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Sample records for proteome coverage attainable

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. Proteomics

    SciTech Connect

    Hixson, Kim K.; Lopez-Ferrer, Daniel; Robinson, Errol W.; Pasa-Tolic, Ljiljana

    2010-02-01

    Proteomics aims to characterize the spatial distribution and temporal dynamics of proteins in biological systems, the protein response to environmental stimuli, and the differences in protein states between diseased and control biological systems. Mass spectrometry (MS) plays a crucial role in enabling the analysis of proteomes and typically is the method of choice for identifying proteins present in biological systems. Peptide (and consequently protein) identifications are made by comparing measured masses to calculated values obtained from genome data. Several methodologies based on MS have been developed for the analysis of proteomes. The complexity of the biological systems requires that the proteome be separated prior to analysis. Both gel based and liquid chromatography based separations have proven very useful in this regard. Typically, separated proteins are analyzed with MS either intact (top-down proteomics) or are digested into peptides (bottom-up) prior to MS analysis. Additionally, several procedures, with and without stable isotopic labeling, have been introduced to facilitate protein quantitation (e.g. characterize changes in protein abundances between given biological states).

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  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. 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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Drug Plan Coverage Rules

    MedlinePlus

    ... Medication Therapy Management programs Drug plan coverage rules , current page Using your drug plan for the first time Filling a prescription without your new plan card Costs for Medicare drug coverage Joining a health or ...

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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 ...

  9. 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.

  10. 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.

  11. 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, ...

  12. A 2-D guinea pig lung proteome map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. 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…

  14. 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

  15. 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…

  16. 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…

  17. 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…

  18. 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.

  19. 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

  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. 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

  2. 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.

  3. 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

  4. 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…

  5. 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)

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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…

  4. 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…

  5. 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

  6. The Platelet Proteome

    PubMed Central

    Senzel, Lisa; Gnatenko, Dmitri V.; Bahou, Wadie F.

    2010-01-01

    Purpose of review The proteome is the pool of proteins expressed at a given time and circumstance. The word “proteomics” summarizes several technologies for visualization, quantitation and identification of these proteins. Recent advances in these techniques are helping to elucidate platelet processes which are relevant to bleeding and clotting disorders, transfusion medicine and regulation of angiogenesis. Recent findings Over 1100 platelet proteins have been identified using proteomic techniques. Various subproteomes have been characterized, including platelet releasates (the “secretome”), alpha and dense granules, membrane and cytoskeletal proteins, platelet-derived microparticles, and the platelet “phosphoproteome”. Proteomic data about platelets have become increasingly available in integrated databases. Summary Proteomic experiments in resting and activated platelets have identified novel signaling pathways and secreted proteins which may represent therapeutic targets, as well as potential cancer biomarkers. PMID:19550320

  7. 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.

  8. [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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  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. 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

  16. 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

  17. Proteomic Assessment of Poultry Spermatozoa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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...

  4. 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".

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. Your Medicare Coverage: Durable Medical Equipment (DME) Coverage

    MedlinePlus

    ... Search Medicare.gov for covered items Durable medical equipment (DME) coverage How often is it covered? Medicare ... B (Medical Insurance) covers medically necessary durable medical equipment (DME) that your doctor prescribes for use in ...

  12. 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

  13. 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.

  14. “Seed Proteomics"

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. [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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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…

  16. 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

  17. 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…

  18. 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…

  19. 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…

  20. 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…

  1. 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...

  2. 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...

  3. 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...

  4. 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

  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. 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.

  7. 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.

  8. 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…

  9. 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)

  10. 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.

  11. Proteomic analysis of Caenorhabditis elegans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  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. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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,

  7. 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.

  8. 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

  9. 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)

  10. 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.

  11. 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 ...

  12. 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

  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. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 1 2014-07-01 2014-07-01 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...

  16. 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...

  17. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 1 2013-07-01 2013-07-01 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...

  18. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 1 2012-07-01 2012-07-01 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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....

  9. 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....

  10. 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....

  11. 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....

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. [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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Salivary proteomics in biomedical research.

    PubMed

    Zhang, Aihua; Sun, Hui; Wang, Ping; Wang, Xijun

    2013-01-16

    Proteins that are important indicators of physiological or pathological states, can provide information for the identification of early and differential markers for disease. Saliva, contains an abundance of proteins, offers an easy, inexpensive, safe, and non-invasive approach for disease detection, and possesses a high potential to revolutionize the diagnostics. Discovery of salivary biomarkers could be used to scrutinize health and disease surveillance. The impact of human saliva proteome analysis in the search for clinically relevant disease biomarkers will be realized through advances made using proteomic technologies. The advancements of emerging proteomic techniques have benefited biomarker research to the point where saliva is now recognized as an excellent diagnostic medium for the detection of disease. This review presents an overview of the value of saliva as a credible diagnostic tool and we aim to summarize the proteomic technologies currently used for global analysis of saliva proteins and to elaborate on the application of saliva proteomics to the discovery of disease biomarkers, and discuss some of the critical challenges and perspectives in this field.

  7. 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

  8. [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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. [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.

  14. 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

  15. 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…

  16. 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…

  17. 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…

  18. 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…

  19. 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…

  20. 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…

  1. 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…

  2. 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…

  3. 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…

  4. 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%…

  5. 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…

  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. 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…

  8. 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.…

  9. 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…

  10. 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.

  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. 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.

  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. 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.

  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. 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.

  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. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. Computational Methods for Analyzing Health News Coverage

    ERIC Educational Resources Information Center

    McFarlane, Delano J.

    2011-01-01

    Researchers that investigate the media's coverage of health have historically relied on keyword searches to retrieve relevant health news coverage, and manual content analysis methods to categorize and score health news text. These methods are problematic. Manual content analysis methods are labor intensive, time consuming, and inherently…

  9. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  10. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  11. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  12. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  13. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  14. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 2 2010-01-01 2010-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  15. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 2 2012-01-01 2012-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  16. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 2 2014-01-01 2014-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  17. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 2 2013-01-01 2013-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  18. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 2 2011-01-01 2011-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  19. 5 CFR 9701.202 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Coverage. 9701.202 Section 9701.202... MANAGEMENT SYSTEM Classification General § 9701.202 Coverage. (a) This subpart applies to eligible DHS... covered by a prevailing rate system established under 5 U.S.C. chapter 53, subchapter IV; (3) Employees...

  20. 5 CFR 9701.402 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Coverage. 9701.402 Section 9701.402 Administrative Personnel DEPARTMENT OF HOMELAND SECURITY HUMAN RESOURCES MANAGEMENT SYSTEM (DEPARTMENT OF... MANAGEMENT SYSTEM Performance Management § 9701.402 Coverage. (a) This subpart applies to eligible...

  1. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 2 2013-04-01 2013-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  2. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  3. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  4. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  5. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  6. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 2 2014-04-01 2014-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  7. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  8. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 1 2013-07-01 2013-07-01 false Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  9. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 1 2012-07-01 2012-07-01 false Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  10. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  11. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  12. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  13. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  14. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  15. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 1 2014-07-01 2013-07-01 true Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  16. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  17. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  18. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  19. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  20. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  1. 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…

  2. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 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....

  3. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 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....

  4. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 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....

  5. 77 FR 16453 - Student Health Insurance Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES 45 CFR Parts 144, 147, and 158 CMS-9981-F RIN 0938-AQ95 Student Health Insurance Coverage... establishes requirements for student health insurance coverage under the Public Health Service (PHS) Act...

  6. 76 FR 7767 - Student Health Insurance Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-11

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES 45 CFR Parts 144 and 147 RIN 0950-AA20 Student Health Insurance Coverage AGENCY: Centers... proposed regulation that would establish rules for student health insurance coverage under the...

  7. 5 CFR 430.302 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 430.302 Section 430.302 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PERFORMANCE MANAGEMENT Managing Senior Executive Performance § 430.302 Coverage. (a) This subpart applies to all senior...

  8. 5 CFR 430.302 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 430.302 Section 430.302 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PERFORMANCE MANAGEMENT Managing Senior Executive Performance § 430.302 Coverage. (a) This subpart applies to all senior...

  9. 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...

  10. 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...

  11. 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...

  12. 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…

  13. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  14. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  15. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  16. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  17. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  18. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  19. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  20. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 1 2011-07-01 2011-07-01 false Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  1. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  2. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  3. 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....

  4. 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....

  5. 5 CFR 831.1612 - Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity computations. 831.1612 Section 831.1612...) RETIREMENT Customs and Border Protection Officers § 831.1612 Elections of Retirement Coverage,...

  6. 5 CFR 831.1612 - Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity computations. 831.1612 Section 831.1612...) RETIREMENT Customs and Border Protection Officers § 831.1612 Elections of Retirement Coverage,...

  7. 5 CFR 831.1612 - Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity computations. 831.1612 Section 831.1612...) RETIREMENT Customs and Border Protection Officers § 831.1612 Elections of Retirement Coverage,...

  8. Financing Universal Coverage in Malaysia: a case study

    PubMed Central

    2012-01-01

    preventive care, in better managing escalating healthcare costs associated with the increasing trend of non-communicable diseases. In tandem, health financing policies need to infuse the element of cost-effectiveness to better manage the purchasing of new medical supplies and equipment. Ultimately, good governance and leadership are needed to ensure adequate public spending on health and maintain the focus on the attainment of universal coverage, as well as making healthcare financing more accountable to the public, particularly in regards to inefficiencies and better utilisation of public funds and resources. PMID:22992444

  9. 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…

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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)

  20. 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

  1. 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

  2. Analyzing the test process using structural coverage

    NASA Technical Reports Server (NTRS)

    Ramsey, James; Basili, Victor R.

    1985-01-01

    A large, commercially developed FORTRAN program was modified to produce structural coverage metrics. The modified program was executed on a set of functionally generated acceptance tests and a large sample of operational usage cases. The resulting structural coverage metrics are combined with fault and error data to evaluate structural coverage. It was shown that in the software environment the functionally generated tests seem to be a good approximation of operational use. The relative proportions of the exercised statement subclasses change as the structural coverage of the program increases. A method was also proposed for evaluating if two sets of input data exercise a program in a similar manner. Evidence was provided that implies that in this environment, faults revealed in a procedure are independent of the number of times the procedure is executed and that it may be reasonable to use procedure coverage in software models that use statement coverage. Finally, the evidence suggests that it may be possible to use structural coverage to aid in the management of the acceptance test processed.

  3. Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer

    PubMed Central

    2013-01-01

    Background In the biopharmaceutical industry, biomarkers define molecular taxonomies of patients and diseases and serve as surrogate endpoints in early-phase drug trials. Molecular biomarkers can be much more sensitive than traditional lab tests. Discriminating disease biomarkers by traditional method such as DNA microarray has proved challenging. Alternative splicing isoform represents a new class of diagnostic biomarkers. Recent scientific evidence is demonstrating that the differentiation and quantification of individual alternative splicing isoforms could improve insights into disease diagnosis and management. Identifying and characterizing alternative splicing isoforms are essential to the study of molecular mechanisms and early detection of complex diseases such as breast cancer. However, there are limitations with traditional methods used for alternative splicing isoform determination such as transcriptome-level, low level of coverage and poor focus on alternative splicing. Results Therefore, we presented a peptidomics approach to searching novel alternative splicing isoforms in clinical proteomics. Our results showed that the approach has significant potential in enabling discovery of new types of high-quality alternative splicing isoform biomarkers. Conclusions We developed a peptidomics approach for the proteomics community to analyze, identify, and characterize alternative splicing isoforms from MS-based proteomics experiments with more coverage and exclusive focus on alternative splicing. The approach can help generate novel hypotheses on molecular risk factors and molecular mechanisms of cancer in early stage, leading to identification of potentially highly specific alternative splicing isoform biomarkers for early detection of cancer. PMID:24565027

  4. Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry

    SciTech Connect

    Burnum-Johnson, Kristin E.; Nie, Song; Casey, Cameron P.; Monroe, Matthew E.; Orton, Daniel J.; Ibrahim, Yehia M.; Gritsenko, Marina A.; Clauss, Therese R. W.; Shukla, Anil K.; Moore, Ronald J.; Purvine, Samuel O.; Shi, Tujin; Qian, Weijun; Liu, Tao; Baker, Erin S.; Smith, Richard D.

    2016-09-25

    Current proteomics approaches are comprised of both broad discovery measurements as well as more quantitative targeted measurements. These two different measurement types are used to initially identify potentially important proteins (e.g., candidate biomarkers) and then enable improved quantification for a limited number of selected proteins. However, both approaches suffer from limitations, particularly the lower sensitivity, accuracy, and quantitation precision for discovery approaches compared to targeted approaches, and the limited proteome coverage provided by targeted approaches. Herein, we describe a new proteomics approach that allows both discovery and targeted monitoring (DTM) in a single analysis using liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled peptides for target ions are spiked into tryptic digests and both the labeled and unlabeled peptides are broadly detected using LC-IMS-MS instrumentation, allowing the benefits of discovery and targeted approaches. To understand the possible improvement of the DTM approach, it was compared to LC-MS broad measurements using an accurate mass and time tag database and selected reaction monitoring (SRM) targeted measurements. The DTM results yielded greater peptide/protein coverage and a significant improvement in the detection of lower abundance species compared to LC-MS discovery measurements. DTM was also observed to have similar detection limits as SRM for the targeted measurements indicating its potential for combining the discovery and targeted approaches.

  5. 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.

  6. 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).

  7. 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

  8. Deciphering diatom biochemical pathways via whole-cell proteomics

    PubMed Central

    Nunn, Brook L.; Aker, Jocelyn R.; Shaffer, Scott A.; Tsai, Shannon; Strzepek, Robert F.; Boyd, Philip W.; Freeman, Theodore Larson; Brittnacher, Mitchell; Malmström, Lars; Goodlett, David R.

    2009-01-01

    Diatoms play a critical role in the oceans’ carbon and silicon cycles; however, a mechanistic understanding of the biochemical processes that contribute to their ecological success remains elusive. Completion of the Thalassiosira pseudonana genome provided ‘blueprints’ for the potential biochemical machinery of diatoms, but offers only a limited insight into their biology under various environmental conditions. Using high-throughput shotgun proteomics, we identified a total of 1928 proteins expressed by T. pseudonana cultured under optimal growth conditions, enabling us to analyze this diatom’s primary metabolic and biosynthetic pathways. Of the proteins identified, 70% are involved in cellular metabolism, while 11% are involved in the transport of molecules. We identified all of the enzymes involved in the urea cycle, thereby describing the complete pathway to convert ammonia to urea, along with urea transporters, and the urea-degrading enzyme urease. Although metabolic exchange between these pathways remains ambiguous, their constitutive presence suggests complex intracellular nitrogen recycling. In addition, all C4 related enzymes for carbon fixation have been identified to be in abundance, with high protein sequence coverage. Quantification of mass spectra acquisitions demonstrated that the 20 most abundant proteins included an unexpectedly high expression of clathrin, which is the primary structural protein involved in endocytic transport. This result highlights a previously overlooked mechanism for the inter- and intra-cellular transport of nutrients and macromolecules in diatoms, potentially providing a missing link to organelle communication and metabolite exchange. Our results demonstrate the power of proteomics, and lay the groundwork for future comparative proteomic studies and directed analyses of specifically expressed proteins and biochemical pathways of oceanic diatoms. PMID:19829762

  9. The Potato Tuber Mitochondrial Proteome1[W][OPEN

    PubMed Central

    Salvato, Fernanda; Havelund, Jesper F.; Chen, Mingjie; Rao, R. Shyama Prasad; Rogowska-Wrzesinska, Adelina; Jensen, Ole N.; Gang, David R.; Thelen, Jay J.; Møller, Ian Max

    2014-01-01

    Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum ‘Folva’) and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more “extreme” proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms. PMID:24351685

  10. Proteome-wide protein concentrations in the human heart.

    PubMed

    Aye, Thin Thin; Scholten, Arjen; Taouatas, Nadia; Varro, Andras; Van Veen, Toon A B; Vos, Marc A; Heck, Albert J R

    2010-10-01

    The largest component of the human heart, the left ventricle (LV), plays a major role in delivering blood throughout the body. Therefore, an in-depth detailed quantitative proteome analysis of the human LV is a valuable resource. For this purpose, a multifaceted proteomics approach combining differential sample fractionations (gel, strong cation exchange (SCX)), enzymatic digestions (trypsin, chymotrypsin, LysN), and peptide fragmentation techniques (CID and ETcaD) was used to enhance protein sequence coverage, identification confidence and quantitative abundance determination. Using stringent criteria, 3584 distinct proteins could be identified from the latest well-annotated Swissprot database (23,000 entries). Commutatively, the over 130,000 identified MS/MS spectra were used to assess concentrations of each identified LV protein through a combination of spectral counting methods. Among the most concentrated proteins, many currently used biomarkers for detection of myocardial infarction reside. These cardiac leakage markers have a good diagnostic power, but their prognostic potential seems limited. Discovery of markers that represent etiological determinants of cardiac disease require a shift of focus towards the signaling proteome. Therefore, a protein-class centered quantitative analysis of kinases, phosphatases and GTPases was adopted. These comparative analyses revealed many cardiac involved kinases (PKA, CaMKII, ERK) to reside among the most abundant signaling proteins, and also to mediate many observed in vivo phosphorylation sites. The abundance chart of signaling proteins may assist in identifying novel functional pathways, for instance through the abundant, but relatively little known, kinases STK38L and OXSR1. The obtained quantitative protein library of the human left ventricle is a valuable resource to isolate signaling based, putative biomarkers with concentrations likely to be detectable in plasma.

  11. Cell wall proteome analysis of Arabidopsis thaliana mature stems.

    PubMed

    Duruflé, Harold; Clemente, Hélène San; Balliau, Thierry; Zivy, Michel; Dunand, Christophe; Jamet, Elisabeth

    2017-02-02

    Plant stems carry flowers necessary for species propagation and need to be adapted to mechanical disturbance and environmental factors. The stem cell walls are different from other organs and can modify their rigidity or viscoelastic properties for the integrity and the robustness required to withstand mechanical impacts and environmental stresses. Plant cell wall is composed of complex polysaccharide networks also containing cell wall proteins (CWPs) crucial to perceive and limit the environmental effects. The CWPs are fundamental players in cell wall remodeling processes, and today, only 86 have been identified from the mature stems of the model plant Arabidopsis thaliana. With a destructive method, this study has enlarged its coverage to 302 CWPs. This new proteome is mainly composed of 27.5% proteins acting on polysaccharides, 16% proteases, 11.6% oxido-reductases, 11% possibly related to lipid metabolism and 11% of proteins with interacting domains with proteins or polysaccharides. Compared to stem cell wall proteomes already available (Brachypodium distachyon, Sacharum officinarum, Linum usitatissimum, Medicago sativa), that of A. thaliana stems has a higher proportion of proteins acting on polysaccharides and of proteases, but a lower proportion of oxido-reductases.

  12. Can museum egg specimens be used for proteomic analyses?

    PubMed Central

    2010-01-01

    Background Mass spectrometry and proteomic analyses have become powerful tools for the analysis of proteins and peptides. Investigation of proteins contained in the various layers of the avian eggshell has focused entirely on domesticated species. It has been widely assumed that this existing research can inform the study of wild bird species despite the fact that the vast majority of the diversity in avian species (~95%) exists outside the Orders to which domestic and poultry species belong. Museum collections offer a potentially valuable source of material for studying composition of wild avian eggshell matrix proteins. We used museum and fresh eggshells of common quails Coturnix coturnix to compare the protein composition of their organic matrices. Four eggs of domestic chickens were analysed simultaneously as a control for comparison to the fresh and museum quail eggs. The determination of the proteins was carried out using enzymatic cleavage followed by high-performance mass spectrometry. Results We found that some of the expected key eggshell proteins (3 out of 11) were not present in the samples of museum quail egg. These proteins were either entirely absent from the museum eggs or the technique was unable to detect them. There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell. Conclusion We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading. PMID:20630081

  13. Animal board invited review: advances in proteomics for animal and food sciences.

    PubMed

    Almeida, A M; Bassols, A; Bendixen, E; Bhide, M; Ceciliani, F; Cristobal, S; Eckersall, P D; Hollung, K; Lisacek, F; Mazzucchelli, G; McLaughlin, M; Miller, I; Nally, J E; Plowman, J; Renaut, J; Rodrigues, P; Roncada, P; Staric, J; Turk, R

    2015-01-01

    Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps

  14. Exploring the potential of public proteomics data

    PubMed Central

    Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Ræder, Helge; Berven, Frode S.; Martens, Lennart; Vizcaíno, Juan A.

    2015-01-01

    In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re‐)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data. PMID:26449181

  15. Proteome of human minor salivary gland secretion.

    PubMed

    Siqueira, W L; Salih, E; Wan, D L; Helmerhorst, E J; Oppenheim, F G

    2008-05-01

    Recent research efforts in oral biology have resulted in elucidation of the proteomes of major human salivary secretions and whole saliva. One might hypothesize that the proteome of minor gland secretions may show significantly different characteristics when compared with the proteomes of parotid or submandibular/sublingual secretions. To test this hypothesis, we conducted the first exploration into the proteome of minor salivary gland secretion. Minor gland secretion was obtained from healthy volunteers, and its components were subjected to liquid-chromatography-electrospray-ionization-tandem-mass-spectrometry. This led to the identification of 56 proteins, 12 of which had never been identified in any salivary secretion. The unique characteristics of the minor salivary gland secretion proteome are related to the types as well as the numbers of components present. The differences between salivary proteomes may be important with respect to specific oral functions.

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

    PubMed Central

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

    2015-01-01

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

  17. Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment

    PubMed Central

    Shevchenko, Anna; Roguev, Assen; Schaft, Daniel; Buchanan, Luke; Habermann, Bianca; Sakalar, Cagri; Thomas, Henrik; Krogan, Nevan J; Shevchenko, Andrej; Stewart, A Francis

    2008-01-01

    Background Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful. Results The Saccharomyces cerevisiae proteome presents the highest quality proteomic data available. To evaluate the accuracy of these data, we intensively mapped a proteomic environment, termed 'Chromatin Central', which encompasses eight protein complexes, including the major histone acetyltransferases and deacetylases, interconnected by twelve proteomic hyperlinks. Using sequential tagging and a new method to eliminate background, we confirmed existing data but also uncovered new subunits and three new complexes, including ASTRA, which we suggest is a widely conserved aspect of telomeric maintenance, and two new variations of Rpd3 histone deacetylase complexes. We also examined the same environment in fission yeast and found a very similar architecture based on a scaffold of orthologues comprising about two-thirds of all proteins involved, whereas the remaining one-third is less constrained. Notably, most of the divergent hyperlinks were found to be due to gene duplications, hence providing a mechanism for the fixation of gene duplications in evolution. Conclusions We define several prerequisites for comparative proteomics and apply them to examine a proteomic environment in unprecedented detail. We suggest that high resolution mapping of proteomic environments will deliver the highest quality data for comparative proteomics. PMID:19040720

  18. Updating the proteome of the uncultivable hemotrophic Mycoplasma suis in experimentally infected pigs.

    PubMed

    Dietz, Stefanie; Lassek, Christian; Mack, Sarah-Lena; Ritzmann, Mathias; Stadler, Julia; Becher, Dörte; Hoelzle, Katharina; Riedel, Katharina; Hoelzle, Ludwig E

    2016-02-01

    Mycoplasma suis belongs to the hemotrophic mycoplasmas that are associated with acute and chronic anemia in a wide range of livestock and wild animals. The inability to culture M. suis in vitro has hindered its characterization at the molecular level. Since the publication of M. suis genome sequences in 2011 only one proteome study has been published. Aim of the presented study was to significantly extend the proteome coverage of M. suis strain KI_3806 during acute infection by applying three different protein extraction methods followed by 1D SDS-PAGE and LC-MS/MS. A total of 404 of 795 M. suis KI_3806 proteins (50.8%) were identified. Data analysis revealed the expression of 83.7% of the predicted ORFs with assigned functions but also highlights the expression of 179 of 523 (34.2%) hypothetical proteins with unknown functions. Computational analyses identified expressed membrane-associated hypothetical proteins that might be involved in adhesion or host-pathogen interaction. Furthermore, analyses of the expressed proteins indicated the existence of a hexose-6-phosphate-transporter and an ECF transporter. In conclusion, our proteome study provides a further step toward the elucidation of the unique life cycle of M. suis and the establishment of an in vitro culture. All MS data have been deposited in the ProteomeXchange with identifier PXD002294 (http://proteomecentral.proteomexchange.org/dataset/PXD002294).

  19. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota

    SciTech Connect

    Xiong, Weili; Abraham, Paul E.; Li, Zhou; Pan, Chongle; Robert L. Hettich

    2015-01-01

    We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs. disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.

  20. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota

    DOE PAGES

    Xiong, Weili; Abraham, Paul E.; Li, Zhou; ...

    2015-01-01

    We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs.more » disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.« less

  1. Proteomic approaches in research of cyanobacterial photosynthesis.

    PubMed

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

    2015-10-01

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

  2. Biospecimen Solicitation - Office of Cancer Clinical Proteomics Research

    Cancer.gov

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

  3. Measuring populations to improve vaccination coverage

    NASA Astrophysics Data System (ADS)

    Bharti, Nita; Djibo, Ali; Tatem, Andrew J.; Grenfell, Bryan T.; Ferrari, Matthew J.

    2016-10-01

    In low-income settings, vaccination campaigns supplement routine immunization but often fail to achieve coverage goals due to uncertainty about target population size and distribution. Accurate, updated estimates of target populations are rare but critical; short-term fluctuations can greatly impact population size and susceptibility. We use satellite imagery to quantify population fluctuations and the coverage achieved by a measles outbreak response vaccination campaign in urban Niger and compare campaign estimates to measurements from a post-campaign survey. Vaccine coverage was overestimated because the campaign underestimated resident numbers and seasonal migration further increased the target population. We combine satellite-derived measurements of fluctuations in population distribution with high-resolution measles case reports to develop a dynamic model that illustrates the potential improvement in vaccination campaign coverage if planners account for predictable population fluctuations. Satellite imagery can improve retrospective estimates of vaccination campaign impact and future campaign planning by synchronizing interventions with predictable population fluxes.

  4. Measuring populations to improve vaccination coverage

    PubMed Central

    Bharti, Nita; Djibo, Ali; Tatem, Andrew J.; Grenfell, Bryan T.; Ferrari, Matthew J.

    2016-01-01

    In low-income settings, vaccination campaigns supplement routine immunization but often fail to achieve coverage goals due to uncertainty about target population size and distribution. Accurate, updated estimates of target populations are rare but critical; short-term fluctuations can greatly impact population size and susceptibility. We use satellite imagery to quantify population fluctuations and the coverage achieved by a measles outbreak response vaccination campaign in urban Niger and compare campaign estimates to measurements from a post-campaign survey. Vaccine coverage was overestimated because the campaign underestimated resident numbers and seasonal migration further increased the target population. We combine satellite-derived measurements of fluctuations in population distribution with high-resolution measles case reports to develop a dynamic model that illustrates the potential improvement in vaccination campaign coverage if planners account for predictable population fluctuations. Satellite imagery can improve retrospective estimates of vaccination campaign impact and future campaign planning by synchronizing interventions with predictable population fluxes. PMID:27703191

  5. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  6. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  7. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  8. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  9. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  10. Universal prescription drug coverage in Canada

    PubMed Central

    Boothe, Katherine

    2016-01-01

    Canada’s universal public healthcare system is unique among developed countries insofar as it does not include universal coverage of prescription drugs. Universal, public coverage of prescription drugs has been recommended by major national commissions in Canada dating back to the 1960s. It has not, however, been implemented. In this article, we extend research on the failure of early proposals for universal drug coverage in Canada to explain failures of calls for reform over the past 20 years. We describe the confluence of barriers to reform stemming from Canadian policy institutions, ideas held by federal policy-makers, and electoral incentives for necessary reforms. Though universal “pharmacare” is once again on the policy agenda in Canada, arguably at higher levels of policy discourse than ever before, the frequently recommended option of universal, public coverage of prescription drugs remains unlikely to be implemented without political leadership necessary to overcome these policy barriers. PMID:27744279

  11. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... DEVELOPMENT GENERAL INTRODUCTION TO FHA PROGRAMS Requirements for Application, Commitment, and Endorsement... Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The mortgage shall cover the entire property included in the project....

  12. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... DEVELOPMENT GENERAL INTRODUCTION TO FHA PROGRAMS Requirements for Application, Commitment, and Endorsement... Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The mortgage shall cover the entire property included in the project....

  13. 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.

  14. Proteomics of Leaf Tissues from Populus

    SciTech Connect

    Hurst, Gregory {Greg} B; Yang, Xiaohan; Tschaplinski, Timothy J; Tuskan, Gerald A; Lankford, Patricia K; Shah, Manesh B; Jawdy, Sara; Gunter, Lee E; Engle, Nancy L

    2010-01-01

    Trees of the genus Populus are farmed commercially for wood and fiber, and are a potential bioenergy crop. As a scientific model organism, P. trichocarpa was the first forest tree for which the genome sequence has been determined. Knowledge of the Populus proteome will provide a deeper understanding of gene expression patterns in various tissues of the plant. To build on our previous profile of the proteome of xylem tissue in Populus (Kalluri et al., Proteomics 2009, 9, 4871), we are currently developing methods for studying the proteome of Populus leaves.

  15. Human saliva proteome and transcriptome.

    PubMed

    Hu, S; Li, Y; Wang, J; Xie, Y; Tjon, K; Wolinsky, L; Loo, R R O; Loo, J A; Wong, D T

    2006-12-01

    This paper tests the hypothesis that salivary proteins and their counterpart mRNAs co-exist in human whole saliva. Global profiling of human saliva proteomes and transcriptomes by mass spectrometry (MS) and expression microarray technologies, respectively, revealed many similarities between saliva proteins and mRNAs. Of the function-known proteins identified in saliva, from 61 to 70% were also found present as mRNA transcripts. For genes not detected at both protein and mRNA levels, we made further efforts to determine if the counterpart is present. Of 19 selected genes detected only at the protein level, the mRNAs of 13 (68%) genes were found in saliva by RT-PCR. In contrast, of many mRNAs detected only by microarrays, their protein products were found in saliva, as reported previously by other investigators. The saliva transcriptome may provide preliminary insights into the boundary of the saliva proteome.

  16. The rat brain hippocampus proteome.

    PubMed

    Fountoulakis, Michael; Tsangaris, George T; Maris, Antony; Lubec, Gert

    2005-05-05

    The hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In humans, the CA1 area of hippocampus is one of the first brain areas to display pathology in Alzheimer's disease. A comprehensive analysis of the hippocampus proteome has not been accomplished yet. We applied proteomics technologies to construct a two-dimensional database for rat brain hippocampus proteins. Hippocampus samples from eight months old animals were analyzed by two-dimensional electrophoresis and the proteins were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The database comprises 148 different gene products, which are in the majority enzymes, structural proteins and heat shock proteins. It also includes 39 neuron specific gene products. The database may be useful in animal model studies of neurological disorders.

  17. Recent developments in quantitative proteomics.

    PubMed

    Becker, Christopher H; Bern, Marshall

    2011-06-17

    Proteomics is the study of proteins on a large scale, encompassing the many interests scientists and physicians have in their expression and physical properties. Proteomics continues to be a rapidly expanding field, with a wealth of reports regularly appearing on technology enhancements and scientific studies using these new tools. This review focuses primarily on the quantitative aspect of protein expression and the associated computational machinery for making large-scale identifications of proteins and their post-translational modifications. The primary emphasis is on the combination of liquid chromatography-mass spectrometry (LC-MS) methods and associated tandem mass spectrometry (LC-MS/MS). Tandem mass spectrometry, or MS/MS, involves a second analysis within the instrument after a molecular dissociative event in order to obtain structural information including but not limited to sequence information. This review further focuses primarily on the study of in vitro digested proteins known as bottom-up or shotgun proteomics. A brief discussion of recent instrumental improvements precedes a discussion on affinity enrichment and depletion of proteins, followed by a review of the major approaches (label-free and isotope-labeling) to making protein expression measurements quantitative, especially in the context of profiling large numbers of proteins. Then a discussion follows on the various computational techniques used to identify peptides and proteins from LC-MS/MS data. This review article then includes a short discussion of LC-MS approaches to three-dimensional structure determination and concludes with a section on statistics and data mining for proteomics, including comments on properly powering clinical studies and avoiding over-fitting with large data sets.

  18. 45 CFR 800.107 - Levels of coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... to offer an MSP pursuant to a contract with OPM. (b) Bronze or platinum metal levels of coverage... coverage or the platinum level of coverage, or both, on any Exchange or SHOP in any State. (c)...

  19. 45 CFR 800.107 - Levels of coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... to offer an MSP pursuant to a contract with OPM. (b) Bronze or platinum metal levels of coverage... coverage or the platinum level of coverage, or both, on any Exchange or SHOP in any State. (c)...

  20. 78 FR 217 - Shared Responsibility for Employers Regarding Health Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-02

    ... Shared Responsibility for Employers Regarding Health Coverage; Proposed Rule #0;#0;Federal Register / Vol... Health Coverage AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice of proposed rulemaking... employers regarding employee health coverage. These proposed regulations would affect only employers...

  1. Forensic Proteomics of Poxvirus Production

    SciTech Connect

    Wunschel, David S.; Tulman, Edan; Engelmann, Heather E.; Clowers, Brian H.; Geary, Steven J.; Robinson, Aaron C.; Liao, Xiaofen

    2013-08-27

    The field of microbial forensics has recently sought to develop methods to discern biological signatures to indicate production methods for biological agents. Viral agents have received less attention to date. Their obligate propagation in living cells makes purification from cellular material a challenge. This leads to potential carryover of protein-rich signature of their production system. Here we have explored a proteomic analysis of Vaccinia virus as a model poxvirus system in which to compare samples of virus propagated in different cell lines and subjected to different purification schemes. The proteomic data sets indicated viral, host cell and culture medium proteins, and several layers of data analysis were applied to build confidence in the peptide identification and capture information on the taxonomic utility of each. The analysis showed clear shifts in protein profiles with virus purification, with successive gradient purification steps showing different levels of viral protein enrichment. Peptides from cellular proteins, including those present in purified virus preparations, provided signatures which enabled discrimination of cell line substrates, including distinguishing between cells derived from different primate species. The ability to discern multiple aspects of viral production demonstrates the potential value of proteomic analysis as tool for microbial forensics.

  2. Protein Neighbors and Proximity Proteomics.

    PubMed

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

    2015-11-01

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

  3. The proteome of human retina.

    PubMed

    Zhang, Pingbo; Dufresne, Craig; Turner, Randi; Ferri, Sara; Venkatraman, Vidya; Karani, Rabia; Lutty, Gerard A; Van Eyk, Jennifer E; Semba, Richard D

    2015-02-01

    The retina is a delicate tissue that detects light, converts photochemical energy into neural signals, and transmits the signals to the visual cortex of the brain. A detailed protein inventory of the proteome of the normal human eye may provide a foundation for new investigations into both the physiology of the retina and the pathophysiology of retinal diseases. To provide an inventory, proteins were extracted from five retinas of normal eyes and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed in duplicate using LC-MS/MS on an Orbitrap Elite mass spectrometer. A total of 3436 nonredundant proteins were identified in the human retina, including 20 unambiguous protein isoforms, of which eight have not previously been demonstrated to exist at the protein level. The proteins identified in the retina included most of the enzymes involved in the visual cycle and retinoid metabolism. One hundred and fifty-eight proteins that have been associated with age-related macular degeneration were identified in the retina. The MS proteome database of the human retina may serve as a valuable resource for future investigations of retinal biology and disease. All MS data have been deposited in the ProteomeXchange with identifier PXD001242 (http://proteomecentral.proteomexchange.org/dataset/PXD001242).

  4. Proteomic patterns associated with heterosis.

    PubMed

    Xing, Jiewen; Sun, Qixin; Ni, Zhongfu

    2016-08-01

    Heterosis is characterized by higher seed yields, plant biomass or other traits in heterozygotes or hybrids compared with their genetically divergent parents, which are often homozygous. Despite extensive investigation of heterosis and its wide application in crops such as maize, rice, wheat and sorghum, its molecular basis is still enigmatic. In the past century, some pioneers have proposed multigene models referring to the complementation of allelic and gene expression variation, which is likely to be an important contributor to heterosis. In addition, there are potential interactions of epigenetic variation involved in heterosis via novel mechanisms. At the level of gene expression, many recent studies have revealed that the heterosis phenomenon can be deciphered not only at the transcriptional level but also at the proteomic level. This review presents an update on the information supporting the involvement of proteomic patterns in heterosis and a possible future direction of the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

  5. Human saliva proteome: an overview

    NASA Astrophysics Data System (ADS)

    Griffin, Timothy J.

    2014-06-01

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

  6. Genomics and proteomics in cancer.

    PubMed

    Baak, J P A; Path, F R C; Hermsen, M A J A; Meijer, G; Schmidt, J; Janssen, E A M

    2003-06-01

    Cancer development is driven by the accumulation of DNA changes in the approximately 40000 chromosomal genes. In solid tumours, chromosomal numerical/structural aberrations are common. DNA repair defects may lead to genome-wide genetic instability, which can drive further cancer progression. The genes code the actual players in the cellular processes, the 100000-10 million proteins, which in (pre)malignant cells can also be altered in a variety of ways. Over the past decade, our knowledge of the human genome and Genomics (the study of the human genome) in (pre)malignancies has increased enormously and Proteomics (the analysis of the protein complement of the genome) has taken off as well. Both will play an increasingly important role. In this article, a short description of the essential molecular biological cell processes is given. Important genomic and proteomic research methods are described and illustrated. Applications are still limited, but the evidence so far is exciting. Will genomics replace classical diagnostic or prognostic procedures? In breast cancers, the gene expression array is stronger than classical criteria, but in endometrial hyperplasia, quantitative morphological features are more cost-effective than genetic testing. It is still too early to make strong statements, the more so because it is expected that genomics and proteomics will expand rapidly. However, it is likely that they will take a central place in the understanding, diagnosis, monitoring and treatment of (pre)cancers of many different sites.

  7. Global proteomic analysis of the chromate response in Arthrobacter sp strain FB24.

    SciTech Connect

    Henne, K. L.; Turse, J. E.; Nicora, C. D.; Lipton, M. S.; Tollaksen, S. L.; Lindberg, C.; Babnigg, G.; Giometti, C. S.; Nakatsu, C. H.; Thompson, D. K.; Konopka, A. E.; Biosciences Division; Purdue Univ.; PNNL

    2009-04-01

    A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO{sub 4}{sup 2-}) transporter by the chromate (CrO{sub 4}{sup 2-}) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceeded 5 mM.

  8. Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24

    SciTech Connect

    Henne, Kristene L.; Turse, Joshua E.; Nicora, Carrie D.; Lipton, Mary S.; Tollaksen, Sandra L.; Lindberg, Carl; Babbnig, Gyorgy; Giometti, Carol S.; Nakatsu, Cindy N.; Thompson, Dorothea K.; Konopka, Allan

    2009-04-01

    A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 mM and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled to tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO42-) transporter by the chromate (CrO42-) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceed 5 mM.

  9. Assessment of adolescents' motivation for educational attainment.

    PubMed

    Cham, Heining; Hughes, Jan N; West, Stephen G; Im, Myung Hee

    2014-06-01

    The Adolescent Motivation for Educational Attainment Questionnaire is a 32-item questionnaire (we drew 20 items from 3 subscales of the Educational Motivation Questionnaire; Murdock, 1999) that was developed to measure multiple potential dimensions of adolescents' motivation to complete high school and enroll in post-secondary education, including competence and effort beliefs; perceived value of education; and peer, teacher, and parent support for educational attainment. We assessed a multiethnic sample (N = 569) of low-achieving students who started 1st grade together in 1 urban and 2 small city school districts. Participants were assessed over 2 consecutive years (Grades 8 and 9 given prior grade retention, or Grades 9 and 10 if not retained). Exploratory factor analyses identified 4 correlated dimensions underlying the questionnaire responses. Subsequent confirmatory factor analyses provided support for a bifactor model, which includes a general factor of students' basic educational motivation, and specific factors of (a) teacher educational expectations, (b) peer aspirations, and (c) value of education. Measurement invariance of the bifactor model was established across students' gender and ethnicity (Caucasian, African American, and Hispanic) and year of testing. Criterion-related validity of the general and specific factors with students' school belonging, student-teacher warmth and conflict, disciplinary practices, letter grade, conduct problems, and behavioral engagement was examined. Practical implications of the measure are discussed.

  10. Expectation and attainment of nursing careers.

    PubMed

    Dunkelberger, J E; Aadland, S C

    1984-01-01

    This study was designed to replicate and extend an investigation completed 15 years ago, which was related to recruitment into the nursing profession. The data are provided by the National Longitudinal Study (NLS) of youths followed from high school through young adulthood. The design involved classification of the NLS sample into three groups based on career interest in nursing and ultimate occupational attainment: (1) those who expected to become nurses when in high school and did so; (2) those who expected to become nurses in high school but did not; and (3) those who had other occupational expectations in high school but became nurses. These three recruitment types were analyzed relative to four demographic variables. Only 34% of those who planned to become nurses did so. Those who did not attain their goal were more often from low socioeconomic backgrounds, had lower aptitudes, and were more often nonwhites than were other nursing recruits. Youth in the other two groups were very similar on all variables. Findings were generally consistent with those found in the earlier study although several differences were noted in the composition of the typologies used, indicating that the pattern of recruitment is changing.

  11. How to attain expertise in clinical communication?

    PubMed

    Wouda, Jan C; van de Wiel, Harry B M

    2013-12-01

    Several factors complicate the attainment of expertise in clinical communication. Medical curricula and postgraduate training insufficiently provide the required learning conditions of deliberate practice to overcome these obstacles. In this paper we provide recommendations for learning objectives and teaching methods for the attainment of professional expertise in patient education. Firstly, we propose to use functional learning objectives derived from the goals and strategies of clinical communication. Secondly, we recommend using teaching and assessment methods which: (1) contain stimulating learning tasks with opportunities for immediate feedback, reflection and corrections, and (2) give ample opportunity for repetition, gradual refinements and practice in challenging situations. Video-on-the-job fits these requirements and can be used to improve the competency in patient education of residents and medical staff in clinical practice. However, video-on-the-job can only be successful if the working environment supports the teaching and learning of communication and if medical staff which supervises the residents, is motivated to improve their own communication and didactic skills.

  12. Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics1[W][OA

    PubMed Central

    Schilmiller, Anthony L.; Miner, Dennis P.; Larson, Matthew; McDowell, Eric; Gang, David R.; Wilkerson, Curtis; Last, Robert L.

    2010-01-01

    Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces β-caryophyllene and α-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells. PMID:20431087

  13. Total and Putative Surface Proteomics of Malaria Parasite Salivary Gland Sporozoites*

    PubMed Central

    Lindner, Scott E.; Swearingen, Kristian E.; Harupa, Anke; Vaughan, Ashley M.; Sinnis, Photini; Moritz, Robert L.; Kappe, Stefan H. I.

    2013-01-01

    Malaria infections of mammals are initiated by the transmission of Plasmodium salivary gland sporozoites during an Anopheles mosquito vector bite. Sporozoites make their way through the skin and eventually to the liver, where they infect hepatocytes. Blocking this initial stage of infection is a promising malaria vaccine strategy. Therefore, comprehensively elucidating the protein composition of sporozoites will be invaluable in identifying novel targets for blocking infection. Previous efforts to identify the proteins expressed in Plasmodium mosquito stages were hampered by the technical difficulty of separating the parasite from its vector; without effective purifications, the large majority of proteins identified were of vector origin. Here we describe the proteomic profiling of highly purified salivary gland sporozoites from two Plasmodium species: human-infective Plasmodium falciparum and rodent-infective Plasmodium yoelii. The combination of improved sample purification and high mass accuracy mass spectrometry has facilitated the most complete proteome coverage to date for a pre-erythrocytic stage of the parasite. A total of 1991 P. falciparum sporozoite proteins and 1876 P. yoelii sporozoite proteins were identified, with >86% identified with high sequence coverage. The proteomic data were used to confirm the presence of components of three features critical for sporozoite infection of the mammalian host: the sporozoite motility and invasion apparatus (glideosome), sporozoite signaling pathways, and the contents of the apical secretory organelles. Furthermore, chemical labeling and identification of proteins on live sporozoites revealed previously uncharacterized complexity of the putative sporozoite surface-exposed proteome. Taken together, the data constitute the most comprehensive analysis to date of the protein expression of salivary gland sporozoites and reveal novel potential surface-exposed proteins that might be valuable targets for antibody blockage

  14. Total and putative surface proteomics of malaria parasite salivary gland sporozoites.

    PubMed

    Lindner, Scott E; Swearingen, Kristian E; Harupa, Anke; Vaughan, Ashley M; Sinnis, Photini; Moritz, Robert L; Kappe, Stefan H I

    2013-05-01

    Malaria infections of mammals are initiated by the transmission of Plasmodium salivary gland sporozoites during an Anopheles mosquito vector bite. Sporozoites make their way through the skin and eventually to the liver, where they infect hepatocytes. Blocking this initial stage of infection is a promising malaria vaccine strategy. Therefore, comprehensively elucidating the protein composition of sporozoites will be invaluable in identifying novel targets for blocking infection. Previous efforts to identify the proteins expressed in Plasmodium mosquito stages were hampered by the technical difficulty of separating the parasite from its vector; without effective purifications, the large majority of proteins identified were of vector origin. Here we describe the proteomic profiling of highly purified salivary gland sporozoites from two Plasmodium species: human-infective Plasmodium falciparum and rodent-infective Plasmodium yoelii. The combination of improved sample purification and high mass accuracy mass spectrometry has facilitated the most complete proteome coverage to date for a pre-erythrocytic stage of the parasite. A total of 1991 P. falciparum sporozoite proteins and 1876 P. yoelii sporozoite proteins were identified, with >86% identified with high sequence coverage. The proteomic data were used to confirm the presence of components of three features critical for sporozoite infection of the mammalian host: the sporozoite motility and invasion apparatus (glideosome), sporozoite signaling pathways, and the contents of the apical secretory organelles. Furthermore, chemical labeling and identification of proteins on live sporozoites revealed previously uncharacterized complexity of the putative sporozoite surface-exposed proteome. Taken together, the data constitute the most comprehensive analysis to date of the protein expression of salivary gland sporozoites and reveal novel potential surface-exposed proteins that might be valuable targets for antibody blockage

  15. Targeted Proteomics Approaches To Monitor Microbial Activity In Basalt Aquifer

    NASA Astrophysics Data System (ADS)

    Paszczynski, A. J.; Paidisetti, R.

    2007-12-01

    communities to allow for better identification of specific proteins. This method not only identified the proteins of interest but also increased the peptide coverage and increased the number of proteins identified. We were able to identify methane monooxygenase proteins within TAN site microbial communities supporting the occurrence of co-metabolic oxidation of TCE in this aquifer. We correlated methane monooxygenase presence with the number of methanotrophs in the samples obtained through quantitative PCR and quantitative proteomic methods. Utilization of this extraction method in combination with UPLC/MS/MS resulted in successful extraction, identification, and quantification of MMO-derived biomarker peptides from both pure cultures and environmental samples. Along with MMO proteins, we identified proteins from non-methanotrophic organisms that may play major roles in macronutrients turnover and the attenuation of TCE in the TAN aquifer.

  16. Genome-scale Proteome Quantification by DEEP SEQ Mass Spectrometry

    PubMed Central

    Zhou, Feng; Lu, Yu; Ficarro, Scott B.; Adelmant, Guillaume; Jiang, Wenyu; Luckey, C. John; Marto, Jarrod A.

    2013-01-01

    Advances in chemistry and massively parallel detection underlie DNA sequencing platforms that are poised for application in personalized medicine. In stark contrast, systematic generation of protein-level data lags well-behind genomics in virtually every aspect: depth of coverage, throughput, ease of sample preparation, and experimental time. Here, to bridge this gap, we develop an approach based on simple detergent lysis and single-enzyme digest, extreme, orthogonal separation of peptides, and true nanoflow LC-MS/MS that provides high peak capacity and ionization efficiency. This automated, deep efficient peptide sequencing and quantification (DEEP SEQ) mass spectrometry platform provides genome-scale proteome coverage equivalent to RNA-seq ribosomal profiling and accurate quantification for multiplexed isotope labels. In a model of the embryonic to epiblast transition in murine stem cells, we unambiguously quantify 11,352 gene products that span 70% of Swiss-Prot and capture protein regulation across the full detectable range of high-throughput gene expression and protein translation. PMID:23863870

  17. Tackling health workforce challenges to universal health coverage: setting targets and measuring progress.

    PubMed

    Cometto, Giorgio; Witter, Sophie

    2013-11-01

    Human resources for health (HRH) will have to be strengthened if universal health coverage (UHC) is to be achieved. Existing health workforce benchmarks focus exclusively on the density of physicians, nurses and midwives and were developed with the objective of attaining relatively high coverage of skilled birth attendance and other essential health services of relevance to the health Millennium Development Goals (MDGs). However, the attainment of UHC will depend not only on the availability of adequate numbers of health workers, but also on the distribution, quality and performance of the available health workforce. In addition, as noncommunicable diseases grow in relative importance, the inputs required from health workers are changing. New, broader health-workforce benchmarks - and a corresponding monitoring framework - therefore need to be developed and included in the agenda for UHC to catalyse attention and investment in this critical area of health systems. The new benchmarks need to reflect the more diverse composition of the health workforce and the participation of community health workers and mid-level health workers, and they must capture the multifaceted nature and complexities of HRH development, including equity in accessibility, sex composition and quality.

  18. HUPO initiatives relevant to clinical proteomics.

    PubMed

    Hanash, Sam

    2004-04-01

    The past few years have seen a tremendous interest in the potential of proteomics to address unmet needs in biomedicine. Such unmet needs include more effective strategies for early disease detection and monitoring and more effective therapies, in addition to developing a better understanding of disease pathogenesis. Proteomics is particularly suited for investigating biological fluids to identify disease-related alterations and to develop molecular signatures for disease processes. However, much of the effort undertaken in clinical proteomics to date represents either demonstrations of principles or relatively small-scale studies when compared with genomics effort and accomplishments or more pertinently when contrasted with the tremendous untapped potential of clinical proteomics. Clearly, we are in the early stages. What seems to be urgently needed is an organized effort to build a solid foundation for proteomics that includes developing a much needed infrastructure with adequate resources. The Human Proteome Organization (HUPO) is fostering an organized international effort in proteomics that includes initiatives around organ systems and biological fluids that have disease relevance as well as development of proteomics resources.

  19. Centennial Paper: Proteomics in animal science

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  20. The promise of proteomics in animal science

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. Current advances in esophageal cancer proteomics.

    PubMed

    Uemura, Norihisa; Kondo, Tadashi

    2015-06-01

    We review the current status of proteomics for esophageal cancer (EC) from a clinician's viewpoint. The ultimate goal of cancer proteomics is the improvement of clinical outcome. The proteome as a functional translation of the genome is a straightforward representation of genomic mechanisms that trigger carcinogenesis. Cancer proteomics has identified the mechanisms of carcinogenesis and tumor progression, detected biomarker candidates for early diagnosis, and provided novel therapeutic targets for personalized treatments. Our review focuses on three major topics in EC proteomics: diagnostics, treatment, and molecular mechanisms. We discuss the major histological differences between EC types, i.e., esophageal squamous cell carcinoma and adenocarcinoma, and evaluate the clinical significance of published proteomics studies, including promising diagnostic biomarkers and novel therapeutic targets, which should be further validated prior to launching clinical trials. Multi-disciplinary collaborations between basic scientists, clinicians, and pathologists should be established for inter-institutional validation. In conclusion, EC proteomics has provided significant results, which after thorough validation, should lead to the development of novel clinical tools and improvement of the clinical outcome for esophageal cancer patients. This article is part of a Special Issue entitled: Medical Proteomics.

  2. Global Proteome Analysis of Leptospira interrogans

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Proteomics: Protein Identification Using Online Databases

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  4. Applications of Proteomic Technologies to Toxicology

    EPA Science Inventory

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

  5. Polar constellations design for discontinuous coverage

    NASA Astrophysics Data System (ADS)

    Sarno, Salvatore; Graziano, Maria Daniela; D'Errico, Marco

    2016-10-01

    A novel constellation design method is developed for discontinuous coverage of the globe and polar caps. It integrates and extends the applicability of the coverage regions and mitigates the limitations of the existing techniques based on streets-of-coverage (SOC) theory. In particular, the visibility conditions of the targets are mapped in the (Ω, u)-domain to identify the number of satellites per plane and the distance between successive orbits, whereas the planes are arranged around the equator exploiting satellites both in ascending and descending phase. The proposed approach is applied to design potential space segments in polar LEO supporting the existing maritime surveillance services over the globe and on the future polar routes. Results show they require a smaller total number of satellites with respect to the SOC-based configurations for revisit times less than one hour and wide range of swaths. In details, it is observed a reduction between 6% and 22% for global coverage and between 24% and 33% for the coverage of polar caps.

  6. On class differentials in educational attainment.

    PubMed

    Erikson, Robert; Goldthorpe, John H; Jackson, Michelle; Yaish, Meir; Cox, D R

    2005-07-05

    Social class differentials in educational attainment have been extensively studied in numerous countries. In this paper, we begin by examining class differentials in the progression to higher secondary education among 16-year-old children in England and Wales. As has been shown for other countries, the differentials result both from the primary effects of differing levels of academic performance of children of different class background and from the secondary effects of differences in the educational choices that these children make at given levels of performance. Through counterfactual analyses in which the performance distribution of one class is combined with the choice distribution of another, primary and secondary effects are decomposed and the former are shown to be roughly three times the size of the latter.

  7. Proteomic Analyses of the Vitreous Humour

    PubMed Central

    Angi, Martina; Kalirai, Helen; Coupland, Sarah E.; Damato, Bertil E.; Semeraro, Francesco; Romano, Mario R.

    2012-01-01

    The human vitreous humour (VH) is a transparent, highly hydrated gel, which occupies the posterior segment of the eye between the lens and the retina. Physiological and pathological conditions of the retina are reflected in the protein composition of the VH, which can be sampled as part of routine surgical procedures. Historically, many studies have investigated levels of individual proteins in VH from healthy and diseased eyes. In the last decade, proteomics analyses have been performed to characterise the proteome of the human VH and explore networks of functionally related proteins, providing insight into the aetiology of diabetic retinopathy and proliferative vitreoretinopathy. Recent proteomic studies on the VH from animal models of autoimmune uveitis have identified new signalling pathways associated to autoimmune triggers and intravitreal inflammation. This paper aims to guide biological scientists through the different proteomic techniques that have been used to analyse the VH and present future perspectives for the study of intravitreal inflammation using proteomic analyses. PMID:22973072

  8. Pros and cons of the proteomics.

    PubMed

    Gupta, Ashish; Kumar, Ashutosh

    2014-01-01

    The number of proteins produced by the 30,000-40,000 genes of the human genome is estimated to be three or four orders of magnitude higher. Proteomics is a rapidly developing science. In principle, two main areas in the field of proteomics have been developed, each of them having its pros and cons. These fields are profiling and functional proteomics. The aim of the proteomic profiling is to describe and index the whole set of proteins of a biological sample, which could be an organism, an organ, or a cell, or parts there of like individual's tissue or organelles. In our understanding, both types of proteomics (profiling and functional) are valuable tools complementing other biological methodologies.

  9. Increasing the Structural Coverage of Tuberculosis Drug Targets

    PubMed Central

    Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

    2015-01-01

    High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

  10. Increasing the structural coverage of tuberculosis drug targets

    SciTech Connect

    Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

    2014-12-19

    High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.

  11. Increasing the structural coverage of tuberculosis drug targets

    DOE PAGES

    Baugh, Loren; Phan, Isabelle; Begley, Darren W.; ...

    2014-12-19

    High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

  12. Rural-Nonrural Disparities in Postsecondary Educational Attainment Revisited

    PubMed Central

    Byun, Soo-yong; Meece, Judith L.; Irvin, Matthew J.

    2013-01-01

    Using data from the National Educational Longitudinal Study, this study revisited rural-nonrural disparities in educational attainment by considering a comprehensive set of factors that constrain and support youth's college enrollment and degree completion. Results showed that rural students were more advantaged in community social resources compared to nonrural students, and these resources were associated with a significant increase in the likelihood of bachelor's degree attainment. Yet results confirmed that rural students lagged behind nonrural students in attaining a bachelor's degree largely due to their lower socioeconomic background. The findings present a more comprehensive picture of the complexity of geographic residence in shaping college enrollment and degree attainment. PMID:24285873

  13. 42 CFR 422.68 - Effective dates of coverage and change of coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 3 2011-10-01 2011-10-01 false Effective dates of coverage and change of coverage. 422.68 Section 422.68 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM MEDICARE ADVANTAGE PROGRAM Eligibility, Election,...

  14. 5 CFR 842.1009 - Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity computations. 842.1009 Section 842.1009... EMPLOYEES RETIREMENT SYSTEM-BASIC ANNUITY Customs and Border Protection Officers § 842.1009 Elections...

  15. 5 CFR 842.1009 - Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity computations. 842.1009 Section 842.1009... EMPLOYEES RETIREMENT SYSTEM-BASIC ANNUITY Customs and Border Protection Officers § 842.1009 Elections...

  16. 5 CFR 842.1009 - Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity computations. 842.1009 Section 842.1009... EMPLOYEES RETIREMENT SYSTEM-BASIC ANNUITY Customs and Border Protection Officers § 842.1009 Elections...

  17. Perplexity analysis of obesity news coverage.

    PubMed

    McFarlane, Delano J; Elhadad, Noémie; Kukafka, Rita

    2009-11-14

    An important task performed during the analysis of health news coverage is the identification of news articles that are related to a specific health topic (e.g. obesity). This is often done using a combination of keyword searching and manual encoding of news content. Statistical language models and their evaluation metric, perplexity, may help to automate this task. A perplexity study of obesity news was performed to evaluate perplexity as a measure of the similarity of news corpora to obesity news content. The results of this study showed that perplexity increased as news coverage became more general relative to obesity news (obesity news approximately 187, general health news approximately 278, general news approximately 378, general news across multiple publishers approximately 382). This indicates that language model perplexity can measure the similarity news content to obesity news coverage, and could be used as the basis for an automated health news classifier.

  18. Learning Time-Varying Coverage Functions

    PubMed Central

    Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

    2015-01-01

    Coverage functions are an important class of discrete functions that capture the law of diminishing returns arising naturally from applications in social network analysis, machine learning, and algorithmic game theory. In this paper, we propose a new problem of learning time-varying coverage functions, and develop a novel parametrization of these functions using random features. Based on the connection between time-varying coverage functions and counting processes, we also propose an efficient parameter learning algorithm based on likelihood maximization, and provide a sample complexity analysis. We applied our algorithm to the influence function estimation problem in information diffusion in social networks, and show that with few assumptions about the diffusion processes, our algorithm is able to estimate influence significantly more accurately than existing approaches on both synthetic and real world data. PMID:25960624

  19. Aspects of coverage in medical DNA sequencing

    PubMed Central

    Wendl, Michael C; Wilson, Richard K

    2008-01-01

    Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations. Results We address the medical sequencing coverage problem via an extension of the standard mathematical theory of haploid coverage. The expected diploid multi-fold coverage, as well as its generalization for aneuploidy are derived and these expressions can be readily evaluated for any project. The resulting theory is used as a scaling law to calibrate performance to that of standard BAC sequencing at 8× to 10× redundancy, i.e. for expected coverages that exceed 99% of the unique sequence. A differential strategy is formalized for tumor/normal studies wherein tumor samples are sequenced more deeply than normal ones. In particular, both tumor alleles should be detected at least twice, while both normal alleles are detected at least once. Our theory predicts these requirements can be met for tumor and normal redundancies of approximately 26× and 21×, respectively. We explain why these values do not differ by a factor of 2, as might intuitively be expected. Future technology developments should prompt even deeper sequencing of tumors, but the 21× value for normal samples is essentially a constant. Conclusion Given the assumptions of standard coverage theory, our model gives pragmatic estimates for required redundancy. The differential strategy should be an efficient means of identifying potential somatic mutations for further study. PMID:18485222

  20. The nature of newspaper coverage of homicide

    PubMed Central

    Taylor, C; Sorenson, S

    2002-01-01

    Objectives: Previous research has shown that some homicides are more likely than others to receive newspaper coverage (for example, homicides by strangers). The present investigation examined whether, once the decision has been made to report on a homicide, the nature of the coverage (that is, how much visibility is given to a story, what information is included, and how a story is written) differs according to two key variables, victim ethnicity, and victim-suspect relationship. Setting: Los Angeles, California (USA). Methods: Homicide articles from the 1990–94 issues of the Los Angeles Times were stratified according to the predictors of interest (victim ethnicity and victim-suspect relationship) and a sample was drawn. Data that characterized two primary aspects of newspaper coverage, prominence and story framing (including background information, story focus, use of opinions, story tone, and "hook" or leading introductory lines) were abstracted from the articles. Descriptive statistics and cross tabulations were generated. Multivariate analyses were conducted to examine the predictive value of victim ethnicity and victim-suspect relationship on the nature of the newspaper coverage. Results: Newspaper coverage of homicide was generally factual, episodic, and unemotional in tone. Victim-suspect relationship, but not victim ethnicity, was related to how a story was covered, particularly the story frame. Homicides by intimates were covered consistently differently from other types of homicides; these stories were less likely to be opinion dominated, be emotional, and begin with a "hook". Conclusion: Victim-suspect relationship was related to the nature of coverage of homicides in a large, metropolitan newspaper. Given the agenda setting and issue framing functions of the news media, these findings have implications for the manner in which the public and policy makers perceive homicides and, consequently, for the support afforded to various types of solutions for

  1. Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines.

    PubMed

    Edwards, Amanda; Haas, Wilhelm

    2016-01-01

    The proteome is the functional entity of the cell, and perturbations of a cellular system almost always cause changes in the proteome. These changes are a molecular fingerprint, allowing characterization and a greater understanding of the effect of the perturbation on the cell as a whole. Monitoring these changes has therefore given great insight into cellular responses to stress and disease states, and analytical platforms to comprehensively analyze the proteome are thus extremely important tools in biological research. Mass spectrometry has evolved as the most relevant technology to characterize proteomes in a comprehensive way. However, due to a lack of throughput capacity of mass spectrometry-based proteomics, researchers frequently use measurement of mRNA levels to approximate proteome changes. Growing evidence of substantial differences between mRNA and protein levels as well as recent improvements in mass spectrometry-based proteomics are heralding an increased use of mass spectrometry for comprehensive proteome mapping. Here we describe the use of multiplexed quantitative proteomics using isobaric labeling with tandem mass tags (TMT) for the simultaneous quantitative analysis of five cancer cell proteomes in biological duplicates in one mass spectrometry experiment.

  2. Toxic metal proteomics: reaction of the mammalian zinc proteome with Cd²⁺.

    PubMed

    Namdarghanbari, Mohammad Ali; Bertling, Joseph; Krezoski, Susan; Petering, David H

    2014-07-01

    The hypothesis was tested that Cd(2+) undergoes measureable reaction with the Zn-proteome through metal ion exchange chemistry. The Zn-proteome of pig kidney LLC-PK1 cells is relatively inert to reaction with competing ligands, including Zinquin acid, EDTA, and apo-metallothionein. Upon reaction of Cd(2+) with the Zn-proteome, Cd(2+) associates with the proteome and near stoichiometric amounts of Zn(2+) become reactive with these chelating agents. The results strongly support the hypothesis that Cd(2+) displaces Zn(2+) from native proteomic binding sites resulting in the formation of a Cd-proteome. Mobilized Zn(2+) becomes adventitiously bound to proteome and available for reaction with added metal binding ligands. Cd-proteome and Zn-metallothionein readily exchange metal ions, raising the possibility that this reaction restores functionality to Cd-proteins. In a parallel experiment, cells were exposed to Cd(2+) and pyrithione briefly to generate substantial proteome-bound Cd(2+). Upon transition to a Cd(2+) free medium, the cells generated new metallothionein protein over time that bound most of the proteomic Cd(2+) as well as additional Zn(2+).

  3. The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community.

    PubMed

    James, Peter

    2011-09-01

    The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org.

  4. Rodeo medicine: considerations in event coverage.

    PubMed

    Young, Eliot J; Markey, Keith L

    2010-01-01

    Rodeo is an increasingly popular but dangerous sport, with injury rates higher than any other sport. While there are several organizations that oversee many of the rodeo competitions in the U.S., most events are non-sanctioned. Several factors contribute to the risk for injury, and medical coverage is usually volunteer-based. This article describes the common events that occur in most rodeo competitions, highlights the injuries most often documented in rodeo injury reporting, and suggests guidelines for preparation of medical coverage of a typical rodeo event.

  5. Extreme sports: injuries and medical coverage.

    PubMed

    Young, Craig C

    2002-10-01

    Extreme sports (including in-line skating, snowboarding, mountain bicycling, extreme skiing, rock climbing, indoor tackle football, kickboxing, skateboarding, and ultra-endurance racing) are growing in popularity. Often these sports are designed to expose athletes to greater thrills and risks than are found in traditional sporting activities. Despite this increased risk of injury, athletes competing in these sports often have little or no formal medical coverage. This article reviews what is known about this emerging area of sports medicine to assist physicians in preparing for medical coverage of these athletes and their competitions.

  6. Controlling the coverage area of a microcell

    NASA Astrophysics Data System (ADS)

    Arowojolu, A. A.; Turkmani, A. M. D.

    A theoretical computer-based study has been undertaken to investigate potential mechanisms for controlling the coverage area of a typical urban microcell. These mechanisms, effected at the base station, include antenna height variation, the use of a directional antenna and antenna downtilt. A signal strength prediction algorithm which is based on geometrical optics and the geometrical theory of diffraction and which makes use of the three-dimensional radiation patterns of antennas has been employed in the study. Results obtained in the form of signal strength profiles demonstrate the effectiveness, in particular, of beam tilting for controlling the microcell coverage area.

  7. 20 CFR 404.1412 - Compensation quarters of coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false Compensation quarters of coverage. 404.1412... the Railroad Retirement Program § 404.1412 Compensation quarters of coverage. As used in this subpart, a compensation quarter of coverage is any quarter of coverage computed with respect to...

  8. 20 CFR 404.1412 - Compensation quarters of coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Compensation quarters of coverage. 404.1412... the Railroad Retirement Program § 404.1412 Compensation quarters of coverage. As used in this subpart, a compensation quarter of coverage is any quarter of coverage computed with respect to...

  9. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 11 2012-01-01 2012-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  10. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 11 2010-01-01 2010-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  11. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 11 2013-01-01 2013-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  12. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 11 2011-01-01 2011-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  13. 42 CFR 457.1010 - Purchase of family coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Purchase of family coverage. 457.1010 Section 457... Waivers: General Provisions § 457.1010 Purchase of family coverage. A State may purchase family coverage... family coverage is cost-effective under the standards described in § 457.1015; (b) The State does...

  14. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  15. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 4 2013-10-01 2013-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  16. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 4 2014-10-01 2014-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  17. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 4 2012-10-01 2012-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  18. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  19. 46 CFR 154.1155 - Hand hose line: Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Hand hose line: Coverage. 154.1155 Section 154.1155... Firefighting System: Dry Chemical § 154.1155 Hand hose line: Coverage. The coverage for the area for a hand hose line under § 154.1150 must not exceed the length of the hand hose line except the coverage for...

  20. 46 CFR 154.1155 - Hand hose line: Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Hand hose line: Coverage. 154.1155 Section 154.1155... Firefighting System: Dry Chemical § 154.1155 Hand hose line: Coverage. The coverage for the area for a hand hose line under § 154.1150 must not exceed the length of the hand hose line except the coverage for...