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Sample records for proteome coverage attainable

  1. NanoLC-FT-ICR MS improves proteome coverage attainable for ~3000 laser microdissected breast carcinoma cells

    SciTech Connect

    Umar, Arzu; Luider, Theo N.; Foekens, J. A.; Pasa-Tolic, Liljiana

    2007-01-29

    Genomics and proteomics assays hold great promise for unrevealing molecular events that underlie human disease. Essential to this quest is the ability to effectively analyze clinical samples, but this task is considerably complicated by tissue heterogeneity. Laser capture microdissection (LCM) can be used to selectively isolate targeted cell populations (such as tumor cells) from their native tissue environment. However, the small number of cells that are typically procured by LCM severely limits the proteome coverage and biomarker discovery potential achievable by conventional proteomics platforms. Herein, we report on the use of a nano liquid chromatography-Fourier transform ion clyclotron resonance mass spectrometry (nLC-FTICR MS) platform for analyzing protein digests of approximately 3,000 LCM-derived tumor cells from breast carcinoma tissue, which corresponds to approximately 300 ng of total protein. A total of 2,836 peptides were identified by matching LC-MS data to accurate mass and time (AMT) tag databases that were previously established for the human mammary epithelium and several breast cancer cell lines. The peptide identifications correspond to 1,139 unique proteins confidently identified with 2 or more peptides. Based on categorization by Gene Ontology, identified proteins appear to cover a wide variety of biological functions and cellular compartments. This work demonstrates that a substantial number of proteins can be identified from a limited number of cells using the AMT tag approach and opens a door for high throughput in-depth proteomics analysis of clinical samples.

  2. Subcellular Fractionation Enhances Proteome Coverage of Pancreatic Duct Cells

    PubMed Central

    Paulo, Joao A.; Gaun, Aleksandr; Kadiyala, Vivek; Ghoulidi, Ali; Banks, Peter A.; Conwell, Darwin L.; Steen, Hanno

    2013-01-01

    Objectives Subcellular fractionation of whole cell lysates offers a means of simplifying protein mixtures, potentially permitting greater depth of proteomic analysis. Here we compare proteins identified from pancreatic duct cells (PaDC) following organelle enrichment to those identified from PaDC whole cell lysates to determine if the additional procedures of subcellular fractionation increases proteome coverage. Methods We used differential centrifugation to enrich for nuclear, mitochondrial, membrane, and cytosolic proteins. We then compared - via mass spectrometry-based analysis - the number of proteins identified from these four fractions with four biological replicates of PaDC whole cell lysates. Results We identified similar numbers of proteins among all samples investigated. In total, 1658 non-redundant proteins were identified in the replicate samples, while 2196 were identified in the subcellular fractionation samples, corresponding to a 30% increase. Additionally, we noted that each organelle fraction was in fact enriched with proteins specific to the targeted organelle. Conclusions Subcellular fractionation of PaDC resulted in greater proteome coverage compared to PaDC whole cell lysate analysis. Although more labor intensive and time consuming, subcellular fractionation provides greater proteome coverage, and enriches for compartmentalized sub-populations of proteins. Application of this subcellular fractionation strategy allows for a greater depth of proteomic analysis and thus a better understanding of the cellular mechanisms of pancreatic disease. PMID:23352835

  3. Parallel proteomics to improve coverage and confidence in the partially annotated Oryctolagus cuniculus mitochondrial proteome.

    PubMed

    White, Melanie Y; Brown, David A; Sheng, Simon; Cole, Robert N; O'Rourke, Brian; Van Eyk, Jennifer E

    2011-02-01

    The ability to decipher the dynamic protein component of any system is determined by the inherent limitations of the technologies used, the complexity of the sample, and the existence of an annotated genome. In the absence of an annotated genome, large-scale proteomic investigations can be technically difficult. Yet the functional and biological species differences across animal models can lead to selection of partially or nonannotated organisms over those with an annotated genome. The outweighing of biology over technology leads us to investigate the degree to which a parallel approach can facilitate proteome coverage in the absence of complete genome annotation. When studying species without complete genome annotation, a particular challenge is how to ensure high proteome coverage while meeting the bioinformatic stringencies of high-throughput proteomics. A protein inventory of Oryctolagus cuniculus mitochondria was created by overlapping "protein-centric" and "peptide-centric" one-dimensional and two-dimensional liquid chromatography strategies; with additional partitioning into membrane-enriched and soluble fractions. With the use of these five parallel approaches, 2934 unique peptides were identified, corresponding to 558 nonredundant protein groups. 230 of these proteins (41%) were identified by only a single technical approach, confirming the need for parallel techniques to improve annotation. To determine the extent of coverage, a side-by-side comparison with human and mouse cardiomyocyte mitochondrial studies was performed. A nonredundant list of 995 discrete proteins was compiled, of which 244 (25%) were common across species. The current investigation identified 142 unique protein groups, the majority of which were detected here by only one technical approach, in particular peptide- and protein-centric two-dimensional liquid chromatography. Although no single approach achieved more than 40% coverage, the combination of three approaches (protein- and

  4. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

    PubMed

    Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

    2008-09-01

    The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

  5. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage.

    PubMed

    Marondedze, Claudius; Wong, Aloysius; Groen, Arnoud; Serrano, Natalia; Jankovic, Boris; Lilley, Kathryn; Gehring, Christoph; Thomas, Ludivine

    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.

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

    PubMed Central

    Marondedze, Claudius; Wong, Aloysius; Groen, Arnoud; Serrano, Natalia; Jankovic, Boris; Lilley, Kathryn; Gehring, Christoph; Thomas, Ludivine

    2014-01-01

    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. PMID:25561235

  7. Expanding proteome coverage with orthogonal-specificity α-Lytic proteases

    SciTech Connect

    Meyer, Jesse G.; Kim, Sangtae; Maltby, David A.; Ghassemian, Majid; Bandeira, Nuno; Komives, Elizabeth A.

    2014-03-01

    Bottom-up proteomics studies traditionally involve proteome digestion with a single protease, trypsin. However, trypsin alone does not generate peptides that encompass the entire proteome. Alternative proteases have been explored, but most have specificity for charged amino acid side chains. Therefore, additional proteases that improve proteome coverage by cleavage at sequences complimentary to trypsin may increase proteome coverage. We demonstrate the novel application of two proteases for bottom-up proteomics: wild type alpha-lytic protease (WaLP), and an active site mutant of WaLP, M190A alpha-lytic protease (MaLP). We assess several relevant factors including MS/MS fragmentation, peptide length, peptide yield, and protease specificity. By combining data from separate digestions with trypsin, LysC, WaLP, and MaLP, proteome coverage was increased 101% compared to trypsin digestion alone. To demonstrate how the gained sequence coverage can access additional PTM information, we show identification of a number of novel phosphorylation sites in the S. pombe proteome and include an illustrative example from the protein MPD2, wherein two novel sites are identified, one in a tryptic peptide too short to identify and the other in a sequence devoid of tryptic sites. The specificity of WaLP and MaLP for aliphatic amino acid side chains was particularly valuable for coverage of membrane protein sequences, which increased 350% when the data from trypsin, LysC, WaLP, and MaLP were combined.

  8. Human fallopian tube proteome shows high coverage of mesenchymal stem cells associated proteins

    PubMed Central

    Wang, Chenyuan; Liu, Yang; Chang, Cheng; Wu, Songfeng; Gao, Jie; Zhang, Yang; Chen, Yingjie; Zhong, Fan; Deng, Gaopi

    2016-01-01

    The object of this research was to report a draft proteome of human fallopian tube (hFT) comprises 5416 identified proteins, which could be considered as a physiological reference to complement Human Proteome Draft. The proteomic raw data and metadata were stored in an integrated proteome resources centre iProX (IPX00034300). This hFT proteome contains many hFT markers newly identified by mass spectrum. This hFT proteome comprises 660 high-, 3605 medium- and 1181 low-abundant proteins. Ribosome, cytoskeleton, vesicle and protein folding associated proteins showed obvious tendency to be higher abundance in hFT. The extraordinary high coverage of mesenchymal stem cells (MSCs)-associated proteins were identified in this hFT proteome, which highly supported that hFT should contain a plenty of MSCs. PMID:26759384

  9. Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments

    NASA Astrophysics Data System (ADS)

    Andrews, Genna L.; Dean, Ralph A.; Hawkridge, Adam M.; Muddiman, David C.

    2011-04-01

    Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms.

  10. Improving proteome coverage on a LTQ-Orbitrap using design of experiments.

    PubMed

    Andrews, Genna L; Dean, Ralph A; Hawkridge, Adam M; Muddiman, David C

    2011-04-01

    Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms. © American Society for Mass Spectrometry, 2011

  11. Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments

    PubMed Central

    Andrews, Genna L.; Dean, Ralph A.; Hawkridge, Adam M.; Muddiman, David C.

    2011-01-01

    Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms. PMID:21472614

  12. Digestion and depletion of abundant proteins improves proteomic coverage

    PubMed Central

    Fonslow, Bryan R.; Stein, Benjamin D.; Webb, Kristofor J.; Xu, Tao; Choi, Jeong; Park, Sung Kyu; Yates, John R.

    2012-01-01

    Two major challenges in proteomics are the large number of proteins and their broad dynamic range within the cell. We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances and observed greater than 3-fold improvement in low abundance human protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases, and proteomic pipelines. PMID:23160281

  13. Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples

    DOE PAGES

    Zhu, Ying; Zhao, Rui; Piehowski, Paul D.; ...

    2017-09-01

    One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here in this study, we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-μm-i.d. columns increase signal intensity by >3-fold relative to those using 75-μm-i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos MS significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap),more » leading to a ~3-fold increase in peptide identifications and 1.7-fold increase in identified protein groups for 2 ng tryptic digests of the bacterium S. oneidensis. The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by ~95% for 0.5 ng samples and by ~42% for 2 ng samples. Using the best combination of the above variables, we were able to identify >3,000 proteins from 10 ng tryptic digests from both HeLa and THP-1 mammalian cell lines. We also identified >950 proteins from subnanogram archaeal/bacterial cocultures. Finally, the present ultrasensitive LC-MS platform achieves a level of proteome coverage not previously realized for ultra-small sample loadings, and is expected to facilitate the analysis of subnanogram samples, including single mammalian cells.« less

  14. Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate.

    PubMed

    Serra, Aida; Zhu, Hongbin; Gallart-Palau, Xavier; Park, Jung Eun; Ho, Hee Haw; Tam, James P; Sze, Siu Kwan

    2016-03-01

    The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics.

  15. Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis

    PubMed Central

    2017-01-01

    The “deep” proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ∼8000–10 000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multienzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth by employing a workflow that addresses current limitations in deep proteome analysis in multiple stages: We used (i) gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, (ii) concatenated high-pH prefractionation, and (iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion (Lumos) mass spectrometer, to achieve 57% median protein sequence coverage in 13 728 protein groups (8949 Unigene IDs) in a single cell line. CHOPIN allows the use of both detectors in the Orbitrap on predefined precursor types that optimizes parallel ion processing, leading to the identification of a total of 179 549 unique peptides covering the deep proteome in unprecedented detail. PMID:28164708

  16. Plant proteomics update (2007-2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge.

    PubMed

    Jorrín-Novo, Jesús V; Maldonado, Ana M; Echevarría-Zomeño, Sira; Valledor, Luis; Castillejo, Mari A; Curto, Miguel; Valero, José; Sghaier, Besma; Donoso, Gabriel; Redondo, Inmaculada

    2009-04-13

    This review is the continuation of three previously published articles [Jorrin JV, Maldonado AM, Castillejo MA. Plant proteome analysis: a 2006 update. Proteomics 2007; 7: 2947-2962; Rossignol M, Peltier JB, Mock HP, Matros A, Maldonado AM, Jorrin JV. Plant proteome analysis: a 2004-2006 update. Proteomics 2006; 6: 5529-5548; Canovas FM, Dumas-Gaudot E, Recorbet G, Jorrin J, Mock HP, Rossignol M. Plant proteome analysis. Proteomics 2004; 4: 285-298] and aims to update the contribution of Proteomics to plant research between 2007 and September 2008 by reviewing most of the papers, which number approximately 250, that appeared in the Plant Proteomics field during that period. Most of the papers published deal with the proteome of Arabidopsis thaliana and rice (Oryza sativa), and focus on profiling organs, tissues, cells or subcellular proteomes, and studying developmental processes and responses to biotic and abiotic stresses using a differential expression strategy. Although the platform based on 2-DE is still the most commonly used, the use of gel-free and second-generation Quantitative Proteomic techniques has increased. Proteomic data are beginning to be validated using complementary -omics or classical biochemical or cellular biology techniques. In addition, appropriate experimental design and statistical analysis are being carried out in accordance with the required Minimal Information about a Proteomic Experiment (MIAPE) standards. As a result, the coverage of the plant cell proteome and the plant biology knowledge is increasing. Compared to human and yeast systems, however, plant biology research has yet to exploit fully the potential of proteomics, in particular its applications to PTMs and Interactomics.

  17. Mapping the Protein Domain Structures of the Respiratory Mucins: a mucin proteome coverage study

    PubMed Central

    Cao, Rui; Wang, T. Tiffany; DeMaria, Genevieve; Sheehan, John K.; Kesimer, Mehmet

    2012-01-01

    Mucin genes encode a family of the largest expressed proteins in the human genome. The proteins are highly substituted with O-linked oligosaccharides which greatly restrict access to the peptide backbones. The genomic organization of the N-terminal, O-glycosylated, and C-terminal regions of most of the mucins has been established and is available in the sequence databases. However, much less is known about the fate of their exposed protein regions after translation and secretion, and, to date, detailed proteomic studies complementary to the genomic studies are rather limited. Using mucins isolated from cultured human airway epithelial cell secretions, trypsin digestion and mass spectrometry, we investigated the proteome coverage of the mucins responsible for the maintenance and protection of the airway epithelia. Excluding the heavily glycosylated mucin domains, up to 85% coverage of the N-terminal region of the gel forming mucins MUC5B and MUC5AC was achieved, and up to 60% of the C-terminal regions were covered, suggesting that more N- and sparsely O-glycosylated regions as well as possible other modifications are available at the C-terminus. All possible peptides from the cysteine-rich regions that interrupt the heavily glycosylated mucin domains were identified. Interestingly, 43 cleavage sites from ten different domains of MUC5B and MUC5AC were identified, which possessed a non-tryptic cleavage site on the N-terminal end of the peptide, indicating potential exposure to proteolytic and/or “spontaneous cleavages”. Some of these non-tryptic cleavages may be important for proper maturation of the molecule, before and/or after secretion. Most of the peptides identified from MUC16 were from the SEA region. Surprisingly, three peptides were clearly identified from its heavily glycosylated regions. Up to 25% coverage of MUC4 was achieved covering seven different domains of the molecule. All peptides from the MUC1 cytoplasmic domain were detected along with the

  18. Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation.

    PubMed

    Blackburn, Kevin; Mbeunkui, Flaubert; Mitra, Srijeet K; Mentzel, Tobias; Goshe, Michael B

    2010-07-02

    Performance differences in protein and proteome characterization achieved by data-independent acquisition (DIA) LC/MS(E) and data-dependent acquisition (DDA) LC/MS/MS approaches were investigated. LC/MS(E) is a novel mode of generating product ion data for all coeluting precursors in parallel as opposed to LC/MS/MS where coeluting precursors must be serially fragmented one at a time. During LC/MS(E) analysis, alternating MS scans of "normal" and "elevated" collision energy are collected at regular intervals, providing nearly a 100% duty cycle for precursor detection and fragmentation because all precursors are fragmented across their full chromatographic elution profile. This is in contrast to DDA-based MS/MS where serial selection of precursor ions is biased toward interrogation and detection of the highest abundance sample components by virtue of the intensity-driven interrogation scheme employed. Both modes of acquisition were applied to a simple four-protein standard mixture with a 16-fold dynamic range in concentration, an in-gel digest of the Arabidopsis thaliana protein FLS2 purified by immunoprecipitation, and a solution-digested tomato leaf proteome sample. Dramatic improvement for individual protein sequence coverage was obtained for all three samples analyzed by the DIA approach, particularly for the lowest abundance sample components. In many instances, precursors readily detected and identified during DIA were either interrogated by MS/MS during DDA at inopportune points in their chromatographic elution profiles resulting in poor quality product ion spectra or not interrogated at all. Detailed evaluation of both DDA and DIA raw data and timing of the MS-to-MS/MS switching events clearly revealed the fundamental limitations of serial MS/MS interrogation and the advantages of parallel fragmentation by DIA for more comprehensive protein identification and characterization which holds promise for enhanced isoform and post-translational modification

  19. Patient Age, Ethnicity, Medical History, and Risk Factor Profile, but Not Drug Insurance Coverage, Predict Successful Attainment of Glycemic Targets

    PubMed Central

    Teoh, Hwee; Braga, Manoela F.B.; Casanova, Amparo; Drouin, Denis; Goodman, Shaun G.; Harris, Stewart B.; Langer, Anatoly; Tan, Mary K.; Ur, Ehud; Yan, Andrew T.; Zinman, Bernard; Leiter, Lawrence A.

    2010-01-01

    OBJECTIVE To identify factors in patients with type 2 diabetes and A1C >7.0% associated with attainment of A1C ≤7.0%. RESEARCH DESIGN AND METHODS We used a prospective registry of 5,280 Canadian patients in primary care settings enrolled in a 12-month glycemic pharmacotherapy optimization strategy based on national guidelines. RESULTS At close out, median A1C was 7.1% (vs. 7.8% at baseline) with 48% of subjects achieving A1C ≤7.0% (P < 0.0001). Older patients of Asian or black origin, those with longer diabetes duration, those with lower baseline A1C, BMI, LDL cholesterol, and blood pressure, and those on angiotensin receptor blockers and a lower number of antihyperglycemic agents, were more likely to achieve A1C ≤7.0% at some point during the study (all P < 0.0235). Access to private versus public drug coverage did not impact glycemic target realization. CONCLUSIONS Patient demography, cardiometabolic health, and ongoing pharmacotherapy, but not access to private drug insurance coverage, contribute to the care gap in type 2 diabetes. PMID:20823344

  20. Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar).

    PubMed

    Nuez-Ortín, Waldo G; Carter, Chris G; Nichols, Peter D; Wilson, Richard

    2016-07-01

    Understanding diet- and environmentally induced physiological changes in fish larvae is a major goal for the aquaculture industry. Proteomic analysis of whole fish larvae comprising multiple tissues offers considerable potential but is challenging due to the very large dynamic range of protein abundance. To extend the coverage of the larval phase of the Atlantic salmon (Salmo salar) proteome, we applied a two-step sequential extraction (SE) method, based on differential protein solubility, using a nondenaturing buffer containing 150 mM NaCl followed by a denaturing buffer containing 7 M urea and 2 M thiourea. Extracts prepared using SE and one-step direct extraction were characterized via label-free shotgun proteomics using nanoLC-MS/MS (LTQ-Orbitrap). SE partitioned the proteins into two fractions of approximately equal amounts, but with very distinct protein composition, leading to identification of ∼40% more proteins than direct extraction. This fractionation strategy enabled the most detailed characterization of the salmon larval proteome to date and provides a platform for greater understanding of physiological changes in whole fish larvae. The MS data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology.

    PubMed

    Agrawal, Ganesh Kumar; Rakwal, Randeep

    2011-05-01

    Growing rice is an important socio-economic activity. Rice proteomics has achieved a tremendous progress in establishing techniques to proteomes of almost all tissues, organs, and organelles during the past one decade (year 2000-2010). We have compiled these progresses time to time over this period. The present compilation discusses proteomics research in rice published between 1st April 2008 and 30th July 2010. Progress continues mainly towards protein cataloging deep into the proteome with high-confident protein assignment and some functional significance than ever before by (i) identifying previously unreported/low-abundance proteins, (ii) quantifying relative/absolute values of proteins, (iii) assigning protein responses to biotic/abiotic stresses, (iv) protein localization into organelles, (v) validating previous proteomes and eliminating false-positive proteins, and (vi) discovering potential biomarkers for tissues, organs, organelles, and for screening transgenic plants and food-safety evaluation. The notable achievements in global mapping of phosphorylation sites and identifying several novel secreted proteins into the extracellular space are worth appreciating. Our ever-increasing knowledge on the rice proteomics is beginning to impact the biology of not only rice, but also crops and plants. These major achievements will be discussed in this review keeping in mind newcomers, young, and established scientists in proteomics and plants. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Collagenase treatment enhances proteomic coverage of low-abundance proteins in decellularized matrix bioscaffolds.

    PubMed

    Kuljanin, Miljan; Brown, Cody F C; Raleigh, Matthew J; Lajoie, Gilles A; Flynn, Lauren E

    2017-11-01

    There is great interest in the application of advanced proteomic techniques to characterize decellularized tissues in order to develop a deeper understanding of the effects of the complex extracellular matrix (ECM) composition on the cellular response to these pro-regenerative bioscaffolds. However, the identification of proteins in ECM-derived bioscaffolds is hindered by the high abundance of collagen in the samples, which can interfere with the detection of lower-abundance constituents that may be important regulators of cell function. To address this limitation, we developed a novel multi-enzyme digestion approach using treatment with a highly-purified collagenase derived from Clostridium Histolyticum to selectively deplete collagen from ECM-derived protein extracts, reducing its relative abundance from up to 90% to below 10%. Moreover, we applied this new method to characterize the proteome of human decellularized adipose tissue (DAT), human decellularized cancellous bone (DCB), and commercially-available bovine tendon collagen (BTC). We successfully demonstrated with all three sources that collagenase treatment increased the depth of detection and enabled the identification of a variety of signaling proteins that were masked by collagen in standard digestion protocols with trypsin/LysC, increasing the number of proteins identified in the DAT by ∼2.2 fold, the DCB by ∼1.3 fold, and the BTC by ∼1.6 fold. In addition, quantitative proteomics using label-free quantification demonstrated that the DAT and DCB extracts were compositionally distinct, and identified a number of adipogenic and osteogenic proteins that were consistently more highly expressed in the DAT and DCB respectively. Overall, we have developed a new processing method that may be applied in advanced mass spectrometry studies to improve the high-throughput proteomic characterization of bioscaffolds derived from mammalian tissues. Further, our study provides new insight into the complex ECM

  3. Effect of surface coatings, grain size, and ionic strength on the maximum attainable coverage of bacteria on sand surfaces.

    PubMed

    Bolster, C H; Mills, A L; Hornberger, G M; Herman, J S

    2001-08-01

    The injection of bacteria in the subsurface has been identified as a potential method for in situ cleanup of contaminated aquifers. For high bacterial loadings, the presence of previously deposited bacteria can result in decreased deposition rates--a phenomenon known as blocking. Miscible displacement experiments were performed on short sand columns (approximately 5 cm) to determine how bacterial deposition on positively charged metal-oxyhydroxide-coated sands is affected by the presence of previously deposited bacteria. Approximately 8 pore volumes of a radiolabeled bacterial suspension at a concentration of approximately 1 x 10(9) cells ml-1 were introduced into the columns followed by a 2-pore-volume flush of cell-free buffer. It was found that the presence of Al- and Fe-coated sand increased both deposition rates and maximum fractional surface coverage of bacteria on the sediment surfaces. The effect of grain size on maximum bacterial retention capacity, however, was not significant. Decreasing ionic strength from 10(-1) to 10(-2) M KCl resulted in noticeable decreases in sticking efficiency (alpha) and maximum surface coverage (thetamax) for clean silica sand--results consistent with DLVO theory. In columns containing positively charged Al- and Fe-coated sands, however, changes in alpha and thetamax due to decreasing ionic strength were minimal. These findings demonstrate the importance of geochemical controls on the maximum bacterial retention capacity of sands.

  4. RuBisCO depletion improved proteome coverage of cold responsive S-nitrosylated targets in Brassica juncea

    PubMed Central

    Sehrawat, Ankita; Abat, Jasmeet K.; Deswal, Renu

    2013-01-01

    Although in the last few years good number of S-nitrosylated proteins are identified but information on endogenous targets is still limiting. Therefore, an attempt is made to decipher NO signaling in cold treated Brassica juncea seedlings. Treatment of seedlings with substrate, cofactor and inhibitor of Nitric-oxide synthase and nitrate reductase (NR), indicated NR mediated NO biosynthesis in cold. Analysis of the in vivo thiols showed depletion of low molecular weight thiols and enhancement of available protein thiols, suggesting redox changes. To have a detailed view, S-nitrosylation analysis was done using biotin switch technique (BST) and avidin-affinity chromatography. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is S-nitrosylated and therefore, is identified as target repeatedly due to its abundance. It also competes out low abundant proteins which are important NO signaling components. Therefore, RuBisCO was removed (over 80%) using immunoaffinity purification. Purified S-nitrosylated RuBisCO depleted proteins were resolved on 2-D gel as 110 spots, including 13 new, which were absent in the crude S-nitrosoproteome. These were identified by nLC-MS/MS as thioredoxin, fructose biphosphate aldolase class I, myrosinase, salt responsive proteins, peptidyl-prolyl cis-trans isomerase and malate dehydrogenase. Cold showed differential S-nitrosylation of 15 spots, enhanced superoxide dismutase activity (via S-nitrosylation) and promoted the detoxification of superoxide radicals. Increased S-nitrosylation of glyceraldehyde-3-phosphate dehydrogenase sedoheptulose-biphosphatase, and fructose biphosphate aldolase, indicated regulation of Calvin cycle by S-nitrosylation. The results showed that RuBisCO depletion improved proteome coverage and provided clues for NO signaling in cold. PMID:24032038

  5. New ammunition for the proteomic reactor: strong anion exchange beads and multiple enzymes enhance protein identification and sequence coverage.

    PubMed

    Zhou, Hu; Hou, Weimin; Lambert, Jean-Philippe; Figeys, Daniel

    2010-08-01

    The enrichment and processing of proteomic samples prior to multi-dimensional chromatography remain a challenge in 'gel-free' proteomics. We previously reported the development of a microfluidic device called the "proteomic reactor" that relied on enriching proteins by using strong cation exchange (SCX) followed by trypsin digestion in an interstitial volume as little as 50 nL. Here, we report a novel proteomic reactor that is based on polymeric strong anion exchange (SAX) material to analyse proteomic samples. We also compare the performance of the SAX proteomic reactor to our previously reported SCX proteomic reactor for analysing complex yeast proteomes. Our results indicate that the SAX protein reactor preferentially identifies more acidic peptides and proteins compared to the SCX reactor. We show that the SAX and SCX reactors are complementary and that their combination increases the number of unique peptides and proteins identified by 50%. Furthermore, we show that the number of protein identified can be increased further by up to 40% using different proteolytic enzymes on the proteomic reactor.

  6. Gains attained in malaria control coverage within settings earmarked for pre-elimination: malaria indicator and prevalence surveys 2012, Eritrea.

    PubMed

    Berhane, Araia; Mihreteab, Selam; Ahmed, Hagos; Zehaie, Assefash; Abdulmumini, Usman; Chanda, Emmanuel

    2015-11-20

    Eritrea, like most countries in sub-Saharan Africa, has expended much effort towards malaria control with the view of transitioning from reduction of the disease burden to elimination. This paper reports on the level of achievement as highlighted by the follow-on, malaria-endemic area representative, survey that aimed to provide data and to assess progress on malaria indicators and parasite prevalence at household level across the country. In 2012, data were collected using a two-stage stratified cluster random sample of 1887 households in 96 clusters (villages in rural areas and census enumeration areas in urban centers) during a malaria indicator and prevalence survey in Eritrea. The survey determined parasite prevalence in vulnerable population groups and evaluated coverage, use and access to malaria control services. Standardized Roll-Back Malaria Monitoring and Evaluation Reference Group household and women's questionnaires were adapted to the local situation and used for collection of data that were analysed and summarized using descriptive statistics. The results of the survey showed that 90% (95% CI 89-91) of households owned at least one mosquito net. The proportion of the population with access to an insecticide-treated net (ITN) in their household was 55% (95% CI 54-56). The utilization of ITNs was 67% (95% CI 65-70) for children under 5 years and 60% (95% CI 58-63) for pregnant women (OR: 0. 73(95% CI 0.62-0.85); P = 0.52). Only 28% (95% CI 26-30) of households were covered by indoor residual spraying (IRS) the previous year with significant heterogeneity by zoba (Debub 50 % (95% CI 45-54) vs Gash Barka 32 % (95% CI 28-36); OR = 0. 47 (95% CI 0.36-0.61), P = 0.05). Malaria parasite prevalence was low; 1.1% (95% CI 0.9-1.3) in the general population and 1.4% (95% CI 1.0-2.0) in children under five and 0.7% (95% CI 0.4-1.1) among women aged 15-49 years. Only 19% (95% CI 15-26) of children under five had fever in the 2 weeks preceding the survey, with 61

  7. A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva

    PubMed Central

    Bandhakavi, Sricharan; Stone, Matthew D.; Onsongo, Getiria; Van Riper, Susan K.; Griffin, Timothy J.

    2009-01-01

    Comprehensive identification of proteins in whole human saliva is critical for appreciating its full diagnostic potential. However, this is challenged by the large dynamic range of protein abundance within this fluid. To address this problem, we used an analysis platform that coupled hexapeptide libraries for dynamic range compression (DRC) with three-dimensional (3D) peptide fractionation. This approach identified 2340 proteins in whole saliva and represents the largest saliva proteomic dataset generated using a single analysis platform. Three dimensional peptide fractionation involving sequential steps of preparative IEF, strong cation exchange, and capillary reversed phase liquid chromatography was essential for maximizing gains from DRC. Compared to saliva not treated with hexapeptide libraries, DRC substantially increased identified proteins across physicochemical and functional categories. Approximately 20% of total salivary proteins are also seen in plasma, and proteins in both fluids show comparable functional diversity and disease-linkage. However, for a subset of diseases, saliva has higher apparent diagnostic potential. These results expand the potential for whole saliva in health monitoring/diagnostics and provide a general platform for improving proteomic coverage of complex biological samples. PMID:19813771

  8. Mouse-Specific Tandem IgY7-SuperMix Immunoaffinity Separations for Improved LC-MS/MS Coverage of the Plasma Proteome

    PubMed Central

    Zhou, Jian-Ying; Petritis, Brianne O.; Petritis, Konstantinos; Norbeck, Angela D.; Weitz, Karl K.; Moore, Ronald J.; Camp, David G.; Kulkarni, Rohit N.; Smith, Richard D.; Qian, Wei-Jun

    2009-01-01

    We report on a mouse specific SuperMix immunoaffinity separation system for separating low abundance proteins from high and moderate abundance proteins in mouse plasma. When applied in tandem with a mouse IgY7 column that removes the seven most abundant proteins in plasma, the SuperMix column captures more than 100 additional moderate abundance proteins, thus allowing significant enrichment of low abundance proteins in the flow-through fraction. A side-by-side comparison of results obtained from 2D-LC-MS/MS analyses of flow-through samples from IgY7 and SuperMix columns revealed a nearly two-fold improvement in the overall proteome coverage. Detection of low abundance proteins was also enhanced, as evidenced by a more than two-fold increase in the coverage of cytokines, growth factors, and other low abundance proteins. Moreover, the tandem separations are automated, reproducible, and allow effective identification of protein abundance differences from LC-MS/MS analyses. Considering the overall reproducibility and increased sensitivity using the IgY7-SuperMix separation system, we anticipate broad applications of this strategy for biomarker discovery using mouse models. PMID:19722698

  9. High pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis

    SciTech Connect

    Yang, Feng; Shen, Yufeng; Camp, David G.; Smith, Richard D.

    2012-04-01

    Orthogonal high-resolution separations are critical for attaining improved analytical dynamic ranges of proteome measurements. Concatenated high pH reversed phase liquid chromatography affords better separations than the strong cation exchange conventionally applied for two-dimensional shotgun proteomic analysis. For example, concatenated high pH reversed phase liquid chromatography increased identification coverage for peptides (e.g., by 1.8-fold) and proteins (e.g., by 1.6-fold) in shotgun proteomics analyses of a digested human protein sample. Additional advantages of concatenated high pH RPLC include improved protein sequence coverage, simplified sample processing, and reduced sample losses, making this an attractive first dimension separation strategy for two-dimensional proteomics analyses.

  10. Advanced proteomic liquid chromatography

    SciTech Connect

    Xie, Fang; Smith, Richard D.; Shen, Yufeng

    2012-10-26

    Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput.

  11. Covering complete proteomes with X-ray structures: a current snapshot

    SciTech Connect

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-11-01

    The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  12. Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer.

    PubMed

    Wei, Wei; Luo, Weijia; Wu, Feilin; Peng, Xuehui; Zhang, Yao; Zhang, Manli; Zhao, Yan; Su, Na; Qi, YingZi; Chen, Lingsheng; Zhang, Yangjun; Wen, Bo; He, Fuchu; Xu, Ping

    2016-11-04

    Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive to MPs exploration, especially for low-abundance proteins. In this study, Q-Exactive HF (HF) was used to survey proteins from the same testis tissues separated by two separating methods (tricine- and glycine-SDS-PAGE), as previously described. A total of 8526 proteins were identified, of which more low-abundance proteins were uniquely detected in HF data but not in our previous LTQ Orbitrap Velos (Velos) reanalysis data. Further transcriptomics analysis showed that these uniquely identified proteins by HF also had lower expression at the mRNA level. Of the 81 total identified MPs, 74 and 39 proteins were listed as MPs in HF and Velos data sets, respectively. Among the above MPs, 47 proteins (43 neXtProt PE2 and 4 PE3) were ranked as confirmed MPs after verifying with the stringent spectra match and isobaric and single amino acid variants filtering. Functional investigation of these 47 MPs revealed that 11 MPs were testis-specific proteins and 7 MPs were involved in spermatogenesis process. Therefore, we concluded that higher scanning speed and resolution of HF might be factors for improving the low-abundance MP identification in future C-HPP studies. All mass-spectrometry data from this study have been deposited in the ProteomeXchange with identifier PXD004092.

  13. Shotgun proteomics in neuroscience.

    PubMed

    Liao, Lujian; McClatchy, Daniel B; Yates, John R

    2009-07-16

    Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.

  14. Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

    PubMed Central

    Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

    2011-01-01

    The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

  15. Untapped Potential of Disordered Proteins in Current Druggable Human Proteome.

    PubMed

    Hu, Gang; Wu, Zhonghua; Wang, Kui; Uversky, Vladimir N; Kurgan, Lukasz

    2016-01-01

    Current efforts in design and characterization of drugs often rely on the structure of their protein targets. However, a large fraction of proteins lack unique 3-D structures and exist as highly dynamic structural ensembles. These intrinsically disordered proteins are involved in pathogenesis of various human diseases and are highly abundant in eukaryotes. Based on a comprehensive analysis of the current druggable human proteome covering 12 drug classes and 18 major classes of drug targets we show a significant bias toward high structural coverage and low abundance of intrinsic disorder. We review reasons for this bias including widespread use of the structural information in various stages of drug development and characterization process and difficulty with attaining structures for the intrinsically disordered proteins. We also discuss future of intrinsically disordered proteins as drug targets. Given the overall high disorder content of the human proteome and current bias of the druggable human proteome toward structural proteins, it is inevitable that disordered proteins will have to raise up on the list of prospective drug targets. The protein disorder-assisted drug design can draw from current rational drug design techniques and would also need novel approaches that no longer rely on a unique protein structure.

  16. Covering complete proteomes with X-ray structures: A current snapshot

    DOE PAGES

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; ...

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

  17. Covering complete proteomes with X-ray structures: A current snapshot

    SciTech Connect

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  18. Covering the Complete Proteomes with X-ray Structures - a Current Snapshot

    SciTech Connect

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Abstract Structural genomics programs developed and applied structure determination pipelines to a wide range of protein targets, facilitating visualization of macromolecular interactions and understanding of their molecular and biochemical functions. We investigate a fundamental question whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography. We performed a first-of-its-kind large scale analysis of crystallization propensity for all proteins encoded in 1,953 fully sequenced genomes. We show that current X-ray crystallography know-how combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling) with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms with 19% in eukaryotes, 35% in bacteria, 49% in archaea, and viruses following coverage values of their hosts. We show that the crystallization propensities of proteomes are distinctive of the taxonomic superkingdoms. The use of knowledge-based target selection is shown to substantially increase ability to produce X-ray structures. We demonstrate that the human proteome has one of the highest attainable coverage values among eukaryotes and we identify GPCR membrane proteins suitable for the X-ray structure determination.

  19. Covering complete proteomes with X-ray structures: a current snapshot

    PubMed Central

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-01-01

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined. PMID:25372670

  20. Sports Coverage

    ERIC Educational Resources Information Center

    Crook, James

    1974-01-01

    Compares the results of a national and state survey on student participation in sports and attendence at sports events at the high school level, concluding that the publications staff should use such data to determine sports coverage in the school press. (RB)

  1. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.

    PubMed

    Gardy, J L; Laird, M R; Chen, F; Rey, S; Walsh, C J; Ester, M; Brinkman, F S L

    2005-03-01

    PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization. An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size. Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. psort-mail@sfu.ca, brinkman@sfu.ca http://www.psort.org/psortb/supplementaryinfo.html.

  2. Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

    PubMed

    Menschaert, Gerben; Van Criekinge, Wim; Notelaers, Tineke; Koch, Alexander; Crappé, Jeroen; Gevaert, Kris; Van Damme, Petra

    2013-07-01

    An increasing number of studies involve integrative analysis of gene and protein expression data, taking advantage of new technologies such as next-generation transcriptome sequencing and highly sensitive mass spectrometry (MS) instrumentation. Recently, a strategy, termed ribosome profiling (or RIBO-seq), based on deep sequencing of ribosome-protected mRNA fragments, indirectly monitoring protein synthesis, has been described. We devised a proteogenomic approach constructing a custom protein sequence search space, built from both Swiss-Prot- and RIBO-seq-derived translation products, applicable for MS/MS spectrum identification. To record the impact of using the constructed deep proteome database, we performed two alternative MS-based proteomic strategies as follows: (i) a regular shotgun proteomic and (ii) an N-terminal combined fractional diagonal chromatography (COFRADIC) approach. Although the former technique gives an overall assessment on the protein and peptide level, the latter technique, specifically enabling the isolation of N-terminal peptides, is very appropriate in validating the RIBO-seq-derived (alternative) translation initiation site profile. We demonstrate that this proteogenomic approach increases the overall protein identification rate 2.5% (e.g. new protein products, new protein splice variants, single nucleotide polymorphism variant proteins, and N-terminally extended forms of known proteins) as compared with only searching UniProtKB-SwissProt. Furthermore, using this custom database, identification of N-terminal COFRADIC data resulted in detection of 16 alternative start sites giving rise to N-terminally extended protein variants besides the identification of four translated upstream ORFs. Notably, the characterization of these new translation products revealed the use of multiple near-cognate (non-AUG) start codons. As deep sequencing techniques are becoming more standard, less expensive, and widespread, we anticipate that mRNA sequencing

  3. Primer: Shotgun Proteomics in Neuroscience

    PubMed Central

    Liao, Lujian; McClatchy, Daniel B.; Yates, John R.

    2009-01-01

    Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and post-translational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun proteomics based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and post-translational modification analysis and discusses several strategies to improve the coverage of the proteome. PMID:19607789

  4. Sideline Coverage

    PubMed Central

    Gould, Sara J.; Cardone, Dennis A.; Munyak, John; Underwood, Philipp J.; Gould, Stephen A.

    2014-01-01

    Context: Sidelines coverage presents unique challenges in the evaluation of injured athletes. Health care providers may be confronted with the question of when to obtain radiographs following an injury. Given that most sidelines coverage occurs outside the elite level, radiographs are not readily available at the time of injury, and the decision of when to send a player for radiographs must be made based on physical examination. Clinical tools have been developed to aid in identifying injuries that are likely to result in radiographically important fractures or dislocations. Evidence Acquisition: A search for the keywords x-ray and decision rule along with the anatomic locations shoulder, elbow, wrist, knee, and ankle was performed using the PubMed database. No limits were set regarding year of publication. We selected meta-analyses, randomized controlled trials, and survey results. Our selection focused on the largest, most well-studied published reports. We also attempted to include studies that reported the application of the rules to the field of sports medicine. Study Design: Retrospective literature review. Level of Evidence: Level 4. Results: The Ottawa Foot and Ankle Rules have been validated and implemented and are appropriate for use in both pediatric and adult populations. The Ottawa Knee Rules have been widely studied, validated, and accepted for evaluation of knee injuries. There are promising studies of decision rules for clinically important fractures of the wrist, but these studies have not been validated. The elbow has been evaluated with good outcomes via the elbow extension test, which has been validated in both single and multicenter studies. Currently, there are no reliable clinical decision tools for traumatic sports injuries to the shoulder to aid in the decision of when to obtain radiographs. Conclusion: Clinical decision tools have been developed to aid in the diagnosis and management of injuries commonly sustained during sporting events

  5. Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

    SciTech Connect

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

    2011-07-22

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

  6. Nanoscale Proteomics

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Masselon, Christophe D.; Pasa-Tolic, Liljiana; Camp, David G.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2004-02-01

    This paper describes efforts to develop a liquid chromatography (LC)/mass spectrometry (MS) technology for ultra-sensitive proteomics studies, i.e. nanoscale proteomics. The approach combines high-efficiency nano-scale LC with advanced MS, including high sensitivity and high resolution Fourier transform ion cyclotron resonance (FTICR) MS, to perform both single-stage MS and tandem MS (MS/MS) proteomic analyses. The technology developed enables large-scale protein identification from nanogram size proteomic samples and characterization of more abundant proteins from sub-picogram size complex samples. Protein identification in such studies using MS is feasible from <75 zeptomole of a protein, and the average proteome measurement throughput is >200 proteins/h and ~3 h/sample. Higher throughput (>1000 proteins/h) and more sensitive detection limits can be obtained using a “accurate mass and time” tag approach developed at our laboratory. These capabilities lay the foundation for studies from single or limited numbers of cells.

  7. Mapping Titan Cloud Coverage

    NASA Image and Video Library

    2010-09-21

    This graphic, constructed from data obtained by NASA Cassini spacecraft, shows the percentage of cloud coverage across the surface of Saturn moon Titan. The color scale from black to yellow signifies no cloud coverage to complete cloud coverage.

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

    PubMed Central

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

    2007-01-01

    Given the growing interest in applying genomic and proteomic approaches for studying the mammalian brain using mouse models, we hereby present a global proteomic approach for analyzing brain tissue and for the first time a comprehensive characterization of the whole mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 non-redundant proteins (∼34% of the predicted mouse proteome). 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models. The proteomic approach presented here may have broad applications for rapid proteomic analyses of various mouse models of human brain diseases. PMID:16457602

  9. The speciation of the proteome

    PubMed Central

    Jungblut, Peter R; Holzhütter, Hermann G; Apweiler, Rolf; Schlüter, Hartmut

    2008-01-01

    Introduction In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function. Discussion Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. Conclusion To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today. PMID:18638390

  10. Air traffic coverage

    SciTech Connect

    George, L.L.

    1988-09-16

    The Federal Aviation Administration plans to consolidate several hundred air traffic control centers and TRACONs into area control facilities while maintaining air traffic coverage. This paper defines air traffic coverage, a performance measure of the air traffic control system. Air traffic coverage measures performance without controversy regarding delay and collision probabilities and costs. Coverage measures help evaluate alternative facility architectures and help schedule consolidation. Coverage measures also help evaluate protocols for handling one facility's air traffic to another facility in case of facility failure. Coverage measures help evaluate radar, communications and other air traffic control systems and procedures. 4 refs., 2 figs.,

  11. Proteome | Office of Cancer Clinical Proteomics Research

    Cancer.gov

    A proteome is the entire complement of proteins, including modifications made to a particular set of proteins, produced by an organism or a cellular system. This will vary with time and distinct requirements such as growth conditions and stresses, and thus is highly dynamic and spatial. Proteomics is the study of the proteome.

  12. Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein-Profiling Technologies

    PubMed Central

    Bruce, Can; Stone, Kathryn; Gulcicek, Erol; Williams, Kenneth

    2013-01-01

    Mass spectrometry has become a major tool in the study of proteomes. The analysis of proteolytic peptides and their fragment ions by this technique enables the identification and quantitation of the precursor proteins in a mixture. However, deducing chemical structures and then protein sequences from mass-to-charge ratios is a challenging computational task. Software tools incorporating powerful algorithms and statistical methods improved our ability to process the large quantities of proteomics data. Repositories of spectral data make both data analysis and experimental design more efficient. New approaches in quantitative and statistical proteomics make possible a greater coverage of the proteome, the identification of more post-translational modifications and a greater sensitivity in the quantitation of targeted proteins. PMID:23504934

  13. Women's Health Insurance Coverage

    MedlinePlus

    ... Medicaid expansions, private insurance reforms, and premium tax credits. This factsheet reviews major sources of coverage for ... individually purchased insurance market by offering premium tax credits to help individuals purchase coverage in state-based ...

  14. Women's Health Insurance Coverage

    MedlinePlus

    ... Home Women's Health Policy Women’s Health Insurance Coverage Women’s Health Insurance Coverage Oct 21, 2016 Facebook Twitter ... for certain low-income uninsured women. 11 Uninsured Women Approximately 11% of women ages 19 to 64 ( ...

  15. Seed proteomics.

    PubMed

    Miernyk, Ján A; Hajduch, Martin

    2011-04-01

    Seeds comprise a protective covering, a small embryonic plant, and a nutrient-storage organ. Seeds are protein-rich, and have been the subject of many mass spectrometry-based analyses. Seed storage proteins (SSP), which are transient depots for reduced nitrogen, have been studied for decades by cell biologists, and many of the complicated aspects of their processing, assembly, and compartmentation are now well understood. Unfortunately, the abundance and complexity of the SSP requires that they be avoided or removed prior to gel-based analysis of non-SSP. While much of the extant data from MS-based proteomic analysis of seeds is descriptive, it has nevertheless provided a preliminary metabolic picture explaining much of their biology. Contemporary studies are moving more toward analysis of protein interactions and posttranslational modifications, and functions of metabolic networks. Many aspects of the biology of seeds make then an attractive platform for heterologous protein expression. Herein we present a broad review of the results from the proteomic studies of seeds, and speculate on a potential future research directions. Copyright © 2010 Elsevier B.V. All rights reserved.

  16. Capillary electrophoresis-based proteomic techniques for biomarker discovery.

    PubMed

    Fang, Xueping; Wang, Chenchen; Lee, Cheng S

    2013-01-01

    Besides proteome complexity, the greatest bioanalytical challenge facing comprehensive proteomic analysis, particularly in the identification of low abundance proteins, is related to the large variation of protein relative abundances. In contrast to universally enriching all analytes by a similar degree, the result of the capillary isotachophoresis (CITP) stacking process is that major components may be diluted, but trace compounds are concentrated. Such selective enhancement toward low abundance proteins drastically reduces the range of relative protein abundances within complex proteomes and greatly enhances the resulting proteome coverage. Furthermore, CITP offers seamless combination with nano-reversed phase liquid chromatography (nano-RPLC) as two highly resolving and completely orthogonal separation techniques critically needed for analyzing complex proteomes.

  17. Biomarker Discovery in Mass Spectrometry-based Urinary Proteomics

    PubMed Central

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

    2016-01-01

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

  18. Design principles for clinical network-based proteomics.

    PubMed

    Goh, Wilson Wen Bin; Wong, Limsoon

    2016-07-01

    Integrating biological networks with proteomics is a tantalizing option for system-level analysis; for example it can help remove false-positives from proteomics data and improve coverage by detecting false-negatives, as well as resolving inconsistent inter-sample protein expression due to biological heterogeneity. Yet, designing a robust network-based analysis strategy on proteomics data is nontrivial. The issues include dealing with test set bias caused by, for example, inappropriate normalization procedure, devising appropriate benchmarking criteria and formulating statistically robust feature-selection techniques. Given the increasing importance of proteomics in contemporary clinical studies, more powerful network-based approaches are needed. We provide some design principles and considerations that can help achieve this, while taking into account the idiosyncrasies of proteomics data.

  19. Proteome-Wide Analysis and Diel Proteomic Profiling of the Cyanobacterium Arthrospira platensis PCC 8005

    PubMed Central

    Matallana-Surget, Sabine; Derock, Jérémy; Leroy, Baptiste; Badri, Hanène; Deschoenmaeker, Frédéric; Wattiez, Ruddy

    2014-01-01

    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. PMID:24914774

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

    PubMed

    Matallana-Surget, Sabine; Derock, Jérémy; Leroy, Baptiste; Badri, Hanène; Deschoenmaeker, Frédéric; Wattiez, Ruddy

    2014-01-01

    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.

  1. Contemporary Network Proteomics and Its Requirements

    PubMed Central

    Goh, Wilson Wen Bin; Wong, Limsoon; Sng, Judy Chia Ghee

    2013-01-01

    The integration of networks with genomics (network genomics) is a familiar field. Conventional network analysis takes advantage of the larger coverage and relative stability of gene expression measurements. Network proteomics on the other hand has to develop further on two critical factors: (1) expanded data coverage and consistency, and (2) suitable reference network libraries, and data mining from them. Concerning (1) we discuss several contemporary themes that can improve data quality, which in turn will boost the outcome of downstream network analysis. For (2), we focus on network analysis developments, specifically, the need for context-specific networks and essential considerations for localized network analysis. PMID:24833333

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

    PubMed

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

    2016-06-01

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

  3. Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case.

    PubMed

    Lopez-Casado, Gloria; Covey, Paul A; Bedinger, Patricia A; Mueller, Lukas A; Thannhauser, Theodore W; Zhang, Sheng; Fei, Zhangjun; Giovannoni, James J; Rose, Jocelyn K C

    2012-03-01

    Effective proteome profiling is generally considered to depend heavily on the availability of a high-quality DNA reference database. As such, proteomics has long been taxonomically restricted, with limited inroads being made into the proteomes of "non-model" organisms. However, next generation sequencing (NGS), and particularly RNA-Seq, now allows deep coverage detection of expressed genes at low cost, which in turn potentially facilitates the matching of peptide mass spectra with cognate gene sequence. To test this, we performed a quantitative analysis of the proteomes of pollen from domesticated tomato (Solanum lycopersicum) and two wild relatives that exhibit differences in mating systems and in interspecific reproductive barriers. Using a custom tomato RNA-Seq database created through 454 pyrosequencing, more than 1200 proteins were identified, with subsets showing expression differences between genotypes or in the accumulation of the corresponding transcripts. Importantly, no major qualitative or quantitative differences were observed in the characterized proteomes when mass spectra were used to interrogate either a highly curated community database of tomato sequences generated through traditional sequencing technologies, or the RNA-Seq database. We conclude that RNA-Seq provides a cost-effective and robust platform for protein identification and will be increasingly valuable to the field of proteomics. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Proteome analysis of Apis mellifera royal jelly.

    PubMed

    Schönleben, Simone; Sickmann, Albert; Mueller, Martin J; Reinders, Joerg

    2007-10-01

    Royal jelly plays a pivotal role in the development of honey bee larvae. However, while various health promoting properties of royal jelly have been reported, most of the active substances within royal jelly that lead to these properties are still unknown. Since up to 50% (dry mass) of royal jelly is protein, royal jelly proteome analysis is a promising starting point for attempts to identify the proteins that provide health-promoting effects. However, the comprehensive analysis of royal jelly proteins is hampered by the enormous abundance of some proteins in the major royal jelly protein family, which constitutes 80-90% of the royal jelly proteome. The high heterogeneity of these proteins is an additional challenge for proteomic analysis, since it necessitates the use of analytical techniques that provide high resolution and a wide dynamic range. The application of individual methods such as 2D-PAGE or multidimensional chromatography can only yield certain subpopulations of a proteome due to the specific bias of each method. We applied different methods for the prefractionation and separation of royal jelly proteins in order to circumvent the shortcomings of the individual techniques and achieve a high coverage of the royal jelly proteome. In this way, we were able to identify 20 different proteins in total, as well as to show a very high degree of cleavage of different proteins of the major royal jelly protein family. Furthermore, we investigated the protein phosphorylation of royal jelly proteins, and identified and located two phosphorylation sites within venom protein 2.

  5. Medicare Prescription Drug Coverage

    MedlinePlus

    ... people also have to pay an additional monthly cost. Private companies provide Medicare prescription drug coverage. You choose the drug plan you like best. Whether or not you should sign up depends on how good your current coverage is. You need to sign up as ...

  6. Education Leaders Applaud ATTAIN Act

    ERIC Educational Resources Information Center

    Curriculum Review, 2007

    2007-01-01

    This article talks about Achievement Through Technology and Innovation (ATTAIN) Act, a bill introduced by Senators Bingaman (D-NM), Burr (R-NC), and Murray (D-WA) and applauded by a coalition of education and industry groups. The proposed ATTAIN Act is similar to its companion in the House (HR 2449), and builds upon the Enhancing Education Through…

  7. Stuttering Severity and Educational Attainment

    ERIC Educational Resources Information Center

    O'Brian, Sue; Jones, Mark; Packman, Ann; Menzies, Ross; Onslow, Mark

    2011-01-01

    Purpose: This study investigated the relationship between self-reported stuttering severity ratings and educational attainment. Method: Participants were 147 adults seeking treatment for stuttering. At pretreatment assessment, each participant reported the highest educational level they had attained and rated their typical and worst stuttering…

  8. Income Sustainability through Educational Attainment

    ERIC Educational Resources Information Center

    Carlson, Ronald H.; McChesney, Christopher S.

    2015-01-01

    The authors examined the sustainability of income, as it relates to educational attainment, from the two recent decades, which includes three significant economic downturns. The data was analyzed to determine trends in the wealth gap, parsed by educational attainment and gender. Utilizing the data from 1991 through 2010, predictions in changes in…

  9. Stuttering Severity and Educational Attainment

    ERIC Educational Resources Information Center

    O'Brian, Sue; Jones, Mark; Packman, Ann; Menzies, Ross; Onslow, Mark

    2011-01-01

    Purpose: This study investigated the relationship between self-reported stuttering severity ratings and educational attainment. Method: Participants were 147 adults seeking treatment for stuttering. At pretreatment assessment, each participant reported the highest educational level they had attained and rated their typical and worst stuttering…

  10. Degree Attainment among Adult Learners

    ERIC Educational Resources Information Center

    O'Conor, Maureen A.

    2009-01-01

    The purpose of this study is to expand understanding and discover knowledge about degree attainment among adult learners. This qualitative inquiry explores what recent non-traditional-age bachelor's degree recipients report contributes to attaining the degree. Professional research and expert material on demographics, motivation, challenges and…

  11. Ethnicity, Gender, Deprivation and Low Educational Attainment in England: Political Arithmetic, Ideological Stances and the Deficient Society

    ERIC Educational Resources Information Center

    Parsons, Carl

    2016-01-01

    Attainment data on England's school pupils are more extensive in coverage, detail, quantity, accessibility and of higher quality than monitoring statistics routinely available in other European countries. These data facilitate investigation of low attainment in England's schools and its relationship to ethnicity, gender and poverty. This article…

  12. Ethnicity, Gender, Deprivation and Low Educational Attainment in England: Political Arithmetic, Ideological Stances and the Deficient Society

    ERIC Educational Resources Information Center

    Parsons, Carl

    2016-01-01

    Attainment data on England's school pupils are more extensive in coverage, detail, quantity, accessibility and of higher quality than monitoring statistics routinely available in other European countries. These data facilitate investigation of low attainment in England's schools and its relationship to ethnicity, gender and poverty. This article…

  13. A 2-D guinea pig lung proteome map

    USDA-ARS?s Scientific Manuscript database

    Guinea pigs represent an important model for a number of infectious and non-infectious pulmonary diseases. The guinea pig genome has recently been sequenced to full coverage, opening up new research avenues using genomics, transcriptomics and proteomics techniques in this species. In order to furth...

  14. Women's Health Insurance Coverage

    MedlinePlus

    ... to be updated by the end of 2016. Abortion services are explicitly prohibited from being included as ... 25 states have laws banning coverage of most abortions from the plans available through the state Marketplaces, ...

  15. Completed | Office of Cancer Clinical Proteomics Research

    Cancer.gov

    Prior to the current Clinical Proteomic Tumor Analysis Consortium (CPTAC), previously funded initiatives associated with clinical proteomics research included: Clinical Proteomic Tumor Analysis Consortium (CPTAC 2.0) Clinical Proteomic Technologies for Cancer Initiative (CPTC) Mouse Proteomic Technologies Initiative

  16. Toward an Optimized Workflow for Middle-Down Proteomics.

    PubMed

    Cristobal, Alba; Marino, Fabio; Post, Harm; van den Toorn, Henk W P; Mohammed, Shabaz; Heck, Albert J R

    2017-03-21

    Mass spectrometry (MS)-based proteomics workflows can crudely be classified into two distinct regimes, targeting either relatively small peptides (i.e., 0.7 kDa < Mw < 3.0 kDa) or small to medium sized intact proteins (i.e., 10 kDa < Mw < 30 kDa), respectively, termed bottom-up and top-down proteomics. Recently, a niche has started to be explored covering the analysis of middle-range peptides (i.e., 3.0 kDa < Mw < 10 kDa), aptly termed middle-down proteomics. Although middle-down proteomics can follow, in principle, a modular workflow similar to that of bottom-up proteomics, we hypothesized that each of these modules would benefit from targeted optimization to improve its overall performance in the analysis of middle-range sized peptides. Hence, to generate middle-range sized peptides from cellular lysates, we explored the use of the proteases Asp-N and Glu-C and a nonenzymatic acid induced cleavage. To increase the depth of the proteome, a strong cation exchange (SCX) separation, carefully tuned to improve the separation of longer peptides, combined with reversed phase-liquid chromatography (RP-LC) using columns packed with material possessing a larger pore size, was used. Finally, after evaluating the combination of potentially beneficial MS settings, we also assessed the peptide fragmentation techniques, including higher-energy collision dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer combined with higher-energy collision dissociation (EThcD), for characterization of middle-range sized peptides. These combined improvements clearly improve the detection and sequence coverage of middle-range peptides and should guide researchers to explore further how middle-down proteomics may lead to an improved proteome coverage, beneficial for, among other things, the enhanced analysis of (co-occurring) post-translational modifications.

  17. Toward an Optimized Workflow for Middle-Down Proteomics

    PubMed Central

    2017-01-01

    Mass spectrometry (MS)-based proteomics workflows can crudely be classified into two distinct regimes, targeting either relatively small peptides (i.e., 0.7 kDa < Mw < 3.0 kDa) or small to medium sized intact proteins (i.e., 10 kDa < Mw < 30 kDa), respectively, termed bottom-up and top-down proteomics. Recently, a niche has started to be explored covering the analysis of middle-range peptides (i.e., 3.0 kDa < Mw < 10 kDa), aptly termed middle-down proteomics. Although middle-down proteomics can follow, in principle, a modular workflow similar to that of bottom-up proteomics, we hypothesized that each of these modules would benefit from targeted optimization to improve its overall performance in the analysis of middle-range sized peptides. Hence, to generate middle-range sized peptides from cellular lysates, we explored the use of the proteases Asp-N and Glu-C and a nonenzymatic acid induced cleavage. To increase the depth of the proteome, a strong cation exchange (SCX) separation, carefully tuned to improve the separation of longer peptides, combined with reversed phase-liquid chromatography (RP-LC) using columns packed with material possessing a larger pore size, was used. Finally, after evaluating the combination of potentially beneficial MS settings, we also assessed the peptide fragmentation techniques, including higher-energy collision dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer combined with higher-energy collision dissociation (EThcD), for characterization of middle-range sized peptides. These combined improvements clearly improve the detection and sequence coverage of middle-range peptides and should guide researchers to explore further how middle-down proteomics may lead to an improved proteome coverage, beneficial for, among other things, the enhanced analysis of (co-occurring) post-translational modifications. PMID:28233997

  18. Bottom-up and Shotgun Proteomics to Identify a Comprehensive Cochlear Proteome

    PubMed Central

    Darville, Lancia N.F.; Sokolowski, Bernd H.A.

    2014-01-01

    Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that transduce the mechanical energy of sound into an electro-chemical energy processed by the peripheral and central nervous systems. Several proteomic techniques have been developed to study the cochlear inner ear, such as two-dimensional difference gel electrophoresis (2D-DIGE), antibody microarray, and mass spectrometry (MS). MS is the most comprehensive and versatile tool in proteomics and in conjunction with separation methods can provide an in-depth proteome of biological samples. Separation methods combined with MS has the ability to enrich protein samples, detect low molecular weight and hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. Different digestion strategies can be applied to whole lysate or to fractionated protein lysate to enhance peptide and protein sequence coverage. Utilization of different separation techniques, including strong cation exchange (SCX), reversed-phase (RP), and gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) can be applied to reduce sample complexity prior to MS analysis for protein identification. PMID:24638115

  19. Bottom-up and shotgun proteomics to identify a comprehensive cochlear proteome.

    PubMed

    Darville, Lancia N F; Sokolowski, Bernd H A

    2014-03-07

    Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that transduce the mechanical energy of sound into an electro-chemical energy processed by the peripheral and central nervous systems. Several proteomic techniques have been developed to study the cochlear inner ear, such as two-dimensional difference gel electrophoresis (2D-DIGE), antibody microarray, and mass spectrometry (MS). MS is the most comprehensive and versatile tool in proteomics and in conjunction with separation methods can provide an in-depth proteome of biological samples. Separation methods combined with MS has the ability to enrich protein samples, detect low molecular weight and hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. Different digestion strategies can be applied to whole lysate or to fractionated protein lysate to enhance peptide and protein sequence coverage. Utilization of different separation techniques, including strong cation exchange (SCX), reversed-phase (RP), and gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) can be applied to reduce sample complexity prior to MS analysis for protein identification.

  20. Large-scale Top-down Proteomics of the Human Proteome: Membrane Proteins, Mitochondria, and Senescence*

    PubMed Central

    Catherman, Adam D.; Durbin, Kenneth R.; Ahlf, Dorothy R.; Early, Bryan P.; Fellers, Ryan T.; Tran, John C.; Thomas, Paul M.; Kelleher, Neil L.

    2013-01-01

    Top-down proteomics is emerging as a viable method for the routine identification of hundreds to thousands of proteins. In this work we report the largest top-down study to date, with the identification of 1,220 proteins from the transformed human cell line H1299 at a false discovery rate of 1%. Multiple separation strategies were utilized, including the focused isolation of mitochondria, resulting in significantly improved proteome coverage relative to previous work. In all, 347 mitochondrial proteins were identified, including ∼50% of the mitochondrial proteome below 30 kDa and over 75% of the subunits constituting the large complexes of oxidative phosphorylation. Three hundred of the identified proteins were found to be integral membrane proteins containing between 1 and 12 transmembrane helices, requiring no specific enrichment or modified LC-MS parameters. Over 5,000 proteoforms were observed, many harboring post-translational modifications, including over a dozen proteins containing lipid anchors (some previously unknown) and many others with phosphorylation and methylation modifications. Comparison between untreated and senescent H1299 cells revealed several changes to the proteome, including the hyperphosphorylation of HMGA2. This work illustrates the burgeoning ability of top-down proteomics to characterize large numbers of intact proteoforms in a high-throughput fashion. PMID:24023390

  1. Soybean seed proteome rebalancing

    PubMed Central

    Herman, Eliot M.

    2014-01-01

    The soybean seed’s protein content and composition are regulated by both genetics and physiology. Overt seed protein content is specified by the genotype’s genetic framework and is selectable as a breeding trait. Within the genotype-specified protein content phenotype soybeans have the capacity to rebalance protein composition to create differing proteomes. Soybeans possess a relatively standardized proteome, but mutation or targeted engineering can induce large-scale proteome rebalancing. Proteome rebalancing shows that the output traits of seed content and composition result from two major types of regulation: genotype and post-transcriptional control of the proteome composition. Understanding the underlying mechanisms that specifies the seed proteome can enable engineering new phenotypes for the production of a high-quality plant protein source for food, feed, and industrial proteins. PMID:25232359

  2. Reducing protein oxidation in low-flow electrospray enables deeper investigation of proteoforms by top down proteomics.

    PubMed

    Kim, Kyunggon; Compton, Philip D; Toby, Timothy K; Thomas, Paul M; Wilkins, John T; Mutharasan, R Kannan; Kelleher, Neil L

    2015-09-01

    Enabling the implementation of top down proteomic techniques within clinical workflows requires a dramatic increase in sensitivity. It has been previously demonstrated that electrospray ionization (ESI) becomes more efficient with decreasing volumetric flow rates at the emitter. Therefore, narrow inner diameter (I.D.) columns used in front-end chromatographic separations yield increased sensitivity. However, the smaller cross-sectional area of a narrow I.D. column places a larger fraction of the eluent in fluid communication with the electrode within the high voltage union that facilitates electrospray ionization (ESI), leading to increased oxidation of solution-phase proteins. Oxidation of proteins alters their chemical state of the protein, complicates data analysis, and reduces the depth of proteome coverage attained in a typical top-down proteomics experiment. Excessive protein oxidation results in poor deconvolution and exact mass calculations from MS1 spectra, interferes with peak isolation for MS/MS fragmentation, and effectively reduces sensitivity by splitting ion current. All of these factors deteriorate top down mass spectral data quality, an effect that becomes more pronounced as column diameter decreases. Artificial protein oxidation can also mislead investigations of in vivo protein oxidation. All of these effects are accentuated in comparison to bottom up proteomics due to the increased probability of having oxidizable residues within a particular species with increasing mass. Herein, we describe a configuration (which we term "Low Protein Oxidation (LPOx)") for proteomics experiments created by re-arranging liquid chromatography (LC) plumbing and present its application to artificial protein oxidation and show a marked improvement in detection sensitivity. Using a standard mixture of five intact proteins, we demonstrate that the LPOx configuration reduces protein oxidation up to 90% using 50 μm I.D. columns when compared to a conventional LC

  3. Immunisation coverage, 2012.

    PubMed

    Hull, Brynley P; Dey, Aditi; Menzies, Rob I; Brotherton, Julia M; McIntyre, Peter B

    2014-09-30

    This, the 6th annual immunisation coverage report, documents trends during 2012 for a range of standard measures derived from Australian Childhood Immunisation Register (ACIR) data, and National Human Papillomavirus (HPV) Vaccination Program Register data. These include coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP) and coverage in adolescents and adults. The proportion of Australian children 'fully vaccinated' at 12, 24 and 60 months of age was 91.7%, 92.5% and 91.2%, respectively. For vaccines available on the NIP but not assessed during 2012 for 'fully vaccinated' status or for eligibility for incentive payments (rotavirus and pneumococcal at 12 months and meningococcal C and varicella at 24 months) coverage varied. Although pneumococcal vaccine had similar coverage at 12 months to other vaccines, coverage was lower for rotavirus at 12 months (83.6%) and varicella at 24 months (84.4%). Although 'fully vaccinated' coverage at 12 months of age was lower among Indigenous children than non-Indigenous children in all jurisdictions, the extent of the difference varied, reaching a 15 percentage point differential in South Australia but only a 0.4 percentage point differential in the Northern Territory. Overall, Indigenous coverage at 24 months of age exceeded that at 12 months of age nationally and for all jurisdictions, but as receipt of varicella vaccine at 18 months is excluded from calculations, this represents delayed immunisation, with some contribution from immunisation incentives. The 'fully vaccinated' coverage estimates for vaccinations due by 60 months of age for Indigenous children exceeded 90% at 91% in 2012. Unlike in 2011, at 60 months of age, there was no dramatic variation in coverage between Indigenous and non-Indigenous children for individual jurisdictions. As previously documented, vaccines recommended for Indigenous children only, hepatitis A and pneumococcal vaccine, had

  4. Yeast Proteome Analysis

    NASA Astrophysics Data System (ADS)

    Matros, Andrea; Mock, Hans-Peter

    Yeast organisms, and specifically Saccharomyces cerevisiae, have become model systems for many aspects in fundamental and applied research. Consistently, many papers have been published applying proteome techniques to study these organisms. The review will give an overview on the proteome research performed on yeast systems so far; however, due to the large number of publications, only selected reports can be cited neglecting many more interesting ones in the interest of space. The review will focus on research involving mass spectrom-etry as a basic proteome technique, although many more approaches are relevant for the functional characterization of proteins in the cell, e.g. the yeast two-hybrid system. We will provide an overview on yeasts as models in the context of pro-teome analysis, and explain the basic techniques currently applied in proteome approaches. The main part of the review will deal with a survey on the current status of proteomic studies in yeasts. In a first part of this chapter, we will deal with the currently available proteome maps of yeasts, and in the following part we will discuss studies dealing with fundamental aspects, but also mention proteome studies related to applied microbiology. Finally, we will envisage future perspectives of the proteome technology for studying yeasts, and draw major conclusion on the current status reached in this field of functional genomics.

  5. The search for coverage

    SciTech Connect

    Laseter, W.S.

    1993-06-01

    Anyone involved with the purchase or management of corporate liability insurance is familiar with the onerous pollution exclusions'' that accompany virtually all liability and property policies issued in recent years. As a result of these provisions, many businesses mistakenly presume their insurance program provides no coverage for environmental losses. Most companies, however, already own substantial sums of environmental coverage in the form of old comprehensive general liability (CGL) and first party, all risks'' property insurance policies issued before the introduction of pollution exclusions in the early 1970s. Unfortunately, due to records destruction policies, office moves, changes in ownership and other opportunities to lose files, most businesses have a difficult time reconstructing their past coverage.

  6. Quantitative plant proteomics.

    PubMed

    Bindschedler, Laurence V; Cramer, Rainer

    2011-02-01

    Quantitation is an inherent requirement in comparative proteomics and there is no exception to this for plant proteomics. Quantitative proteomics has high demands on the experimental workflow, requiring a thorough design and often a complex multi-step structure. It has to include sufficient numbers of biological and technical replicates and methods that are able to facilitate a quantitative signal read-out. Quantitative plant proteomics in particular poses many additional challenges but because of the nature of plants it also offers some potential advantages. In general, analysis of plants has been less prominent in proteomics. Low protein concentration, difficulties in protein extraction, genome multiploidy, high Rubisco abundance in green tissue, and an absence of well-annotated and completed genome sequences are some of the main challenges in plant proteomics. However, the latter is now changing with several genomes emerging for model plants and crops such as potato, tomato, soybean, rice, maize and barley. This review discusses the current status in quantitative plant proteomics (MS-based and non-MS-based) and its challenges and potentials. Both relative and absolute quantitation methods in plant proteomics from DIGE to MS-based analysis after isotope labeling and label-free quantitation are described and illustrated by published studies. In particular, we describe plant-specific quantitative methods such as metabolic labeling methods that can take full advantage of plant metabolism and culture practices, and discuss other potential advantages and challenges that may arise from the unique properties of plants.

  7. The Coverage Issue

    ERIC Educational Resources Information Center

    Yoshinobu, Stan; Jones, Matthew G.

    2012-01-01

    A significant issue mathematics instructors face is how to cover all the material. Mathematics teachers of all levels have some external and internal pressures to "get through" all the required material. The authors define "the coverage issue" to be the set of difficulties that arise in attempting to cover a lengthy list of topics. Principal among…

  8. The Coverage Issue

    ERIC Educational Resources Information Center

    Yoshinobu, Stan; Jones, Matthew G.

    2012-01-01

    A significant issue mathematics instructors face is how to cover all the material. Mathematics teachers of all levels have some external and internal pressures to "get through" all the required material. The authors define "the coverage issue" to be the set of difficulties that arise in attempting to cover a lengthy list of topics. Principal among…

  9. Coverage That Counts.

    ERIC Educational Resources Information Center

    Moss, Nancy

    1990-01-01

    As the shrinking pool of applicants forces colleges to adapt new approaches to recruiting, media campaigns are emerging as an effective way to send key messages to target audiences. Media relations can lend credibility (news coverage is considered more credible than advertising); save money; reach targeted areas; and communicate key themes. (MLW)

  10. Guidance for state attainment plans

    SciTech Connect

    Strait, R.

    1994-06-01

    Title I of the Clean Air act Amendments of 1990 significantly changed requirements for regulatory agencies to prepare state implementation plans that demonstrate attainment of the ozone National Ambient Air Quality Standards. State agencies now are required to submit plans that show how they will meet the standards by their attainment date. EPA has published a series of guidance documents to assist states in preparing their plans. In addition, the agency is developing software to assist states in projecting emissions and tracking reductions. This article summarizes the guidance documents and software program.

  11. Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project.

    PubMed

    Díez, Paula; Droste, Conrad; Dégano, Rosa M; González-Muñoz, María; Ibarrola, Nieves; Pérez-Andrés, Martín; Garin-Muga, Alba; Segura, Víctor; Marko-Varga, Gyorgy; LaBaer, Joshua; Orfao, Alberto; Corrales, Fernando J; De Las Rivas, Javier; Fuentes, Manuel

    2015-09-04

    A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of

  12. A High-Efficiency Cellular Extraction System for Biological Proteomics.

    PubMed

    Dhabaria, Avantika; Cifani, Paolo; Reed, Casie; Steen, Hanno; Kentsis, Alex

    2015-08-07

    Recent developments in quantitative high-resolution mass spectrometry have led to significant improvements in the sensitivity and specificity of the biochemical analyses of cellular reactions, protein-protein interactions, and small-molecule-drug discovery. These approaches depend on cellular proteome extraction that preserves native protein activities. Here, we systematically analyzed mechanical methods of cell lysis and physical protein extraction to identify those that maximize the extraction of cellular proteins while minimizing their denaturation. Cells were mechanically disrupted using Potter-Elvehjem homogenization, probe- or adaptive-focused acoustic sonication, and were in the presence of various detergents, including polyoxyethylene ethers and esters, glycosides, and zwitterions. Using fluorescence spectroscopy, biochemical assays, and mass spectrometry proteomics, we identified the combination of adaptive focused acoustic (AFA) sonication in the presence of a binary poloxamer-based mixture of octyl-β-glucoside and Pluronic F-127 to maximize the depth and yield of the proteome extraction while maintaining native protein activity. This binary poloxamer extraction system allowed for native proteome extraction comparable in coverage to the proteomes extracted using denaturing SDS or guanidine-containing buffers, including the efficient extraction of all major cellular organelles. This high-efficiency cellular extraction system should prove useful for a variety of cell biochemical studies, including structural and functional proteomics.

  13. Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome.

    PubMed

    Moran, Deborah; Cross, Trevor; Brown, Lewis M; Colligan, Ryan M; Dunbar, David

    2014-01-01

    In this work, a method was developed to study the structural proteome of mycobacteriophage Marvin, a recent isolate from soil with 107 predicted coding sequences. This prototype method was applied for semi-quantitative analysis of the composition of this mycobacteriophage virion using ion mobility spectrometry and data-independent acquisition (MS(E)-IMS). MS(E)-IMS was compared to a more conventional proteomics technique employing mass spectrometry with a data-dependent acquisition strategy. MS(E)-IMS provided broad coverage of the virion proteome and high sequence coverage for individual proteins. This shotgun method does not depend on the limited sensitivity of visualization of protein bands by staining reagents inherent in gel-based methods. The method is comprehensive, provides high sequence coverage and is proposed as a particularly efficient method for the study of bacteriophage proteomes. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Proteomics for systems toxicology

    PubMed Central

    Titz, Bjoern; Elamin, Ashraf; Martin, Florian; Schneider, Thomas; Dijon, Sophie; Ivanov, Nikolai V.; Hoeng, Julia; Peitsch, Manuel C.

    2014-01-01

    Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future. PMID:25379146

  15. Proteomics in medical microbiology.

    PubMed

    Cash, P

    2000-04-01

    The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

  16. Educational Attainment: Understanding the Data

    ERIC Educational Resources Information Center

    Baum, Sandy; Cunningham, Alisa; Tanenbaum, Courtney

    2015-01-01

    The level of educational attainment in the United States is a central focus of public policy. The Obama administration, some states, large national foundations, and other organizations have set near-term goals to increase the number of Americans with college degrees. Achieving these goals is likely to involve a combination of increasing…

  17. Educational Attainment: Understanding the Data

    ERIC Educational Resources Information Center

    Baum, Sandy; Cunningham, Alisa; Tanenbaum, Courtney

    2015-01-01

    The level of educational attainment in the United States is a central focus of public policy. The Obama administration, some states, large national foundations, and other organizations have set near-term goals to increase the number of Americans with college degrees. Achieving these goals is likely to involve a combination of increasing…

  18. Educational Attainment and Residential Location

    ERIC Educational Resources Information Center

    Sander, William

    2006-01-01

    The effects of residential location at age 16 and current residential location on measures of educational attainment are estimated. Particular attention is given to the effects of migration and family background on educational outcomes. It is shown that central cities and suburbs of large metropolitan areas in the United States have significantly…

  19. Curriculum of Attainments. Final Report.

    ERIC Educational Resources Information Center

    Peterson, Gary W.

    The final report describes a project at the Florida State University at the end of its third year and an assessment of the degree to which project goals were attained. The project goals were to: (1) establish mastery standards for degree programs; (2) create open, time-variable educational programs; (3) verify that the program product can serve as…

  20. Educational attainment in poor comprehenders

    PubMed Central

    Ricketts, Jessie; Sperring, Rachael; Nation, Kate

    2014-01-01

    To date, only one study has investigated educational attainment in poor (reading) comprehenders, providing evidence of poor performance on national UK school tests at age 11 years relative to peers (Cain and Oakhill, 2006). In the present study, we adopted a longitudinal approach, tracking attainment on such tests from 11 years to the end of compulsory schooling in the UK (age 16 years). We aimed to investigate the proposal that educational weaknesses (defined as poor performance on national assessments) might become more pronounced over time, as the curriculum places increasing demands on reading comprehension. Participants comprised 15 poor comprehenders and 15 controls; groups were matched for chronological age, nonverbal reasoning ability and decoding skill. Children were identified at age 9 years using standardized measures of nonverbal reasoning, decoding and reading comprehension. These measures, along with a measure of oral vocabulary knowledge, were repeated at age 11 years. Data on educational attainment were collected from all participants (n = 30) at age 11 and from a subgroup (n = 21) at 16 years. Compared to controls, educational attainment in poor comprehenders was lower at ages 11 and 16 years, an effect that was significant at 11 years. When poor comprehenders were compared to national performance levels, they showed significantly lower performance at both time points. Low educational attainment was not evident for all poor comprehenders. Nonetheless, our findings point to a link between reading comprehension difficulties in mid to late childhood and poor educational outcomes at ages 11 and 16 years. At these ages, pupils in the UK are making key transitions: they move from primary to secondary schools at 11, and out of compulsory schooling at 16. PMID:24904464

  1. Proteome sequencing goes deep

    PubMed Central

    Richards, Alicia L.; Merrill, Anna E.; Coon, Joshua J.

    2014-01-01

    Advances in mass spectrometry have transformed the scope and impact of protein characterization efforts. Identifying hundreds of proteins from rather simple biological matrices, such as yeast, was a daunting task just a few decades ago. Now, expression of more than half of the estimated ~20,000 human protein coding genes can be confirmed in record time and from minute sample quantities. Access to proteomic information at such unprecedented depths has been fueled by strides in every stage of the shotgun proteomics workflow – from sample processing to data analysis – and promises to revolutionize our understanding of the causes and consequences of proteome variation. PMID:25461719

  2. Proteomic Findings in Melanoma

    PubMed Central

    Sengupta, Deepanwita; Tackett, Alan J

    2016-01-01

    Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients. Here, we have summarized the major contributions of proteomics towards the study of melanoma, which is a deadly variety of skin cancer with a high mortality rate. PMID:27274624

  3. A proteomic glimpse into human ureter proteome

    PubMed Central

    Hirao, Yoshitoshi; Elguoshy, Amr; Xu, Bo; Zhang, Ying; Fujinaka, Hidehiko; Yamamoto, Keiko; Yates, John R.; Yamamoto, Tadashi

    2015-01-01

    Urine has evolved as one of the most important biofluids in clinical proteomics due to its noninvasive sampling and its stability. Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital (UG) tract, determining its precise source within the UG tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease‐associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. All MS data have been deposited in the ProteomeXchange with identifier PXD002620 (http://proteomecentral.proteomexchange.org/dataset/PXD002620). PMID:26442468

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

    SciTech Connect

    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.

  5. Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

    PubMed Central

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

    2013-01-01

    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. PMID:23878158

  6. SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities

    SciTech Connect

    Huang, Eric L.; Piehowski, Paul D.; Orton, Daniel J.; Moore, Ronald J.; Qian, Wei-Jun; Casey, Cameron P.; Sun, Xiaofei; Dey, Sudhansu K.; Burnum-Johnson, Kristin E.; Smith, Richard D.

    2016-03-01

    Global proteomic analyses are now widely applied across biological research to study changes in an organism(s) proteome correlated with a perturbation, phenotype and/or time series of interest.[1-3] Further, it has been broadly established that efficient and reproducible sample preparation workflows are crucial to successful quantitative proteome comparisons, especially when applying label free methods.[4-8] However, clinical samples are often severely limited in quantity and can preclude the application of more robust bulk sample processing workflows due to e.g. contamination, carry-over, or sample losses.[9] This has limited the effective application of global proteomics for many sample types of great interest, e.g. LCM dissected tissues, FACS sorted cells, circulating tumor cells (CTC), and early embryos. In a typical proteomics experiment, bulk homogenization is applied to generate sufficient protein for processing (> 10 µg protein), and can blend the proteomes of many different cell types and disparate tissue regions. The resulting “average” proteome, can effectively render unobservable proteome changes of interest, and preclude important applications. Global proteomic analyses of complex protein samples in nanogram quantities require a fastidious approach to achieve in-depth protein coverage and quantitative reproducibility.

  7. Coverage Metrics for Model Checking

    NASA Technical Reports Server (NTRS)

    Penix, John; Visser, Willem; Norvig, Peter (Technical Monitor)

    2001-01-01

    When using model checking to verify programs in practice, it is not usually possible to achieve complete coverage of the system. In this position paper we describe ongoing research within the Automated Software Engineering group at NASA Ames on the use of test coverage metrics to measure partial coverage and provide heuristic guidance for program model checking. We are specifically interested in applying and developing coverage metrics for concurrent programs that might be used to support certification of next generation avionics software.

  8. Sepsis Through the Eyes of Proteomics: The Progress in the Last Decade.

    PubMed

    Sharma, Narendra Kumar; Salomao, Reinaldo

    2017-01-01

    Sepsis is a systemic inflammatory response caused by infection whose molecular mechanisms are still not completely understood. The early detection of sepsis remains a great challenge for clinicians because no single biomarker capable of its reliable prediction, hence, delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. There are several experimental approaches used to reveal the molecular mechanism of sepsis progression. Proteomics coupled with mass spectrometry made possible to identify differentially expressed proteins in clinical samples. Recent advancement in liquid chromatography-based separation methods and mass spectrometers resolution and sensitivity with absolute quantitation methods, made possible to use proteomics as a powerful tool for study of clinical samples with higher coverage proteome profiles. In recent years, number of proteomic studies have been done under sepsis and/or in response to endotoxin and showed various signaling pathways, functions, and biomarkers. This review enlightened the proteomic progress in the last decade in sepsis.

  9. Proteomics data repositories

    PubMed Central

    Riffle, Michael; Eng, Jimmy K.

    2010-01-01

    The field of proteomics, particularly the application of mass spectrometry analysis to protein samples, is well-established and growing rapidly. Proteomics studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and results accessible to proteomics researchers and biologists alike. This review of proteomics data repositories focuses exclusively on freely-available, centralized data resources that disseminate or store experimental mass spectrometry data and results. The resources chosen reflect a current “snapshot” of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers. Resources are described in terms of their intended purpose and the features and functionality provided to users. PMID:19795424

  10. Proteome Characterization Centers - TCGA

    Cancer.gov

    The centers, a component of NCI’s Clinical Proteomic Tumor Analysis Consortium, will analyze a subset of TCGA samples to define proteins translated from cancer genomes and their related biological processes.

  11. Quantitative proteomics of intracellular Porphyromonas gingivalis

    PubMed Central

    Xia, Qiangwei; Wang, Tiansong; Taub, Fred; Park, Yoonsuk; Capestany, Cindy A.; Lamont, Richard J.; Hackett, Murray

    2009-01-01

    Whole-cell quantitative proteomic analyses were conducted to investigate the change from an extracellular to intracellular lifestyle for Porphyromonas gingivalis, a Gram-negative intracellular pathogen associated with periodontal disease. Global protein abundance data for P. gingivalis strain ATCC 33277 internalized for 18 hours within human gingival epithelial cells and controls exposed to gingival cell culture medium were obtained at sufficient coverage to provide strong evidence that these changes are profound. A total of 385 proteins were over-expressed in internalized P. gingivalis relative to controls; 240 proteins were shown to be under-expressed. This represented in total about 28% of the protein encoding ORFs annotated for this organism, and slightly less than half of the proteins that were observed experimentally. Production of several proteases, including the classical virulence factors RgpA, RgpB, and Kgp, was decreased. A separate validation study was carried out in which a 16-fold dilution of the P. gingivalis proteome was compared to the undiluted sample in order to assess the quantitative false negative rate (all ratios truly alternative). Truly null (no change) abundance ratios from technical replicates were used to assess the rate of quantitative false positives over the entire proteome. A global comparison between the direction of abundance change observed and previously published bioinformatic gene pair predictions for P. gingivalis will assist with future studies of P. gingivalis gene regulation and operon prediction. PMID:17979175

  12. Increasing immunization coverage.

    PubMed

    Hammer, Lawrence D; Curry, Edward S; Harlor, Allen D; Laughlin, James J; Leeds, Andrea J; Lessin, Herschel R; Rodgers, Chadwick T; Granado-Villar, Deise C; Brown, Jeffrey M; Cotton, William H; Gaines, Beverly Marie Madry; Gambon, Thresia B; Gitterman, Benjamin A; Gorski, Peter A; Kraft, Colleen A; Marino, Ronald Vincent; Paz-Soldan, Gonzalo J; Zind, Barbara

    2010-06-01

    In 1977, the American Academy of Pediatrics issued a statement calling for universal immunization of all children for whom vaccines are not contraindicated. In 1995, the policy statement "Implementation of the Immunization Policy" was published by the American Academy of Pediatrics, followed in 2003 with publication of the first version of this statement, "Increasing Immunization Coverage." Since 2003, there have continued to be improvements in immunization coverage, with progress toward meeting the goals set forth in Healthy People 2010. Data from the 2007 National Immunization Survey showed that 90% of children 19 to 35 months of age have received recommended doses of each of the following vaccines: inactivated poliovirus (IPV), measles-mumps-rubella (MMR), varicella-zoster virus (VZB), hepatitis B virus (HBV), and Haemophilus influenzae type b (Hib). For diphtheria and tetanus and acellular pertussis (DTaP) vaccine, 84.5% have received the recommended 4 doses by 35 months of age. Nevertheless, the Healthy People 2010 goal of at least 80% coverage for the full series (at least 4 doses of DTaP, 3 doses of IPV, 1 dose of MMR, 3 doses of Hib, 3 doses of HBV, and 1 dose of varicella-zoster virus vaccine) has not yet been met, and immunization coverage of adolescents continues to lag behind the goals set forth in Healthy People 2010. Despite these encouraging data, a vast number of new challenges that threaten continued success toward the goal of universal immunization coverage have emerged. These challenges include an increase in new vaccines and new vaccine combinations as well as a significant number of vaccines currently under development; a dramatic increase in the acquisition cost of vaccines, coupled with a lack of adequate payment to practitioners to buy and administer vaccines; unanticipated manufacturing and delivery problems that have caused significant shortages of various vaccine products; and the rise of a public antivaccination movement that uses the

  13. Proteomics Research in Schizophrenia

    PubMed Central

    Davalieva, Katarina; Maleva Kostovska, Ivana; Dwork, Andrew J.

    2016-01-01

    Despite intense scientific efforts, the neuropathology and pathophysiology of schizophrenia are poorly understood. Proteomic studies, by testing large numbers of proteins for associations with disease, may contribute to the understanding of the molecular mechanisms of schizophrenia. They may also indicate the types and locations of cells most likely to harbor pathological alterations. Investigations using proteomic approaches have already provided much information on quantitative and qualitative protein patterns in postmortem brain tissue, peripheral tissues and body fluids. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, SELDI-TOF, shotgun proteomics with label-based (ICAT), and label-free (MSE) quantification have been applied to the study of schizophrenia for the past 15 years. This review summarizes the results, mostly from brain but also from other tissues and bodily fluids, of proteomics studies in schizophrenia. Emphasis is given to proteomics platforms, varying sources of material, proposed candidate biomarkers emerging from comparative proteomics studies, and the specificity of the putative markers in terms of other mental illnesses. We also compare proteins altered in schizophrenia with reports of protein or mRNA sequences that are relatively enriched in specific cell types. While proteomic studies of schizophrenia find abnormalities in the expression of many proteins that are not cell type-specific, there appears to be a disproportionate representation of proteins whose synthesis and localization are highly enriched in one or more brain cell type compared with other types of brain cells. Two of the three proteins most commonly altered in schizophrenia are aldolase C and glial fibrillary acidic protein, astrocytic proteins with entirely different functions, but the studies are approximately evenly divided with regard to the direction of the differences and the concordance or discordance between the two proteins. Alterations of common myelin

  14. After-hours coverage

    PubMed Central

    Bordman, Risa; Wheler, David; Drummond, Neil; White, David; Crighton, Eric

    2005-01-01

    OBJECTIVE To determine the prevalence and content of existing or developing policies and guidelines of medical associations and colleges regarding after-hours care by family physicians and general practitioners, especially legal requirements. DESIGN Telephone survey in fall 2002, updated in fall 2004. SETTING Canada. PARTICIPANTS All national and provincial medical associations, Colleges of Family Physicians, Colleges of Physicians and Surgeons, local government offices for the north, and the Canadian Medical Protective Association (CMPA). MAIN OUTCOME MEASURE Response to the question: “Does your agency have a policy in place regarding after-hours health care coverage by FPs/GPs, or are there active discussions regarding such a policy?” RESULTS The College of Physicians and Surgeons of British Columbia was the first to institute a policy, in 1995, requiring physicians to make “specific arrangements” for after-hours care of their patients. The College of Physicians and Surgeons of Alberta adopted a similar policy in 1996 along with a guideline to aid implementation. In 2002, the College of Physicians and Surgeons of Nova Scotia approved a guideline on the Availability of Physicians After Hours. The Saskatchewan Medical Association and the College of Physicians and Surgeons of Saskatchewan formulated a joint policy on medical practice coverage that was released in 2003. Many agencies actively discussed the topic. Provincial and national Colleges of Family Physicians did not have any policies in place. The CMPA does not generate guidelines but released in an information letter in May 2000 a section entitled “Reducing your risk when you’re not available.” CONCLUSION There is increasing interest Canada-wide in setting policy for after-hours care. While provincial Colleges of Physicians and Surgeons have traditionally led the way, a trend toward more collaboration between associations was identified. The effect of policy implementation on physicians

  15. A GPS coverage model

    NASA Technical Reports Server (NTRS)

    Skidmore, Trent A.

    1994-01-01

    The results of several case studies using the Global Positioning System coverage model developed at Ohio University are summarized. Presented are results pertaining to outage area, outage dynamics, and availability. Input parameters to the model include the satellite orbit data, service area of interest, geometry requirements, and horizon and antenna mask angles. It is shown for precision-landing Category 1 requirements that the planned GPS 21 Primary Satellite Constellation produces significant outage area and unavailability. It is also shown that a decrease in the user equivalent range error dramatically decreases outage area and improves the service availability.

  16. Nanoscaled Proteomic Analysis

    NASA Astrophysics Data System (ADS)

    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.

  17. Proteomic research in psychiatry.

    PubMed

    Taurines, Regina; Dudley, Edward; Grassl, Julia; Warnke, Andreas; Gerlach, Manfred; Coogan, Andrew N; Thome, Johannes

    2011-02-01

    Psychiatric disorders such as Alzheimer's disease, schizophrenia and mood disorders are severe and disabling conditions of largely unknown origin and poorly understood pathophysiology. An accurate diagnosis and treatment of these disorders is often complicated by their aetiological and clinical heterogeneity. In recent years proteomic technologies based on mass spectrometry have been increasingly used, especially in the search for diagnostic and prognostic biomarkers in neuropsychiatric disorders. Proteomics enable an automated high-throughput protein determination revealing expression levels, post-translational modifications and complex protein-interaction networks. In contrast to other methods such as molecular genetics, proteomics provide the opportunity to determine modifications at the protein level thereby possibly being more closely related to pathophysiological processes underlying the clinical phenomenology of specific psychiatric conditions. In this article we review the theoretical background of proteomics and its most commonly utilized techniques. Furthermore the current impact of proteomic research on diverse psychiatric diseases, such as Alzheimer's disease, schizophrenia, mood and anxiety disorders, drug abuse and autism, is discussed. Proteomic methods are expected to gain crucial significance in psychiatric research and neuropharmacology over the coming decade.

  18. Antenna Beam Coverage Concepts

    NASA Technical Reports Server (NTRS)

    Estabrook, Polly; Motamedi, Masoud

    1990-01-01

    The strawman Personal Access Satellite System (PASS) design calls for the use of a CONUS beam for transmission between the supplier and the satellite and for fixed beams for transmission between the basic personal terminal and the satellite. The satellite uses a 3 m main reflector for transmission at 20 GHz and a 2 m main reflector for reception at 30 GHz. There are several types of spot beams under consideration for the PASS system besides fixed beams. The beam pattern of a CONUS coverage switched beam is shown along with that of a scanning beam. A switched beam refers to one in which the signal from the satellite is connected alternatively to various feed horns. Scanning beams are taken to mean beams whose footprints are moved between contiguous regions in the beam's coverage area. The advantages and disadvantages of switched and/or scanning beams relative to fixed beams. The consequences of using switched/scanning in lieu of fixed beams in the PASS design and attempts are made to evaluate the listed advantages and disadvantages. Two uses of switched/scanning beams are examined. To illustrate the implications of switched beams use on PASS system design, operation at two beam scan rates is explored.

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

    Cancer.gov

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

  20. 40 CFR 51.1004 - Attainment dates.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 2 2014-07-01 2014-07-01 false Attainment dates. 51.1004 Section 51....5 National Ambient Air Quality Standards § 51.1004 Attainment dates. (a) Consistent with section 172(a)(2)(A) of the Act, the attainment date for an area designated nonattainment for the PM2.5 NAAQS...

  1. Enhanced recovery of lyophilized peptides in shotgun proteomics by using an LC-ESI-MS compatible surfactant.

    PubMed

    Kawashima, Yusuke; Takahashi, Naoyuki; Satoh, Mamoru; Saito, Tatsuya; Kado, Sayaka; Nomura, Fumio; Matsumoto, Hiroyuki; Kodera, Yoshio

    2013-03-01

    LC-ESI/MS/MS-based shotgun proteomics is currently the most commonly used approach for the identification and quantification of proteins in large-scale studies of biomarker discovery. In the past several years, the shotgun proteomics technologies have been refined toward further enhancement of proteome coverage. In the complex series of protocols involved in shotgun proteomics, however, loss of proteolytic peptides during the lyophilization step prior to the LC/MS/MS injection has been relatively neglected despite the fact that the dissolution of the hydrophobic peptides in lyophilized samples is difficult in 0.05-0.1% TFA or formic acid, causing substantial loss of precious peptide samples. In order to prevent the loss of peptide samples during this step, we devised a new protocol using Invitrosol (IVS), a commercially available surfactant compatible with ESI-MS; by dissolving the lyophilized peptides in IVS, we show improved recovery of hydrophobic peptides, leading to enhanced coverage of proteome. Thus, the use of IVS in the recovery step of lyophilized peptides will help the shotgun proteomics analysis by expanding the proteome coverage, which would significantly promote the discovery and development of new diagnostic markers and therapeutic targets. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Have health insurance reforms in Tunisia attained their intended objectives?

    PubMed

    Makhloufi, Khaled; Ventelou, Bruno; Abu-Zaineh, Mohammad

    2015-03-01

    A growing number of developing countries are currently promoting health system reforms with the aim of attaining ' universal health coverage' (UHC). In Tunisia, several reforms have been undertaken over the last two decades to attain UHC with the goals of ensuring financial protection in health and enhancing access to healthcare. The first of these goals has recently been addressed in a companion paper by Abu-Zaineh et al. (Int J Health Care Financ Econ 13(1):73-93, 2013). The present paper seeks to assess whether these reforms have in fact enhanced access to healthcare. The average treatment effects of two insurance schemes, formal-mandatory (MHI) and state-subsidized (MAS) insurance, on the utilization of outpatient and inpatient healthcare are estimated using propensity score matching. Results support the hypothesis that both schemes (MHI and MAS) increase the utilization of healthcare. However, significant variations in the average effect of these schemes are observed across services and areas. For all the matching methods used and compared with those the excluded from cover, the increase in outpatient and inpatient services for the MHI enrollees was at least 19 and 26 %, respectively, in urban areas, while for MAS beneficiaries this increase was even more pronounced (28 and 75 % in the urban areas compared with 27 and 46 % in the rural areas for outpatient and inpatient services, respectively). One important conclusion that emerges is that the current health insurance schemes, despite improving accessibility to healthcare services, are nevertheless incapable of achieving effective coverage of the whole population for all services. Attaining the latter goal requires a strategy that targets the "trees" not the "forest".

  3. Environmental proteomics and metallomics.

    PubMed

    López-Barea, Juan; Gómez-Ariza, José Luis

    2006-04-01

    Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.

  4. Proteomics of human mitochondria.

    PubMed

    Palmfeldt, Johan; Bross, Peter

    2017-03-01

    Proteomics have passed through a tremendous development in the recent years by the development of ever more sensitive, fast and precise mass spectrometry methods. The dramatically increased research in the biology of mitochondria and their prominent involvement in all kinds of diseases and ageing has benefitted from mitochondrial proteomics. We here review substantial findings and progress of proteomic analyses of human cells and tissues in the recent past. One challenge for investigations of human samples is the ethically and medically founded limited access to human material. The increased sensitivity of mass spectrometry technology aids in lowering this hurdle and new approaches like generation of induced pluripotent cells from somatic cells allow to produce patient-specific cellular disease models with great potential. We describe which human sample types are accessible, review the status of the catalog of human mitochondrial proteins and discuss proteins with dual localization in mitochondria and other cellular compartments. We describe the status and developments of pertinent mass spectrometric strategies, and the use of databases and bioinformatics. Using selected illustrative examples, we draw a picture of the role of proteomic analyses for the many disease contexts from inherited disorders caused by mutation in mitochondrial proteins to complex diseases like cancer, type 2 diabetes and neurodegenerative diseases. Finally, we speculate on the future role of proteomics in research on human mitochondria and pinpoint fields where the evolving technologies will be exploited. Copyright © 2016. Published by Elsevier B.V.

  5. Beer and wort proteomics.

    PubMed

    Iimure, Takashi; Kihara, Makoto; Sato, Kazuhiro

    2014-01-01

    Proteome analysis provides a way to identify proteins related to the quality traits of beer. A number of protein species in beer and wort have been identified by two-dimensional gel electrophoresis combined with enzyme digestion such as trypsin, followed by mass spectrometry analyses and/or liquid chromatography mass/mass spectrometry. In addition, low molecular weight polypeptides in beer have been identified by the combination of non-enzyme digestion and mass analyses. These data sets of various molecular weight polypeptides (i.e., proteomes) provide a platform for analyzing protein functions in beer. Several novel proteins related to beer quality traits such as foam stability and haze formation have been identified by analyzing these proteomes. Some of the proteins have been applied to the development of efficient protein or DNA markers for trait selection in malting barley breeding. In this chapter, recent proteome studies of beer and wort are reviewed, and the methods and protocols of beer and wort proteome analysis are described.

  6. The Cysteine Proteome

    PubMed Central

    Go, Young-Mi; Chandler, Joshua D.; Jones, Dean P.

    2015-01-01

    The cysteine (Cys) proteome is a major component of the adaptive interface between the genome and the exposome. The thiol moiety of Cys undergoes a range of biologic modifications enabling biological switching of structure and reactivity. These biological modifications include sulfenylation and disulfide formation, formation of higher oxidation states, S-nitrosylation, persulfidation, metallation, and other modifications. Extensive knowledge about these systems and their compartmentalization now provides a foundation to develop advanced integrative models of Cys proteome regulation. In particular, detailed understanding of redox signaling pathways and sensing networks is becoming available to discriminate network structures. This research focuses attention on the need for atlases of Cys modifications to develop systems biology models. Such atlases will be especially useful for integrative studies linking the Cys proteome to imaging and other omics platforms, providing a basis for improved redox-based therapeutics. Thus, a framework is emerging to place the Cys proteome as a complement to the quantitative proteome in the omics continuum connecting the genome to the exposome. PMID:25843657

  7. Toxoplasma gondii proteomics

    PubMed Central

    Weiss, Louis M; Fiser, Andras; Angeletti, Ruth Hogue; Kim, Kami

    2009-01-01

    Toxoplasma gondii is a ubiquitous, Apicomplexan parasite that, in humans, can cause several clinical syndromes, including encephalitis, chorioretinitis and congenital infection. T. gondii was described a little over 100 years ago in the tissues of the gundi (Ctenodoactylus gundi). There are a large number of applicable experimental techniques available for this pathogen and it has become a model organism for the study of intracellular pathogens. With the completion of the genomes for a type I (GT-1), type II (ME49) and type III (VEG) strains, proteomic studies on this organism have been greatly facilitated. Several subcellular proteomic studies have been completed on this pathogen. These studies have helped elucidate specialized invasion organelles and their composition, as well as proteins associated with the cytoskeleton. Global proteomic studies are leading to improved strategies for genome annotation in this organism and an improved understanding of protein regulation in this pathogen. Web-based resources, such as EPIC-DB and ToxoDB, provide proteomic data and support for studies on T. gondii. This review will summarize the current status of proteomic research on T. gondii. PMID:19489701

  8. Proteomic Assessment of Poultry Spermatozoa

    USDA-ARS?s Scientific Manuscript database

    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...

  9. Proteomics of Foodborne Bacterial Pathogens

    NASA Astrophysics Data System (ADS)

    Fagerquist, Clifton K.

    This chapter is intended to be a relatively brief overview of proteomic techniques currently in use for the identification and analysis of microorganisms with a special emphasis on foodborne pathogens. The chapter is organized as follows. First, proteomic techniques are introduced and discussed. Second, proteomic applications are presented specifically as they relate to the identification and qualitative/quantitative analysis of foodborne pathogens.

  10. The expanding proteome of the molecular chaperone HSP90

    PubMed Central

    Samant, Rahul S; Clarke, Paul A

    2012-01-01

    The molecular chaperone HSP90 maintains the activity and stability of a diverse set of “client” proteins that play key roles in normal and disease biology. Around 20 HSP90 inhibitors that deplete the oncogenic clientele have entered clinical trials for cancer. However, the full extent of the HSP90-dependent proteome, which encompasses not only clients but also proteins modulated by downstream transcriptional responses, is still incompletely characterized and poorly understood. Earlier large-scale efforts to define the HSP90 proteome have been valuable but are incomplete because of limited technical sensitivity. Here, we discuss previous large-scale surveys of proteome perturbations induced by HSP90 inhibitors in light of a significant new study using state-of-the-art stable isotope labeling by amino acids (SILAC) technology combined with more sensitive high-resolution mass spectrometry (MS) that extends the catalog of proteomic changes in inhibitor-treated cancer cells. Among wide-ranging changes, major functional responses include downregulation of protein kinase activity and the DNA damage response alongside upregulation of the protein degradation machinery. Despite this improved proteomic coverage, there was surprisingly little overlap with previous studies. This may be due in part to technical issues but is likely also due to the variability of the HSP90 proteome with the inhibitor conditions used, the cancer cell type and the genetic status of client proteins. We suggest future proteomic studies to address these factors, to help distinguish client protein components from indirect transcriptional components and to address other key questions in fundamental and translational HSP90 research. Such studies should also reveal new biomarkers for patient selection and novel targets for therapeutic intervention. PMID:22421145

  11. Dental care coverage and retirement.

    PubMed

    Manski, Richard J; Moeller, John; Schimmel, Jody; St Clair, Patricia A; Chen, Haiyan; Magder, Larry; Pepper, John V

    2010-01-01

    To examine the convergence of an aging population and a decreased availability of dental care coverage using data from the Health and Retirement Study (HRS). We calculate national estimates of the number and characteristics of those persons age 51 years and above covered by dental insurance by labor force, retirement status, and source of coverage. We also estimate a multivariate model controlling for potentially confounding variables. We show that being in the labor force is a strong predictor of having dental coverage. For older retired adults not in the labor force, the only source for dental coverage is either a postretirement health benefit or spousal coverage. Dental care, generally not covered in Medicare, is an important factor in the decision to seek dental care. It is important to understand the relationship between retirement and dental coverage in order to identify the best ways of improving oral health and access to care among older Americans.

  12. Establishing Substantial Equivalence: Proteomics

    NASA Astrophysics Data System (ADS)

    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.

  13. Subcellular proteomics in neuroscience.

    PubMed

    Li, Ka Wan; Smit, August B

    2008-05-01

    The brain is the most complex and dynamically organized organ of the human body, with a high degree of computation capability enabling the execution of a wide spectrum of physiological processes and behaviors. In the past decades a large number of genomics studies have been undertaken to investigate brain function and brain disorders, but despite these efforts many of the underlying molecular mechanisms still remain largely unknown. The implementation of mass spectrometry based quantitative proteomics in recent years enabled to tap into condition-specific protein trafficking and protein interaction that are the key to organelle proteome (dys)function. The technology for neuroproteomics is still evolving; currently there are no standardized protocols. In this review we describe the most commonly used methods to prepare brain subcellular fractions suitable for proteomics analysis, and highlight the various approaches for quantitative neuroproteomics.

  14. [Insurance and coverage: two critical topics in health care reforms].

    PubMed

    Madies, C V; Chiarvetti, S; Chorny, M

    2000-01-01

    The goal of health for all in the year 2000, which was established at Alma Ata more than two decades ago, has led countries in Latin America and the Caribbean to adopt health sector reforms aimed at extending health coverage to each and every individual citizen. Whereas much has come about as a result of reform policies in the way of theory and legislation, in practice the goals that were established are far from attained, and many countries show large gaps in theoretical coverage on the one hand, and true coverage on the other. This is largely due to organizational features and other "endogenous" characteristics of the various countries' health systems, as well as to "exogenous" factors in the political, macroeconomic, social, epidemiologic, and cultural spheres. This documents takes a close look at the different types of health systems that are currently operating in countries of the Region and their impact on sources of health insurance and health coverage for individuals living in those countries. The end of the article focuses on the different strategies adopted by the countries in an effort to extend health coverage, which in some cases involve policies targeting the most vulnerable social groups.

  15. The Redox Proteome*

    PubMed Central

    Go, Young-Mi; Jones, Dean P.

    2013-01-01

    The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation, and signaling during the life cycle and has a central role in the tolerance and adaptability to diet and environmental challenges. PMID:23861437

  16. [Proteomics in infectious diseases].

    PubMed

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

    2016-04-01

    Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  17. Biophotonics applied to proteomics.

    PubMed

    Faupel, Michel; Bonenfant, Débora; Schindler, Patrick; Bertrand, Eric; Mueller, Dieter; Stoeckli, Markus; Bitsch, Francis; Rohner, Tatiana; Staab, Dieter; Van Oostrum, Jan

    2007-01-01

    Since the completion of the human genome sequencing, our understanding of gene and protein function and their involvement in physiopathological states has increased dramatically, partly due to technological developments in photonics. Photonics is a very active area where new developments occur on a weekly basis, while established tools are adapted to fulfill the needs of other disciplines like genomics and proteomics. Biophotonics emerged at the interface of photonics and biology as a very straightforward and efficient approach to observe and manipulate living systems. In this chapter, we review the current applications of photonics and imaging to proteomics from 2D gels analysis to molecular imaging.

  18. Immunisation coverage annual report, 2009.

    PubMed

    Hull, Brynley; Dey, Aditi; Mahajan, Deepika; Menzies, Rob; McIntyre, Peter B

    2011-06-01

    This, the third annual immunisation coverage report, documents trends during 2009 for a range of standard measures derived from Australian Childhood Immunisation Register data, including overall coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). Coverage by Indigenous status and mapping by smaller geographic areas as well as trends in timeliness is also summarised according to standard templates. With respect to overall coverage, the Immunise Australia Program targets have been reached for children at 12 and 24 months of age but not for children at 5 years of age. Coverage at 24 months of age exceeds that at 12 months of age, but as receipt of varicella vaccine at 18 months is excluded from calculations of 'fully immunised' this probably represents delayed immunisation, with some contribution from immunisation incentives. Similarly, the decrease in coverage estimates for immunisations due at 4 years of age from March 2008 is primarily due to changing the assessment age from 6 years to 5 years of age from December 2007. With respect to individual vaccines, a number of those available on the NIP are not currently assessed for 'fully immunised' status or for eligibility for incentive payments. These include pneumococcal conjugate and meningococcal C conjugate vaccines, for which coverage is comparable with vaccines that are assessed for 'fully immunised' status, and rotavirus and varicella vaccines for which coverage is lower. Coverage is also suboptimal for vaccines recommended for Indigenous children only (i.e. hepatitis A and pneumococcal polysaccharide vaccine) as previously reported for other vaccines for both children and adults. Delayed receipt of vaccines is an important issue for vaccines recommended for Indigenous children and has not improved among non-Indigenous children despite improvements in coverage at the 24-month milestone. Although Indigenous children in Australia have coverage levels

  19. Pressurized Pepsin Digestion in Proteomics

    PubMed Central

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

    2011-01-01

    Integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications. Herein, we describe recent efforts toward efficient integration of bottom-up and top-down LC-MS-based proteomics strategies. Since most proteomics separations utilize acidic conditions, we exploited the compatibility of pepsin (where the optimal digestion conditions are at low pH) for integration into bottom-up and top-down proteomics work flows. Pressure-enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an off-line mode using a Barocycler or an on-line mode using a modified high pressure LC system referred to as a fast on-line digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results were compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultrarapid integrated bottom-up top-down proteomics strategy using a standard mixture of proteins and a monkey pox virus proteome. PMID:20627868

  20. Newspaper Coverage of Racial Injustices.

    ERIC Educational Resources Information Center

    Martindale, Carolyn

    Noting that the press was criticized during the 1960s for failing to convey to white readers the problems and injustices experienced by black Americans, a study analyzed the nature and amount of civil rights coverage in five newspapers from 1963 through 1980. News coverage concerning blacks was examined in 66 issues from four major newspapers in…

  1. The Human Eye Proteome Project: perspectives on an emerging proteome.

    PubMed

    Semba, Richard D; Enghild, Jan J; Venkatraman, Vidya; Dyrlund, Thomas F; Van Eyk, Jennifer E

    2013-08-01

    There are an estimated 285 million people with visual impairment worldwide, of whom 39 million are blind. The pathogenesis of many eye diseases remains poorly understood. The human eye is currently an emerging proteome that may provide key insight into the biological pathways of disease. We review proteomic investigations of the human eye and present a catalogue of 4842 nonredundant proteins identified in human eye tissues and biofluids to date. We highlight the need to identify new biomarkers for eye diseases using proteomics. Recent advances in proteomics do now allow the identification of hundreds to thousands of proteins in tissues and fluids, characterization of various PTMs and simultaneous quantification of multiple proteins. To facilitate proteomic studies of the eye, the Human Eye Proteome Project (HEPP) was organized in September 2012. The HEPP is one of the most recent components of the Biology/Disease-driven Human Proteome Project (B/D-HPP) whose overarching goal is to support the broad application of state-of-the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. The large repertoire of investigative proteomic tools has great potential to transform vision science and enhance understanding of physiology and disease processes that affect sight. © 2013 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Effective coverage: a metric for monitoring Universal Health Coverage.

    PubMed

    Ng, Marie; Fullman, Nancy; Dieleman, Joseph L; Flaxman, Abraham D; Murray, Christopher J L; Lim, Stephen S

    2014-09-01

    A major challenge in monitoring universal health coverage (UHC) is identifying an indicator that can adequately capture the multiple components underlying the UHC initiative. Effective coverage, which unites individual and intervention characteristics into a single metric, offers a direct and flexible means to measure health system performance at different levels. We view effective coverage as a relevant and actionable metric for tracking progress towards achieving UHC. In this paper, we review the concept of effective coverage and delineate the three components of the metric - need, use, and quality - using several examples. Further, we explain how the metric can be used for monitoring interventions at both local and global levels. We also discuss the ways that current health information systems can support generating estimates of effective coverage. We conclude by recognizing some of the challenges associated with producing estimates of effective coverage. Despite these challenges, effective coverage is a powerful metric that can provide a more nuanced understanding of whether, and how well, a health system is delivering services to its populations.

  3. The proteome of lysosomes.

    PubMed

    Schröder, Bernd A; Wrocklage, Christian; Hasilik, Andrej; Saftig, Paul

    2010-11-01

    Lysosomes are organelles of eukaryotic cells that are critically involved in the degradation of macromolecules mainly delivered by endocytosis and autophagocytosis. Degradation is achieved by more than 60 hydrolases sequestered by a single phospholipid bilayer. The lysosomal membrane facilitates interaction and fusion with other compartments and harbours transport proteins catalysing the export of catabolites, thereby allowing their recycling. Lysosomal proteins have been addressed in various proteomic studies that are compared in this review regarding the source of material, the organelle/protein purification scheme, the proteomic methodology applied and the proteins identified. Distinguishing true constituents of an organelle from co-purifying contaminants is a central issue in subcellular proteomics, with additional implications for lysosomes as being the site of degradation of many cellular and extracellular proteins. Although many of the lysosomal hydrolases were identified by classical biochemical approaches, the knowledge about the protein composition of the lysosomal membrane has remained fragmentary for a long time. Using proteomics many novel lysosomal candidate proteins have been discovered and it can be expected that their functional characterisation will help to understand functions of lysosomes at a molecular level that have been characterised only phenomenologically so far and to generally deepen our understanding of this indispensable organelle.

  4. Xylem sap proteomics.

    PubMed

    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.

    PubMed

    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. “Seed Proteomics"

    USDA-ARS?s Scientific Manuscript database

    Proteomic analysis of seeds encounters some specific problems that do not impinge on analyses of other plant cells, tissues, or organs. There are anatomic considerations. Seeds comprise the seed coat, the storage organ(s), and the embryonic axis. Are these to be studied individually or as a compo...

  7. Analyzing the platelet proteome.

    PubMed

    García, Angel; Zitzmann, Nicole; Watson, Steve P

    2004-08-01

    During the last 10 years, mass spectrometry (MS) has become a key tool for protein analysis and has underpinned the emerging field of proteomics. Using high-throughput tandem MS/MS following protein separation, it is potentially possible to analyze hundreds to thousands of proteins in a sample at a time. This technology can be used to analyze the protein content (i.e., the proteome) of any cell or tissue and complements the powerful field of genomics. The technology is particularly suitable for platelets because of the absence of a nucleus. Cellular proteins can be separated by either gel-based methods such as two-dimensional gel electrophoresis or one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by liquid chromatography (LC) -MS/MS or by multidimensional LC-MS/MS. Prefractionation techniques, such as subcellular fractionations or immunoprecipitations, can be used to improve the analysis. Each method has particular advantages and disadvantages. Proteomics can be used to compare the proteome of basal and diseased platelets, helping to reveal information on the molecular basis of the disease.

  8. Genomes to Proteomes

    SciTech Connect

    Panisko, Ellen A.; Grigoriev, Igor; Daly, Don S.; Webb-Robertson, Bobbie-Jo; Baker, Scott E.

    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. Optimization of parameters for coverage of low molecular weight proteins

    PubMed Central

    Müller, Stephan A.; Kohajda, Tibor; Findeiß, Sven; Stadler, Peter F.; Washietl, Stefan; Kellis, Manolis; von Bergen, Martin

    2010-01-01

    Proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption (e.g., temperature reduction) and cell cycle control. Despite their importance, the coverage of smaller proteins in standard proteome studies is rather sparse. Here we investigated biochemical and mass spectrometric parameters that influence coverage and validity of identification. The underrepresentation of low molecular weight (LMW) proteins may be attributed to the low numbers of proteolytic peptides formed by tryptic digestion as well as their tendency to be lost in protein separation and concentration/desalting procedures. In a systematic investigation of the LMW proteome of Escherichia coli, a total of 455 LMW proteins (27% of the 1672 listed in the SwissProt protein database) were identified, corresponding to a coverage of 62% of the known cytosolic LMW proteins. Of these proteins, 93 had not yet been functionally classified, and five had not previously been confirmed at the protein level. In this study, the influences of protein extraction (either urea or TFA), proteolytic digestion (solely, and the combined usage of trypsin and AspN as endoproteases) and protein separation (gel- or non-gel-based) were investigated. Compared to the standard procedure based solely on the use of urea lysis buffer, in-gel separation and tryptic digestion, the complementary use of TFA for extraction or endoprotease AspN for proteolysis permits the identification of an extra 72 (32%) and 51 proteins (23%), respectively. Regarding mass spectrometry analysis with an LTQ Orbitrap mass spectrometer, collision-induced fragmentation (CID and HCD) and electron transfer dissociation using the linear ion trap (IT) or the Orbitrap as the analyzer were compared. IT-CID was found to yield the best identification rate, whereas IT-ETD provided almost comparable results in terms of LMW proteome coverage. The high overlap between the proteins identified with IT

  10. Optimization of parameters for coverage of low molecular weight proteins.

    PubMed

    Müller, Stephan A; Kohajda, Tibor; Findeiss, Sven; Stadler, Peter F; Washietl, Stefan; Kellis, Manolis; von Bergen, Martin; Kalkhof, Stefan

    2010-12-01

    Proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption (e.g., temperature reduction) and cell cycle control. Despite their importance, the coverage of smaller proteins in standard proteome studies is rather sparse. Here we investigated biochemical and mass spectrometric parameters that influence coverage and validity of identification. The underrepresentation of low molecular weight (LMW) proteins may be attributed to the low numbers of proteolytic peptides formed by tryptic digestion as well as their tendency to be lost in protein separation and concentration/desalting procedures. In a systematic investigation of the LMW proteome of Escherichia coli, a total of 455 LMW proteins (27% of the 1672 listed in the SwissProt protein database) were identified, corresponding to a coverage of 62% of the known cytosolic LMW proteins. Of these proteins, 93 had not yet been functionally classified, and five had not previously been confirmed at the protein level. In this study, the influences of protein extraction (either urea or TFA), proteolytic digestion (solely, and the combined usage of trypsin and AspN as endoproteases) and protein separation (gel- or non-gel-based) were investigated. Compared to the standard procedure based solely on the use of urea lysis buffer, in-gel separation and tryptic digestion, the complementary use of TFA for extraction or endoprotease AspN for proteolysis permits the identification of an extra 72 (32%) and 51 proteins (23%), respectively. Regarding mass spectrometry analysis with an LTQ Orbitrap mass spectrometer, collision-induced fragmentation (CID and HCD) and electron transfer dissociation using the linear ion trap (IT) or the Orbitrap as the analyzer were compared. IT-CID was found to yield the best identification rate, whereas IT-ETD provided almost comparable results in terms of LMW proteome coverage. The high overlap between the proteins identified with IT

  11. Market opportunity in computational proteomics.

    PubMed

    Razvi, Enal

    2002-03-01

    The current exuberance on the potential of proteomics as a means to deploy the wealth of the human genome is expected to last into the coming years. Unlike the genome, a finite entity with a fixed number of base pairs of the genetic material, the proteome is "plastic", changing throughout growth and development and environmental stresses, as well as in pathological situations. Our proteomes change over time, and therefore there is no one proteome; the proteome is for practical purposes an infinite entity. It is therefore crucial to build systems that are capable of manipulating the information content that is the proteome, thence the need for computational proteomics as a discipline. In this Market View article, we present the industry landscape that is emerging in the computational proteomics space. This space is still in its infancy and for the most part undefined; therefore we seek to present the market opportunity in informatics in the drug discovery space and then extend that to an examination of industry trends in proteomics. Thus, the gestalt is a set of predictions as to the evolution of the landscape in computational proteomics over the coming years.

  12. Deep proteome and transcriptome mapping of a human cancer cell line

    PubMed Central

    Nagaraj, Nagarjuna; Wisniewski, Jacek R; Geiger, Tamar; Cox, Juergen; Kircher, Martin; Kelso, Janet; Pääbo, Svante; Mann, Matthias

    2011-01-01

    While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. Online liquid chromatography coupled to high-resolution MS and MS/MS yielded 166 420 peptides with unique amino-acid sequence from HeLa cells. These peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. We calculate copy numbers for the expressed proteins and show that the abundances of >90% of them are within a factor 60 of the median protein expression level. Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type. PMID:22068331

  13. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

    PubMed Central

    Lipton, Mary S.; Paša-Tolić, Ljiljana; Anderson, Gordon A.; Anderson, David J.; Auberry, Deanna L.; Battista, John R.; Daly, Michael J.; Fredrickson, Jim; Hixson, Kim K.; Kostandarithes, Heather; Masselon, Christophe; Markillie, Lye Meng; Moore, Ronald J.; Romine, Margaret F.; Shen, Yufeng; Stritmatter, Eric; Tolić, Nikola; Udseth, Harold R.; Venkateswaran, Amudhan; Wong, Kwong-Kwok; Zhao, Rui; Smith, Richard D.

    2002-01-01

    Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical. PMID:12177431

  14. Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags

    SciTech Connect

    Lipton, Mary S.; Pasa-Tolic, Liljiana; Anderson, Gordon A.; Anderson, David J.; Auberry, Deanna L.; Battista, John R.; Daly, Michael J.; Fredrickson, Jim K.; Hixson, Kim K.; Kostandarithes, Heather M.; Masselon, Christophe D.; Markillie, Lye Meng; Moore, Ronald J.; Romine, Margaret F.; Shen, Yufeng; Strittmatter, Eric F.; Tolic, Nikola; Udseth, Harold R.; Venkateswaran, Amudhan; Wong, Kwong-Kwok; Zhao, Rui; Smith, Richard D.

    2002-08-20

    The ability to understand biological systems and their constituents would be greatly facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes e.g. in response to environmental perturbations. To this end we have developed new instrumentation and a high throughput methodology to characterize an organism's dynamic proteome based upon the combination of global enzymatic digestion, high-resolution liquid chromatographic separations and analysis by Fourier transform ion cyclotron resonance mass spectrometry. Using accurate mass tags, 61% of the predicted proteome of the ionizing radiation resistant bacterium Deinococcus radiodurans was characterized with high confidence. This represents the broadest proteome coverage for any organism to date, and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.

  15. Whole proteomes as internal standards in quantitative proteomics.

    PubMed

    Ong, Shao-En

    2010-07-30

    As mass-spectrometry-based quantitative proteomics approaches become increasingly powerful, researchers are taking advantage of well established methodologies and improving instrumentation to pioneer new protein expression profiling methods. For example, pooling several proteomes labeled using the stable isotope labeling by amino acids in cell culture (SILAC) method yields a whole-proteome stable isotope-labeled internal standard that can be mixed with a tissue-derived proteome for quantification. By increasing quantitative accuracy in the analysis of tissue proteomes, such methods should improve integration of protein expression profiling data with transcriptomic data and enhance downstream bioinformatic analyses. An accurate and scalable quantitative method to analyze tumor proteomes at the depth of several thousand proteins provides a powerful tool for global protein quantification of tissue samples and promises to redefine our understanding of tumor biology.

  16. Expanding the bovine milk proteome through extensive fractionation.

    PubMed

    Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne; Røntved, Christine Maria

    2013-01-01

    Bovine milk is an agricultural product of tremendous value worldwide. It contains proteins, fat, lactose, vitamins, and minerals. It provides nutrition and immunological protection (e.g., in the gastrointestinal tract) to the newborn and young calf. It also forms an important part of human nutrition. The repertoire of proteins in milk (i.e., its proteome) is vast and complex. The milk proteome can be described in detail by mass spectrometry-based proteomics. However, the high concentration of dominating proteins in milk reduces mass spectrometry detection sensitivity and limits detection of low abundant proteins. Further, the general health and udder health of the dairy cows delivering the milk may influence the composition of the milk proteome. To gain a more exhaustive and true picture of the milk proteome, we performed an extensive preanalysis fractionation of raw composite milk collected from documented healthy cows in early lactation. Four simple and industrially applicable techniques exploring the physical and chemical properties of milk, including acidification, filtration, and centrifugation, were used for separation of the proteins. This resulted in 5 different fractions, whose content of proteins were compared with the proteins of nonfractionated milk using 2-dimensional liquid chromatography tandem mass spectrometry analysis. To validate the proteome analysis, spectral counts and ELISA were performed on 7 proteins using the ELISA for estimation of the detection sensitivity limit of the 2-dimensional liquid chromatography tandem mass spectrometry analysis. Each fractionation technique resulted in identification of a unique subset of proteins. However, high-speed centrifugation of milk to whey was by far the best method to achieve high and repeatable proteome coverage. The total number of milk proteins initially detected in nonfractionated milk and the fractions were 635 in 2 replicates. Removal of dominant proteins and filtering for redundancy across the

  17. Vaccination coverage rates for 1986.

    PubMed

    1987-10-01

    This article sets forth data on vaccination coverage rates in children under 1 year of age in the individual countries of Latin America and the Caribbean in 1986. In the Region of the Americas as a whole, the 1986 coverage rate was 80% for oral poliovaccine, 54% for DPT, 55% for measles, and 63% for BCG. Vaccination coverage rates increased over 1985 levels for all but measles, which showed a 5% decline due to decreases in Brazil and Mexico. In the Caribbean subregion, the majority of country coverage rates for DPT and oral poliovirus vaccine are equal to or above 80%, while measles coverage rates are generally below 50%. In Central America, vaccine coverage rates with all antigens except BCG showed significant increases between 1985 and 1986. In Central America, coverage ranged from above 80% for oral poliovirus vaccine and DPT in Belize, Costa Rica, and Nicaragua, to below 40% in Guatemala. In general, countries in the region are improving vaccination performance as a result of establishment of vaccination days or campaigns and acceleration of the Expanded Program on Immunization. However, much work remains to be done if the goal of 100% immunization of children and women of childbearing age by 1990 is to be met.

  18. Characterization of the human heart mitochondrial proteome.

    PubMed

    Taylor, Steven W; Fahy, Eoin; Zhang, Bing; Glenn, Gary M; Warnock, Dale E; Wiley, Sandra; Murphy, Anne N; Gaucher, Sara P; Capaldi, Roderick A; Gibson, Bradford W; Ghosh, Soumitra S

    2003-03-01

    To gain a better understanding of the critical role of mitochondria in cell function, we have compiled an extensive catalogue of the mitochondrial proteome using highly purified mitochondria from normal human heart tissue. Sucrose gradient centrifugation was employed to partially resolve protein complexes whose individual protein components were separated by one-dimensional PAGE. Total in-gel processing and subsequent detection by mass spectrometry and rigorous bioinformatic analysis yielded a total of 615 distinct protein identifications. All protein pI values, molecular weight ranges, and hydrophobicities were represented. The coverage of the known subunits of the oxidative phosphorylation machinery within the inner mitochondrial membrane was >90%. A significant proportion of identified proteins are involved in signaling, RNA, DNA, and protein synthesis, ion transport, and lipid metabolism. The biochemical roles of 19% of the identified proteins have not been defined. This database of proteins provides a comprehensive resource for the discovery of novel mitochondrial functions and pathways.

  19. Proteomic analysis of brain mitochondrial proteome and mitochondrial complexes.

    PubMed

    Lopez-Campistrous, Ana; Fernandez-Patron, Carlos

    2013-01-01

    We describe various complementary techniques to achieve multidimensional mitochondrial proteome fractionation and analysis. Previously described methods for 2D-DIGE/mass spectrometry and 1D-SDS-PAGE/Western techniques and protein complex analysis by BN-PAGE/Western and sucrose gradient ultracentrifugation/SDS-PAGE/mass spectrometry are optimized to characterize the brain mitochondrial proteome. This approach allows for a comprehensive identification of mitochondrial proteomic differences between health and disease conditions.

  20. Annual immunisation coverage report, 2010.

    PubMed

    Hull, Brynley; Dey, Aditi; Menzies, Rob; McIntyre, Peter

    2013-03-31

    This, the fourth annual immunisation coverage report, documents trends during 2010 for a range of standard measures derived from Australian Childhood Immunisation Register (ACIR) data. These include coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). For the first time, coverage from other sources for adolescents and the elderly are included. The proportion of children 'fully vaccinated' at 12, 24 and 60 months of age was 91.6%, 92.1% and 89.1% respectively. For vaccines available on the NIP but not currently assessed for 'fully immunised' status or for eligibility for incentive payments (rotavirus and pneumococcal at 12 months and meningococcal C and varicella at 24 months) coverage varied. Although pneumococcal vaccine had similar coverage at 12 months to other vaccines, coverage was lower for rotavirus at 12 months (84.7%) and varicella at 24 months (83.0%). Overall coverage at 24 months of age exceeded that at 12 months of age nationally and for most jurisdictions, but as receipt of varicella vaccine at 18 months is excluded from calculations, this represents delayed immunisation, with some contribution from immunisation incentives. The 'fully immunised' coverage estimates for immunisations due by 60 months increased substantially in 2009, reaching almost 90% in 2010, probably related to completed immunisation by 60 months of age being introduced in 2009 as a requirement for GP incentive payments. As previously documented, vaccines recommended for Indigenous children only (hepatitis A and pneumococcal polysaccharide vaccine) had suboptimal coverage at around 57%. Delayed receipt of vaccines by Indigenous children at the 60-month milestone age improved from 56% to 62% but the disparity in on-time vaccination between Indigenous and non-Indigenous children at earlier age milestones did not improve. Coverage data for human papillomavirus (HPV)from the national HPV register are consistent with high

  1. The Human Eye Proteome Project: Perspectives on an emerging proteome

    PubMed Central

    Semba, Richard D.; Enghild, Jan J.; Venkatraman, Vidya; Dyrlund, Thomas F.; Van Eyk, Jennifer E.

    2013-01-01

    There are an estimated 285 million people with visual impairment worldwide, of whom 39 million are blind. The pathogenesis of many eye diseases remains poorly understood. The human eye is currently an emerging proteome that may provide key insight into the biological pathways of disease. We review proteomic investigations of the human eye and present a catalogue of 4842 non-redundant proteins identified in human eye tissues and biofluids to date. We highlight the need to identify new biomarkers for eye diseases using proteomics. Recent advances in proteomics now allow the identification of hundreds to thousands of proteins in tissues and fluids, characterization of various post-translational modifications, and simultaneous quantification of multiple proteins. To facilitate proteomic studies of the eye, the Human Eye Proteome Project (HEPP) was organized in September 2012. The HEPP is one of the most recent components of the Biology/Disease-driven Human Proteome Project (B/D-HPP) whose overarching goal is to support the broad application of state-of-the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. The large repertoire of investigative proteomic tools has great potential to transform vision science and enhance understanding of physiology and disease processes that affect sight. PMID:23749747

  2. Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine.

    PubMed

    Zhang, Xi

    2017-02-01

    Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Advances in plant proteomics toward improvement of crop productivity and stress resistancex

    PubMed Central

    Hu, Junjie; Rampitsch, Christof; Bykova, Natalia V.

    2015-01-01

    Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein–protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed. PMID:25926838

  4. Sugarcane proteomics: An update on current status, challenges, and future prospects.

    PubMed

    Barnabas, Leonard; Ramadass, Ashwin; Amalraj, Ramesh Sundar; Palaniyandi, Malathi; Rasappa, Viswanathan

    2015-05-01

    Sugarcane is one of the most important commercial crops cultivated worldwide for the production of crystal sugar, ethanol, and other related by-products. Unlike other comparable monocots like sorghum, maize, and rice, sugarcane genome by virtue of its polyploidy nature remains yet to be fully deciphered. Proteomics-an established complementary tool to genomics is at its infancy in sugarcane as compared to the other monocots. However, with the surge in genomics research accomplished by next-generation sequencing platforms, sugarcane proteomics has gained momentum. This review summarizes the available literature from 1970 to 2014, which ensures a comprehensive coverage on sugarcane proteomics-a topic first of its kind to be reviewed. We herewith compiled substantial contributions in different areas of sugarcane proteomics, which include abiotic and biotic stresses, cell wall, organelle, and structural proteomics. The past decade has witnessed a paradigm shift in the pace with which sugarcane proteomics is progressing, as evident by the number of research publications. In addition to extensively reviewing the progress made thus far, we intend to highlight the scope in sugarcane proteomics, with an aspiration to instigate focused research on sugarcane to harness its full potential for the human welfare. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Proteomics as a Systems Approach to Pancreatitis

    PubMed Central

    Williams, John A.

    2013-01-01

    Proteomics is an approach to looking at the identity, amount, proteolysis, compartmentalization and post-translational modification of a large number of proteins simultaneously in a cell or tissue. Recently, proteomics has begun to be applied to the study of pancreatitis to ascertain mechanisms of disease and search for biomarkers of disease. Most mechanistic work has been carried out in animal models of acute pancreatitis. In eight studies, 97 proteins have been reported to increase, 55 to decrease and 23 to undergo proteolysis. Proteins showing increases are most often related to stress, inflammation or the cytoskeleton while decreases are seen in digestive enzymes and proteins related to metabolism. Many protein changes however, are not consistent between studies and only the most recent studies are rigorous and quantitative. By contrast, biomarker studies have focused on pancreatic juice and plasma of humans with disease and often are directed at distinguishing chronic pancreatitis from cancer. Chronic pancreatitis has also been investigated in tissue sections of histological samples. In this review the results of studies to date are described as well as coverage of the methods used and special issues that must be considered. Areas are pointed out that are worthy of future study. PMID:23851428

  6. Urine sample preparation for proteomic analysis.

    PubMed

    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.

  7. Teaching Students to Attain Annual Transition Goals Using the Take Action Goal Attainment Lessons

    ERIC Educational Resources Information Center

    Martin, Jodie D.; Martin, James E.; Osmani, Kimberly J.

    2014-01-01

    This study used the Take Action goal attainment lesson package and assistive technology to teach nine high school students with mild to moderate disabilities to attain annual transition goals. The Take Action lessons increased students' goal attainment knowledge, and this knowledge generalized to improved Plan Organizers, and slightly increased…

  8. Teaching Students to Attain Annual Transition Goals Using the Take Action Goal Attainment Lessons

    ERIC Educational Resources Information Center

    Martin, Jodie D.; Martin, James E.; Osmani, Kimberly J.

    2014-01-01

    This study used the Take Action goal attainment lesson package and assistive technology to teach nine high school students with mild to moderate disabilities to attain annual transition goals. The Take Action lessons increased students' goal attainment knowledge, and this knowledge generalized to improved Plan Organizers, and slightly increased…

  9. Educational Attainment. Indicator of the Month.

    ERIC Educational Resources Information Center

    National Center for Education Statistics (ED), Washington, DC.

    This fact sheet presents data about educational attainment in the United States. The educational attainment of people aged 25 to 29 years increased between 1971 and 1998, and the percentage with a high school diploma or equivalency certificate rose from 78 to 88%. The percentage of high school completers with some college rose from 44% to 66%, and…

  10. Student Attainment in Relation to Rural Education.

    ERIC Educational Resources Information Center

    Cosby, Arthur G.

    Structural and cultural inequalities hinder the attainment of approximately 25 million rural American youth. A characteristic lack of education and employment opportunities is combined with a restricted realm of attainment in rural areas. Rural people are negatively stereotyped by the mass society, as seen in an examination of linguistic terms…

  11. Educational Attainment: Analysis by Immigrant Generation

    ERIC Educational Resources Information Center

    Chiswick, Barry R.; DebBurman, Noyna

    2004-01-01

    This paper presents a theoretical and empirical analysis of the largely ignored issue of the determinants of the educational attainment of adults by immigrant generation. Using current population survey (CPS) data, differences in educational attainment are analyzed by immigrant generation (first, second, and higher order generations), and among…

  12. Inequality and Educational Attainment: Evidence from Massachusetts

    ERIC Educational Resources Information Center

    Papay, John P.; Murnane, Richard J.; Willett, John B.

    2013-01-01

    In the past thirty years educational attainments in the United States have stagnated, particularly for low-income Americans. As a result, income-related gaps in educational attainments have grown. These gaps are important because education has historically been the key mechanism for intergenerational socio-economic mobility in the U.S. While the…

  13. Educational Attainment: Analysis by Immigrant Generation

    ERIC Educational Resources Information Center

    Chiswick, Barry R.; DebBurman, Noyna

    2004-01-01

    This paper presents a theoretical and empirical analysis of the largely ignored issue of the determinants of the educational attainment of adults by immigrant generation. Using current population survey (CPS) data, differences in educational attainment are analyzed by immigrant generation (first, second, and higher order generations), and among…

  14. Projecting manpower to attain quality

    NASA Technical Reports Server (NTRS)

    Rone, K. Y.

    1983-01-01

    The resulting model is useful as a projection tool but must be validated in order to be used as an on-going software cost engineering tool. A procedure is developed to facilitate the tracking of model projections and actual data to allow the model to be tuned. Finally, since the model must be used in an environment of overlapping development activities on a progression of software elements in development and maintenance, a manpower allocation model is developed for use in a steady state development/maintenance environment. In these days of soaring software costs it becomes increasingly important to properly manage a software development project. One element of the management task is the projection and tracking of manpower required to perform the task. In addition, since the total cost of the task is directly related to the initial quality built into the software, it becomes a necessity to project the development manpower in a way to attain that quality. An approach to projecting and tracking manpower with quality in mind is described.

  15. Immunisation coverage annual report, 2008.

    PubMed

    Hull, Brynley P; Mahajan, Deepika; Dey, Aditi; Menzies, Rob I; McIntyre, Peter B

    2010-09-01

    This, the 2nd annual immunisation coverage report, documents trends during 2008 for a range of standard measures derived from Australian Childhood Immunisation Register data, including overall coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). Coverage by indigenous status and mapping by smaller geographic areas as well as trends in timeliness are also summarised according to standard templates. With respect to overall coverage, Immunise Australia Program targets have been reached for children at 12 and 24 months of age but not for children at 5 years of age. Coverage at 24 months of age exceeds that at 12 months of age, but as receipt of varicella vaccine at 18 months is excluded from calculations of 'fully immunised' this probably represents delayed immunisation, with some contribution from immunisation incentives. Similarly, the decrease in coverage estimates for immunisations due at 4 years of age from March 2008, is primarily due to changing the assessment age from 6 years to 5 years of age from December 2007. A number of individual vaccines on the NIP are not currently assessed for 'fully immunised' status or for eligibility for incentive payments. These include pneumococcal conjugate and meningococcal C conjugate vaccines for which coverage is comparable to vaccines which are assessed for 'fully immunised' status, and rotavirus and varicella vaccines for which coverage is lower. Coverage is also suboptimal for vaccines recommended for Indigenous children only (i.e. hepatitis A and pneumococcal polysaccharide vaccine) as previously reported for other vaccines for both children and adults. Delayed receipt of vaccines is an important issue for vaccines recommended for Indigenous children and has not improved among non-Indigenous children despite improvements in coverage at the 24-month milestone. Although Indigenous children in Australia have coverage levels that are similar to non

  16. Medicare coverage for oncology services.

    PubMed

    Bagley, G P; McVearry, K

    1998-05-15

    Medicare's mission is to assure health care security for our beneficiaries. Title XVIII of the Social Security Act (the Act) provides the Health Care Financing Administration (HCFA) with the authority to fulfill this mission. Although Medicare is considered a defined benefit program, the Act vested Medicare with the discretionary authority to make specific policy decisions when necessary. HCFA's discretionary authority, which is found at section 1862(a)(1)(A) of the Act, enables HCFA to provide coverage for services that are reasonable and necessary for the treatment and diagnosis of illness or injury or to improve the functioning of a malformed body member. To determine whether a service is reasonable and necessary, HCFA relies on authoritative evidence. This evidence includes, but is not limited to, approvals from appropriate federal agencies, such as the Food and Drug Administration, and systematic evaluations of scientific literature via technology assessments. HCFA also may decide that a service warrants a unique type of coverage policy, which is referred to as coverage with conditions. This form of coverage is a middle ground between strict noncoverage and general coverage for a medical service that appears promising, but still is evolving. All these policy specifications effect Medicare coverage of oncology services. This means that reasonable and necessary diagnostic and therapeutic cancer-related services that are not otherwise prohibited by Medicare's statute, regulations, and manual instructions are covered and paid for by the program. Prior to the Balanced Budget Act of 1997 (BBA '97), Medicare provided coverage for some beneficiaries to undergo mammography and Papanicolaou smear screening. As a result of BBA '97, Congress has mandated expanding coverage for these services as well as adding coverage for pelvic examinations, prostate cancer screening, colorectal screening, and antiemetic drugs used as part of an anticancer chemotherapy regimen. Other

  17. [Potential coverage and real coverage of ambulatory health care services in the state of Mexico. The case of 3 marginal communities in Atenco and Chalco].

    PubMed

    Nájera-Aguilar, P; Infante-Castañeda, C

    1990-01-01

    Less than a third of the non-insured population studied through a sample in the State of Mexico was covered by the Institute of Health of the State of México. This low coverage was observed in spite the fact that health services were available within 2 kilometer radius. 33 per cent of the non-insured preferred to utilize other services within their own community, and 24 per cent of them traveled to bigger localities to receive care. These results suggest that to attain adequate coverage, utilization patterns should be investigated so that health services can meet the needs of the target population.

  18. Global Routine Vaccination Coverage, 2015.

    PubMed

    Casey, Rebecca M; Dumolard, Laure; Danovaro-Holliday, M Carolina; Gacic-Dobo, Marta; Diallo, Mamadou S; Hampton, Lee M; Wallace, Aaron S

    2016-11-18

    In 1974, the World Health Organization (WHO) established the Expanded Program on Immunization* to provide protection against six vaccine-preventable diseases through routine infant immunization (1). Based on 2015 WHO and United Nations Children's Fund (UNICEF) estimates, global coverage with the third dose of diphtheria-tetanus-pertussis vaccine (DTP3), the first dose of measles-containing vaccine (MCV1) and the third dose of polio vaccine (Pol3) has remained stable (84%-86%) since 2010. From 2014 to 2015, estimated global coverage with the second MCV dose (MCV2) increased from 39% to 43% by the end of the second year of life and from 58% to 61% when older age groups were included. Global coverage was higher in 2015 than 2010 for newer or underused vaccines, including rotavirus vaccine, pneumococcal conjugate vaccine (PCV), rubella vaccine, Haemophilus influenzae type b (Hib) vaccine, and 3 doses of hepatitis B (HepB3) vaccine. Coverage estimates varied widely by WHO Region, country, and district; in addition, for the vaccines evaluated (MCV, DTP3, Pol3, HepB3, Hib3), wide disparities were found in coverage by country income classification. Improvements in equity of access are necessary to reach and sustain higher coverage and increase protection from vaccine-preventable diseases for all persons.

  19. Methods in tubulin proteomics.

    PubMed

    Miller, Leah M; Xiao, Hui; Burd, Berta; Horwitz, Susan Band; Angeletti, Ruth Hogue; Verdier-Pinard, Pascal

    2010-01-01

    New analytical methods are needed for the successful outcome of experiments aimed at characterizing mechanisms of microtubule dynamics and at understanding the effects of drugs on microtubules. The identification of tubulin isotypes and of regions of the microtubule involved in drug interactions has been advanced by proteomic methodologies. The diversity of tubulin sequences and posttranslational modifications (PTMs) can generate a complex mixture of heterodimers with unique molecular dynamics driving specific functions. Mass spectrometry (MS)-based approaches have been developed, and in combination with chromatographic and/or electrophoretic separation of tubulin polypeptides or peptides, they have contributed to our understanding of tubulin proteomics. We present protocols that we have used for the analysis of tubulin isotypes and PTMs present in tubulin isolated from cells in culture or tissues and for the identification of tubulin regions altered by microtubule-stabilizing agents. Tubulin proteomics complements structural and computer modeling information for a high-resolution view of microtubule dynamics and its alteration by drugs. These methodologies will help in providing insights into tubulin isotype-specific functions and in the design of drugs targeting either all tubulin heterodimers indiscriminately or only those containing specific isotypes.

  20. Chromatin enrichment for proteomics

    PubMed Central

    Kustatscher, Georg; Wills, Karen L. H.; Furlan, Cristina; Rappsilber, Juri

    2015-01-01

    During interphase, chromatin hosts fundamental cellular processes, such as gene expression, DNA replication and DNA damage repair. To analyze chromatin on a proteomic scale, we have developed chromatin enrichment for proteomics (ChEP), which is a simple biochemical procedure that enriches interphase chromatin in all its complexity. It enables researchers to take a ‘snapshot’ of chromatin and to isolate and identify even transiently bound factors. In ChEP, cells are fixed with formaldehyde; subsequently, DNA together with all cross-linked proteins is isolated by centrifugation under denaturing conditions. This approach enables the analysis of global chromatin composition and its changes, which is in contrast with existing chromatin enrichment procedures, which either focus on specific chromatin loci (e.g., affinity purification) or are limited in specificity, such as the analysis of the chromatin pellet (i.e., analysis of all insoluble nuclear material). ChEP takes half a day to complete and requires no specialized laboratory skills or equipment. ChEP enables the characterization of chromatin response to drug treatment or physiological processes. Beyond proteomics, ChEP may preclear chromatin for chromatin immunoprecipitation (ChIP) analyses. PMID:25101823

  1. GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide

    PubMed Central

    Lima, D. C.; Duarte, F. T.; Medeiros, V. K. S.; Carvalho, P. C.; Nogueira, F. C. S.; Araujo, G. D. T.; Domont, G. B.; Batistuzzo de Medeiros, S. R.

    2016-01-01

    Chromobacterium violaceum is a free-living bacillus with several genes that enables it survival under different harsh environments such as oxidative and temperature stresses. Here we performed a label-free quantitative proteomic study to unravel the molecular mechanisms that enable C. violaceum to survive oxidative stress. To achieve this, total proteins extracted from control and C. violaceum cultures exposed during two hours with 8 mM hydrogen peroxide were analyzed using GeLC-MS proteomics. Analysis revealed that under the stress condition, the bacterium expressed proteins that protected it from the damage caused by reactive oxygen condition and decreasing the abundance of proteins responsible for bacterial growth and catabolism. GeLC-MS proteomics analysis provided an overview of the metabolic pathways involved in the response of C. violaceum to oxidative stress ultimately aggregating knowledge of the response of this organism to environmental stress. This study identified approximately 1500 proteins, generating the largest proteomic coverage of C. violaceum so far. We also detected proteins with unknown function that we hypothesize to be part of new mechanisms related to oxidative stress defense. Finally, we identified the mechanism of clustered regularly interspaced short palindromic repeats (CRISPR), which has not yet been reported for this organism. PMID:27321545

  2. GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide.

    PubMed

    Lima, D C; Duarte, F T; Medeiros, V K S; Carvalho, P C; Nogueira, F C S; Araujo, G D T; Domont, G B; Batistuzzo de Medeiros, S R

    2016-06-20

    Chromobacterium violaceum is a free-living bacillus with several genes that enables it survival under different harsh environments such as oxidative and temperature stresses. Here we performed a label-free quantitative proteomic study to unravel the molecular mechanisms that enable C. violaceum to survive oxidative stress. To achieve this, total proteins extracted from control and C. violaceum cultures exposed during two hours with 8 mM hydrogen peroxide were analyzed using GeLC-MS proteomics. Analysis revealed that under the stress condition, the bacterium expressed proteins that protected it from the damage caused by reactive oxygen condition and decreasing the abundance of proteins responsible for bacterial growth and catabolism. GeLC-MS proteomics analysis provided an overview of the metabolic pathways involved in the response of C. violaceum to oxidative stress ultimately aggregating knowledge of the response of this organism to environmental stress. This study identified approximately 1500 proteins, generating the largest proteomic coverage of C. violaceum so far. We also detected proteins with unknown function that we hypothesize to be part of new mechanisms related to oxidative stress defense. Finally, we identified the mechanism of clustered regularly interspaced short palindromic repeats (CRISPR), which has not yet been reported for this organism.

  3. A reference map of human nasopharyngeal squamous carcinoma proteome.

    PubMed

    Li, Feng; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Li, Maoyu; Feng, Xueping; Guan, Yongjun; Chen, Zhuchu

    2007-05-01

    In order to conduct a comparative proteomics study of human nasopharyngeal carcinoma (NPC) to understand the molecular mechanisms that participate in the formation of NPC, the two-dimensional gel electrophoresis (2-DE) reference map of human NPC tissue proteome was described. To provide a high level of reproducibility between gels and accurately array each protein expressed in NPC tissue proteome, the two-dimensional polyacrylamide gel electrophoresis system, modified colloidal Coomassie Brilliant Blue staining method and ImageMaster 2D Platinum image analysis software were used. The NPC 2-DE maps show that high quality and good reproducibility of the 2-DE gel pattern was attained. An average total of 1,100 protein spots were separated by 2-DE, visualized by a modified colloidal Coomassie Brilliant Blue staining method. A synthesized 2-DE reference gel was acquired after detailed analysis of the NPC 2-DE gel maps, and 216 medium to high abundant spots were identified as landmark spots of NPC 2-DE gel, which expressed on >75% of gels. To provide an unambiguous identification of the landmark spots in gels, MALDI-TOF, ESI-Q-TOF mass spectrometry and database search were used to identify the proteins expressed in NPC tissue proteome. Between the 216 landmark spots, all proteins were identified with MALDI-TOF at first, 41 of which were identified with both MALDI-TOF and ESI-Q-TOF. All identified proteins were classified in terms of their subcellular localization and physiological function with information from SWISS-PROT and NCBI websites. According to our knowledge this is the first 2-DE reference map of human NPC. This reference map will serve as a basis for further studies of human NPC and the reference map data will be used to expand the proteome database of human NPC, which can be accessed in our website (http://www.xyproteomics.org/).

  4. Perfluorinated alcohol induced coacervates as extraction media for proteomic analysis.

    PubMed

    McCord, James P; Muddiman, David C; Khaledi, Morteza G

    2017-06-12

    We describe a novel method for using hexafluoroisopropanol (HFIP) induced coacervates with a variety of surfactants to extract proteins from a yeast whole cell lysate and conduct a global proteomic investigation on the extracted proteins. Yeast whole cell lysates were prepared and proteins were extracted using two workflows: 1) Proteins were extracted into the coacervate generated from the mixture of HFIP, surfactant, and cell lysate. 2) Proteins were extracted from cell lysate using a surfactant solution, and HFIP was added to the supernatant to generate a coacervate phase with concentrated proteins. Both initial extractions were followed by a modified filter-aided sample preparation (FASP) cleanup. The methodology yields significant protein concentrations in the coacervate phase (2-3 orders of magnitude increase in concentration) and an increase in proteome sequence coverage (+5%), membrane proteins identifications (+50%), and identification of proteins from low abundance cellular subfractions (>10% of total IDs). Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis.

    PubMed

    Wang, Fangjun; Wei, Xiaoluan; Zhou, Hu; Liu, Jing; Figeys, Daniel; Zou, Hanfa

    2012-11-01

    Various enzyme reactors and online enzyme digestion strategies have been developed in recent years. These reactors greatly enhanced the detection sensitivity and proteome coverage in qualitative proteomics. However, these devices have higher rates of miscleavage in protein digestion. Therefore, we investigated the effect of online enzyme digestion on the quantification accuracy of quantitative proteomics using chemical or metabolic isotope labeling approaches. The incomplete digestion would introduce some unexpected variations in comparative quantification when the samples are digested and then chemically isotope labeled in different aliquots. Even when identical protein aliquots are processed on these devices using post-digestion chemical isotope labeling and the CVs of the ratios controlled to less than 50% in replicate analyses, about 10% of the quantified proteins have a ratio greater than two-fold, whereas in theory the ratio is 1:1. Interestingly, the incomplete digestion with enzyme reactor is not a problem when metabolic isotope labeling samples were processed because the proteins are isotopically labeled in vivo prior to their simultaneous digestion within the reactor. Our results also demonstrated that both high quantification accuracy and high proteome coverage can be achieved in comparative proteome quantification using online enzyme digestion even when a limited amount of metabolic isotope labeling samples is used (1683 proteins comparatively quantified from 10(5) Hela cells).

  6. Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP.

    PubMed

    Chang, Cheng; Li, Liwei; Zhang, Chengpu; Wu, Songfeng; Guo, Kun; Zi, Jin; Chen, Zhipeng; Jiang, Jing; Ma, Jie; Yu, Qing; Fan, Fengxu; Qin, Peibin; Han, Mingfei; Su, Na; Chen, Tao; Wang, Kang; Zhai, Linhui; Zhang, Tao; Ying, Wantao; Xu, Zhongwei; Zhang, Yang; Liu, Yinkun; Liu, Xiaohui; Zhong, Fan; Shen, Huali; Wang, Quanhui; Hou, Guixue; Zhao, Haiyi; Li, Guilin; Liu, Siqi; Gu, Wei; Wang, Guibin; Wang, Tong; Zhang, Gong; Qian, Xiaohong; Li, Ning; He, Qing-Yu; Lin, Liang; Yang, Pengyuan; Zhu, Yunping; He, Fuchu; Xu, Ping

    2014-01-03

    To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with varied metastatic potential qualitatively and quantitatively. The results provide a global view of gene expression profiles. The 9064 identified high confident proteins covered 50.2% of all gene products in the translatome. Those proteins with function of adhesion, development, reproduction, and so on are low abundant in transcriptome and translatome but absent in proteome. Taking the translatome as the background of protein expression, we found that the protein abundance plays a decisive role and hydrophobicity has a greater influence than molecular weight and isoelectric point on protein detectability. Thus, the enrichment strategy used for low-abundant transcription factors helped to identify missing proteins. In addition, those peptides with single amino acid polymorphisms played a significant role for the disease research, although they might negligibly contribute to new protein identification. The proteome raw and metadata of proteome were collected using the iProX submission system and submitted to ProteomeXchange (PXD000529, PXD000533, and PXD000535). All detailed information in this study can be accessed from the Chinese Chromosome-Centric Human Proteome Database.

  7. Proteomic analysis of Caenorhabditis elegans

    USDA-ARS?s Scientific Manuscript database

    Proteomic studies of the free-living nematode Caenorhabditis elegans have recently received great attention because this animal is a useful model platform for the in vivo study of various biological problems relevant to human disease. In general, proteomic analysis is performed in order to address a...

  8. Proteomic analysis in cardiovascular research.

    PubMed

    Oda, Teiji; Matsumoto, Ken-ichi

    2016-03-01

    Advances in mass spectrometry technology and bioinformatics using clinical human samples have expanded quantitative proteomics in cardiovascular research. There are two major proteomic strategies: namely, "gel-based" or "gel-free" proteomics coupled with either "top-down" or "bottom-up" mass spectrometry. Both are introduced into the proteomic analysis using plasma or serum sample targeting 'biomarker" searches of aortic aneurysm and tissue samples, such as from the aneurysmal wall, calcific aortic valve, or myocardial tissue, investigating pathophysiological protein interactions and post-translational modifications. We summarize the proteomic studies that analyzed human samples taken during cardiovascular surgery to investigate disease processes, in order to better understand the system-wide changes behind known molecular factors and specific signaling pathways.

  9. Proteome Studies of Filamentous Fungi

    SciTech Connect

    Baker, Scott E.; Panisko, Ellen A.

    2011-04-20

    The continued fast pace of fungal genome sequence generation has enabled proteomic analysis of a wide breadth of organisms that span the breadth of the Kingdom Fungi. There is some phylogenetic bias to the current catalog of fungi with reasonable DNA sequence databases (genomic or EST) that could be analyzed at a global proteomic level. However, the rapid development of next generation sequencing platforms has lowered the cost of genome sequencing such that in the near future, having a genome sequence will no longer be a time or cost bottleneck for downstream proteomic (and transcriptomic) analyses. High throughput, non-gel based proteomics offers a snapshot of proteins present in a given sample at a single point in time. There are a number of different variations on the general method and technologies for identifying peptides in a given sample. We present a method that can serve as a “baseline” for proteomic studies of fungi.

  10. Cysteinyl Peptide Capture for Shotgun Proteomics: Global Assessment of Chemoselective Fractionation

    PubMed Central

    2010-01-01

    The complexity of cell and tissue proteomes presents one of the most significant technical challenges in proteomic biomarker discovery. Multidimensional liquid chromatography−tandem mass spectrometry (LC−MS/MS)-based shotgun proteomics can be coupled with selective enrichment of cysteinyl peptides (Cys-peptides) to reduce sample complexity and increase proteome coverage. Here we evaluated the impact of Cys-peptide enrichment on global proteomic inventories. We employed a new cleavable thiol-reactive biotinylating probe, N-(2-(2-(2-(2-(3-(1-hydroxy-2-oxo-2-phenylethyl)phenoxy)acetamido)ethoxy)-ethoxy)ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide (IBB), to capture Cys-peptides after digestion. Treatment of tryptic digests with the IBB reagent followed by streptavidin capture and mild alkaline hydrolysis releases a highly purified population of Cys-peptides with a residual S-carboxymethyl tag. Isoelectric focusing (IEF) followed by LC−MS/MS of Cys-peptides significantly expanded proteome coverage in Saccharomyces cerevisiae (yeast) and in human colon carcinoma RKO cells. IBB-based fractionation enhanced detection of Cys-proteins in direct proportion to their cysteine content. The degree of enrichment typically was 2−8-fold but ranged up to almost 20-fold for a few proteins. Published copy number annotation for the yeast proteome enabled benchmarking of MS/MS spectral count data to yeast protein abundance and revealed selective enrichment of cysteine-rich, lower abundance proteins. Spectral count data further established this relationship in RKO cells. Enhanced detection of low abundance proteins was due to the chemoselectivity of Cys-peptide capture, rather than simplification of the peptide mixture through fractionation. PMID:20731415

  11. Cysteinyl peptide capture for shotgun proteomics: global assessment of chemoselective fractionation.

    PubMed

    Lin, De; Li, Jing; Slebos, Robbert J C; Liebler, Daniel C

    2010-10-01

    The complexity of cell and tissue proteomes presents one of the most significant technical challenges in proteomic biomarker discovery. Multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based shotgun proteomics can be coupled with selective enrichment of cysteinyl peptides (Cys-peptides) to reduce sample complexity and increase proteome coverage. Here we evaluated the impact of Cys-peptide enrichment on global proteomic inventories. We employed a new cleavable thiol-reactive biotinylating probe, N-(2-(2-(2-(2-(3-(1-hydroxy-2-oxo-2-phenylethyl)phenoxy)acetamido)ethoxy)-ethoxy)ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide (IBB), to capture Cys-peptides after digestion. Treatment of tryptic digests with the IBB reagent followed by streptavidin capture and mild alkaline hydrolysis releases a highly purified population of Cys-peptides with a residual S-carboxymethyl tag. Isoelectric focusing (IEF) followed by LC-MS/MS of Cys-peptides significantly expanded proteome coverage in Saccharomyces cerevisiae (yeast) and in human colon carcinoma RKO cells. IBB-based fractionation enhanced detection of Cys-proteins in direct proportion to their cysteine content. The degree of enrichment typically was 2-8-fold but ranged up to almost 20-fold for a few proteins. Published copy number annotation for the yeast proteome enabled benchmarking of MS/MS spectral count data to yeast protein abundance and revealed selective enrichment of cysteine-rich, lower abundance proteins. Spectral count data further established this relationship in RKO cells. Enhanced detection of low abundance proteins was due to the chemoselectivity of Cys-peptide capture, rather than simplification of the peptide mixture through fractionation.

  12. Proteomics research in India: an update.

    PubMed

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

    2015-09-08

    After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Converging on the optimal attainment of requirements

    NASA Technical Reports Server (NTRS)

    Feather, M. S.; Menzies, T.

    2002-01-01

    Planning for the optimal attainment of requirements is an important early lifecycle activity. However, such planning is difficult when dealing with competing requirements, limited resources, and the incompleteness of information available at requirements time.

  14. Basic Attainment Processes: A Replication and Extension

    ERIC Educational Resources Information Center

    Alexander, Karl L.; Eckland, Bruce

    1975-01-01

    This paper represents the preliminary analysis of a longitudinal data set well-suited for the study of educational and occupational attainment processes. The Blau and Duncan basic model is used. (Author/RM)

  15. Early School Adjustment and Educational Attainment

    PubMed Central

    Magnuson, Katherine; Duncan, Greg; Lee, Kenneth T.H.; Metzger, Molly

    2016-01-01

    Although school attainment is a cumulative process combining mastery of both academic and behavioral skills, most studies have offered only a piecemeal view of the associations between middle childhood capacities and subsequent schooling outcomes. Using a 20-year longitudinal dataset, this study estimates the association between children’s academic skills, anti-social behaviors and attention problems, all averaged across middle childhood, and their long-term educational outcomes. After adjusting for family and individual background measures, we find that high average levels of math and reading achievement, and low average levels of anti-social behavior problems, are positively associated with later attainment. Associations between attention problems and attainment are small. Associations are attenuated somewhat when sibling differences in these skills and behaviors are related to sibling differences in attainment outcomes. PMID:27563151

  16. Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis.

    PubMed

    Facchinelli, Fabio; Pribil, Mathias; Oster, Ulrike; Ebert, Nina J; Bhattacharya, Debashish; Leister, Dario; Weber, Andreas P M

    2013-02-01

    Glaucophytes represent the first lineage of photosynthetic eukaryotes of primary endosymbiotic origin that diverged after plastid establishment. The muroplast of Cyanophora paradoxa represents a primitive plastid that resembles its cyanobacterial ancestor in pigment composition and the presence of a peptidoglycan wall. To attain insights into the evolutionary history of cyanobiont integration and plastid development, it would thus be highly desirable to obtain knowledge on the composition of the glaucophyte plastid proteome. Here, we provide the first proteomic analysis of the muroplast of C. paradoxa. Mass spectrometric analysis of the muroplast proteome identified 510 proteins with high confidence. The protein repertoire of the muroplast revealed novel paths for reduced carbon flow and export to the cytosol through a sugar phosphate transporter of chlamydial origin. We propose that C. paradoxa possesses a primordial plastid mirroring the situation in the early protoalga.

  17. Immunisation coverage annual report, 2011.

    PubMed

    Hull, Brynley P; Dey, Aditi; Menzies, Rob I; Brotherton, Julia M; McIntyre, Peter B

    2013-12-31

    This, the 5th annual immunisation coverage report, documents trends during 2011 for a range of standard measures derived from Australian Childhood Immunisation Register data, and National Human Papillomavirus (HPV) Vaccination Program Register data. The proportion of children 'fully vaccinated' at 12, 24 and 60 months of age was 91.4%, 92.2% and 89.5% respectively. Although pneumococcal vaccine had similar coverage at 12 months to other vaccines, coverage was lower for rotavirus at 12 months (83.8%) and varicella at 24 months (83.9%). By late 2011, the percentage of children who received the 1st dose of DTPa vaccine dose at less than 8 weeks of age was greater than 50% in 3 jurisdictions, the Australian Capital Territory, Victoria, and Queensland and at 70% for New South Wales and Tasmania. Although coverage at 12 months of age was lower among Indigenous children than non-Indigenous children in all jurisdictions, the extent of the difference varied. Overall, coverage at 24 months of age exceeded that at 12 months of age nationally. At 60 months of age, there was dramatic variation between individual jurisdictions, ranging from coverage 8% lower in Indigenous children in South Australia to 6% higher in the Northern Territory. As previously documented, vaccines recommended for Indigenous children only (hepatitis A and pneumococcal polysaccharide vaccine) had suboptimal coverage at 60% and 68%, respectively. On-time receipt (before 49 months of age) of vaccines by Indigenous children at the 60-month milestone age improved between 2010 (18%) and 2011 (19%) but the disparity in on-time vaccination between Indigenous and non-Indigenous children increased at all 3 age milestones. The percentage of vaccine objectors in 2011 (1.7%) has increased from 2007 when it was 1.1%. Coverage data for the 3rd dose of HPV from the national HPV register in the school catch up program was 71% but was substantially lower for the catch-up program for women outside school (39

  18. Proteomics with a pinch of salt: A cyanobacterial perspective

    PubMed Central

    Pandhal, Jagroop; Wright, Phillip C; Biggs, Catherine A

    2008-01-01

    Cyanobacteria are ancient life forms and have adapted to a variety of extreme environments, including high salinity. Biochemical, physiological and genetic studies have contributed to uncovering their underlying survival mechanisms, and as recent studies demonstrate, proteomics has the potential to increase our overall understanding further. To date, most salt-related cyanobacterial proteomic studies have utilised gel electrophoresis with the model organism Synechocystis sp. PCC6803. Moreover, focus has been on 2–4% w/v NaCl concentrations within different cellular compartments. Under these conditions, Synechocystis sp. PCC6803 was found to respond and adapt to salt stress through synthesis of general and specific stress proteins, altering the protein composition of extracellular layers, and re-directing control of complex central intermediary pathways. Post-transcriptional control was also predicted through non-correlating transcript level data and identification of protein isoforms. In this paper, we also review technical developments with emphasis on improving the quality and quantity of proteomic data and overcoming the detrimental effects of salt on sample preparation and analysis. Developments in gel-free methods include protein and peptide fractionation workflows, which can increase coverage of the proteome (20% in Synechocystis sp. PCC6803). Quantitative techniques have also improved in accuracy, resulting in confidence in quantitation approaching or even surpassing that seen in transcriptomic techniques (better than 1.5-fold in differential expression). Furthermore, in vivo metabolic labelling and de novo protein sequencing software have improved the ability to apply proteomics to unsequenced environmental isolates. The example used in this review is a cyanobacterium isolated from a Saharan salt lake. PMID:18412952

  19. 24 CFR 203.205 - Plan coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Plan coverage. 203.205 Section 203... Protection Plans (plan) § 203.205 Plan coverage. (a) Plan coverage must take effect at closing or settlement following the initial sale of the property to the homeowner. (b) During the first year of coverage, a Plan...

  20. 24 CFR 203.205 - Plan coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 2 2014-04-01 2014-04-01 false Plan coverage. 203.205 Section 203... Protection Plans (plan) § 203.205 Plan coverage. (a) Plan coverage must take effect at closing or settlement following the initial sale of the property to the homeowner. (b) During the first year of coverage, a...

  1. 24 CFR 203.205 - Plan coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Plan coverage. 203.205 Section 203... Protection Plans (plan) § 203.205 Plan coverage. (a) Plan coverage must take effect at closing or settlement following the initial sale of the property to the homeowner. (b) During the first year of coverage, a...

  2. Proteome-pI: proteome isoelectric point database.

    PubMed

    Kozlowski, Lukasz P

    2017-01-04

    Proteome-pI is an online database containing information about predicted isoelectric points for 5029 proteomes calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography-mass spectrometry and X-ray protein crystallography. The database, available at http://isoelectricpointdb.org allows the retrieval of virtual 2D-PAGE plots and the development of customised fractions of proteome based on isoelectric point and molecular weight. Moreover, Proteome-pI facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life. For instance, using Proteome-pI data, it is clear that Eukaryotes, which evolved tight control of homeostasis, encode proteins with pI values near the cell pH. In contrast, Archaea living frequently in extreme environments can possess proteins with a wide range of isoelectric points. The database includes various statistics and tools for interactive browsing, searching and sorting. Apart from data for individual proteomes, datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated and made available in CSV format. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Proteome-pI: proteome isoelectric point database

    PubMed Central

    Kozlowski, Lukasz P.

    2017-01-01

    Proteome-pI is an online database containing information about predicted isoelectric points for 5029 proteomes calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography–mass spectrometry and X-ray protein crystallography. The database, available at http://isoelectricpointdb.org allows the retrieval of virtual 2D-PAGE plots and the development of customised fractions of proteome based on isoelectric point and molecular weight. Moreover, Proteome-pI facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life. For instance, using Proteome-pI data, it is clear that Eukaryotes, which evolved tight control of homeostasis, encode proteins with pI values near the cell pH. In contrast, Archaea living frequently in extreme environments can possess proteins with a wide range of isoelectric points. The database includes various statistics and tools for interactive browsing, searching and sorting. Apart from data for individual proteomes, datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated and made available in CSV format. PMID:27789699

  4. The Proteomics of Drusen

    PubMed Central

    Crabb, John W.

    2014-01-01

    The formation of extracellular deposits known as drusen below the macular region of the retina correlates with increased risk of severe visual loss from age-related macular degeneration (AMD). Inflammation and complement dysregulation contribute to AMD progression; however, disease mechanisms remain incompletely defined. Multiple genetic and environmental factors influence AMD pathology, and although immune system processes play a central role, multiple molecular mechanisms appear to be involved. Drusen proteomics, including the analyses of constituent proteins, oxidative protein modifications, and pattern recognition receptors, provide a foundation for deciphering mechanisms of drusen biogenesis and AMD pathology. PMID:24799364

  5. Monitoring Intervention Coverage in the Context of Universal Health Coverage

    PubMed Central

    Boerma, Ties; AbouZahr, Carla; Evans, David; Evans, Tim

    2014-01-01

    Monitoring universal health coverage (UHC) focuses on information on health intervention coverage and financial protection. This paper addresses monitoring intervention coverage, related to the full spectrum of UHC, including health promotion and disease prevention, treatment, rehabilitation, and palliation. A comprehensive core set of indicators most relevant to the country situation should be monitored on a regular basis as part of health progress and systems performance assessment for all countries. UHC monitoring should be embedded in a broad results framework for the country health system, but focus on indicators related to the coverage of interventions that most directly reflect the results of UHC investments and strategies in each country. A set of tracer coverage indicators can be selected, divided into two groups—promotion/prevention, and treatment/care—as illustrated in this paper. Disaggregation of the indicators by the main equity stratifiers is critical to monitor progress in all population groups. Targets need to be set in accordance with baselines, historical rate of progress, and measurement considerations. Critical measurement gaps also exist, especially for treatment indicators, covering issues such as mental health, injuries, chronic conditions, surgical interventions, rehabilitation, and palliation. Consequently, further research and proxy indicators need to be used in the interim. Ideally, indicators should include a quality of intervention dimension. For some interventions, use of a single indicator is feasible, such as management of hypertension; but in many areas additional indicators are needed to capture quality of service provision. The monitoring of UHC has significant implications for health information systems. Major data gaps will need to be filled. At a minimum, countries will need to administer regular household health surveys with biological and clinical data collection. Countries will also need to improve the production of

  6. Monitoring intervention coverage in the context of universal health coverage.

    PubMed

    Boerma, Ties; AbouZahr, Carla; Evans, David; Evans, Tim

    2014-09-01

    Monitoring universal health coverage (UHC) focuses on information on health intervention coverage and financial protection. This paper addresses monitoring intervention coverage, related to the full spectrum of UHC, including health promotion and disease prevention, treatment, rehabilitation, and palliation. A comprehensive core set of indicators most relevant to the country situation should be monitored on a regular basis as part of health progress and systems performance assessment for all countries. UHC monitoring should be embedded in a broad results framework for the country health system, but focus on indicators related to the coverage of interventions that most directly reflect the results of UHC investments and strategies in each country. A set of tracer coverage indicators can be selected, divided into two groups-promotion/prevention, and treatment/care-as illustrated in this paper. Disaggregation of the indicators by the main equity stratifiers is critical to monitor progress in all population groups. Targets need to be set in accordance with baselines, historical rate of progress, and measurement considerations. Critical measurement gaps also exist, especially for treatment indicators, covering issues such as mental health, injuries, chronic conditions, surgical interventions, rehabilitation, and palliation. Consequently, further research and proxy indicators need to be used in the interim. Ideally, indicators should include a quality of intervention dimension. For some interventions, use of a single indicator is feasible, such as management of hypertension; but in many areas additional indicators are needed to capture quality of service provision. The monitoring of UHC has significant implications for health information systems. Major data gaps will need to be filled. At a minimum, countries will need to administer regular household health surveys with biological and clinical data collection. Countries will also need to improve the production of

  7. The Use of a Quantitative Cysteinyl-peptide Enrichment Technology for High-Throughput Quantitative Proteomics

    SciTech Connect

    Liu, Tao; Qian, Weijun; Camp, David G.; Smith, Richard D.

    2007-01-02

    Quantitative proteomic measurements are of significant interest in studies aimed at discovering disease biomarkers and providing new insights into biological pathways. A quantitative cysteinyl-peptide enrichment technology (QCET) can be employed to achieve higher efficiency, greater dynamic range, and higher throughput in quantitative proteomic studies that utilize stable-isotope labeling techniques combined with high-resolution liquid chromatography (LC)-mass spectrometry (MS) measurements. The QCET approach involves specific 16O/18O labeling of tryptic peptides, high-efficiency enrichment of cysteinyl-peptides, and confident protein identification and quantification from high resolution LC-Fourier transform ion cyclotron resonance mass spectrometry (FTICR) measurements and a previously established database of accurate mass and elution time information. This methodology is demonstrated by using proteome profiling of naïve and in vitro-differentiated human mammary epithelial cells (HMEC) as an example, which initially resulted in the identification and quantification of 603 proteins in a single LC-FTICR analysis. QCET provides not only highly efficient enrichment of cysteinyl-peptides for more extensive proteome coverage and improved labeling efficiency for better quantitative measurements, but more importantly, a high-throughput strategy suitable for quantitative proteome analysis where extensive or parallel proteomic measurements are required, such as in time course studies of specific pathways and clinical sample analyses for biomarker discovery.

  8. Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics

    PubMed Central

    Van, Phu T.; Schmid, Amy K.; King, Nichole L.; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T.; Goo, Young-Ah; Deutsch, Eric W.; Reiss, David J.; Mallick, Parag; Baliga, Nitin S.

    2009-01-01

    The relatively small numbers of proteins and fewer possible posttranslational modifications in microbes provides a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has helped highlight plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics. PMID:18652504

  9. Proteome complexity and the forces that drive proteome imbalance.

    PubMed

    Harper, J Wade; Bennett, Eric J

    2016-09-15

    The cellular proteome is a complex microcosm of structural and regulatory networks that requires continuous surveillance and modification to meet the dynamic needs of the cell. It is therefore crucial that the protein flux of the cell remains in balance to ensure proper cell function. Genetic alterations that range from chromosome imbalance to oncogene activation can affect the speed, fidelity and capacity of protein biogenesis and degradation systems, which often results in proteome imbalance. An improved understanding of the causes and consequences of proteome imbalance is helping to reveal how these systems can be targeted to treat diseases such as cancer.

  10. Gene-centric view on the human proteome project: the example of the Russian roadmap for chromosome 18.

    PubMed

    Archakov, Alexander; Aseev, Alexander; Bykov, Victor; Grigoriev, Anatoly; Govorun, Vadim; Ivanov, Vadim; Khlunov, Alexander; Lisitsa, Andrey; Mazurenko, Sergey; Makarov, Alexander A; Ponomarenko, Elena; Sagdeev, Renad; Skryabin, Konstantin

    2011-05-01

    During the 2010 Human Proteome Organization Congress in Sydney, a gene-centric approach emerged as a feasible and tractable scaffold for assemblage of the Human Proteome Project. Bringing the gene-centric principle into practice, a roadmap for the 18th chromosome was drafted, postulating the limited sensitivity of analytical methods, as a serious bottleneck in proteomics. In the context of the sensitivity problem, we refer to the "copy number of protein molecules" as a measurable assessment of protein abundance. The roadmap is focused on the development of technology to attain the low- and ultralow -"copied" portion of the proteome. Roadmap merges the genomic, transcriptomic and proteomic levels to identify the majority of 285 proteins from 18th chromosome - master proteins. Master protein is the primary translation of the coding sequence and resembling at least one of the known isoforms, coded by the gene. The executive phase of the roadmap includes the expansion of the study of the master proteins with alternate splicing, single amino acid polymorphisms (SAPs) and post-translational modifications. In implementing the roadmap, Russian scientists are expecting to establish proteomic technologies for integrating MS and atomic force microscopy (AFM). These technologies are anticipated to unlock the value of new biomarkers at a detection limit of 10(-18) M, i.e. 1 protein copy per 1 μL of plasma. The roadmap plan is posted at www.proteome.ru/en/roadmap/ and a forum for discussion of the document is supported.

  11. Music Coverage in Online Databases.

    ERIC Educational Resources Information Center

    Goudy, Allie Wise

    1982-01-01

    Summarizes the results of a study accessing music coverage in 11 databases--ABI/INFORM, AMERICA--HISTORY AND LIFE, ERIC, HISTORICAL ABSTRACTS, INSPEC, MAGAZINE INDEX, MLA BIBLIOGRAPHY, NATIONAL NEWSPAPER INDEX, PUBLIC AFFAIRS INFORMATION SERVICE INTERNATIONAL, PSYCHINFO, and SOCIOLOGICAL ABSTRACTS. Selection of search terms and relevance of items…

  12. Immunisation coverage annual report, 2014.

    PubMed

    Hull, Brynley P; Hendry, Alexandra J; Dey, Aditi; Beard, Frank H; Brotherton, Julia M; McIntyre, Peter B

    2017-03-31

    This 8th annual immunisation coverage report shows data for 2014 derived from the Australian Childhood Immunisation Register and the National Human Papillomavirus Vaccination Program Register. This report includes coverage data for 'fully immunised' and by individual vaccines at standard age milestones and timeliness of receipt at earlier ages according to Indigenous status. Overall, 'fully immunised' coverage has been mostly stable at the 12- and 24-month age milestones since late 2003, but at 60 months of age, it has increased by more than 10 percentage points since 2009. As in previous years, coverage for 'fully immunised' at 12 months of age among Indigenous children was 3.7% lower than for non-Indigenous children overall, varying from 6.9 percentage points in Western Australia to 0.3 of a percentage point in the Australian Capital Territory. In 2014, 73.4% of Australian females aged 15 years had 3 documented doses of human papillomavirus vaccine (jurisdictional range 67.7% to 77.4%), and 82.7% had at least 1 dose, compared with 71.4% and 81.5%, respectively, in 2013. The disparity in on-time vaccination between Indigenous and non-Indigenous children in 2014 diminished progressively from 20.2% for vaccines due by 12 months to 11.5% for those due by 24 months and 3.0% at 60 months of age.

  13. Crime News Coverage in Perspective.

    ERIC Educational Resources Information Center

    Graber, Doris A.

    According to one sociological model, news is a product of socially determined notions of who and what is important and the organizational structures that result for routinizing news collection; events that deviate from these notions are ignored. This report describes a study of crime news coverage in the media that used this model to examine the…

  14. Is Crime News Coverage Excessive?

    ERIC Educational Resources Information Center

    Graber, Doris A.

    1979-01-01

    Reports on the frequency and manner in which various crime and noncrime news topics were presented in selected newspapers and television newscasts in 1976. Examines news flow data to determine whether news output was inflexible, and whether crime news coverage distorted the amount of real-life crime. (PD)

  15. Tear proteomics in keratoconus.

    PubMed

    Pannebaker, Catherine; Chandler, Heather L; Nichols, Jason J

    2010-10-02

    The purpose of this work was to identify potential tear-film based proteins expressed in keratoconus. Recruited subjects were normal gas permeable (GP) contact lens wearers, keratoconus subjects wearing GP contact lenses, and keratoconus subjects without contact lenses. Subjects wearing soft lenses or having previous ocular surgeries were excluded from participating. Approximately 5 µl of tears were sampled from both eye of each subject using glass microcapillaries. Additional testing included a brief history, visual acuity, slit lamp examination, and topography. Proteomic analyses used to compare samples included Bradford assays, cytokine arrays, SDS-PAGE, and mass spectrometry. Forty-four subjects were enrolled in the study including 20 normals (GP wearers), 18 with keratoconus and wearing GPs, and six with keratoconus (non-lens wearers). Across all proteomic approaches, several proteins were identified as possibly being unique to keratoconus. Increased expression of matrix metalloproteinase-1 (MMP-1) was found in keratoconus subjects with and without gas permeable contact lenses (p=0.02). Unique proteins more associated with keratoconus included several keratins, immunoglobulins alpha and kappa, precursors to prolactin, lysozyme C, and lipocalin. Initial analyses indicate that keratoconus may be associated with the differential expression of several proteins. Further testing is needed to determine any causal relationship or correlation with the etiology of this condition.

  16. Proteomics of the Spermatozoon

    PubMed Central

    Oliva, R; Ballescá, JL

    2012-01-01

    The study of the sperm proteins is crucial for understanding its normal function and alterations in infertile patients. The sperm is a highly specialized cell with a very large flagella, with little cytoplasm and a highly condensed nucleus. The most abundant proteins in the nucleus of mammalian sperm are the protamines. The main functions of the protamines are the condensation of the DNA, possibly contributing to the generation of a more hydrodynamic sperm head and to the protection of the genetic message. However, in addition to protamines, about 5.0–15.0% of the paternal genome is also complexed with histones and histone variants. It has also demonstrated a differential distribution of genes in regions associated with histone and protamine-associated regions, suggesting a potential epigenetic relevance in embryonic development. More recently, detailed lists of proteins have been described corresponding to the different compartments of the sperm cell thanks to the application of recent proteomic techniques based on mass spectrometry (MS). Differential proteomics is also being applied to identify the presence of protein abnormalities found in infertile patients. PMID:24052739

  17. Proteomics of the spermatozoon.

    PubMed

    Oliva, R; Ballescá, Jl

    2012-12-01

    The study of the sperm proteins is crucial for understanding its normal function and alterations in infertile patients. The sperm is a highly specialized cell with a very large flagella, with little cytoplasm and a highly condensed nucleus. The most abundant proteins in the nucleus of mammalian sperm are the protamines. The main functions of the protamines are the condensation of the DNA, possibly contributing to the generation of a more hydrodynamic sperm head and to the protection of the genetic message. However, in addition to protamines, about 5.0-15.0% of the paternal genome is also complexed with histones and histone variants. It has also demonstrated a differential distribution of genes in regions associated with histone and protamine-associated regions, suggesting a potential epigenetic relevance in embryonic development. More recently, detailed lists of proteins have been described corresponding to the different compartments of the sperm cell thanks to the application of recent proteomic techniques based on mass spectrometry (MS). Differential proteomics is also being applied to identify the presence of protein abnormalities found in infertile patients.

  18. The seed nuclear proteome.

    PubMed

    Repetto, Ombretta; Rogniaux, Hélène; Larré, Colette; Thompson, Richard; Gallardo, Karine

    2012-01-01

    Understanding the regulatory networks coordinating seed development will help to manipulate seed traits, such as protein content and seed weight, in order to increase yield and seed nutritional value of important food crops, such as legumes. Because of the cardinal role of the nucleus in gene expression, sub-proteome analyses of nuclei from developing seeds were conducted, taking advantage of the sequences available for model species. In this review, we discuss the strategies used to separate and identify the nuclear proteins at a stage when the seed is preparing for reserve accumulation. We present how these data provide an insight into the complexity and distinctive features of the seed nuclear proteome. We discuss the presence of chromatin-modifying enzymes and proteins that have roles in RNA-directed DNA methylation and which may be involved in modifying genome architecture in preparation for seed filling. Specific features of the seed nuclei at the transition between the stage of cell divisions and that of cell expansion and reserve deposition are described here which may help to manipulate seed quality traits, such as seed weight.

  19. Tear proteomics in keratoconus

    PubMed Central

    Pannebaker, Catherine; Chandler, Heather L.

    2010-01-01

    Purpose The purpose of this work was to identify potential tear-film based proteins expressed in keratoconus. Methods Recruited subjects were normal gas permeable (GP) contact lens wearers, keratoconus subjects wearing GP contact lenses, and keratoconus subjects without contact lenses. Subjects wearing soft lenses or having previous ocular surgeries were excluded from participating. Approximately 5 µl of tears were sampled from both eye of each subject using glass microcapillaries. Additional testing included a brief history, visual acuity, slit lamp examination, and topography. Proteomic analyses used to compare samples included Bradford assays, cytokine arrays, SDS–PAGE, and mass spectrometry. Results Forty-four subjects were enrolled in the study including 20 normals (GP wearers), 18 with keratoconus and wearing GPs, and six with keratoconus (non-lens wearers). Across all proteomic approaches, several proteins were identified as possibly being unique to keratoconus. Increased expression of matrix metalloproteinase-1 (MMP-1) was found in keratoconus subjects with and without gas permeable contact lenses (p=0.02). Unique proteins more associated with keratoconus included several keratins, immunoglobulins alpha and kappa, precursors to prolactin, lysozyme C, and lipocalin. Conclusions Initial analyses indicate that keratoconus may be associated with the differential expression of several proteins. Further testing is needed to determine any causal relationship or correlation with the etiology of this condition. PMID:21031023

  20. Proteomic Biomarkers of Atherosclerosis

    PubMed Central

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

    2008-01-01

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

  1. Proteomic Signatures of Thymomas

    PubMed Central

    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

  2. Global routine vaccination coverage, 2010.

    PubMed

    2011-11-11

    The Expanded Program on Immunization was established by the World Health Organization (WHO) in 1974 to ensure universal access to routinely recommended childhood vaccines. Six vaccine-preventable diseases initially were targeted: tuberculosis, poliomyelitis, diphtheria, tetanus, pertussis, and measles. In 1974, fewer than 5% of the world's infants were fully immunized; by 2005, global coverage with the third dose of diphtheria-tetanus-pertussis (DTP) vaccine (DTP3) was 79%, but many children, especially those living in poorer countries, still were not being reached. That year, WHO and the United Nations Children's Fund (UNICEF) developed the Global Immunization Vision and Strategy (GIVS), with the aim of decreasing vaccine-preventable disease--related morbidity and mortality by improving national immunization programs. One goal of GIVS was for all countries to achieve 90% national DTP3 coverage by 2010. This report summarizes the status of vaccination coverage globally and regionally in 2010 and progress toward meeting the GIVS goal. In 2010, 130 (67%) countries had achieved 90% DTP3 coverage, and an estimated 85% of infants worldwide had received at least 3 doses of DTP vaccine. However, 19.3 million children were not fully vaccinated and remained at risk for diphtheria, tetanus, and pertussis and other vaccine-preventable causes of morbidity and mortality; approximately 50% of these children live in India, Nigeria, and the Democratic Republic of Congo. Despite the overall improvement in vaccination coverage during the past 37 years, routine vaccination programs need to be strengthened globally, especially in countries with the greatest numbers of unvaccinated children.

  3. Immunocapture strategies in translational proteomics

    PubMed Central

    Fredolini, Claudia; Byström, Sanna; Pin, Elisa; Edfors, Fredrik; Tamburro, Davide; Iglesias, Maria Jesus; Häggmark, Anna; Hong, Mun-Gwan; Uhlen, Mathias; Nilsson, Peter; Schwenk, Jochen M

    2016-01-01

    Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field’s current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics. PMID:26558424

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

    Cancer.gov

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

  5. A guide to the Proteomics Identifications Database proteomics data repository.

    PubMed

    Vizcaíno, Juan Antonio; Côté, Richard; Reisinger, Florian; Foster, Joseph M; Mueller, Michael; Rameseder, Jonathan; Hermjakob, Henning; Martens, Lennart

    2009-09-01

    The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.

  6. Comparison of the Membrane Proteome of Virulent Mycobacterium tuberculosis and the Attenuated Mycobacterium bovis BCG Vaccine Strain by Label-free Quantitative Proteomics

    PubMed Central

    Gunawardena, Harsha P.; Feltcher, Meghan E.; Wrobel, John A.; Gu, Sheng; Braunstein, Miriam; Chen, Xian

    2015-01-01

    The Mycobacterium tuberculosis (MTB) membrane is rich in antigens that are potential targets for diagnostics and the development of new vaccines. To better understand the mechanisms underlying MTB virulence and identify new targets for therapeutic intervention we investigated the differential composition of membrane proteomes between virulent M. tuberculosis H37Rv (MTB) and the Mycobacterium bovis BCG vaccine strain. To compare the membrane proteomes, we used LC-MS/MS analysis in combination with label-free quantitative (LFQ) proteomics, utilizing the area-under-curve (AUC) of the extracted ion chromatograms (XIC) of peptides obtained from m/z and retention time alignment of MS1 features. With this approach, we obtained relative abundance ratios for 2,203 identified membrane-associated proteins in high confidence. Of these proteins, 294 showed statistically significant differences of at least 2 fold, in relative abundance between MTB and BCG membrane fractions. Our comparative analysis detected several proteins associated with known genomic regions of difference between MTB and BCG as being absent, which validated the accuracy of our approach. In further support of our label-free quantitative data, we verified select protein differences by immunoblotting. To our knowledge we have generated the first comprehensive and high coverage profile of comparative membrane proteome changes between virulent MTB and its attenuated relative BCG, which helps elucidate the proteomic basis of the intrinsic virulence of the MTB pathogen. PMID:24093440

  7. Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms

    PubMed Central

    Freiberg, Jeffrey A.; Le Breton, Yoann; Tran, Bao Q.; Scott, Alison J.; Harro, Janette M.; Ernst, Robert K.; Goo, Young Ah; Mongodin, Emmanuel F.; Goodlett, David R.; McIver, Kevin S.

    2016-01-01

    . Since the transcriptome level does not usually equal the proteome level, the validity attributed to gene expression studies as well as proteomic studies in microbial analyses must be brought into question. Therefore, the results attained by either approach, whether RNA-seq or shotgun proteomics, must be taken in context and evaluated with particular care since they are by no means interchangeable. PMID:27933318

  8. Unveiling the rat urinary proteome with three complementary proteomics approaches.

    PubMed

    Sánchez-Juanes, Fernando; Muñiz, María Carmen; Raposo, César; Rodríguez-Prieto, Silvia; Paradela, Alberto; Quiros, Yaremi; López-Hernández, Francisco; González-Buitrago, José Manuel; Ferreira, Laura

    2013-09-01

    Urine is a suitable biological fluid to look for markers of physiological and pathological processes, including renal and nonrenal diseases. In addition, it is an optimal body sample for diagnosis, because it is easily obtained without invasive procedures and can be sampled in large quantities at almost any time. Rats are frequently used as a model to study human diseases, and rat urine has been analyzed to search for disease biomarkers. The normal human urinary proteome has been studied extensively, but the normal rat urinary proteome has not been studied in such depth. In light of this, we were prompted to analyze the normal rat urinary proteome using three complementary proteomics platforms: SDS-PAGE separation, followed by LC-ESI-MS/MS; 2DE, followed by MALDI-TOF-TOF and 2D-liquid chromatography-chromatofocusing, followed by LC-ESI-Q-TOF. A total of 366 unique proteins were identified, of which only 5.2% of unique proteins were identified jointly by the three proteomics platforms used. This suggests that simultaneous proteomics techniques provide complementary and nonredundant information. Our analysis affords the most extensive rat urinary protein database currently available and this may be useful in the study of renal physiology and in the search for biomarkers related to renal and nonrenal diseases. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Development of a laser capture microscope-based single-cell-type proteomics tool for studying proteomes of individual cell layers of plant roots

    PubMed Central

    Zhu, Yingde; Li, Hui; Bhatti, Sarabjit; Zhou, Suping; Yang, Yong; Fish, Tara; Thannhauser, Theodore W

    2016-01-01

    Single-cell-type proteomics provides the capability to revealing the genomic and proteomics information at cell-level resolution. However, the methodology for this type of research has not been well-developed. This paper reports developing a workflow of laser capture microdissection (LCM) followed by gel-liquid chromatography-tandem mass spectrometry (GeLC-MS/MS)-based proteomics analysis for the identification of proteomes contained in individual cell layers of tomato roots. Thin-sections (~10-μm thick, 10 sections per root tip) were prepared for root tips of tomato germinating seedlings. Epidermal and cortical cells (5000–7000 cells per tissue type) were isolated under a LCM microscope. Proteins were isolated and then separated by SDS–polyacrylamide gel electrophoresis followed by in-gel-tryptic digestion. The MS and MS/MS spectra generated using nanoLC-MS/MS analysis of the tryptic peptides were searched against ITAG2.4 tomato protein database to identify proteins contained in each single-cell-type sample. Based on the biological functions, proteins with proven functions in root hair development were identified in epidermal cells but not in the cortical cells. Several of these proteins were found in Al-treated roots only. The results demonstrated that the cell-type-specific proteome is relevant for tissue-specific functions in tomato roots. Increasing the coverage of proteomes and reducing the inevitable cross-contamination from adjacent cell layers, in both vertical and cross directions when cells are isolated from slides prepared using intact root tips, are the major challenges using the technology in proteomics analysis of plant roots. PMID:27280026

  10. [The effect of attainability on envy].

    PubMed

    Inoue, Yumi; Murata, Koji

    2014-04-01

    Envy is an unpleasant emotion caused by comparison with a person who possesses something we desire. We conducted two studies to test our prediction that less envy would be felt when the person could attain what others had. In Study 1, participants read scenarios in which their friend could achieve a goal which they could not, and rated their emotions toward the friend. We manipulated the attainability according to whether the goal could be achieved by effort. In Study 2, participants competed with a confederate, and were informed that their performance was worse than that of the confederate. Afterwards the attainability was manipulated by either informing the participants that the possibility of improving their ability was very low or high. Then participants rated their emotions toward the confederate, and we also checked whether the participants had helped the confederate. As predicted, our findings demonstrated that those in the high attainability condition felt envy less than those in the low attainability condition, but showed no significant differences in helping behavior.

  11. Predictors of attainment in rhythmic sportive gymnastics.

    PubMed

    Hume, P A; Hopkins, W G; Robinson, D M; Robinson, S M; Hollings, S C

    1993-12-01

    Correlates of attainment in rhythmic sportive gymnastics (RSG) were investigated in a cross-sectional study of 106 female gymnasts aged 7-27 years. Physical attributes were obtained by anthropometry and from tests of flexibility, leg power, maximum oxygen uptake and visuo-motor proficiency. Training and psychological measures were derived from self-administered questionnaires that included the Leadership Scale for Sport, Psychological Skills Inventory for Sport, General Health Questionnaire, Sport Competition Anxiety Test, and several questions on sport motivation and enjoyment. Attainment was expressed as competition grade level and mean performance score in 4 competitions. The best correlates of attainment were cumulative and current training time (r = 0.84-0.53). Age, lean body mass and composite measures of flexibility, leg power and visuo-motor proficiency were also significant correlates of attainment (r = 0.69-0.29), as were coach democratic and coach social behaviours (r = 0.41-0.28). The significant positive psychometric correlates of attainment were mental preparation, motivation by creativity, and several dimensions of enjoyment (r = 0.35-0.26); significant negative correlates were recent anxiety-depression and enjoyment of training (r = -0.34-(-)0.32). No previous study has identified the relative contributions of such a comprehensive range of physical, psychological and training measures to performance of a sport.

  12. Tetrazine ligation for chemical proteomics.

    PubMed

    Kang, Kyungtae; Park, Jongmin; Kim, Eunha

    2016-01-01

    Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical proteomics.

  13. Proteomics of Plant Pathogenic Fungi

    PubMed Central

    González-Fernández, Raquel; Prats, Elena; Jorrín-Novo, Jesús V.

    2010-01-01

    Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection. PMID:20589070

  14. Urine sample preparation and fractionation for global proteome profiling by LC-MS.

    PubMed

    Court, Magali; Garin, Jérôme; Masselon, Christophe D

    2015-01-01

    Urine has garnered tremendous interest over the past decade as a potential source of protein biomarkers for various pathologies. However, due to its low protein concentration and the presence of interfering compounds, urine constitutes a challenging analyte in proteomics. In the context of a project aimed at the discovery and evaluation of new candidate biomarkers of bladder cancer in urine, our laboratory has implemented and evaluated an array of preparation techniques for urinary proteome analysis. We present here the protocol that, in our hands, yielded the best overall proteome coverage with the lowest analytical effort. It begins with protein precipitation using trichloroacetic acid, in solution digestion and RP-C18 cartridge desalting of the resulting peptides mixture, and is followed by peptide fractionation by gel-free isoelectric focusing, and nano-LC-MS/MS for database compilation.

  15. What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics.

    PubMed

    Hamzeiy, Hamid; Cox, Jürgen

    2017-02-01

    Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps. Despite the similarities, untargeted metabolomics is lagging behind in terms of reliable fully automated quantitative data analysis. We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics. MaxQuant is a popular platform for proteomics data analysis and is widely considered to be superior in achieving high precursor mass accuracies through advanced nonlinear recalibration, usually leading to five to ten-fold better accuracy in complex LC-MS/MS runs. This translates to a sharp decrease in the number of peptide candidates per measured feature, thereby strongly improving the coverage of identified peptides. We argue that similar strategies can be applied to untargeted metabolomics, leading to equivalent improvements in metabolite identification. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  16. An enlarged cell wall proteome of Arabidopsis thaliana rosettes.

    PubMed

    Hervé, Vincent; Duruflé, Harold; San Clemente, Hélène; Albenne, Cécile; Balliau, Thierry; Zivy, Michel; Dunand, Christophe; Jamet, Elisabeth

    2016-12-01

    Plant cells are surrounded by cell walls playing many roles during development and in response to environmental constraints. Cell walls are mainly composed of polysaccharides (cellulose, hemicelluloses and pectins), but they also contain proteins which are critical players in cell wall remodeling processes. Today, the cell wall proteome of Arabidopsis thaliana, a major dicot model plant, comprises more than 700 proteins predicted to be secreted (cell wall proteins-CWPs) identified in different organs or in cell suspension cultures. However, the cell wall proteome of rosettes is poorly represented with only 148 CWPs identified after extraction by vacuum infiltration. This new study allows enlarging its coverage. A destructive method starting with the purification of cell walls has been performed and two experiments have been compared. They differ by the presence/absence of protein separation by a short 1D-electrophoresis run prior to tryptic digestion and different gradient programs for peptide separation before mass spectrometry analysis. Altogether, the rosette cell wall proteome has been significantly enlarged to 361 CWPs, among which 213 newly identified in rosettes and 57 newly described. The identified CWPs fall in four major functional classes: 26.1% proteins acting on polysaccharides, 11.1% oxido-reductases, 14.7% proteases and 11.7% proteins possibly related to lipid metabolism. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Seven perspectives on GPCR H/D-exchange proteomics methods.

    PubMed

    Zhang, Xi

    2017-01-01

    Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor. This article proposes to view bottom-up HDX as two steps to guide choices of detergent buffers and chromatography settings: (I) protein HDX labeling in native buffers, and (II) peptide-centric analysis of HDX labels, which applies (a) bottom-up MS/MS to construct peptide matrix and (b) HDX MS to locate and quantify H/D labels. The detergent-low-TCEP digestion method demystified the challenge of HDX-grade GPCR digestion. GPCR HDX proteomics is a structural approach, thus its choice of experimental conditions should let structure lead and digestion follow, not the opposite.

  18. Imaging beyond the proteome

    PubMed Central

    Chang, Pamela V.; Bertozzi, Carolyn R.

    2013-01-01

    Imaging technologies developed in the early 20th century achieved contrast solely by relying on macroscopic and morphological differences between the tissues of interest and the surrounding tissues. Since then, there has been a movement toward imaging at the cellular and molecular level in order to visualize biological processes. This rapidly growing field is known as molecular imaging. In the last decade, many methodologies for imaging proteins have emerged. However, most of these approaches cannot be extended to imaging beyond the proteome. Here, we highlight some of the recently developed technologies that enable imaging of non-proteinaceous molecules in the cell: lipids, signalling molecules, inorganic ions, glycans, nucleic acids, small-molecule metabolites, and protein post-translational modifications such as phosphorylation and methylation. PMID:22801420

  19. Proteomics of Human Neurodegenerative Diseases

    PubMed Central

    Zhang, Jing; Keene, C. Dirk; Pan, Catherine; Montine, Kathleen S.; Montine, Thomas J.

    2009-01-01

    The technology, experimental approaches, and bioinformatics that support proteomic research are evolving rapidly. The application of these new capabilities to the study of neurodegenerative diseases is providing insight into the biochemical pathogenesis of neurodegeneration as well as fueling major efforts in biomarker discovery. Here, we review the fundamentals of commonly used proteomic approaches and the outcomes of these investigations with autopsy and cerebrospinal fluid samples from patients with neurodegenerative diseases. PMID:18800015

  20. Medical coverage of gymnastics competitions.

    PubMed

    Hecht, Suzanne S; Burton, Monique S

    2009-01-01

    Medical coverage of gymnastics competitions can be a challenging task for the sports medicine physician and other medical personnel because of the complexity and aerial nature of the sport. A broad understanding of the six gymnastics disciplines, along with the type of competitions, injury epidemiology, and the common acute gymnastics injuries will help sports medicine professionals in planning and delivering optimal care to the injured or ill gymnast.

  1. Coverage-adjusted entropy estimation.

    PubMed

    Vu, Vincent Q; Yu, Bin; Kass, Robert E

    2007-09-20

    Data on 'neural coding' have frequently been analyzed using information-theoretic measures. These formulations involve the fundamental and generally difficult statistical problem of estimating entropy. We review briefly several methods that have been advanced to estimate entropy and highlight a method, the coverage-adjusted entropy estimator (CAE), due to Chao and Shen that appeared recently in the environmental statistics literature. This method begins with the elementary Horvitz-Thompson estimator, developed for sampling from a finite population, and adjusts for the potential new species that have not yet been observed in the sample-these become the new patterns or 'words' in a spike train that have not yet been observed. The adjustment is due to I. J. Good, and is called the Good-Turing coverage estimate. We provide a new empirical regularization derivation of the coverage-adjusted probability estimator, which shrinks the maximum likelihood estimate. We prove that the CAE is consistent and first-order optimal, with rate O(P)(1/log n), in the class of distributions with finite entropy variance and that, within the class of distributions with finite qth moment of the log-likelihood, the Good-Turing coverage estimate and the total probability of unobserved words converge at rate O(P)(1/(log n)(q)). We then provide a simulation study of the estimator with standard distributions and examples from neuronal data, where observations are dependent. The results show that, with a minor modification, the CAE performs much better than the MLE and is better than the best upper bound estimator, due to Paninski, when the number of possible words m is unknown or infinite.

  2. Eclipse Photo/Video Coverage

    NASA Image and Video Library

    2017-08-21

    On Monday, Aug. 21, NASA provided coast-to-coast coverage of the solar eclipse across America – featuring views of the phenomenon from unique vantage points, including from the ground, from aircraft, and from spacecraft including the ISS, during a live broadcast seen on NASA Television and the agency’s website. This is footage from the Kennedy Space Center Visitor Complex, KARS Park at Kennedy, and the Vehicle Assembly Building.

  3. Rapid fabrication of glass/PDMS hybrid µIMER for high throughput membrane proteomics.

    PubMed

    Pereira-Medrano, Ana G; Forster, Simon; Fowler, Gregory J S; McArthur, Sally L; Wright, Phillip C

    2010-12-21

    Mass spectrometry (MS) based proteomics has brought a radical approach to systems biology, offering a platform to study complex biological functions. However, key proteomic technical challenges remain, mainly the inability to characterise the complete proteome of a cell due to the thousands of diverse, complex proteins expressed at an extremely wide concentration range. Currently, high throughput and efficient techniques to unambiguously identify and quantify proteins on a proteome-wide scale are in demand. Miniaturised analytical systems placed upstream of MS help us to attain these goals. One time-consuming step in traditional techniques is the in-solution digestion of proteins (4-20 h). This also has other drawbacks, including enzyme autoproteolysis, low efficiency, and manual operation. Furthermore, the identification of α-helical membrane proteins has remained a challenge due to their high hydrophobicity and lack of trypsin cleavage targets in transmembrane helices. We demonstrate a new rapidly produced glass/PDMS micro Immobilised Enzyme Reactor (µIMER) with enzymes covalently immobilised onto polyacrylic acid plasma-modified surfaces for the purpose of rapidly (as low as 30 s) generating peptides suitable for MS analysis. This µIMER also allows, for the first time, rapid digestion of insoluble proteins. Membrane protein identification through this method was achieved after just 4 min digestion time, up to 9-fold faster than either dual-stage in-solution digestion approaches or other commonly used bacterial membrane proteomic workflows.

  4. The Succinated Proteome

    SciTech Connect

    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.

  5. THE SUCCINATED PROTEOME

    PubMed Central

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

    2014-01-01

    The post-translational modifications (PTMs) of cysteine residues include oxidation, S-glutathionylation, S-nitrosylation, and succination, all of which modify protein function or turnover in response to a changing intracellular redox environment. Succination is a chemical modification of cysteine in proteins 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 3T3 adipocytes grown in high glucose medium and in adipose tissue in obesity and diabetes in mice. Increased succination of proteins is also detected in the kidney of a fumarase deficient conditional knock-out mouse which develops renal cysts. A wide range of proteins are subject to succination, including enzymes, adipokines, cytoskeletal proteins, and ER chaperones with functional cysteine residues. There is also some overlap between succinated and glutathionylated proteins, suggesting that the same low pKa thiols are targeted by both. Succination of adipocyte proteins in diabetes increases as a result of nutrient excess derived mitochondrial stress and this is inhibited by uncouplers, which discharge the mitochondrial membrane potential (ΔΨm) and relieve the electron transport chain. 2SC therefore 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 PTM of proteins by proteomics approaches. PMID:24115015

  6. Increasing Coverage of Appropriate Vaccinations

    PubMed Central

    Jacob, Verughese; Chattopadhyay, Sajal K.; Hopkins, David P.; Morgan, Jennifer Murphy; Pitan, Adesola A.; Clymer, John

    2016-01-01

    Context Population-level coverage for immunization against many vaccine-preventable diseases remains below optimal rates in the U.S. The Community Preventive Services Task Force recently recommended several interventions to increase vaccination coverage based on systematic reviews of the evaluation literature. The present study provides the economic results from those reviews. Evidence acquisition A systematic review was conducted (search period, January 1980 through February 2012) to identify economic evaluations of 12 interventions recommended by the Task Force. Evidence was drawn from included studies; estimates were constructed for the population reach of each strategy, cost of implementation, and cost per additional vaccinated person because of the intervention. Analyses were conducted in 2014. Evidence synthesis Reminder systems, whether for clients or providers, were among the lowest-cost strategies to implement and the most cost effective in terms of additional people vaccinated. Strategies involving home visits and combination strategies in community settings were both costly and less cost effective. Strategies based in settings such as schools and managed care organizations that reached the target population achieved additional vaccinations in the middle range of cost effectiveness. Conclusions The interventions recommended by the Task Force differed in reach, cost, and cost effectiveness. This systematic review presents the economic information for 12 effective strategies to increase vaccination coverage that can guide implementers in their choice of interventions to fit their local needs, available resources, and budget. PMID:26847663

  7. Groundwater arsenic and education attainment in Bangladesh.

    PubMed

    Murray, Michael P; Sharmin, Raisa

    2015-10-26

    Thousands of groundwater tube wells serving millions of Bangladeshis are arsenic contaminated. This study investigates the effect of these wells on the education attainment and school attendance of youths who rely on those wells for drinking water. The analysis combines data from the 2006 Bangladesh Multiple Indicator Cluster Survey (2006 MICS) and the National Hydrochemical Survey (NHS) of Bangladeshi tube wells' contamination conducted between 1998 and 2000. The study uses multiple regression analysis to estimate the differences in education attainment and school attendance among the following: (i) youths who live where tube wells are safe, (ii) youths who live where tube wells are unsafe but who report drinking from an arsenic-free source, and (iii) youths who live where tube wells are unsafe but who do not report drinking from an arsenic-free source. Controlling for other determinants of education attainment and school attendance, young Bangladeshi males who live where tube wells are unsafe (by Bangladeshis standards) but who report drinking from arsenic-free sources are found to have the same education attainment (among 19- to 21-year-olds) and school attendance (among 6- to 10-year-olds), on average, as corresponding young Bangladeshi males who live where wells are safe. But young Bangladeshi males who live where tube wells are unsafe and who do not report drinking from an arsenic-free source attain, on average, a half-year less education (among 19- to 21-year-olds) and attend school, on average, five to seven fewer days a year (among 6- to 10-year-olds) than do other Bagladeshi males of those ages. The estimated effects for females are of the same sign but much smaller in magnitude. Bangladeshi public health measures to shift drinking from unsafe to safe wells not only advance good health but also increase males' education attainment.

  8. The proteome of human saliva

    NASA Astrophysics Data System (ADS)

    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.

  9. Challenges and Solutions in Proteomics

    PubMed Central

    Hongzhan, Huang; Shukla, Hem D; Cathy, Wu; Satya, Saxena

    2007-01-01

    The accelerated growth of proteomics data presents both opportunities and challenges. Large-scale proteomic profiling of biological samples such as cells, organelles or biological fluids has led to discovery of numerous key and novel proteins involved in many biological/disease processes including cancers, as well as to the identification of novel disease biomarkers and potential therapeutic targets. While proteomic data analysis has been greatly assisted by the many bioinformatics tools developed in recent years, a careful analysis of the major steps and flow of data in a typical highthroughput analysis reveals a few gaps that still need to be filled to fully realize the value of the data. To facilitate functional and pathway discovery for large-scale proteomic data, we have developed an integrated proteomic expression analysis system, iProXpress, which facilitates protein identification using a comprehensive sequence library and functional interpretation using integrated data. With its modular design, iProXpress complements and can be integrated with other software in a proteomic data analysis pipeline. This novel approach to complex biological questions involves the interrogation of multiple data sources, thereby facilitating hypothesis generation and knowledge discovery from the genomic-scale studies and fostering disease diagnosis and drug development. PMID:18645629

  10. School Choice, School Quality and Postsecondary Attainment

    PubMed Central

    Deming, David J.; Hastings, Justine S.; Kane, Thomas J.; Staiger, Douglas O.

    2015-01-01

    We study the impact of a public school choice lottery in Charlotte-Mecklenburg schools on college enrollment and degree completion. We find a significant overall increase in college attainment among lottery winners who attend their first choice school. Using rich administrative data on peers, teachers, course offerings and other inputs, we show that the impacts of choice are strongly predicted by gains on several measures of school quality. Gains in attainment are concentrated among girls. Girls respond to attending a better school with higher grades and increases in college-preparatory course-taking, while boys do not. PMID:27244675

  11. Proteome Analysis of Subsarcolemmal Cardiomyocyte Mitochondria: A Comparison of Different Analytical Platforms

    PubMed Central

    Giorgianni, Francesco; Koirala, Diwa; Weber, Karl T.; Beranova-Giorgianni, Sarka

    2014-01-01

    Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease. PMID:24865490

  12. Proteome analysis of subsarcolemmal cardiomyocyte mitochondria: a comparison of different analytical platforms.

    PubMed

    Giorgianni, Francesco; Koirala, Diwa; Weber, Karl T; Beranova-Giorgianni, Sarka

    2014-05-26

    Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease.

  13. Less is More: Membrane Protein Digestion Beyond Urea–Trypsin Solution for Next-level Proteomics*

    PubMed Central

    Zhang, Xi

    2015-01-01

    The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting—not destroying—structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics. PMID:26081834

  14. Design and initial characterization of the SC-200 proteomics standard mixture.

    PubMed

    Bauman, Andrew; Higdon, Roger; Rapson, Sean; Loiue, Brenton; Hogan, Jason; Stacy, Robin; Napuli, Alberto; Guo, Wenjin; van Voorhis, Wesley; Roach, Jared; Lu, Vincent; Landorf, Elizabeth; Stewart, Elizabeth; Kolker, Natali; Collart, Frank; Myler, Peter; van Belle, Gerald; Kolker, Eugene

    2011-01-01

    High-throughput (HTP) proteomics studies generate large amounts of data. Interpretation of these data requires effective approaches to distinguish noise from biological signal, particularly as instrument and computational capacity increase and studies become more complex. Resolving this issue requires validated and reproducible methods and models, which in turn requires complex experimental and computational standards. The absence of appropriate standards and data sets for validating experimental and computational workflows hinders the development of HTP proteomics methods. Most protein standards are simple mixtures of proteins or peptides, or undercharacterized reference standards in which the identity and concentration of the constituent proteins is unknown. The Seattle Children's 200 (SC-200) proposed proteomics standard mixture is the next step toward developing realistic, fully characterized HTP proteomics standards. The SC-200 exhibits a unique modular design to extend its functionality, and consists of 200 proteins of known identities and molar concentrations from 6 microbial genomes, distributed into 10 molar concentration tiers spanning a 1,000-fold range. We describe the SC-200's design, potential uses, and initial characterization. We identified 84% of SC-200 proteins with an LTQ-Orbitrap and 65% with an LTQ-Velos (false discovery rate = 1% for both). There were obvious trends in success rate, sequence coverage, and spectral counts with protein concentration; however, protein identification, sequence coverage, and spectral counts vary greatly within concentration levels.

  15. Closing the Prescription Drug Coverage Gap

    MedlinePlus

    ... coverage gap discount work for brand-name drugs? Companies that make brand-name prescription drugs must sign ... Coverage Gap Discount Program. This program requires the companies to offer discounts on brand-name drugs to ...

  16. Bundled automobile insurance coverage and accidents.

    PubMed

    Li, Chu-Shiu; Liu, Chwen-Chi; Peng, Sheng-Chang

    2013-01-01

    This paper investigates the characteristics of automobile accidents by taking into account two types of automobile insurance coverage: comprehensive vehicle physical damage insurance and voluntary third-party liability insurance. By using a unique data set in the Taiwanese automobile insurance market, we explore the bundled automobile insurance coverage and the occurrence of claims. It is shown that vehicle physical damage insurance is the major automobile coverage and affects the decision to purchase voluntary liability insurance coverage as a complement. Moreover, policyholders with high vehicle physical damage insurance coverage have a significantly higher probability of filing vehicle damage claims, and if they additionally purchase low voluntary liability insurance coverage, their accident claims probability is higher than those who purchase high voluntary liability insurance coverage. Our empirical results reveal that additional automobile insurance coverage information can capture more driver characteristics and driving behaviors to provide useful information for insurers' underwriting policies and to help analyze the occurrence of automobile accidents.

  17. Coverage Evaluation of Academic Libraries Survey (ALS).

    ERIC Educational Resources Information Center

    Marston, Christopher C.

    1999-01-01

    Evaluates universe coverage, data coverage, and response rates of the Academic Libraries Survey. Includes examination of survey design and data collection, perceptions of regional survey coordinators, and reporting by public versus private institutions. (Author)

  18. Improved surfaceome coverage with a label-free nonaffinity-purified workflow.

    PubMed

    Glisovic-Aplenc, Tina; Gill, Saar; Spruce, Lynn A; Smith, Ian R; Fazelinia, Hossein; Shestova, Olga; Ding, Hua; Tasian, Sarah K; Aplenc, Richard; Seeholzer, Steven H

    2017-04-01

    The proteins of the cellular plasma membrane (PM) perform important functions relating to homeostasis and intercellular communication. Due to its overall low cellular abundance, amphipathic character, and low membrane-to-cytoplasm ratio, the PM proteome has been challenging to isolate and characterize, and is poorly represented in standard LC-MS/MS analyses. In this study, we employ sucrose gradient ultracentrifugation for the enrichment of the PM proteome, without chemical labeling and affinity purification, together with GeLCMS and use subsequent bioinformatics tools to select proteins associated with the PM/cell surface, herein referred to as the surfaceome. Using this methodology, we identify over 1900 cell surface associated proteins in a human acute myeloid leukemia cell line. These surface proteins comprise almost 50% of all detected cellular proteins, a number that substantially exceeds the depth of coverage in previously published studies describing the leukemia surfaceome.

  19. SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics

    PubMed Central

    Lundström, Susanna L.; Zhang, Bo; Rutishauser, Dorothea; Aarsland, Dag; Zubarev, Roman A.

    2017-01-01

    The human blood proteome is frequently assessed by protein abundance profiling using a combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS). In traditional sequence database search, many good-quality MS/MS data remain unassigned. Here we uncover the hidden part of the blood proteome via novel SpotLight approach. This method combines de novo MS/MS sequencing of enriched antibodies and co-extracted proteins with subsequent label-free quantification of new and known peptides in both enriched and unfractionated samples. In a pilot study on differentiating early stages of Alzheimer’s disease (AD) from Dementia with Lewy Bodies (DLB), on peptide level the hidden proteome contributed almost as much information to patient stratification as the apparent proteome. Intriguingly, many of the new peptide sequences are attributable to antibody variable regions, and are potentially indicative of disease etiology. When the hidden and apparent proteomes are combined, the accuracy of differentiating AD (n = 97) and DLB (n = 47) increased from ≈85% to ≈95%. The low added burden of SpotLight proteome analysis makes it attractive for use in clinical settings. PMID:28167817

  20. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a...

  1. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  2. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  3. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  4. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  5. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and includes...

  6. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 28 Judicial Administration 2 2013-07-01 2013-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  7. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  8. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  9. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 2 Grants and Agreements 1 2013-01-01 2013-01-01 false Insurance coverage. 215.31 Section 215.31... A-110) Post Award Requirements Property Standards § 215.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired...

  10. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 1 2014-10-01 2014-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  11. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 1 2012-10-01 2012-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  12. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  13. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 1 2014-07-01 2014-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  14. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  15. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  16. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  17. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  18. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  19. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  20. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  1. 2 CFR 200.310 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 2 Grants and Agreements 1 2014-01-01 2014-01-01 false Insurance coverage. 200.310 Section 200.310... REQUIREMENTS FOR FEDERAL AWARDS Post Federal Award Requirements Property Standards § 200.310 Insurance coverage. The non-Federal entity must, at a minimum, provide the equivalent insurance coverage for real...

  2. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 1 2014-07-01 2014-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  3. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 2 2013-04-01 2009-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  4. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 1 2013-10-01 2013-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  5. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  6. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 1 2012-07-01 2012-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  7. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 4 2014-01-01 2014-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  8. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 2 2012-04-01 2009-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  9. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 1 2013-07-01 2013-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  10. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  11. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  12. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 20 Employees' Benefits 2 2014-04-01 2014-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  13. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  14. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 1 2013-07-01 2013-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  15. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 1 2014-10-01 2014-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  16. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  17. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  18. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  19. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 2 Grants and Agreements 1 2012-01-01 2012-01-01 false Insurance coverage. 215.31 Section 215.31... A-110) Post Award Requirements Property Standards § 215.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired...

  20. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  1. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 4 2013-01-01 2013-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  2. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  3. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  4. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  5. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  6. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 5 2012-01-01 2012-01-01 false Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  7. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 28 Judicial Administration 2 2014-07-01 2014-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  8. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  9. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 2 2014-04-01 2014-04-01 false Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  10. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 28 Judicial Administration 2 2012-07-01 2012-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  11. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  12. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  13. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  14. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 20 Employees' Benefits 2 2013-04-01 2013-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  15. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  16. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  17. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 1 2012-10-01 2012-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  18. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a General...

  19. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a General...

  20. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a General...

  1. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a General...

  2. 42 CFR 423.566 - Coverage determinations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Coverage determinations. 423.566 Section 423.566... (CONTINUED) MEDICARE PROGRAM VOLUNTARY MEDICARE PRESCRIPTION DRUG BENEFIT Grievances, Coverage Determinations, Redeterminations, and Reconsiderations § 423.566 Coverage determinations. (a) Responsibilities of the Part D plan...

  3. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  4. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  5. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  6. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  7. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  8. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  9. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  10. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  11. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  12. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  13. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  14. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 1 2011-07-01 2011-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  15. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  16. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 1 2011-10-01 2011-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  17. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  18. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  19. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  20. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  1. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  2. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  3. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 2 2011-04-01 2009-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  4. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 1 2011-07-01 2011-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  5. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  6. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  7. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  8. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  9. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 2 Grants and Agreements 1 2011-01-01 2011-01-01 false Insurance coverage. 215.31 Section 215.31... A-110) Post Award Requirements Property Standards § 215.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired...

  10. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  11. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  12. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  13. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  14. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  15. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  16. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  17. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  18. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  19. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  20. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Insurance coverage. 215.31 Section 215.31 Grants and Agreements OFFICE OF MANAGEMENT AND BUDGET CIRCULARS AND GUIDANCE Reserved UNIFORM... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  1. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 2 2014-07-01 2014-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  2. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 2 2013-07-01 2013-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  3. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 2 2011-07-01 2011-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  4. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 2 2012-07-01 2012-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  5. Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings

    PubMed Central

    Ye, Zhujia; Sangireddy, Sasikiran; Okekeogbu, Ikenna; Zhou, Suping; Yu, Chih-Li; Hui, Dafeng; Howe, Kevin J.; Fish, Tara; Thannhauser, Theodore W.

    2016-01-01

    Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the isobaric tags for relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (p < 0.05, fold change <0.6 or >1.7) from the non-treated control to drought-treated conditions. These proteins are involved in the regulation of transcription and translation, cell division, cell wall modification, phyto-hormone metabolism and signaling transduction pathways, and metabolic pathways of carbohydrates, amino acids, and fatty acids. A scheme of abscisic acid (ABA)-biosynthesis and ABA responsive signal transduction pathway was reconstructed using these drought-induced significant proteins, showing systemic regulation at protein level to deploy the respective mechanism. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under

  6. Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings.

    PubMed

    Ye, Zhujia; Sangireddy, Sasikiran; Okekeogbu, Ikenna; Zhou, Suping; Yu, Chih-Li; Hui, Dafeng; Howe, Kevin J; Fish, Tara; Thannhauser, Theodore W

    2016-08-02

    Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a "sandwich" system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the isobaric tags for relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (p < 0.05, fold change <0.6 or >1.7) from the non-treated control to drought-treated conditions. These proteins are involved in the regulation of transcription and translation, cell division, cell wall modification, phyto-hormone metabolism and signaling transduction pathways, and metabolic pathways of carbohydrates, amino acids, and fatty acids. A scheme of abscisic acid (ABA)-biosynthesis and ABA responsive signal transduction pathway was reconstructed using these drought-induced significant proteins, showing systemic regulation at protein level to deploy the respective mechanism. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under soil

  7. College Attainment: Throwing a Complete Game

    ERIC Educational Resources Information Center

    Jones, Stan; Soo, David

    2010-01-01

    The U.S. once had the world's highest percentage of adults with a college degree, but has now dropped to 10th, according to the OECD. In an attempt to reverse this slide, a number of policymakers and foundations have sought to make increased degree attainment a national priority. President Obama has articulated the goal that America will regain…

  8. Attendance and Attainment in a Calculus Course

    ERIC Educational Resources Information Center

    Meulenbroek, Bernard; van den Bogaard, Maartje

    2013-01-01

    In this paper the relationship between attendance and attainment in a standard calculus course is investigated. Calculus could in principle be studied without attending lectures due to the wealth of material available (in hardcopy and online). However, in this study we will show that the pass rate of students attending classes regularly (>75%…

  9. Japanese vs. Caucasian Intelligence and Social Attainment.

    ERIC Educational Resources Information Center

    Nagoshi, Craig T.

    1998-01-01

    Summarizes a series of studies from the Hawaii Family Study of Cognition on possible genetic and social environmental determinants of individual differences in and racial/ethnic differences between groups on intelligence and attainment. These studies, which focused on Japanese and Caucasian Americans, illustrate the complex, interactive, and…

  10. Institutions, Social Norms, and Educational Attainment

    ERIC Educational Resources Information Center

    Zhan, Crystal

    2017-01-01

    Informal institutions are defined as socially shared rules that guide individuals' behaviors outside of officially sanctioned channels. This paper investigates the link between individual educational attainment and education-related informal institutions by examining second-generation immigrants in the USA. I measure the education-related informal…

  11. Birth Order, Family Size and Educational Attainment

    ERIC Educational Resources Information Center

    de Haan, Monique

    2010-01-01

    This paper investigates the effect of family size and birth order on educational attainment. An instrumental variables approach is used to identify the effect of family size. Instruments for the number of children are twins at last birth and the sex mix of the first two children. The effect of birth order is identified, by examining the relation…

  12. 40 CFR 51.1004 - Attainment dates.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... FOR PREPARATION, ADOPTION, AND SUBMITTAL OF IMPLEMENTATION PLANS Provisions for Implementation of PM2.5 National Ambient Air Quality Standards § 51.1004 Attainment dates. (a) Consistent with section 172... demonstrations and associated reasonably available control measures, reasonable further progress plans...

  13. Birth Order, Family Size and Educational Attainment

    ERIC Educational Resources Information Center

    de Haan, Monique

    2010-01-01

    This paper investigates the effect of family size and birth order on educational attainment. An instrumental variables approach is used to identify the effect of family size. Instruments for the number of children are twins at last birth and the sex mix of the first two children. The effect of birth order is identified, by examining the relation…

  14. Differences in STEM Baccalaureate Attainment by Ethnicity

    ERIC Educational Resources Information Center

    Koledoye, Kimberly; Joyner, Sheila; Slate, John R.

    2011-01-01

    In this study, we examined the extent to which differences were present in the science, technology, engineering, and math (STEM) baccalaureate attainment of Black students and of Hispanic students at 82 Texas 4-year colleges from 2008 to 2009. A custom download of data files was conducted on the Integrated Postsecondary Education Data System in…

  15. Attaining the First Community College Presidency

    ERIC Educational Resources Information Center

    Jones, Stephanie J.; Warnick, Erika M.

    2012-01-01

    It would be unusual to read the current literature on community colleges and not find a reference to impending retirements of senior-level administrators, faculty, and staff, as well as what skills and characteristics are important for future leadership. There is limited research on attaining the first community college presidency. This study…

  16. Why Online Education Will Attain Full Scale

    ERIC Educational Resources Information Center

    Sener, John

    2010-01-01

    Online higher education has attained scale and is poised to take the next step in its growth. Although significant obstacles to a full scale adoption of online education remain, we will see full scale adoption of online higher education within the next five to ten years. Practically all higher education students will experience online education in…

  17. The Fiscal Consequences of Adult Educational Attainment

    ERIC Educational Resources Information Center

    Khatiwada, Ishwar; McLaughlin, Joseph; Sum, Andrew; Palma, Sheila

    2007-01-01

    This research monograph prepared for the National Commission on Adult Literacy is primarily designed to describe and analyze the net annual fiscal contributions (tax payments minus cash and in-kind transfers and institutionalization costs) of U.S. adults (ages 16-64) by their educational attainment in recent years. The report begins with an…

  18. Geography Education for "An Attainable Global Perspective"

    ERIC Educational Resources Information Center

    Klein, Phil; Pawson, Eric; Solem, Michael; Ray, Waverly

    2014-01-01

    This article considers approaches to promoting global perspectives as both cognitive and affective learning outcomes within geography education. Particular attention is paid to the work of Robert Hanvey, who proposed "An Attainable Global Perspective" in the 1970s, which explicitly ties to the content and perspectives embedded in…

  19. Japanese vs. Caucasian Intelligence and Social Attainment.

    ERIC Educational Resources Information Center

    Nagoshi, Craig T.

    1998-01-01

    Summarizes a series of studies from the Hawaii Family Study of Cognition on possible genetic and social environmental determinants of individual differences in and racial/ethnic differences between groups on intelligence and attainment. These studies, which focused on Japanese and Caucasian Americans, illustrate the complex, interactive, and…

  20. Early School Adjustment and Educational Attainment

    ERIC Educational Resources Information Center

    Magnuson, Katherine; Duncan, Greg J.; Lee, Kenneth T. H.; Metzger, Molly W.

    2016-01-01

    Although school attainment is a cumulative process combining mastery of both academic and behavioral skills, most studies have offered only a piecemeal view of the associations between middle-childhood capacities and subsequent schooling outcomes. Using a 20-year longitudinal data set, this study estimates the association between children's…

  1. Educational Attainment. Cuyahoga County Data Brief

    ERIC Educational Resources Information Center

    Center on Urban Poverty and Community Development (NJ1), 2010

    2010-01-01

    Educational attainment is reported separately for individuals 18-24 and those 25 and over. Many individuals in the 18-24 year old group are still acquiring their education, but it is still of interest to look at their status in 2000 and 2006-2008 to determine whether more of them have completed high school or more advanced education. The number of…

  2. Life Cycles, Educational Attainment and Labor Markets.

    ERIC Educational Resources Information Center

    Winsborough, H.H., Sweet, J.A.

    Two social changes are cited as particularly important to the projection of college enrollment trends. One is the rising educational attainment of the parents of future potential college attenders; the other is the fact that declines in fertility accompany declines in average family size. Overall, the illustration in this paper suggests that the…

  3. Institutions, Social Norms, and Educational Attainment

    ERIC Educational Resources Information Center

    Zhan, Crystal

    2017-01-01

    Informal institutions are defined as socially shared rules that guide individuals' behaviors outside of officially sanctioned channels. This paper investigates the link between individual educational attainment and education-related informal institutions by examining second-generation immigrants in the USA. I measure the education-related informal…

  4. A Dynamic Analysis of Educational Attainment.

    ERIC Educational Resources Information Center

    Temple, Mark; Polk, Kenneth

    1986-01-01

    Traces the educational attainment experiences of 245 Pacific Northwest males aged 16-31 hypothesizing a main path of educational success coinciding with Rosenbaum's tournament metaphor. Indicates that though early academic success did not ensure later success, early academic failure strongly predicted later failure, but some unsuccessful students…

  5. Adolescents' Sexual Behavior and Academic Attainment

    ERIC Educational Resources Information Center

    Frisco, Michelle L.

    2008-01-01

    High school students have high ambitions but do not always make choices that maximize their likelihood of educational success. This was the motivation for investigating the relationships between high school sexual behavior and two important milestones in academic attainment: earning a high school diploma and enrolling in distinct postsecondary…

  6. High School Socioeconomic Segregation and Student Attainment

    ERIC Educational Resources Information Center

    Palardy, Gregory J.

    2013-01-01

    Using data from the Education Longitudinal Study of 2002, this study examines the association between high school socioeconomic segregation and student attainment outcomes and the mechanisms that mediate those relationships. The results show that socioeconomic segregation has a strong association with high school graduation and college enrollment.…

  7. Influence of Educational Attainment on Consumption

    ERIC Educational Resources Information Center

    Zhang, Xuemin; He, Youning

    2007-01-01

    In market economy, man is both the essential productive factor and the consuming subject. Education promotes the two aspects. As shown by investigations on the influence of educational attainment on consumption, education has great influences on people's consumption level, consumption structure, consumption modes and consumption concepts. The…

  8. Ego Boundaries and Attainments in FL Pronunciation

    ERIC Educational Resources Information Center

    Baran-Lucarz, Malgorzata

    2012-01-01

    The paper reports on a study designed to examine the relationship between the thickness of ego boundaries and attainments in FL pronunciation after a clearly structured form-focused practical course of phonetics. The research involved 45 first-year students of the Institute of English Studies in Wroclaw, Poland, who had attended around thirty…

  9. Degree Attainment. Snapshot™ Report, Winter 2015

    ERIC Educational Resources Information Center

    National Student Clearinghouse, 2015

    2015-01-01

    This Snapshot Report presents information on student degree attainment in science and engineering disciplines for 2004 and 2014. It offers data on the following: (1) Science and Engineering Degrees as Percentage of All Degrees; (2) Gender Distribution of Science and Engineering Degrees by Level; (3) Gender Distribution of Bachelor's Degrees in…

  10. Genetic and Environmental Transactions Underlying Educational Attainment

    ERIC Educational Resources Information Center

    Johnson, Wendy; Deary, Ian J.; Iacono, William G.

    2009-01-01

    This report used a population-representative longitudinal twin study with two birth cohorts to explore the association between intelligence and education by understanding how genetic and environmental influences on intelligence moderate genetic and environmental influences on school grades and educational attainment. Nonshared environmental…

  11. Locus of Control and Status Attainment.

    ERIC Educational Resources Information Center

    Bensman, Miriam Roza; Haller, Archibald O.

    Utilizing data derived from 277 rural, male respondents initially enrolled in Lenawee County, Michigan high schools, the Rotter's Internal-External Locus of Control Scale was employed to test the hypothesis that locus of control will have interactive rather than additive effects on the process of status attainment. Locus of control was defined as…

  12. Attendance and Attainment in a Calculus Course

    ERIC Educational Resources Information Center

    Meulenbroek, Bernard; van den Bogaard, Maartje

    2013-01-01

    In this paper the relationship between attendance and attainment in a standard calculus course is investigated. Calculus could in principle be studied without attending lectures due to the wealth of material available (in hardcopy and online). However, in this study we will show that the pass rate of students attending classes regularly (>75%…

  13. The Fiscal Impacts of College Attainment

    ERIC Educational Resources Information Center

    Trostel, Philip A.

    2010-01-01

    This study quantifies one part of the return to U.S. public investment in college education, namely, the fiscal benefits associated with greater college attainment. College graduates pay much more taxes than those not going to college. Government expenditures are also much less for college graduates than for those without a college education.…

  14. College Attainment: Throwing a Complete Game

    ERIC Educational Resources Information Center

    Jones, Stan; Soo, David

    2010-01-01

    The U.S. once had the world's highest percentage of adults with a college degree, but has now dropped to 10th, according to the OECD. In an attempt to reverse this slide, a number of policymakers and foundations have sought to make increased degree attainment a national priority. President Obama has articulated the goal that America will regain…

  15. Genetic and Environmental Transactions Underlying Educational Attainment

    ERIC Educational Resources Information Center

    Johnson, Wendy; Deary, Ian J.; Iacono, William G.

    2009-01-01

    This report used a population-representative longitudinal twin study with two birth cohorts to explore the association between intelligence and education by understanding how genetic and environmental influences on intelligence moderate genetic and environmental influences on school grades and educational attainment. Nonshared environmental…

  16. The Fiscal Impacts of College Attainment

    ERIC Educational Resources Information Center

    Trostel, Philip A.

    2010-01-01

    This study quantifies one part of the return to U.S. public investment in college education, namely, the fiscal benefits associated with greater college attainment. College graduates pay much more taxes than those not going to college. Government expenditures are also much less for college graduates than for those without a college education.…

  17. Geography Education for "An Attainable Global Perspective"

    ERIC Educational Resources Information Center

    Klein, Phil; Pawson, Eric; Solem, Michael; Ray, Waverly

    2014-01-01

    This article considers approaches to promoting global perspectives as both cognitive and affective learning outcomes within geography education. Particular attention is paid to the work of Robert Hanvey, who proposed "An Attainable Global Perspective" in the 1970s, which explicitly ties to the content and perspectives embedded in…

  18. Challenges to the Attainment of Women's Literacy.

    ERIC Educational Resources Information Center

    Stromquist, Nelly P.

    Literacy for women is a frequently voiced need that most governments recognize officially as a high priority. Despite the expansion of public education, women (particularly poor and rural women) continue to show adult literacy rates lower than those of men. Five key challenges to the attainment of literacy emerge for women. The first challenge is…

  19. Adolescents' Sexual Behavior and Academic Attainment

    ERIC Educational Resources Information Center

    Frisco, Michelle L.

    2008-01-01

    High school students have high ambitions but do not always make choices that maximize their likelihood of educational success. This was the motivation for investigating the relationships between high school sexual behavior and two important milestones in academic attainment: earning a high school diploma and enrolling in distinct postsecondary…

  20. Consolidation of proteomics data in the Cancer Proteomics database.

    PubMed

    Arntzen, Magnus Ø; Boddie, Paul; Frick, Rahel; Koehler, Christian J; Thiede, Bernd

    2015-11-01

    Cancer is a class of diseases characterized by abnormal cell growth and one of the major reasons for human deaths. Proteins are involved in the molecular mechanisms leading to cancer, furthermore they are affected by anti-cancer drugs, and protein biomarkers can be used to diagnose certain cancer types. Therefore, it is important to explore the proteomics background of cancer. In this report, we developed the Cancer Proteomics database to re-interrogate published proteome studies investigating cancer. The database is divided in three sections related to cancer processes, cancer types, and anti-cancer drugs. Currently, the Cancer Proteomics database contains 9778 entries of 4118 proteins extracted from 143 scientific articles covering all three sections: cell death (cancer process), prostate cancer (cancer type) and platinum-based anti-cancer drugs including carboplatin, cisplatin, and oxaliplatin (anti-cancer drugs). The detailed information extracted from the literature includes basic information about the articles (e.g., PubMed ID, authors, journal name, publication year), information about the samples (type, study/reference, prognosis factor), and the proteomics workflow (Subcellular fractionation, protein, and peptide separation, mass spectrometry, quantification). Useful annotations such as hyperlinks to UniProt and PubMed were included. In addition, many filtering options were established as well as export functions. The database is freely available at http://cancerproteomics.uio.no.

  1. The Seed Proteome Web Portal

    PubMed Central

    Galland, Marc; Job, Dominique; Rajjou, Loïc

    2012-01-01

    The Seed Proteome Web Portal (SPWP; http://www.seed-proteome.com/) gives access to information both on quantitative seed proteomic data and on seed-related protocols. Firstly, the SPWP provides access to the 475 different Arabidopsis seed proteins annotated from two dimensional electrophoresis (2DE) maps. Quantitative data are available for each protein according to their accumulation profile during the germination process. These proteins can be retrieved either in list format or directly on scanned 2DE maps. These proteomic data reveal that 40% of seed proteins maintain a stable abundance over germination, up to radicle protrusion. During sensu stricto germination (24 h upon imbibition) about 50% of the proteins display quantitative variations, exhibiting an increased abundance (35%) or a decreasing abundance (15%). Moreover, during radicle protrusion (24–48 h upon imbibition), 41% proteins display quantitative variations with an increased (23%) or a decreasing abundance (18%). In addition, an analysis of the seed proteome revealed the importance of protein post-translational modifications as demonstrated by the poor correlation (r2 = 0.29) between the theoretical (predicted from Arabidopsis genome) and the observed protein isoelectric points. Secondly, the SPWP is a relevant technical resource for protocols specifically dedicated to Arabidopsis seed proteome studies. Concerning 2D electrophoresis, the user can find efficient procedures for sample preparation, electrophoresis coupled with gel analysis, and protein identification by mass spectrometry, which we have routinely used during the last 12 years. Particular applications such as the detection of oxidized proteins or de novo synthesized proteins radiolabeled by [35S]-methionine are also given in great details. Future developments of this portal will include proteomic data from studies such as dormancy release and protein turnover through de novo protein synthesis analyses during germination. PMID

  2. [Proteomics and its application in parasitology].

    PubMed

    Zhao, Qin-ping; Jiang, Ming-sen

    2006-04-30

    Proteomics is an important high throughout method in modern life science. In this paper, the definition, background and methods used in proteomics were introduced, and the last part was focused on its application in parasitology.

  3. CPTAC | Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics.

  4. Proteomics in evolutionary ecology.

    PubMed

    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

  5. Insurance coverage for employment-related claims

    SciTech Connect

    Scheuermann, J.E.

    1993-12-31

    This article analyzes the principal coverage issues arising under CGL policies for employment-related claims. Section I discusses the bases of the duty to defend and the duty to idemnify in the key CGL policy provisions at issue, including the bodily injury and personal injury coverages. Section II examines the three provisions in CGL policies typically raised as defenses to coverage for employment-related claims and two public policy considerations that may affect claims for coverage. The duty to defend is given closer crutiny in section III. Finally, in section IV the effects of settlement on coverage are discussed. 106 refs.

  6. Medical male circumcision coverage in Rakai, Uganda.

    PubMed

    Kong, Xiangrong; Kigozi, Godfrey; Ssekasanvu, Joseph; Nalugoda, Fred; Nakigozi, Gertrude; Chang, Larry W; Latkin, Carl; Serwadda, David; Wawer, Maria J; Gray, Ronald H

    2017-03-13

    We assessed medical male circumcision (MMC) scale-up in Rakai, Uganda using population-based surveys during 2007-2014. MMC coverage increased from 28.5 to 52.0%. Coverage was initially lower in 15-19-year-olds but increased in 2014, was higher in married men and in trading communities, and lowest in the sexually inactive. Coverage did not vary by self-perceived risk of HIV or HIV serostatus. Increasing generalized coverage suggested that MMC became normative, but coverage falls short of WHO/Joint United Nations Programme on HIV and AIDS (UNAIDS) 80% targets, indicating the need for demand generation.

  7. 45 CFR 156.602 - Other coverage that qualifies as minimum essential coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Other coverage that qualifies as minimum essential... essential coverage for plan or policy years beginning on or before December 31, 2014. For coverage beginning after December 31, 2014, sponsors of self-funded student health coverage may apply to be recognized as...

  8. 42 CFR 422.68 - Effective dates of coverage and change of coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... continuity of health benefits coverage. (e) Special election period for individual age 65. For an election of... HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM MEDICARE ADVANTAGE PROGRAM Eligibility, Election, and Enrollment § 422.68 Effective dates of coverage and change of coverage. (a) Initial coverage election...

  9. Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications

    SciTech Connect

    Zhou, Jianying; Dann, Geoffrey P.; Shi, Tujin; Wang, Lu; Gao, Xiaoli; Su, Dian; Nicora, Carrie D.; Shukla, Anil K.; Moore, Ronald J.; Liu, Tao; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2012-03-10

    Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for highly efficient biological sample extraction; however, SDS presents a significant challenge to LC-MS-based proteomic analyses due to its severe interference with reversed-phase LC separations and electrospray ionization interfaces. This study reports a simple SDS-assisted proteomic sample preparation method facilitated by a novel peptide-level SDS removal protocol. After SDS-assisted protein extraction and digestion, SDS was effectively (>99.9%) removed from peptides through ion substitution-mediated DS- precipitation with potassium chloride (KCl) followed by {approx}10 min centrifugation. Excellent peptide recovery (>95%) was observed for less than 20 {mu}g of peptides. Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage from this SDS-assisted protocol was comparable to or better than those obtained from other standard proteomic preparation methods in both mammalian tissues and bacterial samples. These results suggest that this SDS-assisted protocol is a practical, simple, and broadly applicable proteomic sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.

  10. Comprehensive proteomic analysis of Schizosaccharomyces pombe by two-dimensional HPLC-tandem mass spectrometry

    PubMed Central

    Brill, Laurence M.; Motamedchaboki, Khatereh; Wu, Shuangding; Wolf, Dieter A.

    2009-01-01

    We describe a detailed and widely applicable method for comprehensive proteomic profiling of the fission yeast Schizosaccharomyces pombe by 2-dimensional high performance liquid chromatography-electrospray ionization-tandem mass spectrometry that demonstrates high sensitivity and robust operation. Steps ranging from the preparation of total proteins, digestion of proteins to peptides, and separation of peptides by two-dimensional (1. strong cation exchange and 2. reversed-phase) high performance liquid chromatography followed by tandem mass spectrometry and data processing have been optimized for our instrumentation platform. Using this technology, we identify ca. 3400 proteins per sample and have identified an estimated 4600 proteins in vegetative cells (equal to ca. 90 % of the predicted S. pombe proteome) at a false discovery rate of ≤ 0.02. Considering the fact that ~500 genes are strongly induced during sexual differentiation, and sexual differentiation was not included in our experiments, the proteomic profiling technique affords what should be virtually complete coverage of the vegetative S. pombe proteome. In addition, these methods are widely applicable, having been used for proteomic profiling of several other organisms. PMID:19272449

  11. A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition.

    PubMed

    Vidova, Veronika; Spacil, Zdenek

    2017-04-29

    Mass spectrometry (MS) based proteomics have achieved a near-complete proteome coverage in humans and in several other organisms, producing a wealth of information stored in databases and bioinformatics resources. Recent implementation of selected/multiple reaction monitoring (SRM/MRM) technology in targeted proteomics introduced the possibility of quantitatively follow-up specific protein targets in a hypothesis-driven experiment. In contrast to immunoaffinity-based workflows typically used in biological and clinical research for protein quantification, SRM/MRM is characterized by high selectivity, large capacity for multiplexing (approx. 200 proteins per analysis) and rapid, cost-effective transition from assay development to deployment. The concept of SRM/MRM utilizes triple quadrupole (QqQ) mass analyzer to provide inherent reproducibility, unparalleled sensitivity and selectivity to efficiently differentiate isoforms, post-translational modifications and mutated forms of proteins. SRM-like targeted acquisitions such as parallel reaction monitoring (PRM) are pioneered on high resolution/accurate mass (HR/AM) platforms based on the quadrupole-orbitrap (Q-orbitrap) mass spectrometer. The expansion of HR/AM also caused development in data independent acquisition (DIA). This review presents a step-by-step tutorial on development of SRM/MRM protein assay intended for researchers without prior experience in proteomics. We discus practical aspects of SRM-based quantitative proteomics workflow, summarize milestones in basic biological and medical research as well as recent trends and emerging techniques. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS

    SciTech Connect

    Metz, Thomas O.; Jacobs, Jon M.; Gritsenko, Marina A.; Fontes, Ghislaine; Qian, Weijun; Camp, David G.; Poitout, Vincent J.; Smith, Richard D.

    2006-12-01

    Research to elucidate the pathogenesis of type 1 diabetes mellitus has traditionally focused on the genetic and immunological factors associated with the disease, and, until recently, has not considered the target cell. While there have been reports detailing proteomic analyses of established islet cell lines or isolated rodent islets, the information gained is not always easily extrapolated to humans. Therefore, extensive characterization of the human islet proteome could result in better understanding of islet biology and lead to more effective treatment strategies. We have applied a two-dimensional LC-MS/MS-based analysis to the characterization of the human islet proteome, resulting in the detection of 29,021 unique peptides corresponding to 4,925 proteins. As expected, major islet hormones (insulin, glucagon, somatostatin), beta-cell enriched secretory products (IAPP), ion channels (K-ATP channel), and transcription factors (PDX-1, Nkx 6.1, HNF-1 beta) were detected. In addition, significant proteome coverage of metabolic enzymes and cellular pathways was obtained, including the insulin signaling cascade and the MAP kinase, NF-κβ, and JAK/STAT pathways. This work represents the most extensive characterization of the human islet proteome to date and provides a peptide reference library that may be utilized in future studies of islet biology and type 1 diabetes.

  13. Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex.

    PubMed

    Fernández-Irigoyen, Joaquín; Zelaya, María V; Santamaría, Enrique

    2014-01-01

    The amygdaloid complex is a key brain structure involved in the expression of behaviors and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer's disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS), detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a nine-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF). In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.

  14. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

    PubMed Central

    Hernandez-Valladares, Maria; Aasebø, Elise; Selheim, Frode; Berven, Frode S.; Bruserud, Øystein

    2016-01-01

    Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility. PMID:28248234

  15. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia.

    PubMed

    Hernandez-Valladares, Maria; Aasebø, Elise; Selheim, Frode; Berven, Frode S; Bruserud, Øystein

    2016-08-22

    Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.

  16. Subcellular proteomics of Trypanosoma cruzi reservosomes

    PubMed Central

    Sant’Anna, Celso; Nakayasu, Ernesto S.; Pereira, Miria G.; Lourenço, Daniela; de Souza, Wanderley; Almeida, Igor C.; Cunha-e-Silva, Narcisa L.

    2009-01-01

    Reservosomes are the endpoint of the endocytic pathway in Trypanosoma cruzi epimastigotes. These organelles have the particular ability to concentrate proteins and lipids obtained from medium together with the main proteolytic enzymes originated from the secretory pathway, being at the same time a storage organelle and the main site of protein degradation. Subcellular proteomics have been extensively used for profiling organelles in different cell types. Here, we combine cell fractionation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify reservosome-resident proteins. Starting from a purified reservosome fraction, we established a protocol to isolate reservosome membranes. Transmission electron microscopy was applied to confirm the purity of the fractions. To achieve a better coverage of identified proteins we analyzed the fractions separately and combined the results. LC-MS/MS analysis identified in total 709 T. cruzi-specific proteins; of these, 456 had predicted function and 253 were classified as hypothetical proteins. We could confirm the presence of most of the proteins validated by previous work and identify new proteins from different classes such as enzymes, proton pumps, transport proteins and others. The definition of the reservosome protein profile is a good tool to assess their molecular signature, identify molecular markers, and understand their relationship with different organelles. PMID:19288526

  17. Global costs of attaining the Millennium Development Goal for water supply and sanitation

    PubMed Central

    Bartram, Jamie

    2008-01-01

    Abstract Objective Target 10 of the Millennium Development Goals (MDGs) is to “halve by 2015 the proportion of people without sustainable access to safe drinking water and basic sanitation”. Because of its impacts on a range of diseases, it is a health-related MDG target. This study presents cost estimates of attaining MDG target 10. Methods We estimate the population to be covered to attain the MDG target using data on household use of improved water and sanitation for 1990 and 2004, and taking into account population growth. We assume this estimate is achieved in equal annual 
increments from the base year, 2005, until 2014. Costs per capita for investment and recurrent costs are applied. Country data is aggregated to 11 WHO developing country subregions and globally. Findings Estimated spending required in developing countries on new coverage to meet the MDG target is US$ 42 billion for water and US$ 142 billion for sanitation, a combined annual equivalent of US$ 18 billion. The cost of maintaining existing services totals an additional US$ 322 billion for water supply and US $216 billion for sanitation, a combined annual equivalent of US$ 54 billion. Spending for new coverage is largely rural (64%), while for maintaining existing coverage it is largely urban (73%). Additional programme costs, incurred administratively outside the point of delivery of interventions, of between 10% and 30% are required for effective implementation. Conclusion In assessing financing requirements, estimates of cost should include the operation, maintenance and replacement of existing coverage as well as new services and programme costs. Country-level costing studies are needed to guide sector financing. PMID:18235885

  18. Perfluorooctanoic Acid for Shotgun Proteomics

    PubMed Central

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

    2010-01-01

    Here, we describe the novel use of a volatile surfactant, perfluorooctanoic acid (PFOA), for shotgun proteomics. PFOA was found to solubilize membrane proteins as effectively as sodium dodecyl sulfate (SDS). PFOA concentrations up to 0.5% (w/v) did not significantly inhibit trypsin activity. The unique features of PFOA allowed us to develop a single-tube shotgun proteomics method that used all volatile chemicals that could easily be removed by evaporation prior to mass spectrometry analysis. The experimental procedures involved: 1) extraction of proteins in 2% PFOA; 2) reduction of cystine residues with triethyl phosphine and their S-alkylation with iodoethanol; 3) trypsin digestion of proteins in 0.5% PFOA; 4) removal of PFOA by evaporation; and 5) LC-MS/MS analysis of the resulting peptides. The general applicability of the method was demonstrated with the membrane preparation of photoreceptor outer segments. We identified 75 proteins from 1 µg of the tryptic peptides in a single, 1-hour, LC-MS/MS run. About 67% of the proteins identified were classified as membrane proteins. We also demonstrate that a proteolytic 18O labeling procedure can be incorporated after the PFOA removal step for quantitative proteomic experiments. The present method does not require sample clean-up devices such as solid-phase extractions and membrane filters, so no proteins/peptides are lost in any experimental steps. Thus, this single-tube shotgun proteomics method overcomes the major drawbacks of surfactant use in proteomic experiments. PMID:21209883

  19. Proteomic analysis of engineered cartilage

    PubMed Central

    Pu, Xinzhu; Oxford, Julia Thom

    2016-01-01

    Summary Tissue engineering holds promise for the treatment of damaged and diseased tissues, especially for those tissues that do not undergo repair and regeneration readily in situ. Many techniques are available for cell and tissue culturing and differentiation of chondrocytes using a variety of cell types, differentiation methods, and scaffolds. In each case, it is critical to demonstrate the cellular phenotype and tissue composition, with particular attention to the extracellular matrix molecules that play a structural role and that contribute to the mechanical properties of the resulting tissue construct. Mass spectrometry provides an ideal analytical method with which to characterize the full spectrum of proteins produced by tissue engineered cartilage. Using normal cartilage tissue as a standard, tissue engineered cartilage can be optimized according to the entire proteome. Proteomic analysis is a complementary approach to biochemical, immunohistochemical, and mechanical testing of cartilage constructs. Proteomics is applicable as an analysis approach to most cartilage constructs generated from a variety of cellular sources including primary chondrocytes, mesenchymal stem cells from bone marrow, adipose tissue, induced pluripotent stem cells, and embryonic stem cells. Additionally, proteomics can be used to optimize novel scaffolds and bioreactor applications, yielding cartilage tissue with the proteomic profile of natural cartilage. PMID:26445845

  20. [Proteomics: biomarker research in psychiatry].

    PubMed

    Hünnerkopf, R; Grassl, J; Thome, J

    2007-10-01

    Over the last decade, genomics research in psychiatry and neuroscience has provided important insights into genes expressed under different physiological and pathophysiological conditions. Contrary to the great expectations regarding a clinical use of these datasets, genomics failed to improve markedly the diagnostic and therapeutic options in brain disorders. Due to alternative splicing and posttranslational modifications, one single gene determines a multitude of gene products. Therefore, in order to understand molecular processes in neuropsychiatric disorders, it is necessary to unravel signal transduction pathways and complex interaction networks on the level of proteins, not only DNA and mRNA. Proteomics utilises high-throughput mass spectrometric protein identification that can reveal protein expression levels, posttranslational modifications and protein-protein interactions. Proteomic tools have the power to identify quantitative and qualitative protein patterns in postmortem brain tissue, cerebrospinal fluid (CSF) or serum, thus increasing the knowledge about etiology and pathomechanisms of brain diseases. Comparing protein profiles in healthy and disease states provides an opportunity to establish specific diagnostic and prognostic biomarkers. In addition, proteomic studies of the effects of medication - in vitro and in vivo - might help to design specific pharmaceutical agents with fewer side effects. In this overview, we present the most widely used proteomic techniques and illustrate the potential and limitations of this field of research. Furthermore, we provide insight into the contributions of proteomics to the study of psychiatric diseases such as Alzheimer's disease, drug addiction, schizophrenia and depression.

  1. Proteomic approaches to bacterial differentiation

    SciTech Connect

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

    2006-12-01

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

  2. Proteomic Analysis of Engineered Cartilage.

    PubMed

    Pu, Xinzhu; Oxford, Julia Thom

    2015-01-01

    Tissue engineering holds promise for the treatment of damaged and diseased tissues, especially for those tissues that do not undergo repair and regeneration readily in situ. Many techniques are available for cell and tissue culturing and differentiation of chondrocytes using a variety of cell types, differentiation methods, and scaffolds. In each case, it is critical to demonstrate the cellular phenotype and tissue composition, with particular attention to the extracellular matrix molecules that play a structural role and that contribute to the mechanical properties of the resulting tissue construct. Mass spectrometry provides an ideal analytical method with which to characterize the full spectrum of proteins produced by tissue-engineered cartilage. Using normal cartilage tissue as a standard, tissue-engineered cartilage can be optimized according to the entire proteome. Proteomic analysis is a complementary approach to biochemical, immunohistochemical, and mechanical testing of cartilage constructs. Proteomics is applicable as an analysis approach to most cartilage constructs generated from a variety of cellular sources including primary chondrocytes, mesenchymal stem cells from bone marrow, adipose tissue, induced pluripotent stem cells, and embryonic stem cells. Additionally, proteomics can be used to optimize novel scaffolds and bioreactor applications, yielding cartilage tissue with the proteomic profile of natural cartilage.

  3. Proteomics of saliva: personal experience.

    PubMed

    Scarano, E; Fiorita, A; Picciotti, P M; Passali, G C; Calò, L; Cabras, T; Inzitari, R; Fanali, C; Messana, I; Castagnola, M; Paludetti, G

    2010-06-01

    The salivary proteome is a complex protein mixture resulting from the activity of salivary glands with the contribution of other components that form the oral environment such as oral tissues and micro-organisms. For diagnosis purposes, saliva collection has the great advantage of being an easy and non-invasive technique. Human saliva proteomics have proven to be a novel approach in the search for protein biomarkers for detection of different local and systemic diseases. Currently, more than 1400 salivary proteins have been identified. In the last few years, our research group has extensively studied the salivary proteomics in order to analyse the salivary composition, investigating the major families of proteins present in human and mammalian saliva, the post-translational modifications, the different contributions of glands, the physiological and pathological modifications of saliva. The aim of this report is to present our personal experience in salivary proteomics. In conclusion, salivary proteome analysis represents an important field both for diagnosis and monitoring of various diseases and could be considered a novel approach to prevention of various pathological conditions.

  4. Proteomic Analysis of Genistein Mammary Cancer Chemoprevention

    DTIC Science & Technology

    2007-07-01

    to collect a higher yield of proteins and hopefully allow success. 15. SUBJECT TERMS Genistein , Breast Cancer Chemoprevention, Proteomics, Rats ...AD_________________ Award Number: DAMD17-03-1-0433 TITLE: Proteomic Analysis of Genistein ...SUBTITLE 5a. CONTRACT NUMBER Proteomic Analysis of Genistein Mammary Cancer Chemoprevention 5b. GRANT NUMBER DAMD17-03-1-0433 5c. PROGRAM

  5. [Proteomics in cardiology].

    PubMed

    Pinet, F

    2007-01-01

    Cardiovascular diseases are among the major causes of morbidity and mortality in the developed world. The molecular mechanisms responsible for dysfunction of the heart in most cardiac pathologies are still largely unknown, except that the expression of certain genes/proteins is altered. Proteomic analysis is a technology which can provide an overall understanding of changes in the level of protein expression. Especially with differential analysis, it now represents a powerful tool for interpreting all biochemical responses and their regulation. The principal technique employed is two dimensional electrophoresis (2-D gel) to separate the proteins followed by mass spectometry in order to identify them. Recently SELDI-TOF analysis, which is a complementary 2-D electrophoresis technique based on the combination of two principles, chromatography by retention on protein chips and mass spectometry, has allowed the comparison of protein profiles obtained from diverse biological samples. The publication of genome sequences for humans as well as for other species has provided evidence for the biochemical complexity, and in particular the fact that a gene does not just code for a single protein but for several, due to various alternative splicing processes, post-translational modifications etc... The combination of these various approaches has proved to be particularly interesting in the study of cardiovascular diseases with the aim of understanding the molecular mechanisms involved, providing evidence for protein interactions and identifying new biochemical factors / markers involved in the different cardiovascular pathologies.

  6. Proteome of Hydra Nematocyst*

    PubMed Central

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

    2012-01-01

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

  7. Structural Proteomics of Herpesviruses

    PubMed Central

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

    2016-01-01

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

  8. High-throughput proteomics

    NASA Astrophysics Data System (ADS)

    Lesley, Scott A.; Nasoff, Marc; Kreusch, Andreas; Spraggon, Glen

    2001-04-01

    Proteomics has become a major focus as researchers attempt to understand the vast amount of genomic information. Protein complexity makes identifying and understanding gene function inherently difficult. The challenge of studying proteins in a global way is driving the development of new technologies for systematic and comprehensive analysis of protein structure and function. We are addressing this challenge through instrumentation and approaches to rapidly express, purify, crystallize, and mutate large numbers of human gene products. Our approach applies the principles of HTS technologies commonly used in pharmaceutical development. Genes are cloned, expressed, and purified in parallel to achieve a throughput potential of hundreds per day. Our instrumentation allows us to produce tens of milligrams of protein from 96 separate clones simultaneously. Purified protein is used for several applications including a high-throughput crystallographic screening approach for structure determination using automated image analysis. To further understand protein function, we are integrating a mutagenesis and screening approach. By combining these key technologies, we hope to provide a fundamental basis for understanding gene function at the protein level.

  9. Operationalizing universal health coverage in Nigeria through social health insurance

    PubMed Central

    Okpani, Arnold Ikedichi; Abimbola, Seye

    2015-01-01

    Nigeria faces challenges that delay progress toward the attainment of the national government's declared goal of universal health coverage (UHC). One such challenge is system-wide inequities resulting from lack of financial protection for the health care needs of the vast majority of Nigerians. Only a small proportion of Nigerians have prepaid health care. In this paper, we draw on existing evidence to suggest steps toward reforming health care financing in Nigeria to achieve UHC through social health insurance. This article sets out to demonstrate that a viable path to UHC through expanding social health insurance exists in Nigeria. We argue that encouraging the states which are semi-autonomous federating units to setup and manage their own insurance schemes presents a unique opportunity for rapidly scaling up prepaid coverage for Nigerians. We show that Nigeria's federal structure which prescribes a sharing of responsibilities for health care among the three tiers of government presents serious challenges for significantly extending social insurance to uncovered groups. We recommend that rather than allowing this governance structure to impair progress toward UHC, it should be leveraged to accelerate the process by supporting the states to establish and manage their own insurance funds while encouraging integration with the National Health Insurance Scheme. PMID:26778879

  10. Proteome analysis in thyroid pathology.

    PubMed

    Pagni, Fabio; L'Imperio, Vincenzo; Bono, Francesca; Garancini, Mattia; Roversi, Gaia; De Sio, Gabriele; Galli, Manuel; Smith, Andrew James; Chinello, Clizia; Magni, Fulvio

    2015-08-01

    The incidence of thyroid cancer has continuously increased due to its detection in the preclinical stage. Clinical research in thyroid pathology is focusing on the development of new diagnostic tools to improve the stratification of nodules that have biological, practical and economic consequences on the management of patients. Several clinical questions related to thyroid carcinoma remain open and the use of proteomic research in the hunt for new targets with potential diagnostic applications has an important role in the solutions. Many different proteomic approaches are used to investigate thyroid lesions, including mass spectrometry profiling and imaging technologies. These approaches have been applied to different human tissues (cytological specimens, frozen sections, formalin-fixed paraffin embedded tissue or Tissue Micro Arrays). Moreover, other specimens are used for biomarker discovery, such as cell lines and the secretome. Alternative approaches, such as metabolomics and lipidomics, are also used and integrated within proteomics.

  11. Proteomics characterization of exosome cargo.

    PubMed

    Schey, Kevin L; Luther, J Matthew; Rose, Kristie L

    2015-10-01

    Characterization of exosomal cargo is of significant interest because this cargo can provide clues to exosome biogenesis, targeting, and cellular effects and may be a source of biomarkers for disease diagnosis, prognosis and response to treatment. With recent improvements in proteomics technologies, both qualitative and quantitative characterization of exosomal proteins is possible. Here we provide a brief review of exosome proteomics studies and provide detailed protocols for global qualitative, global quantitative, and targeted quantitative analysis of exosomal proteins. In addition, we provide an example application of a standard global quantitative analysis followed by validation via a targeted quantitative analysis of urine exosome samples from human patients. Advantages and limitations of each method are discussed as well as future directions for exosome proteomics analysis.

  12. Proteomics studies of pancreatic cancer

    PubMed Central

    Chen, Ru; Pan, Sheng; Aebersold, Ruedi; Brentnall, Teresa A.

    2008-01-01

    Pancreatic cancer is the fourth leading cause of cancer death in the United States, with 4% survival 5 years after diagnosis. Biomarkers are desperately needed to improve earlier, more curable cancer diagnosis and to develop new effective therapeutic targets. The development of quantitative proteomics technologies in recent years offers great promise for understanding the complex molecular events of tumorigenesis at the protein level, and has stimulated great interest in applying the technology for pancreatic cancer studies. Proteomic studies of pancreatic tissues, juice, serum/plasma, and cell lines have recently attempted to identify differentially expressed proteins in pancreatic cancer to dissect the abnormal signaling pathways underlying oncogenesis, and to detect new biomarkers. It can be expected that the continuing evolution of proteomics technology with better resolution and sensitivity will greatly enhance our capability in combating pancreatic cancer. PMID:18633454

  13. Proteomics, nanotechnology and molecular diagnostics.

    PubMed

    Johnson, Christopher J; Zhukovsky, Nikolay; Cass, Anthony E G; Nagy, Judit M

    2008-02-01

    Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.

  14. Proteomics Characterization of Exosome Cargo

    PubMed Central

    Schey, Kevin L.; Luther, J. Matthew; Rose, Kristie L.

    2015-01-01

    Characterization of exosomal cargo is of significant interest because this cargo can provide clues to exosome biogenesis, targeting, and cellular effects and may be a source of biomarkers for disease diagnosis, prognosis and response to treatment. With recent improvements in proteomics technologies, both qualitative and quantitative characterization of exosomal proteins is possible. Here we provide a brief review of exosome proteomics studies and provide detailed protocols for global qualitative, global quantitative, and targeted quantitative analysis of exosomal proteins. In addition, we provide an example application of a standard global quantitative analysis followed by validation via a targeted quantitative analysis of urine exosome samples from human patients. Advantages and limitations of each method are discussed as well as future directions for exosome proteomics analysis. PMID:25837312

  15. Proteomic Analysis of Menstrual Blood*

    PubMed Central

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

    2012-01-01

    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

  16. Pediatric Ependymoma: A Proteomics Perspective

    PubMed Central

    TSANGARIS, GEORGE TH; PAPATHANASIOU, CHRISSA; ADAMOPOULOS, PANAGIOTIS G; SCORILAS, ANDREAS; VORGIAS, CONSTANTINOS E; PRODROMOU, NEOFYTOS; TZORTZATOU-STATHOPOULOU, FOTEINI; STRAVOPODIS, DIMITRIOS J; ANAGNOSTOPOULOS, ATHANASIOS K

    2017-01-01

    Background/Aim: Proteomics based on high-resolution mass spectrometry (MS) is the tool of choice for the analysis of protein presence, modifications and interactions, with increasing emphasis on the examination of tumor tissues. Application of MS-based proteomics offers a detailed picture of tumor tissue characteristics, facilitating the appreciation of different tumor entities, whilst providing reliable and fast results for therapeutic marker targeting and prognostic factor assessment. Through use of the high analytical resolution of nano-high-pressure liquid chromatography (nanoHPLC) and the high resolution of an Orbitrap Elite mass spectrometer, the present study aimed to provide knowledge on the proteome of the generally unknown entity of pediatric ependymal tumors. Materials and Methods: Ten resected specimens of childhood ependymoma were analyzed through a one-dimensional (1D) nanoLC-MS/MS approach. Method optimization steps were undertaken for both the sample preparation/protein extraction procedure and LC parameters, aiming to achieve the highest possible identification rates. Results: Following method optimization, each nanoLC-MS/MS run resulted in identification of more than 5,000 proteins and more than 25,000 peptides for every analyzed sample, thus detailing the greater part of the ependymoma proteome. Identified proteins were found to spread throughout all known tumor categories regarding their molecular function and subcellular localization. Conclusion: Through the proposed nanoLC-MS/MS method herein we report, for the firs time, the ependymoma proteome database. A large number of similarities regarding proteome content are revealed compared to other two pediatric brain tumor entities; astrocytomas and medulloblastomas. Furthermore, through our approach, the majority of currently proposed markers for ependymoma (e.g. nucleolin, nestin, Ki67 and laminin subunit A2 ) as well as all major key players of the phosphoinositide 3-kinase pathway (seemingly

  17. Attendance and attainment in a Calculus course

    NASA Astrophysics Data System (ADS)

    Meulenbroek, Bernard; van den Bogaard, Maartje

    2013-10-01

    In this paper the relationship between attendance and attainment in a standard calculus course is investigated. Calculus could in principle be studied without attending lectures due to the wealth of material available (in hardcopy and online). However, in this study we will show that the pass rate of students attending classes regularly (>75% of the classes) is much higher than the pass rate of students attending fewer classes. We use a logistic model to investigate whether this correlation is significant. We will argue why we believe that this correlation between attendance and attainment is causal, i.e. why it is necessary for most students to attend classes in order to (improve their chances to) pass the exam.

  18. Advances of Proteomic Sciences in Dentistry

    PubMed Central

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

    2016-01-01

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

  19. Advances of Proteomic Sciences in Dentistry.

    PubMed

    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.

  20. Centennial paper: Proteomics in animal science.

    PubMed

    Lippolis, J D; Reinhardt, T A

    2008-09-01

    Proteomics holds significant promise as a method for advancing animal science research. The use of this technology in animal science is still in its infancy. The ability of proteomics to simultaneously identify and quantify potentially thousands of proteins is unparalleled. In this review, we will discuss basic principles of doing a proteomic experiment. In addition, challenges and limitations of proteomics will be considered, stressing those that are unique to animal sciences. The current proteomic research in animal sciences will be discussed, and the potential uses for this technology will be highlighted.

  1. Scientific Workflow Management in Proteomics

    PubMed Central

    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

  2. Microbial proteomics: the quiet revolution

    SciTech Connect

    Seraphin, Bertrand; Hettich, Robert {Bob} L

    2012-01-01

    Technological developments in DNA sequencing and their application to study thousands of microbial genomes or even microbial ecosystems still today often make the headlines of general newspapers and scientific journals. These revolutionary changes are hiding another revolution that is unfolding more quietly in the background: the development of microbial proteomics to study genome expression products. It is important to recognize that while DNA sequencing reveals extensive details about the genomic potential of an organism or community, proteomic measurements reveal the functional gene products that are present and operational under specific environmental conditions, and thus perhaps better characterize the critical biomolecules that execute the life processes (enzymes, signaling, structural factors, etc.).

  3. Multidimensional peptide separations in proteomics.

    PubMed

    Link, Andrew J

    2002-12-01

    Multidimensional peptide separation will play an increasingly important role in the drive to identify and quantitate the proteome. By increasing the peak and load capacity, multidimensional approaches increase the number and dynamic range of peptides that can be analyzed in a complex biological organism. Separation methods using different physical properties of peptides have been combined with varying degrees of success. The ultimate goal is a rapid separation strategy that can be coupled with analytical methods, such as mass spectrometry, to provide comprehensive monitoring of the changing concentration, interactions, and structures of proteins in the proteome.

  4. Tennessee health plan tobacco cessation coverage.

    PubMed

    Kolade, Folasade M

    2014-01-01

    To evaluate the smoking cessation coverage available from public and private Tennessee health plans. Cross-sectional study. The sampling frame for private plans was a register of licensed plans obtained from the Tennessee Commerce Department. Government websites and reports provided TennCare data. Data were abstracted from plan manuals and formularies for benefit year 2012. Classification of coverage included comprehensive-all seven recommended medications plus individual and group counseling; moderate-at least two forms of nicotine replacement therapy (NRT) plus bupropion and varenicline and one form of counseling; inadequate-at least one treatment, or none-no medications or counseling, or coverage only for pregnant women. Of nine private plans, one provided comprehensive coverage; two, moderate coverage; four, inadequate coverage, as did TennCare; and two plans provided no coverage. Over 362,800 smokers had inadequate access to cessation treatments under TennCare, while 119,094 smokers had inadequate or no cessation coverage under private plans. In 2012, Tennessee fell short of Healthy People goals for total managed care and comprehensive TennCare coverage of smoking cessation. If Tennessee mandates that all health plans provide full coverage, 481,900 smokers may immediately be in a better position to quit. © 2013 Wiley Periodicals, Inc.

  5. Trends in Educational Attainment of Women.

    ERIC Educational Resources Information Center

    Women's Bureau (DOL), Washington, DC.

    Educational attainment of women has risen steadily since the turn of the century. In 1900 about 57,000 girls graduated from high school, and by 1968 the number had increased to 1.4 million. A similar rise occurred in the number of bachelor's degrees received by women. In 1900 about 5,000 graduated from college, and in 1968 the number rose to…

  6. Educational attainment and obesity: A systematic review

    PubMed Central

    Cohen, Alison K.; Rai, Manisha; Rehkopf, David H.; Abrams, Barbara

    2013-01-01

    Background Although previous systematic reviews considered the relationship between socioeconomic status and obesity, almost 200 peer-reviewed articles have been published since the last review on that topic, and this paper focuses specifically on education, which has different implications. Methods The authors systematically review the peer-reviewed literature from around the world considering the association between educational attainment and obesity. Databases from public health and medicine, education, psychology, economics, and other social sciences were searched, and articles published in English, French, Portuguese, and Spanish were included. Results This paper includes 289 articles that report on 410 populations in 91 countries. The relationship between educational attainment and obesity was modified by both gender and the country's economic development level: an inverse association was more common in studies of higher-income countries and a positive association was more common in lower-income countries, with stronger social patterning among women. Relatively few studies reported on lower-income countries, controlled for a comprehensive set of potential confounding variables, and/or attempted to assess causality through the use of quasi-experimental designs. Conclusions Future research should address these gaps to understand if the relationship between educational attainment and obesity may be causal, thus supporting education policy as a tool for obesity prevention. PMID:23889851

  7. Educational attainment and obesity: a systematic review.

    PubMed

    Cohen, A K; Rai, M; Rehkopf, D H; Abrams, B

    2013-12-01

    Although previous systematic reviews considered the relationship between socioeconomic status and obesity, almost 200 peer-reviewed articles have been published since the last review on that topic, and this paper focuses specifically on education, which has different implications. The authors systematically review the peer-reviewed literature from around the world considering the association between educational attainment and obesity. Databases from public health and medicine, education, psychology, economics, and other social sciences were searched, and articles published in English, French, Portuguese and Spanish were included. This paper includes 289 articles that report on 410 populations in 91 countries. The relationship between educational attainment and obesity was modified by both gender and the country's economic development level: an inverse association was more common in studies of higher-income countries and a positive association was more common in lower-income countries, with stronger social patterning among women. Relatively few studies reported on lower-income countries, controlled for a comprehensive set of potential confounding variables and/or attempted to assess causality through the use of quasi-experimental designs. Future research should address these gaps to understand if the relationship between educational attainment and obesity may be causal, thus supporting education policy as a tool for obesity prevention.

  8. Attainable superheat of ethane-methane solutions

    NASA Astrophysics Data System (ADS)

    Baidakov, V. G.; Pankov, A. S.

    2013-12-01

    Methods of measuring lifetime and continuous pressure decrease were used to study kinetics of spontaneous boiling-up of superheated ethane-methane solutions. The attainable superheats of solutions at two pressure values (1.0 and 1.6 MPa) and two concentrations of methane (2.1 and 6.0 mole %) were determined experimentally in the range of nucleation rate J = 1·104-3·108 s-1m-3. At temperatures 266.5, 270.0, and 273.15 K, the attainable stretching of the studied solutions was measured. The experimental results were compared with the theory of homogeneous nucleation. At nucleation rates J ≥ 2.5·106 s-1m-3, there is a fair agreement of the theory and experiment. The discrepancy in attainable superheat temperatures T n does not exceed 0.8 K. It is shown that significant underheating of solution to theoretical values T n at J < 2.5·106 s-1m-3 cannot be bound only with heterogeneous nucleation but is conditioned by other factors as well.

  9. Sideline coverage of youth football.

    PubMed

    Rizzone, Katie; Diamond, Alex; Gregory, Andrew

    2013-01-01

    Youth football is a popular sport in the United States and has been for some time. There are currently more than 3 million participants in youth football leagues according to USA Football. While the number of participants and overall injuries may be higher in other sports, football has a higher rate of injuries. Most youth sporting events do not have medical personnel on the sidelines in event of an injury or emergency. Therefore it is necessary for youth sports coaches to undergo basic medical training in order to effectively act in these situations. In addition, an argument could be made that appropriate medical personnel should be on the sideline for collision sports at all levels, from youth to professional. This article will discuss issues pertinent to sideline coverage of youth football, including coaching education, sideline personnel, emergency action plans, age and size divisions, tackle versus flag football, and injury prevention.

  10. Proteomic Research Funding Opportunity | Office of Cancer Clinical Proteomics Research

    Cancer.gov

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

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

    Cancer.gov

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

  12. Wheat proteomics: proteome modulation and abiotic stress acclimation

    PubMed Central

    Komatsu, Setsuko; Kamal, Abu H. M.; Hossain, Zahed

    2014-01-01

    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. PMID:25538718

  13. What is Proteomics? - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The term "proteome" refers to the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or a cellular system. This will vary with time and distinct requirements, such as stresses, that a cell or organism undergoes.

  14. What is Proteomics? - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The term "proteome" refers to the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or a cellular system. This will vary with time and distinct requirements, such as stresses, that a cell or organism undergoes.

  15. Global Cell Proteome Profiling, Phospho-signaling and Quantitative 
Proteomics for Identification of New Biomarkers in Acute Myeloid 
Leukemia Patients

    PubMed Central

    Aasebø, Elise; Forthun, Rakel B.; Berven, Frode; Selheim, Frode; Hernandez-Valladares, Maria

    2016-01-01

    The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low resolution mass spectrometers. However, most of the studies did not follow up, confirm or validate their candidates with more patient samples. Current proteomics methods, new high resolution and fast mass spectrometers allow the identification and quantification of several thousands of proteins obtained from few tens of μg of AML cell lysate. Enrichment methods for posttranslational modifications (PTM), such as phosphorylation, can isolate several thousands of site-specific phosphorylated peptides from AML patient samples, which subsequently can be quantified with high confidence in new mass spectrometers. While recent reports aiming to propose proteomic or phosphoproteomic biomarkers on the studied AML patient samples have taken advantage of the technological progress, the access to large cohorts of AML patients to sample from and the availability of appropriate control samples still remain challenging. PMID:26306748

  16. Three Dimensional Liquid Chromatography Coupling IEC/HIC/RPC for Effective Protein Separation in Top-Down Proteomics

    PubMed Central

    Gregorich, Zachery R.; Guner, Huseyin; Jin, Song; Ge, Ying

    2015-01-01

    To address the complexity of proteome in mass spectrometry (MS)-based top-down proteomics, multi-dimensional liquid chromatography (MDLC) strategies that can effectively separate proteins with high resolution and automation are highly desirable. Although various MDLC methods that can effectively separate peptides from protein digests exist, very few MDLC strategies, primarily consisting of 2DLC, are available for intact protein separation, which is insufficient to address the proteome complexity. We recently demonstrated that hydrophobic interaction chromatography (HIC) utilizing a MS-compatible salt can provide high resolution separation of intact proteins for top-down proteomics. Herein, we have developed a novel 3DLC strategy by coupling HIC with ion exchange chromatography (IEC) and reverse phase chromatography (RPC) for intact protein separation. We demonstrated that a 3D (IECHIC-RPC) approach greatly outperformed the conventional 2D IEC-RPC approach. For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 non-redundant proteins) as compared to 47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications. Therefore this novel 3DLC method has great potential for effective separation of intact proteins to achieve deep proteome coverage in top-down proteomics. PMID:25867201

  17. Plant proteome analysis: a 2006 update.

    PubMed

    Jorrín, Jesús V; Maldonado, Ana M; Castillejo, Ma Angeles

    2007-08-01

    This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic

  18. Impact of Self-Regulatory Influences on Writing Course Attainment.

    ERIC Educational Resources Information Center

    Zimmerman, Barry J.; Bandura, Albert

    1994-01-01

    Using path analysis, studied the role of self-efficacy beliefs concerning academic attainment and regulation of writing, academic goals, and self-standards in writing-course attainment of 95 college freshmen. Different facets of perceived self-efficacy played a key role in writing-course attainment. (SLD)

  19. 75 FR 45571 - Determination of Attainment for PM10

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-03

    ... AGENCY 40 CFR Part 81 Determination of Attainment for PM 10 for the Las Vegas Valley Nonattainment Area... determine that the Las Vegas Valley nonattainment area in Nevada attained the National Ambient Air Quality... micrometers (PM 10 ) by the applicable attainment date (December 31, 2006), and that the Las Vegas...

  20. 40 CFR 52.577 - Determination of attainment.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...-2010, EPA determined that the Atlanta, Georgia, 1997 8-hour ozone nonattainment Area attained the 1997... attainment date, whether the Area attained the standard. EPA also determined that the Atlanta, Georgia, 1997... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Georgia § 52.577 Determination of...

  1. 40 CFR 52.577 - Determination of attainment.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...-2010, EPA determined that the Atlanta, Georgia, 1997 8-hour ozone nonattainment Area attained the 1997... attainment date, whether the Area attained the standard. EPA also determined that the Atlanta, Georgia, 1997... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Georgia § 52.577 Determination of...

  2. 40 CFR 52.577 - Determination of attainment.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...-2010, EPA determined that the Atlanta, Georgia, 1997 8-hour ozone nonattainment Area attained the 1997... attainment date, whether the Area attained the standard. EPA also determined that the Atlanta, Georgia, 1997... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Georgia § 52.577 Determination of...

  3. Challenges for proteomics core facilities.

    PubMed

    Lilley, Kathryn S; Deery, Michael J; Gatto, Laurent

    2011-03-01

    Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Proteomic Interrogation of Human Chromatin

    PubMed Central

    Torrente, Mariana P.; Zee, Barry M.; Young, Nicolas L.; Baliban, Richard C.; LeRoy, Gary; Floudas, Christodoulos A.; Hake, Sandra B.; Garcia, Benjamin A.

    2011-01-01

    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. PMID:21935452

  5. Proteomics of Saccharomyces cerevisiae Organelles*

    PubMed Central

    Wiederhold, Elena; Veenhoff, Liesbeth M.; Poolman, Bert; Slotboom, Dirk Jan

    2010-01-01

    Knowledge of the subcellular localization of proteins is indispensable to understand their physiological roles. In the past decade, 18 studies have been performed to analyze the protein content of isolated organelles from Saccharomyces cerevisiae. Here, we integrate the data sets and compare them with other large scale studies on protein localization and abundance. We evaluate the completeness and reliability of the organelle proteomics studies. Reliability depends on the purity of the organelle preparations, which unavoidably contain (small) amounts of contaminants from different locations. Quantitative proteomics methods can be used to distinguish between true organellar constituents and contaminants. Completeness is compromised when loosely or dynamically associated proteins are lost during organelle preparation and also depends on the sensitivity of the analytical methods for protein detection. There is a clear trend in the data from the 18 organelle proteomics studies showing that proteins of low abundance frequently escape detection. Proteins with unknown function or cellular abundance are also infrequently detected, indicating that these proteins may not be expressed under the conditions used. We discuss that the yeast organelle proteomics studies provide powerful lead data for further detailed studies and that methodological advances in organelle preparation and in protein detection may help to improve the completeness and reliability of the data. PMID:19955081

  6. Periodontal Proteomics: Wonders Never Cease!

    PubMed Central

    Grover, Harpreet Singh; Kapoor, Shalini; Saksena, Neha

    2013-01-01

    Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. The ongoing research to understand the signalling pathways that allow cells to divide, differentiate, and die in controlled manner has brought us to the era of proteomics. Proteomics is defined as the study of all proteins including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Its application to periodontal science can be used to monitor health status, disease onset, treatment response, and outcome. Proteomics can offer answers to critical, unresolved questions such as the biological basis for the heterogeneity in gingival, alveolar bone, and cemental cell populations. PMID:24490073

  7. Microbial proteomics using mass spectrometry.

    PubMed

    Hines, Harry B

    2012-01-01

    Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subjects, requiring only modifications to or, in some cases, substitution of some of the steps to ensure they are relevant to the desired objective of a study. This fortunate occurrence creates an essential core of proteomic approaches and techniques that are consistently available for most studies, regardless of test subject. In this chapter, an overview of some of these core approaches, techniques, and mass spectrometric instrumentation is given, while indicating how such steps are useful for and applied to bacterial investigations. To exemplify how such proteomic concepts and techniques are applicable to bacterial investigations, a practical, quantitative method useful for bacterial proteomic analysis is presented with a discussion of possibilities, pitfalls, and some emerging technology to provide a compilation of information from the diverse literature that is intermingled with experimental experience.

  8. Soft tissue coverage in abdominal wall reconstruction.

    PubMed

    Baumann, Donald P; Butler, Charles E

    2013-10-01

    Abdominal wall defects requiring soft tissue coverage can be either partial-thickness defects or full-thickness composite defects. Soft tissue flap reconstruction offers significant advantages in defects that cannot be closed primarily. Flap reconstruction is performed in a single-stage procedure obviating chronic wound management. If the defect size exceeds the availability of local soft tissue for coverage, regional pedicled flaps can be delivered into the abdominal wall while maintaining blood supply from their donor site. Microsurgical free tissue transfer increases the capacity to provide soft tissue coverage for abdominal wall defects that are not amenable to either local or regional flap coverage.

  9. Gain in Insurance Coverage and Residual Uninsurance Under the Affordable Care Act: Texas, 2013-2016.

    PubMed

    Pickett, Stephen; Marks, Elena; Ho, Vivian

    2017-01-01

    To examine the effects of the Affordable Care Act's (ACA's) Marketplace on Texas residents and determine which population subgroups benefited the most and which the least. We analyzed insurance coverage rates among nonelderly Texas adults using the Health Reform Monitoring Survey-Texas from September 2013, just before the first open enrollment period in the Marketplace, through March 2016. Texas has experienced a roughly 6-percentage-point increase in insurance coverage (from 74.7% to 80.6%; P = .012) after implementation of the major insurance provisions of the ACA. The 4 subgroups with the largest increases in adjusted insurance coverage between 2013 and 2016 were persons aged 50 to 64 years (12.1 percentage points; P = .002), Hispanics (10.9 percentage points; P = .002), persons reporting fair or poor health status (10.2 percentage points; P = .038), and those with a high school diploma as their highest educational attainment (9.2 percentage points; P = .023). Many population subgroups have benefited from the ACA's Marketplace, but approximately 3 million Texas residents still lack health coverage. Adopting the ACA's Medicaid expansion is a means to address the lack of coverage.

  10. Gain in Insurance Coverage and Residual Uninsurance Under the Affordable Care Act: Texas, 2013–2016

    PubMed Central

    Pickett, Stephen; Marks, Elena

    2017-01-01

    Objectives. To examine the effects of the Affordable Care Act’s (ACA’s) Marketplace on Texas residents and determine which population subgroups benefited the most and which the least. Methods. We analyzed insurance coverage rates among nonelderly Texas adults using the Health Reform Monitoring Survey-Texas from September 2013, just before the first open enrollment period in the Marketplace, through March 2016. Results. Texas has experienced a roughly 6–percentage-point increase in insurance coverage (from 74.7% to 80.6%; P = .012) after implementation of the major insurance provisions of the ACA. The 4 subgroups with the largest increases in adjusted insurance coverage between 2013 and 2016 were persons aged 50 to 64 years (12.1 percentage points; P = .002), Hispanics (10.9 percentage points; P = .002), persons reporting fair or poor health status (10.2 percentage points; P = .038), and those with a high school diploma as their highest educational attainment (9.2 percentage points; P = .023). Conclusions. Many population subgroups have benefited from the ACA’s Marketplace, but approximately 3 million Texas residents still lack health coverage. Adopting the ACA’s Medicaid expansion is a means to address the lack of coverage. PMID:27854535

  11. Formation of hematite nanoparticle monolayers of controlled coverage and structure at polymeric microparticles.

    PubMed

    Sadowska, Marta; Adamczyk, Zbigniew; Nattich-Rak, Małgorzata

    2017-11-01

    The deposition of hematite nanoparticles (22nm and 29nm in diameter) on negatively charged polystyrene microspheres (820nm in diameter) was studied by micro-electrophoretic measurements and AFM. The influence of ionic strength, varied between 10(-4) and 10(-2)M, was determined. Initially, the electrophoretic mobility change of microspheres upon the addition of controlled amount of hematite nanoparticles were measured. These dependencies were quantitatively interpreted in terms of the general electrokinetic model. This allowed to determine the coverage of nanoparticles on microspheres under in situ conditions, which increased with ionic strength attaining 0.35 for the ionic strength of 10(-2)M and 29 in diameter hematite particles. This effect, attributed to the decreasing range of lateral electrostatic repulsion among deposited particles, was accounted for by the random sequential adsorption model. However, the coverages attained for lower ionic strength exceeded the theoretical predictions. This effect was interpreted in terms of an additional electrostatic screening due to polymeric chains present at the microparticle surface. The acid base properties of the hematite monolayers were also acquired by applying thorough micro-electrophoretic measurements. The obtained results confirmed a feasibility of preparing hematite nanoparticle monolayers on polymeric carrier microspheres having well-defined coverage and structure. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Rejuvenating rice proteomics: facts, challenges, and visions.

    PubMed

    Agrawal, Ganesh Kumar; Jwa, Nam-Soo; Iwahashi, Yumiko; Yonekura, Masami; Iwahashi, Hitoshi; Rakwal, Randeep

    2006-10-01

    Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.

  13. Coverage-based constraints for IMRT optimization

    NASA Astrophysics Data System (ADS)

    Mescher, H.; Ulrich, S.; Bangert, M.

    2017-09-01

    Radiation therapy treatment planning requires an incorporation of uncertainties in order to guarantee an adequate irradiation of the tumor volumes. In current clinical practice, uncertainties are accounted for implicitly with an expansion of the target volume according to generic margin recipes. Alternatively, it is possible to account for uncertainties by explicit minimization of objectives that describe worst-case treatment scenarios, the expectation value of the treatment or the coverage probability of the target volumes during treatment planning. In this note we show that approaches relying on objectives to induce a specific coverage of the clinical target volumes are inevitably sensitive to variation of the relative weighting of the objectives. To address this issue, we introduce coverage-based constraints for intensity-modulated radiation therapy (IMRT) treatment planning. Our implementation follows the concept of coverage-optimized planning that considers explicit error scenarios to calculate and optimize patient-specific probabilities q(\\hat{d}, \\hat{v}) of covering a specific target volume fraction \\hat{v} with a certain dose \\hat{d} . Using a constraint-based reformulation of coverage-based objectives we eliminate the trade-off between coverage and competing objectives during treatment planning. In-depth convergence tests including 324 treatment plan optimizations demonstrate the reliability of coverage-based constraints for varying levels of probability, dose and volume. General clinical applicability of coverage-based constraints is demonstrated for two cases. A sensitivity analysis regarding penalty variations within this planing study based on IMRT treatment planning using (1) coverage-based constraints, (2) coverage-based objectives, (3) probabilistic optimization, (4) robust optimization and (5) conventional margins illustrates the potential benefit of coverage-based constraints that do not require tedious adjustment of target volume objectives.

  14. Wing design with attainable thrust considerations

    NASA Technical Reports Server (NTRS)

    Carlson, H. W.; Shrout, B. L.; Darden, C. M.

    1984-01-01

    A CAD process that includes leading-edge thrust considerations for wings with high aerodynamic efficiencies is outlined. Rectangular grids are used for evaluation of both subsonic and supersonic pressure loadings. Account is taken of the Mach number, Re, the wing planform, the presence of camber, the airfoil geometry and the locations and forces induced by shed vortices. Optimization techniques are applied to the candidate surfaces in order to consider the attainable thrust. Inclusion of the optimization techniques permits analyses of mission-adaptive wings and various flap systems and the elimination of singularities in the flight envelope.

  15. Coverage of whole proteome by structural genomics observed through protein homology modeling database

    PubMed Central

    Yamaguchi, Akihiro; Go, Mitiko

    2006-01-01

    We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. However, cases that a modeled 3D structure covers the whole part of an ORF product are rare. When portion of an ORF with 3D structure is compared in three kingdoms of life, in archaebacteria and eubacteria, approximately 60% of the ORFs have modeled 3D structures covering almost the entire amino acid sequences, however, the percentage falls to about 30% in eukaryotes. When annual differences in the number of ORFs with modeled 3D structure are calculated, the fraction of modeled 3D structures of soluble protein for archaebacteria is increased by 5%, and that for eubacteria by 7% in the last 3 years. Assuming that this rate would be maintained and that determination of 3D structures for predicted disordered regions is unattainable, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years. The 3D structures we will have at those times are not the 3D structure of the entire proteins encoded in single ORFs, but the 3D structures of separate structural domains. Measuring or predicting spatial arrangements of structural domains in an ORF will then be a coming issue of structural genomics. PMID:17146617

  16. Proteomic Profiling of Bifidobacterium bifidum S17 Cultivated Under In Vitro Conditions

    PubMed Central

    Wei, Xiao; Wang, Simiao; Zhao, Xiangna; Wang, Xuesong; Li, Huan; Lin, Weishi; Lu, Jing; Zhurina, Daria; Li, Boxing; Riedel, Christian U.; Sun, Yansong; Yuan, Jing

    2016-01-01

    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-Meyerh of 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-interactions and

  17. Protein expression in a transformed trabecular meshwork cell line: proteome analysis.

    PubMed

    Steely, H Thomas; Dillow, Glen W; Bian, Liangqian; Grundstad, Jason; Braun, Terry A; Casavant, Thomas L; McCartney, Mitchell D; Clark, Abbot F

    2006-04-18

    Characterization of the human trabecular meshwork (TM) proteome is hindered by the small mass of intact tissue and the slow growth of cultured cell strains. We have previously characterized a transformed TM cell strain (GTM3) that demonstrates many of the same protein expression and cell signaling systems of nontransformed cell strains. The aim of this study was to initiate a proteomic survey of GTM3 cells as the initial step toward characterization of the complete human TM proteome. GTM3 cells were cultured to confluence, harvested and solubilized in urea/Nonidet. The protein extract (600 mug) was focused in immobilized isoelectric focusing (IEF) strips, separated by 10% SDS PAGE, and visualized with colloidal Coomassie Blue. Spots of interest were excised, destained, and the contained proteins subjected to in-gel reduction, derivatization, and tryptic digestion. Tryptic peptides were extracted and analyzed by electrospray LC/MS/MS. Protein identification was made using the TurboSequest search algorithm and a recent version of the nonredundant human protein database downloaded from the National Center for Biotechnology Information (NCBI). Eighty-seven (87) primary proteins and 93 variants of these proteins were identified. A website was created (TM proteome) that combines data such as graphic spot location within the gel, peptide sequence, apparent and calculated pI, apparent and calculated mass, percentage of coverage, and protein informatic website links. Proteomic analysis of a transformed human TM cell line has been initiated combining preparative two-dimensional PAGE separation, LC/MS/MS analysis of major proteins, and bioinformatic cataloging of the data. Further investigation of data from the transformed cell strain will be used in a comparative fashion for spot identification of analytical proteomic gels of human TM tissue and cultured normal cells. These initial data will form the base from which the characterization of protein expression in the normal

  18. Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry*

    PubMed Central

    Olsson, Niclas; James, Peter; Borrebaeck, Carl A. K.; Wingren, Christer

    2012-01-01

    The development of high-performance technology platforms for generating detailed protein expression profiles, or protein atlases, is essential. Recently, we presented a novel platform that we termed global proteome survey, where we combined the best features of affinity proteomics and mass spectrometry, to probe any proteome in a species independent manner while still using a limited set of antibodies. We used so called context-independent-motif-specific antibodies, directed against short amino acid motifs. This enabled enrichment of motif-containing peptides from a digested proteome, which then were detected and identified by mass spectrometry. In this study, we have demonstrated the quantitative capability, reproducibility, sensitivity, and coverage of the global proteome survey technology by targeting stable isotope labeling with amino acids in cell culture-labeled yeast cultures cultivated in glucose or ethanol. The data showed that a wide range of motif-containing peptides (proteins) could be detected, identified, and quantified in a highly reproducible manner. On average, each of six different motif-specific antibodies was found to target about 75 different motif-containing proteins. Furthermore, peptides originating from proteins spanning in abundance from over a million down to less than 50 copies per cell, could be targeted. It is worth noting that a significant set of peptides previously not reported in the PeptideAtlas database was among the profiled targets. The quantitative data corroborated well with the corresponding data generated after conventional strong cation exchange fractionation of the same samples. Finally, several differentially expressed proteins, with both known and unknown functions, many relevant for the central carbon metabolism, could be detected in the glucose- versus ethanol-cultivated yeast. Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative

  19. Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence

    PubMed Central

    Peters, Julian S.; Calder, Bridget; Gonnelli, Giulia; Degroeve, Sven; Rajaonarifara, Elinambinina; Mulder, Nicola; Soares, Nelson C.; Martens, Lennart; Blackburn, Jonathan M.

    2016-01-01

    Evidence currently suggests that as a species Mycobacterium tuberculosis exhibits very little genomic sequence diversity. Despite limited genetic variability, members of the M. tuberculosis complex (MTBC) have been shown to exhibit vast discrepancies in phenotypic presentation in terms of virulence, elicited immune response and transmissibility. Here, we used qualitative and quantitative mass spectrometry tools to investigate the proteomes of seven clinically-relevant mycobacterial strains—four M. tuberculosis strains, M. bovis, M. bovis BCG, and M. avium—that show varying degrees of pathogenicity and virulence, in an effort to rationalize the observed phenotypic differences. Following protein preparation, liquid chromatography mass spectrometry (LC MS/MS) and data capture were carried out using an LTQ Orbitrap Velos. Data analysis was carried out using a novel bioinformatics strategy, which yielded high protein coverage and was based on high confidence peptides. Through this approach, we directly identified a total of 3788 unique M. tuberculosis proteins out of a theoretical proteome of 4023 proteins and identified an average of 3290 unique proteins for each of the MTBC organisms (representing 82% of the theoretical proteomes), as well as 4250 unique M. avium proteins (80% of the theoretical proteome). Data analysis showed that all major classes of proteins are represented in every strain, but that there are significant quantitative differences between strains. Targeted selected reaction monitoring (SRM) assays were used to quantify the observed differential expression of a subset of 23 proteins identified by comparison to gene expression data as being of particular relevance to virulence. This analysis revealed differences in relative protein abundance between strains for proteins which may promote bacterial fitness in the more virulent W. Beijing strain. These differences may contribute to this strain's capacity for surviving within the host and resisting

  20. Advancing Proteomics Research through Collaboration | Office of Cancer Clinical Proteomics Research

    Cancer.gov

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

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

    Cancer.gov

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

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

    Cancer.gov

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

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

    Cancer.gov

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

  4. First insight into the human liver proteome from PROTEOME(SKY)-LIVER(Hu) 1.0, a publicly available database.

    PubMed

    2010-01-01

    Herein, we report proteome and transcriptome profiles of the human adult liver and present an initial analysis. Overall, the human liver proteome (HLP) data set comprises 6788 identified proteins with at least two peptides matches at 95% confidence, including 3721 proteins newly identified in liver. The human liver transcriptome (HLT) data set consists of 11 205 expressed genes. The HLP is the largest proteome data set for a human organ and is the first direct association between a proteome and its transcriptome derived from the same sample. Although it is hard to approach complete coverage of the HLP currently, several conclusions based on this data set are clearly reached: (1) The 5816 protein-encoding genes (PEGs) represented by the HLP and the 11 104 PEGs represented in the HLT have been identified from 20 070 PEGs in IPI Human v3.07 and 19 478 PEGs in the integrated human transcriptome database, respectively. (2) The patterns of chromosomal distribution of the genes corresponding to the HLP are highly consistent with those of the HLT. Some chromosomal regions, such as 16p13.3, 19q13.31, 19q13.42, and Xq28, exhibit particularly high densities of liver-specific genes, which perform the important functions related to normal physiology or/and pathology in this organ. (3) The HLP spans 6 orders of magnitude in relative protein abundance and 78% of the proteins fall in the middle of this range. Of newly identified liver proteins, 82.5% are of low abundance. (4) Proteins involving in metabolism, transport, and coagulation and those containing active domains for metabolism, transport, and biosynthesis are significantly enriched in liver. (5) All 94 metabolic pathways in KEGG are touched to different extent. Of which, for 48 pathways, particularly those involved in metabolism of carbohydrates and amino acids, more than 80% of the component proteins have been detected. The liver-specific pathways, such as those participating in metabolism of bile acid and bilirubin and

  5. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Mortgage coverage. 200.17 Section... Generally Applicable to Multifamily and Health Care Facility Mortgage Insurance Programs; and Continuing Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The mortgage...

  6. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Mortgage coverage. 200.17 Section... Generally Applicable to Multifamily and Health Care Facility Mortgage Insurance Programs; and Continuing Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The mortgage...

  7. HEALTH INSURANCE COVERAGE FOR WORKERS ON LAYOFF.

    ERIC Educational Resources Information Center

    KOLODRUBETZ, WALTER W.

    ESTIMATES OF GROUP HEALTH INSURANCE COVERAGE BY INDUSTRY INDICATE THAT EXTENDED PROTECTION DURING LAYOFF IS GUARANTEED TO NO MORE THAN A TENTH OF THE APPROXIMATELY 50 MILLION WORKERS COVERED BY GROUP HEALTH INSURANCE PLANS. THIS COVERAGE HAS LARGELY DEVELOPED DURING THE PAST 15 YEARS. FRAGMENTARY DATA SUGGEST THAT INCREASED COST ATTRIBUTABLE TO…

  8. 32 CFR 2001.71 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Coverage. 2001.71 Section 2001.71 National Defense Other Regulations Relating to National Defense INFORMATION SECURITY OVERSIGHT OFFICE, NATIONAL... Training § 2001.71 Coverage. (a) General. Each department or agency shall establish and maintain a...

  9. 32 CFR 2001.71 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Coverage. 2001.71 Section 2001.71 National Defense Other Regulations Relating to National Defense INFORMATION SECURITY OVERSIGHT OFFICE, NATIONAL... Training § 2001.71 Coverage. (a) General. Each department or agency shall establish and maintain a...

  10. 32 CFR 2001.71 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Coverage. 2001.71 Section 2001.71 National Defense Other Regulations Relating to National Defense INFORMATION SECURITY OVERSIGHT OFFICE, NATIONAL... Training § 2001.71 Coverage. (a) General. Each department or agency shall establish and maintain a...

  11. 5 CFR 319.201 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 319.201 Section 319.201 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT IN SENIOR-LEVEL AND SCIENTIFIC AND PROFESSIONAL POSITIONS Position Allocations and Establishment § 319.201 Coverage. This section...

  12. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage. This...

  13. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage....

  14. Abstract Journals: A Survey of Patent Coverage.

    ERIC Educational Resources Information Center

    Rimmer, Brenda M.

    1988-01-01

    Describes a survey of 33 British, French, German, and U.S. abstract journals that examined their coverage of patent specifications. The standards for the identification of patent documents developed by the World Intellectual Property Organization are discussed, and an appendix provides a listing of the patent coverage by the country of each…

  15. 5 CFR 550.802 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 550.802 Section 550.802...) Back Pay § 550.802 Coverage. (a) Except as provided in paragraph (b) of this section, this subpart applies to employees, as defined in § 550.803 of this subpart. (b) This subpart does not apply to— (1...

  16. 5 CFR 550.802 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 550.802 Section 550.802...) Back Pay § 550.802 Coverage. (a) Except as provided in paragraph (b) of this section, this subpart applies to employees, as defined in § 550.803 of this subpart. (b) This subpart does not apply to— (1...

  17. 5 CFR 550.802 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 550.802 Section 550.802...) Back Pay § 550.802 Coverage. (a) Except as provided in paragraph (b) of this section, this subpart applies to employees, as defined in § 550.803 of this subpart. (b) This subpart does not apply to— (1...

  18. 5 CFR 550.802 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 550.802 Section 550.802...) Back Pay § 550.802 Coverage. (a) Except as provided in paragraph (b) of this section, this subpart applies to employees, as defined in § 550.803 of this subpart. (b) This subpart does not apply to— (1...

  19. 5 CFR 630.802 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 630.802 Section 630.802 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Funeral Leave § 630.802 Coverage. This subpart applies to: (a) An employee as defined in section 2105 of title 5...

  20. 5 CFR 630.802 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 630.802 Section 630.802 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Funeral Leave § 630.802 Coverage. This subpart applies to: (a) An employee as defined in section 2105 of title 5...