization. Withdrawal from cocaine in cocaine-sensitized rats induced an apparent time-dependent rebound of the MAOB protein level to about 200% over control on day 14 after withdrawal. Treatment of cocaine-withdrawn rats with the MAOB inhibitor deprenyl completely alleviated the behavioral sensitization to cocaine. Our results demonstrate a role of Sig-1R in transcriptional regulation and suggest cocaine may work through this newly discovered genomic action to achieve its addictive action. Results also suggest the MAOB inhibitor deprenyl as a therapeutic agent to block certain actions of cocaine during withdrawal.

  6. Proteomic analysis of Rac1 signaling regulation by guanine nucleotide exchange factors.

    Science.gov (United States)

    Marei, Hadir; Carpy, Alejandro; Macek, Boris; Malliri, Angeliki

    2016-08-02

    The small GTPase Rac1 is implicated in various cellular processes that are essential for normal cell function. Deregulation of Rac1 signaling has also been linked to a number of diseases, including cancer. The diversity of Rac1 functioning in cells is mainly attributed to its ability to bind to a multitude of downstream effectors following activation by Guanine nucleotide Exchange Factors (GEFs). Despite the identification of a large number of Rac1 binding partners, factors influencing downstream specificity are poorly defined, thus hindering the detailed understanding of both Rac1's normal and pathological functions. In a recent study, we demonstrated a role for 2 Rac-specific GEFs, Tiam1 and P-Rex1, in mediating Rac1 anti- versus pro-migratory effects, respectively. Importantly, via conducting a quantitative proteomic screen, we identified distinct changes in the Rac1 interactome following activation by either GEF, indicating that these opposing effects are mediated through GEF modulation of the Rac1 interactome. Here, we present the full list of identified Rac1 interactors together with functional annotation of the differentially regulated Rac1 binding partners. In light of this data, we also provide additional insights into known and novel signaling cascades that might account for the GEF-mediated Rac1-driven cellular effects.

  7. Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis.

    Science.gov (United States)

    Aviner, Ranen; Hofmann, Sarah; Elman, Tamar; Shenoy, Anjana; Geiger, Tamar; Elkon, Ran; Ehrlich, Marcelo; Elroy-Stein, Orna

    2017-06-02

    Precise regulation of mRNA translation is critical for proper cell division, but little is known about the factors that mediate it. To identify mRNA-binding proteins that regulate translation during mitosis, we analyzed the composition of polysomes from interphase and mitotic cells using unbiased quantitative mass-spectrometry (LC-MS/MS). We found that mitotic polysomes are enriched with a subset of proteins involved in RNA processing, including alternative splicing and RNA export. To demonstrate that these may indeed be regulators of translation, we focused on heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a test case and confirmed that it is recruited to elongating ribosomes during mitosis. Then, using a combination of pulsed SILAC, metabolic labeling and ribosome profiling, we showed that knockdown of hnRNP C affects both global and transcript-specific translation rates and found that hnRNP C is specifically important for translation of mRNAs that encode ribosomal proteins and translation factors. Taken together, our results demonstrate how proteomic analysis of polysomes can provide insight into translation regulation under various cellular conditions of interest and suggest that hnRNP C facilitates production of translation machinery components during mitosis to provide daughter cells with the ability to efficiently synthesize proteins as they enter G1 phase. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Barrier to auto integration factor becomes dephosphorylated during HSV-1 Infection and Can Act as a host defense by impairing viral DNA replication and gene expression.

    Science.gov (United States)

    Jamin, Augusta; Thunuguntla, Prasanth; Wicklund, April; Jones, Clinton; Wiebe, Matthew S

    2014-01-01

    BAF (Barrier to Autointegration Factor) is a highly conserved DNA binding protein that senses poxviral DNA in the cytoplasm and tightly binds to the viral genome to interfere with DNA replication and transcription. To counteract BAF, a poxviral-encoded protein kinase phosphorylates BAF, which renders BAF unable to bind DNA and allows efficient viral replication to occur. Herein, we examined how BAF phosphorylation is affected by herpes simplex virus type 1 (HSV-1) infection and tested the ability of BAF to interfere with HSV-1 productive infection. Interestingly, we found that BAF phosphorylation decreases markedly following HSV-1 infection. To determine whether dephosphorylated BAF impacts HSV-1 productive infection, we employed cell lines stably expressing a constitutively unphosphorylated form of BAF (BAF-MAAAQ) and cells overexpressing wild type (wt) BAF for comparison. Although HSV-1 production in cells overexpressing wtBAF was similar to that in cells expressing no additional BAF, viral growth was reduced approximately 80% in the presence of BAF-MAAAQ. Experiments were also performed to determine the mechanism of the antiviral activity of BAF with the following results. BAF-MAAAQ was localized to the nucleus, whereas wtBAF was dispersed throughout cells prior to infection. Following infection, wtBAF becomes dephosphorylated and relocalized to the nucleus. Additionally, BAF was associated with the HSV-1 genome during infection, with BAF-MAAAQ associated to a greater extent than wtBAF. Importantly, unphosphorylated BAF inhibited both viral DNA replication and gene expression. For example, expression of two regulatory proteins, ICP0 and VP16, were substantially reduced in cells expressing BAF-MAAAQ. However, other viral genes were not dramatically affected suggesting that expression of certain viral genes can be differentially regulated by unphosphorylated BAF. Collectively, these results suggest that BAF can act in a phosphorylation-regulated manner to impair

  9. Proteomic Alterations in Response to Hypoxia Inducible Factor 2α in Normoxic Neuroblastoma Cells.

    Science.gov (United States)

    Cimmino, Flora; Pezone, Lucia; Avitabile, Marianna; Persano, Luca; Vitale, Monica; Sassi, Mauro; Bresolin, Silvia; Serafin, Valentina; Zambrano, Nicola; Scaloni, Andrea; Basso, Giuseppe; Iolascon, Achille; Capasso, Mario

    2016-10-07

    Hypoxia inducible factor (HIF)-2α protein expression in solid tumors promotes stem-like phenotype in cancer stem cells and increases tumorigenic potential in nonstem cancer cells. Recently, we have shown that HIF-1/2α gene expression is correlated to neuroblastoma (NB) poor survival and to undifferentiated tumor state; HIF-2α protein was demonstrated to enhance aggressive features of the disease. In this study, we used proteomic experiments on NB cells to investigate HIF-2α downstream-regulated proteins or pathways with the aim of providing novel therapeutic targets or bad prognosis markers. We verified that pathways mostly altered by HIF-2α perturbation are involved in tumor progression. In particular, HIF-2α induces alteration of central metabolism and splicing control pathways. Simultaneously, WNT, RAS/MAPK, and PI3K/AKT activity or expression are affected and may impact the sensitivity and the intensity of HIF-2α-regulated pathways. Furthermore, genes coding the identified HIF-2α-related markers built a signature able to stratify NB patients with unfavorable outcome. Taken together, our findings underline the relevance of dissecting the downstream effects of a poor survival marker in developing targeted therapy and improving patient stratification. Future prospective studies are needed to translate the use of these data into the clinical practice.

  10. Identification of pathogenic factors potentially involved in Staphylococcus aureus keratitis using proteomics.

    Science.gov (United States)

    Khan, Shamila; Cole, Nerida; Hume, Emma B H; Garthwaite, Linda L; Nguyen-Khuong, Terry; Walsh, Bradley J; Willcox, Mark D P

    2016-10-01

    Staphylococcus is a leading cause of microbial keratitis, characterized by destruction of the cornea by bacterial exoproteins and host-associated factors. The aim of this study was to compare extracellular and cell-associated proteins produced by two different isolates of S. aureus, a virulent clinical isolate (Staph 38) and a laboratory strain (Staphylococcus aureus 8325-4) of weaker virulence in the mouse keratitis model. Proteins were analyzed using 2D polyacrylamide gel electrophoresis and identified by subsequent mass spectrometry. Activity of staphylococcal adhesins was assessed by allowing strains to bind to various proteins adsorbed onto polymethylmethacrylate squares. Thirteen proteins in the extracellular fraction and eight proteins in the cell-associated fractions after bacterial growth were produced in increased amounts in the clinical isolate Staph 38. Four of these proteins were S. aureus virulence factor adhesins, fibronectin binding protein A, staphopain, glyceraldehyde-3-phosphate dehydrogenase 2 and extracellular adherence protein. The clinical isolate Staph 38 adhered to a greater extent to all mammalian proteins tested, indicating the potential of the adhesins to be active on its surface. Other proteins with increased expression in Staph 38 included potential moonlighting proteins and proteins involved in transcription or translation. This is the first demonstration of the proteome of S. aureus isolates from keratitis. These results indicate that the virulent clinical isolate produces more potentially important virulence factors compared to the less virulent laboratory strain and these may be associated with the ability of a S. aureus strain to cause more severe keratitis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Electroconvulsive therapy modulates plasma pigment epithelium-derived factor in depression: a proteomics study.

    Science.gov (United States)

    Ryan, K M; Glaviano, A; O'Donovan, S M; Kolshus, E; Dunne, R; Kavanagh, A; Jelovac, A; Noone, M; Tucker, G M; Dunn, M J; McLoughlin, D M

    2017-03-28

    Electroconvulsive therapy (ECT) is the most effective treatment for severe depression, yet its mechanism of action is not fully understood. Peripheral blood proteomic analyses may offer insights into the molecular mechanisms of ECT. Patients with a major depressive episode were recruited as part of the EFFECT-Dep trial (enhancing the effectiveness of electroconvulsive therapy in severe depression; ISRCTN23577151) along with healthy controls. As a discovery-phase study, patient plasma pre-/post-ECT (n=30) was analyzed using 2-dimensional difference in gel electrophoresis and mass spectrometry. Identified proteins were selected for confirmation studies using immunodetection methods. Samples from a separate group of patients (pre-/post-ECT; n=57) and matched healthy controls (n=43) were then used to validate confirmed changes. Target protein mRNA levels were also assessed in rat brain and blood following electroconvulsive stimulation (ECS), the animal model of ECT. We found that ECT significantly altered 121 protein spots with 36 proteins identified by mass spectrometry. Confirmation studies identified a post-ECT increase (P<0.01) in the antiangiogenic and neuroprotective mediator pigment epithelium-derived factor (PEDF). Validation work showed an increase (P<0.001) in plasma PEDF in depressed patients compared with the controls that was further increased post-ECT (P=0.03). PEDF levels were not associated with mood scores. Chronic, but not acute, ECS increased PEDF mRNA in rat hippocampus (P=0.02) and dentate gyrus (P=0.03). This study identified alterations in blood levels of PEDF in depressed patients and further alterations following ECT, as well as in an animal model of ECT. These findings implicate PEDF in the biological response to ECT for depression.

  12. Energy Metabolism Disorder as a Contributing Factor of Rheumatoid Arthritis: A Comparative Proteomic and Metabolomic Study.

    Directory of Open Access Journals (Sweden)

    Xin Yu Yang

    Full Text Available To explore the pathogenesis of rheumatoid arthritis (RA, the different metabolites were screened in synovial fluid by metabolomics.Synovial fluid from 25 RA patients and 10 normal subjects were analyzed by GC/TOF MS analysis so as to give a broad overview of synovial fluid metabolites. The metabolic profiles of RA patients and normal subjects were compared using multivariate statistical analysis. Different proteins were verified by qPCR and western blot. Different metabolites were verified by colorimetric assay kit in 25 inactive RA patients, 25 active RA patients and 20 normal subjects. The influence of hypoxia-inducible factor (HIF-1α pathway on catabolism was detected by HIF-1α knockdown.A subset of 58 metabolites was identified, in which the concentrations of 7 metabolites related to energy metabolism were significantly different as shown by importance in the projection (VIP (VIP ≥ 1 and Student's t-test (p<0.05. In the 7 metabolites, the concentration of glucose was decreased, and the concentration of lactic acid was increased in the synovial fluid of RA patients than normal subjects verified by colorimetric assay Kit. Receiver operator characteristic (ROC analysis shows that the concentration of glucose and lactic acid in synovial fluid could be used as dependable biomarkers for the diagnosis of active RA, provided an AUC of 0.906 and 0.922. Sensitivity and specificity, which were determined by cut-off points, reached 84% and 96% in sensitivity and 95% and 85% in specificity, respectively. The verification of different proteins identified in our previous proteomic study shows that the enzymes of anaerobic catabolism were up-regulated (PFKP and LDHA, and the enzymes of aerobic oxidation and fatty acid oxidation were down-regulated (CS, DLST, PGD, ACSL4, ACADVL and HADHA in RA patients. The expression of HIF-1α and the enzymes of aerobic oxidation and fatty acid oxidation were decreased and the enzymes of anaerobic catabolism were

  13. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue.

    Science.gov (United States)

    Thompson, Seonaid M; Craven, Rachel A; Nirmalan, Niroshini J; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

    2013-04-01

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response

    DEFF Research Database (Denmark)

    Beli, Petra; Lukashchuk, Natalia; Wagner, Sebastian A

    2012-01-01

    The regulatory networks of the DNA damage response (DDR) encompass many proteins and posttranslational modifications. Here, we use mass spectrometry-based proteomics to analyze the systems-wide response to DNA damage by parallel quantification of the DDR-regulated phosphoproteome, acetylome......, and proteome. We show that phosphorylation-dependent signaling networks are regulated more strongly compared to acetylation. Among the phosphorylated proteins identified are many putative substrates of DNA-PK, ATM, and ATR kinases, but a majority of phosphorylated proteins do not share the ATM/ATR/DNA......-PK target consensus motif, suggesting an important role of downstream kinases in amplifying DDR signals. We show that the splicing-regulator phosphatase PPM1G is recruited to sites of DNA damage, while the splicing-associated protein THRAP3 is excluded from these regions. Moreover, THRAP3 depletion causes...

  15. Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics

    DEFF Research Database (Denmark)

    Akimov, Vyacheslav; Rigbolt, Kristoffer T G; Nielsen, Mogens M

    2011-01-01

    Protein ubiquitination is a dynamic reversible post-translational modification that plays a key role in the regulation of numerous cellular processes including signal transduction, endocytosis, cell cycle control, DNA repair and gene transcription. The conjugation of the small protein ubiquitin...... investigating ubiquitination on a proteomic scale, mainly due to the inherited complexity and heterogeneity of ubiquitination. We describe here a quantitative proteomics strategy based on the specificity of ubiquitin binding domains (UBDs) and Stable Isotope Labeling by Amino acids in Cell culture (SILAC...... as ubiquitination-dependent events in signaling pathways. In addition to a detailed seven time-point profile of EGFR ubiquitination over 30 minutes of ligand stimulation, our data determined prominent involvement of Lysine-63 ubiquitin branching in EGF signaling. Furthermore, we found two centrosomal proteins, PCM1...

  16. Proteomics analysis of human obesity reveals the epigenetic factor HDAC4 as a potential target for obesity.

    Directory of Open Access Journals (Sweden)

    Mohamed Abu-Farha

    Full Text Available Sedentary lifestyle and excessive energy intake are prominent contributors to obesity; a major risk factors for the development of insulin resistance, type 2 diabetes and cardiovascular diseases. Elucidating the molecular mechanisms underlying these chronic conditions is of relevant importance as it might lead to the identification of novel anti-obesity targets. The purpose of the current study is to investigate differentially expressed proteins between lean and obese subjects through a shot-gun quantitative proteomics approach using peripheral blood mononuclear cells (PBMCs extracts as well as potential modulation of those proteins by physical exercise. Using this approach, a total of 47 proteins showed at least 1.5 fold change between lean and obese subjects. In obese, the proteomic profiling before and after 3 months of physical exercise showed differential expression of 38 proteins. Thrombospondin 1 (TSP1 was among the proteins that were upregulated in obese subjects and then decreased by physical exercise. Conversely, the histone deacetylase 4 (HDAC4 was downregulated in obese subjects and then induced by physical exercise. The proteomic data was further validated by qRT-PCR, Western blot and immunohistochemistry in both PBMCs and adipose tissue. We also showed that HDAC4 levels correlated positively with maximum oxygen consumption (VO2 Max but negatively with body mass index, percent body fat, and the inflammatory chemokine RANTES. In functional assays, our data indicated that ectopic expression of HDAC4 significantly impaired TNF-α-dependent activation of NF-κB, establishing thus a link between HDAC4 and regulation of the immune system. Together, the expression pattern of HDAC4 in obese subjects before and after physical exercise, its correlation with various physical, clinical and metabolic parameters along with its inhibitory effect on NF-κB are suggestive of a protective role of HDAC4 against obesity. HDAC4 could therefore represent

  17. In vitro culture may be the major contributing factor for transgenic versus nontransgenic proteomic plant differences.

    Science.gov (United States)

    Fonseca, Cátia; Planchon, Sébastien; Serra, Tânia; Chander, Subhash; Saibo, Nelson J M; Renaut, Jenny; Oliveira, M Margarida; Batista, Rita

    2015-01-01

    Identification of differences between genetically modified plants and their original counterparts plays a central role in risk assessment strategy. Our main goal was to better understand the relevance of transgene presence, genetic, and epigenetic changes induced by transgene insertion, and in vitro culture in putative unintended differences between a transgenic and its comparator. Thus, we have used multiplex fluorescence 2DE coupled with MS to characterize the proteome of three different rice lines (Oryza sativa L. ssp. japonica cv. Nipponbare): a control conventional line (C), an Agrobacterium-transformed transgenic line (Ta) and a negative segregant (NSb). We observed that Ta and NSb appeared identical (with only one spot differentially abundant--fold difference ≥ 1.5), contrasting with the control (49 spots with fold difference ≥ 1.5, in both Ta and NSb vs. control). Given that in vitro culture was the only event in common between Ta and NSb, we hypothesize that in vitro culture stress was the most relevant condition contributing for the observed proteomic differences. MS protein identification support our hypothesis, indicating that Ta and NSb lines adjusted their metabolic pathways and altered the abundance of several stress related proteins in order to cope with in vitro culture. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Proteomic Analysis and Identification of Paracrine Factors in Mesenchymal Stem Cell-Conditioned Media under Hypoxia

    Directory of Open Access Journals (Sweden)

    Suk-Won Song

    2016-11-01

    Full Text Available Background/Aims: We previously showed that a hypoxic environment modulates the antiarrhythmic potential of mesenchymal stem cells. Methods: To investigate the mechanism by which secreted proteins contribute to the pathogenesis of antiarrhythmic potential in mesenchymal stem cells, we used two-dimensional electrophoresis combined with MALDI-TOF-MS to perform a proteomic analysis to compare the paracrine media produced by normoxic and hypoxic cells. Results: The proteomic analysis revealed that 66 protein spots out of a total of 231 matched spots indicated differential expression between the normoxic and hypoxic conditioned media of mesenchymal stem cells. Interestingly, two tropomyosin isoforms were dramatically increased in the hypoxic conditioned medium of mesenchymal stem cells. An increase in tropomyosin was confirmed using Western blot to analyze the conditioned media between normoxic and hypoxic cells. In a network analysis based on gene ontology (GO Molecular Function by GeneMANIA analysis, most of the identified proteins were found to be involved in the regulation of heart processes. Conclusion: Our results show that hypoxia up-regulates tropomyosin and other secreted proteins which suggests that tropomyosin may be involved in regulating proarrhythmic and antiarrhythmic functions.

  19. Comparative proteomic analysis of alfalfa revealed new salt and drought stress-related factors involved in seed germination.

    Science.gov (United States)

    Ma, Qiaoli; Kang, Junmei; Long, Ruicai; Zhang, Tiejun; Xiong, Junbo; Zhang, Kun; Wang, Tenghua; Yang, Qingchuan; Sun, Yan

    2017-07-01

    Salinity and drought are two major environmental factors that limit the growth and yield of many forage crops in semi-arid and arid regions. Alfalfa (Medicago sativa L.) is one of the most important forage crops in many countries. We aim to investigate the molecular mechanisms of alfalfa in response to salt and drought stresses in this study. Physiological and proteomic analyses were applied to examine the Zhongmu NO.3 alfalfa seed germination stage with 200 mM NaCl and 180 g·L -1 polyethylene glycol (PEG) treatments. The germination ability of the seed and the accumulation of osmotic solutes were quite different between the NaCl and PEG treatments. More than 800 protein spots were detected by proteomics technology on two-dimensional electrophoresis (2-DE) gels. The abundance of twenty-eight proteins were decreased or increased after salt and drought stress. Seventeen of these proteins were identified and classified into six functional categories through mass spectrometry (MS). The six groups involved in salt- and PEG-mediated stress included defense response, energy metabolism, protein synthesis and degradation, oxidative stress, carbohydrate metabolism-associated proteins, and unknown proteins. We discovered that some proteins related to carbohydrate metabolism and energy production increased in abundance under salt- and PEG-mediated drought stress. This demonstrates a common mechanism of energy consumption during abiotic stresses. Further study of these proteins with unknown function will provide insights into the molecular mechanisms of abiotic stress and the discovery of new candidate markers.

  20. Proteomics dataset

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

    2017-01-01

    The datasets presented in this article are related to the research articles entitled “Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies” (Bennike et al., 2015 [1]), and “Proteome Analysis of Rheumatoid Arthritis Gut Mucosa” (Bennike et al., 2017 [2])...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

  1. Plasmid vectors for proteomic analyses in Giardia: purification of virulence factors and analysis of the proteasome.

    Science.gov (United States)

    Jerlström-Hultqvist, Jon; Stadelmann, Britta; Birkestedt, Sandra; Hellman, Ulf; Svärd, Staffan G

    2012-07-01

    In recent years, proteomics has come of age with the development of efficient tools for purification, identification, and characterization of gene products predicted by genome projects. The intestinal protozoan Giardia intestinalis can be transfected, but there is only a limited set of vectors available, and most of them are not user friendly. This work delineates the construction of a suite of cassette-based expression vectors for use in Giardia. Expression is provided by the strong constitutive ornithine carbamoyltransferase (OCT) promoter, and tagging is possible in both N- and C-terminal configurations. Taken together, the vectors are capable of providing protein localization and production of recombinant proteins, followed by efficient purification by a novel affinity tag combination, streptavidin binding peptide-glutathione S-transferase (SBP-GST). The option of removing the tags from purified proteins was provided by the inclusion of a PreScission protease site. The efficiency and feasibility of producing and purifying endogenous recombinant Giardia proteins with the developed vectors was demonstrated by the purification of active recombinant arginine deiminase (ADI) and OCT from stably transfected trophozoites. Moreover, we describe the tagging, purification by StrepTactin affinity chromatography, and compositional analysis by mass spectrometry of the G. intestinalis 26S proteasome by employing the Strep II-FLAG-tandem affinity purification (SF-TAP) tag. This is the first report of efficient production and purification of recombinant proteins in and from Giardia, which will allow the study of specific parasite proteins and protein complexes.

  2. Shotgun proteomic analysis of plasma from dairy cattle suffering from footrot: characterization of potential disease-associated factors.

    Directory of Open Access Journals (Sweden)

    Dongbo Sun

    Full Text Available The plasma proteome of healthy dairy cattle and those with footrot was investigated using a shotgun LC-MS/MS approach. In total, 648 proteins were identified in healthy plasma samples, of which 234 were non-redundant proteins and 123 were high-confidence proteins; 712 proteins were identified from footrot plasma samples, of which 272 were non-redundant proteins and 138 were high-confidence proteins. The high-confidence proteins showed significant differences between healthy and footrot plasma samples in molecular weight, isoelectric points and the Gene Ontology categories. 22 proteins were found that may differentiate between the two sets of plasma proteins, of which 16 potential differential expression (PDE proteins from footrot plasma involved in immunoglobulins, innate immune recognition molecules, acute phase proteins, regulatory proteins, and cell adhesion and cytoskeletal proteins; 6 PDE proteins from healthy plasma involved in regulatory proteins, cytoskeletal proteins and coagulation factors. Of these PDE proteins, haptoglobin, SERPINA10 protein, afamin precursor, haptoglobin precursor, apolipoprotein D, predicted peptidoglycan recognition protein L (PGRP-L and keratan sulfate proteoglycan (KS-PG were suggested to be potential footrot-associated factors. The PDE proteins PGRP-L and KS-PG were highlighted as potential biomarkers of footrot in cattle. The resulting protein lists and potential differentially expressed proteins may provide valuable information to increase understanding of plasma protein profiles in cattle and to assist studies of footrot-associated factors.

  3. Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri.

    Science.gov (United States)

    Facincani, Agda P; Moreira, Leandro M; Soares, Márcia R; Ferreira, Cristiano B; Ferreira, Rafael M; Ferro, Maria I T; Ferro, Jesus A; Gozzo, Fabio C; de Oliveira, Julio C F

    2014-03-01

    The bacteria Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. The disease symptoms are characterized by localized host cell hyperplasia followed by tissue necrosis at the infected area. An arsenal of bacterial pathogenicity- and virulence-related proteins is expressed to ensure a successful infection process. At the post-genomic stage of Xac, we used a proteomic approach to analyze the proteins that are displayed differentially over time when the pathogen attacks the host plant. Protein extracts were prepared from infectious Xac grown in inducing medium (XAM1) for 24 h or from host citrus plants for 3 or 5 days after infection, detached times to evaluate the adaptation and virulence of the pathogen. The protein extracts were proteolyzed, and the peptides derived from tryptic digestion were investigated using liquid chromatography and tandem mass spectrometry. Changes in the protein expression profile were compared with the Xac genome and the proteome recently described under non-infectious conditions. An analysis of the proteome of Xac under infectious conditions revealed proteins directly involved in virulence such as the type III secretion system (T3SS) and effector proteins (T3SS-e), the type IV pilus (Tfp), and xanthan gum biosynthesis. Moreover, four new mutants related to proteins detected in the proteome and with different functions exhibited reduced virulence relative to the wild-type proteins. The results of the proteome analysis of infectious Xac define the processes of adaptation to the host and demonstrate the induction of the virulence factors of Xac involved in plant-pathogen interactions.

  4. Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants

    Energy Technology Data Exchange (ETDEWEB)

    Niemann, George; Brown, Roslyn N.; Gustin, Jean K.; Stufkens, Afke; Shaikh-Kidwai, Afshan S.; Li, Jie; McDermott, Jason E.; Brewer, Heather M.; Schepmoes, Athena A.; Smith, Richard D.; Adkins, Joshua N.; Heffron, Fred

    2011-01-01

    The intracellular pathogen Salmonella enterica serovar Typhimurium is a leading cause of acute gastroenteritis in the world. This pathogen has two type-III secretion systems (TTSS) necessary for virulence that are encoded in Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) and are expressed during extracellular or intracellular infectious states, respectively, to deliver virulence factors (effectors) to the host cell cytoplasm. While many have been identified and at least partially characterized, the full repertoire of effectors has not been catalogued. In this mass spectrometry-based proteomics study, we identified effector proteins secreted under minimal acidic medium growth conditions that induced the SPI-2 TTSS and its effectors, and compared the secretome from the parent strain to the secretome from strains missing either essential (SsaK) or regulatory components (SsaL) of the SPI-2 secretion apparatus. We identified 75% of the known TTSS effector repertoire. Excluding translocon components, 95% of the known effectors were biased for identification in the ssaL mutant background, which demonstrated that SsaL regulates SPI-2 type III secretion. To confirm secretion to animal cells, we made translational fusions of several of the best candidates to the calmodulin-dependent adenylate cyclase of Bordetella pertussis and assayed cAMP levels of infected J774 macrophage-like cells. From these infected cells we identified six new TTSS effectors and two others that are secreted independent of TTSS. Our results substantiate reports of additional secretion systems encoded by Salmonella other than TTSS.

  5. Search for a platelet-activating factor receptor in the Trypanosoma cruzi proteome: a potential target for Chagas disease chemotherapy

    Directory of Open Access Journals (Sweden)

    Daniel Fábio Kawano

    2011-12-01

    Full Text Available Chagas disease (CD causes the highest burden of parasitic diseases in the Western Hemisphere and is therefore a priority for drug research and development. Platelet-activating factor (PAF causes the CD parasite Trypanosoma cruzi to differentiate, which suggests that the parasite may express PAF receptors. Here, we explored the T. cruzi proteome for PAF receptor-like proteins. From a total of 23,000 protein sequences, we identified 29 hypothetical proteins that are predicted to have seven transmembrane domains (TMDs, which is the main characteristic of the G protein-coupled receptors (GPCRs, including the PAF receptor. The TMDs of these sequences were independently aligned with domains from 25 animal PAF receptors and the sequences were analysed for conserved residues. The conservation score mean values for the TMDs of the hypothetical proteins ranged from 31.7-44.1%, which suggests that if the putative T. cruzi PAF receptor is among the sequences identified, the TMDs are not highly conserved. These results suggest that T. cruzi contains several GPCR-like proteins and that one of these GPCRs may be a PAF receptor. Future studies may further validate the PAF receptor as a target for CD chemotherapy.

  6. Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders.

    Science.gov (United States)

    Estruch, Sara B; Graham, Sarah A; Quevedo, Martí; Vino, Arianna; Dekkers, Dick H W; Deriziotis, Pelagia; Sollis, Elliot; Demmers, Jeroen; Poot, Raymond A; Fisher, Simon E

    2018-04-01

    FOXP transcription factors play important roles in neurodevelopment, but little is known about how their transcriptional activity is regulated. FOXP proteins cooperatively regulate gene expression by forming homo- and hetero-dimers with each other. Physical associations with other transcription factors might also modulate the functions of FOXP proteins. However, few FOXP-interacting transcription factors have been identified so far. Therefore, we sought to discover additional transcription factors that interact with the brain-expressed FOXP proteins, FOXP1, FOXP2 and FOXP4, through affinity-purifications of protein complexes followed by mass spectrometry. We identified seven novel FOXP-interacting transcription factors (NR2F1, NR2F2, SATB1, SATB2, SOX5, YY1 and ZMYM2), five of which have well-estabslished roles in cortical development. Accordingly, we found that these transcription factors are co-expressed with FoxP2 in the deep layers of the cerebral cortex and also in the Purkinje cells of the cerebellum, suggesting that they may cooperate with the FoxPs to regulate neural gene expression in vivo. Moreover, we demonstrated that etiological mutations of FOXP1 and FOXP2, known to cause neurodevelopmental disorders, severely disrupted the interactions with FOXP-interacting transcription factors. Additionally, we pinpointed specific regions within FOXP2 sequence involved in mediating these interactions. Thus, by expanding the FOXP interactome we have uncovered part of a broader neural transcription factor network involved in cortical development, providing novel molecular insights into the transcriptional architecture underlying brain development and neurodevelopmental disorders.

  7. Proteomics dataset

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

    2017-01-01

    The datasets presented in this article are related to the research articles entitled “Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies” (Bennike et al., 2015 [1]), and “Proteome Analysis of Rheumatoid Arthritis Gut Mucosa” (Bennike et al., 2017 [2...... conducted the sample preparation and liquid chromatography mass spectrometry (LC-MS/MS) analysis of all samples in one batch, enabling label-free comparison between all biopsies. The datasets are made publicly available to enable critical or extended analyses. The proteomics data and search results, have...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

  8. Proteomes: A New Proteomic Journal

    Directory of Open Access Journals (Sweden)

    Jacek R. Wiśniewski

    2012-10-01

    Full Text Available In the early years of proteomics, mass spectrometry served only as a technique in protein chemistry facilitating the characterization of purified proteins and mapping their posttranslational modifications (PTMs. A bit later this technique almost completely replaced Edman degradation and amino acid analysis. The continuous development of the mass spectrometry techniques created a huge analytical potential allowing the study of nearly complete proteomes in single experiments. This evolution distanced proteomics from protein chemistry and placed it in a novel position. Its capability to identify and quantify in parallel thousands of proteins and their modifications at minute sample amount requirements is one of the most fascinating technological advances in biology today.

  9. Identification of Virulence Factors in Nematode-Trapping Fungi - Insights from Genomics, Transcriptomics and Proteomics

    OpenAIRE

    Andersson, Karl-Magnus

    2013-01-01

    Nematode-trapping fungi are soil-living organisms with the unique ability to capture and infect free-living nematodes. The interest in studying these fungi arises from their potential use as biological control agents for plant- and animal-parasitic nematodes. To enter the parasitic stage, nematode-trapping fungi develop different kinds of trapping structures. In order to understand more about the evolution of parasitism in the nematode-trapping fungi and to identify virulence factors in these...

  10. Serum Proteome Signature of Radiation Response: Upregulation of Inflammation-Related Factors and Downregulation of Apolipoproteins and Coagulation Factors in Cancer Patients Treated With Radiation Therapy—A Pilot Study

    Energy Technology Data Exchange (ETDEWEB)

    Widlak, Piotr, E-mail: widlak@io.gliwice.pl [Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice (Poland); Jelonek, Karol; Wojakowska, Anna; Pietrowska, Monika [Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice (Poland); Polanska, Joanna [Institute of Automatics Control, Silesian University of Technology, Gliwice (Poland); Marczak, Łukasz [Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan (Poland); Miszczyk, Leszek; Składowski, Krzysztof [Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice (Poland)

    2015-08-01

    features of serum proteome. The signature included upregulation of factors involved in acute or inflammatory response but also downregulation of plasma apolipoproteins and factors involved in blood coagulation.

  11. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics.

    Science.gov (United States)

    Brand, Marjorie; Ranish, Jeffrey A; Kummer, Nicolas T; Hamilton, Joan; Igarashi, Kazuhiko; Francastel, Claire; Chi, Tian H; Crabtree, Gerald R; Aebersold, Ruedi; Groudine, Mark

    2004-01-01

    During erythroid differentiation, beta-globin gene expression is regulated by the locus control region (LCR). The transcription factor NF-E2p18/MafK binds within this region and is essential for beta-globin expression in murine erythroleukemia (MEL) cells. Here we use the isotope-coded affinity tag (ICAT) technique of quantitative mass spectrometry to compare proteins interacting with NF-E2p18/MafK during differentiation. Our results define MafK as a 'dual-function' molecule that shifts from a repressive to an activating mode during erythroid differentiation. The exchange of MafK dimerization partner from Bach1 to NF-E2p45 is a key step in the switch from the repressed to the active state. This shift is associated with changes in the interaction of MafK with co-repressors and co-activators. Thus, our results suggest that in addition to its role as a cis-acting activator of beta-globin gene expression in differentiated erythroid cells, the LCR also promotes an active repression of beta-globin transcription in committed cells before terminal differentiation.

  12. 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

  13. Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells.

    Science.gov (United States)

    Wang, Bingyuan; Pfeiffer, Martin J; Drexler, Hannes C A; Fuellen, Georg; Boiani, Michele

    2016-08-05

    The reprogramming process that leads to induced pluripotent stem cells (iPSCs) may benefit from adding oocyte factors to Yamanaka's reprogramming cocktail (OCT4, SOX2, KLF4, with or without MYC; OSK(M)). We previously searched for such facilitators of reprogramming (the reprogrammome) by applying label-free LC-MS/MS analysis to mouse oocytes, producing a catalog of 28 candidates that are (i) able to robustly access the cell nucleus and (ii) shared between mature mouse oocytes and pluripotent embryonic stem cells. In the present study, we hypothesized that our 28 reprogrammome candidates would also be (iii) abundant in mature oocytes, (iv) depleted after the oocyte-to-embryo transition, and (v) able to potentiate or replace the OSKM factors. Using LC-MS/MS and isotopic labeling methods, we found that the abundance profiles of the 28 proteins were below those of known oocyte-specific and housekeeping proteins. Of the 28 proteins, only arginine methyltransferase 7 (PRMT7) changed substantially during mouse embryogenesis and promoted the conversion of mouse fibroblasts into iPSCs. Specifically, PRMT7 replaced SOX2 in a factor-substitution assay, yielding iPSCs. These findings exemplify how proteomics can be used to prioritize the functional analysis of reprogrammome candidates. The LC-MS/MS data are available via ProteomeXchange with identifier PXD003093.

  14. Silac mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function

    OpenAIRE

    Krüger, M.; Moser, M.; Ussar, S.; Thievessen, I.; Luber, C.A.; Forner, F.; Schmidt, S.; Zanivan, S.; Fässler, R.; Mann, M.

    2008-01-01

    Stable isotope labeling by amino acids in cell culture (SILAC) has become a versatile tool for quantitative, mass spectrometry (MS)-based proteomics. Here, we completely label mice with a diet containing either the natural or the 13C6-substituted version of lysine. Mice were labeled over four generations with the heavy diet, and development, growth, and behavior were not affected. MS analysis of incorporation levels allowed for the determination of incorporation rates of proteins from blood c...

  15. Proteomics identifies Bacillus cereus EntD as a pivotal protein for the production of numerous virulence factors

    Directory of Open Access Journals (Sweden)

    Hélène eOmer

    2015-10-01

    Full Text Available Bacillus cereus is a gram-positive pathogen that causes a wide variety of diseases in humans. It secretes into the extracellular milieu proteins that may contribute directly or indirectly to its virulence. EntD is a novel exoprotein identified by proteogenomics of B. cereus ATCC 14579. We constructed a ΔentD mutant and analyzed the impact of entD disruption on the cellular proteome and exoproteome isolated from early, late and stationary-phase cultures. We identified 308 and 79 proteins regulated by EntD in the cellular proteome and the exoproteome, respectively. The contribution of these proteins to important virulence-associated functions, including central metabolism, cell structure, antioxidative ability, cell motility and toxin production, are presented. The proteomic data were correlated with the growth defect, cell morphology change, reduced motility and reduced cytotoxicity of the ΔentD mutant strain. We conclude that EntD is an important player in B. cereus virulence. The function of EntD and the putative EntD-dependent regulatory network are discussed. To our knowledge, this study is the first characterization of an Ent family protein in a species of the B. cereus group.

  16. Proteomics identifies Bacillus cereus EntD as a pivotal protein for the production of numerous virulence factors.

    Science.gov (United States)

    Omer, Hélène; Alpha-Bazin, Béatrice; Brunet, Jean-Luc; Armengaud, Jean; Duport, Catherine

    2015-01-01

    Bacillus cereus is a Gram-positive pathogen that causes a wide variety of diseases in humans. It secretes into the extracellular milieu proteins that may contribute directly or indirectly to its virulence. EntD is a novel exoprotein identified by proteogenomics of B. cereus ATCC 14579. We constructed a ΔentD mutant and analyzed the impact of entD disruption on the cellular proteome and exoproteome isolated from early, late, and stationary-phase cultures. We identified 308 and 79 proteins regulated by EntD in the cellular proteome and the exoproteome, respectively. The contribution of these proteins to important virulence-associated functions, including central metabolism, cell structure, antioxidative ability, cell motility, and toxin production, are presented. The proteomic data were correlated with the growth defect, cell morphology change, reduced motility, and reduced cytotoxicity of the ΔentD mutant strain. We conclude that EntD is an important player in B. cereus virulence. The function of EntD and the putative EntD-dependent regulatory network are discussed. To our knowledge, this study is the first characterization of an Ent family protein in a species of the B. cereus group.

  17. 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: 3.849, year: 2016

  18. 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 g...

  19. Proteomic analysis of menstrual blood.

    Science.gov (United States)

    Yang, Heyi; Zhou, Bo; Prinz, Mechthild; Siegel, Donald

    2012-10-01

    Menstruation is the expulsion of the endometrial lining of the uterus following a nearly month long preparation for embryo implantation and pregnancy. Increasingly, the health of the endometrium is being recognized as a critical factor in female fertility, and proteomes and transcriptomes from endometrial biopsies at different stages of the menstrual cycle have been studied for both diagnostic and therapeutic purposes (1 Kao, L. C., et al. 2003 Endocrinology 144, 2870-2881; Strowitzki, Tet al. 2006 Hum. Reprod. Update 12, 617-630; DeSouza, L., et al. 2005 Proteomics 5, 270-281). Disorders of the uterus ranging from benign to malignant tumors, as well as endometriosis, can cause abnormal menstrual bleeding and are frequently diagnosed through endometrial biopsy (Strowitzki, Tet al. 2006 Hum. Reprod. Update 12, 617-630; Ferenczy, A. 2003 Maturitas 45, 1-14). Yet the proteome of menstrual blood, an easily available noninvasive source of endometrial tissue, has yet to be examined for possible causes or diagnoses of infertility or endometrial pathology. This study employed five different methods to define the menstrual blood proteome. A total of 1061 proteins were identified, 361 were found by at least two methods and 678 were identified by at least two peptides. When the menstrual blood proteome was compared with those of circulating blood (1774 proteins) and vaginal fluid (823 proteins), 385 proteins were found unique to menstrual blood. Gene ontology analysis and evaluation of these specific menstrual blood proteins identified pathways consistent with the processes of the normal endometrial cycle. Several of the proteins unique to menstrual blood suggest that extramedullary uterine hematopoiesis or parenchymal hemoglobin synthesis may be occurring in late endometrial tissue. The establishment of a normal menstrual blood proteome is necessary for the evaluation of its usefulness as a diagnostic tool for infertility and uterine pathologies. Identification of unique

  20. 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.

  1. Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E

    DEFF Research Database (Denmark)

    Fierro-Monti, Ivo; Mohammed, Shabaz; Matthiesen, Rune

    2006-01-01

    Protein complexes are dynamic entities; identification and quantitation of their components is critical in elucidating functional roles under specific cellular conditions. We report the first quantitative proteomic analysis of the human cap-binding protein complex. Components and proteins associa...

  2. [Proteomics and transfusion medicine].

    Science.gov (United States)

    Lion, N; Prudent, M; Crettaz, D; Tissot, J-D

    2011-04-01

    The term "proteomics" covers tools and techniques that are used to analyze and characterize complex mixtures of proteins from various biological samples. In this short review, a typical proteomic approach, related to the study of particular and illustrative situation related to transfusion medicine is reported. This "case report" will allow the reader to be familiar with a practical proteomic approach of a real situation, and will permit to describe the tools that are usually used in proteomic labs, and, in a second part, to present various proteomic applications in transfusion medicine. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  3. Transcriptome and proteome dynamics in chemostat culture reveal how Campylobacter jejuni modulates metabolism, stress responses and virulence factors upon changes in oxygen availability.

    Science.gov (United States)

    Guccione, Edward J; Kendall, John J; Hitchcock, Andrew; Garg, Nitanshu; White, Michael A; Mulholland, Francis; Poole, Robert K; Kelly, David J

    2017-10-01

    Campylobacter jejuni, the most frequent cause of food-borne bacterial gastroenteritis worldwide, is a microaerophile that has to survive high environmental oxygen tensions, adapt to oxygen limitation in the intestine and resist host oxidative attack. Here, oxygen-dependent changes in C. jejuni physiology were studied at constant growth rate using carbon (serine)-limited continuous chemostat cultures. We show that a perceived aerobiosis scale can be calibrated by the acetate excretion flux, which becomes zero when metabolism is fully aerobic (100% aerobiosis). Transcriptome changes in a downshift experiment from 150% to 40% aerobiosis revealed many novel oxygen-regulated genes and highlighted re-modelling of the electron transport chains. A label-free proteomic analysis showed that at 40% aerobiosis, many proteins involved in host colonisation (e.g., PorA, CadF, FlpA, CjkT) became more abundant. PorA abundance increased steeply below 100% aerobiosis. In contrast, several citric-acid cycle enzymes, the peptide transporter CstA, PEB1 aspartate/glutamate transporter, LutABC lactate dehydrogenase and PutA proline dehydrogenase became more abundant with increasing aerobiosis. We also observed a co-ordinated response of oxidative stress protection enzymes and Fe-S cluster biogenesis proteins above 100% aerobiosis. Our approaches reveal key virulence factors that respond to restricted oxygen availability and specific transporters and catabolic pathways activated with increasing aerobiosis. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. 1st Central and Eastern European Proteomic Conference and 3rd Czech Proteomic Conference

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Hana; Gadher, S. J.; Archakov, A.

    2008-01-01

    Roč. 5, č. 1 (2008), s. 25-28 ISSN 1478-9450 Institutional research plan: CEZ:AV0Z50450515 Keywords : proteomic conference Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.848, year: 2008

  5. Proteomics: a subcellular look at spermatozoa

    Directory of Open Access Journals (Sweden)

    Yadav Satya P

    2011-03-01

    Full Text Available Abstract Background Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting. Methods Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry. Results Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome. Conclusion Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites

  6. 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

  7. The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF).

    Science.gov (United States)

    Rosenling, Therese; Slim, Christiaan L; Christin, Christin; Coulier, Leon; Shi, Shanna; Stoop, Marcel P; Bosman, Jan; Suits, Frank; Horvatovich, Peter L; Stockhofe-Zurwieden, Norbert; Vreeken, Rob; Hankemeier, Thomas; van Gool, Alain J; Luider, Theo M; Bischoff, Rainer

    2009-12-01

    To standardize the use of cerebrospinal fluid (CSF) for biomarker research, a set of stability studies have been performed on porcine samples to investigate the influence of common sample handling procedures on proteins, peptides, metabolites and free amino acids. This study focuses at the effect on proteins and peptides, analyzed by applying label-free quantitation using microfluidics nanoscale liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (chipLC-MS) as well as matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) and Orbitrap LC-MS/MS to trypsin-digested CSF samples. The factors assessed were a 30 or 120 min time delay at room temperature before storage at -80 degrees C after the collection of CSF in order to mimic potential delays in the clinic (delayed storage), storage at 4 degrees C after trypsin digestion to mimic the time that samples remain in the cooled autosampler of the analyzer, and repeated freeze-thaw cycles to mimic storage and handling procedures in the laboratory. The delayed storage factor was also analyzed by gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) for changes of metabolites and free amino acids, respectively. Our results show that repeated freeze/thawing introduced changes in transthyretin peptide levels. The trypsin digested samples left at 4 degrees C in the autosampler showed a time-dependent decrease of peak areas for peptides from prostaglandin D-synthase and serotransferrin. Delayed storage of CSF led to changes in prostaglandin D-synthase derived peptides as well as to increased levels of certain amino acids and metabolites. The changes of metabolites, amino acids and proteins in the delayed storage study appear to be related to remaining white blood cells. Our recommendations are to centrifuge CSF samples immediately after collection to remove white blood cells, aliquot, and then

  8. Cellular Proteome Dynamics during Differentiation of Human Primary Myoblasts

    DEFF Research Database (Denmark)

    Le Bihan, Marie-Catherine; Barrio, Inigo; Mortensen, Tenna Pavia

    2015-01-01

    withdrawal, RNA metabolism, cell adhesion, proteolysis, and cytoskeletal organization. In silico transcription factor target analysis demonstrated that the observed dynamic changes in the proteome could be attributed to a cascade of transcriptional events involving key myogenic regulatory factors as well...

  9. 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. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. ProteomicsDB.

    Science.gov (United States)

    Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias

    2018-01-04

    ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. PROTEOMICS in aquaculture

    DEFF Research Database (Denmark)

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

    2012-01-01

    Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous...... of 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...

  12. Proteomics studies on stress responses in diatoms.

    Science.gov (United States)

    Muhseen, Ziyad Tariq; Xiong, Qian; Chen, Zhuo; Ge, Feng

    2015-12-01

    Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Bacterial membrane proteomics.

    Science.gov (United States)

    Poetsch, Ansgar; Wolters, Dirk

    2008-10-01

    About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

  14. Nanoscaled Proteomic Analysis

    Science.gov (United States)

    Xu, Yan; Jia, Lee

    2013-09-01

    Global proteomics research is currently hampered by the extremely complexity of the proteome and the absence of techniques like the polymerase chain reaction in genomics which enables multiplication of a single protein molecule. Since all the existing analytical technologies cannot overcome the detection limit and the dynamic concentration barrier, development of improved analytical technologies at nanoscale, ideally those that could recognize single protein molecule in the presence of high abundant of others, is a high priority for proteomics. In this chapter, we will show the state-of-the-art of nanoproteomics, i.e., the application of nanotechnologies to proteomics. Various nanomaterials including carbon nanomaterials, magnetic nanoparticles, silica nanoparticles, polymer and copolymer nanoparticles, metal and metal oxide nanoparticles have been used to improve sensitivity, specificity, and repeatability of proteomic analysis especially when the multidimensional separation system coupled with MALDI-TOF-MS is used. Among them, gold nanoparticles (GNPs) and carbon nanotubes (CNTs) are the two most important nanomaterials: while GNPs are frequently utilized for enzyme immobilization, high throughput bioassay, selection of target-peptides and target-protein, CNTs including single-walled carbon nanotubes (SWCNTs) and mutiple-walled carbon nanotubes (MWCNTs) have wide applications to electronic sensor, sensitive immunodetection, nanobiocatalysis, affinity probes, MALDI matrices, protein digestion, peptides enrichment and analysis. In perspectives, a deep understanding of the structures and property of nanomaterials and interdisciplinary applications of nanotechnology to proteomics will certainly be revolutionary and intellectually rewarding.

  15. Directed proteomic analysis of the human nucleolus

    DEFF Research Database (Denmark)

    Andersen, Jens S; Lyon, Carol E; Fox, Archa H

    2002-01-01

    of their structure and function remain uncharacterized. RESULTS: We report a proteomic analysis of human nucleoli. Using a combination of mass spectrometry (MS) and sequence database searches, including online analysis of the draft human genome sequence, 271 proteins were identified. Over 30% of the nucleolar...... proteins were encoded by novel or uncharacterized genes, while the known proteins included several unexpected factors with no previously known nucleolar functions. MS analysis of nucleoli isolated from HeLa cells in which transcription had been inhibited showed that a subset of proteins was enriched....... These data highlight the dynamic nature of the nucleolar proteome and show that proteins can either associate with nucleoli transiently or accumulate only under specific metabolic conditions. CONCLUSIONS: This extensive proteomic analysis shows that nucleoli have a surprisingly large protein complexity...

  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. 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

  18. Quantitative proteomics of fractionated membrane and lumen exosome proteins from isogenic metastatic and non-metastatic bladder cancer cells reveal differential expression of EMT factors

    DEFF Research Database (Denmark)

    Jeppesen, Dennis Kjølhede; Nawrocki, Arkadiusz; Jensen, Steffen Grann

    2014-01-01

    T24 without metastatic capacity and its two isogenic derivate cell lines SLT4 and FL3, which form metastases in the lungs and liver of mice, respectively. Cultivation in CLAD1000 bioreactors rather than conventional culture flasks resulted in a 13-16-fold increased exosome yield and facilitated......, with changes in cellular mRNA expression. Our proteomic approach may help identification of proteins in the membrane and lumen of exosomes potentially involved in the metastatic process. This article is protected by copyright. All rights reserved....

  19. 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; Brenes Murillo, Alejandro; Gartner, Anton; Kenyon, Cynthia J.

    2016-01-01

    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

  20. Proteomics - new analytical approaches

    International Nuclear Information System (INIS)

    Hancock, W.S.

    2001-01-01

    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

  1. Proteomic Assessment of Poultry Spermatozoa

    Science.gov (United States)

    Fully characterizing the protein composition of spermatozoa is the first step in utilizing proteomics to delineate the function of sperm proteins. To date, sperm proteome maps have been partially developed for the human, mouse, rat, bull and several invertebrates. Here we report the first proteomic...

  2. 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.

  3. 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.

  4. Xylem sap proteomics.

    Science.gov (United States)

    de Bernonville, Thomas Dugé; Albenne, Cécile; Arlat, Matthieu; Hoffmann, Laurent; Lauber, Emmanuelle; Jamet, Elisabeth

    2014-01-01

    Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

  5. Proteomic approach to nanotoxicity.

    Science.gov (United States)

    Matysiak, Magdalena; Kapka-Skrzypczak, Lucyna; Brzóska, Kamil; Gutleb, Arno C; Kruszewski, Marcin

    2016-03-30

    In recent years a large number of engineered nanomaterials (NMs) have been developed with promising technical benefits for consumers and medical appliances. In addition to already known potentially advantageous biological properties (antibiotic, antifungal and antiviral activity) of NMs, many new medical applications of NMs are foreseen, such as drug carriers, contrast agents, radiopharmaceuticals and many others. However, there is increasing concern about potential environmental and health effects due to NMs exposure. An increasing body of evidence suggests that NMs may trigger undesirable hazardous interactions with biological systems with potential to generate harmful effects. In this review we summarized a current state of knowledge on the proteomics approaches to nanotoxicity, including protein corona formation, in vitro and in vivo effects of exposure to NMs on proteome of different classes of organisms, from bacteria and plants to mammals. The effects of NMs on the proteome of environmentally relevant organisms are also described. Despite the benefit that development of nanotechnology may bring to the society, there are still major gaps of knowledge on the influence of nanomaterials on human health and the environment. Thus, it seems necessary to conduct further interdisciplinary research to fill the knowledge gaps in NM toxicity, using more holistic approaches than offered by conventional biological techniques. “OMICS” techniques will certainly help researchers in this field. In this paper we summarized the current stage of knowledge of the effects of nanoparticles on the proteome of different organisms, including those commonly used as an environmentally relevant indicator organisms.

  6. Arabidopsis peroxisome proteomics

    Directory of Open Access Journals (Sweden)

    John D. Bussell

    2013-04-01

    Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

  7. Sperm Surface Proteomics 2

    NARCIS (Netherlands)

    Brewis, I.A.; Gadella, B.M.|info:eu-repo/dai/nl/115389873

    2017-01-01

    This contribution will focus exclusively on the total (global) protein composition (the proteome) of the sperm surface. Immune responses directed towards sperm surface proteins may cause infertility since functionally intact sperm are under immune attack. The immune attack can be achieved directly

  8. 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

  9. A Review: Proteomics in Retinal Artery Occlusion, Retinal Vein Occlusion, Diabetic Retinopathy and Acquired Macular Disorders.

    Science.gov (United States)

    Cehofski, Lasse Jørgensen; Honoré, Bent; Vorum, Henrik

    2017-04-28

    Retinal artery occlusion (RAO), retinal vein occlusion (RVO), diabetic retinopathy (DR) and age-related macular degeneration (AMD) are frequent ocular diseases with potentially sight-threatening outcomes. In the present review we discuss major findings of proteomic studies of RAO, RVO, DR and AMD, including an overview of ocular proteome changes associated with anti-vascular endothelial growth factor (VEGF) treatments. Despite the severe outcomes of RAO, the proteome of the disease remains largely unstudied. There is also limited knowledge about the proteome of RVO, but proteomic studies suggest that RVO is associated with remodeling of the extracellular matrix and adhesion processes. Proteomic studies of DR have resulted in the identification of potential therapeutic targets such as carbonic anhydrase-I. Proliferative diabetic retinopathy is the most intensively studied stage of DR. Proteomic studies have established VEGF, pigment epithelium-derived factor (PEDF) and complement components as key factors associated with AMD. The aim of this review is to highlight the major milestones in proteomics in RAO, RVO, DR and AMD. Through large-scale protein analyses, proteomics is bringing new important insights into these complex pathological conditions.

  10. Proteomics as a Tool for Understanding Schizophrenia

    OpenAIRE

    Martins-de-Souza, Daniel

    2011-01-01

    Schizophrenia is likely to be a multifactorial disorder, consequence of alterations in gene and protein expression since the neurodevelopment that together to environmental factors will trigger the establishment of the disease. In the post-genomic era, proteomics has emerged as a promising strategy for revealing disease and treatment biomarkers as well as a tool for the comprehension of the mechanisms of schizophrenia pathobiology. Here, there is a discussion of the potential pathways and str...

  11. 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

  12. Plant redox proteomics

    DEFF Research Database (Denmark)

    Navrot, Nicolas; Finnie, Christine; Svensson, Birte

    2011-01-01

    In common with other aerobic organisms, plants are exposed to reactive oxygen species resulting in formation of post-translational modifications related to protein oxidoreduction (redox PTMs) that may inflict oxidative protein damage. Accumulating evidence also underscores the importance of redox...... PTMs in regulating enzymatic activities and controlling biological processes in plants. Notably, proteins controlling the cellular redox state, e.g. thioredoxin and glutaredoxin, appear to play dual roles to maintain oxidative stress resistance and regulate signal transduction pathways via redox PTMs....... To get a comprehensive overview of these types of redox-regulated pathways there is therefore an emerging interest to monitor changes in redox PTMs on a proteome scale. Compared to some other PTMs, e.g. protein phosphorylation, redox PTMs have received less attention in plant proteome analysis, possibly...

  13. Sperm cell proteomics.

    Science.gov (United States)

    Oliva, Rafael; de Mateo, Sara; Estanyol, Josep Maria

    2009-02-01

    The spermatozoon is an accessible cell which can be easily purified and therefore it is particularly well suited for proteomic analysis. It is also an extremely differentiated cell with very marked genetic, cellular, functional and chromatin changes as compared to other cells, and has profound implications for fertility, embryo development and heredity. The recent developments in MS have boosted the potential for identification and study of the sperm proteins. Catalogues of hundreds to thousands of spermatozoan proteins in human and in model species are becoming available setting up the basis for subsequent research, diagnostic applications and the development of specific treatments. The present article reviews the available scientific publications dealing with the composition and function of the sperm cell using an MS proteomic approach.

  14. 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....

  15. Dentistry proteomics: from laboratory development to clinical practice.

    Science.gov (United States)

    Rezende, Taia M B; Lima, Stella M F; Petriz, Bernardo A; Silva, Osmar N; Freire, Mirna S; Franco, Octávio L

    2013-12-01

    Despite all the dental information acquired over centuries and the importance of proteome research, the cross-link between these two areas only emerged around mid-nineties. Proteomic tools can help dentistry in the identification of risk factors, early diagnosis, prevention, and systematic control that will promote the evolution of treatment in all dentistry specialties. This review mainly focuses on the evolution of dentistry in different specialties based on proteomic research and how these tools can improve knowledge in dentistry. The subjects covered are an overview of proteomics in dentistry, specific information on different fields in dentistry (dental structure, restorative dentistry, endodontics, periodontics, oral pathology, oral surgery, and orthodontics) and future directions. There are many new proteomic technologies that have never been used in dentistry studies and some dentistry areas that have never been explored by proteomic tools. It is expected that a greater integration of these areas will help to understand what is still unknown in oral health and disease. Copyright © 2013 Wiley Periodicals, Inc.

  16. 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...... tendinopathies, and to evaluate perspectives of proteomics – the comprehensive study of protein composition - in tendon research. Materials and Methods We conducted a systematic search of the literature published between 1 January 1990 and 18 December 2012 in PubMed, Embase, and Web of Science. We included......), tissue inhibitor of metalloproteinase (TIMP)-1 (4 of 7), and vascular endothelial growth factor (4 of 7), and a decrease in MMP-3 (10 of 12). Fourteen proteomics studies of tendon tissues/cells failed inclusion, mostly because they were conducted in animals or in vitro. Conclusions Based on methods...

  17. New heights and horizons in fostering proteomics in central and eastern Europe

    Czech Academy of Sciences Publication Activity Database

    Gadher, S. J.; Kovářová, Hana

    2013-01-01

    Roč. 10, č. 1 (2013), s. 13-15 ISSN 1478-9450. [Central and Eastern European Proteomics conference /6./. Budapest, 14.10.2012-17.10.2012] Institutional support: RVO:67985904 Keywords : proteomics Subject RIV: CE - Biochemistry Impact factor: 3.542, year: 2013

  18. Proteomic identification of gender molecular markers in Bothrops jararaca venom.

    Science.gov (United States)

    Zelanis, André; Menezes, Milene C; Kitano, Eduardo S; Liberato, Tarcísio; Tashima, Alexandre K; Pinto, Antonio F M; Sherman, Nicholas E; Ho, Paulo L; Fox, Jay W; Serrano, Solange M T

    2016-04-29

    larger than males. This sexual size dimorphism suggests the tendency for female specimens to feed on larger prey, and for male specimens to go on a diet similar to that of juveniles. Variation in the snake venom proteome is a ubiquitous phenomenon occurring at all taxonomic levels. At the intraspecific variation level, the individual contribution to the venom proteome is important but effects contributed by age and feeding habits may also affect the proteome phenotype. Whether sex-based factors play a role in venom variation of a species that shows sexual size dimorphism is poorly known. The use of proteomic strategies supported by transcriptomic data allows a more comprehensive assessment of venom proteomes uncovering components that are gender-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. 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.

  20. Proteomics of Maize Root Development.

    Science.gov (United States)

    Hochholdinger, Frank; Marcon, Caroline; Baldauf, Jutta A; Yu, Peng; Frey, Felix P

    2018-01-01

    Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

  1. Proteomics of Maize Root Development

    Directory of Open Access Journals (Sweden)

    Frank Hochholdinger

    2018-03-01

    Full Text Available Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

  2. Proteomic Signatures of Thymomas

    Science.gov (United States)

    Shilo, Konstantin; Hitchcock, Charles L.; Freitas, Michael A.

    2016-01-01

    Based on the histological features and outcome, the current WHO classification separates thymomas into A, AB, B1, B2 and B3 subtypes. It is hypothesized that the type A thymomas are derived from the thymic medulla while the type B thymomas are derived from the cortex. Due to occasional histological overlap between the tumor subtypes creating difficulties in their separation, the aim of this study was to provide their proteomic characterization and identify potential immunohistochemical markers aiding in tissue diagnosis. Pair-wise comparison of neoplastic and normal thymus by liquid chromatography tandem mass spectrometry (LC-MS/MS) of formalin fixed paraffin embedded tissue revealed 61 proteins differentially expressed in thymomas compared to normal tissue. Hierarchical clustering showed distinct segregation of subtypes AB, B1 and B2 from that of A and B3. Most notably, desmoyokin, a protein that is encoded by the AHNAK gene, was associated with type A thymomas and medulla of normal thymus, by LC-MS/MS and immunohistochemistry. In this global proteomic characterization of the thymoma, several proteins unique to different thymic compartments and thymoma subtypes were identified. Among differentially expressed proteins, desmoyokin is a marker specific for thymic medulla and is potentially promising immunohistochemical marker in separation of type A and B3 thymomas. PMID:27832160

  3. Proteomic Signatures of Thymomas.

    Directory of Open Access Journals (Sweden)

    Linan Wang

    Full Text Available Based on the histological features and outcome, the current WHO classification separates thymomas into A, AB, B1, B2 and B3 subtypes. It is hypothesized that the type A thymomas are derived from the thymic medulla while the type B thymomas are derived from the cortex. Due to occasional histological overlap between the tumor subtypes creating difficulties in their separation, the aim of this study was to provide their proteomic characterization and identify potential immunohistochemical markers aiding in tissue diagnosis. Pair-wise comparison of neoplastic and normal thymus by liquid chromatography tandem mass spectrometry (LC-MS/MS of formalin fixed paraffin embedded tissue revealed 61 proteins differentially expressed in thymomas compared to normal tissue. Hierarchical clustering showed distinct segregation of subtypes AB, B1 and B2 from that of A and B3. Most notably, desmoyokin, a protein that is encoded by the AHNAK gene, was associated with type A thymomas and medulla of normal thymus, by LC-MS/MS and immunohistochemistry. In this global proteomic characterization of the thymoma, several proteins unique to different thymic compartments and thymoma subtypes were identified. Among differentially expressed proteins, desmoyokin is a marker specific for thymic medulla and is potentially promising immunohistochemical marker in separation of type A and B3 thymomas.

  4. Opportunities and Challenges for Nutritional Proteomics in Cancer Prevention12

    Science.gov (United States)

    Romagnolo, Donato F.; Milner, John A.

    2012-01-01

    Knowledge gaps persist about the efficacy of cancer prevention strategies based on dietary food components. Adaptations to nutrient supply are executed through tuning of multiple protein networks that include transcription factors, histones, modifying enzymes, translation factors, membrane and nuclear receptors, and secreted proteins. However, the simultaneous quantitative and qualitative measurement of all proteins that regulate cancer processes is not practical using traditional protein methodologies. Proteomics offers an attractive opportunity to fill this knowledge gap and unravel the effects of dietary components on protein networks that impinge on cancer. The articles presented in this supplement are from talks proffered in the “Nutrition Proteomics and Cancer Prevention” session at the American Institute for Cancer Research Annual Research Conference on Food, Nutrition, Physical Activity and Cancer held in Washington, DC on October 21 and 22, 2010. Recent advances in MS technologies suggest that studies in nutrition and cancer prevention may benefit from the adoption of proteomic tools to elucidate the impact on biological processes that govern the transition from normal to malignant phenotype; to identify protein changes that determine both positive and negative responses to food components; to assess how protein networks mediate dose-, time-, and tissue-dependent responses to food components; and, finally, for predicting responders and nonresponders. However, both the limited accessibility to proteomic technologies and research funding appear to be hampering the routine adoption of proteomic tools in nutrition and cancer prevention research. PMID:22649262

  5. A proteome study of secreted prostatic factors affecting osteoblastic activity: galectin-1 is involved in differentiation of human bone marrow stromal cells

    DEFF Research Database (Denmark)

    Andersen, H; Jensen, Ole N; Moiseeva, Elena P

    2003-01-01

    Prostate cancer cells metastasize to bone causing a predominantly osteosclerotic response. It has been shown that cells from the human prostate cancer cell line PC3 secrete factors that influence the behavior of osteoblast-like cells. Some of these factors with mitogenic activity have been found...... to be proteins with molecular weights between 20 and 30 kDa, but the identity of the osteoblastic mitogenic factor or factors produced by prostate cancer cells is still unknown. Therefore, the aim of this study was to characterize the protein profile of conditioned medium (CM) from PC3 cells in the molecular......BMS) cells. Furthermore, we tested whether adhesion of PC3 cells to plastic, laminin, fibronectin, and collagen type I was influenced by lactose, which inhibits galectin-1. Galectin-1 (1000 ng/ml) inhibited the proliferation of hBMS cells up to 70 +/- 12% (treated/control) of control in contrast to PC3 CM...

  6. Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

    Science.gov (United States)

    Nuss, Jonathan E; Kehn-Hall, Kylene; Benedict, Ashwini; Costantino, Julie; Ward, Michael; Peyser, Brian D; Retterer, Cary J; Tressler, Lyal E; Wanner, Laura M; McGovern, Hugh F; Zaidi, Anum; Anthony, Scott M; Kota, Krishna P; Bavari, Sina; Hakami, Ramin M

    2014-01-01

    Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV). Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry) with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90), as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

  7. Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

    Directory of Open Access Journals (Sweden)

    Jonathan E Nuss

    Full Text Available Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV. Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90, as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

  8. 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.

  9. Proteomics of early zebrafish embryos

    Directory of Open Access Journals (Sweden)

    Heisenberg Carl-Philipp

    2006-01-01

    Full Text Available Abstract Background Zebrafish (D. rerio has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D gel electrophoresis and proteomics have yet to be developed. Results As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS, including a comparison of databases for MS identification of zebrafish proteins. Conclusion The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.

  10. 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.

  11. Proteome Characterization of a Chromatin Locus Using the Proteomics of Isolated Chromatin Segments Approach.

    Science.gov (United States)

    Kan, Sophie L; Saksouk, Nehmé; Déjardin, Jérome

    2017-01-01

    The biological functions of given genomic regions are ruled by the local chromatin composition. The Proteomics of Isolated Chromatin segments approach (PICh) is a powerful and unbiased method to analyze the composition of chosen chromatin segments, provided they are abundant (repeated) or that the organism studied has a small genome. PICh can be used to identify novel and unexpected regulatory factors, or when combined with quantitative mass spectrometric approaches, to characterize the function of a defined factor at the chosen locus, by quantifying composition changes at the locus upon removal/addition of that factor.

  12. Comparative Study of the Life Cycle Dependent Post-Translation Modifications of Protein Synthesis Elongation Factor Tu Present in the Membrane Proteome of Streptomycetes and Mycobacteria

    Czech Academy of Sciences Publication Activity Database

    Holub, Martin; Bezoušková, Silvia; Petráčková, Denisa; Kalachová, Ladislava; Kofroňová, Olga; Benada, Oldřich; Weiser, Jaroslav

    2010-01-01

    Roč. 55, č. 3 (2010), s. 203-210 ISSN 0015-5632 R&D Projects: GA AV ČR IAA600200702; GA AV ČR IAA500200913 Institutional research plan: CEZ:AV0Z50200510 Keywords : ESCHERICHIA-COLI * COELICOLOR A3(2) * OUTER-MEMBRANE Subject RIV: EE - Microbiology, Virology Impact factor: 0.977, year: 2010

  13. 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.

  14. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. The proteome of human saliva

    Science.gov (United States)

    Griffin, Timothy J.

    2013-05-01

    Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

  16. Evolution of clinical proteomics and its role in medicine.

    Science.gov (United States)

    Boja, Emily; Hiltke, Tara; Rivers, Robert; Kinsinger, Christopher; Rahbar, Amir; Mesri, Mehdi; Rodriguez, Henry

    2011-01-07

    Significant progress has been made in characterizing and sequencing genomic alterations of biospecimens from several types of cancer. Understanding the functional changes in the human proteome that arise from the genomic alterations or other factors is the next logical step in the development of high-value protein biomarkers that can be transitioned to clinical studies for biomarker qualification. Linking advances in genomic analysis to proteomic analysis will provide a pathway for qualified biomarkers which can drive the rational development of new diagnostics and therapies. The availability of these multidimensional data to the scientific community sets the stage for the development of new molecularly targeted cancer interventions.

  17. Quantitative proteomic assessment of very early cellular signaling events

    DEFF Research Database (Denmark)

    Dengjel, Joern; Akimov, Vyacheslav; Olsen, Jesper V

    2007-01-01

    Technical limitations have prevented proteomic analyses of events occurring less than 30 s after signal initiation. We developed an automated, continuous quench-flow system allowing quantitative proteomic assessment of very early cellular signaling events (qPACE) with a time resolution of 1 s....... Using this technique, we determined that autophosphorylation of the epidermal growth factor receptor occurs within 1 s after ligand stimulation and is followed rapidly by phosphorylation of the downstream signaling intermediates Src homologous and collagen-like protein and phospholipase C gamma 1....

  18. Overexpression of nuclear apoptosis-inducing factor 1 altered the proteomic profile of human gastric cancer cell MKN45 and induced cell cycle arrest at G1/S phase.

    Directory of Open Access Journals (Sweden)

    Mei Yang

    Full Text Available Nuclear apoptosis-inducing factor 1 (NAIF1 was previously reported to induce apoptosis. Moreover, the expression of NAIF1 was significantly down-regulated in human gastric cancer tissues compared to adjacent normal tissues. However, the mechanism by which the NAIF1 gene induces apoptosis is not fully understood. Our results show that NAIF1 was minimally expressed in all the tested gastric cancer cell lines. Our data also demonstrates that NAIF1 is localized in the nuclei of cells as detected by monitoring the green fluorescence of NAIF1-GFP fusion protein using fluorescent confocal microscopy. Next, a comparative proteomic approach was used to identify the differential expression of proteins between gastric cancer cell lines MKN45/NAIF1 (- and MKN45/NAIF1 (+. We found five proteins (proteasome 26S subunit 2, proteasome 26S subunit 13, NADH dehydrogenase Fe-S protein 1, chaperonin containing TCP1 subunit 3 and thioredoxin reductase 1 that were up-regulated and three proteins (ribonuclease inhibitor 1, 14-3-3 protein epsilon isoform and apolipoprotein A-I binding protein that were down-regulated in the MKN45 cells overexpressing NAIF1. We also discovered that NAIF1 could induce cell cycle arrest at G1/S phase by altering the expression of cell cycle proteins cyclinD1, cdc2 and p21. The differentially expressed proteins identified here are related to various cellular programs involving cell cycle, apoptosis, and signal transduction regulation and suggest that NAIF1 may be a tumor suppressor in gastric cancer. Our research provides evidence that elucidates the role of how NAIF1 functions in gastric cancer.

  19. A comparison of the bovine uterine and plasma proteome using iTRAQ proteomics.

    Science.gov (United States)

    Faulkner, Simon; Elia, Giuliano; Mullen, Michael P; O'Boyle, Padraic; Dunn, Michael J; Morris, Dermot

    2012-06-01

    Early embryo loss is a key factor affecting fertility in dairy and beef herds. Prior to implantation, the bovine embryo spends around 16 days free-floating in the uterine environment and is dependent on the composition of uterine fluid for normal growth and development. However, there is a lack of information regarding the protein composition of the bovine uterus and how it relates to plasma. In this study, uterine flushings (UF) (n = 6) and blood plasma (n = 4) were collected from beef heifers on day 7 of the oestrous cycle, albumin depleted and compared using iTRAQ proteomics. A total of 35 proteins were higher and 18 were lower in UF including metabolic enzymes, proteins with anti-oxidant activity and those involved in modulation of the immune response. This study confirms the dynamic nature of the bovine uterine proteome and that it differs from plasma. Factors affecting the uterine proteome and how it impacts on embryo survival warrant further study. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Dynamics of the proteome in human and farm animal milk

    NARCIS (Netherlands)

    Zhang, L.

    2015-01-01

    Abstract

    The milk proteome changes due to many factors, such as lactation, individual, health status, processing, and species differences. The objective of the work described in this thesis was to increase our

  1. Dynamics of the proteome in human and farm animal milk

    NARCIS (Netherlands)

    Zhang, L.

    2015-01-01

    Abstract

    The milk proteome changes due to many factors, such as lactation, individual, health status, processing, and species differences. The objective of the work described in this thesis was to increase our

  2. Proteome analysis of Bordetella pertussis isolated from human macrophages

    Czech Academy of Sciences Publication Activity Database

    Lamberti, Y.; Cafiero, J.H.; Surmann, K.; Valdez, H.; Holubová, Jana; Večerek, Branislav; Šebo, Peter; Schmidt, F.; Völker, U.; Rodriguez, M.E.

    2016-01-01

    Roč. 136, MAY16 (2016), s. 55-67 ISSN 1874-3919 R&D Projects: GA MŠk(CZ) 7AMB14AR028 Institutional support: RVO:61388971 Keywords : Bordetella pertussis * Intracellular survival * Proteomics Subject RIV: EE - Microbiology, Virology Impact factor: 3.914, year: 2016

  3. An efficient proteomic approach to analyze agriculture crop biomass

    Czech Academy of Sciences Publication Activity Database

    Flodrová, Dana; Bobálová, Janette

    2013-01-01

    Roč. 32, č. 5 (2013), s. 365-372 ISSN 1572-3887 R&D Projects: GA MŠk 1M0570 Institutional support: RVO:68081715 Keywords : MALDI * biomass * proteomics * identification * hemicellulases Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.039, year: 2013

  4. Proteomic techniques for characterisation of mesenchymal stem cell secretome.

    Czech Academy of Sciences Publication Activity Database

    Kupcová Skalníková, Helena

    2013-01-01

    Roč. 95, č. 12 (2013), s. 2196-2211 ISSN 0300-9084 R&D Projects: GA MŠk ED2.1.00/03.0124; GA TA ČR TA01011466 Institutional support: RVO:67985904 Keywords : mesenchymal stem cells * secretome * exosome * conditioned medium * proteomics Subject RIV: CE - Biochemistry Impact factor: 3.123, year: 2013

  5. Tribolium castaneum larval gut transcriptome and proteome: A resource for the study of the Coleopteran gut

    Czech Academy of Sciences Publication Activity Database

    Morris, K.; Lorenzen, M. D.; Hiromasa, Y.; Tomich, J. M.; Oppert, C.; Elpidina, E. N.; Vinokurov, Konstantin; Jurat-Fuentes, J. L.; Fabrick, J.; Oppert, B.

    2009-01-01

    Roč. 8, č. 8 (2009), s. 3889-3898 ISSN 1535-3893 Institutional research plan: CEZ:AV0Z50070508 Keywords : Tribolium castaneum * microarray * proteomics Subject RIV: ED - Physiology Impact factor: 5.132, year: 2009

  6. Plant responses to ambient temperature fluctuations and water-limiting conditions: A proteome-wide perspective

    Czech Academy of Sciences Publication Activity Database

    Johnova, P.; Skalák, J.; Saiz-Fernandez, I.; Brzobohatý, Břetislav

    2016-01-01

    Roč. 1864, č. 8 (2016), s. 916-931 ISSN 1570-9639 Institutional support: RVO:68081707 Keywords : Plant proteome * Heat stress * Cold stress Subject RIV: BO - Biophysics Impact factor: 2.773, year: 2016

  7. Proteomic analysis of human tooth pulp proteomes – Comparison of caries-resistant and caries-susceptible

    Czech Academy of Sciences Publication Activity Database

    Jágr, Michal; Eckhardt, Adam; Pataridis, Statis; Foltán, R.; Myšák, J.; Mikšík, Ivan

    2016-01-01

    Roč. 145, Aug 11 (2016), s. 127-136 ISSN 1874-3919 R&D Projects: GA MZd(CZ) NT14324 Institutional support: RVO:67985823 Keywords : human tooth pulp * DIGE * proteome * caries * resistance Subject RIV: FF - HEENT, Dentistry Impact factor: 3.914, year: 2016

  8. A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary

    Czech Academy of Sciences Publication Activity Database

    Gadher, S. J.; Drahos, L.; Vékey, K.; Kovářová, Hana

    2017-01-01

    Roč. 14, č. 7 (2017), s. 567-569 ISSN 1478-9450 R&D Projects: GA MŠk(CZ) LO1609 Institutional support: RVO:67985904 Keywords : CEEPC * proteomics * neuroproteomics * mass spectrometry imaging Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemical research methods Impact factor: 3.849, year: 2016

  9. Proteomic analysis of human tooth pulp: proteomics of human tooth.

    Science.gov (United States)

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

    2014-12-01

    The unique pulp-dentin complex demonstrates strong regenerative potential, which enables it to respond to disease and traumatic injury. Identifying the proteins of the pulp-dentin complex is crucial to understanding the mechanisms of regeneration, tissue calcification, defense processes, and the reparation of dentin by dental pulp. The lack of knowledge of these proteins limits the development of more efficient therapies. The proteomic profile of human tooth pulp was investigated and compared with the proteome of human dentin and blood. The samples of tooth pulp were obtained from 5 sound permanent human third molars of 5 adults (n = 5). The extracted proteins were separated by 2-dimensional gel electrophoresis, analyzed by nano-liquid chromatography tandem mass spectrometry, and identified by correlating mass spectra to the proteomic databases. A total of 342 proteins were identified with high confidence, and 2 proteins were detected for the first time in an actual human sample. The identified tooth pulp proteins have a variety of functions: structural, catalytic, transporter, protease activity, immune response, and many others. In a comparison with dentin and blood plasma, 140 (pulp/dentin) shared proteins were identified, 37 of which were not observed in plasma. It can be suggested that they might participate in the unique pulp-dentin complex. This proteomic investigation of human tooth pulp, together with the previously published study of human dentin, is one of the most comprehensive proteome lists of human teeth to date. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  10. Multipotent adult germline stem cells and embryonic stem cells functional proteomics revealed an important role of eukaryotic initiation factor 5A (Eif5a) in stem cell differentiation.

    Science.gov (United States)

    Dihazi, Hassan; Dihazi, Gry H; Jahn, Olaf; Meyer, Sandra; Nolte, Jessica; Asif, Abdul R; Mueller, Gerhard A; Engel, Wolfgang

    2011-04-01

    Multipotent adult germline stem cells (maGSCs) are pluripotent cells that can be differentiated into somatic cells of the three primary germ layers. To highlight the protein profile changes associated with stem cell differentiation, retinoic acid (RA) treated mouse stem cells (maGSCs and ESCs) were compared to nontreated stem cells. 2-DE and DIGE reference maps were created, and differentially expressed proteins were further processed for identification. In both stem cell types, the RA induced differentiation resulted in an alteration of 36 proteins of which 18 were down-regulated and might be potential pluripotency associated proteins, whereas the other 18 proteins were up-regulated. These might be correlated to stem cell differentiation. Surprisingly, eukaryotic initiation factor 5A (Eif5a), a protein which is essential for cell proliferation and differentiation, was significantly down-regulated under RA treatment. A time-dependent investigation of Eif5a showed that the RA treatment of stem cells resulted in a significant up-regulation of the Eif5a in the first 48 h followed by a progressive down-regulation thereafter. This effect could be blocked by the hypusination inhibitor ciclopirox olamine (CPX). The alteration of Eif5a hypusination, as confirmed by mass spectrometry, exerts an antiproliferative effect on ESCs and maGSCs in vitro, but does not affect the cell pluripotency. Our data highlights the important role of Eif5a and its hypusination for stem cell differentiation and proliferation.

  11. 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

  12. Proteomic Analysis of Chinese Hamster Ovary Cells

    DEFF Research Database (Denmark)

    Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama

    2012-01-01

    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, multidimens......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...

  13. Proteomics in pulmonary research: selected methodical aspects

    Directory of Open Access Journals (Sweden)

    Martin Petrek

    2007-10-01

    Full Text Available Recent years witness rapid expansion of applications of proteomics to clinical research including non-malignant lung disorders. These developments bring along the need for standardisation of proteomic experiments. This paper briefly reviews basic methodical aspects of appliedproteomic studies using SELDI-TOF mass spectrometry platform as example but also emphasizes general aspects of quality assurance in proteomics. Key-words: lung proteome, quality assurance, SELDI-TOF MS

  14. The proteome browser web portal.

    Science.gov (United States)

    Goode, Robert J A; Yu, Simon; Kannan, Anitha; Christiansen, Jeffrey H; Beitz, Anthony; Hancock, William S; Nice, Edouard; Smith, A Ian

    2013-01-04

    In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), aimed at identifying and characterizing the proteome of the human body. To support complete coverage, one arm of the project will take a gene- or chromosomal-centric strategy (C-HPP) aimed at identifying at least one protein product from each protein-coding gene. Despite multiple large international biological databases housing genomic and protein data, there is currently no single system that integrates updated pertinent information from each of these data repositories and assembles the information into a searchable format suitable for the type of global proteomics effort proposed by the C-HPP. We have undertaken the goal of producing a data integration and analysis software system and browser for the C-HPP effort and of making data collections from this resource discoverable through metadata repositories, such as Australian National Data Service's Research Data Australia. Here we present our vision and progress toward the goal of developing a comprehensive data integration and analysis software tool that provides a snapshot of currently available proteomic related knowledge around each gene product, which will ultimately assist in analyzing biological function and the study of human physiology in health and disease.

  15. Maillard Proteomics: Opening New Pages

    Directory of Open Access Journals (Sweden)

    Alena Soboleva

    2017-12-01

    Full Text Available Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer’s disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus, proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.

  16. An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes.

    Directory of Open Access Journals (Sweden)

    Lulu Jia

    Full Text Available BACKGROUND: With the help of proteomics technology, the human plasma and urine proteomes, which closely represent the protein compositions of the input and output of the kidney, respectively, have been profiled in much greater detail by different research teams. Many datasets have been accumulated to form "reference profiles" of the plasma and urine proteomes. Comparing these two proteomes may help us understand the protein handling aspect of kidney function in a way, however, which has been unavailable until the recent advances in proteomics technology. METHODOLOGY/PRINCIPAL FINDINGS: After removing secreted proteins downstream of the kidney, 2611 proteins in plasma and 1522 in urine were identified with high confidence and compared based on available proteomic data to generate three subproteomes, the plasma-only subproteome, the plasma-and-urine subproteome, and the urine-only subproteome, and they correspond to three groups of proteins that are handled in three different ways by the kidney. The available experimental molecular weights of the proteins in the three subproteomes were collected and analyzed. Since the functions of the overrepresented proteins in the plasma-and-urine subproteome are probably the major functions that can be routinely regulated by excretion from the kidney in physiological conditions, Gene Ontology term enrichment in the plasma-and-urine subproteome versus the whole plasma proteome was analyzed. Protease activity, calcium and growth factor binding proteins, and coagulation and immune response-related proteins were found to be enriched. CONCLUSION/SIGNIFICANCE: The comparison method described in this paper provides an illustration of a new approach for studying organ functions with a proteomics methodology. Because of its distinctive input (plasma and output (urine, it is reasonable to predict that the kidney will be the first organ whose functions are further elucidated by proteomic methods in the near future. It

  17. Proteomics of Eosinophil Activation

    Directory of Open Access Journals (Sweden)

    Deane F. Mosher

    2017-09-01

    Full Text Available We recently identified and quantified >7,000 proteins in non-activated human peripheral blood eosinophils using liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS and described phosphoproteomic changes that accompany acute activation of eosinophils by interleukin-5 (IL5 (1. These data comprise a treasure trove of information about eosinophils. We illustrate the power of label-free LC–MS/MS quantification by considering four examples: complexity of eosinophil STATs, contribution of immunoproteasome subunits to eosinophil proteasomes, complement of integrin subunits, and contribution of platelet proteins originating from platelet–eosinophil complexes to the overall proteome. We describe how isobaric labeling enables robust sample-to-sample comparisons and relate the 220 phosphosites that changed significantly upon treatment with IL5 to previous studies of eosinophil activation. Finally, we review previous attempts to leverage the power of mass spectrometry to discern differences between eosinophils of healthy subjects and those with eosinophil-associated conditions and point out features of label-free quantification and isobaric labeling that are important in planning future mass spectrometric studies.

  18. Structural Proteomics of Herpesviruses

    Directory of Open Access Journals (Sweden)

    Baptiste Leroy

    2016-02-01

    Full Text Available 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.

  19. Leaf proteome profiling of transgenic mint infected with Alternaria alternata.

    Science.gov (United States)

    Sinha, Ragini; Bhattacharyya, Dipto; Majumdar, Aparupa Bose; Datta, Riddhi; Hazra, Saptarshi; Chattopadhyay, Sharmila

    2013-11-20

    The genus Mentha has been widely used in food, flavor, culinary, cosmetic and pharmaceutical industries. Substantial damage to this crop happened regularly due to environmental stresses like metal toxicity and pathogen attack. Here, an approach has been taken to raise transgenic mint over-expressing γ-glutamyl-cysteine synthetase (γ-ECS), the rate-limiting enzyme of GSH biosynthesis, resulted enhanced GSH content and its in planta expression confers significant tolerance towards abiotic/biotic stresses viz. metal toxicity - Cd, Zn as well as against infection of Alternaria alternata and Rhizoctonia solani. A differential proteomic analysis through 2-DE and MALDI TOF-TOF MSMS was performed to focus on the altered abundance of functionally important protein species in control and infected transgenic mint. Results showed a significant variation in the protein profile of the infected transgenic plant as compared to the wild/control transgenic counterpart. In addition to protein species related to stress and defense, redox regulation, transcription factors and energy & metabolism, protein species related to signaling and gene regulation as well as cell division also showed differential accumulation in infected transgenic. Hence, proteomics can be used as a tool to decipher the mechanism of action of GSH in providing tolerance against a necrotrophic fungus, A. alternata in transgenic mint. The reported work describes a comparative proteomics of non-model unsequenced plants like Mentha. There is a comparative protein profile between transgenic and its wild counterparts under control and infected condition. The work has an impact in crop proteomics and also tries to explain the application of proteomic approach to decipher the mechanism by which a foreign metabolite mediates stress tolerance in plant under control and infected condition. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Deciphering animal development through proteomics: requirements and prospects

    Directory of Open Access Journals (Sweden)

    Mandato Craig A

    2008-07-01

    Full Text Available Abstract In recent years proteomic techniques have started to become very useful tools in a variety of model systems of developmental biology. Applications cover many different aspects of development, including the characterization of changes in the proteome during early embryonic stages. During early animal development the embryo becomes patterned through the temporally and spatially controlled activation of distinct sets of genes. Patterning information is then translated, from gastrulation onwards, into regional specific morphogenetic cell and tissue movements that give the embryo its characteristic shape. On the molecular level, patterning is the outcome of intercellular communication via signaling molecules and the local activation or repression of transcription factors. Genetic approaches have been used very successfully to elucidate the processes behind these events. Morphogenetic movements, on the other hand, have to be orchestrated through regional changes in the mechanical properties of cells. The molecular mechanisms that govern these changes have remained much more elusive, at least in part due to the fact that they are more under translational/posttranslational control than patterning events. However, recent studies indicate that proteomic approaches can provide the means to finally unravel the mechanisms that link patterning to the generation of embryonic form. To intensify research in this direction will require close collaboration between proteome scientists and developmental researchers. It is with this aim in mind that we first give an outline of the classical questions of patterning and morphogenesis. We then summarize the proteomic approaches that have been applied in developmental model systems and describe the pioneering studies that have been done to study morphogenesis. Finally we discuss current and future strategies that will allow characterizing the changes in the embryonic proteome and ultimately lead to a deeper

  1. Advances of Proteomic Sciences in Dentistry.

    Science.gov (United States)

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

    2016-05-13

    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.

  2. Scientific Workflow Management in Proteomics

    Science.gov (United States)

    de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

    2012-01-01

    Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

  3. 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.

  4. Wheat Proteomics: Proteome modulation and abiotic stress acclimation

    Directory of Open Access Journals (Sweden)

    Setsuko eKomatsu

    2014-12-01

    Full Text Available Cellular mechanisms of stress sensing and signaling represent the initial plant responses to adverse conditions. The development of high-throughput Omics techniques has initiated a new era of the study of plant molecular strategies for adapting to environmental changes. However, the elucidation of stress adaptation mechanisms in plants requires the accurate isolation and characterization of stress-responsive proteins. Because the functional part of the genome, namely the proteins and their post-translational modifications, are critical for plant stress responses, proteomic studies provide comprehensive information about the fine-tuning of cellular pathways that primarily involved in stress mitigation. This review summarizes the major proteomic findings related to alterations in the wheat proteomic profile in response to abiotic stresses. Moreover, the strengths and weaknesses of different sample preparation techniques, including subcellular protein extraction protocols, are discussed in detail. The continued development of proteomic approaches in combination with rapidly evolving bioinformatics tools and interactive databases will facilitate understanding of the plant mechanisms underlying stress tolerance.

  5. Optimization and Modeling of Quadrupole Orbitrap Parameters for Sensitive Analysis toward Single-Cell Proteomics.

    Science.gov (United States)

    Sun, Bingyun; Kovatch, Jessica Rae; Badiong, Albert; Merbouh, Nabyl

    2017-10-06

    Single-cell proteomics represents a field of extremely sensitive proteomic analysis, owing to the minute amount of yet complex proteins in a single cell. Without amplification potential as of nucleic acids, single-cell mass spectrometry (MS) analysis demands special instrumentation running with optimized parameters to maximize the sensitivity and throughput for comprehensive proteomic discovery. To facilitate such analysis, we here investigated two factors critical to peptide sequencing and protein detection in shotgun proteomics, i.e. precursor ion isolation window (IW) and maximum precursor ion injection time (ITmax), on an ultrahigh-field quadrupole Orbitrap (Q-Exactive HF). Counterintuitive to the frequently used proteomic parameters for bulk samples (>100 ng), our experimental data and subsequent modeling suggested a universally optimal IW of 4.0 Th for sample quantity ranging from 100 ng to 1 ng, and a sample-quantity dependent ITmax of more than 250 ms for 1-ng samples. Compared with the benchmark condition of IW = 2.0 Th and ITmax = 50 ms, our optimization generated up to 300% increase to the detected protein groups for 1-ng samples. The additionally identified proteins allowed deeper penetration of proteome for better revealing crucial cellular functions such as signaling and cell adhesion. We hope this effort can prompt single-cell and trace proteomic analysis and enable a rational selection of MS parameters.

  6. Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction.

    Science.gov (United States)

    Gendron, Joshua M; Webb, Kristofor; Yang, Bing; Rising, Lisa; Zuzow, Nathan; Bennett, Eric J

    2016-08-01

    Protein homeostasis dysfunction has been implicated in the development and progression of aging related human pathologies. There is a need for the establishment of quantitative methods to evaluate global protein homoeostasis function. As the ubiquitin (ub) proteasome system plays a key role in regulating protein homeostasis, we applied quantitative proteomic methods to evaluate the sensitivity of site-specific ubiquitylation events as markers for protein homeostasis dysfunction. Here, we demonstrate that the ub-modified proteome can exceed the sensitivity of engineered fluorescent reporters as a marker for proteasome dysfunction and can provide unique signatures for distinct proteome challenges which is not possible with engineered reporters. We demonstrate that combining ub-proteomics with subcellular fractionation can effectively separate degradative and regulatory ubiquitylation events on distinct protein populations. Using a recently developed potent inhibitor of the critical protein homeostasis factor p97/VCP, we demonstrate that distinct insults to protein homeostasis function can elicit robust and largely unique alterations to the ub-modified proteome. Taken together, we demonstrate that proteomic approaches to monitor the ub-modified proteome can be used to evaluate global protein homeostasis and can be used to monitor distinct functional outcomes for spatially separated protein populations. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. 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.

  8. Phenotypic Analysis of Organoids by Proteomics.

    Science.gov (United States)

    Gonneaud, Alexis; Asselin, Claude; Boudreau, François; Boisvert, François-Michel

    2017-10-01

    The development of 3D cell cultures into self-organizing organ-like structures named organoids provides a model that better reflects in vivo organ physiology and their functional properties. Organoids have been established from several organs, such as the intestine, prostate, brain, liver, kidney and pancreas. With recent advances in high-throughput and -omics profiling technologies, it is now possible to study the mechanisms of cellular organisation at the systems level. It is therefore not surprising that these methods are now used to characterize organoids at the transcriptomic, proteomic, chromatin state and transcription factor DNA-binding levels. These approaches can therefore provide a wealth of information regarding both the mechanisms involved in different diseases, and those involved in cell responses to different conditions, in a more in vivo setting. The authors provide an overview of the potential applications of quantitative mass spectrometry with organoid culture, and how the use of large-scale proteome measurements is emerging in different organoid systems. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. A proteomic approach to study parathyroid glands.

    Science.gov (United States)

    Giusti, Laura; Cetani, Filomena; Ciregia, Federica; Da Valle, Ylenia; Donadio, Elena; Giannaccini, Gino; Banti, Chiara; Pardi, Elena; Saponaro, Federica; Basolo, Fulvio; Berti, Piero; Miccoli, Paolo; Pinchera, Aldo; Marcocci, Claudio; Lucacchini, Antonio

    2011-03-01

    Parathyroid tumours are heterogeneous and in some cases the diagnosis may be difficult using histological features. In this study we used a two-dimensional electrophoresis (2D)/mass spectrometry (MS)-based approach to examine the global changes of parathyroid adenoma tissues protein profile compared to the parathyroid normal tissues. Validation of protein expression was performed by immunoblotting using specific antibodies. Ingenuity software was used to identify the biological processes to which these proteins belong and to construct a potential network. A total of 30 proteins were found to be differentially expressed, of which 22 resulted in being over-expressed. Proteins identified by 2D/MS/MS proteomics were classified into functional categories and a major change (≥ 2-fold) in terms of expression was found in proteins involved in response to biotic stimuli, cell organization and signal transduction. After Ingenuity analysis, 14-3-3 ζ/δ appears to be a key protein in the network of parathyroid adenoma, where it is linked to other proteins such as annexin A2, B box and SPRY domain-containing protein (BSPRY), p53 and epidermal growth factor receptor (EGFR). Our results suggest that the proteomic approach was able to differentiate the protein profiles of normal parathyroid and parathyroid adenoma and identify a panel of proteins which are differentially expressed. The functional role of these proteins in the network of intracellular pathways is discussed.

  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 g...

  11. 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...

  12. Unravelling the nuclear matrix proteome

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Knol, Jaco C; Jimenez, Connie R

    2009-01-01

    The nuclear matrix (NM) model posits the presence of a protein/RNA scaffold that spans the mammalian nucleus. The NM proteins are involved in basic nuclear function and are a promising source of protein biomarkers for cancer. Importantly, the NM proteome is operationally defined as the proteins...

  13. Crop and medicinal plants proteomics in response to salt stress

    Directory of Open Access Journals (Sweden)

    Keyvan eAghaei

    2013-01-01

    Full Text Available Increasing of world population marks a serious need to create new crop cultivars and medicinal plants with high growth and production at any environmental situations. Among the environmental unfavorable conditions, salinity is the most widespread in the world. Crop production and growth severely decreases under salt stress; however, some crop cultivars show significant tolerance against the negative effects of salinity. Among salt stress responses of crops, proteomic responses play a pivotal role in their ability to cope with it and have become the main center of notification. Many physiological responses are detectable in terms of protein increase and decrease even before physiological responses take place. Thus proteomic approach makes a short cut in the way of inferring how crops response to salt stress. Nowadays many salt-responsive proteins such as heat shock proteins, pathogen related proteins, protein kinases, ascorbate peroxidase, osmotin, ornithine decarboxylase and some transcription factors, have been detected in some major crops which are thought to give them the ability of withstanding against salt stress. Proteomic analysis of medicinal plants also revealed that alkaloid biosynthesis related proteins such as tryptophan synthase, codeinone reductase, strictosidine synthase and 12-oxophytodienoate reductase might have major role in production of secondary metabolites. In this review we are comparing some different or similar proteomic responses of several crops and medicinal plants to salt stress and discuss about the future prospects.

  14. Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data.

    Science.gov (United States)

    Alessio, Massimo; Cannistraci, Carlo Vittorio

    2016-01-01

    Dimensionality reduction is largely and successfully employed for the visualization and discrimination of patterns, hidden in multidimensional proteomics datasets. Principal component analysis (PCA), which is the preferred approach for linear dimensionality reduction, may present serious limitations, in particular when samples are nonlinearly related, as often occurs in several two-dimensional electrophoresis (2-DE) datasets. An aggravating factor is that PCA robustness is impaired when the number of samples is small in comparison to the number of proteomic features, and this is the case in high-dimensional proteomic datasets, including 2-DE ones. Here, we describe the use of a nonlinear unsupervised learning machine for dimensionality reduction called minimum curvilinear embedding (MCE) that was successfully applied to different biological samples datasets. In particular, we provide an example where we directly compare MCE performance with that of PCA in disclosing neuropathic pain patterns, hidden in a multidimensional proteomic dataset.

  15. Proteomics data exchange and storage: the need for common standards and public repositories.

    Science.gov (United States)

    Jiménez, Rafael C; Vizcaíno, Juan Antonio

    2013-01-01

    Both the existence of data standards and public databases or repositories have been key factors behind the development of the existing "omics" approaches. In this book chapter we first review the main existing mass spectrometry (MS)-based proteomics resources: PRIDE, PeptideAtlas, GPMDB, and Tranche. Second, we report on the current status of the different proteomics data standards developed by the Proteomics Standards Initiative (PSI): the formats mzML, mzIdentML, mzQuantML, TraML, and PSI-MI XML are then reviewed. Finally, we present an easy way to query and access MS proteomics data in the PRIDE database, as a representative of the existing repositories, using the workflow management system (WMS) tool Taverna. Two different publicly available workflows are explained and described.

  16. Aging synaptic mitochondria exhibit dynamic proteomic changes while maintaining bioenergetic function.

    Science.gov (United States)

    Stauch, Kelly L; Purnell, Phillip R; Fox, Howard S

    2014-04-01

    Aging correlates with a progressive impairment of mitochondrial homeostasis and is an influential factor for several forms of neurodegeneration. However, the mechanisms underlying age-related alterations in synaptosomal mitochondria, a neuronal mitochondria population highly susceptible to insults and critical for brain function, remain incompletely understood. Therefore this study investigates the synaptic mitochondrial proteomic and bioenergetic alterations that occur with age. The utilization of a state of the art quantitative proteomics approach allowed for the comparison of protein expression levels in synaptic mitochondria isolated from 5 (mature), 12 (old), and 24 (aged) month old mice. During the process of aging we find that dynamic proteomic alterations occur in synaptic mitochondria. Despite direct (mitochondrial DNA deletions) and indirect (increased antioxidant protein levels) signs of mitochondrial damage in the aged mice, there was an overall maintenance of mitochondrial function. Therefore the synaptic mitochondrial proteomic changes that occur with aging correlate with preservation of synaptic mitochondrial function.

  17. Building ProteomeTools based on a complete synthetic human proteome

    Science.gov (United States)

    Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

    2018-01-01

    The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

  18. Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs

    OpenAIRE

    Gerszten, Robert E.; Accurso, Frank; Bernard, Gordon R.; Caprioli, Richard M.; Klee, Eric W.; Klee, George G.; Kullo, Iftikhar; Laguna, Theresa A.; Roth, Frederick P.; Sabatine, Marc; Srinivas, Pothur; Wang, Thomas J.; Ware, Lorraine B.

    2008-01-01

    The emerging scientific field of proteomics encompasses the identification, characterization, and quantification of the protein content or proteome of whole cells, tissues, or body fluids. The potential for proteomic technologies to identify and quantify novel proteins in the plasma that can function as biomarkers of the presence or severity of clinical disease states holds great promise for clinical use. However, there are many challenges in translating plasma proteomics from bench to bedsid...

  19. Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

  20. Differential proteome analysis of chikungunya virus infection on host cells.

    Directory of Open Access Journals (Sweden)

    Christina Li-Ping Thio

    Full Text Available BACKGROUND: Chikungunya virus (CHIKV is an emerging mosquito-borne alphavirus that has caused multiple unprecedented and re-emerging outbreaks in both tropical and temperate countries. Despite ongoing research efforts, the underlying factors involved in facilitating CHIKV replication during early infection remains ill-characterized. The present study serves to identify host proteins modulated in response to early CHIKV infection using a proteomics approach. METHODOLOGY AND PRINCIPAL FINDINGS: The whole cell proteome profiles of CHIKV-infected and mock control WRL-68 cells were compared and analyzed using two-dimensional gel electrophoresis (2-DGE. Fifty-three spots were found to be differentially modulated and 50 were successfully identified by MALDI-TOF/TOF. Eight were significantly up-regulated and 42 were down-regulated. The mRNA expressions of 15 genes were also found to correlate with the corresponding protein expression. STRING network analysis identified several biological processes to be affected, including mRNA processing, translation, energy production and cellular metabolism, ubiquitin-proteasome pathway (UPP and cell cycle regulation. CONCLUSION/SIGNIFICANCE: This study constitutes a first attempt to investigate alteration of the host cellular proteome during early CHIKV infection. Our proteomics data showed that during early infection, CHIKV affected the expression of proteins that are involved in mRNA processing, host metabolic machinery, UPP, and cyclin-dependent kinase 1 (CDK1 regulation (in favour of virus survival, replication and transmission. While results from this study complement the proteomics results obtained from previous late host response studies, functional characterization of these proteins is warranted to reinforce our understanding of their roles during early CHIKV infection in humans.

  1. Proteomic Investigation of Ram Spermatozoa and the Proteins Conferred by Seminal Plasma.

    Science.gov (United States)

    Pini, Taylor; Leahy, Tamara; Soleilhavoup, Clement; Tsikis, Guillaume; Labas, Valerie; Combes-Soia, Lucie; Harichaux, Gregoire; Rickard, Jessica P; Druart, Xavier; de Graaf, Simon P

    2016-10-07

    Sperm proteomes have emerged for several species; however, the extent of species similarity is unknown. Sheep are an important agricultural species for which a comprehensive sperm proteome has not been produced. In addition, potential proteomic factors from seminal plasma that may contribute to improved fertility after cervical insemination are yet to be explored. Here we use liquid chromatography-tandem mass spectrometry to investigate the proteome of ejaculated ram spermatozoa, with quantitative comparison to epididymal spermatozoa. We also present a comparison to published proteomes of five other species. We identified 685 proteins in ejaculated ram spermatozoa, with the most abundant proteins involved in metabolic pathways. Only 5% of ram sperm proteins were not detected in other species, which suggest highly conserved structures and pathways. Of the proteins present in both epididymal and ejaculated ram spermatozoa, 7% were more abundant in ejaculated spermatozoa. Only two membrane-bound proteins were detected solely in ejaculated sperm lysates: liver enriched gene 1 (LEG1/C6orf58) and epidermal growth factor-like repeats and discoidin I-like domains 3 (EDIL3). This is the first evidence that despite its relatively complex proteomic composition, seminal plasma exposure leads to few novel proteins binding tightly to the ram sperm plasma membrane.

  2. 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...... 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....

  3. Proteome reference map of Drosophila melanogaster head.

    Science.gov (United States)

    Lee, Tian-Ren; Huang, Shun-Hong; Lee, Chi-Ching; Lee, Hsiao-Yun; Chan, Hsin-Tzu; Lin, Kuo-Sen; Chan, Hong-Lin; Lyu, Ping-Chiang

    2012-06-01

    Drosophila melanogaster has been used as a genetic model organism to understand the fundamental molecular mechanisms in human biology including memory formation that has been reported involving protein synthesis and/or post-translational modification. In this study, we employed a proteomic platform based on fluorescent 2DE and MALDI-TOF MS to build a standard D. melanogaster head proteome map for proteome-proteome comparison. In order to facilitate the comparison, an interactive database has been constructed for systematically integrating and analyzing the proteomes from different conditions and further implicated to study human diseases related to D. melanogaster model. In summary, the fundamental head proteomic database and bioinformatic analysis will be useful for further elucidating the biological mechanisms such as memory formation and neurodegenerative diseases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Application of proteomics to hordein screening in the malting process

    Czech Academy of Sciences Publication Activity Database

    Flodrová, Dana; Šalplachta, Jiří; Benkovská, Dagmar; Bobálová, Janette

    2012-01-01

    Roč. 18, č. 3 (2012), s. 323-332 ISSN 1469-0667 R&D Projects: GA MŠk 1M0570; GA MŠk(CZ) EE2.3.20.0182; GA ČR(CZ) GPP503/12/P395 Institutional research plan: CEZ:AV0Z40310501 Keywords : barley * hordein * proteomics * mass spectrometry Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.259, year: 2012

  5. The biology of milk synthesis from a proteomics perspective

    OpenAIRE

    Lu, J.

    2013-01-01

    Large variation in bovine milk composition of Dutch Holstein cows has been observed. The factors influencing the milk synthesis and secretion process in the mammary gland and the variations in this process lead to variation in milk composition. The understanding of milk synthesis was improved during the last decades, however, much is still unknown, especially with regard to lipid synthesis and secretion. In this research, a proteomics technique (FASP-Dimethyl labeling-NanoLC-Orbitrap-MS/MS) w...

  6. T3: Targeted Proteomics of DNA-Binding Proteins

    OpenAIRE

    Nagore, Linda I.; Jarrett, Harry W.

    2015-01-01

    A technique that allows the inclusion of a specific DNA to enrich and direct proteomic identification of transcription factors (TF) while providing a route for high throughput screening on a single platform would be valuable in investigations of gene expression and regulation. Polyvinylpyrrolidone binds DNA avidly while binding negligible amounts of protein. This observation is used in a proof-of-concept method to enrich for TF by combining nuclear extract with a specific DNA sequence and imm...

  7. Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples

    Energy Technology Data Exchange (ETDEWEB)

    Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora; Kitzmiller, Joseph A.; Huang, Eric L.; Zink, Erika M.; Sontag, Ryan L.; Orton, Daniel J.; Moore, Ronald J.; Carson, James P.; Smith, Richard D.; Whitsett, Jeffrey A.; Corley, Richard A.; Ambalavanan, Namasivayam; Ansong, Charles

    2016-12-22

    Global proteomics approaches allow characterization of whole tissue lysates to an impressive depth. However, it is now increasingly recognized that to better understand the complexity of multicellular organisms, global protein profiling of specific spatially defined regions/substructures of tissues (i.e. spatially-resolved proteomics) is essential. Laser capture microdissection (LCM) enables microscopic isolation of defined regions of tissues preserving crucial spatial information. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, and that impact measurement robustness, quantification, and throughput. Here, we coupled LCM with a fully automated sample preparation workflow that with a single manual step allows: protein extraction, tryptic digestion, peptide cleanup and LC-MS/MS analysis of proteomes from microdissected tissues. Benchmarking against the current state of the art in ultrasensitive global proteomic analysis, our approach demonstrated significant improvements in quantification and throughput. Using our LCM-SNaPP proteomics approach, we characterized to a depth of more than 3,400 proteins, the ontogeny of protein changes during normal lung development in laser capture microdissected alveolar tissue containing ~4,000 cells per sample. Importantly, the data revealed quantitative changes for 350 low abundance transcription factors and signaling molecules, confirming earlier transcript-level observations and defining seven modules of coordinated transcription factor/signaling molecule expression patterns, suggesting that a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes. Our LCM-proteomics approach facilitates efficient, spatially-resolved, ultrasensitive global proteomics analyses in high-throughput that will be enabling for several clinical and

  8. Proteomic approaches in research of cyanobacterial photosynthesis.

    Science.gov (United States)

    Battchikova, Natalia; Angeleri, Martina; Aro, Eva-Mari

    2015-10-01

    Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.

  9. Host Proteome Research in HIV Infection

    OpenAIRE

    Zhang, Lijun; Zhang, Xiaojun; Ma, Qing; Zhou, Honghao

    2010-01-01

    Proteomics has been widely used in the last few years to look for new biomarkers and decipher the mechanism of HIV?host interaction. Herein, we review the recent developments of HIV/AIDS proteomic research, including the samples used in HIV/AIDS related research, the technologies used for proteomic study, the diagnosis biomarkers of HIV-associated disease especially HIV-associated neurocognitive impairment, the mechanisms of HIV?host interaction, HIV-associated dementia, substance abuse, and ...

  10. Farm animal proteomics - A review

    DEFF Research Database (Denmark)

    Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin

    2011-01-01

    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......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...... 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...

  11. Analysis of Peanut Leaf Proteome

    DEFF Research Database (Denmark)

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

    2010-01-01

    Peanut (Arachis hypogaea) is one of the most important sources of plant protein. Current selection of genotypes requires molecular characterization of available populations. Peanut genome database has several EST cDNAs which can be used to analyze gene expression. Analysis of proteins is a direct...... 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...... electrophoresis in combination with sequence identification using MALDI/TOF to determine their identity and function related to growth, development and responses to stresses. Peanut leaf proteins were resolved into 300 polypeptides with pI values between 3.5 and 8.0 and relative molecular masses from 12 to 100 k...

  12. Proteomic Investigations into Hemodialysis Therapy

    Science.gov (United States)

    Bonomini, Mario; Sirolli, Vittorio; Pieroni, Luisa; Felaco, Paolo; Amoroso, Luigi; Urbani, Andrea

    2015-01-01

    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(in)compatibility. 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. PMID:26690416

  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. Protein Neighbors and Proximity Proteomics*

    Science.gov (United States)

    Rees, Johanna S.; Li, Xue-Wen; Perrett, Sarah; Lilley, Kathryn S.; Jackson, Antony P.

    2015-01-01

    Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest. PMID:26355100

  15. Proteome analysis of Aspergillus ochraceus.

    Science.gov (United States)

    Rizwan, Muhammad; Miller, Ingrid; Tasneem, Fareeha; Böhm, Josef; Gemeiner, Manfred; Razzazi-Fazeli, Ebrahim

    2010-08-01

    Genome sequencing for many important fungi has begun during recent years; however, there is still some deficiency in proteome profiling of aspergilli. To obtain a comprehensive overview of proteins and their expression, a proteomic approach based on 2D gel electrophoresis and MALDI-TOF/TOF mass spectrometry was used to investigate A. ochraceus. The cell walls of fungi are exceptionally resistant to destruction, therefore two lysis protocols were tested: (1) lysis via manual grinding using liquid nitrogen, and (2) mechanical lysis via rapid agitation with glass beads using MagNalyser. Mechanical grinding with mortar and pestle using liquid nitrogen was found to be a more efficient extraction method for our purpose, resulting in extracts with higher protein content and a clear band pattern in SDS-PAGE. Two-dimensional electrophoresis gave a complex spot pattern comprising proteins of a broad range of isoelectric points and molecular masses. The most abundant spots were subjected to mass spectrometric analysis. We could identify 31 spots representing 26 proteins, most of them involved in metabolic processes and response to stress. Seventeen spots were identified by de novo sequencing due to a lack of DNA and protein database sequences of A. ochraceus. The proteins identified in our study have been reported for the first time in A. ochraceus and this represents the first proteomic approach with identification of major proteins, when the fungus was grown under submerged culture.

  16. The beta subunit of glyceraldehyde 3-phosphate dehydrogenase is an important factor for maintaining photosynthesis and plant development under salt stress-Based on an integrative analysis of the structural, physiological and proteomic changes in chloroplasts in Thellungiella halophila.

    Science.gov (United States)

    Chang, Lili; Guo, Anping; Jin, Xiang; Yang, Qian; Wang, Dan; Sun, Yong; Huang, Qixing; Wang, Limin; Peng, Cunzhi; Wang, Xuchu

    2015-07-01

    Thellungiella halophila, a new model halophyte, can survive under highly saline conditions. We performed comparative proteomics of chloroplasts from plants grown under different saline conditions. Seventy-five salt-responsive proteins were positively identified by mass spectrometry, which represented 43 unique ones. These proteins were categorized into 7 main pathways: light reaction, carbon fixation, energy metabolism, antenna proteins, cell structure, and protein degradation and folding. Saline conditions increased the abundance of proteins involved in photosynthesis, energy metabolism and cell structure. The results indicated that Thellungiella could withstand high salinity by maintaining normal or high photosynthetic capacity, reducing ROS production, as well as enhancing energy usage. Meanwhile, the ultrastructural and physiological data also agree with chloroplast proteomics results. Subsequently, the glyceraldehydes 3-phosphate dehydrogenase beta subunit (GAPB) involved in carbon fixation was selected and its role in salt tolerance was clarified by over-expressing it in Arabidopsis. ThGAPB-overexpressing plants had higher total chlorophyll contents, dry weights, water contents and survival rates than that of wild type plants. These results indicated that ThGAPB might improve plant salt tolerance by maintaining higher recycling rates of ADP and NADP(+) to decrease ROS production, helping to maintain photosynthetic efficiency and plant development under saline conditions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. 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

  18. Proteomics reveals the effects of sustained weight loss on the human plasma proteome

    DEFF Research Database (Denmark)

    Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

    2016-01-01

    Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed...... in the plasma proteome, and eight plasma proteins correlated better with insulin resistance than the known marker adiponectin. Nearly all study participants benefited from weight loss regarding a ten-protein inflammation panel defined from the proteomics data. We conclude that plasma proteome profiling broadly...... by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...

  19. Effects of three commonly-used diuretics on the urinary proteome.

    Science.gov (United States)

    Li, Xundou; Zhao, Mindi; Li, Menglin; Jia, Lulu; Gao, Youhe

    2014-06-01

    Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F; hydrochlorothiazide, H; and spirolactone, S) on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Based on the criteria of P≤0.05, a fold change ≥2, a spectral count ≥5, and false positive rate (FDR) ≤1%, 14 proteins (seven for F, five for H, and two for S) were identified by Progenesis LC-MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics. Copyright © 2014. Production and hosting by Elsevier Ltd.

  20. Effects of Three Commonly-used Diuretics on the Urinary Proteome

    Directory of Open Access Journals (Sweden)

    Xundou Li

    2014-06-01

    Full Text Available Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F; hydrochlorothiazide, H; and spirolactone, S on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography–tandem mass spectrometry (LC–MS/MS. Based on the criteria of P ⩽ 0.05, a fold change ⩾2, a spectral count ⩾5, and false positive rate (FDR ⩽1%, 14 proteins (seven for F, five for H, and two for S were identified by Progenesis LC–MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics.

  1. Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells

    International Nuclear Information System (INIS)

    Liu, Xia; Zhao, Libo; Yang, Yongtao; Bode, Liv; Huang, Hua; Liu, Chengyu; Huang, Rongzhong; Zhang, Liang

    2014-01-01

    Background: Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. Methods: Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. Results: Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. Conclusions: BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells. - Highlights: • A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). • This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells. • BDV infection affected the expression of many transcription factors and several HATs and HDACs

  2. Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xia [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Department of Neurology, The Fifth People' s Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, 200240 (China); Zhao, Libo [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Department of Neurology, The Third People' s Hospital of Chongqing, 400014 (China); Yang, Yongtao [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); Bode, Liv [Bornavirus Research Group affiliated to the Free University of Berlin, Berlin (Germany); Huang, Hua [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); Liu, Chengyu [Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); Huang, Rongzhong [Department of Rehabilitative Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010 (China); Zhang, Liang [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 (China); Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, 400016 (China); Institute of Neuroscience, Chongqing Medical University, Chongqing, 400016 (China); and others

    2014-09-15

    Background: Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. Methods: Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. Results: Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. Conclusions: BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells. - Highlights: • A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). • This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells. • BDV infection affected the expression of many transcription factors and several HATs and HDACs.

  3. Integrating cell biology and proteomic approaches in plants.

    Science.gov (United States)

    Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

    2017-10-03

    Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

  4. A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin*

    Science.gov (United States)

    Völker-Albert, Moritz Carl; Pusch, Miriam Caroline; Fedisch, Andreas; Schilcher, Pierre; Schmidt, Andreas; Imhof, Axel

    2016-01-01

    The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone proteins that associate with it. These factors help to establish and maintain a largely DNA sequence-independent but surprisingly stable structure. Chromatin is extensively disassembled and reassembled during DNA replication, repair, recombination or transcription in order to allow the necessary factors to gain access to their substrate. Despite such constant interference with chromatin structure, the epigenetic information is generally well maintained. Surprisingly, the mechanisms that coordinate chromatin assembly and ensure proper assembly are not particularly well understood. Here, we use label free quantitative mass spectrometry to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos. The use of a data independent acquisition method for proteome wide quantitation allows a time resolved comparison of in vitro chromatin assembly. A comparison of our in vitro data with proteomic studies of replicative chromatin assembly in vivo reveals an extensive overlap showing that the in vitro system can be used for investigating the kinetics of chromatin assembly in a proteome-wide manner. PMID:26811354

  5. Proteomic and Genetic Approaches Identify Syk as an AML Target

    Science.gov (United States)

    Hahn, Cynthia K.; Berchuck, Jacob E.; Ross, Kenneth N.; Kakoza, Rose M.; Clauser, Karl; Schinzel, Anna C.; Ross, Linda; Galinsky, Ilene; Davis, Tina N.; Silver, Serena J.; Root, David E.; Stone, Richard M.; DeAngelo, Daniel J.; Carroll, Martin; Hahn, William C.; Carr, Steven A.; Golub, Todd R.; Kung, Andrew L.; Stegmaier, Kimberly

    2009-01-01

    SUMMARY Cell-based screening can facilitate rapid identification of compounds inducing complex cellular phenotypes. Advancing a compound toward the clinic, however, generally requires identification of precise mechanisms of action. We previously found that epidermal growth factor receptor (EGFR) inhibitors induce acute myeloid leukemia (AML) differentiation via a non-EGFR mechanism. In this report, we integrated proteomic and RNAi-based strategies to identify their off-target anti-AML mechanism. These orthogonal approaches identified Syk as a target in AML. Genetic and pharmacological inactivation of Syk with a drug in clinical trial for other indications promoted differentiation of AML cells and attenuated leukemia growth in vivo. These results demonstrate the power of integrating diverse chemical, proteomic, and genomic screening approaches to identify therapeutic strategies for cancer. PMID:19800574

  6. 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...

  7. 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...

  8. Dynamics of nuclear matrix proteome during embryonic ...

    Indian Academy of Sciences (India)

    Drosophila melanogaster embryos and show that 65% of the NuMat proteome is dynamic during development. Our ... [Varma P and Mishra RK 2011 Dynamics of nuclear matrix proteome during embryonic development in Drosophila melanogaster. J. Biosci. 36 .... functional group X, D = Number of proteins unique to late.

  9. Applications of Proteomic Technologies to Toxicology

    Science.gov (United States)

    Proteomics is the large-scale study of gene expression at the protein level. This cutting edge technology has been extensively applied to toxicology research recently. The up-to-date development of proteomics has presented the toxicology community with an unprecedented opportunit...

  10. 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...

  11. 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…

  12. Comparative mitochondrial proteomics: perspective in human diseases

    Directory of Open Access Journals (Sweden)

    Jiang Yujie

    2012-03-01

    Full Text Available Abstract Mitochondria are the most complex and the most important organelles of eukaryotic cells, which are involved in many cellular processes, including energy metabolism, apoptosis, and aging. And mitochondria have been identified as the "hot spot" by researchers for exploring relevant associated dysfunctions in many fields. The emergence of comparative proteomics enables us to have a close look at the mitochondrial proteome in a comprehensive and effective manner under various conditions and cellular circumstances. Two-dimensional electrophoresis combined with mass spectrometry is still the most popular techniques to study comparative mitochondrial proteomics. Furthermore, many new techniques, such as ICAT, MudPIT, and SILAC, equip researchers with more flexibilities inselecting proper methods. This article also reviews the recent development of comparative mitochondrial proteomics on diverse human diseases. And the results of mitochondrial proteomics enhance a better understanding of the pathogenesis associated with mitochondria and provide promising therapeutic targets.

  13. Proteomic Analyses of the Vitreous Humour

    Directory of Open Access Journals (Sweden)

    Martina Angi

    2012-01-01

    Full Text Available The human vitreous humour (VH is a transparent, highly hydrated gel, which occupies the posterior segment of the eye between the lens and the retina. Physiological and pathological conditions of the retina are reflected in the protein composition of the VH, which can be sampled as part of routine surgical procedures. Historically, many studies have investigated levels of individual proteins in VH from healthy and diseased eyes. In the last decade, proteomics analyses have been performed to characterise the proteome of the human VH and explore networks of functionally related proteins, providing insight into the aetiology of diabetic retinopathy and proliferative vitreoretinopathy. Recent proteomic studies on the VH from animal models of autoimmune uveitis have identified new signalling pathways associated to autoimmune triggers and intravitreal inflammation. This paper aims to guide biological scientists through the different proteomic techniques that have been used to analyse the VH and present future perspectives for the study of intravitreal inflammation using proteomic analyses.

  14. 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.

  15. Proteomic Studies on Human and Experimental Cerebral Malaria

    KAUST Repository

    Moussa, Ehab

    2012-07-01

    Cerebral malaria (CM) is a severe neurological complication of malaria infection that results from interrelated pathologies. Despite extensive research efforts, the mechanism of the disease is not completely understood. Clinical studies, postmortem analysis, and animal models have been the main research arenas in CM. In this thesis, shotgun proteomics approach was used to further understand the pathology of human and experimental CM. The mechanism by which CM turns fatal is yet to be identified. A clinical proteomics study was conducted on pooled plasma samples from children with reversible or fatal CM from the Gambia. The results show that depletion of coagulation factors and increased levels of circulating proteasomes are associated with fatal pediatric CM. This data suggests that the ongoing coagulation during CM might be a disseminated intravascular coagulation state that eventually causes depletion of the coagulation factors leading to petechial hemorrhages. In addition, the mechanism(s) by which blood transfusion benefits CM in children was investigated. To that end, the concentration and multimerization pattern of von-willebrand factor, and the concentration of haptoglobin in the plasma of children with CM who received blood transfusions were measured. In addition to clinical studies, experimental cerebral malaria (ECM) in mice has been long used as a model for the disease. A shotgun proteomics workflow was optimized to identify the proteomic signature of the brain tissue of mice with ECM.Because of the utmost importance of membrane proteins in the pathology of the disease, sample fractionation and filter aided sample preparation were used to recover them. The proteomic signature of the brains of mice infected with P. berghei ANKA that developed neurological syndrome, mice infected with P. berghei NK56 that developed severe malaria but without neurological signs, and non-infected mice, were compared to identify CM specific proteins. Among the differentially

  16. Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

    Science.gov (United States)

    Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

    2017-01-01

    No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as

  17. The proteome of Populus nigra woody root: response to bending

    Science.gov (United States)

    Trupiano, Dalila; Rocco, Mariapina; Renzone, Giovanni; Scaloni, Andrea; Viscosi, Vincenzo; Chiatante, Donato; Scippa, Gabriella S.

    2012-01-01

    Background and Aims Morphological and biomechanical alterations occurring in woody roots of many plant species in response to mechanical stresses are well documented; however, little is known about the molecular mechanisms regulating these important alterations. The first forest tree genome to be decoded is that of Populus, thereby providing a tool with which to investigate the mechanisms controlling adaptation of woody roots to changing environments. The aim of this study was to use a proteomic approach to investigate the response of Populus nigra woody taproot to mechanical stress. Methods To simulate mechanical perturbations, the taproots of 30 one-year-old seedlings were bent to an angle of 90 ° using a steel net. A spatial and temporal two-dimensional proteome map of the taproot axis was obtained. We compared the events occurring in the above-bending, central bending and below-bending sectors of the taproot. Key Results The first poplar woody taproot proteome map is reported here; a total of 207 proteins were identified. Spatial and temporal proteomic analysis revealed that factors involved in plant defence, metabolism, reaction wood formation and lateral root development were differentially expressed in the various sectors of bent vs. control roots, seemingly in relation to the distribution of mechanical forces along the stressed woody taproots. A complex interplay among different signal transduction pathways involving reactive oxygen species appears to modulate these responses. Conclusions Poplar woody root uses different temporal and spatial mechanisms to respond to mechanical stress. Long-term bending treatment seem to reinforce the defence machinery, thereby enabling the taproot to better overcome winter and to be ready to resume growth earlier than controls. PMID:22437664

  18. A decade of Central and Eastern European Proteomic Conference (CEEPC): Credibility, cohesion and vision for the next decade

    Czech Academy of Sciences Publication Activity Database

    Gadher, S. J.; Kovářová, Hana

    2017-01-01

    Roč. 153, S1 (2017), s. 2-7 ISSN 1874-3919. [Central and Eastern European Proteomics Conference /10./. Budapest, 11.10.2016-14.10.2016] R&D Projects: GA MŠk(CZ) LO1609 Institutional support: RVO:67985904 Keywords : CEEPC * protein diveristy * proteome Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemical research methods Impact factor: 3.914, year: 2016

  19. Exploring the potential of public proteomics data.

    Science.gov (United States)

    Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Raeder, Helge; Berven, Frode S; Martens, Lennart; Vizcaíno, Juan A; Barsnes, Harald

    2016-01-01

    In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data. © 2015 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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.

  2. 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.

  3. Principles of proteome allocation are revealed using proteomic data and genome-scale models

    DEFF Research Database (Denmark)

    Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

    2016-01-01

    , prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and "hedging" against uncertain environments and stresses, as indicated by significant enrichment...... of these sectors for the general stress response sigma factor sigma(S). Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally......-related protein groups) as demonstrated here. This flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models....

  4. Identification of redox-sensitive cysteines in the arabidopsis proteome using OxiTRAQ, a quantitative redox proteomics method

    KAUST Repository

    Liu, Pei

    2014-01-28

    Cellular redox status plays a key role in mediating various physiological and developmental processes often through modulating activities of redox-sensitive proteins. Various stresses trigger over-production of reactive oxygen/nitrogen species which lead to oxidative modifications of redox-sensitive proteins. Identification and characterization of redox-sensitive proteins are important steps toward understanding molecular mechanisms of stress responses. Here, we report a high-throughput quantitative proteomic approach termed OxiTRAQ for identifying proteins whose thiols undergo reversible oxidative modifications in Arabidopsis cells subjected to oxidative stress. In this approach, a biotinylated thiol-reactive reagent is used for differential labeling of reduced and oxidized thiols. The biotin-tagged peptides are affinity purified, labeled with iTRAQ reagents, and analyzed using a paralleled HCD-CID fragmentation mode in an LTQ-Orbitrap. With this approach, we identified 195 cysteine-containing peptides from 179 proteins whose thiols underwent oxidative modifications in Arabidopsis cells following the treatment with hydrogen peroxide. A majority of those redox-sensitive proteins, including several transcription factors, were not identified by previous redox proteomics studies. This approach allows identification of the specific redox-regulated cysteine residues, and offers an effective tool for elucidation of redox proteomes. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Proteomics reveals the effects of sustained weight loss on the human plasma proteome

    DEFF Research Database (Denmark)

    Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

    2016-01-01

    in the plasma proteome, and eight plasma proteins correlated better with insulin resistance than the known marker adiponectin. Nearly all study participants benefited from weight loss regarding a ten-protein inflammation panel defined from the proteomics data. We conclude that plasma proteome profiling broadly...... affected proteins. The adipocyte-secreted SERPINF1 and apolipoprotein APOF1 were most significantly regulated with fold changes of -16% and +37%, respectively (P

  6. Proteome Regulation during Olea europaea Fruit Development

    DEFF Research Database (Denmark)

    Bianco, Linda; Alagna, Fiammetta; Baldoni, Luciana

    2013-01-01

    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 different...... 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 of cv...

  7. Accounting for Population Variation in Targeted Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Fujimoto, Grant M.; Monroe, Matthew E.; Rodriguez, Larissa; Wu, Chaochao; MacLean, Brendan; Smith, Richard D.; MacCoss, Michael J.; Payne, Samuel H.

    2014-01-03

    Individual proteomes typically differ from the reference human proteome at ~10,000 single amino acid variants. When viewed at the population scale, this individual variation results in a wide variety of protein sequences. In targeted proteomics experiments, such variability would confound accurate protein quantification. To facilitate researchers in identifying target peptides with high variability within the human population we have created the Population Variation plug-in for Skyline, which provides easy access to the polymorphisms stored in dbSNP. Given a set of peptides, the tool reports minor allele frequency for common polymorphisms. We highlight the importance of considering genetic variation by applying the tool to public datasets.

  8. 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....

  9. 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 describes...

  10. A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration.

    Science.gov (United States)

    Petersen, Hendrik O; Höger, Stefanie K; Looso, Mario; Lengfeld, Tobias; Kuhn, Anne; Warnken, Uwe; Nishimiya-Fujisawa, Chiemi; Schnölzer, Martina; Krüger, Marcus; Özbek, Suat; Simakov, Oleg; Holstein, Thomas W

    2015-08-01

    The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Proteomics and posttranslational proteomics of seed dormancy and germination.

    Science.gov (United States)

    Rajjou, Loïc; Belghazi, Maya; Catusse, Julie; Ogé, Laurent; Arc, Erwann; Godin, Béatrice; Chibani, Kamel; Ali-Rachidi, Sonia; Collet, Boris; Grappin, Philippe; Jullien, Marc; Gallardo, Karine; Job, Claudette; Job, Dominique

    2011-01-01

    The seed is the dispersal unit of plants and must survive the vagaries of the environment. It is the object of intense genetic and genomic studies because processes related to seed quality affect crop yield and the seed itself provides food for humans and animals. Presently, the general aim of postgenomics analyses is to understand the complex biochemical and molecular processes underlying seed quality, longevity, dormancy, and vigor. Due to advances in functional genomics, the recent past years have seen a tremendous progress in our understanding of several aspects of seed development and germination. Here, we describe the proteomics protocols (from protein extraction to mass spectrometry) that can be used to investigate several aspects of seed physiology, including germination and its hormonal regulation, dormancy release, and seed longevity. These techniques can be applied to the study of both model plants (such as Arabidopsis) and crops.

  12. Proteomics-grade de novo sequencing approach

    DEFF Research Database (Denmark)

    Savitski, Mikhail M; Nielsen, Michael L; Kjeldsen, Frank

    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...

  13. Proteomic survey of metabolic pathways in rice.

    Science.gov (United States)

    Koller, Antonius; Washburn, Michael P; Lange, B Markus; Andon, Nancy L; Deciu, Cosmin; Haynes, Paul A; Hays, Lara; Schieltz, David; Ulaszek, Ryan; Wei, Jing; Wolters, Dirk; Yates, John R

    2002-09-03

    A systematic proteomic analysis of rice (Oryza sativa) leaf, root, and seed tissue using two independent technologies, two-dimensional gel electrophoresis followed by tandem mass spectrometry and multidimensional protein identification technology, allowed the detection and identification of 2,528 unique proteins, which represents the most comprehensive proteome exploration to date. A comparative display of the expression patterns indicated that enzymes involved in central metabolic pathways are present in all tissues, whereas metabolic specialization is reflected in the occurrence of a tissue-specific enzyme complement. For example, tissue-specific and subcellular compartment-specific isoforms of ADP-glucose pyrophosphorylase were detected, thus providing proteomic confirmation of the presence of distinct regulatory mechanisms involved in the biosynthesis and breakdown of separate starch pools in different tissues. In addition, several previously characterized allergenic proteins were identified in the seed sample, indicating the potential of proteomic approaches to survey food samples with regard to the occurrence of allergens.

  14. Proteomics Applications in Dental Derived Stem Cells.

    Science.gov (United States)

    Li, Jie; Tian, Weidong; Song, Jinlin

    2017-07-01

    At present, the existence of a variety of dental derived stem cells has been documented. These cells displayed promising clinical application potential not only for teeth and its surrounding tissue regeneration, but also for other tissues, such as nerve and bone regeneration. Proteomics is an unbiased, global informatics tool that provides information on all protein expression levels as well as post-translational modification in cells or tissues and is applicable to dental derived stem cells research. Over the last decade, considerable progress has been made to study the global proteome, secrotome, and membrane proteome of dental derived stem cells. Here, we present an overview of the proteomics studies in the context of stem cell research. Particular attention is given to dental derived stem cell types as well as current challenges and opportunities. J. Cell. Physiol. 232: 1602-1610, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  15. 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. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Media | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The Office of Cancer Clinical Proteomics Research (OCCPR) is committed to providing the media with timely and accurate information.  This section offers key resources for patients, cancer researchers, physicians, and media professionals.

  17. Plasma proteome analysis of cervical intraepithelial neoplasia

    Indian Academy of Sciences (India)

    ... Malaysia and University of Malaya Centre For Proteomics Research (UMCPR), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia; Department of Clinical Oral Biology, Faculty of Dentistry; Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia; Department of Obstetrics and Gynecology; Universiti Kebangsaan ...

  18. Subnuclear proteomics in colorectal cancer

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Knol, Jaco C; Piersma, Sander R

    2010-01-01

    for early cancer detection. Here we evaluate a proteomics work flow for profiling protein constituents in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples. First, we......Abnormalities in nuclear phenotype and chromosome structure are key features of cancer cells. Investigation of the protein determinants of nuclear subfractions in cancer may yield molecular insights into aberrant chromosome function and chromatin organization and in addition may yield biomarkers...... with statistics, we identified proteins that are significantly enriched in the nuclear matrix fraction relative to two earlier fractions (the chromatin-binding and intermediate filament fractions) isolated from six colorectal tissue samples. The total data set contained 2,059 non-redundant proteins. Gene ontology...

  19. Embryology in the era of proteomics.

    Science.gov (United States)

    Katz-Jaffe, Mandy G; McReynolds, Susanna

    2013-03-15

    Proteomic technologies have begun providing evidence that viable embryos possess unique protein profiles. Some of these potential protein biomarkers have been identified as extracellular and could be used in the development of a noninvasive quantitative method for embryo assessment. The field of assisted reproductive technologies would benefit from defining the human embryonic proteome and secretome, thereby expanding our current knowledge of embryonic cellular processes. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  20. 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.

  1. Proteomics

    DEFF Research Database (Denmark)

    Tølbøll, Trine H; Danscher, Anne Mette; Andersen, Pia H

    2012-01-01

    Claw horn disruption (CHD) is a common underlying cause of lameness in dairy cattle which leads to compromised animal welfare and production losses. Despite an intense research effort over the last two decades, progress in reducing the prevalence of lameness due to CHD has been limited. In additi...

  2. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Embryology in the era of proteomics.

    Science.gov (United States)

    Katz-Jaffe, M G; Gardner, D K

    2007-09-01

    Currently, relatively little is known regarding the protein production of mammalian embryos. Unlike the genome, the proteome itself is dynamic reflecting both internal and external environmental stimuli. Until now the lack of sensitivity has remained a stumbling block for the global introduction of proteomics into the field of mammalian embryology. However, new developments in mass spectrometry have been revolutionary, utilizing protein profiling and peptide sequencing to elucidate underlying biological processes. The sensitivity of these platforms have allowed for the development of new protocols that are capable of profiling the proteome of individual mammalian oocytes and embryos. This information is fundamental to unravelling the complexity of embryo physiology including the dialogue between the developing embryo and its maternal environment. Such proteomic approaches are also assisting in the optimization of ART techniques, including oocyte cryopreservation and in vitro maturation. Embryo selection for transfer is another area of ART that should benefit in this era of proteomics. Currently, mammalian embryos are selected for transfer based on morphological grading systems. Although of great value, analysis of morphology alone cannot determine the embryo's physiological state or chromosomal complement. Subsequently, there is a need to identify in culture those embryos with the highest implantation potential. Proteomic analysis of the embryonic secretome (proteins produced by the embryo and secreted into the surrounding medium) followed by the identification of specific proteins critical for implantation, may lead to the development of a non-invasive viability assay to assist in the selection of embryos for transfer.

  4. Proteomics methods applied to malaria: Plasmodium falciparum

    International Nuclear Information System (INIS)

    Cuesta Astroz, Yesid; Segura Latorre, Cesar

    2012-01-01

    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.

  5. 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

    2015-09-04

    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.

  6. Proteomics: A new perspective for cancer

    Directory of Open Access Journals (Sweden)

    Basavaradhya Sahukar Shruthi

    2016-01-01

    Full Text Available In the past decades, several ground breaking discoveries in life science were made. The completion of sequencing the human genome certainly belongs to the key tasks successfully completed, representing a true milestone in the biomedicine. The accomplishment of the complete genome also brings along a new, even more challenging task for scientists: The characterization of the human proteome. Proteomics, the main tool for proteome research, is a relatively new and extremely dynamically evolving branch of science, focused on the evaluation of gene expression at proteome level. Due to the specific properties of proteins, current proteomics deals with different issues, such as protein identification, quantification, characterization of post-translational modification, structure and function elucidation, and description of possible interactions. This field incorporates technologies that can be applied to serum and tissue in order to extract important biological information in the form of biomarkers to aid clinicians and scientists in understanding the dynamic biology of their system of interest, such as a patient with cancer. The present review article provides a detail description of proteomics and its role in cancer research.

  7. Ozone inhalation modifies the rat liver proteome

    Directory of Open Access Journals (Sweden)

    Whitney S. Theis

    2014-01-01

    Full Text Available Ozone (O3 is a serious public health concern. Recent findings indicate that the damaging health effects of O3 extend to multiple systemic organ systems. Herein, we hypothesize that O3 inhalation will cause downstream alterations to the liver. To test this, male Sprague-Dawley rats were exposed to 0.5 ppm O3 for 8 h/day for 5 days. Plasma liver enzyme measurements showed that 5 day O3 exposure did not cause liver cell death. Proteomic and mass spectrometry analysis identified 10 proteins in the liver that were significantly altered in abundance following short-term O3 exposure and these included several stress responsive proteins. Glucose-regulated protein 78 and protein disulfide isomerase increased, whereas glutathione S-transferase M1 was significantly decreased by O3 inhalation. In contrast, no significant changes were detected for the stress response protein heme oxygenase-1 or cytochrome P450 2E1 and 2B in liver of O3 exposed rats compared to controls. In summary, these results show that an environmentally-relevant exposure to inhaled O3 can alter the expression of select proteins in the liver. We propose that O3 inhalation may represent an important unrecognized factor that can modulate hepatic metabolic functions.

  8. Impact of urbanization of the proteome of birch pollen and its chemotactic activity on human granulocytes

    NARCIS (Netherlands)

    Bryce, M.; Drews, O.; Schenk, M.F.; Menzel, A.; Estrella, N.; Weichenmeier, I.; Smulders, M.J.M.; Buters, J.; Ring, J.; Gorg, A.; Behrendt, H.; Traidl-Hoffmann, C.

    2010-01-01

    Background: Epidemiologic studies reveal a dramatic increase in allergies in the last decades. Air pollution is considered to be one of the factors responsible for this augmentation. The aim of this study was to analyze the impact of urbanization on birch pollen. The birch pollen proteome was

  9. Identification and functionality of proteomes secreted by rat cardiac stem cells and neonatal cardiomyocytes

    Czech Academy of Sciences Publication Activity Database

    Šťastná, Miroslava; Chimenti, I.; Marban, E.; Van Eyk, J.E.

    2010-01-01

    Roč. 10, č. 2 (2010), s. 245-253 ISSN 1615-9853 Institutional research plan: CEZ:AV0Z40310501 Keywords : animal proteomics * cardiac stem cells * neonatal cardiomyocytes Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.815, year: 2010

  10. Specificity of secreted proteomes from cardiac stem cells and neonatal myocytes

    Czech Academy of Sciences Publication Activity Database

    Šťastná, Miroslava; Chimenti, I.; Marban, E.; Van Eyk, J.

    2009-01-01

    Roč. 276, Suppl.1 (2009), s. 346 ISSN 1742-464X. [FEBS Congress /34./. 04.07.2009-09.07.2009, Prague] Institutional research plan: CEZ:AV0Z40310501 Keywords : cardiac stem cells * secreted paracrine/autocrine factors * proteomics Subject RIV: CB - Analytical Chemistry, Separation

  11. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics

    DEFF Research Database (Denmark)

    Blagoev, Blagoy; Ong, S.E.; Kratchmarova, Irina

    2004-01-01

    To study the global dynamics of phosphotyrosine-based signaling events in early growth factor stimulation, we developed a mass spectrometric method that converts temporal changes to differences in peptide isotopic abundance. The proteomes of three cell populations were metabolically encoded with ...

  12. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

    DEFF Research Database (Denmark)

    Blagoev, B.; Kratchmarova, I.; Ong, S.E.

    2003-01-01

    Mass spectrometry-based proteomics can reveal protein-protein interactions on a large scale, but it has been difficult to separate background binding from functionally important interactions and still preserve weak binders. To investigate the epidermal growth factor receptor (EGFR) pathway, we em...

  13. Proteome modification in tomato plants upon long-term aluminum treatment

    Science.gov (United States)

    This study aimed to identify the aluminum (Al)-induced proteomes in tomato (Solanum lycopersicum, “Micro-Tom”) after long-term exposure to the stress factor. Plants were treated in Magnavaca’s solution (pH 4.5) supplemented with 7.5 uM Al3+ ion activity over a 4 month period beginning at the emergen...

  14. Microbial genomics, transcriptomics and proteomics: new discoveries in microbial decomposition research using complementary methods

    Czech Academy of Sciences Publication Activity Database

    Baldrian, Petr; López-Mondéjar, Rubén

    2014-01-01

    Roč. 98, č. 4 (2014), s. 1531-1537 ISSN 0175-7598 R&D Projects: GA MŠk LD12050; GA MŠk(CZ) EE2.3.30.0003 Institutional support: RVO:61388971 Keywords : decomposition * genomics * proteomics * saprotrophic fungi * bacteria Subject RIV: EE - Microbiology, Virology Impact factor: 3.337, year: 2014

  15. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

    DEFF Research Database (Denmark)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

    2014-01-01

    replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors...

  16. Global Changes in the Rat Heart Proteome Induced by Prolonged Morphine Treatment and Withdrawal

    Czech Academy of Sciences Publication Activity Database

    Drastichová, Z.; Škrabalová, J.; Jedelský, P.; Neckář, Jan; Kolář, František; Novotný, J.

    2012-01-01

    Roč. 7, č. 10 (2012), e47167 E-ISSN 1932-6203 R&D Projects: GA AV ČR(CZ) IAA501110901 Institutional support: RVO:67985823 Keywords : morphine * rat * heart * proteome Subject RIV: ED - Physiology Impact factor: 3.730, year: 2012

  17. Tribute to Michael Dunn for his dedication and contribution to proteomics and stem cell focus

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Hana; Gadher, S. J.

    2016-01-01

    Roč. 16, č. 22 (2016), s. 2840-2841 ISSN 1615-9853 R&D Projects: GA MŠk(CZ) LO1609 Institutional support: RVO:67985904 Keywords : proteomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.041, year: 2016

  18. Effective Removal of Nonionic Detergents in Protein Mass Spectrometry, Hydrogen/Deuterium Exchange, and Proteomics

    Czech Academy of Sciences Publication Activity Database

    Rey, M.; Mrázek, H.; Pompach, Petr; Novák, P.; Pelosi, L.; Brandolin, G.; Forest, E.; Havlíček, Vladimír; Man, P.

    2010-01-01

    Roč. 82, č. 12 (2010), s. 5107-5116 ISSN 0003-2700 R&D Projects: GA AV ČR KJB500200612; GA MŠk LC545 Institutional research plan: CEZ:AV0Z50200510 Keywords : mass spectrometry * proteomics * peptides Subject RIV: CE - Biochemistry Impact factor: 5.874, year: 2010

  19. The iron-regulated transcriptome and proteome of Neisseria meningitidis serogroup C

    Czech Academy of Sciences Publication Activity Database

    Basler, Marek; Linhartová, Irena; Halada, Petr; Novotná, Jana; Bezoušková, Silvia; Osička, Radim; Weiser, Jaroslav; Vohradský, Jiří; Šebo, Peter

    2006-01-01

    Roč. 6, č. 23 (2006), s. 6194-6206 ISSN 1615-9853 R&D Projects: GA ČR GA310/04/0804; GA MZe 1G46068 Institutional research plan: CEZ:AV0Z50200510 Keywords : iron regulation * Neisseria meningitidis * proteome Subject RIV: EE - Microbiology, Virology Impact factor: 5.735, year: 2006

  20. 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.

  1. 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. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Next-generation proteomics: towards an integrative view of proteome dynamics

    NARCIS (Netherlands)

    Altelaar, A.F.M.|info:eu-repo/dai/nl/304833517; Munoz-Peralta, J.; Heck, A.J.R.|info:eu-repo/dai/nl/105189332

    2013-01-01

    Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is

  3. A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

    Science.gov (United States)

    Gadher, Suresh Jivan; Drahos, László; Vékey, Károly; Kovarova, Hana

    2017-07-01

    The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

  4. Data from proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis

    Directory of Open Access Journals (Sweden)

    Yongxin Yang

    2015-06-01

    Full Text Available Milk fat globules memebrane (MFGM-enriched proteomes from Holstein, Jersey, yak, buffalo, goat, camel, horse, and human were extracted and identified by an iTRAQ quantification proteomic approach. Proteomes data were analyzed by bioinformatic and multivariate statistical analysis and used to present the characteristic traits of the MFGM proteins among the studied mammals. The data of this study are also related to the research article “Proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis” in the Journal of Proteomics [1].

  5. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

    DEFF Research Database (Denmark)

    Welker, F.

    2018-01-01

    not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against...... positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications...

  6. Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer

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    Stobiecki Maciej

    2009-07-01

    Full Text Available Abstract Background Mass spectrometric analysis of the blood proteome is an emerging method of clinical proteomics. The approach exploiting multi-protein/peptide sets (fingerprints detected by mass spectrometry that reflect overall features of a specimen's proteome, termed proteome pattern analysis, have been already shown in several studies to have applicability in cancer diagnostics. We aimed to identify serum proteome patterns specific for early stage breast cancer patients using MALDI-ToF mass spectrometry. Methods Blood samples were collected before the start of therapy in a group of 92 patients diagnosed at stages I and II of the disease, and in a group of age-matched healthy controls (104 women. Serum specimens were purified and the low-molecular-weight proteome fraction was examined using MALDI-ToF mass spectrometry after removal of albumin and other high-molecular-weight serum proteins. Protein ions registered in a mass range between 2,000 and 10,000 Da were analyzed using a new bioinformatic tool created in our group, which included modeling spectra as a sum of Gaussian bell-shaped curves. Results We have identified features of serum proteome patterns that were significantly different between blood samples of healthy individuals and early stage breast cancer patients. The classifier built of three spectral components that differentiated controls and cancer patients had 83% sensitivity and 85% specificity. Spectral components (i.e., protein ions that were the most frequent in such classifiers had approximate m/z values of 2303, 2866 and 3579 Da (a biomarker built from these three components showed 88% sensitivity and 78% specificity. Of note, we did not find a significant correlation between features of serum proteome patterns and established prognostic or predictive factors like tumor size, nodal involvement, histopathological grade, estrogen and progesterone receptor expression. In addition, we observed a significantly (p = 0

  7. Quantitative Proteomics of the E. coli Membranome.

    Science.gov (United States)

    Tsolis, K C; Economou, A

    2017-01-01

    Due to their physicochemical properties, membrane protein proteomics analyses often require extensive sample preparation protocols resulting in sample loss and introducing technical variation. Several methods for membrane proteomics have been described, designed to meet the needs of specific sample types and experimental designs. Here, we present a complete membrane proteomics pipeline starting from the membrane sample preparation to the protein identification/quantification and also discuss about annotation of proteomics data. The protocol has been developed using Escherichia coli samples but is directly adaptable to other bacteria including pathogens. We describe a method for the preparation of E. coli inner membrane vesicles (IMVs) central to our pipeline. IMVs are functional membrane vesicles that can also be used for biochemical studies. Next, we propose methods for membrane protein digestion and describe alternative experimental approaches that have been previously tested in our lab. We highlight a surface proteolysis protocol for the identification of inner membrane and membrane-bound proteins. This is a simple, fast, and reproducible method for the membrane sample characterization that has been previously used for the E. coli inner membrane proteome characterization (Papanastasiou et al., 2013) and the experimental validation of E. coli membrane proteome (Orfanoudaki & Economou, 2014). It provides a reduced load on MS-time and allows for multiple repeats. Then we discuss membrane protein quantification approaches and tools that can be used for the functional annotation of identified proteins. Overall, membrane proteome quantification can be fast, simplified, and reproducible; however, optimization steps should be performed for a given sample type. © 2017 Elsevier Inc. All rights reserved.

  8. Scientific Approaches | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    CPTAC employs two complementary scientific approaches, a "Targeting Genome to Proteome" (Targeting G2P) approach and a "Mapping Proteome to Genome" (Mapping P2G) approach, in order to address biological questions from data generated on a sample.

  9. 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.

  10. 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. © 2016 Elsevier Inc. All rights reserved.

  11. Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity.

    Science.gov (United States)

    Howden, Andrew J M; Stam, Remco; Martinez Heredia, Victor; Motion, Graham B; Ten Have, Sara; Hodge, Kelly; Marques Monteiro Amaro, Tiago M; Huitema, Edgar

    2017-07-01

    Plant-pathogen interactions are complex associations driven by the interplay of host and microbe-encoded factors. With secreted pathogen proteins (effectors) and immune signalling components found in the plant nucleus, this compartment is a battleground where susceptibility is specified. We hypothesized that, by defining changes in the nuclear proteome during infection, we can pinpoint vital components required for immunity or susceptibility. We tested this hypothesis by documenting dynamic changes in the tomato (Solanum lycopersicum) nuclear proteome during infection by the oomycete pathogen Phytophthora capsici. We enriched nuclei from infected and noninfected tissues and quantitatively assessed changes in the nuclear proteome. We then tested the role of candidate regulators in immunity through functional assays. We demonstrated that the host nuclear proteome dynamically changes during P. capsici infection. We observed that known nuclear immunity factors were differentially expressed and, based on this observation, selected a set of candidate regulators that we successfully implicated in immunity to P. capsici. Our work exemplifies a powerful strategy to gain rapid insight into important nuclear processes that underpin complex crop traits such as resistance. We have identified a large set of candidate nuclear factors that may underpin immunity to pathogens in crops. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  12. Proteomics of protein secretion by Aggregatibacter actinomycetemcomitans.

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    Vincent Zijnge

    Full Text Available The extracellular proteome (secretome of periodontitis-associated bacteria may constitute a major link between periodontitis and systemic diseases. To obtain an overview of the virulence potential of Aggregatibacter actinomycetemcomitans, an oral and systemic human pathogen implicated in aggressive periodontitis, we used a combined LC-MS/MS and bioinformatics approach to characterize the secretome and protein secretion pathways of the rough-colony serotype a strain D7S. LC-MS/MS revealed 179 proteins secreted during biofilm growth. Further to confirming the release of established virulence factors (e.g. cytolethal distending toxin [CDT], and leukotoxin [LtxA], we identified additional putative virulence determinants in the secretome. These included DegQ, fHbp, LppC, Macrophage infectivity protein (MIP, NlpB, Pcp, PotD, TolB, and TolC. This finding indicates that the number of extracellular virulence-related proteins is much larger than previously demonstrated, which was also supported by in silico analysis of the strain D7S genome. Moreover, our LC-MS/MS and in silico data revealed that at least Type I, II, and V secretion are actively used to excrete proteins directly into the extracellular space, or via two-step pathways involving the Sec/Tat systems for transport across the inner membrane, and outer membrane factors, secretins and auto-transporters, respectively for delivery across the outer membrane. Taken together, our results provide a molecular basis for further elucidating the role of A. actinomycetemcomitans in periodontal and systemic diseases.

  13. Proteomic View of the Crosstalk between Lactobacillus mucosae and Intestinal Epithelial Cells in Co-culture Revealed by Q Exactive-Based Quantitative Proteomics

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    Edward Alain B. Pajarillo

    2017-12-01

    Full Text Available Lactobacilli are bacteria that are beneficial to host health, but information on communication between Lactobacilli and host cells in the intestine is lacking. In this study, we examined the proteomes of the Lactobacillus mucosae strain LM1, as a model of beneficial bacteria, and the intestinal porcine epithelial cell line (IPEC-J2 after co-culture. Label-free proteomics demonstrated the high-throughput capability of the technique, and robust characterization of the functional profiles and changes in the bacteria and intestinal cells was achieved in pure and mixed cultures. After co-culture, we identified totals of 376 and 653 differentially expressed proteins in the LM1 and IPEC-J2 proteomes, respectively. The major proteomic changes in the LM1 strain occurred in the functional categories of transcription, general function, and translation, whereas those in IPEC-J2 cells involved metabolic and cellular processes, and cellular component organization/biogenesis. Among them, elongation factor Tu, glyceraldehyde 3-phosphate dehydrogenase, and phosphocarrier protein HPr, which are known to be involved in bacterial adhesion, were upregulated in LM1. In contrast, proteins involved in tight junction assembly, actin organization, and genetic information processing (i.e., histones and signaling pathways were significantly upregulated in IPEC-J2 cells. Furthermore, we identified functional pathways that are possibly involved in host–microbe crosstalk and response. These findings will provide novel insights into host–bacteria communication and the molecular mechanism of probiotic establishment in the intestine.

  14. Proteomic View of the Crosstalk betweenLactobacillus mucosaeand Intestinal Epithelial Cells in Co-culture Revealed by Q Exactive-Based Quantitative Proteomics.

    Science.gov (United States)

    Pajarillo, Edward Alain B; Kim, Sang Hoon; Valeriano, Valerie Diane; Lee, Ji Yoon; Kang, Dae-Kyung

    2017-01-01

    Lactobacilli are bacteria that are beneficial to host health, but information on communication between Lactobacilli and host cells in the intestine is lacking. In this study, we examined the proteomes of the Lactobacillus mucosae strain LM1, as a model of beneficial bacteria, and the intestinal porcine epithelial cell line (IPEC-J2) after co-culture. Label-free proteomics demonstrated the high-throughput capability of the technique, and robust characterization of the functional profiles and changes in the bacteria and intestinal cells was achieved in pure and mixed cultures. After co-culture, we identified totals of 376 and 653 differentially expressed proteins in the LM1 and IPEC-J2 proteomes, respectively. The major proteomic changes in the LM1 strain occurred in the functional categories of transcription, general function, and translation, whereas those in IPEC-J2 cells involved metabolic and cellular processes, and cellular component organization/biogenesis. Among them, elongation factor Tu, glyceraldehyde 3-phosphate dehydrogenase, and phosphocarrier protein HPr, which are known to be involved in bacterial adhesion, were upregulated in LM1. In contrast, proteins involved in tight junction assembly, actin organization, and genetic information processing (i.e., histones and signaling pathways) were significantly upregulated in IPEC-J2 cells. Furthermore, we identified functional pathways that are possibly involved in host-microbe crosstalk and response. These findings will provide novel insights into host-bacteria communication and the molecular mechanism of probiotic establishment in the intestine.

  15. Detection of Nuclear Protein Profile Changes by Human Metapneumovirus M2-2 Protein Using Quantitative Differential Proteomics

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    Yuping Ren

    2017-12-01

    Full Text Available Human metapneumovirus (hMPV is a leading cause of lower respiratory infection in pediatric populations globally. This study examined proteomic profile changes in A549 cells infected with hMPV and two attenuated mutants with deleted PDZ domain-binding motif(s in the M2-2 protein. These motifs are involved in the interruption of antiviral signaling, namely the interaction between the TNF receptor associated factor (TRAF and mitochondrial antiviral-signaling (MAVS proteins. The aim of this study was to provide insight into the overall and novel impact of M2-2 motifs on cellular responses via an unbiased comparison. Tandem mass tagging, stable isotope labeling, and high-resolution mass spectrometry were used for quantitative proteomic analysis. Using quantitative proteomics and Venn analysis, 1248 common proteins were detected in all infected samples of both technical sets. Hierarchical clustering of the differentiated proteome displayed distinct proteomic signatures that were controlled by the motif(s. Bioinformatics and experimental analysis confirmed the differentiated proteomes, revealed novel cellular biological events, and implicated key pathways controlled by hMPV M2-2 PDZ domain-binding motif(s. This provides further insight for evaluating M2-2 mutants as potent vaccine candidates.

  16. Mitochondrial Proteome Studies in Seeds during Germination

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    Malgorzata Czarna

    2016-06-01

    Full Text Available Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs and the regulation of seed germination.

  17. Shotgun Proteomics and Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    W. Hayes McDonald

    2002-01-01

    Full Text Available Coupling large-scale sequencing projects with the amino acid sequence information that can be gleaned from tandem mass spectrometry (MS/MS has made it much easier to analyze complex mixtures of proteins. The limits of this “shotgun” approach, in which the protein mixture is proteolytically digested before separation, can be further expanded by separating the resulting mixture of peptides prior to MS/MS analysis. Both single dimensional high pressure liquid chromatography (LC and multidimensional LC (LC/LC can be directly interfaced with the mass spectrometer to allow for automated collection of tremendous quantities of data. While there is no single technique that addresses all proteomic challenges, the shotgun approaches, especially LC/LC-MS/MS-based techniques such as MudPIT (multidimensional protein identification technology, show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range. Advances in the ability to quantitate differences between samples and to detect for an array of post-translational modifications allow for the discovery of classes of protein biomarkers that were previously unassailable.

  18. Magnetoresistive biosensors for quantitative proteomics

    Science.gov (United States)

    Zhou, Xiahan; Huang, Chih-Cheng; Hall, Drew A.

    2017-08-01

    Quantitative proteomics, as a developing method for study of proteins and identification of diseases, reveals more comprehensive and accurate information of an organism than traditional genomics. A variety of platforms, such as mass spectrometry, optical sensors, electrochemical sensors, magnetic sensors, etc., have been developed for detecting proteins quantitatively. The sandwich immunoassay is widely used as a labeled detection method due to its high specificity and flexibility allowing multiple different types of labels. While optical sensors use enzyme and fluorophore labels to detect proteins with high sensitivity, they often suffer from high background signal and challenges in miniaturization. Magnetic biosensors, including nuclear magnetic resonance sensors, oscillator-based sensors, Hall-effect sensors, and magnetoresistive sensors, use the specific binding events between magnetic nanoparticles (MNPs) and target proteins to measure the analyte concentration. Compared with other biosensing techniques, magnetic sensors take advantage of the intrinsic lack of magnetic signatures in biological samples to achieve high sensitivity and high specificity, and are compatible with semiconductor-based fabrication process to have low-cost and small-size for point-of-care (POC) applications. Although still in the development stage, magnetic biosensing is a promising technique for in-home testing and portable disease monitoring.

  19. Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

    Science.gov (United States)

    Fadda, Silvina; Almeida, André M

    2015-11-01

    Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Comparative analysis of the uropathogenic Escherichia coli surface proteome by tandem mass-spectrometry of artificially induced outer membrane vesicles.

    Science.gov (United States)

    Wurpel, Daniël J; Moriel, Danilo G; Totsika, Makrina; Easton, Donna M; Schembri, Mark A

    2015-02-06

    Uropathogenic Escherichia coli (UPEC) are the major cause of urinary tract infections. For successful colonisation of the urinary tract, UPEC employ multiple surface-exposed or secreted virulence factors, including adhesins and iron uptake systems. Whilst individual UPEC strains and their virulence factors have been the focus of extensive research, there have been no outer membrane (OM) proteomic studies based on large clinical UPEC collections, primarily due to limitations of traditional methods. In this study, a high-throughput method based on tandem mass-spectrometry of EDTA heat-induced outer membrane vesicles (OMVs) was developed for the characterisation of the UPEC surface-associated proteome. The method was applied to compare the OM proteome of fifty-four UPEC isolates, resulting in the identification of 8789 proteins, consisting of 619 unique proteins, which were subsequently interrogated for their subcellular origin, prevalence and homology to characterised virulence factors. Multiple distinct virulence-associated proteins were identified, including two novel putative iron uptake proteins, an uncharacterised type of chaperone-usher fimbriae and various highly prevalent hypothetical proteins. Our results give fundamental insight into the physiology of UPEC and provide a framework for understanding the composition of the UPEC OM proteome. In this study a high-throughput method based on tandem mass-spectrometry of EDTA heat-induced outer membrane vesicles was used to define the outer membrane proteome of a large uropathogenic E. coli (UPEC) collection. Our results provide an inventory of proteins expressed on the surface of UPEC, and provide a framework for understanding the composition of the UPEC OM proteome. The method enables the rapid characterisation of the E. coli surface proteome and could easily be applied to the large-scale outer membrane protein profiling of other Gram-negative bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Proteomic profiling of Bifidobacterium bifidum S17 cultivated under in vitro conditions

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    Xiao eWei

    2016-02-01

    Full Text Available Bifidobacteria are frequently used in probiotic food and dairy products. Bifidobacterium bifidum S17 is a promising probiotic candidate strain that displays strong adhesion to intestinal epithelial cells and elicits potent anti-inflammatory capacity both in vitro and in murine models of colitis. The recently sequenced genome of B. bifidum S17 has a size of about 2.2 Mb and encodes 1,782 predicted protein-coding genes. In the present study, a comprehensive proteomic profiling was carried out to identify and characterize proteins expressed by B. bifidum S17. A total of 1148 proteins entries were identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS, representing 64.4% of the predicted proteome. 719 proteins could be assigned to functional categories according to cluster of orthologous groups of proteins (COGs. The COG distribution of the detected proteins highly correlates with that of the complete predicted proteome suggesting a good coverage and representation of the genomic content of B. bifidum S17 by the proteome. COGs that were highly present in the proteome of B. bifidum S17 were Translation, Amino Acid Transport and Metabolism, and Carbohydrate Transport and Metabolism. Complete sets of enzymes for both the bifidus shunt and the Embden-Meyerhof pathway were identified. Further bioinformatic analysis yielded 28 proteins with a predicted extracellular localization including 14 proteins with an LPxTG-motif for cell wall anchoring and two proteins (elongation factor Tu and enolase with a potential moonlighting function in adhesion. Amongst the predicted extracellular proteins were five of six pilin proteins encoded in the B. bifidum S17 genome as well as several other proteins with a potential role in interaction with host structures. The presented results are the first compilation of a proteomic reference profile for a B. bifidum strain and will facilitate analysis of the molecular mechanisms of physiology, host

  2. Proteome analysis of Lactobacillus plantarum strain under cheese-like conditions.

    Science.gov (United States)

    Wu, Zhen; Wang, Pingping; He, Jiayi; Pan, Daodong; Zeng, Xiaoqun; Cao, Jinxuan

    2016-09-02

    As a food grade fermentation starter, Lactobacillus plantarum (L. plantarum) also named as the secondary starters during cheese ripening. In this study, the concentration of NaCl was screened as the main factor in the cheese-like conditions (15°C, pH5.2, 6% NaCl) to assess the potential properties of L. plantarum. A comprehensive proteome profile of L. plantarum strain was analyzed with iTRAQ proteomics methods fractionated by SCX chromatography. Proteins involved in carbohydrate transport and metabolism, cell envelope, peptide-glycan biosynthesis and lipid transport and metabolism were found significant changes. Meanwhile, the same trends were found in mRNA expression levels analyzed by RT-PCR. Some general transportation proteins related to ion transporters were detected as more abundant, which may reveal a rescue mechanism of the microbe in sodium-dependent glucose transfer. The understanding of L. plantarum proteome in salt tolerance could be useful to get strain adapted for specific applications. The bacterial biota has a primary role in affecting cheese quality. Under cheese-like conditions, L. plantarum mainly increased the levels of enzymes that responsible for the flavour development during cheese ripening. However, the mechanisms of proteomic adaptation remain largely unclear in unraveling details of the salt tolerance of L. plantarum. This study revealed a dramatic change involved in carbohydrate transport and metabolism, cell envelope, peptide-glycan biosynthesis, lipid transport and metabolism, and glycolysis. Meanwhile, these pathways provide a comprehensive proteome profile of L. plantarum survived under cheese-like conditions. Furthermore, this study shows that iTRAQ proteomics provide more reliable information in describing the molecular rescue strategy of L. plantarum in sodium-dependent glucose transfer. Copyright © 2016. Published by Elsevier B.V.

  3. Prediction of acute coronary syndromes by urinary proteome analysis.

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    Nay M Htun

    Full Text Available Identification of individuals who are at risk of suffering from acute coronary syndromes (ACS may allow to introduce preventative measures. We aimed to identify ACS-related urinary peptides, that combined as a pattern can be used as prognostic biomarker. Proteomic data of 252 individuals enrolled in four prospective studies from Australia, Europe and North America were analyzed. 126 of these had suffered from ACS within a period of up to 5 years post urine sampling (cases. Proteomic analysis of 84 cases and 84 matched controls resulted in the discovery of 75 ACS-related urinary peptides. Combining these to a peptide pattern, we established a prognostic biomarker named Acute Coronary Syndrome Predictor 75 (ACSP75. ACSP75 demonstrated reasonable prognostic discrimination (c-statistic = 0.664, which was similar to Framingham risk scoring (c-statistics = 0.644 in a validation cohort of 42 cases and 42 controls. However, generating by a composite algorithm named Acute Coronary Syndrome Composite Predictor (ACSCP, combining the biomarker pattern ACSP75 with the previously established urinary proteomic biomarker CAD238 characterizing coronary artery disease as the underlying aetiology, and age as a risk factor, further improved discrimination (c-statistic = 0.751 resulting in an added prognostic value over Framingham risk scoring expressed by an integrated discrimination improvement of 0.273 ± 0.048 (P < 0.0001 and net reclassification improvement of 0.405 ± 0.113 (P = 0.0007. In conclusion, we demonstrate that urinary peptide biomarkers have the potential to predict future ACS events in asymptomatic patients. Further large scale studies are warranted to determine the role of urinary biomarkers in clinical practice.

  4. Proteomics of secretory and endocytic organelles in Giardia lamblia.

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    Petra B Wampfler

    Full Text Available Giardia lamblia is a flagellated protozoan enteroparasite transmitted as an environmentally resistant cyst. Trophozoites attach to the small intestine of vertebrate hosts and proliferate by binary fission. They access nutrients directly via uptake of bulk fluid phase material into specialized endocytic organelles termed peripheral vesicles (PVs, mainly on the exposed dorsal side. When trophozoites reach the G2/M restriction point in the cell cycle they can begin another round of cell division or encyst if they encounter specific environmental cues. They induce neogenesis of Golgi-like organelles, encystation-specific vesicles (ESVs, for regulated secretion of cyst wall material. PVs and ESVs are highly simplified and thus evolutionary diverged endocytic and exocytic organelle systems with key roles in proliferation and transmission to a new host, respectively. Both organelle systems physically and functionally intersect at the endoplasmic reticulum (ER which has catabolic as well as anabolic functions. However, the unusually high degree of sequence divergence in Giardia rapidly exhausts phylogenomic strategies to identify and characterize the molecular underpinnings of these streamlined organelles. To define the first proteome of ESVs and PVs we used a novel strategy combining flow cytometry-based organelle sorting with in silico filtration of mass spectrometry data. From the limited size datasets we retrieved many hypothetical but also known organelle-specific factors. In contrast to PVs, ESVs appear to maintain a strong physical and functional link to the ER including recruitment of ribosomes to organelle membranes. Overall the data provide further evidence for the formation of a cyst extracellular matrix with minimal complexity. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000694.

  5. FSHD myotubes with different phenotypes exhibit distinct proteomes.

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    Alexandra Tassin

    Full Text Available Facioscapulohumeral muscular dystrophy (FSHD is a progressive muscle disorder linked to a contraction of the D4Z4 repeat array in the 4q35 subtelomeric region. This deletion induces epigenetic modifications that affect the expression of several genes located in the vicinity. In each D4Z4 element, we identified the double homeobox 4 (DUX4 gene. DUX4 expresses a transcription factor that plays a major role in the development of FSHD through the initiation of a large gene dysregulation cascade that causes myogenic differentiation defects, atrophy and reduced response to oxidative stress. Because miRNAs variably affect mRNA expression, proteomic approaches are required to define the dysregulated pathways in FSHD. In this study, we optimized a differential isotope protein labeling (ICPL method combined with shotgun proteomic analysis using a gel-free system (2DLC-MS/MS to study FSHD myotubes. Primary CD56(+ FSHD myoblasts were found to fuse into myotubes presenting various proportions of an atrophic or a disorganized phenotype. To better understand the FSHD myogenic defect, our improved proteomic procedure was used to compare predominantly atrophic or disorganized myotubes to the same matching healthy control. FSHD atrophic myotubes presented decreased structural and contractile muscle components. This phenotype suggests the occurrence of atrophy-associated proteolysis that likely results from the DUX4-mediated gene dysregulation cascade. The skeletal muscle myosin isoforms were decreased while non-muscle myosin complexes were more abundant. In FSHD disorganized myotubes, myosin isoforms were not reduced, and increased proteins were mostly involved in microtubule network organization and myofibrillar remodeling. A common feature of both FSHD myotube phenotypes was the disturbance of several caveolar proteins, such as PTRF and MURC. Taken together, our data suggest changes in trafficking and in the membrane microdomains of FSHD myotubes. Finally, the

  6. The Use of Proteomics in Assisted Reproduction.

    Science.gov (United States)

    Kosteria, Ioanna; Anagnostopoulos, Athanasios K; Kanaka-Gantenbein, Christina; Chrousos, George P; Tsangaris, George T

    2017-01-01

    Despite the explosive increase in the use of Assisted Reproductive Technologies (ART) over the last 30 years, their success rates remain suboptimal. Proteomics is a rapidly-evolving technology-driven science that has already been widely applied in the exploration of human reproduction and fertility, providing useful insights into its physiology and leading to the identification of numerous proteins that may be potential biomarkers and/or treatment targets of a successful ART pregnancy. Here we present a brief overview of the techniques used in proteomic analyses and attempt a comprehensive presentation of recent data from mass spectrometry-based proteomic studies in humans, regarding all components of ARTs, including the male and female gamete, the derived zygote and embryo, the endometrium and, finally, the ART offspring both pre- and postnatally. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  7. 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.

  8. Introduction to mass spectrometry-based proteomics

    DEFF Research Database (Denmark)

    Matthiesen, R.; Bunkenborg, J.

    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...

  9. Proteomics and syndrome of Chinese medicine.

    Science.gov (United States)

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

    2010-12-01

    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 systemic context, proteomics have a convergence with traditional Chinese medicine (TCM) syndrome, which could overcome the one-sidedness and singleness of TCM and avoid the complication and tedious processes. Chinese medicine has a wealth of experience and proteomics has a substantial research potential, the integration of the two aspects will bring a great enhancement of our knowledge of disease. © 2010 The Authors Journal compilation © 2010 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

  10. Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data.

    Directory of Open Access Journals (Sweden)

    Jason W Locasale

    2009-08-01

    Full Text Available Advances in mass spectrometry among other technologies have allowed for quantitative, reproducible, proteome-wide measurements of levels of phosphorylation as signals propagate through complex networks in response to external stimuli under different conditions. However, computational approaches to infer elements of the signaling network strictly from the quantitative aspects of proteomics data are not well established. We considered a method using the principle of maximum entropy to infer a network of interacting phosphotyrosine sites from pairwise correlations in a mass spectrometry data set and derive a phosphorylation-dependent interaction network solely from quantitative proteomics data. We first investigated the applicability of this approach by using a simulation of a model biochemical signaling network whose dynamics are governed by a large set of coupled differential equations. We found that in a simulated signaling system, the method detects interactions with significant accuracy. We then analyzed a growth factor mediated signaling network in a human mammary epithelial cell line that we inferred from mass spectrometry data and observe a biologically interpretable, small-world structure of signaling nodes, as well as a catalog of predictions regarding the interactions among previously uncharacterized phosphotyrosine sites. For example, the calculation places a recently identified tumor suppressor pathway through ARHGEF7 and Scribble, in the context of growth factor signaling. Our findings suggest that maximum entropy derived network models are an important tool for interpreting quantitative proteomics data.

  11. Quantitative proteomics of delirium cerebrospinal fluid

    Science.gov (United States)

    Poljak, A; Hill, M; Hall, R J; MacLullich, A M; Raftery, M J; Tai, J; Yan, S; Caplan, G A

    2014-01-01

    Delirium is a common cause and complication of hospitalization in older people, being associated with higher risk of future dementia and progression of existing dementia. However relatively little data are available on which biochemical pathways are dysregulated in the brain during delirium episodes, whether there are protein expression changes common among delirium subjects and whether there are any changes which correlate with the severity of delirium. We now present the first proteomic analysis of delirium cerebrospinal fluid (CSF), and one of few studies exploring protein expression changes in delirium. More than 270 proteins were identified in two delirium cohorts, 16 of which were dysregulated in at least 8 of 17 delirium subjects compared with a mild Alzheimer's disease neurological control group, and 31 proteins were significantly correlated with cognitive scores (mini-mental state exam and acute physiology and chronic health evaluation III). Bioinformatics analyses revealed expression changes in several protein family groups, including apolipoproteins, secretogranins/chromogranins, clotting/fibrinolysis factors, serine protease inhibitors and acute-phase response elements. These data not only provide confirmatory evidence that the inflammatory response is a component of delirium, but also reveal dysregulation of protein expression in a number of novel and unexpected clusters of proteins, in particular the granins. Another surprising outcome of this work is the level of similarity of CSF protein profiles in delirium patients, given the diversity of causes of this syndrome. These data provide additional elements for consideration in the pathophysiology of delirium as well as potential biomarker candidates for delirium diagnosis. PMID:25369144

  12. A comprehensive compilation of SUMO proteomics

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Vertegaal, Alfred C O

    2016-01-01

    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...

  13. The Human Skeletal Muscle Proteome Project

    DEFF Research Database (Denmark)

    Gonzalez-Freire, Marta; Semba, Richard D.; Ubaida-Mohien, Ceereena

    2017-01-01

    of the literature and analysed publically available protein databases. A systematic search of peer-reviewed studies was performed using PubMed. Search terms included ‘human’, ‘skeletal muscle’, ‘proteome’, ‘proteomic(s)’, and ‘mass spectrometry’, ‘liquid chromatography-mass spectrometry (LC-MS/MS)’. A catalogue...... of 5431 non-redundant muscle proteins identified by mass spectrometry-based proteomics from 38 peer-reviewed scientific publications from 2002 to November 2015 was created. We also developed a nosology system for the classification of muscle proteins based on localization and function. Such inventory...

  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. Considerations about gastric cancer proteomics.

    Science.gov (United States)

    Carvalho, Carlos Eduardo; McCormick, Thaís Messias; Carvalho, Paulo Costa; Fischer, Juliana DE Saldanha DA Gama; Aquino, Priscila Ferreira DE; Bravo, Guilherme Pinto; Carvalho, Maria DA Glória DA Costa

    2016-01-01

    The frequency of molecular studies aimed to analyze promoter methylation of tumor suppressor genes and global proteomics in gastric carcinogenesis is increasing. Nonetheless, only a few considered the different types of stomach cells, the tumor location and the influence of Helicobacter pylori and Epstein Barr virus infection (EBV). Molecular differences relating to anatomical and histological tumor areas were also recently described. The authors propose a molecular classification of gastric cancer, dividing it into four subtypes: tumors positive for EBV; microsatellite unstable tumors; genomically stable tumors and tumors with chromosomal instability. RESUMO A frequência de estudos moleculares visando a analisar os promotores de metilação de genes supressores de tumor e proteômica globais na carcinogênese gástrica está aumentando. No entanto, apenas alguns consideraram os diferentes tipos de células do estômago, a localização do tumor e a influência da infecção por Helicobacter pylori e pelo vírus Epstein-Barr (EBV). Diferenças moleculares relacionadas com áreas tumorais anatômicas e histológicas também foram recentemente descritas. Os autores propõem uma classificação molecular de câncer gástrico, dividindo-o em quatro subtipos: tumores positivos para o EBV; tumores microssatélite instáveis; tumores genomicamente estáveis ​​e tumores com instabilidade cromossômica.

  16. Proteomic screening for amyloid proteins.

    Directory of Open Access Journals (Sweden)

    Anton A Nizhnikov

    Full Text Available Despite extensive study, progress in elucidation of biological functions of amyloids and their role in pathology is largely restrained due to the lack of universal and reliable biochemical methods for their discovery. All biochemical methods developed so far allowed only identification of glutamine/asparagine-rich amyloid-forming proteins or proteins comprising amyloids that form large deposits. In this article we present a proteomic approach which may enable identification of a broad range of amyloid-forming proteins independently of specific features of their sequences or levels of expression. This approach is based on the isolation of protein fractions enriched with amyloid aggregates via sedimentation by ultracentrifugation in the presence of strong ionic detergents, such as sarkosyl or SDS. Sedimented proteins are then separated either by 2D difference gel electrophoresis or by SDS-PAGE, if they are insoluble in the buffer used for 2D difference gel electrophoresis, after which they are identified by mass-spectrometry. We validated this approach by detection of known yeast prions and mammalian proteins with established capacity for amyloid formation and also revealed yeast proteins forming detergent-insoluble aggregates in the presence of human huntingtin with expanded polyglutamine domain. Notably, with one exception, all these proteins contained glutamine/asparagine-rich stretches suggesting that their aggregates arose due to polymerization cross-seeding by human huntingtin. Importantly, though the approach was developed in a yeast model, it can easily be applied to any organism thus representing an efficient and universal tool for screening for amyloid proteins.

  17. Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis

    NARCIS (Netherlands)

    Low, T.Y.; van Heesch, S.; van den Toorn, H.; Giansanti, P.; Cristobal, A.; Toonen, P.; Schafer, S.; Hubner, N.; van Breukelen, B.; Mohammed, S.; Cuppen, E.; Heck, A.J.R.; Guryev, V.

    2013-01-01

    Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We

  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...... 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...

  19. 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.

    2015-01-01

    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

  20. 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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Oxidative Stress in Aging: Advances in Proteomic Approaches

    Directory of Open Access Journals (Sweden)

    Daniel Ortuño-Sahagún

    2014-01-01

    Full Text Available Aging is a gradual, complex process in which cells, tissues, organs, and the whole organism itself deteriorate in a progressive and irreversible manner that, in the majority of cases, implies pathological conditions that affect the individual’s Quality of Life (QOL. Although extensive research efforts in recent years have been made, the anticipation of aging and prophylactic or treatment strategies continue to experience major limitations. In this review, the focus is essentially on the compilation of the advances generated by cellular expression profile analysis through proteomics studies (two-dimensional [2D] electrophoresis and mass spectrometry [MS], which are currently used as an integral approach to study the aging process. Additionally, the relevance of the oxidative stress factors is discussed. Emphasis is placed on postmitotic tissues, such as neuronal, muscular, and red blood cells, which appear to be those most frequently studied with respect to aging. Additionally, models for the study of aging are discussed in a number of organisms, such as Caenorhabditis elegans, senescence-accelerated probe-8 mice (SAMP8, naked mole-rat (Heterocephalus glaber, and the beagle canine. Proteomic studies in specific tissues and organisms have revealed the extensive involvement of reactive oxygen species (ROS and oxidative stress in aging.

  2. Proteomics of seed development, desiccation tolerance, germination and vigor.

    Science.gov (United States)

    Wang, Wei-Qing; Liu, Shu-Jun; Song, Song-Quan; Møller, Ian Max

    2015-01-01

    Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  3. Proteomics analysis of the zebrafish skeletal extracellular matrix.

    Directory of Open Access Journals (Sweden)

    Maurijn Y Kessels

    Full Text Available The extracellular matrix of the immature and mature skeleton is key to the development and function of the skeletal system. Notwithstanding its importance, it has been technically challenging to obtain a comprehensive picture of the changes in skeletal composition throughout the development of bone and cartilage. In this study, we analyzed the extracellular protein composition of the zebrafish skeleton using a mass spectrometry-based approach, resulting in the identification of 262 extracellular proteins, including most of the bone and cartilage specific proteins previously reported in mammalian species. By comparing these extracellular proteins at larval, juvenile, and adult developmental stages, 123 proteins were found that differed significantly in abundance during development. Proteins with a reported function in bone formation increased in abundance during zebrafish development, while analysis of the cartilage matrix revealed major compositional changes during development. The protein list includes ligands and inhibitors of various signaling pathways implicated in skeletogenesis such as the Int/Wingless as well as the insulin-like growth factor signaling pathways. This first proteomic analysis of zebrafish skeletal development reveals that the zebrafish skeleton is comparable with the skeleton of other vertebrate species including mammals. In addition, our study reveals 6 novel proteins that have never been related to vertebrate skeletogenesis and shows a surprisingly large number of differences in the cartilage and bone proteome between the head, axis and caudal fin regions. Our study provides the first systematic assessment of bone and cartilage protein composition in an entire vertebrate at different stages of development.

  4. Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection

    Energy Technology Data Exchange (ETDEWEB)

    Sigdel, Tara K.; Kaushal, Amit; Gritsenko, Marina A.; Norbeck, Angela D.; Qian, Weijun; Xiao, Wenzhong; Camp, David G.; Smith, Richard D.; Sarwal, Minnie M.

    2010-01-04

    Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non-invasive diagnostic biomarkers for AR is an unmet need. We used shotgun proteomics using LC-MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls (HC). A total of 1446 urinary proteins were identified along with a number of NS specific, renal transplantation specific and AR specific proteins. Relative abundance of identified urinary proteins was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific urinary proteins in AR, primarily relating to MHC antigens, the complement cascade and extra-cellular matrix proteins. A subset of proteins (UMOD, SERPINF1 and CD44), have been further cross-validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these urinary proteins in AR. This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of urinary proteins for serial, non-invasive clinical monitoring for graft rejection after

  5. Proteomic analysis of the shistosome tegument and its surface membranes

    Directory of Open Access Journals (Sweden)

    Simon Braschi

    2006-10-01

    Full Text Available The tegument surface of the adult schistosome, bounded by a normal plasma membrane overlain by a secreted membranocalyx, holds the key to understanding how schistosomes evade host immune responses. Recent advances in mass spectrometry (MS, and the sequencing of the Schistosoma mansoni transcriptome/genome, have facilitated schistosome proteomics. We detached the tegument from the worm body and enriched its surface membranes by differential extraction, before subjecting the preparation to liquid chromatography-based proteomics to identify its constituents. The most exposed proteins on live worms were labelled with impearmeant biotinylation reagents, and we also developed methods to isolate the membranocalyx for analysis. We identified transporters for sugars, amino acids, inorganic ions and water, which confirm the importance of the tegument plasma membrane in nutrient acquisition and solute balance. Enzymes, including phosphohydrolases, esterases and carbonic anhydrase were located with their catalytic domains external to the plasma membrane, while five tetraspanins, annexin and dysferlin were implicated in membrane architecture. In contrast, few parasite proteins could be assigned to the membranocalyx but mouse immune response proteins, including three immunoglobulins and two complement factors, were detected, plus host membrane proteins such as CD44, integrin and a complement regulatory protein, testifying to the acquisitive properties of the secreted bilayer.

  6. Functional proteomic analysis of Ankaferd® Blood Stopper

    Directory of Open Access Journals (Sweden)

    Duygu Özel Demiralp

    2010-06-01

    Full Text Available Objective: Ankaferd® Blood Stopper (ABS comprises a standardized mixture of the plants Thymus vulgaris, Glycyrrhiza glabra, Vitis vinifera, Alpinia officinarum, and Urtica dioica. The basic mechanism of action for ABS is the formation of an encapsulated protein network that provides focal points for vital erythrocyte aggregation. ABS–induced protein network formation with blood cells, particularly erythrocytes, covers the primary and secondary hemostatic system without disturbing individual coagulation factors. Materials and Methods: To understand the effect mechanisms of ABS on hemostasis, a proteomic analysis using 2D gel electrophoresis and mass spectrometer was performed. Results: Proteins of plant origin in Ankaferd® were NADP-dependent-malic enzyme, ribulose bisphosphate-carboxylase-large chain, maturase K, ATP synthase subunit-beta, ATP synthase subunit-alpha, chalcone-flavanone isomerase-1, chalcone-flavanone isomerase-2, and actin-depolymerizing factor. Furthermore, functional proteomic studies revealed that proteins resembling human peptides have been detected within Ankaferd®, including ATP synthase, mucin-16 (CD164 sialomucin-like 2 protein, coiled-coil domain containing 141 hypothetical protein LOC283638 isoform 1, hypothetical protein LOC283638 isoform 2, dynactin 5, complex I intermediate-associated protein 30, mitochondrial, NADH dehydrogenase (ubiquinone 1 alpha subcomplex, TP synthase, H+ transporting, mitochondrial actin binding 1 isoform, LIM domain and actin binding 1 isoform a, LIM domain and actin binding 1 isoform b, spectrin alpha non erythrocytic 1, prolactin releasing hormone receptor, utrophin, tet oncogene family member 2 isoform b, protein phosphatase 1 regulatory subunit 12A, NIMA (never in mitosis gene a-related kinase, ATP-binding cassette protein C12, Homo sapiens malic enzyme 1, mitochondrial NADP(+-dependent malic enzyme 3, ME2 protein, nuclear factor 1 B-type, abhydrolase domain-containing protein 12B, E

  7. The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics.

    Science.gov (United States)

    Brenes, Alejandro; Afzal, Vackar; Kent, Robert; Lamond, Angus I

    2018-01-04

    Driven by improvements in speed and resolution of mass spectrometers (MS), the field of proteomics, which involves the large-scale detection and analysis of proteins in cells, tissues and organisms, continues to expand in scale and complexity. There is a resulting growth in datasets of both raw MS files and processed peptide and protein identifications. MS-based proteomics technology is also used increasingly to measure additional protein properties affecting cellular function and disease mechanisms, including post-translational modifications, protein-protein interactions, subcellular and tissue distributions. Consequently, biologists and clinicians need innovative tools to conveniently analyse, visualize and explore such large, complex proteomics data and to integrate it with genomics and other related large-scale datasets. We have created the Encyclopedia of Proteome Dynamics (EPD) to meet this need (https://peptracker.com/epd/). The EPD combines a polyglot persistent database and web-application that provides open access to integrated proteomics data for >30 000 proteins from published studies on human cells and model organisms. It is designed to provide a user-friendly interface, featuring graphical navigation with interactive visualizations that facilitate powerful data exploration in an intuitive manner. The EPD offers a flexible and scalable ecosystem to integrate proteomics data with genomics information, RNA expression and other related, large-scale datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

    Science.gov (United States)

    Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

    2012-05-15

    The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

  9. In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

    Directory of Open Access Journals (Sweden)

    Lindo Micheal

    2003-08-01

    Full Text Available Abstract Proteomics experiments typically involve protein or peptide separation steps coupled to the identification of many hundreds to thousands of peptides by mass spectrometry. Development of methodology and instrumentation in this field is proceeding rapidly, and effective software is needed to link the different stages of proteomic analysis. We have developed an application, proteogest, written in Perl that generates descriptive and statistical analyses of the biophysical properties of multiple (e.g. thousands protein sequences submitted by the user, for instance protein sequences inferred from the complete genome sequence of a model organism. The application also carries out in silico proteolytic digestion of the submitted proteomes, or subsets thereof, and the distribution of biophysical properties of the resulting peptides is presented. proteogest is customizable, the user being able to select many options, for instance the cleavage pattern of the digestion treatment or the presence of modifications to specific amino acid residues. We show how proteogest can be used to compare the proteomes and digested proteome products of model organisms, to examine the added complexity generated by modification of residues, and to facilitate the design of proteomics experiments for optimal representation of component proteins.

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

    Directory of Open Access Journals (Sweden)

    Chuming Chen

    2011-04-01

    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.

  11. Proteomic analysis of chromate response in Staphylococcus ...

    African Journals Online (AJOL)

    Staphylococci species resistant to chromate were previously isolated from a fly ash dumping site. To further understand the mechanisms developed by these bacteria to tolerate chromate, a proteomic analysis was performed to identify proteins involved in chromate stress response of Staphylococcus saprophyticus isolated ...

  12. Protein synthesis in synaptosomes: a proteomics analysis

    NARCIS (Netherlands)

    Jimenez, C.R.; Eyman, M.; Lavina, Z.S.; Goio, A.; Li, K.W.; van der Schors, R.C.; Geraerts, W.P.M.; Giuditta, A.; Kaplan, B.B.; van Minnen, J.

    2002-01-01

    A proteomics approach was used to identify the translation products of a unique synaptic model system, squid optic lobe synaptosomes. Unlike its vertebrate counterparts, this preparation is largely free of perikaryal cell fragments and consists predominantly of pre-synaptic terminals derived from

  13. Bacterial Electron Transfer Chains Primed by Proteomics.

    Science.gov (United States)

    Wessels, H J C T; de Almeida, N M; Kartal, B; Keltjens, J T

    2016-01-01

    Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities. © 2016 Elsevier Ltd. All rights reserved.

  14. A proteomic analysis of human bile

    DEFF Research Database (Denmark)

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

    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 87...... of cancer biomarkers from any body fluid. Udgivelsesdato: 2004-Jul...

  15. Barley seed proteomics from spots to structures

    DEFF Research Database (Denmark)

    Finnie, Christine; Svensson, Birte

    2009-01-01

    forms on 2D-gels. Specific protein families, including peroxidases and alpha-amylases have been subjected to in-depth analysis resulting in characterisation of different isozymes, post-translational. modifications and processing. A functional proteomics study focusing on the seed thioredoxin system has...

  16. Eukaryotic expression : developments for structural proteomics

    NARCIS (Netherlands)

    Aricescu, A. R.; Assenberg, R.; Bill, R. M.; Busso, D.; Chang, V. T.; Davis, S. J.; Dubrovsky, A.; Gustafsson, L.L.; Hedfalk, K.; Heinemann, U.; Jones, I. M.; Ksiazek, D.; Lang, Chim C; Maskos, K.; Messerschmidt, A.; Macieira, S.; Peleg, Y.; Perrakis, A.; Poterszman, A.; Schneider, G.; Sixma, Titia K; Sussman, Joel L.; Sutton, G.; Tarboureich, N.; Zeev-Ben-Mordehai, T.; Jones, E. Yvonne

    2006-01-01

    The production of sufficient quantities of protein is an essential prelude to a structure determination, but for many viral and human proteins this cannot be achieved using prokaryotic expression systems. Groups in the Structural Proteomics In Europe (SPINE) consortium have developed and implemented

  17. 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.

  18. 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...

  19. Human maternal plasma proteomic changes with parturition

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    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. Recent advances in proteomics of cereals.

    Science.gov (United States)

    Bansal, Monika; Sharma, Madhu; Kanwar, Priyanka; Goyal, Aakash

    Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.

  1. Proteomics insights into plant signaling and development.

    NARCIS (Netherlands)

    Kaufmann, K.; Smaczniak, C.D.; Vries, de S.C.; Angenent, G.C.; Karlova, R.B.

    2011-01-01

    Mass spectrometry-based proteomics is used to gain insight into the abundance and subcellular localization of cellular signaling components, the composition of molecular complexes and the regulation of signaling pathways. Multicellular organisms have evolved signaling networks and fast responses to

  2. Skeletal muscle proteomics in livestock production.

    Science.gov (United States)

    Picard, Brigitte; Berri, Cécile; Lefaucheur, Louis; Molette, Caroline; Sayd, Thierry; Terlouw, Claudia

    2010-05-01

    Proteomics allows studying large numbers of proteins, including their post-translational modifications. Proteomics has been, and still are, used in numerous studies on skeletal muscle. In this article, we focus on its use in the study of livestock muscle development and meat quality. Changes in protein profiles during myogenesis are described in cattle, pigs and fowl using comparative analyses across different ontogenetic stages. This approach allows a better understanding of the key stages of myogenesis and helps identifying processes that are similar or divergent between species. Genetic variability of muscle properties analysed by the study of hypertrophied cattle and sheep are discussed. Biological markers of meat quality, particularly tenderness in cattle, pigs and fowl are presented, including protein modifications during meat ageing in cattle, protein markers of PSE meat in turkeys and of post-mortem muscle metabolism in pigs. Finally, we discuss the interest of proteomics as a tool to understand better biochemical mechanisms underlying the effects of stress during the pre-slaughter period on meat quality traits. In conclusion, the study of proteomics in skeletal muscles allows generating large amounts of scientific knowledge that helps to improve our understanding of myogenesis and muscle growth and to control better meat quality.

  3. DNA damage response: multilevel proteomics gains momentum.

    Science.gov (United States)

    Daub, Henrik

    2012-04-27

    In this issue of Molecular Cell, Beli et al. (2012) introduce a multilevel proteomics approach for parallel quantification of protein phosphorylation, acetylation, and abundance and apply this to the complex signaling network of the DNA damage response. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Proteome Analysis of Rheumatoid Arthritis Gut Mucosa

    DEFF Research Database (Denmark)

    Bjerg Bennike, Tue; Ellingsen, Torkell; Glerup, Henning

    2017-01-01

    Rheumatoid arthritis (RA) is an inflammatory joint disease leading to cartilage damage and ultimately impaired joint function. To gain new insight into the systemic immune manifestations of RA, we characterized the colon mucosa proteome from 11 RA-patients and 10 healthy controls. The biopsies were...

  5. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Bioinformatics applications in proteomics data analysis

    NARCIS (Netherlands)

    Peng, M.

    2015-01-01

    In this thesis, I detail my 4-year efforts in developing bioinformatics tools and algorithms to address the growing demands of current proteomics endeavors, covering a range of facets such as large-scale protein expression profiling, charting post-translation modifications as well as

  7. Reconciling proteomics with next generation sequencing

    NARCIS (Netherlands)

    Low, Teck Yew; Heck, Albert Jr

    2015-01-01

    Both genomics and proteomics technologies have matured in the last decade to a level where they are able to deliver system-wide data on the qualitative and quantitative abundance of their respective molecular entities, that is DNA/RNA and proteins. A next logical step is the collective use of these

  8. 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.

  9. Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids.

    Science.gov (United States)

    Sedeek, Khalid E M; Qi, Weihong; Schauer, Monica A; Gupta, Alok K; Poveda, Lucy; Xu, Shuqing; Liu, Zhong-Jian; Grossniklaus, Ueli; Schiestl, Florian P; Schlüter, Philipp M

    2013-01-01

    Sexually deceptive orchids of the genus Ophrys mimic the mating signals of their pollinator females to attract males as pollinators. This mode of pollination is highly specific and leads to strong reproductive isolation between species. This study aims to identify candidate genes responsible for pollinator attraction and reproductive isolation between three closely related species, O. exaltata, O. sphegodes and O. garganica. Floral traits such as odour, colour and morphology are necessary for successful pollinator attraction. In particular, different odour hydrocarbon profiles have been linked to differences in specific pollinator attraction among these species. Therefore, the identification of genes involved in these traits is important for understanding the molecular basis of pollinator attraction by sexually deceptive orchids. We have created floral reference transcriptomes and proteomes for these three Ophrys species using a combination of next-generation sequencing (454 and Solexa), Sanger sequencing, and shotgun proteomics (tandem mass spectrometry). In total, 121 917 unique transcripts and 3531 proteins were identified. This represents the first orchid proteome and transcriptome from the orchid subfamily Orchidoideae. Proteome data revealed proteins corresponding to 2644 transcripts and 887 proteins not observed in the transcriptome. Candidate genes for hydrocarbon and anthocyanin biosynthesis were represented by 156 and 61 unique transcripts in 20 and 7 genes classes, respectively. Moreover, transcription factors putatively involved in the regulation of flower odour, colour and morphology were annotated, including Myb, MADS and TCP factors. Our comprehensive data set generated by combining transcriptome and proteome technologies allowed identification of candidate genes for pollinator attraction and reproductive isolation among sexually deceptive orchids. This includes genes for hydrocarbon and anthocyanin biosynthesis and regulation, and the development of

  10. Plasma proteome changes in cardiovascular disease patients: novel isoforms of apolipoprotein A1

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    Oravec Milan

    2011-06-01

    Full Text Available Abstract Background The aim of this proteomic study was to look for changes taking place in plasma proteomes of patients with acute myocardial infarction (AMI, unstable angina pectoris (UAP, and stable angina pectoris (SAP. Methods Depleted plasma proteins were separated by 2D SDS-PAGE (pI 4-7, and proteomes were compared using Progenesis SameSpots statistical software. Proteins were identified by nanoLC-MS/MS. Proteins were quantified using commercial kits. Apolipoprotein A1 was studied using 1D and 2D SDS-PAGE, together with western blotting. Results Reciprocal comparison revealed 46 unique, significantly different spots; proteins in 34 spots were successfully identified and corresponded to 38 different proteins. Discrete comparisons of patient groups showed 45, 41, and 8 significantly different spots when AMI, UAP, and SAP were compared with the control group. On the basis of our proteomic data, plasma levels of two of them, alpha-1 microglobulin and vitamin D-binding protein, were determined. The data, however, failed to prove the proteins to be suitable markers or risk factors in the studied groups. The plasma level and isoform representation of apolipoprotein A1 were also estimated. Using 1D and 2D SDS-PAGE, together with western blotting, we observed extra high-molecular weight apolipoprotein A1 fractions presented only in the patient groups, indicating that the novel high-molecular weight isoforms of apolipoprotein A1 may be potential new markers or possible risk factors of cardiovascular disease. Conclusion The reported data show plasma proteome changes in patients with AMI, UAP, and SAP. We propose some apolipoprotein A1 fractions as a possible new disease-associated marker of cardiovascular disorders.

  11. The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique.

    Science.gov (United States)

    Huang, Eric L; Orsat, Valérie; Shah, Manesh B; Hettich, Robert L; VerBerkmoes, Nathan C; Lefsrud, Mark G

    2012-09-18

    System biology and bioprocess technology can be better understood using shotgun proteomics as a monitoring system during the fermentation. We demonstrated a shotgun proteomic method to monitor the temporal yeast proteome in early, middle and late exponential phases. Our study identified a total of 1389 proteins combining all 2D-LC-MS/MS runs. The temporal Saccharomyces cerevisiae proteome was enriched with proteolysis, radical detoxification, translation, one-carbon metabolism, glycolysis and TCA cycle. Heat shock proteins and proteins associated with oxidative stress response were found throughout the exponential phase. The most abundant proteins observed were translation elongation factors, ribosomal proteins, chaperones and glycolytic enzymes. The high abundance of the H-protein of the glycine decarboxylase complex (Gcv3p) indicated the availability of glycine in the environment. We observed differentially expressed proteins and the induced proteins at mid-exponential phase were involved in ribosome biogenesis, mitochondria DNA binding/replication and transcriptional activator. Induction of tryptophan synthase (Trp5p) indicated the abundance of tryptophan during the fermentation. As fermentation progressed toward late exponential phase, a decrease in cell proliferation was implied from the repression of ribosomal proteins, transcription coactivators, methionine aminopeptidase and translation-associated proteins. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project.

    Science.gov (United States)

    Lee, Hyoung-Joo; Jeong, Seul-Ki; Na, Keun; Lee, Min Jung; Lee, Sun Hee; Lim, Jong-Sun; Cha, Hyun-Jeong; Cho, Jin-Young; Kwon, Ja-Young; Kim, Hoguen; Song, Si Young; Yoo, Jong Shin; Park, Young Mok; Kim, Hail; Hancock, William S; Paik, Young-Ki

    2013-06-07

    As a starting point of the Chromosome-Centric Human Proteome Project (C-HPP), we established strategies of genome-wide proteomic analysis, including protein identification, quantitation of disease-specific proteins, and assessment of post-translational modifications, using paired human placental tissues from healthy and preeclampsia patients. This analysis resulted in identification of 4239 unique proteins with high confidence (two or more unique peptides with a false discovery rate less than 1%), covering 21% of approximately 20, 059 (Ensembl v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially expressed preeclampsia-specific proteins. When these proteins are assigned to all human chromosomes, the pattern of the newly identified placental protein population is proportional to that of the gene count distribution of each chromosome. We also identified 219 unique N-linked glycopeptides, 592 unique phosphopeptides, and 66 chromosome 13-specific proteins. In particular, protein evidence of 14 genes previously known to be specifically up-regulated in human placenta was verified by mass spectrometry. With respect to the functional implication of these proteins, 38 proteins were found to be involved in regulatory factor biosynthesis or the immune system in the placenta, but the molecular mechanism of these proteins during pregnancy warrants further investigation. As far as we know, this work produced the highest number of proteins identified in the placenta and will be useful for annotating and mapping all proteins encoded in the human genome.

  13. Examining hemodialyzer membrane performance using proteomic technologies.

    Science.gov (United States)

    Bonomini, Mario; Pieroni, Luisa; Di Liberato, Lorenzo; Sirolli, Vittorio; Urbani, Andrea

    2018-01-01

    The success and the quality of hemodialysis therapy are mainly related to both clearance and biocompatibility properties of the artificial membrane packed in the hemodialyzer. Performance of a membrane is strongly influenced by its interaction with the plasma protein repertoire during the extracorporeal procedure. Recognition that a number of medium-high molecular weight solutes, including proteins and protein-bound molecules, are potentially toxic has prompted the development of more permeable membranes. Such membrane engineering, however, may cause loss of vital proteins, with membrane removal being nonspecific. In addition, plasma proteins can be adsorbed onto the membrane surface upon blood contact during dialysis. Adsorption can contribute to the removal of toxic compounds and governs the biocompatibility of a membrane, since surface-adsorbed proteins may trigger a variety of biologic blood pathways with pathophysiologic consequences. Over the last years, use of proteomic approaches has allowed polypeptide spectrum involved in the process of hemodialysis, a key issue previously hampered by lack of suitable technology, to be assessed in an unbiased manner and in its full complexity. Proteomics has been successfully applied to identify and quantify proteins in complex mixtures such as dialysis outflow fluid and fluid desorbed from dialysis membrane containing adsorbed proteins. The identified proteins can also be characterized by their involvement in metabolic and signaling pathways, molecular networks, and biologic processes through application of bioinformatics tools. Proteomics may thus provide an actual functional definition as to the effect of a membrane material on plasma proteins during hemodialysis. Here, we review the results of proteomic studies on the performance of hemodialysis membranes, as evaluated in terms of solute removal efficiency and blood-membrane interactions. The evidence collected indicates that the information provided by proteomic

  14. The nuclear proteome of Trypanosoma brucei.

    Science.gov (United States)

    Goos, Carina; Dejung, Mario; Janzen, Christian J; Butter, Falk; Kramer, Susanne

    2017-01-01

    Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes.

  15. Proteomics of Trypanosoma evansi infection in rodents.

    Directory of Open Access Journals (Sweden)

    Nainita Roy

    2010-03-01

    Full Text Available 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.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.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 first ever proteomic study reported thus far. In addition to providing a

  16. Hypothalamus proteomics from mouse models with obesity and anorexia reveals therapeutic targets of appetite regulation.

    Science.gov (United States)

    Manousopoulou, A; Koutmani, Y; Karaliota, S; Woelk, C H; Manolakos, E S; Karalis, K; Garbis, S D

    2016-04-25

    This study examined the proteomic profile of the hypothalamus in mice exposed to a high-fat diet (HFD) or with the anorexia of acute illness. This comparison could provide insight on the effects of these two opposite states of energy balance on appetite regulation. Four to six-week-old male C56BL/6J mice were fed a normal (control 1 group; n=7) or a HFD (HFD group; n=10) for 8 weeks. The control 2 (n=7) and lipopolysaccharide (LPS) groups (n=10) were fed a normal diet for 8 weeks before receiving an injection of saline and LPS, respectively. Hypothalamic regions were analysed using a quantitative proteomics method based on a combination of techniques including iTRAQ stable isotope labeling, orthogonal two-dimensional liquid chromatography hyphenated with nanospray ionization and high-resolution mass spectrometry. Key proteins were validated with quantitative PCR. Quantitative proteomics of the hypothalamous regions profiled a total of 9249 protein groups (q<0.05). Of these, 7718 protein groups were profiled with a minimum of two unique peptides for each. Hierachical clustering of the differentiated proteome revealed distinct proteomic signatures for the hypothalamus under the HFD and LPS nutritional conditions. Literature research with in silico bioinformatics interpretation of the differentiated proteome identified key biological relevant proteins and implicated pathways. Furthermore, the study identified potential pharmacologic targets. In the LPS groups, the anorexigen pro-opiomelanocortin was downregulated. In mice with obesity, nuclear factor-κB, glycine receptor subunit alpha-4 (GlyR) and neuropeptide Y levels were elevated, whereas serotonin receptor 1B levels decreased. High-precision quantitative proteomics revealed that under acute systemic inflammation in the hypothalamus as a response to LPS, homeostatic mechanisms mediating loss of appetite take effect. Conversely, under chronic inflammation in the hypothalamus as a response to HFD, mechanisms

  17. Proteomic definition of a desmoglein linear determinant common to Pemphigus vulgaris and Pemphigus foliaceous

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    Sinha Animesh A

    2006-08-01

    Full Text Available Abstract Background A number of autoimmune diseases have been clinically and pathologically characterized. In contrast, target antigens have been identified only in a few cases and, in these few cases, the knowledge of the exact epitopic antigenic sequence is still lacking. Thus the major objective of current work in the autoimmunity field is the identification of the epitopic sequences that are related to autoimmune reactions. Our labs propose that autoantigen peptide epitopes able to evoke humoral (autoimmune response are defined by the sequence similarity to the host proteome. The underlying scientific rationale is that antigen peptides acquire immunoreactivity in the context of their proteomic similarity level. Sequences uniquely owned by a protein will have high potential to evoke an immune reaction, whereas motifs with high proteomic redundancy should be immunogenically silenced by the tolerance phenomenon. The relationship between sequence redundancy and peptide immunoreactivity has been successfully validated in a number of experimental models. Here the hypothesis has been applied to pemphigus diseases and the corresponding desmoglein autoantigens. Methods Desmoglein 3 sequence similarity analysis to the human proteome followed by dot-blot/NMR immunoassays were carried out to identify and validate possible epitopic sequences. Results Computational analysis led to identifying a linear immunodominant desmoglein-3 epitope highly reactive with the sera from Pemphigus vulgaris as well as Pemphigus foliaceous. The epitopic peptide corresponded to the amino acid REWVKFAKPCRE sequence, was located in the extreme N-terminal region (residues 49 to 60, and had low redundancy to the human proteome. Sequence alignment showed that human desmoglein 1 and 3 share the REW-KFAK–RE sequence as a common motif with 75% residue identity. Conclusion This study 1 validates sequence redundancy to autoproteome as a main factor in shaping desmoglein peptide

  18. Biogeoscience from a Metallomic and Proteomic Perspective

    Science.gov (United States)

    Anbar, A. D.; Shock, E.

    2004-12-01

    In the wake of the genomics revolution, life scientists are expanding their focus from the genome to the "proteome" - the assemblage of all proteins in a cell - and the "metallome" - the distribution of inorganic species in a cell. The proteome and metallome are tightly connected because proteins and protein products are intimately involved in the transport and homeostasis of inorganic elements, and because many enzymes depend on inorganic elements for catalytic activity. Together, they are at the heart of metabolic function. Unlike the relatively static genome, the proteome and metallome are extremely dynamic, changing rapidly in response to environmental cues. They are substantially more complex than the genome; for example, in humans, some 30,000 genes code for approximately 500,000 proteins. Metaphorically, the proteome and metallome constitute the complex, dynamic "language" by which the genome and the environment communicate. Therefore biogeochemists, like life scientists, are moving beyond a strictly genomic perspective. Research guided by proteomic and metallomic perspectives and methodologies should provide new insights into the connections between life and the inorganic Earth in modern environments, and the evolution of these connections through time. For example, biogeochemical research in modern environments, such as Yellowstone hot springs, is hindered by the gap between genomic determinations of metabolic potential in ecosystems and geochemical characterizations of the energetic boundary conditions faced by these ecosystems; genomics tells us "who is there" and geochemistry tells us "what they might be doing", but neither genomics nor geochemistry easily provide quantitative information about which metabolisms are actually active or a framework for understanding why ecosystems do not fully exploit the energy available in their surroundings. Such questions are fundamentally kinetic rather than thermodynamic and therefore demand that we characterize and

  19. Proteome identification of the silkworm middle silk gland

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    Jian-ying Li

    2016-03-01

    Full Text Available 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].

  20. Proteomics studies in inner ear disorders: pathophysiology and biomarkers.

    Science.gov (United States)

    Alawieh, Ali; Mondello, Stefania; Kobeissy, Firas; Shibbani, Kamel; Bassim, Marc

    2015-04-01

    Although proteomics has been exploited in a wide range of diseases for identification of biomarkers and pathophysiological mechanisms, there are still biomedical disciplines such as otology where proteomics platforms are underused due to technical challenges and/or complex features of the disease. Thus, in the past few years, healthcare and scientific agencies have advocated the development and adoption of proteomic technologies in otological research. However, few studies have been conducted and limited literature is available in this area. Here, we present the state of the art of proteomics in otology, discussing the substantial evidence from recent experimental models and clinical studies in inner-ear conditions. We also delineate a series of critical issues including minute size of the inner ear, delicacy and poor accessibility of tissue that researchers face while undertaking otology proteomics research. Furthermore, we provide perspective to enhance the impact and lead to the clinical implementation of these proteomics-based strategies.

  1. Large pore dermal microdialysis and liquid chromatography-tandem mass spectroscopy shotgun proteomic analysis: a feasibility study

    DEFF Research Database (Denmark)

    Petersen, Lars J.; Sorensen, Mette A.; Codrea, Marius C.

    2013-01-01

    Background/AimsThe purpose of the present pilot study was to investigate the feasibility of combining large pore dermal microdialysis with shotgun proteomic analysis in human skin. MethodsDialysate was recovered from human skin by 2000 kDa microdialysis membranes from one subject at three different......, and complement factors, make up the major load of proteins in all three test conditions. ConclusionShotgun proteomics allowed the identification of more than 150 proteins in microdialysis samples from human skin. This highlights the opportunities of LC-MS/MS to study the complex molecular interactions...... in the skin....

  2. The colostrum proteome, ruminant nutrition and immunity: a review.

    Science.gov (United States)

    Hernández-Castellano, Lorenzo E; Almeida, Andrè M; Castro, Noemi; Argüello, Anastasio

    2014-02-01

    In this review authors address colostrum proteins implications in different domestic ruminant species. The colostrogenesis process and how different factors, such as litter size or nutrition during gestation can alter the different components concentrations in colostrum are also reviewed. The different colostrum fractions will be described, focusing on high and low abundant proteins. This review describes the major function of such proteins and their role on the passive immune transfer and nutrition in the newborn animal. It will be also performed a comprehensive review on different techniques and commercial kits available for high abundant protein depletion in colostrum. We will finally focus on how proteomics has been used to address this issue and how it can contribute to the major questions about colostrum associated immunology.

  3. Application of proteomics to investigate barley-Fusarium graminearum interaction

    DEFF Research Database (Denmark)

    Yang, Fen

    that i) spots increasing in intensity in the infected plants included fungal proteins and proteolytic fragments of plant proteins, ii) spots decreasing in intensity contained plant proteins possibly degraded by fungal proteases, iii) greater spot volume changes in response to the fungus were observed......-wall-degrading enzymes and proteases. Besides Tri5 gene, ten selected genes encoding protein expressed in vitro were also expressed in the F. graminearum-infected wheat and barley from 2-6 day after inoculation (dai), suggesting the in vitro proteome approach may be an ideal strategy to discover pathogenicity factors....... In addition, sharper increase in fungal biomass was observed in barley than in wheat and fungal induced proteolytic fragments of - amylases were only observed in barley not in wheat. Furthermore, a barley PR17 protein and a fungal hypothetical protein were expressed in E. coli and purified in Chapter 5...

  4. Core proteome of the minimal cell: comparative proteomics of three mollicute species.

    Directory of Open Access Journals (Sweden)

    Gleb Y Fisunov

    Full Text Available Mollicutes (mycoplasmas have been recognized as highly evolved prokaryotes with an extremely small genome size and very limited coding capacity. Thus, they may serve as a model of a 'minimal cell': a cell with the lowest possible number of genes yet capable of autonomous self-replication. We present the results of a comparative analysis of proteomes of three mycoplasma species: A. laidlawii, M. gallisepticum, and M. mobile. The core proteome components found in the three mycoplasma species are involved in fundamental cellular processes which are necessary for the free living of cells. They include replication, transcription, translation, and minimal metabolism. The members of the proteome core seem to be tightly interconnected with a number of interactions forming core interactome whether or not additional species-specific proteins are located on the periphery. We also obtained a genome core of the respective organisms and compared it with the proteome core. It was found that the genome core encodes 73 more proteins than the proteome core. Apart of proteins which may not be identified due to technical limitations, there are 24 proteins that seem to not be expressed under the optimal conditions.

  5. Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005.

    Directory of Open Access Journals (Sweden)

    Sabine Matallana-Surget

    Full Text Available The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.

  6. Proteomic Profiling of Sugar Beet (Beta vulgaris) Leaves during Rhizomania Compatible Interactions

    OpenAIRE

    Webb, Kimberly M.; Broccardo, Carolyn J.; Prenni, Jessica E.; Wintermantel, William M.

    2014-01-01

    Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), severely impacts sugar beet (Beta vulgaris) production throughout the world, and is widely prevalent in most production regions. Initial efforts to characterize proteome changes focused primarily on identifying putative host factors that elicit resistant interactions with BNYVV, but as resistance breaking strains become more prevalent, effective disease control strategies will require the application of novel methods based on be...

  7. Recent developments and applications of capillary and microchip electrophoresis in proteomic and peptidomic analyses

    Czech Academy of Sciences Publication Activity Database

    Štěpánová, Sille; Kašička, Václav

    2016-01-01

    Roč. 39, č. 1 (2016), s. 198-211 ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA13-17224S; GA ČR(CZ) GA15-01948S Institutional support: RVO:61388963 Keywords : capillary electrophoresis * mass spectrometry * microchip electrophoresis * peptidomics * proteomics Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.557, year: 2016

  8. Dependence of molecular properties on proteomic family for marketed oral drugs.

    Science.gov (United States)

    Vieth, Michal; Sutherland, Jeffrey J

    2006-06-15

    An association of drugs with their proteomic family reveals that molecular properties of drugs targeting proteases, lipid and peptide G-protein-coupled receptors (GPCRs), and nuclear hormone receptors significantly exceed limits for some properties in the "rule of five", while drugs targeting cytochrome P450s, biogenic amine GPCRs, and transporters have significantly lower values for certain properties. Also, the variation in drug targets appears to be a factor explaining increasing molecular weight over time.

  9. Impact of homogenization and protein extraction conditions on the obtained tobacco pollen proteomic patterns

    Czech Academy of Sciences Publication Activity Database

    Fíla, Jan; Čapková, Věra; Feciková, Jana; Honys, David

    2011-01-01

    Roč. 55, č. 3 (2011), s. 499-506 ISSN 0006-3134 R&D Projects: GA MŠk OC08011; GA ČR(CZ) GAP501/11/1462 Institutional research plan: CEZ:AV0Z50380511 Keywords : proteomics * Roche MagNA Lyser Instrument * ARABIDOPSIS-THALIANA Subject RIV: ED - Physiology Impact factor: 1.974, year: 2011

  10. Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping

    Czech Academy of Sciences Publication Activity Database

    Schräder, Ch.U.; Lee, L.; Rey, M.; Sarpe, V.; Man, Petr; Sharma, S.; Zabrouskov, V.; Larsen, B.; Schrimer, D.C.

    2017-01-01

    Roč. 16, č. 6 (2017), s. 1162-1171 ISSN 1535-9476 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk(CZ) LQ1604 Institutional support: RVO:61388971 Keywords : EXCHANGE MASS-SPECTROMETRY * POSTTRANSLATIONAL MODIFICATIONS * SHOTGUN PROTEOMICS Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 6.540, year: 2016

  11. The use of carrier ampholyte-free isoelectric focusing for proteomic analysis

    Czech Academy of Sciences Publication Activity Database

    Procházková, B.; Šalplachta, Jiří

    2008-01-01

    Roč. 67, Suppl. (2008), S55-S61 ISSN 0009-5893. [ Advances in Chromatography and Electrophoresis 2007 and Chiranal 2007. Olomouc, 24.06.2007-27.06.2007] Institutional research plan: CEZ:AV0Z40310501 Keywords : MALDI-TOF-TOF-MS * proteomics * carrier ampholyte-free IEF Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.312, year: 2008

  12. Advances in Proteomic Techniques for Cytokine Analysis: Focus on Melanoma Research

    Czech Academy of Sciences Publication Activity Database

    Kupcová Skalníková, Helena; Čížková, Jana; Červenka, Jakub; Vodička, Petr

    2017-01-01

    Roč. 18, č. 12 (2017), č. článku 2697. E-ISSN 1422-0067 R&D Projects: GA ČR GA16-05534S; GA MŠk(CZ) LO1609 Institutional support: RVO:67985904 Keywords : cytokine * cancer * melanoma * secretome * proteomics Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemical research methods Impact factor: 3.226, year: 2016

  13. Comparative analysis of proteomic changes in contrasting flax cultivars upon cadmium exposure

    Czech Academy of Sciences Publication Activity Database

    Hradilová, Jana; Řehulka, Pavel; Řehulková, Helena; Vrbová, M.; Griga, M.; Brzobohatý, Břetislav

    2010-01-01

    Roč. 31, č. 2 (2010), s. 421-431 ISSN 0173-0835 R&D Projects: GA MŠk 1M06030 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40310501 Keywords : 2-DE analysis * proteomic identification * cadmium Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.569, year: 2010

  14. Environmental stress is the major cause of transcriptomic and proteomic changes in GM and non-GM plants

    KAUST Repository

    Batista, Rita

    2017-08-31

    The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such

  15. Analysis of peptide mixtures for proteomics research using LC–ESI-MS with a simple microgradient device

    Czech Academy of Sciences Publication Activity Database

    Lenobel, R.; Řehulková, H.; Šebela, M.; Franc, V.; Kahle, Vladislav; Moravcová, Dana; Řehulka, P.

    2015-01-01

    Roč. 33, č. 6 (2015), s. 420-428 ISSN 1527-5949 R&D Projects: GA MV VG20112015021 Institutional support: RVO:68081715 Keywords : LC-ESI-MS * proteomics * peptide Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 0.519, year: 2014 http://hdl.handle.net/11104/0249120

  16. A high-quality catalog of the Drosophila melanogaster proteome

    DEFF Research Database (Denmark)

    Brunner, Erich; Ahrens, Christian H.; Mohanty, Sonaly

    2007-01-01

    % of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis...... matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism....

  17. 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....

  18. Marine proteomics: a critical assessment of an emerging technology.

    Science.gov (United States)

    Slattery, Marc; Ankisetty, Sridevi; Corrales, Jone; Marsh-Hunkin, K Erica; Gochfeld, Deborah J; Willett, Kristine L; Rimoldi, John M

    2012-10-26

    The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.

  19. Update in research and methods in proteomics and bioinformatics.

    Science.gov (United States)

    Bencharit, Sompop; Border, Michael B; Edelmann, Alex; Byrd, Warren C

    2013-10-01

    The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013) Philadelphia, PA, USA, 15-17 July 2013 The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.

  20. PRIDE: quality control in a proteomics data repository.

    Science.gov (United States)

    Csordas, Attila; Ovelleiro, David; Wang, Rui; Foster, Joseph M; Ríos, Daniel; Vizcaíno, Juan Antonio; Hermjakob, Henning

    2012-01-01

    The PRoteomics IDEntifications (PRIDE) database is a large public proteomics data repository, containing over 270 million mass spectra (by November 2011). PRIDE is an archival database, providing the proteomics data supporting specific scientific publications in a computationally accessible manner. While PRIDE faces rapid increases in data deposition size as well as number of depositions, the major challenge is to ensure a high quality of data depositions in the context of highly diverse proteomics work flows and data representations. Here, we describe the PRIDE curation pipeline and its practical application in quality control of complex data depositions. DATABASE URL: http://www.ebi.ac.uk/pride/.

  1. Single Electron Transistor Platform for Microgravity Proteomics, Phase I

    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,...

  2. Genomics, proteomics, and metabolomics in nutraceuticals and functional foods

    National Research Council Canada - National Science Library

    Bagchi, Debasis; Lau, Francis; Bagchi, Manashi

    2010-01-01

    .... Genomics, proteomics, and metobolomics represent three major scientific research areas that contribute to nutraceutical and functional food research for studies of effectiveness and safety"--Provided by publisher.

  3. Proteomics of Uveal Melanoma: A Minireview

    Directory of Open Access Journals (Sweden)

    Søren K. O. Abildgaard

    2013-01-01

    Full Text Available Uveal melanoma (UM continues to be associated with a high mortality rate of up to 50% due to metastatic spread primarily to the liver. Currently there are relatively effective treatments for the primary tumor, though the management of the metastatic disease remains inadequate. Conventional diagnostic tools have a low sensitivity for detecting metastasis, and early detection of metastatic spread would allow more treatment options that could ultimately increase survival of UM patients. Advanced proteomic methods have already helped to find potential biomarkers associated with UM pathogenesis and metastasis. In the present review we discuss the field of proteomics in relation to studies elucidating biomarkers of UM, where proteins such as S-100β, osteopontin (OPN, and melanoma inhibitory activity (MIA have been shown to be associated with metastasis.

  4. Lessons from the proteomic study of osteoarthritis.

    Science.gov (United States)

    Ruiz-Romero, Cristina; Fernández-Puente, Patricia; Calamia, Valentina; Blanco, Francisco J

    2015-08-01

    Osteoarthritis is the most common rheumatic pathology and one of the leading causes of disability worldwide. It is a very complex disease whose etiopathogenesis is not fully understood. Furthermore, there are serious limitations for its management, since it lacks specific and sensitive biomarkers for early diagnosis, prognosis and therapeutic monitoring. Proteomic approaches performed in the last few decades have contributed to the knowledge on the molecular mechanisms that participate in this pathology and they have also led to interesting panels of putative biomarker candidates. In the next few years, further efforts should be made for translating these findings into the clinical routines. It is expected that targeted proteomics strategies will be highly valuable for the verification and qualification of biomarkers of osteoarthritis.

  5. Proteomic maps of breast cancer subtypes

    DEFF Research Database (Denmark)

    Tyanova, Stefka; Albrechtsen, Reidar; Kronqvist, Pauliina

    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...

  6. Using the Proteomics Identifications Database (PRIDE).

    Science.gov (United States)

    Martens, Lennart; Jones, Phil; Côté, Richard

    2008-03-01

    The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer-reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE.

  7. Proteomic applications in food allergy: food allergenomics.

    Science.gov (United States)

    Di Girolamo, Francesco; Muraca, Maurizio; Mazzina, Oscar; Lante, Isabella; Dahdah, Lamia

    2015-06-01

    To familiarize the reader with the recent developments in the identification of food protein allergens by proteomics mass spectrometry-based methods, named allergenomics. The proteomic analysis of food protein allergens has became a hot topic in the food safety field in recent years. Indeed, food allergies represent a current and relevant problem in clinical medicine. Several food allergenomics studies have recently been performed, aiming at better understanding the cause of sensitization to cow's milk in breastfed infants and at assessing both the safety of food (e.g. transgenic) and in particular the allergenic properties of processed fish and seafood. Food protein allergen characterization and quantification, together with the immunoglobulin E epitope mapping, will contribute to the diagnosis/prognosis of food allergy and will lead to a better safety assessment of foods (e.g. novel transgenic foods).

  8. 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...

  9. Proteomic analysis of integrin adhesion complexes.

    Science.gov (United States)

    Byron, Adam; Humphries, Jonathan D; Bass, Mark D; Knight, David; Humphries, Martin J

    2011-04-05

    Integrin receptors regulate cell fate by coupling the binding of extracellular adhesion proteins to the assembly of intracellular cytoskeletal and signaling complexes. A detailed, integrative view of adhesion complexes will provide insight into the molecular mechanisms that control cell morphology, survival, movement, and differentiation. To date, membrane receptor-associated signaling complexes have been refractory to proteomic analysis because of their inherent lability and inaccessibility. We developed a methodology to isolate ligand-induced integrin adhesion complexes, and we used this technique to analyze the composition of complexes associated with multiple receptor-ligand pairs and define core and receptor-specific subnetworks. In particular, we identified regulator of chromosome condensation-2 (RCC2) as a component of fibronectin-activated signaling pathways that regulate directional cell movement. The development of this proteomics pipeline provides the means to investigate the molecular composition and function of various adhesion complexes.

  10. 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.

  11. Proteomics in studying cancer stem cell biology.

    Science.gov (United States)

    Kranenburg, Onno; Emmink, Benjamin L; Knol, Jaco; van Houdt, Winan J; Rinkes, Inne H M Borel; Jimenez, Connie R

    2012-06-01

    Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and how these are affected by cancer-specific genetic alterations and by treatment. Proteomics is emerging as a powerful tool to identify the signaling complexes and pathways that control multi- and pluri-potency and SC differentiation. Here, the authors review the novel insights that these studies have provided and present a comprehensive strategy for the use of proteomics in studying cancer SC biology.

  12. An update of the macaque testis proteome

    Directory of Open Access Journals (Sweden)

    Tao Zhou

    2015-12-01

    Full Text Available The genome sequence of rhesus macaque is a draft version with many errors and is lack of Y chromosome annotation. In the present dataset, we reanalyzed the previously published macaque testis proteome. We searched for refined protein sequences, potential Y chromosome proteins and transcripts predicted proteins in addition to the latest Ensembl protein sequences of macaque. A total of 74,433 peptides corresponding to 9247 protein groups were identified, and the data are supplied in this paper. The updated version of macaque testis proteome provided evidences for predicted genes or transcripts at the peptide level. It can be used for further in-depth proteogenomic annotation of macaque genome and is useful for studying the mechanisms of macaque spermatogenesis.

  13. Autophagy is highly targeted among host comparative proteomes during infection with different virulent RABV strains.

    Science.gov (United States)

    Li, Ling; Jin, Hongli; Wang, Hualei; Cao, Zengguo; Feng, Na; Wang, Jianzhong; Zhao, Yongkun; Zheng, Xuexing; Hou, Pengfei; Li, Nan; Chi, Hang; Huang, Pei; Jiao, Cuicui; Li, Qian; Wang, Lina; Wang, Tiecheng; Sun, Weiyang; Gao, Yuwei; Tu, Changchun; Hu, Guixue; Yang, Songtao; Xia, Xianzhu

    2017-03-28

    Rabies virus (RABV) is a neurotropic virus that causes serious disease in humans and animals worldwide. It has been reported that different RABV strains can result in divergent prognoses in animal model. To identify host factors that affect different infection processes, a kinetic analysis of host proteome alterations in mouse brains infected with different virulent RABV strains was performed using isobaric tags for a relative and absolute quantification (iTRAQ)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach, and this analysis identified 147 differentially expressed proteins (DEPs) between the pathogenic challenge virus standard (CVS)-11 strain and the attenuated SRV9 strain. Bioinformatics analyses of these DEPs revealed that autophagy and several pathways associated with autophagy, such as mammalian target of rapamycin (mTOR) signaling, p70S6K signaling, nuclear factor erythroid 2-related factor 2 (NRF2)-mediated oxidative stress and superoxide radical degradation, were dysregulated. Validation of the proteomic data showed that attenuated SRV9 induced more autophagosome accumulation than CVS-11 in an in vitro model. Our findings provide new insights into the pathogenesis of RABV and encourage further studies on this topic.

  14. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    Science.gov (United States)

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  15. Label-free quantitative proteomic analysis reveals strong involvement of complement alternative and terminal pathways in human glomerular sclerotic lesions.

    Science.gov (United States)

    Zhang, Ying; Xu, Bo; Kinoshita, Naohiko; Yoshida, Yutaka; Tasaki, Masayuki; Fujinaka, Hidehiko; Magdeldin, Sameh; Yaoita, Eishin; Yamamoto, Tadashi

    2015-06-18

    Since glomerular sclerosis frequently accompanies various glomerular diseases at the end stages, it is challenging to differentiate ubiquitous biological processes underlying this pathology from those critically involved in specific diseases. Furthermore, in-depth proteomic profile of human glomerular sclerosis remains limited. In this study, human glomeruli with intermediate (i-GS) and advanced (GS) sclerotic lesions, which were excluded from specific renal diseases and assumed to be aging-related, were laser captured from macroscopically normal cortex distant from urological carcinoma, and subjected to label-free quantitative proteomic analysis. We explicate an evident increase of membrane attack complex in i-GS and GS with an up-going tendency, which is accompanied by increasing of inhibitory regulators of alternative and terminal pathways. GO annotation and IPA pathway analysis agree to these results. Proteomic findings are validated by immunohistochemical studies which indicate that alternative and terminal pathways are positively involved in the glomerular sclerosis seen in distinct renal diseases. Furthermore, proteomic analysis also demonstrates remarkable increases of complement factor B in GS and TGF-ß1 in both GS and i-GS. Identification of complement factor B implicates that on-site activation of alternative pathway may occur in injured glomeruli and stepwise increase of TGF-ß1 suggests its contribution to the progression of glomerulosclerosis. This study provides in-depth quantitative proteomic profiles of human glomeruli with intermediate and advanced sclerotic lesions. It reveals that the over-expression of alternative and terminal pathway components is significantly involved in human glomerulosclerosis seen in distinct renal diseases. Proteomic identification of the increased TGF-ß1 provides supporting evidence for the role of podocyte apoptosis leading to human glomerulosclerosis. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Proteomic profiling of the epileptic dentate gyrus

    OpenAIRE

    Li, Aiqing; Choi, Yun-Sik; Dziema, Heather; Cao, Ruifeng; Cho, Hee-Yeon; Jung, Yeon Joo; Obrietan, Karl

    2010-01-01

    The development of epilepsy is often associated with marked changes in central nervous system cell structure and function. Along these lines, reactive gliosis and granule cell axonal sprouting within the dentate gyrus of the hippocampus are commonly observed in individuals with temporal lobe epilepsy. Here we used the pilocarpine model of temporal lobe epilepsy in mice to screen the proteome and phosphoproteome of the dentate gyrus to identify molecular events that are altered as part of the ...

  17. Proteomics of anti-cancer drugs

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Hana; Martinková, Jiřina; Hrabáková, Rita; Skalníková, Helena; Novák, Petr; Hajdůch, M.; Gadher, S. J.

    2009-01-01

    Roč. 276, Supplement 1 (2009), s. 84-84 E-ISSN 1742-4658. [34th FEBS Congress. 04.07.2009-09.07.2009, Praha] R&D Projects: GA MŠk LC07017 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50200510 Keywords : proteomics * anti-cancer drugs * biomarkers Subject RIV: FD - Oncology ; Hematology

  18. Hydrophilic interaction liquid chromatography (HILIC) in proteomics

    OpenAIRE

    Boersema, Paul J.; Mohammed, Shabaz; Heck, Albert J. R.

    2008-01-01

    In proteomics, nanoflow multidimensional chromatography is now the gold standard for the separation of complex mixtures of peptides as generated by in-solution digestion of whole-cell lysates. Ideally, the different stationary phases used in multidimensional chromatography should provide orthogonal separation characteristics. For this reason, the combination of strong cation exchange chromatography (SCX) and reversed-phase (RP) chromatography is the most widely used combination for the separa...

  19. Proteome profiling of embryo chick retina

    OpenAIRE

    Mizukami, Mina; Kanamoto, Takashi; Souchelnytskyi, Nazariy; Kiuchi, Yoshiaki

    2008-01-01

    Abstract Background Little is known regarding the molecular pathways that underlie the process of retinal development. The purpose of this study was to identify proteins which may be involved in development of retina. We used a proteomics-based approach to identify proteins that are up- or down-regulated during the development of the embryo chick retina. Results Two-dimensional gel electrophoresis was performed with the retina of embryo chicken, which was obtained from embryos of day 7 (ED7) ...

  20. Proteomics Development and Application for Bioforensics

    Energy Technology Data Exchange (ETDEWEB)

    Wahl, Karen L.; Wunschel, David S.; Clowers, Brian H.

    2010-09-15

    Proteomics is a relatively new scientific discipline dedicated to the comprehensive study of the protein composition of biological systems. While genomic sequencing is an invaluable tool for bioforensic sample identification, proteomics complements genomics in that the genes present in an organism code for the proteins that can be present in a microorganism. Many proteins are conserved for general identification while other protein expression varies with environment/growth state/growth conditions (i.e. not all proteins are expressed at any given time or condition) providing additional information beyond genomic analysis. This expression specificity and the relative stability of proteins with respect to genetic material make them attractive targets for microorganism identification and forensic applications to complement genomic approaches. Proteomic analysis depends upon the availability of genome sequences of the relevant organisms or their near relatives. The known amino acid sequences for potential proteins within the database can be compared to amino acid sequences of actual proteins present in a sample as determined with high mass accuracy by mass spectrometry for identification of the proteins in the sample. With the development of technology for rapid genome sequencing of organisms, the known protein database is growing, supporting improved identification of the proteins present in a sample. Recent developments in mass spectrometry instrumentation and microbial sequencing are leading to an increased growth in application of proteomics to microbiology, pathogen detection, disease diagnosis and microbial forensics as well as other biological disciplines. Mass spectrometry analysis does not require a priori knowledge of the sample or expected targets to gain meaningful.

  1. 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.

  2. 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

  3. Synaptic proteome changes in the hypothalamus of mother rats.

    Science.gov (United States)

    Udvari, Edina Brigitta; Völgyi, Katalin; Gulyássy, Péter; Dimén, Diána; Kis, Viktor; Barna, János; Szabó, Éva Rebeka; Lubec, Gert; Juhász, Gábor; Kékesi, Katalin Adrienna; Dobolyi, Árpád

    2017-04-21

    To establish synaptic proteome changes associated with motherhood, we isolated synaptosome fractions from the hypothalamus of mother rats and non-maternal control females at the 11th postpartum day. Proteomic analysis by two-dimensional differential gel electrophoresis combined with mass spectrometric protein identification established 26 significant proteins, 7 increasing and 19 decreasing protein levels in the dams. The altered proteins are mainly involved in energy homeostasis, protein folding, and metabolic processes suggesting the involvement of these cellular processes in maternal adaptations. The decrease in a significantly altered protein, complement component 1q subcomponent-binding protein (C1qbp) was validated with Western blotting. Furthermore, immunohistochemistry showed its presence in hypothalamic fibers and terminals in agreement with its presence in synaptosomes. We also found the expression of C1qbp in different hypothalamic nuclei including the preoptic area and the paraventricular hypothalamic nucleus at the protein and at the mRNA level using immunohistochemistry and in situ hybridization histochemistry, respectively. Bioinformatical network analysis revealed that cytokines, growth factors, and protein kinases are common regulators, which indicates a complex regulation of the proteome change in mothers. The results suggest that maternal responsiveness is associated with synaptic proteins level changes in the hypothalamus, and that growth factors and cytokines may govern these alterations. The period of motherhood is accompanied with several behavioral, neuroendocrine, emotional and metabolic adaptations in the brain. Although it is established that various hypothalamic networks participate in the maternal adaptations of the rodent brain, our knowledge on the molecular background of these alterations remains seriously limited. In the present study, we first determined that the functional alterations of the maternal brain can be detected at the

  4. Latex beads internalization and quantitative proteomics join forces to decipher the endosomal proteome.

    Science.gov (United States)

    Guimarães de Araújo, Mariana Eça; Huber, Lukas Alfons; Stasyk, Taras

    2011-06-01

    The proteome analysis of endocytic compartments has been constrained by the limited purity of the organelle fractions obtained by current biochemical methods. Duclos and coworkers have developed a novel method to isolate highly purified endosomal organelles based on small latex beads internalization followed by gradient centrifugation and successfully combined it with a redundant peptide counting method to compare the relative abundance of proteins in organelles. The presence of bona fide markers in their respective subcellular organelles and the identification of several new endosomal-associated proteins, attested the applicability of their combinatory approach. Future applications of this strategy may deliver a comprehensive endosomal proteome chart: from the identification of the key players to the determination of time and signaling-dependent proteome changes. As a long-term perspective, such an approach may unveil new clues to the molecular mechanisms underlining human diseases associated with endosomal biogenesis defects.

  5. How to submit MS proteomics data to ProteomeXchange via the PRIDE database.

    Science.gov (United States)

    Ternent, Tobias; Csordas, Attila; Qi, Da; Gómez-Baena, Guadalupe; Beynon, Robert J; Jones, Andrew R; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2014-10-01

    The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission and dissemination of MS-based proteomics data in the public domain. In the consortium, the PRIDE database at the European Bioinformatics Institute, acts as the initial submission point of MS/MS data sets. In this manuscript, we explain step by step the submission process of MS/MS data sets to PX via PRIDE. We describe in detail the two available workflows: 'complete' and 'partial' submissions, together with the available tools to streamline the process. Throughout the manuscript, we will use one example data set containing identification and quantification data, which has been deposited in PRIDE/ProteomeXchange with the accession number PXD000764 (http://proteomecentral.proteomexchange.org/dataset/PXD000764). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. CPTAC Collaborates with Molecular & Cellular Proteomics to Address Reproducibility in Targeted Assay Development | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The journal Molecular & Cellular Proteomics (MCP), in collaboration with the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), part of the National Institutes of Health, announce new guidelines and requirements for papers describing the development and application of targeted mass spectrometry measurements of peptides, modified peptides and proteins (Mol Cell Proteomics 2017; PMID: 28183812).  NCI’s participation is part of NIH’s overall effort to address the r

  7. A Proposal of the Ur-proteome

    Science.gov (United States)

    Palacios-Pérez, Miryam; Andrade-Díaz, Fernando; José, Marco V.

    2017-11-01

    Herein we outline a plausible proteome, encoded by assuming a primeval RNY genetic code. We unveil the primeval phenotype by using only the RNA genotype; it means that we recovered the most ancestral proteome, mostly made of the 8 amino acids encoded by RNY triplets. By looking at those fragments, it is noticeable that they are positioned, not at catalytic sites, but in the cofactor binding sites. It implies that the stabilization of a molecule appeared long before its catalytic activity, and therefore the Ur-proteome comprised a set of proteins modules that corresponded to Cofactor Stabilizing Binding Sites (CSBSs), which we call the primitive bindome. With our method, we reconstructed the structures of the "first protein modules" that Sobolevsky and Trifonov (2006) found by using only RMSD. We also examine the probable cofactors that bound to them. We discuss the notion of CSBSs as the first proteins modules in progenotes in the context of several proposals about the primitive forms of life.

  8. Fungal proteomics: from identification to function.

    Science.gov (United States)

    Doyle, Sean

    2011-08-01

    Some fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of 'unknown function protein' as opposed to 'hypothetical protein' - once any protein has been identified by protein mass spectrometry. A combination of approaches including comparative proteomics, pathogen-induced protein expression and immunoproteomics are outlined, which, when used in combination with a variety of other techniques (e.g. functional genomics, microarray analysis, immunochemical and infection model systems), appear to yield comprehensive and definitive information on protein function in fungi. The relative advantages of proteomic, as opposed to transcriptomic-only, analyses are also described. In the future, combined high-throughput, quantitative proteomics, allied to transcriptomic sequencing, are set to reveal much about protein function in fungi. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  9. Organelle proteomics experimental designs and analysis.

    Science.gov (United States)

    Gatto, Laurent; Vizcaíno, Juan Antonio; Hermjakob, Henning; Huber, Wolfgang; Lilley, Kathryn S

    2010-11-01

    In biology, localisation is function: knowledge of the localisation of proteins is of paramount importance to assess and study their function. This supports the need for reliable protein sub-cellular localisation assignment. Concomitant with recent technological advances in organelle proteomics, there is a requirement for more rigorous experimental and analysis design planning and description. In this review, we present an overview of current experimental designs in qualitative and quantitative organelle proteomics as well as associated data analysis. We also consider the major benefits associated with careful description and dissemination of the experiment and analysis designs, namely (i) comparison and optimisation of experimental designs and analysis pipelines, (ii) data validation, (iii) reproducible research, (iv) efficient repository submission and retrieval and (v) meta analysis. Formalization of experimental design and analysis work flows is of direct benefit for the organelle proteomics researchers and will result in providing organelle localisation data of highest quality for the wider research community. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Proteomics for the authentication of fish species.

    Science.gov (United States)

    Mazzeo, Maria Fiorella; Siciliano, Rosa Anna

    2016-09-16

    Assessment of seafood authenticity and origin, mainly in the case of processed products (fillets, sticks, baby food) represents the crucial point to prevent fraudulent deceptions thus guaranteeing market transparency and consumers health. The most dangerous practice that jeopardies fish safety is intentional or unintentional mislabeling, originating from the substitution of valuable fish species with inferior ones. Conventional analytical methods for fish authentication are becoming inadequate to comply with the strict regulations issued by the European Union and with the increase of mislabeling due to the introduction on the market of new fish species and market globalization. This evidence prompts the development of high-throughput approaches suitable to identify unambiguous biomarkers of authenticity and screen a large number of samples with minimal time consumption. Proteomics provides suitable and powerful tools to investigate main aspects of food quality and safety and has given an important contribution in the field of biomarkers discovery applied to food authentication. This report describes the most relevant methods developed to assess fish identity and offers a perspective on their potential in the evaluation of fish quality and safety thus depicting the key role of proteomics in the authentication of fish species and processed products. The assessment of fishery products authenticity is a main issue in the control quality process as deceptive practices could imply severe health risks. Proteomics based methods could significantly contribute to detect falsification and frauds, thus becoming a reliable operative first-line testing resource in food authentication. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Proteome compression via protein domain compositions.

    Science.gov (United States)

    Hayashida, Morihiro; Ruan, Peiying; Akutsu, Tatsuya

    2014-06-01

    In this paper, we study domain compositions of proteins via compression of whole proteins in an organism for the sake of obtaining the entropy that the individual contains. We suppose that a protein is a multiset of domains. Since gene duplication and fusion have occurred through evolutionary processes, the same domains and the same compositions of domains appear in multiple proteins, which enables us to compress a proteome by using references to proteins for duplicated and fused proteins. Such a network with references to at most two proteins is modeled as a directed hypergraph. We propose a heuristic approach by combining the Edmonds algorithm and an integer linear programming, and apply our procedure to 14 proteomes of Dictyostelium discoideum, Escherichia coli, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Oryza sativa, Danio rerio, Xenopus laevis, Gallus gallus, Mus musculus, Pan troglodytes, and Homo sapiens. The compressed size using both of duplication and fusion was smaller than that using only duplication, which suggests the importance of fusion events in evolution of a proteome. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. The broccoli (Brassica oleracea) phloem tissue proteome.

    Science.gov (United States)

    Anstead, James A; Hartson, Steven D; Thompson, Gary A

    2013-11-07

    The transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloem. To better understand these processes a comprehensive understanding of the proteins involved is required. While a considerable amount of data has been obtained from proteomic analyses of phloem sap, this has mainly served to identify the soluble proteins that are translocated through the phloem network. In order to obtain more comprehensive proteomic data from phloem tissue we developed a simple dissection procedure to isolate phloem tissue from Brassica oleracea. The presence of a high density of phloem sieve elements was confirmed using light microscopy and fluorescently labeled sieve element-specific antibodies. To increase the depth of the proteomic analysis for membrane bound and associated proteins, soluble proteins were extracted first and subsequent extractions were carried out using two different detergents (SDS and CHAPSO). Across all three extractions almost four hundred proteins were identified and each extraction method added to the analysis demonstrating the utility of an approach combining several extraction protocols. The phloem was found to be enriched in proteins associated with biotic and abiotic stress responses and structural proteins. Subsequent expression analysis identified a number of genes that appear to be expressed exclusively or at very high levels in phloem tissue, including genes that are known to express specifically in the phloem as well as novel phloem genes.

  13. 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.

  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. Extending mass spectrometry's reach in proteome analysis

    International Nuclear Information System (INIS)

    Downard, K.M.

    2001-01-01

    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

  16. Impact of cryopreservation on bull () semen proteome.

    Science.gov (United States)

    Westfalewicz, B; Dietrich, M A; Ciereszko, A

    2015-11-01

    Cryopreservation of bull spermatozoa is a well-established technique, allowing artificial insemination of cattle on a commercial scale. However, the extent of proteome changes in seminal plasma and spermatozoa during cryopreservation are not yet fully known. The objective of this study was to compare the proteomes of fresh, equilibrated, and cryopreserved bull semen (spermatozoa and seminal plasma) to establish the changes in semen proteins during the cryopreservation process. Semen was collected from 6 mature Holstein Friesian bulls. After sample processing, comparative analysis and identification of proteins was performed using 2-dimensional difference in-gel electrophoresis coupled with matrix-assisted laser desorption/ionization mass spectrometry. Analysis of spermatozoa extracts revealed that 25 identified protein spots, representing 16 proteins, underwent significant ( cryopreservation. Eighteen protein spots decreased in abundance, 5 protein spots increased in abundance, and 2 protein spots showed different, specific patterns of abundance changes. Analysis of seminal fluid containing seminal plasma showed that 6 identified protein spots, representing 4 proteins, underwent significant ( cryopreservation. Two protein spots increased in abundance and 4 decreased in abundance. Semen extending and equilibration seems to be responsible for a significant portion of the proteome changes related to cryopreservation technology. Most sperm proteins affected by equilibration and cryopreservation are membrane bound, and loss of those proteins may reduce natural spermatozoa coating. Further research is needed to unravel the mechanisms of the particular protein changes described in this study and establish the relationship between those changes and sperm quality.

  17. 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.

  18. Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication*

    Science.gov (United States)

    Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

    2016-01-01

    Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under

  19. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

    Science.gov (United States)

    Deutsch, Eric W; Csordas, Attila; Sun, Zhi; Jarnuczak, Andrew; Perez-Riverol, Yasset; Ternent, Tobias; Campbell, David S; Bernal-Llinares, Manuel; Okuda, Shujiro; Kawano, Shin; Moritz, Robert L; Carver, Jeremy J; Wang, Mingxun; Ishihama, Yasushi; Bandeira, Nuno; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2017-01-04

    The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components.We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective.

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-09-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

  1. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-01-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed. PMID:26340626

  2. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    Directory of Open Access Journals (Sweden)

    Klára Kosová

    2015-09-01

    Full Text Available Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum, durum wheat (Triticum durum, barley (Hordeum vulgare, maize (Zea mays; leguminous plants: alfalfa (Medicago sativa, soybean (Glycine max, common bean (Phaseolus vulgaris, pea (Pisum sativum; oilseed rape (Brassica napus; potato (Solanum tuberosum; tobacco (Nicotiana tabaccum; tomato (Lycopersicon esculentum; and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

  3. Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains.

    Science.gov (United States)

    González-Fernández, Raquel; Aloria, Kerman; Valero-Galván, José; Redondo, Inmaculada; Arizmendi, Jesús M; Jorrín-Novo, Jesús V

    2014-01-31

    The necrotrophic fungus Botrytis cinerea is a very damaging phytopathogen of wide host range and environmental persistence. It is difficult to control because of its genetic versatility, expressed in the many phenotypical differences among isolates. The genomes of the B. cinerea B05.10 and T4 strains have been recently sequenced, becoming a model system for necrotrophic pathogens, and thus opening new alternatives for functional genomics analysis. In this work, the mycelium and secreted proteome of six wild-type strains with different host range, and grown in liquid minimal medium, have been analyzed by using complementary gel-based (1-DE and 2-DE) and gel-free/label-free (nUPLC-MS(E)) approaches. We found differences in the protein profiles among strains belonging to both the mycelium and the secretome. A total of 47 and 51 variable proteins were identified in the mycelium and the secretome, respectively. Some of them, such as malate dehydrogenase or peptidyl-prolyl cis-trans isomerase from the mycelium, and endopolygalacturonase, aspartic protease or cerato-platanin protein from the secretome have been reported as virulence factors, which are involved in host-tissue invasion, pathogenicity or fungal development. The necrotrophic fungus Botrytis cinerea is an important phytopathogen of wide host range and environmental persistence, causing substantial economic losses worldwide. In this work, the mycelium and secreted proteome of six B. cinerea wild-type strains with different host range have been analyzed by using complementary gel-based and gel-free/label-free approaches. Fungal genetic versatility was confirmed at the proteome level for both mycelium proteome and secreted proteins. A high number of hypothetical proteins with conserved domains related to toxin compounds or to unknown functions were identified, having qualitative differences among strains. The identification of hypothetical proteins suggests that the B. cinerea strains differ mostly in processes

  4. Proteomic profiling of human intraschisis cavity fluid.

    Science.gov (United States)

    Sudha, Dhandayuthapani; Kohansal-Nodehi, Mahdokht; Kovuri, Purnima; Manda, Srikanth Srinivas; Neriyanuri, Srividya; Gopal, Lingam; Bhende, Pramod; Chidambaram, Subbulakshmi; Arunachalam, Jayamuruga Pandian

    2017-01-01

    X-linked retinoschisis (XLRS) is a vitreoretinal degenerative disorder causing vision deterioration, due to structural defects in retina. The hallmark of this disease includes radial streaks arising from the fovea and splitting of inner retinal layers (schisis). Although these retinal changes are attributed to mutations in the retinoschisin gene, schisis is also observed in patients who do not carry mutations. In addition, the origin of intraschisis fluid, the triggering point of schisis formation and its progression are largely unknown still. So far, there is no report on the complete proteomic analysis of this fluid. Schisis fluid proteome could reflect biochemical changes in the disease condition, helping in better understanding and management of retinoschisis. Therefore it was of interest to investigate the intraschisis fluid proteome using high-resolution mass spectrometry. Two male XLRS patients (aged 4 and 40 years) underwent clinical and genetic evaluation followed by surgical extraction of intraschisis fluids. The two fluid samples were resolved on a SDS-PAGE and the processed peptides were analyzed by Q-Exactive plus hybrid quadrupole-Orbitrap mass spectrometry. Functional annotation of the identified proteins was performed using Ingenuity pathway analysis software. Mass spectrometry analysis detected 770 nonredundant proteins in the intraschisis fluid. Retinol dehydrogenase 14 was found to be abundant in the schisis fluid. Gene ontology based analysis indicated that 19% of the intraschisis fluid proteins were localized to the extracellular matrix and 15% of the proteins were involved in signal transduction. Functional annotation identified three primary canonical pathways to be associated with the schisis fluid proteome viz., LXR/RXR activation, complement system and acute phase response signalling, which are involved in immune and inflammatory responses. Collectively, our results show that intraschisis fluid comprises specific inflammatory proteins

  5. Proteomics of neural stem cells

    Czech Academy of Sciences Publication Activity Database

    Skalníková, Helena; Vodička, Petr; Gadher, S. J.; Kovářová, Hana

    2008-01-01

    Roč. 5, č. 2 (2008), s. 175-186 ISSN 1478-9450 R&D Projects: GA MŠk 1M0538 Institutional research plan: CEZ:AV0Z50450515 Keywords : cell-based regnerative and reparative therapy * conditioned media * differentiation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.848, year: 2008

  6. Identification and proteomic analysis of osteoblast-derived exosomes

    Energy Technology Data Exchange (ETDEWEB)

    Ge, Min; Ke, Ronghu; Cai, Tianyi; Yang, Junyi; Mu, Xiongzheng, E-mail: cranio@vip.163.com

    2015-11-06

    Exosomes are nanometer-sized vesicles with the function of intercellular communication, and they are released by various cell types. To reveal the knowledge about the exosomes from osteoblast, and explore the potential functions of osteogenesis, we isolated microvesicles from supernatants of mouse Mc3t3 by ultracentrifugation, characterized exosomes by electron microscopy and immunoblotting and presented the protein profile by proteomic analysis. The result demonstrated that microvesicles were between 30 and 100 nm in diameter, round shape with cup-like concavity and expressed exosomal marker tumor susceptibility gene (TSG) 101 and flotillin (Flot) 1. We identified a total number of 1069 proteins among which 786 proteins overlap with ExoCarta database. Gene Oncology analysis indicated that exosomes mostly derived from plasma membrane and mainly involved in protein localization and intracellular signaling. The Ingenuity Pathway Analysis showed pathways are mostly involved in exosome biogenesis, formation, uptake and osteogenesis. Among the pathways, eukaryotic initiation factor 2 pathways played an important role in osteogenesis. Our study identified osteoblast-derived exosomes, unveiled the content of them, presented potential osteogenesis-related proteins and pathways and provided a rich proteomics data resource that will be valuable for further studies of the functions of individual proteins in bone diseases. - Highlights: • We for the first time identified exosomes from mouse osteoblast. • Osteoblasts-derived exosomes contain osteoblast peculiar proteins. • Proteins from osteoblasts-derived exosomes are intently involved in EIF2 pathway. • EIF2α from the EIF2 pathway plays an important role in osteogenesis.

  7. Novel effects of hormonal contraceptive use on the plasma proteome.

    Directory of Open Access Journals (Sweden)

    Andrea R Josse

    Full Text Available Hormonal contraceptive (HC use may increase cardiometabolic risk; however, the effect of HC on emerging cardiometabolic and other disease risk factors is not clear.To determine the association between HC use and plasma proteins involved in established and emerging disease risk pathways.Concentrations of 54 high-abundance plasma proteins were measured simultaneously by LC-MRM/MS in 783 women from the Toronto Nutrigenomics and Health Study. C-reactive protein (CRP was measured separately. ANCOVA was used to test differences in protein concentrations between users and non-users, and among HC users depending on total hormone dose. Linear regression was used to test the association between duration (years of HC use and plasma protein concentrations. Principal components analysis (PCA was used to identify plasma proteomic profiles in users and non-users.After Bonferroni correction, 19 proteins involved in inflammation, innate immunity, coagulation and blood pressure regulation were significantly different between users and non-users (P<0.0009. These differences were replicated across three distinct ethnocultural groups. Traditional markers of glucose and lipid metabolism were also significantly higher among HC users. Neither hormone dose nor duration of use affected protein concentrations. PCA identified 4 distinct proteomic profiles in users and 3 in non-users.HC use was associated with different concentrations of plasma proteins along various disease-related pathways, and these differences were present across different ethnicities. Aside from the known effect of HC on traditional biomarkers of cardiometabolic risk, HC use also affects numerous proteins that may be biomarkers of dysregulation in inflammation, coagulation and blood pressure.

  8. Proteome analysis of early lineage specification in bovine embryos.

    Science.gov (United States)

    Demant, Myriam; Deutsch, Daniela R; Fröhlich, Thomas; Wolf, Eckhard; Arnold, Georg J

    2015-02-01

    During mammalian embryo development, the zygote undergoes embryonic cleavage in the oviduct and reaches the uterus at the morula stage, when compaction and early lineage specification take place. To increase knowledge about the associated changes of the embryonic protein repertoire, we performed a comprehensive proteomic analysis of in vitro produced bovine morulae and blastocysts (six biological replicates), using an iTRAQ-based approach. A total of 560 proteins were identified of which 502 were quantified. The abundance of 140 proteins was significantly different between morulae and blastocysts, among them nucleophosmin (NPM1), eukaryotic translation initiation factor 5A-1 (EIF5A), receptor of activated protein kinase C 1 (GNB2L1/RACK1), and annexin A6 (ANXA6) with increased, and glutathione S-transferase mu 3 (GSTM3), peroxiredoxin 2 (PRDX2), and aldo-keto reductase family 1 member B1 (AKR1B1) with decreased abundance in blastocysts. Seventy-three percent of abundance altered proteins increased, reflecting an increase of translation activity in this period. This is further supported by an increase in the abundance of proteins involved in the translation machinery and the synthesis of ATP. Additionally, a complementary 2D saturation DIGE analysis led to the detection of protein isoforms, e.g. of GSTM3 and PRDX2, relevant for this period of mammalian development, and exemplarily verified the results of the iTRAQ approach. In summary, our systematic differential proteome analysis of bovine morulae and blastocysts revealed new molecular correlates of early lineage specification and differentiation events during bovine embryogenesis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea ...

    African Journals Online (AJOL)

    A two-dimensional liquid chromatography (2D LC) system, ProteomeLab PF 2D, was employed to study the defence proteome of Arabidopsis following infection with the necrotrophic fungal pathogen, Botrytis cinerea. This system demonstrated differential protein expression in control and treated samples in some fractions.

  10. The promise of targeted proteomics for quantitative network biology.

    Science.gov (United States)

    Matsumoto, Masaki; Nakayama, Keiichi I

    2018-03-15

    Proteomics is a powerful tool for obtaining information on a large number of proteins with regard to their expression levels, interactions with other molecules, and posttranslational modifications. Whereas nontargeted, discovery proteomics uncovers differences in the proteomic landscape under different conditions, targeted proteomics has been developed to overcome the limitations of this approach with regard to quantitation. In addition to technical advances in instruments and informatics tools, the advent of the synthetic proteome composed of synthetic peptides or recombinant proteins has advanced the adoption of targeted proteomics across a wide range of research fields. Targeted proteomics can now be applied to measurement of the dynamics of any proteins of interest under a variety of conditions as well as to estimation of the absolute abundance or stoichiometry of proteins in a given network. Multiplexed targeted proteomics assays of high reproducibility and accuracy can provide insight at the quantitative level into entire networks that govern biological phenomena or diseases. Such assays will establish a new paradigm for data-driven science. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Exploring signal transduction networks using mass spectrometry-based proteomics

    NARCIS (Netherlands)

    Meijer, L.A.T.

    2012-01-01

    Mass spectrometry (MS)-based proteomics can be used to answer a diversity of biological questions. In this thesis, we describe the application of several MS-based proteomics approaches to get insight into several aspects of signal transduction. In Chapter 2, quantitative global phosphoproteomics are

  12. Teaching molecular genetics: Chapter 3--Proteomics in nephrology.

    NARCIS (Netherlands)

    Groenen, P.J.T.A.; Heuvel, L.P.W.J. van den

    2006-01-01

    The novel discipline of proteomics has experienced a rapid growth in the recent past and has great potentials for the future. The study of proteins on a genomic scale enables a large number of proteins to be analysed simultaneously. Moreover, proteomic analysis reveals the presence of protein

  13. PRIME-XS, a European infrastructure for proteomics

    NARCIS (Netherlands)

    Raijmakers, Reinout; Olsen, Jesper V; Aebersold, Ruedi; Heck, Albert J R

    The PRIME-XS consortium is a pan-European infrastructure for proteomics. As a prologue to this special issue of Molecular & Cellular Proteomics on the research activities of the PRIME-XS consortium, we, as the guest editors of this issue, provide an overview of the structure and activities of this

  14. Tissue-based map of the human proteome

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Fagerberg, Linn; Hallström, Björn M.

    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...

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

    DEFF Research Database (Denmark)

    Roepstorff, Peter

    2012-01-01

    LC-MS is described. A number of challenging problems which have been solved using different proteomics strategies including the advantage of organell enrichment or modifications specific peptide isolation to get deeper into the proteome are described. Finally the present status and future needs discussed....

  16. 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...

  17. Extracellular proteome of a highly invasive multidrug-resistant clinical strain of Acinetobacter baumannii.

    Science.gov (United States)

    Mendez, Jose Antonio; Soares, Nelson C; Mateos, Jesús; Gayoso, Carmen; Rumbo, Carlos; Aranda, Jesús; Tomas, Maria; Bou, Germán

    2012-12-07

    The study of the extracellular proteomes of pathogenic bacteria is essential for gaining insights into the mechanisms of pathogenesis and for the identification of virulence factors. Through the use of different proteomic approaches, namely Nano-LC and 2DE combined with MALDI-TOF/TOF, we have characterized the extracellular proteome of a highly invasive, multidrug-resistant strain of A. baumannii (clone AbH12O-A2). This study focused on two main protein fractions of the extracellular proteome: proteins that are exported by outer membrane vesicles (OMVs) and freely soluble extracellular proteins (FSEPs) present in the culture medium of A. baumannii. Herein, a total of 179 nonredundant proteins were identified in the OMV protein fraction and a total of 148 nonredundant proteins were identified in FSEP fraction. Of the OMV proteins, 39 were associated with pathogenesis and virulence, including proteins associated with attachment to host cells (e.g., CsuE, CsuB, CsuA/B) and specialized secretion systems for delivery of virulence factors (e.g., P. pilus assembly and FilF), whereas the FSEP fraction possesses extracellular enzymes with degradative activity, such as alkaline metalloprotease. Furthermore, among the FSEP we have detected at least 18 proteins with a known role in oxidative stress response (e.g., catalase, thioredoxin, oxidoreductase, superoxide dismutase). Further assays demonstrated that in the presence of FSEPs, bacterial cells withstand much higher concentrations of H2O2 showing higher survival rate (approximately 2.5 fold) against macrophages. In this study we have identified an unprecedented number of novel extracellular proteins of A. baumannii and we provide insight into their potential role in relevant processes such as oxidative stress response and defense against macrophage attack.

  18. 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.

  19. Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

    NARCIS (Netherlands)

    Low, Teck Yew; van Heesch, Sebastiaan; van den Toorn, Henk; Giansanti, Piero; Cristobal, Alba; Toonen, Pim; Schafer, Sebastian; Huebner, Norbert; van Breukelen, Bas; Mohammed, Shabaz; Cuppen, Edwin; Heck, Albert J. R.; Guryev, Victor

    2013-01-01

    Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and post-transcriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We

  20. 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.

  1. Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

    Science.gov (United States)

    Mayer, Gerhard; Jones, Andrew R; Binz, Pierre-Alain; Deutsch, Eric W; Orchard, Sandra; Montecchi-Palazzi, Luisa; Vizcaíno, Juan Antonio; Hermjakob, Henning; Oveillero, David; Julian, Randall; Stephan, Christian; Meyer, Helmut E; Eisenacher, Martin

    2014-01-01

    This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Erin Shammel; Liu, Tao; Petyuk, Vladislav A.; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; Anderson, Gordon A.; Smith, Richard D.

    2012-08-31

    Mass spectrometry (MS)-based proteomics measurements have become increasingly utilized in a wide range of biological and biomedical applications, and have significantly enhanced the understanding of the complex and dynamic nature of the proteome and its connections to biology and diseases. While some MS techniques such as those for targeted analysis are increasingly applied with great success, others such as global quantitative analysis (for e.g. biomarker discovery) are more challenging and continue to be developed and refined to provide the desired throughput, sensitivity and/ or specificity. New MS capabilities and proteomics-based pipelines/strategies also keep enhancing for the advancement of clinical proteomics applications such as protein biomarker discovery and validation. Herein, we provide a brief review to summarize the current state of MS-based proteomics with respect to its advantages and present limitations, while highlighting its potential in future clinical applications.

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

    Science.gov (United States)

    Gharbi, Myriam; Deberg, Michelle; Henrotin, Yves

    2011-01-01

    After the genomic era, proteomic corresponds to a wide variety of techniques that study the protein content of cells, tissue, or organism and that allow the isolation of 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 or underlying mechanisms leading to a disease or associated with 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 osteoarthritis 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.

  4. A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics.

    Science.gov (United States)

    Reddy, Panga Jaipal; Ray, Sandipan; Sathe, Gajanan J; Gajbhiye, Akshada; Prasad, T S Keshava; Rapole, Srikanth; Panda, Dulal; Srivastava, Sanjeeva

    2015-01-30

    The rapid emergence of microbial drug resistance indicates the urgent need for development of new antimicrobial agents. Bacterial cell division machinery is considered as a promising antimicrobial target. Totarol is a naturally existing diterpenoid, which has the ability to restrain bacterial growth by perturbing the cell division. The present study was conducted to investigate the proteomic alterations in Bacillus subtilis as a consequence of totarol treatment to decipher its mechanism of action and possible molecular targets. Cellular proteome of the totarol treated B. subtilis AH75 strain was analyzed by using multiple complementary proteomic approaches. After the drug treatment, 12, 38 and 139 differentially expressed (1.5 fold change) proteins were identified using 2-DE, DIGE and iTRAQ analyses, respectively. In silico functional analysis of the identified differentially expressed proteins indicated a possible effect of totarol on the central metabolism for energy production, heme biosynthesis and chemotaxis. Interestingly, the primary dehydrogenases, which play a vital role in generating the reducing equivalent, were found to be repressed after totarol treatment indicating an apparent metabolic shutdown. Consequently, multiple cellular assays including resazurin assay and FACS analysis of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) staining confirmed the effect of totarol on respiratory activity and cellular metabolism. The exact mechanism of action of totarol is still unclear and further investigations are essential to identify the molecular/cellular targets of this potential antimicrobial agent. The present study demonstrates the application of differential proteome to decipher the mechanism of action and molecular targets of totarol in B. subtilis. Our quantitative proteome analysis revealed that totarol induced alterations in the expression levels of 139 proteins (1.5 fold change and ≥2 peptides) in B. subtilis. Findings obtained from this study

  5. Insights into islet differentiation and maturation through proteomic characterization of a human iPSC-derived pancreatic endocrine model.

    Science.gov (United States)

    Haller, Corinne; Chaskar, Prasad; Piccand, Julie; Cominetti, Ornella; Macron, Charlotte; Dayon, Loïc; Kraus, Marine R-C

    2018-03-26

    Great progresses have been made for generating in vitro pluripotent stem cell pancreatic β-like cells. However, the maturation stage of the cells still requires in vivo maturation to recreate the environmental niche. A deeper understanding of the factors promoting maturation of the cells is of great interest for clinical applications. We performed label-free mass spectrometry-based proteomic analysis of samples from a longitudinal study of differentiation of human-induced pluripotent stem cells towards glucose-responsive insulin producing cells. Proteome patterns correlated with specific transcription factor gene expression levels during in vitro differentiation, showing the relevance of the technology for identification of pancreatic-specific markers. We analyzed proteomes of the implanted cells in a longitudinal study and showed that the neovascularization process linked to the extracellular matrix environment is time-dependent and conditions the proper maturation of the cells in β-like cells secreting insulin in response to glucose. Proteomic profiling is valuable to qualify and better understand in vivo maturation of progenitor cells towards β-cells. This is critical for future clinical trials where in vivo maturation still needs to be improved for robustness and effectiveness of cell therapy. Novel biomarkers for predicting the efficiency of maturation represents non-invasive monitoring tools for following efficiency of the implant. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  6. Advancing translational research and precision medicine with targeted proteomics.

    Science.gov (United States)

    Uzozie, Anuli Christiana; Aebersold, Ruedi

    2018-02-22

    Remarkable advances in quantitative mass spectrometry have shifted the focus of proteomics from the characterization of protein expression profiles to detailed investigations on the spatial and temporal organization of the proteome. Demands for precision therapy and personalized medicine are challenged by heterogeneity in the larger population, which have led to drawbacks in biomarker performance and therapeutic efficacy. The consistent adaptation of the cellular proteome in response to distinctive signals defines a phenotype. Acquisition of quantitative multi-layered omics data on multiple individuals over defined time scales has made it possible to establish means to probe the extent to which the genome, transcriptome and environment influence the variability of the proteome in given conditions, over time. Comprehensive, reproducible datasets generated with contemporary quantitative, massively parallel, targeted proteomic approaches offer as yet untapped benefits for biomarker discovery, development, and validation. The objective of this review is to recapitulate on advances in targeted proteomics approaches for quantifying the cellular proteome and to address ways to incorporate these data towards improving present day methodologies for biomarker evaluation and precision medicine. Advances in quantitative mass spectrometry have shifted the focus of proteomics from the characterization of protein expression profiles to detailed investigations on the spatial and temporal organization of the proteome. This review expounds on avenues through which targeted proteomic methodologies can be constructively implemented in translational research and precision medicine to overcome existing challenges that hinder the success of protein biomarkers in clinics, and to develop precise therapeutics for future applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Proteome Profile and Quantitative Proteomic Analysis of Buffalo (Bubalusbubalis Follicular Fluid during Follicle Development

    Directory of Open Access Journals (Sweden)

    Qiang Fu

    2016-04-01

    Full Text Available Follicular fluid (FF accumulates in the antrum of the ovarian follicle and provides the microenvironment for oocyte development. FF plays an important role in follicle growth and oocyte maturation. The FF provides a unique window to investigate the processes occurring during buffalo follicular development. The observed low quality of buffalo oocytes may arise from the poor follicular microenvironment. Investigating proteins found in buffalo FF (BFF should provide insight into follicular development processes and provide further understanding of intra-follicular maturation and oocytes quality. Here, a proteomic-based approach was used to analyze the proteome of BFF. SDS-PAGE separation combined with mass spectrometry was used to generate the proteomic dataset. In total, 363 proteins were identified and classified by Gene Ontology terms. The proteins were assigned to 153 pathways, including signaling pathways. To evaluate difference in proteins expressed between BFF with different follicle size (small, <4 mm; and large, >8 mm, a quantitative proteomic analysis based on multi-dimensional liquid chromatography pre-fractionation tandem Orbitrap mass spectrometry identification was performed. Eleven differentially expressed proteins (six downregulated and five upregulated in large BFF were identified and assigned to a variety of functional processes, including serine protease inhibition, oxidation protection and the complement cascade system. Three differentially expressed proteins, Vimentin, Peroxiredoxin-1 and SERPIND1, were verified by Western blotting, consistent with the quantitative proteomics results. Our datasets offers new information about proteins present in BFF and should facilitate the development of new biomarkers. These differentially expressed proteins illuminate the size-dependent protein changes in follicle microenvironment.

  8. Proteome Profile and Quantitative Proteomic Analysis of Buffalo (Bubalusbubalis) Follicular Fluid during Follicle Development.

    Science.gov (United States)

    Fu, Qiang; Huang, Yulin; Wang, Zhiqiang; Chen, Fumei; Huang, Delun; Lu, Yangqing; Liang, Xianwei; Zhang, Ming

    2016-04-29

    Follicular fluid (FF) accumulates in the antrum of the ovarian follicle and provides the microenvironment for oocyte development. FF plays an important role in follicle growth and oocyte maturation. The FF provides a unique window to investigate the processes occurring during buffalo follicular development. The observed low quality of buffalo oocytes may arise from the poor follicular microenvironment. Investigating proteins found in buffalo FF (BFF) should provide insight into follicular development processes and provide further understanding of intra-follicular maturation and oocytes quality. Here, a proteomic-based approach was used to analyze the proteome of BFF. SDS-PAGE separation combined with mass spectrometry was used to generate the proteomic dataset. In total, 363 proteins were identified and classified by Gene Ontology terms. The proteins were assigned to 153 pathways, including signaling pathways. To evaluate difference in proteins expressed between BFF with different follicle size (small, 8 mm), a quantitative proteomic analysis based on multi-dimensional liquid chromatography pre-fractionation tandem Orbitrap mass spectrometry identification was performed. Eleven differentially expressed proteins (six downregulated and five upregulated in large BFF) were identified and assigned to a variety of functional processes, including serine protease inhibition, oxidation protection and the complement cascade system. Three differentially expressed proteins, Vimentin, Peroxiredoxin-1 and SERPIND1, were verified by Western blotting, consistent with the quantitative proteomics results. Our datasets offers new information about proteins present in BFF and should facilitate the development of new biomarkers. These differentially expressed proteins illuminate the size-dependent protein changes in follicle microenvironment.

  9. Positional proteomics in the era of the human proteome project on the doorstep of precision medicine.

    Science.gov (United States)

    Eckhard, Ulrich; Marino, Giada; Butler, Georgina S; Overall, Christopher M

    2016-03-01

    Proteolytic processing is a pervasive and irreversible post-translational modification that expands the protein universe by generating new proteoforms (protein isoforms). Unlike signal peptide or prodomain removal, protease-generated proteoforms can rarely be predicted from gene sequences. Positional proteomic techniques that enrich for N- or C-terminal peptides from proteomes are indispensable for a comprehensive understanding of a protein's function in biological environments since protease cleavage frequently results in altered protein activity and localization. Proteases often process other proteases and protease inhibitors which perturbs proteolytic networks and potentiates the initial cleavage event to affect other molecular networks and cellular processes in physiological and pathological conditions. This review is aimed at researchers with a keen interest in state of the art systems level positional proteomic approaches that: (i) enable the study of complex protease-protease, protease-inhibitor and protease-substrate crosstalk and networks; (ii) allow the identification of proteolytic signatures as candidate disease biomarkers; and (iii) are expected to fill the Human Proteome Project missing proteins gap. We predict that these methodologies will be an integral part of emerging precision medicine initiatives that aim to customize healthcare, converting reactive medicine into a personalized and proactive approach, improving clinical care and maximizing patient health and wellbeing, while decreasing health costs by eliminating ineffective therapies, trial-and-error prescribing, and adverse drug effects. Such initiatives require quantitative and functional proteome profiling and dynamic disease biomarkers in addition to current pharmacogenomics approaches. With proteases at the pathogenic center of many diseases, high-throughput protein termini identification techniques such as TAILS (Terminal Amine Isotopic Labeling of Substrates) and COFRADIC (COmbined

  10. Proteomic profiling of the rat hypothalamus

    Directory of Open Access Journals (Sweden)

    Pedroso Amanda P

    2012-04-01

    Full Text Available Abstract Background The hypothalamus plays a pivotal role in numerous mechanisms highly relevant to the maintenance of body homeostasis, such as the control of food intake and energy expenditure. Impairment of these mechanisms has been associated with the metabolic disturbances involved in the pathogenesis of obesity. Since rodent species constitute important models for metabolism studies and the rat hypothalamus is poorly characterized by proteomic strategies, we performed experiments aimed at constructing a two-dimensional gel electrophoresis (2-DE profile of rat hypothalamus proteins. Results As a first step, we established the best conditions for tissue collection and protein extraction, quantification and separation. The extraction buffer composition selected for proteome characterization of rat hypothalamus was urea 7 M, thiourea 2 M, CHAPS 4%, Triton X-100 0.5%, followed by a precipitation step with chloroform/methanol. Two-dimensional (2-D gels of hypothalamic extracts from four-month-old rats were analyzed; the protein spots were digested and identified by using tandem mass spectrometry and database query using the protein search engine MASCOT. Eighty-six hypothalamic proteins were identified, the majority of which were classified as participating in metabolic processes, consistent with the finding of a large number of proteins with catalytic activity. Genes encoding proteins identified in this study have been related to obesity development. Conclusion The present results indicate that the 2-DE technique will be useful for nutritional studies focusing on hypothalamic proteins. The data presented herein will serve as a reference database for studies testing the effects of dietary manipulations on hypothalamic proteome. We trust that these experiments will lead to important knowledge on protein targets of nutritional variables potentially able to affect the complex central nervous system control of energy homeostasis.

  11. 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.

  12. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

    KAUST Repository

    Komatsu, Setsuko

    2017-05-10

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

  13. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

    Science.gov (United States)

    Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

    2017-06-23

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

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

    Science.gov (United States)

    Gadher, Suresh Jivan; Marczak, Łukasz; Łuczak, Magdalena; Stobiecki, Maciej; Widlak, Piotr; Kovarova, Hana

    2016-01-01

    Every year since 2007, the Central and Eastern European Proteomic Conference (CEEPC) has excelled in representing state-of-the-art proteomics in and around Central and Eastern Europe, and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including traditional and often-revisited methodologies as well as the latest technological achievements in clinical, quantitative and structural proteomics with a view to systems biology of a variety of processes. The 9th CEEPC was held from June 15th to 18th, 2015, at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznań, Poland. The scientific program stimulated exchange of proteomic knowledge whilst the spectacular venue of the conference allowed participants to enjoy the cobblestoned historical city of Poznań.

  15. Tissue proteomics of the human mammary gland

    DEFF Research Database (Denmark)

    Moreira, José Manuel Alfonso; Cabezón, Teresa; Gromova, Irina

    2010-01-01

    Our limited understanding of the biological impact of the whole spectrum of early breast lesions together with a lack of accurate molecular-based risk criteria for the diagnosis and assignment of prognostic significance to biopsy findings presents an important problem in the clinical management...... of these limitations and here we present our efforts to search for biomarkers using normal fresh tissue from non-neoplastic breast samples. From the data generated by the 2D gel-based proteomic profiling we were able to compile a protein database of normal human breast epithelial tissue that was used to support...

  16. Proteomic and genomic analysis of cardiovascular disease

    National Research Council Canada - National Science Library

    Van Eyk, Jennifer; Dunn, M. J

    2003-01-01

    ... to cardiovascular disease. By exploring the various strategies and technical aspects of both, using examples from cardiac or vascular biology, the limitations and the potential of these methods can be clearly seen. The book is divided into three sections: the first focuses on genomics, the second on proteomics, and the third provides an overview of the importance of these two scientific disciplines in drug and diagnostic discovery. The goal of this book is the transfer of their hard-earned lessons to the growing num...

  17. Exhaled Breath Condensate for Proteomic Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    Sean W. Harshman

    2014-07-01

    Full Text Available Exhaled breath condensate (EBC has been established as a potential source of respiratory biomarkers. Compared to the numerous small molecules identified, the protein content of EBC has remained relatively unstudied due to the methodological and technical difficulties surrounding EBC analysis. In this review, we discuss the proteins identified in EBC, by mass spectrometry, focusing on the significance of those proteins identified. We will also review the limitations surrounding mass spectral EBC protein analysis emphasizing recommendations to enhance EBC protein identifications by mass spectrometry. Finally, we will provide insight into the future directions of the EBC proteomics field.

  18. Proteomics of pollen development and germination.

    Science.gov (United States)

    Dai, Shaojun; Wang, Tai; Yan, Xiufeng; Chen, Sixue

    2007-12-01

    In higher plants, pollen grains represent the vestiges of a highly reduced male gametophyte generation. After germination, the pollen tube delivers the sperm cells by tip-growing to the embryo sac for fertilization. Besides the intrinsic importance for sexual reproduction, pollen development and germination serve as an attractive system to address important questions related to cell division, cell differentiation, polar growth, cell-cell interaction, and cell fate. Recently, pollen functional specification has been well-studied using multidisciplinary approaches. Here, we review recent advances in proteomics of pollen development and germination.

  19. The Proteome of Primary Prostate Cancer.

    Science.gov (United States)

    Iglesias-Gato, Diego; Wikström, Pernilla; Tyanova, Stefka; Lavallee, Charlotte; Thysell, Elin; Carlsson, Jessica; Hägglöf, Christina; Cox, Jürgen; Andrén, Ove; Stattin, Pär; Egevad, Lars; Widmark, Anders; Bjartell, Anders; Collins, Colin C; Bergh, Anders; Geiger, Tamar; Mann, Matthias; Flores-Morales, Amilcar

    2016-05-01

    Clinical management of the prostate needs improved prognostic tests and treatment strategies. Because proteins are the ultimate effectors of most cellular reactions, are targets for drug actions and constitute potential biomarkers; a quantitative systemic overview of the proteome changes occurring during prostate cancer (PCa) initiation and progression can result in clinically relevant discoveries. To study cellular processes altered in PCa using system-wide quantitative analysis of changes in protein expression in clinical samples and to identify prognostic biomarkers for disease aggressiveness. 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. Over 9000 proteins were identified as expressed in the human prostate. Tumor tissue exhibited elevated expression of proteins involved in multiple anabolic processes including fatty acid and protein synthesis, ribosomal biogenesis and protein secretion but no overt evidence of increased proliferation was observed. Tumors also showed increased levels of mitochondrial proteins, which was associated with elevated oxidative phosphorylation capacity measured in situ. Molecular analysis indicated that some of the proteins overexpressed in tumors, such as carnitine palmitoyltransferase 2 (CPT2, fatty acid transporter), coatomer protein complex, subunit alpha (COPA, vesicle secretion), and mitogen- and stress-activated protein kinase 1 and 2 (MSK1/2, protein kinase) regulate the proliferation of PCa cells. Additionally, pro-NPY was found overexpressed in PCa (5-fold, pcancer and as such constitutes a valuable resource for understanding the complex metabolic

  20. Cotton proteomics for deciphering the mechanism of environment stress response and fiber development.

    Science.gov (United States)

    Zhou, Meiliang; Sun, Guoqing; Sun, Zhanmin; Tang, Yixiong; Wu, Yanmin

    2014-06-13

    Cotton fiber is considered as the backbone of the textile industry. The productivity of cotton crop is severely hampered by the occurrence of pathogens, pests, and various environmental factors. Nevertheless, cotton plant has developed sophisticated mechanisms to respond to environment stresses to avoid detrimental effects on its growth and development. Therefore, understanding the mechanisms of cotton fiber development and environment stress response is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in cotton fiber development and abiotic/biotic stress tolerance has increased dramatically in the last 5years as evidenced by the large amount of publications in this area. This review summarizes the work which has been reported for cotton proteomics and evaluates the findings in context of the approaches that are widely employed with the aim to generate novel insight useful for cotton improvement. Cotton (Gossypium spp.) is considered as the foremost commercially important fiber crop grown all over the world and is deemed as the backbone of the textile industry. Cotton is also an important source of edible oil seed and a nutrient-rich food crop as cottonseed contains high-quality protein and oil. The growth and productivity of cotton crop are often hampered by various biotic stress factors, such as insect pests and pathogens. In addition, cotton plants are frequently subjected to unavoidable environmental factors that cause abiotic stress, such as salt, heat and drought. Proteomic techniques provide one of the best options for understanding the gene function and phenotypic changes during cotton fiber development and stress response. This review first summarizes the work which has been reported for cotton proteomics about cotton fiber development and abiotic/biotic stress tolerance, and also evaluates the findings in context of the approaches

  1. Proteomic Analyses using High-Efficiency Separations and Accurate Mass Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Jacobs, Jon M.; Smith, Richard D.

    2006-08-01

    While the development of analytical techniques for detecting and identifying proteins has been an actively pursued area of research for many years, a recent and concerted reemergence of work in this area has resulted in an explosion of new developments that can be applied across multiple disciplines. The advent of numerous mass spectrometric and separation advances may be viewed as the technical driving force behind these developments, but other factors are perhaps equally crucial. These factors include the increasing availability of sequences for many organisms as a result of recent advancements in genome analysis, recognition that there are limitations to using sequence/transcriptome information alone, and the more apparent value of directly characterizing the biomolecules and pathways that actually drive cellular events. Direct identification of structural and functional proteins allows perturbations at the protein level to be linked to responses at the cellular level, and provides a method for analyzing global proteomic changes in virtually any model system. The field of proteomics, in particular, has benefited from numerous recent analytical advances that have provided increased sensitivity and dynamic range of proteins detected, as well as analysis throughput. Traditional approaches typically have involved separations using two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in conjunction with a mass spectrometric (MS) component for protein identification.[1] These seminal techniques set the foundation for the advancing field of proteomics. The limitations associated with the gel-based techniques are well known and stem mostly from a lack of sufficient dynamic range needed for in-depth proteome coverage and [2] and from the large amount of time needed for analysis, which dramatically limits throughput. Significant developments have been made in an attempt to address both these and other issues. With the advent of electrospray ionization, researchers

  2. Proteomic Profiling of Sugar Beet (Beta vulgaris Leaves during Rhizomania Compatible Interactions

    Directory of Open Access Journals (Sweden)

    Kimberly M. Webb

    2014-04-01

    Full Text Available Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV, severely impacts sugar beet (Beta vulgaris production throughout the world, and is widely prevalent in most production regions. Initial efforts to characterize proteome changes focused primarily on identifying putative host factors that elicit resistant interactions with BNYVV, but as resistance breaking strains become more prevalent, effective disease control strategies will require the application of novel methods based on better understanding of disease susceptibility and symptom development. Herein, proteomic profiling was conducted on susceptible sugar beet, infected with two strains of BNYVV, to clarify the types of proteins prevalent during compatible virus-host plant interactions. Total protein was extracted from sugar beet leaf tissue infected with BNYVV, quantified, and analyzed by mass spectrometry. A total of 203 proteins were confidently identified, with a predominance of proteins associated with photosynthesis and energy, metabolism, and response to stimulus. Many proteins identified in this study are typically associated with systemic acquired resistance and general plant defense responses. These results expand on relatively limited proteomic data available for sugar beet and provide the ground work for additional studies focused on understanding the interaction of BNYVV with sugar beet.

  3. Proteomic Profiling of Sugar Beet (Beta vulgaris) Leaves during Rhizomania Compatible Interactions.

    Science.gov (United States)

    Webb, Kimberly M; Broccardo, Carolyn J; Prenni, Jessica E; Wintermantel, William M

    2014-04-09

    Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), severely impacts sugar beet ( Beta vulgaris ) production throughout the world, and is widely prevalent in most production regions. Initial efforts to characterize proteome changes focused primarily on identifying putative host factors that elicit resistant interactions with BNYVV, but as resistance breaking strains become more prevalent, effective disease control strategies will require the application of novel methods based on better understanding of disease susceptibility and symptom development. Herein, proteomic profiling was conducted on susceptible sugar beet, infected with two strains of BNYVV, to clarify the types of proteins prevalent during compatible virus-host plant interactions. Total protein was extracted from sugar beet leaf tissue infected with BNYVV, quantified, and analyzed by mass spectrometry. A total of 203 proteins were confidently identified, with a predominance of proteins associated with photosynthesis and energy, metabolism, and response to stimulus. Many proteins identified in this study are typically associated with systemic acquired resistance and general plant defense responses. These results expand on relatively limited proteomic data available for sugar beet and provide the ground work for additional studies focused on understanding the interaction of BNYVV with sugar beet.

  4. Differentially delayed root proteome responses to salt stress in sugar cane varieties.

    Science.gov (United States)

    Pacheco, Cinthya Mirella; Pestana-Calsa, Maria Clara; Gozzo, Fabio Cesar; Mansur Custodio Nogueira, Rejane Jurema; Menossi, Marcelo; Calsa, Tercilio

    2013-12-06

    Soil salinity is a limiting factor to sugar cane crop development, although in general plants present variable mechanisms of tolerance to salinity stress. The molecular basis underlying these mechanisms can be inferred by using proteomic analysis. Thus, the objective of this work was to identify differentially expressed proteins in sugar cane plants submitted to salinity stress. For that, a greenhouse experiment was established with four sugar cane varieties and two salt conditions, 0 mM (control) and 200 mM NaCl. Physiological and proteomics analyses were performed after 2 and 72 h of stress induction by salt. Distinct physiological responses to salinity stress were observed in the varieties and linked to tolerance mechanisms. In proteomic analysis, the roots soluble protein fraction was extracted, quantified, and analyzed through bidimensional electrophoresis. Gel images analyses were done computationally, where in each contrast only one variable was considered (salinity condition or variety). Differential spots were excised, digested by trypsin, and identified via mass spectrometry. The tolerant variety RB867515 showed the highest accumulation of proteins involved in growth, development, carbohydrate and energy metabolism, reactive oxygen species metabolization, protein protection, and membrane stabilization after 2 h of stress. On the other hand, the presence of these proteins in the sensitive variety was verified only in stress treatment after 72 h. These data indicate that these stress responses pathways play a role in the tolerance to salinity in sugar cane, and their effectiveness for phenotypical tolerance depends on early stress detection and activation of the coding genes expression.

  5. Difference of proteomics vernalization-induced in bolting and flowering transitions of Beta vulgaris.

    Science.gov (United States)

    Liang, Naiguo; Cheng, Dayou; Liu, Qiaohong; Cui, Jie; Luo, Chengfei

    2018-02-01

    Sugar beet (Beta vulgaris) is a biennial crop that accounts for 30% sugar production of the world. Vernalization is an essential factor for sugar beet reproductative growth under long days. Although genes association with bolting and flowering were well explored, the difference of proteomics in the two growth stages were still poorly understood. To address the molecular mechanism at the level of proteins, an isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics approach was employed to the three different growth stages (germination, bolting, flowering) of vernalized samples and the corresponding stage germination (17W weeks), 19W and 20W of nonvernalized samples. A total of 1110 peptides, 842 unique peptides and 570 proteins were identified. Most of them were assigned to phenylpropanoid biosynthesis, hormone metabolism and protein processing pathway. IAA and Gibberellins (GA3) promoted growth and development in a threshold manner at growth stage germination after vernalization. A novel discovery was that IAA biosynthetic pathway of sugar beet was the Trp-dependent. In addition, two predominant pathways of protein processing association with vernalization were also identified in sugar beet at growth stage flowering. This study provided an in-depth understanding of the molecular mechanism of vernalization at the level of proteomics. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  6. Mass spectrometry-based bacterial proteomics: focus on dermatological associated microbial pathogens

    Directory of Open Access Journals (Sweden)

    Youcef eSoufi

    2016-02-01

    Full Text Available The composition of human skin acts as a natural habitat for various bacterial species that function in a commensal and symbiotic fashion. In a healthy individual, bacterial flora serves to protect the host. Under certain conditions such as minor trauma, impaired host immunity, or environmental factors, the risk of developing skin infections is increased. Although a large majority of bacterial associated skin infections are common, a portion can potentially manifest into clinically significant morbidity. For example, Gram positive species that typically reside on the skin such as Staphylococcus and Streptococcus can cause numerous epidermal (impetigo, ecthyma and dermal (cellulitis, necrotizing fasciitis, erysipelas skin infections. Moreover, the increasing incidence of bacterial antibiotic resistance represents a serious challenge to modern medicine and threatens the health care system. Therefore, it is critical to develop tools and strategies that can allow us to better elucidate the nature and mechanism of bacterial virulence. To this end, mass spectrometry (MS-based proteomics has been revolutionizing biomedical research, and has positively impacted the microbiology field. Advances in MS technologies have paved the way for numerous bacterial proteomes and their respective post translational modifications (PTMs to be accurately identified and quantified in a high throughput and robust fashion. This technological platform offers critical information with regards to signal transduction, adherence, and microbial-host interactions associated with bacterial pathogenesis. This mini-review serves to highlight the current progress proteomics has contributed towards the understanding of bacteria that are associated with skin related diseases, infections, and antibiotic resistance.

  7. Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579.

    Directory of Open Access Journals (Sweden)

    Sabrina Laouami

    Full Text Available The facultative anaerobe, Bacillus cereus, causes diarrheal diseases in humans. Its ability to deal with oxygen availability is recognized to be critical for pathogenesis. The B. cereus genome comprises a gene encoding a protein with high similarities to the redox regulator, Rex, which is a central regulator of anaerobic metabolism in Bacillus subtilis and other Gram-positive bacteria. Here, we showed that B. cereus rex is monocistronic and down-regulated in the absence of oxygen. The protein encoded by rex is an authentic Rex transcriptional factor since its DNA binding activity depends on the NADH/NAD+ ratio. Rex deletion compromised the ability of B. cereus to cope with external oxidative stress under anaerobiosis while increasing B. cereus resistance against such stress under aerobiosis. The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Δrex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.

  8. Redox proteomics and the dynamic molecular landscape of the aging brain.

    Science.gov (United States)

    Perluigi, Marzia; Swomley, Aaron M; Butterfield, D Allan

    2014-01-01

    It is well established that the risk to develop neurodegenerative disorders increases with chronological aging. Accumulating studies contributed to characterize the age-dependent changes either at gene and protein expression level which, taken together, show that aging of the human brain results from the combination of the normal decline of multiple biological functions with environmental factors that contribute to defining disease risk of late-life brain disorders. Finding the "way out" of the labyrinth of such complex molecular interactions may help to fill the gap between "normal" brain aging and development of age-dependent diseases. To this purpose, proteomics studies are a powerful tool to better understand where to set the boundary line of healthy aging and age-related disease by analyzing the variation of protein expression levels and the major post translational modifications that determine "protein" physio/pathological fate. Increasing attention has been focused on oxidative modifications due to the crucial role of oxidative stress in aging, in addition to the fact that this type of modification is irreversible and may alter protein function. Redox proteomics studies contributed to decipher the complexity of brain aging by identifying the proteins that were increasingly oxidized and eventually dysfunctional as a function of age. The purpose of this review is to summarize the most important findings obtained by applying proteomics approaches to murine models of aging with also a brief overview of some human studies, in particular those related to dementia. Copyright © 2014. Published by Elsevier B.V.

  9. Clinical proteomics for liver disease: a promising approach for discovery of novel biomarkers

    Directory of Open Access Journals (Sweden)

    Tsubouchi Hirohito

    2010-12-01

    Full Text Available Abstract Hepatocellular carcinoma (HCC is the fifth most common cancer and advanced hepatic fibrosis is a major risk factor for HCC. Hepatic fibrosis including liver cirrhosis and HCC are mainly induced by persistent hepatitis B or C virus infection, with approximately 500 million people infected with hepatitis B or C virus worldwide. Furthermore, the number of patients with non-alcoholic fatty liver disease (NAFLD has recently increased and NAFLD can progress to cirrhosis and HCC. These chronic liver diseases are major causes of morbidity and mortality, and the identification of non-invasive biomarkers is important for early diagnosis. Recent advancements in quantitative and large-scale proteomic methods could be used to optimize the clinical application of biomarkers. Early diagnosis of HCC and assessment of the stage of hepatic fibrosis or NAFLD can also contribute to more effective therapeutic interventions and an improve prognosis. Furthermore, advancements of proteomic techniques contribute not only to the discovery of clinically useful biomarkers, but also in clarifying the molecular mechanisms of disease pathogenesis by using body fluids, such as serum, and tissue samples and cultured cells. In this review, we report recent advances in quantitative proteomics and several findings focused on liver diseases, including HCC, NAFLD, hepatic fibrosis and hepatitis B or C virus infections.

  10. Proteome data to explore the impact of pBClin15 on Bacillus cereus ATCC 14579.

    Science.gov (United States)

    Madeira, Jean-Paul; Alpha-Bazin, Béatrice; Armengaud, Jean; Omer, Hélène; Duport, Catherine

    2016-09-01

    This data article reports changes in the cellular and exoproteome of B. cereus cured from pBClin15.Time-course changes of proteins were assessed by high-throughput nanoLC-MS/MS. We report all the peptides and proteins identified and quantified in B. cereus with and without pBClin15. Proteins were classified into functional groups using the information available in the KEGG classification and we reported their abundance in term of normalized spectral abundance factor. The repertoire of experimentally confirmed proteins of B. cereus presented here is the largest ever reported, and provides new insights into the interplay between pBClin15 and its host B. cereus ATCC 14579. The data reported here is related to a published shotgun proteomics analysis regarding the role of pBClin15, "Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics" Madeira et al. [1]. All the associated mass spectrometry data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (http://www.ebi.ac.uk/pride/), with the dataset identifier PRIDE: PXD001568, PRIDE: PXD002788 and PRIDE: PXD002789.

  11. Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579.

    Science.gov (United States)

    Laouami, Sabrina; Clair, Géremy; Armengaud, Jean; Duport, Catherine

    2014-01-01

    The facultative anaerobe, Bacillus cereus, causes diarrheal diseases in humans. Its ability to deal with oxygen availability is recognized to be critical for pathogenesis. The B. cereus genome comprises a gene encoding a protein with high similarities to the redox regulator, Rex, which is a central regulator of anaerobic metabolism in Bacillus subtilis and other Gram-positive bacteria. Here, we showed that B. cereus rex is monocistronic and down-regulated in the absence of oxygen. The protein encoded by rex is an authentic Rex transcriptional factor since its DNA binding activity depends on the NADH/NAD+ ratio. Rex deletion compromised the ability of B. cereus to cope with external oxidative stress under anaerobiosis while increasing B. cereus resistance against such stress under aerobiosis. The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Δrex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.

  12. Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Pandey, Aarti; Chakraborty, Subhra; Datta, Asis; Chakraborty, Niranjan

    2008-01-01

    Dehydration or water-deficit is one of the most important environmental stress factors that greatly influences plant growth and development and limits crop productivity. Plants respond and adapt to such stress by altering their cellular metabolism and activating various defense machineries. Mechanisms that operate signal perception, transduction, and downstream regulatory events provide valuable information about the underlying pathways involved in environmental stress responses. The nuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. To gain a better understanding of dehydration response in plants, we have developed a comparative nuclear proteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water and the changes in the nuclear proteome were examined using two-dimensional gel electrophoresis. Approximately 205 protein spots were found to be differentially regulated under dehydration. Mass spectrometry analysis allowed the identification of 147 differentially expressed proteins, presumably involved in a variety of functions including gene transcription and replication, molecular chaperones, cell signaling, and chromatin remodeling. The dehydration responsive nuclear proteome of chickpea revealed a coordinated response, which involves both the regulatory as well as the functional proteins. This study, for the first time, provides an insight into the complex metabolic network operating in the nucleus during dehydration.

  13. Proteome Characteristics of Non-Alcoholic Steatohepatitis Liver Tissue and Associated Hepatocellular Carcinomas

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    Anna Kakehashi

    2017-02-01

    Full Text Available To uncover mechanisms of nonalcoholic steatohepatitis (NASH associated hepatocarcinogenesis, we compared the proteomes of human NASH-associated liver biopsies, resected hepatocellular carcinomas (HCCs and HCCs of HCV+ patients with normal liver tissue of patients with gastrointestinal tumor metastasis, in formalin-fixed paraffin-embedded samples obtained after surgery in our hospital during the period from 2006 to 2011. In addition, proteome analysis of liver tumors in male STAM NASH-model mice was performed. Similar changes in the proteome spectrum such as overexpression of enzymes involved in lipid, cholesterol and bile acid biosynthesis and examples associated with suppression of fatty acid oxidation and catabolism, alcohol metabolism, mitochondrial function as well as low expression levels of cytokeratins 8 and 18 were observed in both human NASH biopsies and NASH HCCs, but not HCV+ HCCs. Alterations in downstream protein expression pointed to significant activation of transforming growth factor β, SMAD family member 3, β-catenin, Nrf2, SREBP-LXRα and nuclear receptor-interacting protein 1 (NRIP1, and inhibition of PPARs and p53 in human NASH biopsies and/or HCCs, suggesting their involvement in accumulation of lipids, development of fibrosis, oxidative stress, cell proliferation and suppression of apoptosis in NASH hepatocarcinogenesis. In STAM mice, PPARs inhibition was not obvious, while expression of cytokeratins 8 and 18 was elevated, indicative of essential differences between human and mouse NASH pathogenesis.

  14. Role of the visual experience-dependent nascent proteome in neuronal plasticity.

    Science.gov (United States)

    Liu, Han-Hsuan; McClatchy, Daniel B; Schiapparelli, Lucio; Shen, Wanhua; Yates, John R; Cline, Hollis T

    2018-02-07

    Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling. Functional analysis of select CPPs revealed the requirement for eukaryotic initiation factor three subunit A (eIF3A), fused in sarcoma (FUS), and ribosomal protein s17 (RPS17) in experience-dependent structural plasticity in tectal neurons and behavioral plasticity in tadpoles. These results demonstrate that the nascent proteome is dynamic in response to visual experience and that de novo synthesis of machinery that regulates RNA splicing and protein translation is required for experience-dependent plasticity. © 2018, Liu et al.

  15. neXtProt: organizing protein knowledge in the context of human proteome projects.

    Science.gov (United States)

    Gaudet, Pascale; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek, Paula; Evalet, Olivier; Gateau, Alain; Gleizes, Anne; Pereira, Mario; Zahn-Zabal, Monique; Zwahlen, Catherine; Bairoch, Amos; Lane, Lydie

    2013-01-04

    About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.

  16. Proteomic and bioinformatics analysis of human saliva for the dental-risk assessment

    Directory of Open Access Journals (Sweden)

    Laputková Galina

    2017-10-01

    Full Text Available Background: Dental caries disease is a dynamic process with a multi-factorial etiology. It is manifested by demineralization of enamel followed by damage spreading into the tooth inner structure. Successful early diagnosis could identify caries-risk and improve dental screening, providing a baseline for evaluating personalized dental treatment and prevention strategies. Methodology:\tSalivary proteome of the whole unstimulated saliva (WUS samples was assessed in caries-free and caries-susceptible individuals of older adolescent age with permanent dentition using a nano-HPLC and MALDI-TOF/TOF mass spectrometry. Results: 554 proteins in the caries-free and 695 proteins in the caries-susceptible group were identified. Assessment using bioinformatics tools and Gene Ontology (GO term enrichment analysis revealed qualitative differences between these two proteomes. Members of the caries-susceptible group exhibited a branch of cytokine binding gene products responsible for the regulation of immune and inflammatory responses to infections. Inspection of molecular functions and biological processes of caries-susceptible saliva samples revealed significant categories predominantly related to the activity of proteolytic peptidases, and the regulation of metabolic and catabolic processes of carbohydrates. Conclusions: Proteomic analysis of the whole saliva revealed information about potential risk factors associated with the development of caries-susceptibility and provides a better understanding of tooth protection mechanisms.

  17. Effects of human and porcine bile on the proteome of Helicobacter hepaticus

    Directory of Open Access Journals (Sweden)

    Okoli Arinze S

    2012-04-01

    Full Text Available Abstract Background Helicobacter hepaticus colonizes the intestine and liver of mice causing hepatobiliary disorders such as hepatitis and hepatocellular carcinoma, and has also been associated with inflammatory bowel disease in children. In its habitat, H. hepaticus must encounter bile which has potent antibacterial properties. To elucidate virulence and host-specific adaptation mechanisms of H. hepaticus modulated by human or porcine bile, a proteomic study of its response to the two types of bile was performed employing two-dimensional gel electrophoresis (2-DE and mass spectrometry. Results The 2-DE and mass spectrometry analyses of the proteome revealed that 46 proteins of H. hepaticus were differentially expressed in human bile, 18 up-regulated and 28 down-regulated. In the case of porcine bile, 32 proteins were differentially expressed of which 19 were up-regulated, and 13 were down-regulated. Functional classifications revealed that identified proteins participated in various biological functions including stress response, energy metabolism, membrane stability, motility, virulence and colonization. Selected genes were analyzed by RT-PCR to provide internal validation for the proteomic data as well as provide insight into specific expressions of motility, colonization and virulence genes of H. hepaticus in response to human or porcine bile. Conclusions Overall, the data suggested that bile is an important factor that determines virulence, host adaptation, localization and colonization of specific niches within host environment.

  18. [A review of current methods for nutrimetabolomic and proteomic research in biochemistry of nutrition].

    Science.gov (United States)

    Kirbaeva, N V; Sharanova, N É; Pertsov, S S

    2014-01-01

    At present biochemistry of nutrition involves the use of OMICs to investigate food quality, safety, bioactivity and nutrition mechanisms. In this context, nutrimetabolomics is one of the latest directions of nutrition development and provides a better understanding of the influence of nutritional factors on the metabolic pathways of the organism. Proteomic methods play an important role in nutrimetabolomics and allow to detect, identify and quantify proteins under different conditions. Variety of technical and methodological advances, improvements in bioinformatics and possibility of tandem use of different methods helps to solve a number of basic and applied science's problems. Currently huge amount of qualitative and quantitative data on the structure, functions and activities of proteins and their interactions is accumulated. Proteomics aims to establish and characterize a complete set of proteins of the organism. This review summarizes the basic applications of proteomics used in nutrimetabolomic researches. The advantages and disadvantages of the most common techniques of protein separation and sample ionization, types of mass analyzers, basic approaches to the identification of proteins and most widely used databases of known biological sequences are overviewed with a critical assessment of challenges and potential applications.

  19. Proteome Modification in Tomato Plants upon Long-Term Aluminum Treatment.

    Science.gov (United States)

    Zhou, Suping; Okekeogbu, Ikenna; Sangireddy, Sasikiran; Ye, Zhujia; Li, Hui; Bhatti, Sarabjit; Hui, Dafeng; McDonald, Daniel W; Yang, Yong; Giri, Shree; Howe, Kevin J; Fish, Tara; Thannhauser, Theodore W

    2016-05-06

    This study aimed to identify the aluminum (Al)-induced proteomes in tomato (Solanum lycopersicum, "Micro-Tom") after long-term exposure to the stress factor. Plants were treated in Magnavaca's solution (pH 4.5) supplemented with 7.5 μM Al(3+) ion activity over a 4 month period beginning at the emergence of flower buds and ending when the lower mature leaves started to turn yellow. Proteomes were identified using a 8-plex isobaric tags for relative and absolute quantification (iTRAQ) labeling strategy followed by a two-dimensional (high- and low-pH) chromatographic separation and final generation of tandem mass spectrometry (MS/MS) spectra of tryptic peptides on an LTQ-Orbitrap Elite mass spectrometer. Principal component analysis revealed that the Al-treatment had induced systemic alterations in the proteomes from roots and leaves but not seed tissues. The significantly changed root proteins were shown to have putative functions in Al(3+) ion uptake and transportation, root development, and a multitude of other cellular processes. Changes in the leaf proteome indicate that the light reaction centers of photosynthetic machinery are the primary targets of Al-induced stress. Embryo and seed-coat tissues derived from Al-treated plants were enriched with stress proteins. The biological processes involving these Al-induced proteins concur with the physiological and morphological changes, such as the disturbance of mineral homeostasis (higher contents of Al, P, and Fe and reduced contents of S, Zn, and Mn in Al-treated compared to nontreated plants) in roots and smaller sizes of roots and the whole plants. More importantly, the identified significant proteins might represent a molecular mechanism for plants to develop toward establishing the Al tolerance and adaptation mechanism over a long period of stress treatment.

  20. A novel approach to the study of the functional proteome in breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Hennessy, Bryan; Lu, Yiling; Gonzalez-Angulo, Ana Maria; Carey, Mark; Myhre, Simen; Ju, Zhenlin; Coombes, Kevin; Meric-Bernstam, Funda; Bedrosian, Isabelle; Davies, Michael A.; Siwak, Doris; Agarwal, Roshan; Zhang, Fan; Overgaard, Jens; Alsner, Jan; Neve, Richard M.; Kuo, Wen-Lin; Gray, Joe W.; Borresen-Dale, Anne-Lise; Mills, Gordon B.

    2008-10-10

    Factors including intratumoral heterogeneity and variability in tissue handling potentially hamper the application of reverse phase protein arrays (RPPA) to study of the solid tumor functional proteome. To address this, RPPA was applied to quantify protein expression and activation in 233 human breast tumors and 52 breast cancer cell lines. Eighty-two antibodies that recognize kinase and steroid signaling events and their effectors were validated for RPPA because of the importance of these proteins to breast carcinogenesis. Reproducibility in replicate lysates was excellent. Intratumoral protein expression was less variable than intertumoral expression, and prognostic biomarkers retained the ability to accurately predict patient outcomes when analyzed in different tumor sites. Although 21/82 total and phosphoproteins demonstrated time-dependent instability in breast tumors that were placed at room temperature after surgical excision for 24 hours prior to freezing, the functional proteomic 'fingerprint' was robust in most tumors until at least 24 hours before tissue freezing. Correlations between RPPA and immunohistochemistry were statistically significant for assessed proteins but RPPA demonstrated a superior dynamic range and detected, for example, an 866-fold difference in estrogen receptor alpha level across breast tumors. Protein and mRNA levels were concordant (at p {le} 0.05) for 41.3% and 61.1% of assayed targets in breast tumors and cell lines, respectively. Several phosphorylation and cleavage products did not correlate with the corresponding transcript levels. In conclusion, the reproducibility of RPPA, the faithfulness with which proteins and the functional proteomic 'fingerprint' are preserved in different sections derived from primary breast tumors, and the surprising stability of this 'fingerprint' with increasing time to freezing all facilitate the application of RPPA to the accurate study of protein biomarkers in non

  1. Proteomic profiling of bone marrow mesenchymal stem cells upon TGF-beta stimulation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Daojing; Park, Jennifer S.; Chu, Julia S.F.; Ari, Krakowski; Luo, Kunxin; Chen, David J.; Li, Song

    2004-08-08

    Bone marrow mesenchymal stem cells (MSCs) can differentiate into different types of cells, and have tremendous potential for cell therapy and tissue engineering. Transforming growth factor {beta}1 (TGF-{beta}) plays an important role in cell differentiation and vascular remodeling. We showed that TGF-{beta} induced cell morphology change and an increase in actin fibers in MSCs. To determine the global effects of TGF-{beta} on MSCs, we employed a proteomic strategy to analyze the effect of TGF-{beta} on the human MSC proteome. By using two-dimensional gel electrophoresis and electrospray ionization coupled to Quadrupole/time-of-flight tandem mass spectrometers, we have generated a proteome reference map of MSCs, and identified {approx}30 proteins with an increase or decrease in expression or phosphorylation in response to TGF-{beta}. The proteins regulated by TGF-{beta} included cytoskeletal proteins, matrix synthesis proteins, membrane proteins, metabolic enzymes, etc. TGF-{beta} increased the expression of smooth muscle (SM) {alpha}-actin and decreased the expression of gelsolin. Over-expression of gelsolin inhibited TGF-{beta}-induced assembly of SM {alpha}-actin; on the other hand, knocking down gelsolin expression enhanced the assembly of {alpha}-actin and actin filaments without significantly affecting {alpha}-actin expression. These results suggest that TGF-{beta} coordinates the increase of {alpha}-actin and the decrease of gelsolin to promote MSC differentiation. This study demonstrates that proteomic tools are valuable in studying stem cell differentiation and elucidating the underlying molecular mechanisms.

  2. Convergent transcriptomics and proteomics of environmental enrichment and cocaine identifies novel therapeutic strategies for addiction.

    Science.gov (United States)

    Zhang, Yafang; Crofton, Elizabeth J; Fan, Xiuzhen; Li, Dingge; Kong, Fanping; Sinha, Mala; Luxon, Bruce A; Spratt, Heidi M; Lichti, Cheryl F; Green, Thomas A

    2016-12-17

    Transcriptomic and proteomic approaches have separately proven effective at identifying novel mechanisms affecting addiction-related behavior; however, it is difficult to prioritize the many promising leads from each approach. A convergent secondary analysis of proteomic and transcriptomic results can glean additional information to help prioritize promising leads. The current study is a secondary analysis of the convergence of recently published separate transcriptomic and proteomic analyses of nucleus accumbens (NAc) tissue from rats subjected to environmental enrichment vs. isolation and cocaine self-administration vs. saline. Multiple bioinformatics approaches (e.g. Gene Ontology (GO) analysis, Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA)) were used to interrogate these rich data sets. Although there was little correspondence between mRNA vs. protein at the individual target level, good correspondence was found at the level of gene/protein sets, particularly for the environmental enrichment manipulation. These data identify gene sets where there is a positive relationship between changes in mRNA and protein (e.g. glycolysis, ATP synthesis, translation elongation factor activity, etc.) and gene sets where there is an inverse relationship (e.g. ribosomes, Rho GTPase signaling, protein ubiquitination, etc.). Overall environmental enrichment produced better correspondence than cocaine self-administration. The individual targets contributing to mRNA and protein effects were largely not overlapping. As a whole, these results confirm that robust transcriptomic and proteomic data sets can provide similar results at the gene/protein set level even when there is little correspondence at the individual target level and little overlap in the targets contributing to the effects. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  3. Multilineage potential and proteomic profiling of human dental stem cells derived from a single donor

    Energy Technology Data Exchange (ETDEWEB)

    Patil, Rajreddy; Kumar, B. Mohana; Lee, Won-Jae; Jeon, Ryoung-Hoon; Jang, Si-Jung; Lee, Yeon-Mi [Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701 (Korea, Republic of); Park, Bong-Wook; Byun, June-Ho [Department of Oral and Maxillofacial Surgery, School of Medicine and Institute of Health Science, Gyeongsang National University, Jinju 660-702 (Korea, Republic of); Ahn, Chun-Seob; Kim, Jae-Won [Department of Microbiology, Division of Life Sciences, Research Institute of Life Science, Gyeongsang National University, Jinju 660-701 (Korea, Republic of); Rho, Gyu-Jin, E-mail: jinrho@gnu.ac.kr [Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701 (Korea, Republic of); Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701 (Korea, Republic of)

    2014-01-01

    Dental tissues provide an alternative autologous source of mesenchymal stem cells (MSCs) for regenerative medicine. In this study, we isolated human dental MSCs of follicle, pulp and papilla tissue from a single donor tooth after impacted third molar extraction by excluding the individual differences. We then compared the morphology, proliferation rate, expression of MSC-specific and pluripotency markers, and in vitro differentiation ability into osteoblasts, adipocytes, chondrocytes and functional hepatocyte-like cells (HLCs). Finally, we analyzed the protein expression profiles of undifferentiated dental MSCs using 2DE coupled with MALDI-TOF-MS. Three types of dental MSCs largely shared similar morphology, proliferation potential, expression of surface markers and pluripotent transcription factors, and differentiation ability into osteoblasts, adipocytes, and chondrocytes. Upon hepatogenic induction, all MSCs were transdifferentiated into functional HLCs, and acquired hepatocyte functions by showing their ability for glycogen storage and urea production. Based on the proteome profiling results, we identified nineteen proteins either found commonly or differentially expressed among the three types of dental MSCs. In conclusion, three kinds of dental MSCs from a single donor tooth possessed largely similar cellular properties and multilineage potential. Further, these dental MSCs had similar proteomic profiles, suggesting their interchangeable applications for basic research and call therapy. - Highlights: • Isolated and characterized three types of human dental MSCs from a single donor. • MSCs of dental follicle, pulp and papilla had largely similar biological properties. • All MSCs were capable of transdifferentiating into functional hepatocyte-like cells. • 2DE proteomics with MALDI-TOF/MS identified 19 proteins in three types of MSCs. • Similar proteomic profiles suggest interchangeable applications of dental MSCs.

  4. Multilineage potential and proteomic profiling of human dental stem cells derived from a single donor

    International Nuclear Information System (INIS)

    Patil, Rajreddy; Kumar, B. Mohana; Lee, Won-Jae; Jeon, Ryoung-Hoon; Jang, Si-Jung; Lee, Yeon-Mi; Park, Bong-Wook; Byun, June-Ho; Ahn, Chun-Seob; Kim, Jae-Won; Rho, Gyu-Jin

    2014-01-01

    Dental tissues provide an alternative autologous source of mesenchymal stem cells (MSCs) for regenerative medicine. In this study, we isolated human dental MSCs of follicle, pulp and papilla tissue from a single donor tooth after impacted third molar extraction by excluding the individual differences. We then compared the morphology, proliferation rate, expression of MSC-specific and pluripotency markers, and in vitro differentiation ability into osteoblasts, adipocytes, chondrocytes and functional hepatocyte-like cells (HLCs). Finally, we analyzed the protein expression profiles of undifferentiated dental MSCs using 2DE coupled with MALDI-TOF-MS. Three types of dental MSCs largely shared similar morphology, proliferation potential, expression of surface markers and pluripotent transcription factors, and differentiation ability into osteoblasts, adipocytes, and chondrocytes. Upon hepatogenic induction, all MSCs were transdifferentiated into functional HLCs, and acquired hepatocyte functions by showing their ability for glycogen storage and urea production. Based on the proteome profiling results, we identified nineteen proteins either found commonly or differentially expressed among the three types of dental MSCs. In conclusion, three kinds of dental MSCs from a single donor tooth possessed largely similar cellular properties and multilineage potential. Further, these dental MSCs had similar proteomic profiles, suggesting their interchangeable applications for basic research and call therapy. - Highlights: • Isolated and characterized three types of human dental MSCs from a single donor. • MSCs of dental follicle, pulp and papilla had largely similar biological properties. • All MSCs were capable of transdifferentiating into functional hepatocyte-like cells. • 2DE proteomics with MALDI-TOF/MS identified 19 proteins in three types of MSCs. • Similar proteomic profiles suggest interchangeable applications of dental MSCs

  5. Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen

    LENUS (Irish Health Repository)

    O'Toole, Paul W

    2010-03-10

    Abstract Background Helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. H. mustelae remains the only helicobacter other than H. pylori that causes gastric ulceration and cancer in its natural host. To improve understanding of H. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. Results The H. mustelae genome lacks orthologs of major H. pylori virulence factors including CagA, VacA, BabA, SabA and OipA. However, it encodes ten autotransporter surface proteins, seven of which were detected in the expressed proteome, and which, except for the Hsr protein, are of unknown function. There are 26 putative outer membrane proteins in H. mustelae, some of which are most similar to the Hof proteins of H. pylori. Although homologs of putative virulence determinants of H. pylori (NapA, plasminogen adhesin, collagenase) and Campylobacter jejuni (CiaB, Peb4a) are present in the H. mustelae genome, it also includes a distinct complement of virulence-related genes including a haemagglutinin\\/haemolysin protein, and a glycosyl transferase for producing blood group A\\/B on its lipopolysaccharide. The most highly expressed 264 proteins in the cytosolic proteome included many corresponding proteins from H. pylori, but the rank profile in H. mustelae was distinctive. Of 27 genes shown to be essential for H. pylori colonization of the gerbil, all but three had orthologs in H. mustelae, identifying a shared set of core proteins for gastric persistence. Conclusions The determination of the genome sequence and expressed proteome of the ulcerogenic species H mustelae provides a comparative model for H. pylori to investigate bacterial gastric carcinogenesis in mammals, and to suggest ways whereby cag minus H. pylori strains might cause ulceration and cancer. The genome sequence was

  6. Proteomic approaches to the study of renal mitochondria.

    Science.gov (United States)

    Tuma, Zdenek; Kuncova, Jitka; Mares, Jan; Grundmanova, Martina; Matejovic, Martin

    2016-06-01

    Dysfunction of kidney mitochondria plays a critical role in the pathogenesis of a number of renal diseases. Proteomics represents an untargeted attempt to reveal the remodeling of mitochondrial proteins during disease. Combination of separation methods and mass spectrometry allows identification and quantitative analysis of mitochondrial proteins including protein complexes. The aim of this review is to summarize the methods and applications of proteomics to renal mitochondria. Using keywords "mitochondria", "kidney", "proteomics", scientific databases (PubMed and Web of knowledge) were searched from 2000 to August 2015 for articles describing methods and applications of proteomics to analysis of mitochondrial proteins in kidney. Included were publications on mitochondrial proteins in kidneys of humans and animal model in health and disease. Proteomics of renal mitochondria has been/is mostly used in diabetes, hypertension, acidosis, nephrotoxicity and renal cancer. Integration of proteomics with other methods for examining protein activity is promising for insight into the role of renal mitochondria in pathological states. Several challenges were identified: selection of appropriate model organism, sensitivity of analytical methods and analysis of mitochondrial proteome in different renal zones/biopsies in the course of various kidney disorders.

  7. Clinical proteomics: Current status, challenges, and future perspectives

    Directory of Open Access Journals (Sweden)

    Shyh-Horng Chiou

    2011-01-01

    Full Text Available This account will give an overview and evaluation of the current advances in mass spectrometry (MS-based proteomics platforms and technology. A general review of some background information concerning the application of these methods in the characterization of molecular sizes and related protein expression profiles associated with different types of cells under varied experimental conditions will be presented. It is intended to provide a concise and succinct overview to those clinical researchers first exposed to this foremost powerful methodology in modern life sciences of postgenomic era. Proteomic characterization using highly sophisticated and expensive instrumentation of MS has been used to characterize biological samples of complex protein mixtures with vastly different protein structure and composition. These systems are then used to highlight the versatility and potential of the MS-based proteomic strategies for facilitating protein expression analysis of various disease-related organisms or tissues of interest. Major MS-based strategies reviewed herein include (1 matrix-assisted laser desorption ionization-MS and electron-spray ionization proteomics; (2 one-dimensional or two-dimensional gel-based proteomics; (3 gel-free shotgun proteomics in conjunction with liquid chromatography/tandem MS; (4 Multiple reaction monitoring coupled tandem MS quantitative proteomics and; (5 Phosphoproteomics based on immobilized metal affinity chromatography and liquid chromatography-MS/MS.

  8. Quantitative proteomics in cardiovascular research: global and targeted strategies

    Science.gov (United States)

    Shen, Xiaomeng; Young, Rebeccah; Canty, John M.; Qu, Jun

    2014-01-01

    Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases (CVD) and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation. PMID:24920501

  9. 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.

  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. 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.

  12. Deep coverage of the beer proteome.

    Science.gov (United States)

    Grochalová, Martina; Konečná, Hana; Stejskal, Karel; Potěšil, David; Fridrichová, Danuše; Srbová, Eva; Ornerová, Kateřina; Zdráhal, Zbyněk

    2017-06-06

    We adopted an approach based on peptide immobilized pH gradient-isoelectric focusing (IPG-IEF) separation, coupled with LC-MS/MS, in order to maximize coverage of the beer proteome. A lager beer brewed using traditional Czech technology was degassed, desalted and digested. Tryptic peptides were separated by isoelectric focusing on an immobilized pH gradient strip and, after separation, the gel strip was divided into seven equally sized parts. Peptides extracted from gel fractions were analyzed by LC-MS/MS. This approach resulted in a three-fold increase in the number of proteins identified (over 1700) when compared to analysis of unfractionated beer processed by a filter-aided sample preparation (FASP). Over 1900 protein groups (PGs) in total were identified by both approaches. The study significantly extends knowledge about the beer proteome and demonstrates its complexity. Detailed knowledge of the protein content, especially gluten proteins, will enhance the evaluation of potential health risks related to beer consumption (coeliac disease) and will contribute to improving beer quality. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Urine sample preparation for proteomic analysis.

    Science.gov (United States)

    Olszowy, Pawel; Buszewski, Boguslaw

    2014-10-01

    Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross-reactions that should be taken into consideration. The incorporation of new post-translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. 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.

  15. 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.

  16. 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.

  17. Plant iTRAQ-based proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Handakumbura, Pubudu; Hixson, Kim K.; Purvine, Samuel O.; Jansson, Georg C.; Pasa Tolic, Ljiljana

    2017-06-21

    We present a simple one-­pot extraction protocol, which rapidly isolates hydrophyllic metabolites, lipids, and proteins from the same pulverized plant sample. Also detailed is a global plant proteomics sample preparation method utilizing iTRAQ multiplexing reagents that enables deep proteome coverage due to the use of HPLC fractionation of the peptides prior to mass spectrometric analysis. We have successfully used this protocol on several different plant tissues (e.g., roots, stems, leaves) from different plants (e.g., sorghum, poplar, Arabidopsis, soybean), and have been able to successfully detect and quantify thousands of proteins. Multiplexing strategies such as iTRAQ and the bioinformatics strategy outlined here, ultimately provide insight into which proteins are significantly changed in abundance between two or more groups (e.g., control, perturbation). Our bioinformatics strategy yields z-­score values, which normalize the expression data into a format that can easily be cross-­compared with other expression data (i.e., metabolomics, transcriptomics) obtained from different analytical methods and instrumentation.

  18. Finding Our Way in the Dark Proteome.

    Science.gov (United States)

    Bhowmick, Asmit; Brookes, David H; Yost, Shane R; Dyson, H Jane; Forman-Kay, Julie D; Gunter, Daniel; Head-Gordon, Martin; Hura, Gregory L; Pande, Vijay S; Wemmer, David E; Wright, Peter E; Head-Gordon, Teresa

    2016-08-10

    The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.

  19. Sperm Proteome Maturation in the Mouse Epididymis.

    Science.gov (United States)

    Skerget, Sheri; Rosenow, Matthew A; Petritis, Konstantinos; Karr, Timothy L

    2015-01-01

    In mammals, transit through the epididymis, which involves the acquisition, loss and modification of proteins, is required to confer motility and fertilization competency to sperm. The overall dynamics of maturation is poorly understood, and a systems level understanding of the complex maturation process will provide valuable new information about changes occurring during epididymal transport. We report the proteomes of sperm collected from the caput, corpus and cauda segments of the mouse epididymis, identifying 1536, 1720 and 1234 proteins respectively. This study identified 765 proteins that are present in sperm obtained from all three segments. We identified 1766 proteins that are potentially added (732) or removed (1034) from sperm during epididymal transit. Phenotypic analyses of the caput, corpus and cauda sperm proteomes identified 60 proteins that have known sperm phenotypes when mutated, or absent from sperm. Our analysis indicates that as much as one-third of proteins with known sperm phenotypes are added to sperm during epididymal transit. GO analyses revealed that cauda sperm are enriched for specific functions including sperm-egg recognition and motility, consistent with the observation that sperm acquire motility and fertilization competency during transit through the epididymis. In addition, GO analyses revealed that the immunity protein profile of sperm changes during sperm maturation. Finally, we identified components of the 26S proteasome, the immunoproteasome, and a proteasome activator in mature sperm.

  20. A HaloTag-Based Multicolor Fluorogenic Sensor Visualizes and Quantifies Proteome Stress in Live Cells Using Solvatochromic and Molecular Rotor-Based Fluorophores.

    Science.gov (United States)

    Liu, Yu; Miao, Kun; Li, Yinghao; Fares, Matthew; Chen, Shuyuan; Zhang, Xin

    2018-02-28

    Protein homeostasis, or proteostasis, is essential for cellular fitness and viability. Many environmental factors compromise proteostasis, induce global proteome stress, and cause diseases. The proteome stress sensor is a powerful tool for dissecting the mechanism of cellular stress and finding therapeutics that ameliorate these diseases. In this work, we present a multicolor HaloTag-based sensor (named AgHalo) to visualize and quantify proteome stresses in live cells. The current AgHalo sensor is equipped with three fluorogenic probes that turn on fluorescence when the sensor forms either soluble oligomers or insoluble aggregates upon exposure to stress conditions, both in vitro and in cellulo. In addition, AgHalo probes can be combined with commercially available always-fluorescent HaloTag ligands to enable two-color imaging, allowing for direct visualization of the AgHalo sensor both before and after cells are subjected to stress conditions. Finally, pulse-chase experiments can be performed to discern changes in the cellular proteome in live cells by first forming the AgHalo conjugate and then either applying or removing stress at any desired time point. In summary, the AgHalo sensor can be used to visualize and quantify proteome stress in live cells, a task that is difficult to accomplish using previous always-fluorescent methods. This sensor should be suited to evaluating cellular proteostasis under various exogenous stresses, including chemical toxins, drugs, and environmental factors.

  1. Proteomic interactions in the mouse vitreous-retina complex.

    Directory of Open Access Journals (Sweden)

    Jessica M Skeie

    Full Text Available Human vitreoretinal diseases are due to presumed abnormal mechanical interactions between the vitreous and retina, and translational models are limited. This study determined whether nonstructural proteins and potential retinal biomarkers were expressed by the normal mouse vitreous and retina.Vitreous and retina samples from mice were collected by evisceration and analyzed by liquid chromatography-tandem mass spectrometry. Identified proteins were further analyzed for differential expression and functional interactions using bioinformatic software.We identified 1,680 unique proteins in the retina and 675 unique proteins in the vitreous. Unbiased clustering identified protein pathways that distinguish retina from vitreous including oxidative phosphorylation and neurofilament cytoskeletal remodeling, whereas the vitreous expressed oxidative stress and innate immunology pathways. Some intracellular protein pathways were found in both retina and vitreous, such as glycolysis and gluconeogenesis and neuronal signaling, suggesting proteins might be shuttled between the retina and vitreous. We also identified human disease biomarkers represented in the mouse vitreous and retina, including carbonic anhydrase-2 and 3, crystallins, macrophage inhibitory factor, glutathione peroxidase, peroxiredoxins, S100 precursors, and von Willebrand factor.Our analysis suggests the vitreous expresses nonstructural proteins that functionally interact with the retina to manage oxidative stress, immune reactions, and intracellular proteins may be exchanged between the retina and vitreous. This novel proteomic dataset can be used for investigating human vitreoretinopathies in mouse models. Validation of vitreoretinal biomarkers for human ocular diseases will provide a critical tool for diagnostics and an avenue for therapeutics.

  2. Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media.

    Science.gov (United States)

    Kalule, John Bosco; Fortuin, Suereta; Calder, Bridget; Robberts, Lourens; Keddy, Karen H; Nel, Andrew J M; Garnett, Shaun; Nicol, Mark; Warner, Digby F; Soares, Nelson C; Blackburn, Jonathan M

    2017-09-05

    Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains. Label-free proteomic analysis allowed the identification of virulence and drug resistance proteins that were unique to each of the clinical isolates compared in this study. The B subunit of Shiga toxin, ToxB, was uniquely detected in the STEC strain while several other virulence factors including SheA, OmpF, OmpC and OmpX were significantly more abundant in the STEC strain. The ciprofloxacin resistant EPEC isolate possessed reduced levels of key virulence proteins compared to the ciprofloxacin susceptible EPEC and STEC strains. Parallel reaction monitoring assays validated the presence of biologically relevant proteins across biologically-replicated cultures. Propagation of clinical isolates on a relevant solid medium followed by mass spectrometry analysis represents a convenient means to quantify virulence factors and drug resistance determinants that might otherwise be lost through extensive in vitro passage in enteropathogenic bacteria. Through the use of quantitative proteomics, we have characterized the virulence and antimicrobial resistance attributes of three clinically isolated, pathogenic E. coli strains cultured on solid media. Our results provide new, quantitative data on the expressed proteomes of these tellurite-resistant, diarrhoeagenic E. coli strains and reveal a subset of antimicrobial resistance and virulence proteins that are differentially abundant between these clinical strains. Our quantitative proteomics-based approach should thus have

  3. [Preparation of monolithic materials and their applications in proteomic analysis].

    Science.gov (United States)

    Liang, Yu; Zhang, Lihua; Zhang, Yukui

    2011-09-01

    Proteomics is one of the core contents of life science in the post-genomic era, among which it is very important to develop the analytical techniques with high resolution, high sensitivity, high accuracy and high throughput. With the advantages of facile preparation, fast mass transfer, low backpressure and easy modification, monolithic materials have been widely used in proteomic analysis. This review summarizes the preparation methods of different kinds of monolithic materials (including organic polymer monoliths, silica-based monoliths, organic-inorganic hybrid silica monoliths) and their applications in proteomic study such as the digestion of proteins, the separation of proteins or peptides, high throughput analysis integrating online digestion, separation and identification.

  4. A community proposal to integrate proteomics activities in ELIXIR

    DEFF Research Database (Denmark)

    Vizcaíno, Juan Antonio; Walzer, Mathias; Jiménez, Rafael C.

    2017-01-01

    in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case...... in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders...

  5. [LEGUME-RHIZOBIUM SYMBIOSIS PROTEOMICS: ACHIEVEMENTS AND PERSPECTIVES].

    Science.gov (United States)

    Kondratiuk, Iu Iu; Mamenko, P M; Kots, S Ya

    2015-01-01

    The present review contains results of proteomic researches of legume-rhizobium symbiosis. The technical difficulties associated with the methods of obtaining protein extracts from symbiotic structures and ways of overcoming them were discussed. The changes of protein synthesis under formation and functioning of symbiotic structures were shown. Special attention has been given to the importance of proteomic studies of plant-microbe structures in the formation of adaptation strategies under adverse environmental conditions. The technical and conceptual perspectives of legume-rhizobium symbiosis proteomics were shown.

  6. Interlaboratory studies and initiatives developing standards for proteomics

    Science.gov (United States)

    Ivanov, Alexander R.; Colangelo, Christopher M.; Dufresne, Craig P.; Friedman, David B.; Lilley, Kathryn S.; Mechtler, Karl; Phinney, Brett S.; Rose, Kristie L.; Rudnick, Paul A.; Searle, Brian C.; Shaffer, Scott A.; Weintraub, Susan T.

    2013-01-01

    Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This view-point article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG). PMID:23319436

  7. Single muscle fiber proteomics reveals unexpected mitochondrial specialization

    DEFF Research Database (Denmark)

    Murgia, Marta; Nagaraj, Nagarjuna; Deshmukh, Atul S

    2015-01-01

    Mammalian skeletal muscles are composed of multinucleated cells termed slow or fast fibers according to their contractile and metabolic properties. Here, we developed a high-sensitivity workflow to characterize the proteome of single fibers. Analysis of segments of the same fiber by traditional...... and unbiased proteomics methods yielded the same subtype assignment. We discovered novel subtype-specific features, most prominently mitochondrial specialization of fiber types in substrate utilization. The fiber type-resolved proteomes can be applied to a variety of physiological and pathological conditions...

  8. The Arabidopsis cytosolic proteome

    DEFF Research Database (Denmark)

    Ito, Jun; Parsons, Harriet Tempé; Heazlewood, Joshua L.

    2014-01-01

    compartments. However, a detailed study of enriched cytosolic fractions from Arabidopsis cell culture has been performed only recently, with over 1,000 proteins reproducibly identified by mass spectrometry. The number of proteins allocated to the cytosol nearly doubles to 1,802 if a series of targeted...... proteomic characterizations of complexes is included. Despite this, few groups are currently applying advanced proteomic approaches to this important metabolic space. This review will highlight the current state of the Arabidopsis cytosolic proteome since its initial characterization a few years ago....

  9. In silico analysis of the core signaling proteome from the barley powdery mildew pathogen (Blumeria graminis f.sp. hordei).

    Science.gov (United States)

    Kusch, Stefan; Ahmadinejad, Nahal; Panstruga, Ralph; Kuhn, Hannah

    2014-10-02

    Compared to other ascomycetes, the barley powdery mildew pathogen Blumeria graminis f.sp. hordei (Bgh) has a large genome (ca. 120 Mbp) that harbors a relatively small number of protein-coding genes (ca. 6500). This genomic assemblage is thought to be the result of numerous gene losses, which likely represent an evolutionary adaptation to a parasitic lifestyle in close association with its host plant, barley (Hordeum vulgare). Approximately 8% of the Bgh genes are predicted to encode virulence effectors that are secreted into host tissue and/or cells to promote pathogenesis; the remaining proteome is largely uncharacterized at present. We provide a comparative analysis of the conceptual Bgh proteome, with an emphasis on proteins with known roles in fungal development and pathogenicity, for example heterotrimeric G proteins and G protein coupled receptors; components of calcium and cAMP signaling; small monomeric GTPases; mitogen-activated protein cascades and transcription factors. The predicted Bgh proteome lacks a number of proteins that are otherwise conserved in filamentous fungi, including two proteins that are required for the formation of anastomoses (somatic hyphal connections). By contrast, apart from minor modifications, all major canonical signaling pathways are retained in Bgh. A family of kinases that preferentially occur in pathogenic species of the fungal clade Leotiomyceta is unusually expanded in Bgh and its close relative, Blumeria graminis f.sp. tritici. Our analysis reveals characteristic features of the proteome of a fungal phytopathogen that occupies an extreme habitat: the living plant cell.

  10. Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition.

    Science.gov (United States)

    Kronja, Iva; Whitfield, Zachary J; Yuan, Bingbing; Dzeyk, Kristina; Kirkpatrick, Joanna; Krijgsveld, Jeroen; Orr-Weaver, Terry L

    2014-11-11

    The onset of development is marked by two major, posttranscriptionally controlled, events: oocyte maturation (release of the prophase I primary arrest) and egg activation (release from the secondary meiotic arrest). Using quantitative mass spectrometry, we previously described proteome remodeling during Drosophila egg activation. Here, we describe our quantitative mass spectrometry-based analysis of the changes in protein levels during Drosophila oocyte maturation. This study presents the first quantitative survey, to our knowledge, of proteome changes accompanying oocyte maturation in any organism and provides a powerful resource for identifying both key regulators and biological processes driving this critical developmental window. We show that Muskelin, found to be up-regulated during oocyte maturation, is required for timely nurse cell nuclei clearing from mature egg chambers. Other proteins up-regulated at maturation are factors needed not only for late oogenesis but also completion of meiosis and early embryogenesis. Interestingly, the down-regulated proteins are predominantly involved in RNA processing, translation, and RNAi. Integrating datasets on the proteome changes at oocyte maturation and egg activation uncovers dynamics in proteome remodeling during the change from oocyte to embryo. Notably, 66 proteins likely act uniquely during late oogenesis, because they are up-regulated at maturation and down-regulated at activation. We find down-regulation of this class of proteins to be mediated partially by APC/C(CORT), a meiosis-specific form of the E3 ligase anaphase promoting complex/cyclosome (APC/C).

  11. The importance of accounting for sex in the search of proteomic signatures of mycotoxin exposure.

    Science.gov (United States)

    Soler, L; Oswald, I P

    2017-12-27

    Mycotoxins are natural food and feed contaminants that are toxic to human and animals. Proteomics is an adequate toolbox to investigate the mode of action and the effects of mycotoxins, as these toxicants often alter protein synthesis and degradation, as well as induce changes of important post-translational modifications. For instance, the contaminant deoxynivalenol induces a severe ribosomal stress that affects protein production, whereas the toxin Fumonisin B1 can alter the phosphorylation of a large number of proteins, and patulin is a potent proteotoxic molecule. The response to most mycotoxins is sex-dependent, males being generally more sensitive than females. In addition, for some toxins, the toxic effects observed were different for each sex. Nevertheless, the importance of accounting for a sex-dependent response is often overlooked in toxicology studies involving mycotoxins. Here we review the information that proteomics has provided in pre-clinical studies of mycotoxin exposure as well as the differential response of males and females to these molecules to highlight the need of including male and female individuals when evaluating the impact of mycotoxins in the cell proteome. The current trend in mycotoxicology is the combination of several -omics techniques in order to understand the mechanism of action and effects of these toxic natural food contaminants. One of the goals of these experiments is to determine "potential biomarkers" of mycotoxicoses. Nevertheless, the strategy followed in biomarker research must take into account as many possible factors as possible in order to find robust biomarkers for differential diagnosis. Among the factors that can have an influence in the response to mycotoxins, one of the most important is sex. Traditionally, males are preferentially used in research, as they are more sensitive to mycotoxins and their response is not dependent on hormonal levels, thus less variable. However the intrinsic and hormonal differences

  12. Proteomic responses of drought-tolerant and drought-sensitive cotton varieties to drought stress.

    Science.gov (United States)

    Zhang, Haiyan; Ni, Zhiyong; Chen, Quanjia; Guo, Zhongjun; Gao, Wenwei; Su, Xiujuan; Qu, Yanying

    2016-06-01

    Drought, one of the most widespread factors reducing agricultural crop productivity, affects biological processes such as development, architecture, flowering and senescence. Although protein analysis techniques and genome sequencing have made facilitated the proteomic study of cotton, information on genetic differences associated with proteomic changes in response to drought between different cotton genotypes is lacking. To determine the effects of drought stress on cotton seedlings, we used two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry to comparatively analyze proteome of drought-responsive proteins during the seedling stage in two cotton (Gossypium hirsutum L.) cultivars, drought-tolerant KK1543 and drought-sensitive Xinluzao26. A total of 110 protein spots were detected on 2-DE maps, of which 56 were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified proteins were mainly associated with metabolism (46.4 %), antioxidants (14.2 %), and transport and cellular structure (23.2 %). Some key proteins had significantly different expression patterns between the two genotypes. In particular, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, UDP-D-glucose pyrophosphorylase and ascorbate peroxidase were up-regulated in KK1543 compared with Xinluzao26. Under drought stress conditions, the vacuolar H(+)-ATPase catalytic subunit, a 14-3-3g protein, translation initiation factor 5A and pathogenesis-related protein 10 were up-regulated in KK1543, whereas ribosomal protein S12, actin, cytosolic copper/zinc superoxide dismutase, protein disulfide isomerase, S-adenosylmethionine synthase and cysteine synthase were down-regulated in Xinluzao26. This work represents the first characterization of proteomic changes that occur in response to drought in roots of cotton plants. These differentially expressed proteins may be related to

  13. DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.

    Science.gov (United States)

    Samwer, Matthias; Schneider, Maximilian W G; Hoefler, Rudolf; Schmalhorst, Philipp S; Jude, Julian G; Zuber, Johannes; Gerlich, Daniel W

    2017-08-24

    Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF's association with inner nuclear membrane proteins but instead relies on BAF's ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis.

    Science.gov (United States)

    Clark, David J; Fondrie, William E; Liao, Zhongping; Hanson, Phyllis I; Fulton, Amy; Mao, Li; Yang, Austin J

    2015-10-20

    Exosomes are microvesicles of endocytic origin constitutively released by multiple cell types into the extracellular environment. With evidence that exosomes can be detected in the blood of patients with various malignancies, the development of a platform that uses exosomes as a diagnostic tool has been proposed. However, it has been difficult to truly define the exosome proteome due to the challenge of discerning contaminant proteins that may be identified via mass spectrometry using various exosome enrichment strategies. To better define the exosome proteome in breast cancer, we incorporated a combination of Tandem-Mass-Tag (TMT) quantitative proteomics approach and Support Vector Machine (SVM) cluster analysis of three conditioned media derived fractions corresponding to a 10 000g cellular debris pellet, a 100 000g crude exosome pellet, and an Optiprep enriched exosome pellet. The quantitative analysis identified 2 179 proteins in all three fractions, with known exosomal cargo proteins displaying at least a 2-fold enrichment in the exosome fraction based on the TMT protein ratios. Employing SVM cluster analysis allowed for the classification 251 proteins as "true" exosomal cargo proteins. This study provides a robust and vigorous framework for the future development of using exosomes as a potential multiprotein marker phenotyping tool that could be useful in breast cancer diagnosis and monitoring disease progression.

  15. Soybean Proteome Database 2012: Update on the comprehensive data repository for soybean proteomics

    Directory of Open Access Journals (Sweden)

    Hajime eOhyanagi

    2012-05-01

    Full Text Available The Soybean Proteome Database (SPD was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei proteins collected from several organs, tissues and organelles including the maps for plasma membrane, cell wall, chloroplast and mitochondrion, which were electrophoresed on two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. An omics table also has been provided to reveal relationships among mRNAs, proteins and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of multiple omes in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean/.

  16. 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

  17. 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

  18. Proteomic identification of secreted proteins of Propionibacterium acnes

    Science.gov (United States)

    2010-01-01

    Background The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal that resides preferentially within sebaceous follicles; however, it also exhibits many traits of an opportunistic pathogen, playing roles in a variety of inflammatory diseases such as acne vulgaris. To date, the underlying disease-causing mechanisms remain ill-defined and knowledge of P. acnes virulence factors remains scarce. Here, we identified proteins secreted during anaerobic cultivation of a range of skin and clinical P. acnes isolates, spanning the four known phylogenetic groups. Results Culture supernatant proteins of P. acnes were separated by two-dimensional electrophoresis (2-DE) and all Coomassie-stained spots were subsequently identified by MALDI mass spectrometry (MALDI-MS). A set of 20 proteins was secreted in the mid-exponential growth phase by the majority of strains tested. Functional annotation revealed that many of these common proteins possess degrading activities, including glycoside hydrolases with similarities to endoglycoceramidase, β-N-acetylglucosaminidase and muramidase; esterases such as lysophospholipase and triacylglycerol lipase; and several proteases. Other secreted factors included Christie-Atkins-Munch-Petersen (CAMP) factors, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and several hypothetical proteins, a few of which are unique to P. acnes. Strain-specific differences were apparent, mostly in the secretion of putative adhesins, whose genes exhibit variable phase variation-like sequence signatures. Conclusions Our proteomic investigations have revealed that the P. acnes secretome harbors several proteins likely to play a role in host-tissue degradation and inflammation. Despite a large overlap between the secretomes of all four P. acnes phylotypes, distinct differences between predicted host-tissue interacting proteins were identified, providing potential insight into the differential virulence properties of P. acnes isolates

  19. Proteomic identification of secreted proteins of Propionibacterium acnes

    Directory of Open Access Journals (Sweden)

    Holland Carsten

    2010-08-01

    Full Text Available Abstract Background The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal that resides preferentially within sebaceous follicles; however, it also exhibits many traits of an opportunistic pathogen, playing roles in a variety of inflammatory diseases such as acne vulgaris. To date, the underlying disease-causing mechanisms remain ill-defined and knowledge of P. acnes virulence factors remains scarce. Here, we identified proteins secreted during anaerobic cultivation of a range of skin and clinical P. acnes isolates, spanning the four known phylogenetic groups. Results Culture supernatant proteins of P. acnes were separated by two-dimensional electrophoresis (2-DE and all Coomassie-stained spots were subsequently identified by MALDI mass spectrometry (MALDI-MS. A set of 20 proteins was secreted in the mid-exponential growth phase by the majority of strains tested. Functional annotation revealed that many of these common proteins possess degrading activities, including glycoside hydrolases with similarities to endoglycoceramidase, β-N-acetylglucosaminidase and muramidase; esterases such as lysophospholipase and triacylglycerol lipase; and several proteases. Other secreted factors included Christie-Atkins-Munch-Petersen (CAMP factors, glyceraldehyde 3-phosphate dehydrogenase (GAPDH, and several hypothetical proteins, a few of which are unique to P. acnes. Strain-specific differences were apparent, mostly in the secretion of putative adhesins, whose genes exhibit variable phase variation-like sequence signatures. Conclusions Our proteomic investigations have revealed that the P. acnes secretome harbors several proteins likely to play a role in host-tissue degradation and inflammation. Despite a large overlap between the secretomes of all four P. acnes phylotypes, distinct differences between predicted host-tissue interacting proteins were identified, providing potential insight into the differential virulence

  20. Proteomics analysis of bodily fluids in pancreatic cancer.

    Science.gov (United States)

    Pan, Sheng; Brentnall, Teresa A; Chen, Ru

    2015-08-01

    Proteomics study of pancreatic cancer using bodily fluids emphasizes biomarker discovery and clinical application, presenting unique prospect and challenges. Depending on the physiological nature of the bodily fluid and its proximity to pancreatic cancer, the proteomes of bodily fluids, such as pancreatic juice, pancreatic cyst fluid, blood, bile, and urine, can be substantially different in terms of protein constitution and the dynamic range of protein concentration. Thus, a comprehensive discovery and specific detection of cancer-associated proteins within these varied fluids is a complex task, requiring rigorous experiment design and a concerted approach. While major challenges still remain, fluid proteomics studies in pancreatic cancer to date have provided a wealth of information in revealing proteome alterations associated with pancreatic cancer in various bodily fluids. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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

  2. Plasma proteome analysis of cervical intraepithelial neoplasia and ...

    Indian Academy of Sciences (India)

    ... Malaysia and University of Malaya Centre For Proteomics Research (UMCPR), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia; Department of Clinical Oral Biology, Faculty of Dentistry; Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia; Department of Obstetrics and Gynecology; Universiti Kebangsaan ...

  3. C4 photosynthetic machinery: insights from maize chloroplast proteomics

    Directory of Open Access Journals (Sweden)

    Qi eZhao

    2013-04-01

    Full Text Available C4 plants exhibit much higher CO2 assimilation rates than C3 plants. The specialized differentiation of mesophyll cell (M and bundle sheath cell (BS type chloroplasts is unique to C4 plants and improves photosynthesis efficiency. Maize (Zea mays is an important crop and model with C4 photosynthetic machinery. Current high-throughput quantitative proteomics approaches (e.g., 2DE, iTRAQ, and shotgun proteomics have been employed to investigate maize chloroplast structure and function. These proteomic studies have provided valuable information on C4 chloroplast protein components, photosynthesis, and other metabolic mechanisms underlying chloroplast biogenesis, stromal and membrane differentiation, as well as response to salinity, high/low temperature, and light stress. This review presents an overview of proteomics advances in maize chloroplast biology.

  4. Proteome research : two-dimensional gel electrophoresis and identification methods

    National Research Council Canada - National Science Library

    Rabilloud, Thierry, 1961

    2000-01-01

    "Two-dimensional electrophoresis is the central methodology in proteome research, and the state of the art is described in detail in this text, together with extensive coverage of the detection methods available...

  5. 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

  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. Critical evaluation of proteomic protocols for passion fruit ( Passiflora ...

    African Journals Online (AJOL)

    Critical evaluation of proteomic protocols for passion fruit (Passiflora edulis Sims) leaves, a crop with juice market benefits. VA Perdizio, OLT Machado, JS Araujo, AEA Oliveira, LR Monteiro, MN Costa, AT Ferreira, J Perales, T Jacinto ...

  8. CPTAC Teams | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The following are the current CPTAC teams, representing a network of Proteome Characterization Centers (PCCs), Proteogenomic Translational Research Centers (PTRCs), and Proteogenomic Data Analysis Centers (PGDACs). Teams are listed alphabetically by institution, with their respective Principal Investigators:

  9. Introduction to proteomics : tools for the new biology

    National Research Council Canada - National Science Library

    Liebler, Daniel C

    2002-01-01

    This is an introductory, single-authored introduction to proteomics, which is currently the hottest area in the biological sciences as it enable scientists to study the protein complement of the genome...

  10. Review of recent proteomic applications in aquatic toxicology.

    Science.gov (United States)

    Sanchez, Brian C; Ralston-Hooper, Kimberly; Sepúlveda, María S

    2011-02-01

    Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates. © 2010 SETAC.

  11. Autocorrelated logistic ridge regression for prediction based on proteomics spectra.

    Science.gov (United States)

    Goeman, Jelle J

    2008-01-01

    This paper presents autocorrelated logistic ridge regression, an extension of logistic ridge regression for ordered covariates that is based on the assumption that adjacent covariates have similar regression coefficients. The method is applied to the analysis of proteomics mass spectra.

  12. Application of bioinformatics to optimization of serum proteome in ...

    African Journals Online (AJOL)

    Conclusively, researches are encouraged to launch a proteomics assistance and guidance in modern molecular diagnostic approaches for understanding and controlling the mucosa lesions especially in conquering the malignant progress. Keywords: Oral squamous cell carcinoma (OSCC); oral leukoplakia (OLK), ...

  13. Application of bioinformatics to optimization of serum proteome in ...

    African Journals Online (AJOL)

    SAM

    2014-05-14

    OSCC) from oral leukoplakia ... study the sera proteomes of 32 healthy volunteers, 6 patients with oral mucosa leukoplakia, 28 OSCC patients, and 8 .... American Ciphergen SELDI Protein Biology System II plus (PBS. II plus) and ...

  14. Plasma-based proteomics reveals immune response, complement and coagulation cascades pathway shifts in heat-stressed lactating dairy cows.

    Science.gov (United States)

    Min, Li; Cheng, Jianbo; Zhao, Shengguo; Tian, He; Zhang, Yangdong; Li, Songli; Yang, Hongjian; Zheng, Nan; Wang, Jiaqi

    2016-09-02

    Heat stress (HS) has an enormous economic impact on the dairy industry. In recent years, many researchers have investigated changes in the gene expression and metabolomics profiles in dairy cows caused by HS. However, the proteomics profiles of heat-stressed dairy cows have not yet been completely elucidated. We compared plasma proteomics from HS-free and heat-stressed dairy cows using an iTRAQ labeling approach. After the depletion of high abundant proteins in the plasma, 1472 proteins were identified. Of these, 85 proteins were differentially abundant in cows exposed to HS relative to HS-free. Database searches combined with GO and KEGG pathway enrichment analyses revealed that many components of the complement and coagulation cascades were altered in heat-stressed cows compared with HS-free cows. Of these, many factors in the complement system (including complement components C1, C3, C5, C6, C7, C8, and C9, complement factor B, and factor H) were down-regulated by HS, while components of the coagulation system (including coagulation factors, vitamin K-dependent proteins, and fibrinogens) were up-regulated by HS. In conclusion, our results indicate that HS decreases plasma levels of complement system proteins, suggesting that immune function is impaired in dairy cows exposed to HS. Though many aspects of heat stress (HS) have been extensively researched, relatively little is known about the proteomics profile changes that occur during heat exposure. In this work, we employed a proteomics approach to investigate differential abundance of plasma proteins in HS-free and heat-stressed dairy cows. Database searches combined with GO and KEGG pathway enrichment analyses revealed that HS resulted in a decrease in complement components, suggesting that heat-stressed dairy cows have impaired immune function. In addition, through integrative analyses of proteomics and previous metabolomics, we showed enhanced glycolysis, lipid metabolic pathway shifts, and nitrogen

  15. 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...

  16. Capillary electrophoresis of proteins for proteomic studies.

    Science.gov (United States)

    Manabe, T

    1999-10-01

    Analyses of proteins in complex mixtures such as cell lyzates are presently performed mainly by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. For structural analysis, each protein in a spot is digested with proteases and the fragment peptides are subjected to Edman sequencing and/or mass spectrometry. These works aim at the total analysis of proteins in a complex mixture and reconstruction of their cooperative functions. Genomic studies are now being combined with these proteomic studies. This review article focuses on the application of capillary electrophoresis aiming at the total analysis of complex protein systems or structural analysis of each separated protein. From this viewpoint, articles on capillary zone electrophoresis, capillary isoelectric focusing, and sieving SDS capillary electrophoresis are reviewed. Since these techniques of capillary electrophoresis have been thoroughly reviewed previously, papers published in 1997 and 1998 are mainly covered.

  17. Genomes, proteomes, and the central dogma.

    Science.gov (United States)

    Franklin, Sarah; Vondriska, Thomas M

    2011-10-01

    Systems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology. Rather than studying individual molecules or even single reactions, a systems approach allows integration of orthogonal data sets from distinct tiers of biological data, including gene, RNA, protein, metabolite, and other component networks. Together these networks give rise to emergent properties of cellular function, and it is their reprogramming that causes disease. We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the role of modules of molecules as opposed to individual proteins acting in isolation; (3) it enables discovery of novel emergent properties; (4) it demonstrates the importance of networks in biology; and (5) it adds new dimensionality to the study of biological systems.

  18. Application of proteomics to translational research

    International Nuclear Information System (INIS)

    Liotta, L.A.; Petricoin, E.; Garaci, E.; De Maria, R.; Belluco, C.

    2009-01-01

    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

  19. Proteome analysis of the hypercholestrolemic rat, RICO

    International Nuclear Information System (INIS)

    Cho, S.Y.; Park, K.-S.; Paik, Y.-K.; Seong, J.-K.

    2001-01-01

    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

  20. Proteomics of a fuzzy organelle: interphase chromatin

    Science.gov (United States)

    Kustatscher, Georg; Hégarat, Nadia; Wills, Karen L H; Furlan, Cristina; Bukowski-Wills, Jimi-Carlo; Hochegger, Helfrid; Rappsilber, Juri

    2014-01-01

    Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology. PMID:24534090