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Sample records for adrian proteomics myers

  1. [Adrian Stokes and 'trench jaundice'].

    PubMed

    Wever, Peter C

    2015-01-01

    On the day that Great Britain declared war on Germany in 1914, the Irish physician and bacteriologist Adrian Stokes travelled to London to volunteer. One week later he left for France with the first British troops as an officer with the Royal Army Medical Corps. He spent most of the First World War attached to No. 1 Mobile Bacteriological Laboratory at the Remy Siding British-Canadian field hospital in Flanders. In April 1916, he was confronted with an outbreak of trench jaundice, also known as epidemic jaundice (Weil's disease). Conditions in the trenches contributed to the hundred cases identified by Stokes in a short period. In 1917, he was the first to publish (in The Lancet) the finding that the bacterium Spirochaeta icterohaemorrhagiae, the causative agent of epidemic jaundice, could be isolated from the kidneys of rats. A subsequent rat control campaign in the trenches successfully curbed the disease.

  2. 78 FR 14304 - Adrian Vela: Debarment Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-05

    ... HUMAN SERVICES Food and Drug Administration Adrian Vela: Debarment Order AGENCY: Food and Drug Administration, HHS. ACTION: Notice. SUMMARY: The Food and Drug Administration (FDA) is issuing an order under... at Sea Food Center's Tampa facility to divide the shrimp received from Thailand, Malaysia,...

  3. Adrian Public Library Literacy Education and Development (LEAD) Program.

    ERIC Educational Resources Information Center

    Adrian Public Library, MI.

    Project LEAD (Literacy Education and Development) is an organization of volunteer tutors in English literacy for limited-English-proficient migrant workers, primarily Spanish-speakers. The report details project implementation in Lenawee County (Michigan) by the Adrian Public Library. The report is organized according to the project's eight stated…

  4. Collective Bargaining Agreement between Adrian College and Adrian College Association of Professors (MEA/NEA), September 1, 1984-September 1, 1986.

    ERIC Educational Resources Information Center

    Michigan Education Association, East Lansing.

    The collective bargaining agreement between Adrian College and Adrian College Association of Professors, an affiliate of the Michigan and National Education Associations, covering the period September 1, 1984-September 1, 1986 is presented. Items covered in the agreement include: unit recognition; definitions; rights of the Board of Trustees;…

  5. Adrian Stokes and the portrait of Melanie Klein.

    PubMed

    Sayers, Janet

    2015-08-01

    This paper focuses on the offer by the art writer Adrian Stokes to commission and pay for a portrait of the psychoanalyst Melanie Klein by the artist William Coldstream. It details some of the precursors of this offer in Stokes's preceding involvement first with Klein and then with Coldstream; her response to this offer; and its outcome and aftermath in Stokes's subsequent writing about Klein and Coldstream.

  6. 33 CFR 100.736 - Annual Fort Myers Beach air show; Fort Myers Beach, FL.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Annual Fort Myers Beach air show; Fort Myers Beach, FL. 100.736 Section 100.736 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... Fort Myers Beach air show; Fort Myers Beach, FL. (a)(1) Regulated Area. The regulated area is formed...

  7. 33 CFR 100.736 - Annual Fort Myers Beach air show; Fort Myers Beach, FL.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Annual Fort Myers Beach air show; Fort Myers Beach, FL. 100.736 Section 100.736 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... Fort Myers Beach air show; Fort Myers Beach, FL. (a)(1) Regulated Area. The regulated area is formed...

  8. 33 CFR 100.736 - Annual Fort Myers Beach air show; Fort Myers Beach, FL.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Annual Fort Myers Beach air show; Fort Myers Beach, FL. 100.736 Section 100.736 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... Fort Myers Beach air show; Fort Myers Beach, FL. (a)(1) Regulated Area. The regulated area is formed...

  9. 33 CFR 100.736 - Annual Fort Myers Beach air show; Fort Myers Beach, FL.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Annual Fort Myers Beach air show; Fort Myers Beach, FL. 100.736 Section 100.736 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... Fort Myers Beach air show; Fort Myers Beach, FL. (a)(1) Regulated Area. The regulated area is formed...

  10. 33 CFR 100.736 - Annual Fort Myers Beach air show; Fort Myers Beach, FL.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Annual Fort Myers Beach air show; Fort Myers Beach, FL. 100.736 Section 100.736 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... Fort Myers Beach air show; Fort Myers Beach, FL. (a)(1) Regulated Area. The regulated area is formed...

  11. 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).

  12. Fort Myer, Virginia: Historic Landscape Inventory.

    DTIC Science & Technology

    1998-06-01

    the Martin Luther King , Jr. Public Library, the Virginia Room of the Arlington Library. Other important sources at Fort Myer itself include the Third...Myer, 1909 ( Martin Luther King , Jr. Library, Washington, DC, Washingtoniana Room). 57 Figure 26. Equestrian excellence at Fort Myer in the 1920s...U.S. Army Posts 1925). 58 Figure 27. The Machine Gun Troop of the Tenth Cavalry on Summerall Field, 1931 ( Martin Luther King , Jr. Library, Washington

  13. Myers-Briggs typology and Jungian individuation.

    PubMed

    Myers, Steve

    2016-06-01

    Myers-Briggs typology is widely seen as equivalent to and representative of Jungian theory by the users of the Myers-Briggs Type Indicator (MBTI) and similar questionnaires. However, the omission of the transcendent function from the theory, and the use of typological functions as its foundation, has resulted in an inadvertent reframing of the process of individuation. This is despite some attempts to integrate individuation and typology, and reintroduce the transcendent function into Myers-Briggs theory. This paper examines the differing views of individuation in Myers-Briggs and Jungian theory, and some of the challenges of reconciling those differences, particularly in the context of normality. It proposes eight principles, drawn mainly from Jungian and classical post-Jungian work, that show how individuation as a process can be integrated with contemporary Myers-Briggs typology. These principles show individuation as being a natural process that can be encouraged outside of the analytic process. They make use of a wide range of opposites as well as typological functions, whilst being centred on the transcendent function. Central to the process is the alchemical image of the caduceus and a practical interpretation of the axiom of Maria, both of which Jung used to illustrate the process of individuation.

  14. The Myers-Briggs Type of College Student Leaders.

    ERIC Educational Resources Information Center

    Darst, Kimberly Vess

    2001-01-01

    Determined the Myers-Briggs type for 149 undergraduate students holding leadership positions in student organizations. Found that college student leaders tent to be Extraverted, Sensing, Thinking, and Judging on the Myers-Briggs Type Indicator. (EV)

  15. Using the Myers Briggs Type Indicator - part of the solution.

    PubMed

    Allen, Judy

    1994-05-12

    The Myers Briggs Type Indicator, which is based on the work of Jung, is used in an infinite variety of settings to enhance learning, personal development and team building. This article describes its particular relevance to the nursing profession. (N.B. Isabel Myers used the name Isabel Briggs Myers for publication purposes. The Indicator is termed Myers Briggs in order to indicate the involvement of her mother in its development.).

  16. 33 CFR 100.717 - Annual Fort Myers Beach Offshore Grand Prix; Fort Myers, FL.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... involved with the Fort Myers Beach Offshore Grand Prix, exiting Big Carlos Pass between 11 a.m. and 3 p.m... until finally past and clear of the racecourse. All coordinates referenced use datum: NAD 83. (5)...

  17. 33 CFR 100.717 - Annual Fort Myers Beach Offshore Grand Prix; Fort Myers, FL.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...°58.30′ W). All coordinates referenced use datum: NAD 83. (b) Special local regulations. (1) No vessel... coordinates referenced use datum: NAD 83. (3) All vessel traffic, not involved with the Fort Myers Beach... clear of the racecourse. All coordinates referenced use datum: NAD 83. (4) All vessel traffic,...

  18. 33 CFR 100.717 - Annual Fort Myers Beach Offshore Grand Prix; Fort Myers, FL.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...°58.30′ W). All coordinates referenced use datum: NAD 83. (b) Special local regulations. (1) No vessel... coordinates referenced use datum: NAD 83. (3) All vessel traffic, not involved with the Fort Myers Beach... clear of the racecourse. All coordinates referenced use datum: NAD 83. (4) All vessel traffic,...

  19. 33 CFR 100.717 - Annual Fort Myers Beach Offshore Grand Prix; Fort Myers, FL.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...°58.30′ W). All coordinates referenced use datum: NAD 83. (b) Special local regulations. (1) No vessel... coordinates referenced use datum: NAD 83. (3) All vessel traffic, not involved with the Fort Myers Beach... clear of the racecourse. All coordinates referenced use datum: NAD 83. (4) All vessel traffic,...

  20. 33 CFR 100.717 - Annual Fort Myers Beach Offshore Grand Prix; Fort Myers, FL.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...°58.30′ W). All coordinates referenced use datum: NAD 83. (b) Special local regulations. (1) No vessel... coordinates referenced use datum: NAD 83. (3) All vessel traffic, not involved with the Fort Myers Beach... clear of the racecourse. All coordinates referenced use datum: NAD 83. (4) All vessel traffic,...

  1. 9. Photocopy of architectural drawing (from blueprint at Fort Myer ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Photocopy of architectural drawing (from blueprint at Fort Myer Engineer Activity) 'Double Set of Non-Commissioned Officers Qrs.' Quartermaster Generals Office, sheet 1 and unnumbered sheet, standard plan 23, June 1891. lithograph on linen architectural drawing 2. PLANS, 1 SECTION, 2 DETAILS - Fort Myer, Non-Commissioned Officers Quarters, Washington Avenue between Johnson Lane & Custer Road, Arlington, Arlington County, VA

  2. 8. Photocopy of architectural drawing (from blueprint at Fort Myer ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Photocopy of architectural drawing (from blueprint at Fort Myer Engineer Activity) 'Double set of Non-Commissioned Officers Qrs.' Quartermaster Generals Office, sheets 2 and 3, standard plan 23, June 1891, Lithographed on linen architectural drawing. 1 PLAN, 3 ELEVATIONS - Fort Myer, Non-Commissioned Officers Quarters, Washington Avenue between Johnson Lane & Custer Road, Arlington, Arlington County, VA

  3. An assessment of the Myers-Briggs Type indicator.

    PubMed

    Carlyn, M

    1977-10-01

    A comprehensive assessment of the Myers-Briggs Type indicator is presented, including a description of the four personality scales measured by the instrument, a summary of the scoring process, and an extensive review of intercorrelation studies, reliability studies, and validity studies conducted with the Indicator. Results of the studies indicate that the Myers-Briggs Type Indicator is an adequately reliable self-report inventory. The Extraversion-Introversion Sensation-Intuition, and Thinking-Feeling scales appear to be relatively independent of each other, measuring dimensions of personality which seem to be quite similar to those postulated by Carl Jung.

  4. The rigid Horowitz-Myers conjecture

    NASA Astrophysics Data System (ADS)

    Woolgar, Eric

    2017-03-01

    The new positive energy conjecture was first formulated by Horowitz and Myers in the late 1990s to probe for a possible extended, nonsupersymmetric AdS/CFT correspondence. We consider a version formulated for complete, asymptotically Poincaré-Einstein Riemannian metrics ( M, g) with bounded scalar curvature R ≥ - n( n - 1) and with no (inner) boundary except possibly a finite union of compact, totally geodesic hypersurfaces (horizons). This version then asserts that any such ( M, g) must have mass not less than a certain bound which is realized as the mass m 0 of a metric g 0 induced on a time-symmetric slice of a spacetime called an AdS soliton. This conjecture remains unproved, having so far resisted standard techniques. Little is known other than that the conjecture is true for metrics which are sufficiently small perturbations of g 0. We pose another test for the conjecture. We assume its validity and attempt to prove as a corollary the corresponding scalar curvature rigidity statement, which is that g 0 is the unique asymptotically Poincaré-Einstein metric with mass m 0 obeying R ≥ - n( n - 1). Were a second such metric g 1 not isometric to g 0 to exist, it then may well admit perturbations of lower mass, contradicting the assumed validity of the conjecture. We find enough rigidity to show that the minimum mass metric must be static Einstein, so the problem is reduced to that of static uniqueness. When n = 3 the manifold must be isometric to a time-symmetric slice of an AdS soliton spacetime, or must have a non-compact horizon. En route we study the mass aspect, obtaining and generalizing known results: (i) we relate the mass aspect of static metrics to the holographic energy density, (ii) we obtain the conformal invariance of the mass aspect when the bulk dimension is odd, and (iii) we show the vanishing of the mass aspect for negative Einstein manifolds with Einstein conformal boundary.

  5. Myers-Briggs Type Inventory Personality Preferences and Academic Performance.

    ERIC Educational Resources Information Center

    Lowenthal, Werner; Meth, Hilda

    1989-01-01

    A study to determine if there are any relationships between the Myers-Briggs Type Inventory personality preferences and academic performance in schools of pharmacy is discussed. Differences in academic performance that could be related to gender are reported. (Author/MLW)

  6. The Utility of the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Pittenger, David J.

    1993-01-01

    The Myers Briggs Type Indicator (MBTI) is evaluated using a unified view of test validity that requires that validity be considered from an approach requiring many sources of corroboration. A review of available literature suggests insufficient evidence to support the tenets and claims about the utility of the MBTI. (SLD)

  7. The Myers-Briggs type indicator--a management tool.

    PubMed

    Costello, K

    1993-05-01

    The Myers-Briggs Type Indicator can be an enlightening experience for managers as it uncovers blind spots as well as provides insight into managerial styles. This tool offers a way to build communication patterns that meet nurse managers' needs and the needs of the people they supervise.

  8. Item validity of the Myers-Briggs Type Indicator.

    PubMed

    Tzeng, O C; Outcalt, D; Boyer, S L; Ware, R; Landis, D

    1984-06-01

    The present study presents a brief summary of four extensive psychometric analyses of the Myers-Briggs Type Indicator (MBTI) items. Positive empirical evidence supports the MBTI item validity. However, several measurement issues on item construction were raised to caution the future users.

  9. "Monsters'" Ink: How Walter Dean Myers Made "Frankenstein" Fun.

    ERIC Educational Resources Information Center

    Phillips, Nathan

    2003-01-01

    Describes an effective but new twist on the use of young adult books as bridges to the classics. Considers how "Frankenstein" is a novel written for today. Aims for his students to see that literature can be a way to discuss important issues. Discusses how to bridge Walter Dean Myers' novel "Monster" to…

  10. An Assessment of the Myers-Briggs Type Indicator

    ERIC Educational Resources Information Center

    Carlyn, Marcia

    1977-01-01

    The Myers Briggs Type Indicator is a self-report inventory developed to measure variables in Carl Jung's personality typology. The four personality scales measured by the instrument, and the scoring process are described, and an extensive review of the intercorrelation, reliability, and validity research is presented. (Author/MV)

  11. Myers Briggs Type Indicator, burnout, and satisfaction in Illinois dentists.

    PubMed

    Baran, Ronald B

    2005-01-01

    There is conflicting research concerning satisfaction and burnout levels in dentistry. High levels of burnout can have deleterious effects on the dentist, his or her family, and patients. A random sample of Illinois general dentists was examined using the Myers Briggs Type Indicator, the Maslach Burnout Inventory, the Dentist Satisfaction Survey, and a demographic questionnaire. Areas examined were the frequency of types compared to a base population as well as the relationship of type to levels of satisfaction, burnout, and demographic items. Three of the 16 Myers Briggs types were overrepresented in this sample, while two types were underrepresented. Slightly less than half of the dentists were satisfied with their profession; 7.4% had reached significant levels of burnout and 83% perceived dentistry as being "very stressful." The personality types overrepresented in dentistry tended to have a higher level of satisfaction and a lower level of burnout compared to their cohort group.

  12. Rethinking communication apprehension: a Myers-Briggs perspective.

    PubMed

    Opt, S K; Loffredo, D A

    2000-09-01

    This study is an examination of relationships between Myers-Briggs personality type preferences, based on Jungian theory, and communication apprehension. Results showed that participants who preferred introversion or sensing reported significantly higher levels of communication apprehension in general and across the group, dyadic, meeting, and public contexts than did participants who preferred extraversion or intuition. In addition, participants who preferred feeling reported higher levels of communication anxiety in the public context than those who preferred thinking. Findings support the assumption that communication apprehension is biologically based, suggest that the Myers-Briggs type preference framework offers an alternative way of understanding communication apprehension, and point out the need for new approaches to understanding the phenomenon of communication apprehension.

  13. The Myers-Briggs type indicator and coronary heart disease.

    PubMed

    Thorne, B M; Fyfe, J H; Carskadon, T G

    1987-01-01

    Researchers have for many years attempted to establish a relationship between coronary heart disease (CHD) and personality type. In our study, 103 subjects completed Form G of the Myers-Briggs Type Indicator (MBTI). Comparisons were made between 93 CHD patients and an age-appropriate control group (Group C) on each of the four MBTI dimensions: Extraversion-Introversion, Sensing-Intuition, Thinking-Feeling, and Judging-Perceiving. The comparison between CHD patients and Group C showed that CHD patients were significantly more likely to prefer sensing and feeling.

  14. Myers-Briggs personality types of art collectors.

    PubMed

    Gridley, Mark C

    2004-04-01

    27 art collectors (13 men, 14 women) completed the Myers-Briggs Type Indicator. Their age range was 37 to 86 years and the mean 59.5 yr. Seventy percent were classified as Intuition types instead of Sensation types (versus its 25% incidence in the general population). This corresponds to personality profiles of artists and the disproportionately high incidence of high scores on the related Openness to Experience factor in studies of creative personalities, thereby supporting the contention that persons creating art and appreciating art have personality traits in common.

  15. 33 CFR 100.740 - Annual Offshore Super Series Boat Race; Fort Myers Beach, FL.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. 100.740 Section 100.740 Navigation and Navigable Waters COAST GUARD... Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. (a) Regulated area. (1) The regulated...

  16. 33 CFR 100.740 - Annual Offshore Super Series Boat Race; Fort Myers Beach, FL.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. 100.740 Section 100.740 Navigation and Navigable Waters COAST GUARD... Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. (a) Regulated area. (1) The regulated...

  17. 33 CFR 100.740 - Annual Offshore Super Series Boat Race; Fort Myers Beach, FL.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. 100.740 Section 100.740 Navigation and Navigable Waters COAST GUARD... Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. (a) Regulated area. (1) The regulated...

  18. 33 CFR 100.740 - Annual Offshore Super Series Boat Race; Fort Myers Beach, FL.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. 100.740 Section 100.740 Navigation and Navigable Waters COAST GUARD... Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. (a) Regulated area. (1) The regulated...

  19. 33 CFR 100.740 - Annual Offshore Super Series Boat Race; Fort Myers Beach, FL.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. 100.740 Section 100.740 Navigation and Navigable Waters COAST GUARD... Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. (a) Regulated area. (1) The regulated...

  20. A Technical Review of the Myers-Briggs Type Indicator(tm).

    ERIC Educational Resources Information Center

    Denham, Thomas J.

    This paper describes the Myers-Briggs Type Indicator (MBTI), developed by I. Myers and K. Briggs (1940s) to assess personality type. Based on Jungian theory, the MBTI has become a tool for identifying the 16 different patterns of action into which every person fits. The 16 personality types are based on patterns of: (1) extraversion-introversion;…

  1. Myers-Briggs® Preferences and Academic Success in the First College Semester

    ERIC Educational Resources Information Center

    Sanborn, Debra K.

    2013-01-01

    This research examined aspects of Myers-Briggs® preferences and academic success in the first college semester. Academic aptitude as measured by precollege characteristics of ACT and class rank, academic performance during the first semester of college, and Myers-Briggs preference were analyzed for their significance within a learning community at…

  2. 77 FR 3324 - Release of Airport Property: Page Field, Fort Myers, FL

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-23

    ... Property: Page Field, Fort Myers, FL AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Request... properties 1.52 acres at Page Field, Fort Myers, FL from the conditions, release certain properties from all... the Lee County Port Authority, owner of Page Field, to dispose of the property for other...

  3. Making Connections in the Life and Works of Walter Dean Myers.

    ERIC Educational Resources Information Center

    Greever, Ellen A.; Austin, Patricia

    1998-01-01

    Discusses the life and works of acclaimed writer Walter Dean Myers. Describes his struggles growing up, his time in the army, his decision to become a writer, and the father/son relationships in his books. Discusses how Myers' concern for African-American heritage, identity, and pride led to biographies of Sarah Forbes and of Malcolm X. (SR)

  4. Writing through the Labyrinth of Fears: The Legacy of Walter Dean Myers

    ERIC Educational Resources Information Center

    Tatum, Alfred W.

    2015-01-01

    This commentary discusses the legacy of Walter Dean Myers in relationship to advancing writing as an intellectual tool of protection for black male teens. Multiple implications are provided for teachers who want to engage black male teens to write fearlessly to extend the legacy of Walter Dean Myers.

  5. Performance Monitoring of a Nearshore Berm at Ft. Myers Beach, Florida

    DTIC Science & Technology

    2013-08-01

    ER D C/ CH L TR - 1 3 - 1 1 Performance Monitoring of a Nearshore Berm at Ft. Myers Beach, Florida: Final Report C oa st al a n d H yd...xiv  1   Introduction... 1   2  Review of General Guidelines for Nearshore Berm Design and Performance ........................ 3  3  Overview of Ft. Myers

  6. Quantum gravity effects in Myers-Perry space-times

    NASA Astrophysics Data System (ADS)

    Litim, Daniel F.; Nikolakopoulos, Konstantinos

    2014-04-01

    We study quantum gravity effects for Myers-Perry black holes assuming that the leading contributions arise from the renormalization group evolution of Newton's coupling. Provided that gravity weakens following the asymptotic safety conjecture, we find that quantum effects lift a degeneracy of higher-dimensional black holes, and dominate over kinematical ones induced by rotation, particularly for small black hole mass, large angular momentum, and higher space-time dimensionality. Quantum-corrected space-times display inner and outer horizons, and show the existence of a black hole of smallest mass in any dimension. Ultra-spinning solutions no longer persist. Thermodynamic properties including temperature, specific heat, the Komar integrals, and aspects of black hole mechanics are studied as well. Observing a softening of the ring singularity, we also discuss the validity of classical energy conditions.

  7. Recent assessments of the Myers-Briggs Type Indicator.

    PubMed

    Carlson, J G

    1985-08-01

    The present paper focuses on approximately two dozen recent published studies that examined reliability and validity of the Myers-Briggs Type Indicator (MBTI) in clinical, counseling, and research settings. Several assessments of split-half and test-retest reliability of the standard Form F and shorter Form G of the Inventory have yielded generally satisfactory correlations for all four scales. A larger number of studies of construct validity of the MBTI have yielded support for research hypotheses in situations ranging from correlations of the MBTI with a personality inventory, to couples problems in a counseling setting, to line judgment in groups, and others. Therefore, the applications of the MBTI have been broad, although somewhat unsystematic, and with generally favorable validity assessment. Continued attempts to validate the instrument in a variety of settings are needed.

  8. Using the Myers Briggs Type Indicator--part of the solution?

    PubMed

    Allen, J

    The Myers Briggs Type Indicator, which is based on the work of Jung, is used in an infinite variety of settings to enhance learning, personal development and team building. This article describes its particular relevance to the nursing profession.

  9. Self-Selection Patterns of College Roommates as Identified by the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Anchors, W. Scott; Hale, John, Jr.

    1985-01-01

    Investigated patterns and processes by which students (N=422) made unassisted roommate pairings within residence halls using the Myers-Briggs Type Indicator. Results indicated introverts, intuitives, feelers, and perceivers each tended to self-select. (BL)

  10. Levi Myers (1767-1822): An eighteenth century Glasgow medical graduate from South Carolina.

    PubMed

    Collins, Kenneth

    2016-05-01

    Levi Myers, a native of Georgetown, South Carolina, was the first Jewish medical graduate at the University of Glasgow, obtaining the MD, in 1787. Myers had been registered for studies at the University of Edinburgh for three years, from 1785/1786 to 1787/1788, after some years of training with a physician in Charleston, South Carolina. Recent studies of Jewish life in Edinburgh have revealed the evidence of a settled group of Jewish inhabitants in the city during the last quarter of the eighteenth century, during the time of Myers' sojourn in Edinburgh and thirty years before the formal inauguration of Scotland's first Jewish community. This paper examines the context of Myers' studies in Edinburgh as an American medical student and as a Jew.

  11. Myers-Briggs Type Indicator and dental school performance.

    PubMed

    Jones, A C; Courts, F J; Sandow, P L; Watson, R E

    1997-12-01

    The Myers-Briggs Type Indicator (MBTI) was administered to 256 dental students, representing four classes, at the University of Florida College of Dentistry. The results of this psychological instrument were then correlated with overall dental school performance based on results from the National Dental Board Examinations Part I and II (NB-I, NB-II), yearly class rank, and specific academic difficulties as measured by the Student Performance Evaluation Committee. Introverted students were found to display a significantly increased performance on NB-I (p = .038) and NB-II (p = .044). They were also found, however, to demonstrate a progressively lower class rank over the four-year period than extroverted students and were more likely to experience major academic difficulties as well. Judging and sensing individuals were found to earn a higher class rank over the four-year period than perceiving and intuitive students, respectively. Perceiving students were found to exhibit major difficulties or were placed on probation more often than judging individuals. These results may prove useful in counseling students to recognize potential problems before they commence their dental education or to anticipate and address specific weaknesses during the course of their education.

  12. 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.

  13. Effects of Joint Interpretation of the Strong Interest Inventory and the Myers-Briggs Type Indicator in Career Choice.

    ERIC Educational Resources Information Center

    Katz, Louise; Joyner, John W.; Seaman, Nancy

    1999-01-01

    Students completed either the Strong Interest Inventory (n=114) or Myers-Briggs Type Indicator (n=108), both (n=99), or none (n=106). Twelve weeks after interpretation, those who completed both showed more change, specificity, or certainty in their career goal. The Myers-Briggs proved as helpful as Strong in career decision making. (SK)

  14. Relationship between Myers-Briggs Type Indicator and Gregorc Style Delineator.

    PubMed

    Harasym, P H; Leong, E J; Juschka, B B; Lucier, G E; Lorscheider, F L

    1996-06-01

    The relationship between the Myers-briggs Type Indicator and Gregorc Style Delineator, and achievement was examined by administering these instruments to 259 first-year nursing students enrolled in an introductory human anatomy and physiology course. A principal component factor analysis using a varimax rotation of the scores from the two psychometric instruments, achievement examinations and an over-all grade point average indicated that each learning style from the Gregorc Style Delineator corresponds to certain traits on the Myers-Briggs Type Indicator. An individual who had a preference for the learning style of Concrete Sequential tended to have the traits of sensing and judging on the Myers-Briggs Type Indicator, while an individual who used the learning style of Concrete Random tended to have the traits of intuition and perceiving on the Myers-Briggs Type Indicator. One who had a preference for the learning style of Abstract Sequential tended to use the trait of thinking while another who used the learning style of Abstract Random tended to have the trait of feeling. The factor analysis also indicates no relationship of any scores of the traits on the Myers-Briggs Type Indicator or learning styles of the Gregorc Style Delineator with the examination scores achieved in the human anatomy and physiology course or to the students' over-all grade point average. However, factor analysis indicates that the Myers-Briggs Type Indicator traits of Judging vs Perceiving collapsed into the Sensing vs Intuition scale, and that the Gregorc Style Delineator consists of two bipolar scales that are different from those proposed by Gregorc.

  15. Personality characteristics of hospice volunteers as measured by Myers-Briggs Type Indicator.

    PubMed

    Mitchell, C W; Shuff, I M

    1995-12-01

    A sample of hospice volunteers (n = 99) was administered the Myers-Briggs Type Indicator (Myers & McCaulley, 1985). Frequencies of types observed were compared to population sample (n = 1,105) frequencies. Results indicated that, as a whole, hospice volunteers preferred extraversion over introversion, intuition over sensing, and feeling over thinking. Analysis of four-and two-letter preference combinations also yielded statistically significant differences. Most notably, the sensing-intuitive function appeared pivotal in determining of hospice volunteering. Suggestions are offered as to why the sensing-intuition function appeared central to hospice volunteering. Results appeared consistent with Jungian personality theory.

  16. Instability in near-horizon geometries of even-dimensional Myers-Perry black holes

    NASA Astrophysics Data System (ADS)

    Tanahashi, Norihiro; Murata, Keiju

    2012-12-01

    We study the gravitational, electromagnetic and scalar field perturbations on the near-horizon geometries of the even-dimensional extremal Myers-Perry black holes. By dimensional reduction, the perturbation equations are reduced to effective equations of motion in AdS2. We find that some modes in the gravitational perturbations violate the Breitenlöhner-Freedman bound in AdS2. This result suggests that the even-dimensional (near-)extremal Myers-Perry black holes are unstable against gravitational perturbations. We also discuss implications of our results to the Kerr-CFT correspondence.

  17. Utilizing the Myers-Briggs Personality Inventory in Employee Assistance Program Workplace Seminars.

    ERIC Educational Resources Information Center

    Aviles, Christopher B.

    Social work educators are being called upon more often to deliver employee workplace seminars for community agencies on a variety of topics ranging from burnout and stress management to improving workplace communication and managing workplace conflicts. One tool that addresses workplace communication is the Myers-Briggs Type Indicator (MBTI). It…

  18. Eysenck Personality Questionnaire and Jungian Myers-Briggs Type Indicator Correlation of Extraversion-Introversion

    ERIC Educational Resources Information Center

    Steele, Robert S.; Kelly, Thomas J.

    1976-01-01

    C. G. Jung and H. J. Eysenck developed concepts of extraversion-introversion from radically different theoretical orientations. It is hypothesized that given the methods and content similarity of the Eysenck Personality Questionnaire and the Myers-Briggs Type Indicator. Extraversion-Introversion scales of the inventories will be significantly…

  19. Use of the Myers-Briggs Type Indicator (MBTI) with Physicians: A Review of the Literature.

    ERIC Educational Resources Information Center

    Howard, David H.

    This document reviews the research on the use of the Myers-Briggs Type Indicator (MBTI), with medical students and physicians. The MBTI is a paper-and-pencil instrument based on C. G. Jung's theory of personality typology. The introductory section of the review describes the MBTI and explains its dimensions (extroverted versus introverted, sensing…

  20. A Description and Evaluation of the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Stricker, Lawrence J.; Ross, John

    The Myers-Briggs Type Indicator is a Jungian-oriented self-report inventory which classifies people into dichotomous categories along four scales: extraversion-introversion, sensation-intuition, thinking-feeling, and judgment-perception. Introduced in 1942, the scoring and items have changed after several items analyses. Form F contains 51 phrase…

  1. Affirmative: In Support of Researching the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Carlson, John G.

    1989-01-01

    Updates 1985 review of Myers-Briggs Type Indicator (MBTI) noting recent criterion-based assessments of the MBTI remain largely unsystematic theoretically but generally positive. Claims more methodologically sophisticated approaches have been developed. Concludes that it seems premature to reject the MBTI owing either to its dichotomous approach to…

  2. General Psychology Assessment and Course Satisfaction Compared with the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Whitney, Gloria D.

    A study involving 211 students enrolled in eight sections of a general psychology course at Brevard Community College was conducted to determine if the course activities and testing methods were biased toward certain personality types, as defined by the Myers-Briggs Type Inventory (MBTI); and to evaluate the usefulness of the MBTI as a learning…

  3. Enhancing Student Team Effectiveness: Application of Myers-Briggs Personality Assessment in Business Courses

    ERIC Educational Resources Information Center

    Amato, Christie H.; Amato, Louis H.

    2005-01-01

    This article examines the relationship between student perceptions of team learning experience and communication style. Student group learning perceptions were evaluated and team communication style was measured using dyads derived from Myers-Briggs personality profiles. Groups containing similar personalities were classified as compatible,…

  4. Teacher's Myers-Briggs Personality Profiles: Identifying Effective Teacher Personality Traits

    ERIC Educational Resources Information Center

    Rushton, Stephen; Morgan, Jackson; Richard, Michael

    2007-01-01

    The Myers-Briggs Type Inventory (MBTI) and Beiderman Risk Taking (BRT) scale were administered to 58 teachers living in the state of Florida, USA. These teachers are considered part of prestigious group of educators who were nominated into the Florida League of Teachers by their superintendents/directors. Descriptive data includes frequency and…

  5. Differences in Myers-Briggs Personality Types among High School Band, Orchestra, and Choir Members

    ERIC Educational Resources Information Center

    MacLellan, Christin Reardon

    2011-01-01

    The purpose of this study was to explore personality type differences among high school band, string orchestra, and choir students according to ensemble membership. Participants (N = 355) were high school students who had participated in their school's band, orchestra, or choir for 1 year or more. The author administered the Myers-Briggs Type…

  6. Opposition from Christians to Myers-Briggs Personality Typing: An Analysis and Evaluation

    ERIC Educational Resources Information Center

    Lloyd, John B.

    2007-01-01

    Myers-Briggs personality typing is widely used in the Christian church as an aid to individual self-understanding and spiritual formation. However, some Christian leaders have expressed doubt about its validity in understanding human personality and also opposition to its use in nurturing spiritual growth. The aim of the work reported was to…

  7. Examination of the relationship between the Myers-Briggs Type Indicator and empathetic response.

    PubMed

    Jenkins, S J; Stephens, J C; Chew, A L; Downs, E

    1992-06-01

    This study investigated the potential relationship between the Myers-Briggs Type Indicator and level of empathetic responding. Analyses indicated that the Thinking-Feeling scale was significantly associated with ratings of empathy for 49 graduate students in counselor education. Sex and graduate grade point average were also related significantly to empathic responding. Results are discussed in terms of their significance for research.

  8. Predicting dentists' career choices using the Myers-Briggs type indicator.

    PubMed

    Grandy, T G; Westerman, G H; Ocanto, R A; Erskine, C G

    1996-02-01

    The Myers-Briggs Type Indicator is a psychological measure designed to determine personality preferences, learning styles and management styles and to assist with career choices. The authors surveyed 1,117 practicing dentists to determine if the MBTI was useful in determining which respondents were most likely to be specialists. They found no significant differences between general practitioners and specialists.

  9. Personality Characteristics of South Korean Students with Visual Impairments Using the Myers-Briggs Type Indicator

    ERIC Educational Resources Information Center

    Bak, Sunhi

    2012-01-01

    Introduction: The study presented here was designed to determine whether there were significant differences in the frequency and preference scores of personality functions and the frequency of personality types, as measured by the Myers-Briggs Type Indicator (MBTI), by gender, school level, and level of visual function, of students with visual…

  10. Correlations between the Myers-Briggs Type Indicator and the Neo Personality Inventory facets.

    PubMed

    MacDonald, D A; Anderson, P E; Tsagarakis, C I; Holland, C J

    1995-04-01

    Using data obtained from 48 male and 161 female undergraduate students in psychology, correlations between scores on the scales of the Myers-Briggs Type Indicator and the facets of the Neuroticism, Extraversion, and Openness domains of the NEO Personality Inventory were low to moderate.

  11. Two Approaches to Examining the Stability of Myers-Briggs Type Indicator Scores

    ERIC Educational Resources Information Center

    Salter, Daniel W.; Forney, Deanna S.; Evans, Nancy J.

    2005-01-01

    In this study, two approaches are used to assess the stability of Myers-Briggs Type Indicator scores across 3 administrations (N = 231): longitudinal configural frequency analysis with categorical scores and generalizability theory with the Preference Clarity Indices and continuous scores. The results are generally positive. Evaluation of…

  12. Myers-Briggs Type Indicator Score Reliability across Studies: A Meta-Analytic Reliability.

    ERIC Educational Resources Information Center

    Capraro, Robert M.; Capraro, Mary Margaret

    2002-01-01

    Submitted the Myers-Briggs Type Indicator (MBTI) to a descriptive reliability generalization analysis to characterize the variability of measurement error in MBTI scores across administrations. In general the MBTI and its scales yielded scores with strong internal consistency and test-retest reliability estimates. (SLD)

  13. A Higher Order Analysis of the Factor Structure of the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Johnson, William L.; Mauzey, Edward; Johnson, Annabel M.; Murphy, Stanley D.; Zimmerman, Kurt J.

    2001-01-01

    Examines the higher order structure of Form G of the Myers Briggs Type Indicator. A third order component analysis of a sample (N=926) found two higher order components. This higher order analysis contributes to the research literature pertaining to the generalized structure of the personality measure. (Contains 44 references and 1 table.) (GCP)

  14. Interpreting the Myers-Briggs Type Indicator to Help Clients in Understanding Their Strong Interest Inventory.

    ERIC Educational Resources Information Center

    Healy, Charles C.

    2000-01-01

    Scores of 370 adults on the Myers Briggs Type Indicator (MBTI) were correlated with General Occupational Theme (GOT) scores on the Strong Interest Inventory. Simple categorical MBTI scores were related modestly to Strong GOT scores as expected; individual continuous scores did not account for more variance in GOT than in categorical scores. (SK)

  15. Relationship Between Personality Types on the Strong-Campbell and Myers-Briggs Instruments.

    ERIC Educational Resources Information Center

    Dillon, Michael; Weissman, Shel

    1987-01-01

    Examined relationship between Holland's personality types as measured by the Strong-Campbell Interest Inventory and Jung's personality types as measured by the Myers-Briggs Type Indicator. College students' (N=394) responses to the two instruments revealed significant associations between certain types based on interests and preferences.…

  16. No ISCOs in Charged Myers Perry Spacetimes by Measuring Lyapunov Exponent

    NASA Astrophysics Data System (ADS)

    Pradhan, Parthapratim

    2015-01-01

    By computing coordinate time Lyapunov exponent, we prove that for more than four spacetime dimensions (N ≥ 3), there are no Innermost Stable Circular Orbit (ISCO) in charged Myers Perry blackhole spacetime.Using it, we show that the instability of equatorial circular geodesics, both massive and massless particles for such types of blackhole space-times.

  17. Failure of the Ingard-Myers boundary condition for a lined duct: an experimental investigation.

    PubMed

    Renou, Ygaäl; Aurégan, Yves

    2011-07-01

    This paper deals with experimental investigation of the lined wall boundary condition in flow duct applications such as aircraft engine systems or automobile mufflers. A first experiment, based on a microphone array located in the liner test section, is carried out in order to extract the axial wavenumbers with the help of an "high-accurate" singular value decomposition Prony-like algorithm. The experimental axial wavenumbers are then used to provide the lined wall impedance for both downstream and upstream acoustic propagation by means of a straightforward impedance education method involving the classical Ingard-Myers boundary condition. The results show that the Ingard-Myers boundary condition fails to predict with accuracy the acoustic behavior in a lined duct with flow. An effective lined wall impedance, valid whatever the direction of acoustic propagation, can be suitably found from experimental axial wavenumbers and a modified version of the Ingard-Myers condition with the form inspired from a previous theoretical study [Aurégan et al., J. Acoust. Soc. Am. 109, 59-64 (2001)]. In a second experiment, the scattering matrix of the liner test section is measured and is then compared to the predicted scattering matrix using the multimodal approach and the lined wall impedances previously deduced. A large discrepancy is observed between the measured and the predicted scattering coefficients that confirms the poor accuracy provided from the Ingard-Myers boundary condition widely used in lined duct applications.

  18. Myers-Briggs Attitude Typology: The Influence of Birth Order with Other Family Variables.

    ERIC Educational Resources Information Center

    Stansbury, Virginia K.; Coll, Kenneth M.

    1998-01-01

    Investigates the influence of birth order with parenting style, age spacing, gender, and socioeconomic status on the Myers-Briggs attitude scales of Extroversion/Introversion and Judging/Perceiving. Results indicate that age spacing interacted with birth order to influence Extroversion/Introversion scores. Parenting style and gender interacted…

  19. The Complex and Elusive Nature of Religious Prosociality: Reply to Myers (2012) and Saroglou (2012)

    ERIC Educational Resources Information Center

    Galen, Luke W.

    2012-01-01

    This reply explores issues raised in comments by Myers (2012) and Saroglou (2012) on Galen (2012) regarding whether religiosity has any influence on prosociality. Areas of contention include (a) the distinction between religious belief and other influences, mainly the socialization effects of group behavior; (b) whether behavior largely restricted…

  20. The Myers-Briggs Type Indicator: A Measure for Individuals and Groups.

    ERIC Educational Resources Information Center

    McCaulley, Mary H.

    1990-01-01

    Describes Myers-Briggs Type Indicator (MBTI). Looks at history and development of the MBTI, characteristics, scores, Jung's theory of lifelong development, the dynamic interaction of the four functions measured by the MBTI, the construction of the MBTI, use with groups, how to use type tables, and use of the MBTI in career counseling. (NB)

  1. Essentials of Myers-Briggs Type Indicator[R] Assessment. Essentials of Psychological Assessment Series.

    ERIC Educational Resources Information Center

    Quenk, Naomi L.

    This book provides step-by-step guidance on the administration, scoring, and interpretation of the Myers-Briggs Type Indicator[R] (MBTI). The book also contains assessment of the test's strengths and weaknesses, advice on its clinical applications, and several case reports. The chapters are: (1) "Overview"; (2) "How To Administer…

  2. Using the Myers-Briggs Type Indicator in the Social Work Classroom.

    ERIC Educational Resources Information Center

    Aviles, Christopher B.

    The Myers-Briggs Type Indicator (MBTI) is one of the most popular measures of personality available today and has been taken by over 12 million people. The MBTI has been successfully utilized for personal and marriage counseling, conflict and stress management, and understanding learning styles. It is perfect for the social work classroom because…

  3. Queens University of Charlotte--Myers Park Traditional Elementary School Partnership

    ERIC Educational Resources Information Center

    Horn, Suzanne E.; Wooten-Thornburg, Amy; Bonner, Paul; Boyd, Irma; Gerald, Jamie; Perkins, Shavonn; Mercer, Elizabeth; Hunter, Laura

    2010-01-01

    Great work can be accomplished with little budgets and big dreams and desires for increased student achievement. The focus of the Queens University of Charlotte and Myers Park Traditional School (MPTS) partnership was excellent teacher development that centered on learning as a community of teachers (both pre-service and in-service). What they…

  4. Survey of Librarians Using the Myers-Briggs Type Indicator (Form G Self-Scorable).

    ERIC Educational Resources Information Center

    Johns, Alan

    A survey conducted in February 1990 asked 100 librarians to respond to a mailed Myers-Briggs Type Indicator (MBTI), a widely used personality survey that determines Jungian personality types. The results of the MBTI can be applied to building work teams in the library. Forty-eight librarians responded to the survey. Their responses were tallied…

  5. The Myers-Briggs Type Indicator and the Teaching-Learning Process.

    ERIC Educational Resources Information Center

    McCaulley, Mary H.

    The Myers-Briggs Type Indicator (MBTI) was developed specifically to make possible the implementation of Carl Jung's theory of type and is concerned mainly with conscious elements of the personality. It assumes that to function well, an individual must have a well-developed system for perception and a well-developed system for making decisions or…

  6. 75 FR 37521 - Culturally Significant Objects Imported for Exhibition Determinations: “Eton College Myers...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-29

    ... Culturally Significant Objects Imported for Exhibition Determinations: ``Eton College Myers Collection at Johns Hopkins University'' SUMMARY: Notice is hereby given of the following determinations: Pursuant to... 15, 2003 , I hereby determine that the objects to be included in the exhibition ``Eton College...

  7. Painleve-gullstrand-type Coordinates for the Five-dimensional Myers-Perry Black Hole

    NASA Technical Reports Server (NTRS)

    Finch, Tehani Kahi

    2013-01-01

    The Painleve-Gullstrand coordinates provide a convenient framework for presenting the Schwarzschild geometry because of their flat constant-time hypersurfaces, and the fact that they are free of coordinate singularities outside r=0. Generalizations of Painlev´e-Gullstrand coordinates suitable for the Kerr geometry have been presented by Doran and Nat´ario. These coordinate systems feature a time coordinate identical to the proper time of zero-angular-momentum observers that are dropped from infinity. Here, the methods of Doran and Nat´ario are extended to the five-dimensional rotating black hole found by Myers and Perry. The result is a new formulation of the Myers-Perry metric. The properties and physical significance of these new coordinates are discussed.

  8. Over-representation of Myers Briggs Type Indicator introversion in social phobia patients.

    PubMed

    Janowsky, D S; Morter, S; Tancer, M

    2000-01-01

    The purpose of this study is to profile the personalities of patients with social phobia. Sixteen patients with social phobia were compared with a normative population of 55,971, and with 24 hospitalized Major Depressive Disorder inpatients, using the Myers Briggs Type Indicator. The Myers Briggs Type Indicator, a popular personality survey, divides individuals into eight categories: Extroverts versus Introverts, Sensors versus Intuitives, Thinkers versus Feelers, and Judgers versus Perceivers. Social phobia patients were significantly more often Introverts (93.7%) than were subjects in the normative population (46.2%). In addition, using continuous scores, the social phobia patients scored as significantly more introverted than did the patients with Major Depressive Disorder, who also scored as Introverted. Introversion is a major component of social phobia, and this observation may have both etiological and therapeutic significance.

  9. Bipolarity in Jungian type theory and the Myers-Briggs Type Indicator.

    PubMed

    Girelli, S A; Stake, J E

    1993-04-01

    The standard form of the Myers-Briggs Type Indicator (MBTI; Myers & McCaulley, 1985) was constructed to measure introversion/extroversion, sensing/intuiting, and thinking/feeling as single, bipolar dimensions. We tested this assumption of bipolarity with a Likert form of the MBTI that allowed for the independent assessment of each attitude and function. A total of 106 female and 59 male undergraduate and graduate students completed the standard and Likert MBTI forms approximately 3 weeks apart. Evidence for the bipolarity of the introversion/extroversion dimension was weak, and findings did not support the bipolarity of the sensing/intuiting or thinking/feeling dimensions. Results provide evidence that high negative correlations within MBTI dimensions are an artifact of its forced-choice format. Implications of the findings for typology measurement are discussed.

  10. Use of the Myers-Briggs Type Indicator to develop a continuing education department.

    PubMed

    Schoessler, M; Conedera, F; Bell, L F; Marshall, D; Gilson, M

    1993-01-01

    Myers-Briggs concepts are useful for understanding and managing individual and group strengths, preferences, and "blind spots." Requirements of the work to be accomplished can be matched to the strengths and preferences of the individual or group. Work groups can be selected to enhance individual strengths and to counterbalance blind spots. This article describes the experience of one hospital-based continuing education department that uses the Myers-Briggs Personality Trait Inventory to explore department members' strengths and preferences. Understanding individual preferences has helped group members to understand, anticipate, and work with one another. The ideal mix of profiles challenges and stimulates both the individual and the department. Maximizing diversity increases the potential for conflict between individuals with opposite preferences; recognizing strengths and blind spots, willingness to talk about work style differences, and a little humor all make peaceful coexistence possible.

  11. Relationship of Myers Briggs type indicator personality characteristics to suicidality in affective disorder patients.

    PubMed

    Janowsky, David S; Morter, Shirley; Hong, Liyi

    2002-01-01

    The current study characterized the Myers Briggs Type Indicator (MBTI) personality profiles of 64 suicidal and 30 non-suicidal psychiatric inpatients with affective disorder diagnoses. The MBTI divides individuals categorically into eight personality preferences (Extroverted and Introverted, Sensing and Intuitive, Thinking and Feeling, and Judging and Perceiving). Compared to the group of non-suicidal affective disorder patients, suicidal affective disorder patients were significantly more Introverted and Perceiving using ANCOVA analyses, and significantly more Introverted alone using Chi Square analyses.

  12. Reexamination of relations between the Myers-Briggs type indicator and field dependence-independence.

    PubMed

    Schmidt, C P; McCutcheon, J W

    1988-12-01

    The Group Embedded Figures Test and the Myers-Briggs Type Indicator were administered to 210 undergraduate and graduate students. Bivariate relations between the embedded figures test and the Indicator scales of Extraversion-Introversion (EI), Thinking-Feeling (TF), and Judgment-Perception (JP) were nonsignificant while the relation between scores on embedded figures and Sensing-Intuition (SN) was statistically significant. ESFP, ISFJ, and ESFJ types were significantly more field-dependent than the INFP and ENTP types.

  13. Hawking Radiation of Scalar and Vector Particles from 5D Myers-Perry Black Holes

    NASA Astrophysics Data System (ADS)

    Jusufi, Kimet; Övgün, Ali

    2017-02-01

    In the present paper we explore the Hawking radiation as a quantum tunneling effect from a rotating 5 dimensional Myers-Perry black hole (5D-MPBH) with two independent angular momentum components. First, we investigate the Hawking temperature by considering the tunneling of massive scalar particles and spin-1 vector particles from the 5D-MPBH in the Painlevé coordinates and then in the corotating frames. More specifically, we solve the Klein-Gordon and Proca equations by applying the WKB method and Hamilton-Jacobi equation in both cases. Finally, we recover the Hawking temperature and show that coordinates systems do not affect the Hawking temperature.

  14. Communicator image and Myers-Briggs Type Indicator extraversion-introversion.

    PubMed

    Opt, Susan K; Loffredo, Donald A

    2003-11-01

    This study is an examination of the relationship between communicator image and Myers-Briggs Type Indicator (MBTI) dimensions of extraversion-introversion. The authors found that individuals who prefer extraversion tend to have a more positive communicator image than those who prefer introversion. The results of this study support other research results showing that personality preferences differ in communication behaviors and traits, which could have implications for the individual's comfort and success in society. Results of this research also support the contention that communication behavior has biological aspects.

  15. The upper bound of radiation energy in the Myers-Perry black hole collision

    NASA Astrophysics Data System (ADS)

    Gwak, Bogeun; Lee, Bum-Hoon

    2016-07-01

    We have investigated the upper bound of the radiation energy in the head-on collision of two Myers-Perry black holes. Initially, the two black holes are far away from each other, and they become one black hole after the collision. We have obtained the upper bound of the radiation energy thermodynamically allowed in the process. The upper bound of the radiation energy is obtained in general dimensions. The radiation bound depends on the alignments of rotating axes for a given initial condition due to spin-spin interaction. We have found that the collision may not be occurred for a initially ultra-spinning black hole.

  16. Nonintellective intelligence and personality: variance shared by the Constructive Thinking Inventory and the Myers-Briggs Type Indicator.

    PubMed

    Spirrison, C L; Gordy, C C

    1994-04-01

    The Constructive Thinking Inventory (CTI; Epstein & Meier, 1989), a recently developed scale assessing patterns of habitual everyday thoughts, was compared with the Myers-Briggs Type Indicator (MBTI; Myers & McCaulley, 1985) to ascertain areas of common variance. CTI and MBTI data from 65 men and 109 women were evaluated. A series of standard multiple regression procedures indicated that, in most instances, CTI scales were predictive of MBTI continuous scores, although gender mediated several of the effects. The results suggest that the variance assessed by the CTI is similar to that addressed by traditional measures of personality but that the CTI partitions the variance in an atypical, yet coherent, manner.

  17. A partial replication of Lippin (1990) using the Myers-Briggs type indicator with a sample of female prisoners.

    PubMed

    Long, C K; Lenoir, C; Phung, T; Witherspoon, A D

    1995-10-01

    A sample of 108 women incarcerated in a state prison who volunteered to participate in an employment seminar were given the Myers-Briggs Type Indicator. Comparison of the distribution of types here and in Myers and McCaulley's 1985 sample using a Selection Ratio Type Table for analysis indicated an overrepresentation of ISTJ, ISFJ, and ISTP. The ESFP and ESFJ types were underrepresented. Further analysis of the types and the relationship to criminal offense was not significant. Results are compared with those of Lippin from 1990.

  18. Myers-Pospelov model as an ensemble of Pais-Uhlenbeck oscillators: unitarity and Lorentz invariance violation

    NASA Astrophysics Data System (ADS)

    Lopez-Sarrion, Justo; Reyes, Carlos M.

    2013-04-01

    We study a generalization of the Pais-Uhlenbeck oscillator for fermionic variables. Next, we consider an ensemble of these oscillators and we identify a particular case of the Myers-Pospelov model which is relevant for effective theories of quantum gravity. Finally, by taking advantage of this connection, we analyze, for this model, unitarity at one loop order in the low energy regime where no ghost states can be created on-shell. This energy regime is the relevant one when we consider the Myers-Pospelov model as a true effective theory coming from a new space-time structure.

  19. The relationship between life satisfaction, self-consciousness, and the Myers-Briggs type inventory dimensions.

    PubMed

    Harrington, R; Loffredo, D A

    2001-07-01

    The study was an investigation of the relationship between psychological well-being, life satisfaction, self-consciousness, and the four Myers-Briggs Type Indicator dimensions (MBTI; I. B. Myers & M. H. McCaulley, 1985). The participants were 97 college students (79 women and 18 men whose mean age was 31.4 years). All the students were administered four instruments, the Psychological Well-Being Inventory (C. D. Ryff, 1989), the Satisfaction With Life Scale (E. Diener, R. A. Emmons, R. J. Larsen, & S. Griffin, 1985), the Self-Consciousness Scale-Revised (M. F. Scheier & C. S. Carver, 1985), and the MBTI (Form G Self-Scoring). MANOVAs revealed significant differences on three of the four dimensions of the MBTI with extraverts showing higher psychological well-being and life satisfaction and lower self-consciousness than introverts. Intuition types scored higher in psychological well-being and lower in self-consciousness than Sensing types. Judging types scored higher in psychological well-being than Perceiving types. Correlational analyses showed that most dimensions of psychological well-being were negatively related to self-consciousness. The relationship between life satisfaction and personality variables is discussed.

  20. A Review of the Myers-Briggs Type Inventory: A Potential Training Tool for Human Services Organizations.

    ERIC Educational Resources Information Center

    Aviles, Christopher B.

    The Myers-Briggs Type Inventory (MBTI) can be helpful in personal, career, and marriage counseling; conflict and stress management; team building; and understanding managerial and learning styles. It has great potential to be utilized in human services organizations for training purposes because it offers a way to conceptualize employee…

  1. The Multifactorial Nature of Extraversion-Introversion in the Myers-Briggs Type Indicator and Eysenck Personality Inventory.

    ERIC Educational Resources Information Center

    Sipps, Gary J.; Alexander, Ralph A.

    1987-01-01

    The construct validity of extraversion-introversion was explored, as measured by the Myers Briggs Type Indicator (MBTI) and the Eysenck Personality Inventory. Findings supported the complexity of extraversion-introversion. Two MBTI scales, Extraversion Introversion and Judging Perceiving, were factorially valid measures of impulsivity…

  2. Considering Personality Type in Adult Learning: Using the Myers-Briggs Type Indicator in Instructor Preparation at PricewaterhouseCoopers

    ERIC Educational Resources Information Center

    Daisley, Richard J.

    2011-01-01

    This article explores the feasibility of using the Myers-Briggs Type Indicator (MBTI) as a framework for instructor development in a professional services training environment. It explores the consistency of MBTI with common adult learning theory, addresses questions on MBTI's reliability and validity, and explores the applicability of MBTI to the…

  3. The Myers-Briggs Type Indicator as a Tool to Facilitate Learning Outcomes for Team Building in the Classroom

    ERIC Educational Resources Information Center

    Berry, Priscilla; Wood, Cindy; Thornton, Barry

    2007-01-01

    Globalization and domestic competition are forcing businesses to rethink the human resources utilization process, and one method for considering again this challenge is creating a team culture. One key to this process for human resources development is the understanding of how to create the most successful teams. The use of the Myers-Briggs Type…

  4. A Longitudinal Study of Learning Style Preferences on the Myers-Briggs Type Indicator and Learning Style Inventory

    ERIC Educational Resources Information Center

    Salter, Daniel W.; Evans, Nancy J.; Forney, Deanna S.

    2006-01-01

    The stability of learning style preferences, as measured by the Myers-Briggs Type Indicator (MBTI) and Learning Style Inventory (LSI), was examined using a configural frequency analysis of differences. Thirteen cohorts (222 graduate students) completed the instruments 3 times during their programs. Implications for use of learning style measures…

  5. Incremental Validity of the Myers-Briggs Type Indicator in Predicting Academic Major Selection of Undecided University Students

    ERIC Educational Resources Information Center

    Pulver, Chad A.; Kelly, Kevin R.

    2008-01-01

    This study examined the incremental validity of the Myers-Briggs Type Indicator (MBTI) as a predictor of academic major choice. Undecided university students were administered the MBTI and Strong Interest Inventory (SII). Their academic major choice was recorded at the end of their fourth semester and categorized as realistic, investigative,…

  6. Log-Linear Techniques for the Analysis of Categorical Data: A Demonstration with the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Salter, Daniel W.

    2003-01-01

    Log-linear analysis (LLA) techniques for categorical variables are demonstrated and evaluated using data from the Myers-Briggs Type Indicator. Symmetrical LLA and asymmetrical LLA address questions of association and inference, respectively. Configural frequency analysis is examined as a strategy for whole types research. LLA approaches seem…

  7. 74 FR 16384 - Myers, Max J.; Perkins, Jr., Melvin H.; Brockman, Carla D.; Forbes, Scott H.; Notice of Filing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2009-04-10

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Myers, Max J.; Perkins, Jr., Melvin H.; Brockman, Carla D.; Forbes, Scott H.; Notice of Filing April 3, 2009. Take notice that on April 1, 2009, the above applicants, submitted...

  8. Harlem Connections: Teaching Walter Dean Myers'"Scorpions" with Paul Laurence Dunbar's "The Sport of the Gods."

    ERIC Educational Resources Information Center

    West, Mark I.

    1999-01-01

    Describes how the author, in a course titled "Literature for Adolescents" paired Walter Dean Myers' 1988 young adult novel, "Scorpions," with Paul Laurence Dunbar's 1902 novel for adults, "The Sport of the Gods." Describes student readers' responses to the pair of books, which focus on the difficulties of growing up…

  9. Comparing University Students and Community College Students Learning Styles and Myers-Briggs Type Indicator (MBTI) Preferences.

    ERIC Educational Resources Information Center

    Herbster, Douglas L.; And Others

    This document reports on a study to determine if there is a pattern between specific learning styles and Myers-Briggs Type Indicator preferences. The learning style inventory used for the study, "The Teaching and Learning Styles Survey for Adolescents (TLC)," is based on Jungian style preferences--thinker, feeler, sensor, and…

  10. The Myers-Briggs Type Indicator[R] and Mainstream Psychology: Analysis and Evaluation of an Unresolved Hostility

    ERIC Educational Resources Information Center

    Lloyd, John B.

    2012-01-01

    The Myers-Briggs Type Indicator (MBTI[R]) is widely used as a staff-development tool in the business and voluntary sectors. Its Psychological Type approach is found to be a valuable aid to understanding self and others and thus to enhancing effective team-working. This continuing and growing popularity is surprising in view of the disdain with…

  11. 76 FR 79701 - Bristol-Myers Squibb Co. et al.; Withdrawal of Approval of 70 New Drug Applications and 97...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-22

    ... is still in effect. FOR FURTHER INFORMATION CONTACT: Florine Purdie, Center for Drug Evaluation and... HUMAN SERVICES Food and Drug Administration Bristol-Myers Squibb Co. et al.; Withdrawal of Approval of 70 New Drug Applications and 97 Abbreviated New Drug Applications; Correction AGENCY: Food and...

  12. Gathering the Force Fields of Energy in Student Affairs: Staff Development Using the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    McNickle, Phyllis J.; Veltman, Gayle C.

    1988-01-01

    Discusses application of the Myers-Briggs Type Indicator (MBTI) as a staff development tool at Wichita State University in Kansas. Describes procedure for implementing the MBTI in staff development and presents results from MBTI use with 39 staff members. Recommends that student affairs divisions at other institutions use the MBTI in staff…

  13. Third Response to "The Teacher as a Service Professional," by Donald A. Myers: Defining "Professionalism" Does Not Make It So

    ERIC Educational Resources Information Center

    Houston, W. Robert

    2008-01-01

    It has been generally accepted that teaching does not meet the criteria of a profession, at least as exemplified by the more mature professions of medicine and law (Abbott, 1988; Darling-Hammond & Youngs, 2002; Etzioni, 1969; Howsam, Corrigan, Denemark, & Nash, 1976). Teaching is most often referred to as a semiprofession; Myers's (2008 [this…

  14. Water quality study at the Congaree Swamp National monument of Myers Creek, Reeves Creek and Toms Creek. Technical report

    SciTech Connect

    Rikard, M.

    1991-11-01

    The Congaree Swamp National Monument is one of the last significant near virgin tracts of bottom land hardwood forests in the Southeast United States. The study documents a water quality monitoring program on Myers Creek, Reeves Creek and Toms Creek. Basic water quality parameters were analyzed. High levels of aluminum and iron were found, and recommendations were made for further monitoring.

  15. 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

  16. 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.

  17. Bimodal score distributions and the Myers-Briggs Type Indicator: fact or artifact?

    PubMed

    Bess, Tammy L; Harvey, Robert J

    2002-02-01

    We examined Myers-Briggs Type Indicator (MBTI) score distributions computed using item response theory (IRT) to assess the generalizability of earlier bimodality reports that have been cited in support of the "type" versus "trait" view of personality. Using the BILOG IRT program to score a sample of approximately 12,000 individuals who participated in leadership development programs, theta score distributions for the 4 dimensions of the MBTI computed using 10 (the BILOG default) versus 50 quadrature points were compared. Results indicated that past reports of bimodality were artifacts caused by BILOG's default use of a small number of quadrature points; when larger numbers of points were used, score distributions became strongly center-weighted. Although our findings are not supportive of the "type"-based hypothesis, the extremely high correlations between theta scores (rs > .996) suggest that no practical differences would be expected as a function of the number-of-quadrature-points decision.

  18. Myers-Briggs psychological type and achievement in anatomy and physiology.

    PubMed

    Harasym, P H; Leong, E J; Juschka, B B; Lucier, G E; Lorscheider, F L

    1995-06-01

    Results from the Myers-Briggs Type Indicator (MBTI) for 259 nursing students were compared with their achievement on examinations in an undergraduate course in anatomy and physiology. Factor analysis demonstrated that no relationship existed between any of the eight individual personality traits purported to be measured by MBTI (i.e., E, Extrovert; I, Introvert; S, Sensing; N, Intuition; T, Thinking; F, Feeling; J, Judging; P, Perceiving) and examination scores in this course. The analysis also showed that the bipolar scales S vs. N and J vs. P collapsed into a single bipolar scale (S/J vs. N/P). This means that the MBTI is only capable of measuring three bipolar scales of personality traits instead of four scales as currently claimed. Contrary to other findings, results from an analysis of variance revealed no meaningful relationship between course achievement and psychological types.

  19. Relationship between Myers-Briggs psychological traits and use of course objectives in anatomy and physiology.

    PubMed

    Harasym, P H; Leong, E J; Lucier, G E; Lorscheider, F L

    1996-06-01

    The results from the Myers-Briggs Type Indicator (MBTI), which identified preferred psychological traits for 131 nursing students, were compared to their usage levels of course objectives in an undergraduate course in anatomy and physiology. The three usage levels (user, occasional user, and nonuser) were also compared to exam scores in the course, overall grade point averages (GPA) in first-year nursing, and the various psychological traits measured by the MBTI. A multivariate analysis of variance (MANOVA) indicated that users of objectives achieved significantly higher exam scores and maintained a higher GPA than occasional and nonusers. The MANOVA also indicated that users of course objectives preferred a sensing judging modality, whereas nonusers preferred an intuiting perceiving style to guide their studying and learning.

  20. Stable bound orbits in six-dimensional Myers-Perry black holes

    NASA Astrophysics Data System (ADS)

    Igata, Takahisa

    2015-07-01

    The existence of stable bound orbits of test particles is one of the most characteristic properties in black hole spacetimes. In higher-dimensional black holes, due to the dependence of gravity on the spacetime dimensions, there is no stable bound orbit balanced by Newtonian gravitational monopole force and centrifugal force, although this balance occurs in the four-dimensional Kerr black hole. In this paper, however, the existence of stable bound orbits of massive and massless particles is shown in six-dimensional singly spinning Myers-Perry black holes with a value of the spin parameter larger than a critical value. The innermost stable bound orbits and the outermost stable bound orbits are found on the rotational axis.

  1. Perturbations of near-horizon geometries and instabilities of Myers-Perry black holes

    NASA Astrophysics Data System (ADS)

    Durkee, Mark N.; Reall, Harvey S.

    2011-05-01

    It is shown that the equations governing linearized gravitational (or electromagnetic) perturbations of the near-horizon geometry of any known extreme vacuum black hole (allowing for a cosmological constant) can be Kaluza-Klein reduced to give the equation of motion of a charged scalar field in AdS2 with an electric field. One can define an effective Breitenlöhner-Freedman bound for such a field. We conjecture that if a perturbation preserves certain symmetries then a violation of this bound should imply an instability of the full black hole solution. Evidence in favor of this conjecture is provided by the extreme Kerr solution and extreme cohomogeneity-1 Myers-Perry solution. In the latter case, we predict an instability in seven or more dimensions and, in five dimensions, we present results for operator conformal weights assuming the existence of a conformal field theory dual. We sketch a proof of our conjecture for scalar field perturbations.

  2. Astyanax hastatus Myers, 1928 (Teleostei, Characidae): A new species complex within the genus Astyanax?

    PubMed Central

    2009-01-01

    Four populations of Astyanax hastatus Myers 1928 from the Guapimirim River basin (Rio de Janeiro State) were analyzed and three distinct cytotypes identified. These cytotypes presented 2n = 50 chromosomes, with 4M+8SM+10ST+28A (Cytotype A), 8M+10SM+14ST+18A (Cytotype B), 6M+8SM+4ST+32A (Cytotype C) and scanty heterochromatin, mainly located throughout pericentromeric regions of several chromosomal pairs. No homologies with the As-51 satellite DNA were observed in the three cytotypes, although all of them presented multiple 18S rDNA sites, as detected by both silver nitrate staining and FISH (fluorescent in situ hybridization). The application of the term “species complex” in Astyanax is discussed from a cytotaxonomic viewpoint. PMID:21637509

  3. 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.

  4. 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.

  5. Algenol in Fort Myers, Fla. Among Winners of the 20th Annual Presidential Green Chemistry Challenge Awards/Innovative technologies tackle climate change, water, and chemical issues

    EPA Pesticide Factsheets

    ATLANTA - Algenol in Fort Myers, Florida is among the winners to be recognized by the U.S. Environmental Protection Agency (EPA) for landmark green chemistry technologies developed by industrial pioneers and leading scientists that turn climate risk

  6. 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

  7. 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.

  8. Affirming Psychological Science--For Students, Teachers, and the Larger World: An Interview With David G. Myers

    ERIC Educational Resources Information Center

    Miller, Jr., Harold L.

    2005-01-01

    David G. Myers received a BA in chemistry, magna cum laude from Whitworth College and an MA and PhD in psychology from the University of Iowa. Since 1982 he has been the John Dirk Werkman Professor of Psychology at Hope College. He is best known for his authorship of Psychology (2004), now in its 7th edition, and Social Psychology (2005a), now in…

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. [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.

  15. 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

  16. Personality types of family practice residents as measured by the Myers-Briggs type indicator.

    PubMed

    Harris, D L; Ebbert, P

    1985-01-01

    This study was initiated to test the hypothesis that individuals currently choosing family practice as a career are likely to have different personality types than those who previously pursued general practice. Incoming residents to the University of Utah Family Practice Residency Program were compared to a group of private primary care physicians serving rural areas. Personality types were determined by administering the Myers-Briggs Type Indicator to both groups. Results showed that the current resident group differed significantly from the primary care physician group and that the residents' personality types were similar to personality types of faculty in other studies. This raises the concern that many family practice residents may not choose to practice in underserved areas. Further studies need to follow personality types through medical school and residency training and into practice to help determine which prospective physicians are likely to choose a primary care career and a rural practice. This information may be useful in health manpower planning and in examining admissions policies of medical schools and residencies.

  17. The association between Myers-Briggs Type Indicator and Psychiatry as the specialty choice

    PubMed Central

    Richard, George; Durkin, Martin

    2016-01-01

    Objectives The purpose of this pilot study is to examine the association between Myers-Briggs Type Indicator (MBTI) and prospective psychiatry residents. Methods Forty-six American medical schools were contacted and asked to participate in this study. Data were collected and an aggregated list was compiled that included the following information: date of MBTI administration, academic year, MBTI form/version, residency match information and student demographic information. The data includes 835 American medical students who completed the MBTI survey and matched into a residency training program in the United States. All analyses were performed using R 3.1.2. Results The probability of an introvert matching to a psychiatry residency is no different than that of an extravert (p= 0.30). The probability of an intuitive individual matching to a psychiatry residency is no different than that of a sensing type (p=0.20). The probability of a feeling type matching to a psychiatry residency is no different than that of a thinking type (p= 0.50). The probability of a perceiving type matching to a psychiatry residency is no different than that of a judging type (p= 0.60). Conclusions Further analyses may elicit more accurate information regarding the personality profile of prospective psychiatry residents. The improvement in communication, team dynamics, mentor-mentee relationships and reduction in workplace conflicts are possible with the awareness of MBTI personality profiles. PMID:26851600

  18. Health-hazard evaluation report HETA 91-090-2175, Caisson Platoon, Ft Myer, Virginia

    SciTech Connect

    Echt, A.

    1992-01-01

    In response to a request from an industrial hygiene technician with the Walter Reed Army Medical Center, an investigation was made of possible hazardous working conditions at the Caisson Platoon (SIC-0752), Ft. Myer, Virginia. The Caisson Platoon had 34 horses used in ceremonies. Specific concern was expressed about exposure of soldiers to air contaminants while cleaning the stables, levelling the grain bin, and working in the tack room. Exposures experienced by blacksmiths in the execution of their duties were also monitored. The author concludes that soldiers dyeing leather in the tack room were exposed to methylene-chloride (75092) and 2-ethoxyethanol (110805) above the NIOSH recommended exposure limits. Soldiers cleaning the stables were not overexposed to nuisance dust or endotoxin. Soldiers involved in levelling grain in the grain bin were exposed to grain dust for a brief period of nearly 7 times the 8 hour recommended exposure limit of 4mg/cu m. The exposures in the tack room could be reduced through the substitution of less hazardous ingredients in leather dyes, lacquers, and spray paints or through the use of local exhaust ventilation. The grain dust exposure can be controlled through the use of engineering controls, such as a vibratory shaker applied to the outside of the bin thus eliminating the need to enter the grain bin to level the grain. Local exhaust ventilation should be provided for welding operations in the blacksmith shop.

  19. Myers-Perry black holes with scalar hair and a mass gap: Unequal spins

    NASA Astrophysics Data System (ADS)

    Herdeiro, Carlos; Kunz, Jutta; Radu, Eugen; Subagyo, Bintoro

    2015-09-01

    We construct rotating boson stars and Myers-Perry black holes with scalar hair (MPBHsSH) as fully non-linear solutions of five dimensional Einstein gravity minimally coupled to a complex, massive scalar field. The MPBHsSH are, in general, regular on and outside the horizon, asymptotically flat, and possess angular momentum in a single rotation plane. They are supported by rotation and have no static limit. Such hairy BHs may be thought of as bound states of boson stars and singly spinning, vacuum MPBHs and inherit properties of both these building blocks. When the horizon area shrinks to zero, the solutions reduce to (in a single plane) rotating boson stars; but the extremal limit also yields a zero area horizon, as for singly spinning MPBHs. Similarly to the case of equal angular momenta, and in contrast to Kerr black holes with scalar hair, singly spinning MPBHsSH are disconnected from the vacuum black holes, due to a mass gap. We observe that for the general case, with two unequal angular momenta, the equilibrium condition for the existence of MPBHsSH is w =m1Ω1 +m2Ω2, where Ωi are the horizon angular velocities in the two independent rotation planes and w ,mi, i = 1 , 2, are the scalar field's frequency and azimuthal harmonic indices.

  20. Geodesic motion in equal angular momenta Myers-Perry-AdS spacetimes

    NASA Astrophysics Data System (ADS)

    Delsate, Térence; Rocha, Jorge V.; Santarelli, Raphael

    2015-10-01

    We study the geodesic motion of massive and massless test particles in the background of equally spinning Myers-Perry-anti-de Sitter (AdS) black holes in five dimensions. By adopting a coordinate system that makes manifest the cohomogeneity-1 property of these spacetimes, the equations of motion simplify considerably. This allows us to easily separate the radial motion from the angular part and to obtain solutions for angular trajectories in a compact closed form. For the radial motion, we focus our attention on spherical orbits. In particular, we determine the timelike innermost stable circular orbits (ISCOs) for these asymptotically AdS spacetimes, as well as the location of null circular orbits. We find that the ISCO dives below the ergosurface for black holes rotating close to extremality and merges with the event horizon exactly at extremality, in analogy with the four-dimensional Kerr case. For sufficiently massive black holes in AdS, there exists a spin parameter range in which the background spacetime is stable against super-radiance and the ISCO lies inside the ergoregion. Our results for massless geodesics show that there are no stable circular null orbits outside the horizon, but there exist such orbits inside the horizon, as well as around overextremal spacetimes, i.e., naked singularities. We also discuss how these orbits deform from the static to the rotating case.

  1. 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.

  2. 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.

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Chronology, supertubes and the Breckenridge-Myers-Peet-Vafa (BMPV) black hole

    NASA Astrophysics Data System (ADS)

    Finch, Tehani K.

    String theory has provided a precise quantum description of supersymmetric black holes. One particular example is a rotating charged black hole in five dimensions called the Breckenridge-Myers-Peet-Vafa (BMPV) black hole. Its unusual properties make it amenable to scattering calculations that involve string theoretical probes. The probe of this investigation is a charged D-brane configuration called a supertube. The low velocity scattering of a two-charge supertube in the vicinity of a BMPV black hole has been considered by previous authors; here the objective is to determine to what extent such results apply to the three-charge supertube. We utilize the Dirac-Born-Infeld (DBI) action to describe the supertube in the background of a BMPV black hole in five dimensions. We expand the action to second order in the velocities and then perform a Legendre transformation to obtain a Hamiltonian and an effective potential. We find that, similarly to the two-charge case, there is a critical value of the supertube circumferential angular momentum; above this value an adiabatic merger with the black hole is not allowed. In the case of a moving supertube, on the other hand, such a merger is possible, but only when accompanied by a potential barrier. An important class of these mergers are fragmentation mergers, which naively appear to decrease the black hole entropy but instead trigger a thermodynamic instability that causes the black hole to fission. This group of mergers includes, but is not limited to, those that violate the angular momentum bound of the black hole. Thus it can be concluded that the thermodynamic instability found for the two-charge supertube appears for the three-charge case as well. Moreover, since this instability does not require violation of the angular momentum bound, it occurs under circumstances somewhat more general than described in previous work.

  11. 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.

  12. Establishing Substantial Equivalence: Proteomics

    NASA Astrophysics Data System (ADS)

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

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

  13. 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

  14. Examination of the relations of the Myers-Briggs type indicator and the NEO-4 Personality Inventory in a Polish sample.

    PubMed

    Klinkosz, Waldemar; Iskra, Justyna

    2010-10-01

    The present study was designed to replicate McCrae and Costa's research findings on the relation of NEO-4 domains with the Myers-Briggs Type Indicator scales in a Polish sample of 300 psychology student volunteers (175 women, 125 men). Their mean age was 22.3 yr. (SD = 4.5). Correlations for scores on the MBTI scales with NEO-4 domains ranged from .72 to .02 for Extraversion, from -.60 to -.16 for Openness to experience, from -.56 to -.04 for Agreeableness, and from .55 to -.07 for Conscientiousness. Two domains assessed with the NEO-4 correspond to preferences measured by the Myers-Briggs Type Indicator.

  15. 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.

  16. “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...

  17. 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.

  18. 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.

  19. 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

  20. Reinterpreting the Myers-Briggs Type Indicator from the perspective of the five-factor model of personality.

    PubMed

    McCrae, R R; Costa, P T

    1989-03-01

    The Myers-Briggs Type Indicator (MBTI; Myers & McCaulley, 1985) was evaluated from the perspectives of Jung's theory of psychological types and the five-factor model of personality as measured by self-reports and peer ratings on the NEO Personality Inventory (NEO-PI; Costa & McCrae, 1985b). Data were provided by 267 men and 201 women ages 19 to 93. Consistent with earlier research and evaluations, there was no support for the view that the MBTI measures truly dichotomous preferences or qualitatively distinct types; instead, the instrument measures four relatively independent dimensions. The interpretation of the Judging-Perceiving index was also called into question. The data suggest that Jung's theory is either incorrect or inadequately operationalized by the MBTI and cannot provide a sound basis for interpreting it. However, correlational analyses showed that the four MBTI indices did measure aspects of four of the five major dimensions of normal personality. The five-factor model provides an alternative basis for interpreting MBTI findings within a broader, more commonly shared conceptual framework.

  1. 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.

  2. 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.

  3. 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.

  4. Analyzing the Relationship of Strengths to Personality Preferences and Vocational Interests Utilizing Clifton StrengthsFinder, Myers-Briggs Type Indicator, and Strong Interest Inventory

    ERIC Educational Resources Information Center

    Schenck, Paulette M.

    2009-01-01

    Throughout the history of vocational psychology, career counselors have constantly searched for, devised, and implemented practices and techniques to best prepare clients for the world of work. The purpose of this study was to explore the relationship between strengths to personality preference and vocational interests utilizing the Myers-Briggs…

  5. Teaching Teams To Be Teams: An Exercise Using the Myers-Briggs Type Indicator and the Five-Factor Personality Traits.

    ERIC Educational Resources Information Center

    Clinebell, Sharon; Stecher, Mary

    2003-01-01

    Management students formed teams after completing exercises based on the Myers-Briggs Type Indicator and the Five-Factor Model of Personality. Team members examined how types and traits might affect performance. Most students indicated that understanding personality increased awareness of behavior. Teams that used extreme division of labor were…

  6. The Relationship between Personality Type and Software Usability Using the Myers-Briggs Type Indicator (MBTI) and the Software Usability Measurement Inventory (SUMI)

    ERIC Educational Resources Information Center

    Lindsey, William H.

    2011-01-01

    The study attempted to determine if there is a relationship between user's psychological personality types, measured by the Myers Briggs Type Indicator[R] (MBTI[R]) and distinct measures of usability measured by the Software Usability Measurement Inventory (SUMI). The study was expected to provide an answer to the following basic research…

  7. Holland's Vocational Preference Inventory and the Myers-Briggs Type Indicator as Predictors of Vocational Choice among Master's of Business Administration.

    ERIC Educational Resources Information Center

    Martin, David C.; Bartol, Kathryn M.

    1986-01-01

    Tested the ability of Holland's Vocational Preference Inventory (VPI) and the Myers-Briggs Type Indicator (MBTI) to predict student business concentration. Significant discriminant analysis results were obtained for both instruments. Classification analyses supported the potential usefulness of the VPI for counseling students regarding…

  8. Using the Career Orientation and Planning Profile (COPP) and the Myers-Briggs Type Indicator (MBTI) To Strengthen Adult Students' Knowledge of Self and of the Work World.

    ERIC Educational Resources Information Center

    Hayslip, Jo

    A study worked with three groups of female students to determine whether using the Career Orientation and Planning Profile (COPP) and the Myers-Briggs Type Indicator (MBTI) would enable adults to make better career choices the second time around. The students were women in the Access to Careers and Training (ACT) program for unemployed or…

  9. 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.

  10. 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

  11. Comparative study of operative treatment [corrected] of varicose veins according to the Klapp and Smetana method versus Myers method.

    PubMed

    Solaković, Emir; Totić, Dragan; Solaković, Sid

    2008-08-01

    Venous abnormalities in lower extremities are among the most frequent disorders that affects general population with significant morbidity and mortality. Usually, the problem consists of a mild form of varicose veins and teleangiectasis. Treatment in this stage of disease is highly recommended since progression can lead to chronic venous insufficiency and chronic disability with very few effective treatment options. The most effective and popular treatment of varicose veins is operative treatment; specifically two different operative procedures: method according to Myers and method according to Klapp and Smetana. We designed this study in order to determine which method is superior based on clinical parameters and patients satisfaction. Our evidence strongly support clinical superiority, as well as patient satisfaction, of Klapp and Smetana method.

  12. Similarity between partners in real and perceived personality traits as measured by the Myers-Briggs type indicator.

    PubMed

    Nordvik, H

    1996-12-01

    From 90 couples, 90 male and 90 female subjects, two sets of scores on the four personality dimensions measured by the Myers-Briggs Type Indicator (MBTI) were obtained by letting each person answer each item twice, first in the ordinary way and then as he or she believed the partner would answer the item. Correlations between partners' self-reported scores were all close to zero, whereas the correlations between the partner-reported scores and the self-reported scores were high for both males and females and for all the four dimensions measured by the MBTI, thus indicating that partners were not similar in personality traits, but they had a realistic perception of each other. The results support the hypothesis that mating is random in terms of personality traits.

  13. Case study: technology initiative led to advanced lead optimization screening processes at Bristol-Myers Squibb, 2004-2009.

    PubMed

    Zhang, Litao; Cvijic, Mary Ellen; Lippy, Jonathan; Myslik, James; Brenner, Stephen L; Binnie, Alastair; Houston, John G

    2012-07-01

    In this paper, we review the key solutions that enabled evolution of the lead optimization screening support process at Bristol-Myers Squibb (BMS) between 2004 and 2009. During this time, technology infrastructure investment and scientific expertise integration laid the foundations to build and tailor lead optimization screening support models across all therapeutic groups at BMS. Together, harnessing advanced screening technology platforms and expanding panel screening strategy led to a paradigm shift at BMS in supporting lead optimization screening capability. Parallel SAR and structure liability relationship (SLR) screening approaches were first and broadly introduced to empower more-rapid and -informed decisions about chemical synthesis strategy and to broaden options for identifying high-quality drug candidates during lead optimization.

  14. 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...

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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,

  3. 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.

  4. The Role of the Myers-Briggs Personality Type and Emotional Intelligence in Marital Satisfaction among Married Female Students at Tehran University.

    PubMed

    Shirzad, Galin

    2016-10-01

    The present descriptive correlational study was conducted to predict the role of emotional intelligence and the Myers-Briggs personality type in marital satisfaction in married female students Tehran University in 2015. The study population consisted of all the married female students at Tehran University who visited Iran MBTI center between 22.04.2015 and 21.06.2015. A total of 140 students were selected as the study samples. Data were collected using the Myer-Briggs Type Indicator, the Bar-On Emotional Intelligence Questionnaire and the Enrich Marital Satisfaction Scale and were then analyzed in SPSS-20 using the multivariate regression analysis. The results obtained showed that emotional intelligence (interpersonal and intra-personal skills) and personality type (extraverted and structured) can predict marital satisfaction.

  5. Supporting open access to clinical trial data for researchers: The Duke Clinical Research Institute-Bristol-Myers Squibb Supporting Open Access to Researchers Initiative.

    PubMed

    Pencina, Michael J; Louzao, Darcy M; McCourt, Brian J; Adams, Monique R; Tayyabkhan, Rehbar H; Ronco, Peter; Peterson, Eric D

    2016-02-01

    There are growing calls for sponsors to increase transparency by providing access to clinical trial data. In response, Bristol-Myers Squibb and the Duke Clinical Research Institute have collaborated on a new initiative, Supporting Open Access to Researchers. The aim is to facilitate open sharing of Bristol-Myers Squibb trial data with interested researchers. Key features of the Supporting Open Access to Researchers data sharing model include an independent review committee that ensures expert consideration of each proposal, stringent data deidentification/anonymization and protection of patient privacy, requirement of prespecified statistical analysis plans, and independent review of manuscripts before submission for publication. We believe that these approaches will promote open science by allowing investigators to verify trial results as well as to pursue interesting secondary uses of trial data without compromising scientific integrity.

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Physician personality types in physical medicine and rehabilitation as measured by the Myers-Briggs Type Indicator.

    PubMed

    Sliwa, J A; Shade-Zeldow, Y

    1994-01-01

    Personality is one variable that correlates with specialty selection and practice type. To test our hypothesis that there has been a change in the personality type of those entering Physical Medicine and Rehabilitation (PM&R) and to identify the academic potential of those in rehabilitation, we invited all residents and graduates of our training program to participate in a study of personality types within PM&R by completing a Myers-Briggs Type Indicator (MBTI). Thirty residents and 48 graduates completed the questionnaire. A wide range of personality types were represented in our sample. The most common types are shared by a number of other people-oriented, primary care specialties. There was a statistically significant difference between residents and graduates on two of the four MBTI indexes, with graduates more introverted (P < 0.05) and judging (P < 0.001) than the present residents. Intuition, previously correlated with research and academic practice, was the dominant process for the majority of graduates and residents. This would confirm, according to type theory, the academic potential of both graduates and residents in our training program.

  13. 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

  14. 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.

  15. 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

  16. For the relief of Adrian Rodriguez.

    THOMAS, 111th Congress

    Rep. Filner, Bob [D-CA-51

    2009-02-03

    02/20/2009 Referred to the Subcommittee on Immigration, Citizenship, Refugees, Border Security, and International Law. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  17. 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.

  18. Perfluorooctanoic Acid for Shotgun Proteomics

    PubMed Central

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

    2010-01-01

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

  19. [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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. [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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. Relationship between DHI production values and Myers-Briggs type indicator as a measure of management ability.

    PubMed

    Young, A J; Walters, J L

    2002-08-01

    Associations between owners' Myers-Briggs Type Indicator (MBTI) preferences (E = extraversion vs. I = introversion; S = sensing vs. N = intuition; T = thinking vs F = feeling; J = judging vs. P = perceiving) and 21 Dairy Herd Improvement (DHI) production variables were determined on 60 farms. Of 60 dairy farmers participating, 51 were from Holstein farms (85%) and nine from farms with other breeds, primarily Jersey. Cows were milked either twice (n = 44 herds, 73%) or three times (n = 16) per day. Farmers were evenly split between the "E" and "I" dimension, whereas 93% of the farmers were "S," 75% "T," and 62% "J.". Individuals with a preference for the "I" dimension were associated with higher peak and mature equivalent milk yield than those individuals with a preference for the "E" dimension. The "T" and "J" dimensions had a significantly higher percentage of the herd with records usable by USDA and a lower percentage of animals pregnant by the goal set by the dairy producer than the "F" and "P" dimensions. Herds managed by individuals with a combination preference of "E" and "P" produced 7 to 10 kg of 3.5% FCM/cow per day less or 1,820 to 2,752 kg/ cow RHA ECM less than other combinations of the "E-I" and "J-P" dimensions. Those herds also had longer days dry and a lower percentage of records usable by USDA, suggesting that the "E-P" preference is less favorably associated to those measures of herd performance. The MBTI had limited association with many DHI production variables, but relationships to measures of labor and business management should be examined.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. A comparison of music education and music therapy majors: personality types as described by the Myers-Briggs Type Indicator and demographic profiles.

    PubMed

    Steele, Anita Louise; Young, Sylvester

    2008-01-01

    The purpose of this study was to develop both personality and demographic profiles for students who are interested in majoring in music education or music therapy. Two primary questions were addressed in the study: (a) Are there similarities and differences in the personality types of music education and music therapy majors as measured by the Myers Briggs Type Indicator (MBTI )? (b) Are there similarities and differences in demographic characteristics of music education and music therapy majors in regard to (i) principal instrument studied in college, (ii) grade point average, (iii) scholarship awards, (iv) high school participation in private study and (v) ensembles, (vi) church/community participation, and (vii) volunteerism in high school?

  3. 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

  4. 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

  5. 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

  6. University studies science course selection and academic achievement in relation to the Myers-Briggs Type Indicator

    NASA Astrophysics Data System (ADS)

    Skauge, Suzanne Elizabeth

    This research conducted at a southern regional university studied general education (University Studies - US) science course selection and academic success in US science in relation to Myers-Briggs Type Indicator (MBTI) preference categories (SF, ST, NF and NT). Additionally, differences in type preferences among students with mathematics and/or reading competency were explored. Data was examined for 755 students enrolled in the freshman success seminar course between Fall 1989 and Spring 1995 who had completed the MBTI test as part of that class. US science courses examined were grouped by science study: earth science, biology, chemistry and physics. Academic success was defined as a grade of "C" or higher and proficiency criteria were dictated by the university catalog. The study's nonparametric test results did not find any significant differences between MBTI type preferences and the two main areas of focus, US science course selection and academic success in US science courses. However, significant proportional differences were found between type preferences in relation to student reading competency (sig. = .03), as well as, reading competency and academic success in science (sig. = .04) even though fairly weak relationships existed between the variables with contingency coefficients of .11 and .10 respectively. All other relationships tested proved not significant. Each type's course selection closely reflected the overall sample: Earth Science 52.3%, Biology 34%, Chemistry 7.5% and Physics 6.1%. Nearly one-fifth (19.7%) of the sample were not successful in their selected science course. Less than two-fifths (37.7%) of student sample were not mathematics and/or reading competent. Academically in science intuitive types tended to do better than sensing types and feeling types tended to better than thinking types (NF 2.41, NT 2.36, SF 2.29 and ST 2.23). Further analysis found the TF preference scale contributed more toward the significant differences in reading

  7. The rigorous bound on the transmission probability for massless scalar field of non-negative-angular-momentum mode emitted from a Myers-Perry black hole

    NASA Astrophysics Data System (ADS)

    Ngampitipan, Tritos; Boonserm, Petarpa; Chatrabhuti, Auttakit; Visser, Matt

    2016-06-01

    Hawking radiation is the evidence for the existence of black hole. What an observer can measure through Hawking radiation is the transmission probability. In the laboratory, miniature black holes can successfully be generated. The generated black holes are, most commonly, Myers-Perry black holes. In this paper, we will derive the rigorous bounds on the transmission probabilities for massless scalar fields of non-negative-angular-momentum modes emitted from a generated Myers-Perry black hole in six, seven, and eight dimensions. The results show that for low energy, the rigorous bounds increase with the increase in the energy of emitted particles. However, for high energy, the rigorous bounds decrease with the increase in the energy of emitted particles. When the black holes spin faster, the rigorous bounds decrease. For dimension dependence, the rigorous bounds also decrease with the increase in the number of extra dimensions. Furthermore, as comparison to the approximate transmission probability, the rigorous bound is proven to be useful.

  8. 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.

  9. 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).

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. 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.

  8. 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...

  9. 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...

  10. 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.

  11. 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...

  12. 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…

  13. 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...

  14. Genetic and environmental influences on the continuous scales of the Myers-Briggs Type Indicator: an analysis based on twins reared apart.

    PubMed

    Bouchard, T J; Hur, Y M

    1998-04-01

    The Myers-Briggs Type Indicator was administered to a sample of 61 monozygotic twins reared apart (MZA), 49 dizygotic twins reared apart (DZA), and 92 spouses, who participated in the Minnesota Study of Twins Reared Apart (MISTRA) from 1979 to 1995. Twins' scores on the continuous scales were subjected to behavior genetic model-fitting procedures. Extraversion-Introversion and Thinking-Feeling yielded heritabilities of about .60, consisting largely of nonadditive genetic variance. Sensing-Intuition and Judgment-Perception yielded heritabilities of about .40, consisting largely of additive genetic variance. Spouse correlations for three of the four scales were near zero and not statistically significant; one spouse correlation (Sensing-Intuition) was modestly positive and statistically significant.

  15. Separability of the massive Dirac equation in 5-dimensional Myers-Perry black hole geometry and its relation to a rank-three Killing-Yano tensor

    SciTech Connect

    Wu Shuangqing

    2008-09-15

    The Dirac equation for the electron around a five-dimensional rotating black hole with two different angular momenta is separated into purely radial and purely angular equations. The general solution is expressed as a superposition of solutions derived from these two decoupled ordinary differential equations. By separating variables for the massive Klein-Gordon equation in the same spacetime background, I derive a simple and elegant form for the Staeckel-Killing tensor, which can be easily written as the square of a rank-three Killing-Yano tensor. I have also explicitly constructed a symmetry operator that commutes with the scalar Laplacian by using the Staeckel-Killing tensor, and the one with the Dirac operator by the Killing-Yano tensor admitted by the five-dimensional Myers-Perry metric, respectively.

  16. 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

  17. 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.

  18. 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.

  19. 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+).

  20. 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.

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

    PubMed

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

    2017-01-01

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

  2. Ultrasensitive proteome analysis using paramagnetic bead technology

    PubMed Central

    Hughes, Christopher S; Foehr, Sophia; Garfield, David A; Furlong, Eileen E; Steinmetz, Lars M; Krijgsveld, Jeroen

    2014-01-01

    In order to obtain a systems-level understanding of a complex biological system, detailed proteome information is essential. Despite great progress in proteomics technologies, thorough interrogation of the proteome from quantity-limited biological samples is hampered by inefficiencies during processing. To address these challenges, here we introduce a novel protocol using paramagnetic beads, termed Single-Pot Solid-Phase-enhanced Sample Preparation (SP3). SP3 provides a rapid and unbiased means of proteomic sample preparation in a single tube that facilitates ultrasensitive analysis by outperforming existing protocols in terms of efficiency, scalability, speed, throughput, and flexibility. To illustrate these benefits, characterization of 1,000 HeLa cells and single Drosophila embryos is used to establish that SP3 provides an enhanced platform for profiling proteomes derived from sub-microgram amounts of material. These data present a first view of developmental stage-specific proteome dynamics in Drosophila at a single-embryo resolution, permitting characterization of inter-individual expression variation. Together, the findings of this work position SP3 as a superior protocol that facilitates exciting new directions in multiple areas of proteomics ranging from developmental biology to clinical applications. PMID:25358341

  3. Quantitative Proteomics of the E. coli Membranome.

    PubMed

    Tsolis, K C; Economou, A

    2017-01-01

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

  4. Proteomics: a review and an example using the reticulocyte membrane proteome.

    PubMed

    Prenni, Jessica E; Avery, Anne C; Olver, Christine S

    2007-03-01

    Proteomics is a rapidly expanding field of scientific study that combines techniques in protein solubilization and separation, mass spectrometry, and genome and protein database searching. The proteome is most commonly defined as the entire complement of proteins expressed in a given cell type or tissue under a given condition. A proteomics experiment may be as simple as identifying a single protein or as complex as identifying thousands of proteins in a cell lysate. In this review, we describe the general principles of proteomics and its analytic methods and present an example of an experiment to characterize the murine reticulocyte membrane proteome. A brief summary of proteomics applications and their clinical potential and relevance to clinical pathology is also presented.

  5. Recent advances in cardiovascular proteomics.

    PubMed

    Sharma, Parveen; Cosme, Jake; Gramolini, Anthony O

    2013-04-09

    Cardiovascular diseases (CVDs) are the major source of global morbidity and death and more people die annually from CVDs than from any other cause. These diseases can occur quickly, as seen in acute myocardial infarction (AMI), or progress slowly over years as with chronic heart failure. Advances in mass spectrometry detection and analysis, together with improved isolation and enrichment techniques allowing for the separation of organelles and membrane proteins, now allow for the indepth analysis of the cardiac proteome. Here we outline current insights that have been provided through cardiovascular proteomics, and discuss studies that have developed innovative technologies which permit the examination of the protein complement in specific organelles including exosomes and secreted proteins. We highlight these foundational studies and illustrate how they are providing the technologies and tools which are now being applied to further study cardiovascular disease; provide new diagnostic markers and potentially new methods of cardiac patient management with identification of novel drug targets. This article is part of a Special Issue entitled: From protein structures to clinical applications.

  6. Proteomics in prostate cancer research.

    PubMed

    Hellström, Magnus; Lexander, Helena; Franzén, Bo; Egevad, Lars

    2007-02-01

    The incidence of early prostate cancer (PCa) among middle-aged men has increased rapidly. For many of these men, curatively intended treatment does more harm than good. Established prognostic factors are tumor stage and grade. As a result of earlier detection a majority of patients now have nonpalpable tumors (T1c) of intermediate grade (Gleason score 6). Prostate specific antigen in serum in such cases is generally at a low level and not a reliable predictor of prognosis. Altogether there is an urgent need for adjunctive prognostic indicators. In the search for relevant tumor markers for improved patient selection an exploration of the proteome (the human proteins) could be fruitful. This paper critically reviews the use of 2-dimensional gel electrophoresis (2-DE) for proteome research. Additional steps such as image analysis and mass spectrometry are described. Techniques based on non-2-DE platforms: surface-enhanced laser desorption/ionization (SELDI), isotope coded affinity tags (ICAT) and array-based technologies are also summarized. Although labor-intensive and time-consuming, 2-DE is presently the most powerful method for analysis of cellular protein phenotype and may potentially reveal gene regulations that cannot be detected on a genetic level.

  7. Radiation proteomics: a brief overview.

    PubMed

    Leszczynski, Dariusz

    2014-03-01

    Acute biological effects caused by the exposure to high doses of radiation, either ionizing or nonionizing, are relatively well-known but the delayed effects, occurring decades after exposure, are difficult to predict. The knowledge of the acute and delayed effects of the low doses of ionizing radiation (e.g. bystander effect) or nonionizing radiation (e.g. radiation emitted by wireless communication devices) is not yet reliably established. Often the acute effects of low doses are small and difficult to discover and replicate in scientific studies. Chronic effects of prolonged exposures to low-dose radiation for decades are virtually unknown and often not possible to predict on the basis of the knowledge gained from acute exposures to high doses of radiation. Physiological significance of the biological effects induced by low doses of radiation is not known. The same lack of predictability of outcomes applies to the delayed effects of high-dose radiation exposures. Proteomics, supplemented with other "omics" techniques, might be the best way forward to find out the target molecules of radiation, the biomarkers of radiation exposure and the physiological and health significance of the acute and delayed biological effects caused by the exposures to high- and low-dose radiation. However, the currently available database of radiation effects on proteomes is far too small to be useful in formulation of new hypotheses concerning health consequences of radiation exposures.

  8. Surface plasmon resonance for proteomics.

    PubMed

    de Mol, Nico J

    2012-01-01

    Surface plasmon resonance (SPR) is a well-established label-free technique to detect mass changes near an SPR surface. For 20 years the benefits of SPR have been proven in biomolecular interaction analysis, including measurements of affinity and kinetics. The emergence of proteomics and a need for high throughput analysis drives the development of SPR systems capable of analyzing microarrays. The use of SPR imaging (also known as SPR microscopy) makes it possible to use multiplexed arrays to follow binding reactions. As SPR only analyzes the binding process, but not the identity of captured molecules on the SPR surface, technologies have been developed to integrate SPR with mass spectrometric (MS) analysis. Such approaches involve the recovery of analytes from the SPR surface and subsequent MALDI-TOF MS analysis, or LC-MS/MS after tryptic digestion of recovered proteins. An approach compatible with SPR arrays is on-chip MALDI-TOF MS, from arrayed spots on an SPR surface. This review describes some exciting developments in the application of SPR to proteomics, using instruments which are on the market already, or are expected to be available in the years to come.

  9. Threshold-avoiding proteomics pipeline.

    PubMed

    Suits, Frank; Hoekman, Berend; Rosenling, Therese; Bischoff, Rainer; Horvatovich, Peter

    2011-10-15

    We present a new proteomics analysis pipeline focused on maximizing the dynamic range of detected molecules in liquid chromatography-mass spectrometry (LC-MS) data and accurately quantifying low-abundance peaks to identify those with biological relevance. Although there has been much work to improve the quality of data derived from LC-MS instruments, the goal of this study was to extend the dynamic range of analyzed compounds by making full use of the information available within each data set and across multiple related chromatograms in an experiment. Our aim was to distinguish low-abundance signal peaks from noise by noting their coherent behavior across multiple data sets, and central to this is the need to delay the culling of noise peaks until the final peak-matching stage of the pipeline, when peaks from a single sample appear in the context of all others. The application of thresholds that might discard signal peaks early is thereby avoided, hence the name TAPP: threshold-avoiding proteomics pipeline. TAPP focuses on quantitative low-level processing of raw LC-MS data and includes novel preprocessing, peak detection, time alignment, and cluster-based matching. We demonstrate the performance of TAPP on biologically relevant sample data consisting of porcine cerebrospinal fluid spiked over a wide range of concentrations with horse heart cytochrome c.

  10. Neural Stem Cells (NSCs) and Proteomics*

    PubMed Central

    Shoemaker, Lorelei D.; Kornblum, Harley I.

    2016-01-01

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

  11. Selected reaction monitoring applied to proteomics.

    PubMed

    Gallien, Sebastien; Duriez, Elodie; Domon, Bruno

    2011-03-01

    Selected reaction monitoring (SRM) performed on triple quadrupole mass spectrometers has been the reference quantitative technique to analyze small molecules for several decades. It is now emerging in proteomics as the ideal tool to complement shotgun qualitative studies; targeted SRM quantitative analysis offers high selectivity, sensitivity and a wide dynamic range. However, SRM applied to proteomics presents singularities that distinguish it from small molecules analysis. This review is an overview of SRM technology and describes the specificities and the technical aspects of proteomics experiments. Ongoing developments aiming at increasing multiplexing capabilities of SRM are discussed; they dramatically improve its throughput and extend its field of application to directed or supervised discovery experiments.

  12. Accounting for population variation in targeted proteomics

    SciTech Connect

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

    2014-01-03

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

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

    PubMed

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

    2011-01-01

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

  14. APPLICATION OF PROTEOMICS TO NEUTROPHIL BIOLOGY

    PubMed Central

    Luerman, Gregory C.; Uriarte, Silvia M.; Rane, Madhavi J.; McLeish, Kenneth R.

    2009-01-01

    Polymorphonuclear leukocytes or neutrophils are a primary effector cell of the innate immune system and contribute to the development of adaptive immunity. Neutrophils participate in both the initiation and resolution of inflammatory responses through a series of highly coordinated molecular and phenotypic changes. To accomplish these changes, neutrophils express numerous receptors and use multiple overlapping and redundant signal transduction pathways. Dysregulation of the activation or resolution pathways plays a role in a number of human diseases. A comprehensive understanding of the regulation of neutrophil responses can be provided by high throughput proteomic technologies and sophisticated computational analysis. The first steps in the application of proteomics to understanding neutrophil biology have been taken. Here we review the application of expression, structural, and functional proteomic studies to neutrophils. Although defining the complex molecular events associated with neutrophil activation is in the early stages, the data generated to date suggest that proteomic technologies will dramatically enhance our understanding of neutrophil biology. PMID:19580889

  15. Clinical proteomics in obstetrics and neonatology.

    PubMed

    Klein, Julie; Buffin-Meyer, Benedicte; Mullen, William; Carty, David M; Delles, Christian; Vlahou, Antonia; Mischak, Harald; Decramer, Stéphane; Bascands, Jean-Loup; Schanstra, Joost P

    2014-02-01

    Clinical proteomics has been applied to the identification of biomarkers of obstetric and neonatal disease. We will discuss a number of encouraging studies that have led to potentially valid biomarkers in the context of Down's syndrome, preterm birth, amniotic infections, preeclampsia, intrauterine growth restriction and obstructive uropathies. Obtaining noninvasive biomarkers (e.g., from the maternal circulation, urine or cervicovaginal fluid) may be more feasible for obstetric diseases than for diseases of the fetus, for which invasive methods are required (e.g., amniotic fluid, fetal urine). However, studies providing validated proteomics-identified biomarkers are limited. Efforts should be made to save well-characterized samples of these invasive body fluids so that many valid biomarkers of pregnancy-related diseases will be identified in the coming years using proteomics based analysis upon adoption of 'clinical proteomics guidelines'.

  16. Characterization of individual mouse cerebrospinal fluid proteomes

    SciTech Connect

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

    2014-03-20

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

  17. The proteomics of pediatric brain tumors.

    PubMed

    Anagnostopoulos, Athanasios K; Tsangaris, George T

    2014-10-01

    Pediatric tumors of the CNS are the leading cause of cancer-related mortality in children. In pediatric pathology, brain tumors constitute the most frequent solid malignancy. An unparalleled outburst of information in pediatric neuro-oncology research has been witnessed over the last few years, largely due to increased use of high-throughput technologies such as genomics, proteomics and meta-analysis tools. Input from these technologies gives scientists the advantage of early prognosis assessment, more accurate diagnosis and prospective curative intent in the pediatric brain tumor clinical setting. The present review aims to summarize current knowledge on research applying proteomics techniques or proteomics-based approaches performed on pediatric brain tumors. Proteins that can be used as potential disease markers or molecular targets, and their biological significance, are herein listed and discussed. Furthermore, future perspectives that proteomics technologies may offer regarding this devastating disorder are presented.

  18. The Clinical Proteomic Technologies for Cancer | Partners

    Cancer.gov

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

  19. The Clinical Proteomic Technologies for Cancer | About

    Cancer.gov

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

  20. Proteome Characterization of Leaves in Common Bean

    PubMed Central

    Robison, Faith M.; Heuberger, Adam L.; Brick, Mark A.; Prenni, Jessica E.

    2015-01-01

    Dry edible bean (Phaseolus vulgaris L.) is a globally relevant food crop. The bean genome was recently sequenced and annotated allowing for proteomics investigations aimed at characterization of leaf phenotypes important to agriculture. The objective of this study was to utilize a shotgun proteomics approach to characterize the leaf proteome and to identify protein abundance differences between two bean lines with known variation in their physiological resistance to biotic stresses. Overall, 640 proteins were confidently identified. Among these are proteins known to be involved in a variety of molecular functions including oxidoreductase activity, binding peroxidase activity, and hydrolase activity. Twenty nine proteins were found to significantly vary in abundance (p-value < 0.05) between the two bean lines, including proteins associated with biotic stress. To our knowledge, this work represents the first large scale shotgun proteomic analysis of beans and our results lay the groundwork for future studies designed to investigate the molecular mechanisms involved in pathogen resistance. PMID:28248269

  1. Unexpected features of the dark proteome.

    PubMed

    Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S; Buckley, Michael J; Tabor, Bruce; Signal, Beth; Gloss, Brian S; Hammang, Christopher J; Rost, Burkhard; Schafferhans, Andrea; O'Donoghue, Seán I

    2015-12-29

    We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.

  2. Proteomics in the genome engineering era.

    PubMed

    Vandemoortele, Giel; Gevaert, Kris; Eyckerman, Sven

    2016-01-01

    Genome engineering experiments used to be lengthy, inefficient, and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected. In this review, we describe the main applications of genome engineering in proteomics, including the use of engineered disease models and endogenous epitope tagging. In addition, we provide an overview on current literature and highlight important considerations when launching genome engineering technologies in proteomics workflows.

  3. Integrated multifunctional microfluidics for automated proteome analyses.

    PubMed

    Osiri, John K; Shadpour, Hamed; Witek, Małgorzata A; Soper, Steven A

    2011-01-01

    Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device

  4. Proteome analysis of wheat lemma.

    PubMed

    Woo, Sun-Hee; Kimura, Makoto; Higa-Nishiyama, Arisa; Dohmae, Naoshi; Hamamoto, Hiroshi; Jong, Seung-Keun; Yamaguchi, Isamu

    2003-11-01

    We report here for the first time on the construction of proteomes from wheat lemma at the anthesis stage. After transfer of lemma proteins to polyvinylidene difluoride membranes, seventy larger spots were subjected to peptide sequence analysis; the amino acid sequences could be described for forty-eight of these proteins. The result suggested that wheat proteins were less N-terminally blocked compared to rice proteins, which are known to have a much higher ratio of N-terminal blocks. We further analyzed the internal sequences of eight blocked proteins by the Cleveland peptide mapping method. Out of these total 56 amino acid sequences, forty-one could be assigned to the corresponding expressed sequence tags (ESTs). The expression profile of lemma proteins was generally similar to that of leaf, and the majority of identified proteins were related to cellular metabolisms. We analyzed the internal sequences of one protein spot present in lemma, which was not present in leaf.

  5. Bioinformatic analysis of proteomics data

    PubMed Central

    2014-01-01

    Most biochemical reactions in a cell are regulated by highly specialized proteins, which are the prime mediators of the cellular phenotype. Therefore the identification, quantitation and characterization of all proteins in a cell are of utmost importance to understand the molecular processes that mediate cellular physiology. With the advent of robust and reliable mass spectrometers that are able to analyze complex protein mixtures within a reasonable timeframe, the systematic analysis of all proteins in a cell becomes feasible. Besides the ongoing improvements of analytical hardware, standardized methods to analyze and study all proteins have to be developed that allow the generation of testable new hypothesis based on the enormous pre-existing amount of biological information. Here we discuss current strategies on how to gather, filter and analyze proteomic data sates using available software packages. PMID:25033288

  6. Collaboration - Office of Cancer Clinical Proteomics Research

    Cancer.gov

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

  7. Selected reaction monitoring applied to quantitative proteomics.

    PubMed

    Kiyonami, Reiko; Domon, Bruno

    2010-01-01

    Proteomics is gradually shifting from pure qualitative studies (protein identification) to large-scale quantitative experiments, prompted by the growing need to analyze consistently and precisely a large set of proteins in biological samples. The selected reaction monitoring (SRM) technique is increasingly applied to quantitative proteomics because of its selectivity (two levels of mass selection), its sensitivity (non-scanning mode), and its wide dynamic range. This account describes the different steps in the design and the experimental setup of SRM experiments.

  8. Proteomics boosts translational and clinical microbiology.

    PubMed

    Del Chierico, F; Petrucca, A; Vernocchi, P; Bracaglia, G; Fiscarelli, E; Bernaschi, P; Muraca, M; Urbani, A; Putignani, L

    2014-01-31

    The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

  9. Personalized Proteomics: The Future of Precision Medicine.

    PubMed

    Duarte, Trevor T; Spencer, Charles T

    2016-01-01

    Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient's response to disease and treatment. As more analytical and diagnostic techniques are incorporated into medical practice, the personalized medicine initiative transitions to precision medicine giving a holistic view of the patient's condition. The high accuracy and sensitivity of mass spectrometric analysis of proteomes is well suited for the incorporation of proteomics into precision medicine. This review begins with an overview of the advance to precision medicine and the current state of the art in technology and instrumentation for mass spectrometry analysis. Thereafter, it focuses on the benefits and potential uses for personalized proteomic analysis in the diagnostic and treatment of individual patients. In conclusion, it calls for a synthesis between basic science and clinical researchers with practicing clinicians to design proteomic studies to generate meaningful and applicable translational medicine. As clinical proteomics is just beginning to come out of its infancy, this overview is provided for the new initiate.

  10. Personalized Proteomics: The Future of Precision Medicine

    PubMed Central

    Duarte, Trevor T.; Spencer, Charles T.

    2016-01-01

    Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient’s response to disease and treatment. As more analytical and diagnostic techniques are incorporated into medical practice, the personalized medicine initiative transitions to precision medicine giving a holistic view of the patient’s condition. The high accuracy and sensitivity of mass spectrometric analysis of proteomes is well suited for the incorporation of proteomics into precision medicine. This review begins with an overview of the advance to precision medicine and the current state of the art in technology and instrumentation for mass spectrometry analysis. Thereafter, it focuses on the benefits and potential uses for personalized proteomic analysis in the diagnostic and treatment of individual patients. In conclusion, it calls for a synthesis between basic science and clinical researchers with practicing clinicians to design proteomic studies to generate meaningful and applicable translational medicine. As clinical proteomics is just beginning to come out of its infancy, this overview is provided for the new initiate. PMID:27882306

  11. Polyphemus, Odysseus and the ovine milk proteome.

    PubMed

    Cunsolo, Vincenzo; Fasoli, Elisa; Di Francesco, Antonella; Saletti, Rosaria; Muccilli, Vera; Gallina, Serafina; Righetti, Pier Giorgio; Foti, Salvatore

    2017-01-30

    In the last years the amount of ovine milk production, mainly used to formulate a wide range of different and exclusive dairy products often categorized as gourmet food, has been progressively increasing. Taking also into account that sheep milk (SM) also appears to be potentially less allergenic than cow's one, an in-depth information about its protein composition is essential to improve the comprehension of its potential benefits for human consumption. The present work reports the results of an in-depth characterization of SM whey proteome, carried out by coupling the CPLL technology with SDS-PAGE and high resolution UPLC-nESI MS/MS analysis. This approach allowed the identification of 718 different protein components, 644 of which are from unique genes. Particularly, this identification has expanded literature data about sheep whey proteome by 193 novel proteins previously undetected, many of which are involved in the defence/immunity mechanisms or in the nutrient delivery system. A comparative analysis of SM proteome known to date with cow's milk proteome, evidenced that while about 29% of SM proteins are also present in CM, 71% of the identified components appear to be unique of SM proteome and include a heterogeneous group of components which seem to have health-promoting benefits. The data have been deposited to the ProteomeXchange with identifier .

  12. Sub-cellular proteomics of Medicago truncatula

    PubMed Central

    Lee, Jeonghoon; Lei, Zhentian; Watson, Bonnie S.; Sumner, Lloyd W.

    2013-01-01

    Medicago truncatula is a leading model species and substantial molecular, genetic, genomics, proteomics, and metabolomics resources have been developed for this species to facilitate the study of legume biology. Currently, over 60 proteomics studies of M. truncatula have been published. Many of these have focused upon the unique symbiosis formed between legumes and nitrogen fixing rhizobia bacteria, while others have focused on seed development and the specialized proteomes of distinct tissues/organs. These include the characterization of sub-cellular organelle proteomes such as nuclei and mitochondria, as well as proteins distributed in plasma or microsomal membranes from various tissues. The isolation of sub-cellular proteins typically requires a series of steps that are labor-intensive. Thus, efficient protocols for sub-cellular fractionation, purification, and enrichment are necessary for each cellular compartment. In addition, protein extraction, solubilization, separation, and digestion prior to mass spectral identification are important to enhance the detection of low abundance proteins and to increase the overall detectable proportion of the sub-cellular proteome. This review summarizes the sub-cellular proteomics studies in M. truncatula. PMID:23641248

  13. [Progress in stable isotope labeled quantitative proteomics methods].

    PubMed

    Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

    2013-06-01

    Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

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

    PubMed

    Altelaar, A F Maarten; Munoz, Javier; Heck, Albert J R

    2013-01-01

    Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the interconnectivity of proteins into complexes and signalling networks that are highly divergent in time and space. Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis. Here we describe this emerging next generation of proteomics and highlight recent applications.

  15. 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

  16. Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

    NASA Astrophysics Data System (ADS)

    Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

    2014-12-01

    The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.

  17. Unitarity and Lee-Wick prescription at one loop level in the effective Myers-Pospelov electrodynamics: The e++e- annihilation

    NASA Astrophysics Data System (ADS)

    Reyes, Carlos M.; Urrutia, L. F.

    2017-01-01

    We study perturbative unitarity in a Lorentz-symmetry-violating QED model with higher-order derivative operators in the light of the results of Lee and Wick to preserve unitarity in indefinite metric theories. Specifically, we consider the fermionic sector of the Myers-Pospelov model, which includes dimension-five operators, coupled to standard photons. We canonically quantize the model, paying attention to its effective character, and show that its Hamiltonian is stable, emphasizing the exact stage at which the indefinite metric appears and decomposes into a positive-metric sector and a negative-metric sector. Finally, we verify the optical theorem at the one-loop level in the annihilation channel of the forward-scattering process e+(p2,r )+e-(p1,s ) by applying the Lee-Wick prescription, in which the states associated with the negative metric are left out from the asymptotic Hilbert space, but nevertheless are considered in the loop integration via the propagator.

  18. The Escherichia coli Peripheral Inner Membrane Proteome*

    PubMed Central

    Papanastasiou, Malvina; Orfanoudaki, Georgia; Koukaki, Marina; Kountourakis, Nikos; Sardis, Marios Frantzeskos; Aivaliotis, Michalis; Karamanou, Spyridoula; Economou, Anastassios

    2013-01-01

    Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ∼19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ∼25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with

  19. Top-Down Proteomics and Farm Animal and Aquatic Sciences.

    PubMed

    Campos, Alexandre M O; de Almeida, André M

    2016-12-21

    Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

  20. Integrated Proteomic Approaches for Understanding Toxicity of Environmental Chemicals

    EPA Science Inventory

    To apply quantitative proteomic analysis to the evaluation of toxicity of environmental chemicals, we have developed an integrated proteomic technology platform. This platform has been applied to the analysis of the toxic effects and pathways of many important environmental chemi...

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

    PubMed

    Jain, Kewal K

    2016-01-01

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

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

    Cancer.gov

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

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

    Cancer.gov

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

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

    Cancer.gov

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

  5. Top-Down Proteomics and Farm Animal and Aquatic Sciences

    PubMed Central

    Campos, Alexandre M.O.; de Almeida, André M.

    2016-01-01

    Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences. PMID:28248248

  6. Proteomics for everyday use: activities of the HUPO Brain Proteome Project during the 5th HUPO World Congress.

    PubMed

    Hamacher, Michael; Stephan, Christian; Eisenacher, Martin; van Hall, Andre; Marcus, Katrin; Martens, Lennart; Park, Young Mok; Gutstein, Howard B; Herberg, Friedrich; Meyer, Helmut E

    2007-04-01

    Long Beach hosted this year's annual congress of the Human Proteome Organisation (HUPO). In addition to the numerous sessions, talks and poster presentations organized by HUPO itself, several events were arranged by the HUPO initiatives. The Brain Proteome Project (HUPO BPP) was very active, initiating three pre-congress workshops: (i) the kick-off meeting of the EU-funded ProDaC consortium (Proteomics Data Collection) that is aiming at the bioinformatics Standardization in the proteomics field; (ii) the workshop "Standardization Issues in Proteomics: Perspectives from Vendors" giving an overview about the lessons learned by proteomics industrial partners; (iii) the 6th HUPO BPP Workshop "New Proteomics Approaches for further HUPO BPP Studies" offering new concepts for brain-related proteomics studies.

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

    Cancer.gov

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

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

    Cancer.gov

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

  9. 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.

  10. Application of mass spectrometry in proteomics.

    PubMed

    Guerrera, Ida Chiara; Kleiner, Oliver

    2005-01-01

    Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.

  11. PROTEOMICS in aquaculture: applications and trends.

    PubMed

    Rodrigues, Pedro M; Silva, Tomé S; Dias, Jorge; Jessen, Flemming

    2012-07-19

    Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

  12. Translational Research and Plasma Proteomic in Cancer.

    PubMed

    Santini, Annamaria Chiara; Giovane, Giancarlo; Auletta, Adelaide; Di Carlo, Angelina; Fiorelli, Alfonso; Cito, Letizia; Astarita, Carlo; Giordano, Antonio; Alfano, Roberto; Feola, Antonia; Di Domenico, Marina

    2016-04-01

    Proteomics is a recent field of research in molecular biology that can help in the fight against cancer through the search for biomarkers that can detect this disease in the early stages of its development. Proteomic is a speedily growing technology, also thanks to the development of even more sensitive and fast mass spectrometry analysis. Although this technique is the most widespread for the discovery of new cancer biomarkers, it still suffers of a poor sensitivity and insufficient reproducibility, essentially due to the tumor heterogeneity. Common technical shortcomings include limitations in the sensitivity of detecting low abundant biomarkers and possible systematic biases in the observed data. Current research attempts are trying to develop high-resolution proteomic instrumentation for high-throughput monitoring of protein changes that occur in cancer. In this review, we describe the basic features of the proteomic tools which have proven to be useful in cancer research, showing their advantages and disadvantages. The application of these proteomic tools could provide early biomarkers detection in various cancer types and could improve the understanding the mechanisms of tumor growth and dissemination.

  13. Proteomics: bases for protein complexity understanding.

    PubMed

    Rotilio, Domenico; Della Corte, Anna; D'Imperio, Marco; Coletta, Walter; Marcone, Simone; Silvestri, Cristian; Giordano, Lucia; Di Michele, Michela; Donati, Maria Benedetta

    2012-03-01

    In the post genomic era we became aware that the genomic sequence and protein functions cannot be correlated. One gene can encode multiple protein functions mainly because of mRNA splice variants, post translational modifications (PTM) and moonlighting functions. To study the whole population of proteins present in a cell to a specific time point and under defined conditions it is necessary to investigate the proteome. Comprehensive analysis of the proteome requires the use of emerging high technologies because of the complexity and wide dynamic range of protein concentrations. Proteomics provides the tools to study protein identification and quantitation, protein-protein interactions, protein modifications and localization. The most widespread strategy for studying global protein expression employs two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) allowing thousands of proteins to be resolved and their expression quantified. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) has emerged as a high throughput technique for protein identification and characterization because of its high sensitivity, precision and accuracy. LC-MS/MS is well suited for accurate quantitation of protein expression levels, post-translational modifications and comparative and absolute quantitative analysis of peptides. Bioinformatic tools are required to elaborate the growing number of proteomic data. Here, we give an overview of the current status of the wide range of technologies that define and characterize the modern proteomics.

  14. A Cell-type-resolved Liver Proteome*

    PubMed Central

    Ding, Chen; Li, Yanyan; Guo, Feifei; Jiang, Ying; Ying, Wantao; Li, Dong; Yang, Dong; Xia, Xia; Liu, Wanlin; Zhao, Yan; He, Yangzhige; Li, Xianyu; Sun, Wei; Liu, Qiongming; Song, Lei; Zhen, Bei; Zhang, Pumin; Qian, Xiaohong; Qin, Jun; He, Fuchu

    2016-01-01

    Parenchymatous organs consist of multiple cell types, primarily defined as parenchymal cells (PCs) and nonparenchymal cells (NPCs). The cellular characteristics of these organs are not well understood. Proteomic studies facilitate the resolution of the molecular details of different cell types in organs. These studies have significantly extended our knowledge about organogenesis and organ cellular composition. Here, we present an atlas of the cell-type-resolved liver proteome. In-depth proteomics identified 6000 to 8000 gene products (GPs) for each cell type and a total of 10,075 GPs for four cell types. This data set revealed features of the cellular composition of the liver: (1) hepatocytes (PCs) express the least GPs, have a unique but highly homogenous proteome pattern, and execute fundamental liver functions; (2) the division of labor among PCs and NPCs follows a model in which PCs make the main components of pathways, but NPCs trigger the pathways; and (3) crosstalk among NPCs and PCs maintains the PC phenotype. This study presents the liver proteome at cell resolution, serving as a research model for dissecting the cell type constitution and organ features at the molecular level. PMID:27562671

  15. Integrated and Quantitative Proteomics of Human Tumors.

    PubMed

    Yakkioui, Y; Temel, Y; Chevet, E; Negroni, L

    2017-01-01

    Quantitative proteomics represents a powerful approach for the comprehensive analysis of proteins expressed under defined conditions. These properties have been used to investigate the proteome of disease states, including cancer. It has become a major subject of studies to apply proteomics for biomarker and therapeutic target identification. In the last decades, technical advances in mass spectrometry have increased the capacity of protein identification and quantification. Moreover, the analysis of posttranslational modification (PTM), especially phosphorylation, has allowed large-scale identification of biological mechanisms. Even so, increasing evidence indicates that global protein quantification is often insufficient for the explanation of biology and has shown to pose challenges in identifying new and robust biomarkers. As a consequence, to improve the accuracy of the discoveries made using proteomics in human tumors, it is necessary to combine (i) robust and reproducible methods for sample preparation allowing statistical comparison, (ii) PTM analyses in addition to global proteomics for additional levels of knowledge, and (iii) use of bioinformatics for decrypting protein list. Herein, we present technical specificities for samples preparation involving isobaric tag labeling, TiO2-based phosphopeptides enrichment and hydrazyde-based glycopeptides purification as well as the key points for the quantitative analysis and interpretation of the protein lists. The method is based on our experience with tumors analysis derived from hepatocellular carcinoma, chondrosarcoma, human embryonic intervertebral disk, and chordoma experiments.

  16. PPDB, the Plant Proteomics Database at Cornell.

    PubMed

    Sun, Qi; Zybailov, Boris; Majeran, Wojciech; Friso, Giulia; Olinares, Paul Dominic B; van Wijk, Klaas J

    2009-01-01

    The Plant Proteomics Database (PPDB; http://ppdb.tc.cornell.edu), launched in 2004, provides an integrated resource for experimentally identified proteins in Arabidopsis and maize (Zea mays). Internal BLAST alignments link maize and Arabidopsis information. Experimental identification is based on in-house mass spectrometry (MS) of cell type-specific proteomes (maize), or specific subcellular proteomes (e.g. chloroplasts, thylakoids, nucleoids) and total leaf proteome samples (maize and Arabidopsis). So far more than 5000 accessions both in maize and Arabidopsis have been identified. In addition, more than 80 published Arabidopsis proteome datasets from subcellular compartments or organs are stored in PPDB and linked to each locus. Using MS-derived information and literature, more than 1500 Arabidopsis proteins have a manually assigned subcellular location, with a strong emphasis on plastid proteins. Additional new features of PPDB include searchable posttranslational modifications and searchable experimental proteotypic peptides and spectral count information for each identified accession based on in-house experiments. Various search methods are provided to extract more than 40 data types for each accession and to extract accessions for different functional categories or curated subcellular localizations. Protein report pages for each accession provide comprehensive overviews, including predicted protein properties, with hyperlinks to the most relevant databases.

  17. Comparative profiling of the sperm proteome.

    PubMed

    Holland, Ashling; Ohlendieck, Kay

    2015-02-01

    The highly complex and species-selective mechanism of fertilization is a central theme of developmental biology. Gametogenesis, sperm activation, and egg-sperm recognition are fundamental biological processes, warranting detailed studies into the molecular composition of gametes. Biological MS has been instrumental for the comprehensive itemizing of gamete proteomes. The protein constellation of sperm cells and its subcellular structures has been established for a variety of animal species. Spermatogenesis and the crucial activation of sperm cells as a prerequisite of successful fertilization and physiological adaptations to external stressors was investigated using proteomics, as well as the underlying mechanisms of male infertility with respect to proteome-wide alterations. This review outlines recent achievements of sperm proteomics and exemplifies the usefulness of gel-based surveys by outlining the comparative analysis of abnormal spermatozoa in globozoospermia. Besides label-free MS techniques and cell-based labeling methodology, high-resolution fluorescence 2DE has been shown to be highly suitable as a proteomic biomarker discovery tool in sperm protein research. The appropriateness of novel protein markers for improving our understanding of normal spermatogenesis and sperm activation versus the molecular pathogenesis of male infertility will be discussed. New biomarker candidates might be useful to improve diagnostic, prognostic, and therapeutic aspects of infertility.

  18. Proteomic profile of dormant Trichophyton Rubrum conidia

    PubMed Central

    Leng, Wenchuan; Liu, Tao; Li, Rui; Yang, Jian; Wei, Candong; Zhang, Wenliang; Jin, Qi

    2008-01-01

    Background Trichophyton rubrum is the most common dermatophyte causing fungal skin infections in humans. Asexual sporulation is an important means of propagation for T. rubrum, and conidia produced by this way are thought to be the primary cause of human infections. Despite their importance in pathogenesis, the conidia of T. rubrum remain understudied. We intend to intensively investigate the proteome of dormant T. rubrum conidia to characterize its molecular and cellular features and to enhance the development of novel therapeutic strategies. Results The proteome of T. rubrum conidia was analyzed by combining shotgun proteomics with sample prefractionation and multiple enzyme digestion. In total, 1026 proteins were identified. All identified proteins were compared to those in the NCBI non-redundant protein database, the eukaryotic orthologous groups database, and the gene ontology database to obtain functional annotation information. Functional classification revealed that the identified proteins covered nearly all major biological processes. Some proteins were spore specific and related to the survival and dispersal of T. rubrum conidia, and many proteins were important to conidial germination and response to environmental conditions. Conclusion Our results suggest that the proteome of T. rubrum conidia is considerably complex, and that the maintenance of conidial dormancy is an intricate and elaborate process. This data set provides the first global framework for the dormant T. rubrum conidia proteome and is a stepping stone on the way to further study of the molecular mechanisms of T. rubrum conidial germination and the maintenance of conidial dormancy. PMID:18578874

  19. Mitochondrial Proteome Studies in Seeds during Germination

    PubMed Central

    Czarna, Malgorzata; Kolodziejczak, Marta; Janska, Hanna

    2016-01-01

    Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination. PMID:28248229

  20. Proteomics studies on stress responses in diatoms.

    PubMed

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

    2015-12-01

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

  1. Proteome studies of bacterial antibiotic resistance mechanisms.

    PubMed

    Vranakis, Iosif; Goniotakis, Ioannis; Psaroulaki, Anna; Sandalakis, Vassilios; Tselentis, Yannis; Gevaert, Kris; Tsiotis, Georgios

    2014-01-31

    Ever since antibiotics were used to help humanity battle infectious diseases, microorganisms straight away fought back. Antibiotic resistance mechanisms indeed provide microbes with possibilities to by-pass and survive the action of antibiotic drugs. Several methods have been employed to identify these microbial resistance mechanisms in an ongoing effort to reduce the steadily increasing number of treatment failures due to multi-drug-resistant microbes. Proteomics has evolved to an important tool for this area of research. Following rapid advances in whole genome sequencing, proteomic technologies have been widely used to investigate microbial gene expression. This review highlights the contribution of proteomics in identifying microbial drug resistance mechanisms. It summarizes different proteomic studies on bacteria resistant to different antibiotic drugs. The review further includes an overview of the methodologies used, as well as lists key proteins identified, thus providing the reader not only a summary of research already done, but also directions for future research. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

  2. The Tetrahymena thermophila phagosome proteome.

    PubMed

    Jacobs, Mary Ellen; DeSouza, Leroi V; Samaranayake, Haresha; Pearlman, Ronald E; Siu, K W Michael; Klobutcher, Lawrence A

    2006-12-01

    In vertebrates, phagocytosis occurs mainly in specialized cells of the immune system and serves as a primary defense against invading pathogens, but it also plays a role in clearing apoptotic cells and in tissue remodeling during development. In contrast, unicellular eukaryotes, such as the ciliate Tetrahymena thermophila, employ phagocytosis to ingest and degrade other microorganisms to meet their nutritional needs. To learn more about the protein components of the multistep process of phagocytosis, we carried out an analysis of the Tetrahymena phagosome proteome. Tetrahymena cells were fed polystyrene beads, which allowed for the efficient purification of phagosomes. The protein composition of purified phagosomes was then analyzed by multidimensional separation coupled with tandem mass spectrometry. A total of 453 peptides were identified that resulted in the identification of 73 putative phagosome proteins. Twenty-eight of the proteins have been implicated in phagocytosis in other organisms, indicating that key aspects of phagocytosis were conserved during evolution. Other identified proteins have not previously been associated with phagocytosis, including some of unknown function. Live-cell confocal fluorescence imaging of Tetrahymena strains expressing green fluorescent protein-tagged versions of four of the identified phagosome proteins provided evidence that at least three of the proteins (including two with unknown functions) are associated with phagosomes, indicating that the bulk of the proteins identified in the analyses are indeed phagosome associated.

  3. A proteomic Ramachandran plot (PRplot).

    PubMed

    Carugo, Oliviero; Djinović-Carugo, Kristina

    2013-02-01

    Each protein structure can be characterized by the average values of the main chain torsion angles ϕ and ψ and, as a consequence, be plotted on a bidimensional diagram, which resembles the Ramachandran plot. Here, we describe a proteomic ϕ-ψ plot (PRplot) where each protein structure is associated with one point, allowing in this way to represent the entire protein structure universe. It was verified that the PRplot is a robust tool since it does not depend on the dimension of the proteins, on the crystallographic resolution of the structures, nor on the biological source; moreover, it is little affected by disordered and structurally uncharacterized residues. The proteins mapped on the PRplot tend to cluster in three regions that correspond to the structures rich in alpha-helices, in beta-strands, and in both helices and strands, and are distributed along a sigmoidal curve that connect these three highly populated regions. PRplots are a unique instrument to project all protein structures on a single bidimensional plane where the entire structural complexity is reduced to a striking simplicity, with the sigmoid curve clearly delineating the space fraction accessible to a stable protein.

  4. [Proteomic biomarkers in Parkinson's disease].

    PubMed

    Bandrés, Sara; Durán, Raquel; Barrero, Francisco; Ramírez, Manuel; Vives, Francisco

    2014-02-16

    Parkinson's disease (PD) is a neurodegenerative disorder that affects movement and is caused by the death of the dopaminergic neurons in the compact part of the substantia nigra. Its diagnosis is essentially clinical, but although the signs and symptoms of PD are well known, the rate of diagnostic error is relatively high. It is estimated that 10-30% of patients initially diagnosed with PD are later reclassified. This disease has a high prevalence beyond the age of 60, and one of its biggest problems is that it is diagnosed when the degenerative process is already at a very advanced stage. Therefore, it is necessary to look for other biomarkers that make it possible to carry out an early diagnosis of PD, follow up its development, distinguish it from other related pathologies (parkinsonisms) and help monitor the effect of novel therapies. The fact that there are mutations that lead to PD, as well as polygenetic combinations that can act as risk factors, suggests the possibility of measuring the proteins resulting from the expression of these genes in peripheral tissues. And once their sensitivity and specificity have been proved they could be used as biomarkers for PD, even in the early phases of the disease. The aim of this work is to focus on a detailed review of the main candidate proteomic biomarkers researched to date by discussing the most recent literature.

  5. Proteomic Analysis of Hair Follicles

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  6. Prefractionation techniques in proteome analysis.

    PubMed

    Righetti, Pier Giorgio; Castagna, Annalisa; Herbert, Ben; Reymond, Frederic; Rossier, Joël S

    2003-08-01

    The present review deals with a number of prefractionation protocols in preparation for two-dimensional map analysis, both in the fields of chromatography and in the field of electrophoresis. In the first case, Fountoulaki's groups has reported just about any chromatographic procedure useful as a prefractionation step, including affinity, ion-exchange, and reversed-phase resins. As a result of the various enrichment steps, several hundred new species, previously undetected in unfractionated samples, could be revealed for the first time. Electrophoretic prefractionation protocols include all those electrokinetic methodologies which are performed in free solution, essentially all relying on isoelectric focusing steps. The devices here reviewed include multichamber apparatus, such as the multicompartment electrolyzer with Immobiline membranes, Off-Gel electrophoresis in a multicup device and the Rotofor, an instrument also based on a multichamber system but exploiting the conventional technique of carrier-ampholyte-focusing. Other instruments of interest are the Octopus, a continuous-flow device for isoelectric focusing in a upward flowing liquid curtain, and the Gradiflow, where different pI cuts are obtained by a multistep passage through two compartments buffered at different pH values. It is felt that this panoply of methods could offer a strong step forward in "mining below the tip of the iceberg" for detecting the "unseen proteome".

  7. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology.

    PubMed

    Lacerda, Carla M R; Reardon, Kenneth F

    2009-01-01

    In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.

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

    PubMed Central

    Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; Ebrahim, Ali; Saunders, Michael A.; Palsson, Bernhard O.

    2016-01-01

    Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. This flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models. PMID:27857205

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

    PubMed

    Fadda, Silvina; Almeida, André M

    2015-11-01

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

  10. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

    PubMed Central

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

    2015-01-01

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

  11. University of Victoria Genome British Columbia Proteomics Centre Partners with CPTAC - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    University of Victoria Genome British Columbia Proteomics Centre, a leader in proteomic technology development, has partnered with the U.S. National Cancer Institute (NCI) to make targeted proteomic assays accessible to the community through NCI’s CPTAC Assay Portal.

  12. Anthelmintic metabolism in parasitic helminths: proteomic insights.

    PubMed

    Brophy, Peter M; MacKintosh, Neil; Morphew, Russell M

    2012-08-01

    Anthelmintics are the cornerstone of parasitic helminth control. Surprisingly, understanding of the biochemical pathways used by parasitic helminths to detoxify anthelmintics is fragmented, despite the increasing global threat of anthelmintic resistance within the ruminant and equine industries. Reductionist biochemistry has likely over-estimated the enzymatic role of glutathione transferases in anthelmintic metabolism and neglected the potential role of the cytochrome P-450 superfamily (CYPs). Proteomic technologies offers the opportunity to support genomics, reverse genetics and pharmacokinetics, and provide an integrated insight into both the cellular mechanisms underpinning response to anthelmintics and also the identification of biomarker panels for monitoring the development of anthelmintic resistance. To date, there have been limited attempts to include proteomics in anthelmintic metabolism studies. Optimisations of membrane, post-translational modification and interaction proteomic technologies in helminths are needed to especially study Phase I CYPs and Phase III ABC transporter pumps for anthelmintics and their metabolites.

  13. Comparative proteomics and difference gel electrophoresis.

    PubMed

    Minden, Jonathan

    2007-12-01

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

  14. Proteomics and metabolomics in inflammatory bowel disease.

    PubMed

    Yau, Yunki; Leong, Rupert W; Zeng, Ming; Wasinger, Valerie C

    2013-07-01

    Genome-wide studies in inflammatory bowel disease (IBD) have allowed us to understand Crohn's disease and ulcerative colitis as forms of related autoinflammatory disorders that arise from a multitude of pathogenic origins. Proteomics and metabolomics are the offspring of genomics that possess unprecedented possibilities to characterize unknown pathogenic pathways. It has been about a decade since proteomics was first applied to IBD, and 5 years for metabolomics. These techniques have yielded novel and potentially important findings, but turning these results into beneficial patient outcomes remains challenging. This review recounts the history and context of clinical IBD developments before and after proteomics and metabolomics IBD in this field, discusses the challenges in consolidating high complexity data with physiological understanding, and provides an outlook on the emerging principles that will help interface the bioanalytical laboratory with IBD prognosis.

  15. Proteomic Technologies for the Study of Osteosarcoma

    PubMed Central

    Byrum, Stephanie D.; Washam, Charity L.; Montgomery, Corey O.; Tackett, Alan J.; Suva, Larry J.

    2012-01-01

    Osteosarcoma is the most common primary bone cancer of children and is established during stages of rapid bone growth. The disease is a consequence of immature osteoblast differentiation, which gives way to a rapidly synthesized incompletely mineralized and disorganized bone matrix. The mechanism of osteosarcoma tumorogenesis is poorly understood, and few proteomic studies have been used to interrogate the disease thus far. Accordingly, these studies have identified proteins that have been known to be associated with other malignancies, rather than being osteosarcoma specific. In this paper, we focus on the growing list of available state-of-the-art proteomic technologies and their specific application to the discovery of novel osteosarcoma diagnostic and therapeutic targets. The current signaling markers/pathways associated with primary and metastatic osteosarcoma that have been identified by early-stage proteomic technologies thus far are also described. PMID:22550414

  16. Characterization of human pineal gland proteome.

    PubMed

    Yelamanchi, Soujanya D; Kumar, Manish; Madugundu, Anil K; Gopalakrishnan, Lathika; Dey, Gourav; Chavan, Sandip; Sathe, Gajanan; Mathur, Premendu P; Gowda, Harsha; Mahadevan, Anita; Shankar, Susarla K; Prasad, T S Keshava

    2016-11-15

    The pineal gland is a neuroendocrine gland located at the center of the brain. It is known to regulate various physiological functions in the body through secretion of the neurohormone melatonin. Comprehensive characterization of the human pineal gland proteome has not been undertaken to date. We employed a high-resolution mass spectrometry-based approach to characterize the proteome of the human pineal gland. A total of 5874 proteins were identified from the human pineal gland in this study. Of these, 5820 proteins were identified from the human pineal gland for the first time. Interestingly, 1136 proteins from the human pineal gland were found to contain a signal peptide domain, which indicates the secretory nature of these proteins. An unbiased global proteomic profile of this biomedically important organ should benefit molecular research to unravel the role of the pineal gland in neuropsychiatric and neurodegenerative diseases.

  17. A Review: Proteomics in Nasopharyngeal Carcinoma

    PubMed Central

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

    2015-01-01

    Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In this review, an overview of proteomics with different samples related to NPC and common proteomics methods was made. In conclusion, identical proteins are sorted as follows: Keratin is ranked the highest followed by such proteins as annexin, heat shock protein, 14-3-3σ, nm-23 protein, cathepsin, heterogeneous nuclear ribonucleoproteins, enolase, triosephosphate isomerase, stathmin, prohibitin, and vimentin. This ranking indicates that these proteins may be NPC-related proteins and have potential value for further studies. PMID:26184160

  18. Sperm proteome and reproductive technologies in mammals.

    PubMed

    Li, Chun-Jin; Wang, Dong; Zhou, Xu

    2016-10-01

    Sperm is highly differentiated cell that can be easily obtained and purified. Mature sperm is considered to be transcriptionally and translationally silent and incapable of protein synthesis. Recently, a large number of proteins have been identified in sperm from different species by using the proteomic approaches. Clinically, sperm proteins can be used as markers for male infertility due to different protein profiles identified in sperm from fertile and infertile male animals. Recent evidences have shown that the conditions of sperm preservation in vitro can also change the sperm protein profiles. This paper reviews the recent scientific publications available to address sperm proteome and their relationship with sperm cryopreservation, capacitation, fertilization, and separation of X and Y sperm. Future directions in the application of sperm proteomics to develop or optimize reproductive technologies in mammals are also discussed.

  19. Supporting tool suite for production proteomics

    PubMed Central

    Ma, Ze-Qiang; Tabb, David L.; Burden, Joseph; Chambers, Matthew C.; Cox, Matthew B.; Cantrell, Michael J.; Ham, Amy-Joan L.; Litton, Michael D.; Oreto, Michael R.; Schultz, William C.; Sobecki, Scott M.; Tsui, Tina Y.; Wernke, Gregory R.; Liebler, Daniel C.

    2011-01-01

    Summary: The large amount of data produced by proteomics experiments requires effective bioinformatics tools for the integration of data management and data analysis. Here we introduce a suite of tools developed at Vanderbilt University to support production proteomics. We present the Backup Utility Service tool for automated instrument file backup and the ScanSifter tool for data conversion. We also describe a queuing system to coordinate identification pipelines and the File Collector tool for batch copying analytical results. These tools are individually useful but collectively reinforce each other. They are particularly valuable for proteomics core facilities or research institutions that need to manage multiple mass spectrometers. With minor changes, they could support other types of biomolecular resource facilities. Availability and Implementation: Source code and executable versions are available under Apache 2.0 License at http://www.vicc.org/jimayersinstitute/data/ Contact: daniel.liebler@vanderbilt.edu PMID:21965817

  20. Unexpected features of the dark proteome

    PubMed Central

    Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S.; Buckley, Michael J.; Tabor, Bruce; Signal, Beth; Gloss, Brian S.; Hammang, Christopher J.; Rost, Burkhard; Schafferhans, Andrea

    2015-01-01

    We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology. PMID:26578815

  1. Salivary and pellicle proteome: A datamining analysis

    PubMed Central

    Schweigel, Hardy; Wicht, Michael; Schwendicke, Falk

    2016-01-01

    We aimed to comprehensively compare two compartmented oral proteomes, the salivary and the dental pellicle proteome. Systematic review and datamining was used to obtain the physico-chemical, structural, functional and interactional properties of 1,515 salivary and 60 identified pellicle proteins. Salivary and pellicle proteins did not differ significantly in their aliphatic index, hydrophaty, instability index, or isoelectric point. Pellicle proteins were significantly more charged at low and high pH and were significantly smaller (10–20 kDa) than salivary proteins. Protein structure and solvent accessible molecular surface did not differ significantly. Proteins of the pellicle were more phosphorylated and glycosylated than salivary proteins. Ion binding and enzymatic activities also differed significantly. Protein-protein-ligand interaction networks relied on few key proteins. The identified differences between salivary and pellicle proteins could guide proteome compartmentalization and result in specialized functionality. Key proteins could be potential targets for diagnostic or therapeutic application. PMID:27966577

  2. Proteomic profiling of skeletal muscle plasticity.

    PubMed

    Ohlendieck, Kay

    2011-10-01

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

  3. Salivary and pellicle proteome: A datamining analysis.

    PubMed

    Schweigel, Hardy; Wicht, Michael; Schwendicke, Falk

    2016-12-14

    We aimed to comprehensively compare two compartmented oral proteomes, the salivary and the dental pellicle proteome. Systematic review and datamining was used to obtain the physico-chemical, structural, functional and interactional properties of 1,515 salivary and 60 identified pellicle proteins. Salivary and pellicle proteins did not differ significantly in their aliphatic index, hydrophaty, instability index, or isoelectric point. Pellicle proteins were significantly more charged at low and high pH and were significantly smaller (10-20 kDa) than salivary proteins. Protein structure and solvent accessible molecular surface did not differ significantly. Proteins of the pellicle were more phosphorylated and glycosylated than salivary proteins. Ion binding and enzymatic activities also differed significantly. Protein-protein-ligand interaction networks relied on few key proteins. The identified differences between salivary and pellicle proteins could guide proteome compartmentalization and result in specialized functionality. Key proteins could be potential targets for diagnostic or therapeutic application.

  4. Advances in Proteomics of Mycobacterium leprae.

    PubMed

    Parkash, O; Singh, B P

    2012-04-01

    Although Mycobacterium leprae was the first bacterial pathogen identified causing human disease, it remains one of the few that is non-cultivable. Understanding the biology of M. leprae is one of the primary challenges in current leprosy research. Genomics has been extremely valuable, nonetheless, functional proteins are ultimately responsible for controlling most aspects of cellular functions, which in turn could facilitate parasitizing the host. Furthermore, bacterial proteins provide targets for most of the vaccines and immunodiagnostic tools. Better understanding of the proteomics of M. leprae could also help in developing new drugs against M. leprae. During the past nearly 15 years, there have been several developments towards the identification of M. leprae proteins employing contemporary proteomics tools. In this review, we discuss the knowledge gained on the biology and pathogenesis of M. leprae from current proteomic studies.

  5. Proteome Profiling—Pitfalls and Progress

    PubMed Central

    Yates III, John R.

    2000-01-01

    In this review we examine the current state of analytical methods in proteomics. The conventional methodology using two-dimensional electrophoresis gels and mass spectrometry is discussed, with particular reference to the advantages and shortcomings thereof. Two recently published methods which offer an alternative approach are presented and discussed, with emphasis on how they can provide information not available via two-dimensional gel electrophoresis. These two methods are the isotope-coded affinity tags approach of Gygi et al. and the two-dimensional liquid chromatography–tandem mass spectrometry approach as presented by Link et al. We conclude that both of these new techniques represent significant advances in analytical methodology for proteome analysis. Furthermore, we believe that in the future biological research will continue to be enhanced by the continuation of such developments in proteomic analytical technology. PMID:10900454

  6. Proteome of the Caenorhabditis elegans oocyte.

    PubMed

    Chik, John K; Schriemer, David C; Childs, Sarah J; McGhee, James D

    2011-05-06

    Oocytes were purified from the temperature-sensitive fertilization-defective fer-1(b232ts) mutant of the nematode Caenorhabditis elegans and used for comprehensive mass spectrometric analysis. Using stringent criteria, 1165 C. elegans proteins were identified; at lower stringency, an additional 288 proteins were identified. We validate the high degree of sample purity and evaluate several possible sources of bias in the proteomic data. We compare the classes of proteins identified in the current oocyte proteome with protein classes identified in our previously determined oocyte transcriptome. The oocyte proteome appears enriched in proteins likely to be needed immediately upon fertilization, whereas the transcriptome appears enriched in molecules and processes needed later in embryogenesis. The current study provides fundamental background information for future more detailed studies of oocyte biology.

  7. Complementary Proteomic Analysis of Protein Complexes

    PubMed Central

    Greco, Todd M.; Miteva, Yana; Conlon, Frank L.; Cristea, Ileana M.

    2013-01-01

    Proteomic characterization of protein complexes leverages the versatile platform of liquid chromatography-tandem mass spectrometry to elucidate molecular and cellular signaling processes underlying the dynamic regulation of macromolecular assemblies. Here, we describe a complementary proteomic approach optimized for immunoisolated protein complexes. As the relative complexity, abundance, and physiochemical properties of proteins can vary significantly between samples, we have provided (1) complementary sample preparation workflows, (2) detailed steps for HPLC and mass spectrometric method development, and (3) a bioinformatic workflow that provides confident peptide/protein identification paired with unbiased functional gene ontology analysis. This protocol can also be extended for characterization of larger complexity samples from whole cell or tissue Xenopus proteomes. PMID:22956100

  8. Integrated Analysis of Transcriptomic and Proteomic Data

    PubMed Central

    Haider, Saad; Pal, Ranadip

    2013-01-01

    Until recently, understanding the regulatory behavior of cells has been pursued through independent analysis of the transcriptome or the proteome. Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions. However, recent studies have shown that the correlation between mRNA and Protein expressions can be low due to various factors such as different half lives and post transcription machinery. Thus, a joint analysis of the transcriptomic and proteomic data can provide useful insights that may not be deciphered from individual analysis of mRNA or protein expressions. This article reviews the existing major approaches for joint analysis of transcriptomic and proteomic data. We categorize the different approaches into eight main categories based on the initial algorithm and final analysis goal. We further present analogies with other domains and discuss the existing research problems in this area. PMID:24082820

  9. Proteomics in diagnosis of prostate cancer.

    PubMed

    Davalieva, K; Polenakovic, M

    2015-01-01

    Prostate cancer (PCa) is the second most frequently diagnosed malignancy in men worldwide. The introduction of prostate specific antigen (PSA) has greatly increased the number of men diagnosed with PCa but at the same time, as a result of the low specificity, led to overdiagnosis, resulting to unnecessary biopsies and high medical cost treatments. The primary goal in PCa research today is to find a biomarker or biomarker set for clear and effecttive diagnosis of PCa as well as for distinction between aggressive and indolent cancers. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, MALDI MS profiling, shotgun proteomics with label-based (ICAT, iTRAQ) and label-free (SWATH) quantification, MudPIT, CE-MS have been applied to the study of PCa in the past 15 years. Various biological samples, including tumor tissue, serum, plasma, urine, seminal plasma, prostatic secretions and prostatic-derived exosomes were analyzed with the aim of identifying diagnostic and prognostic biomarkers and developing a deeper understanding of the disease at the molecular level. This review is focused on the overall analysis of expression proteomics studies in the PCa field investigating all types of human samples in the search for diagnostics biomarkers. Emphasis is given on proteomics platforms used in biomarker discovery and characterization, explored sources for PCa biomarkers, proposed candidate biomarkers by comparative proteomics studies and the possible future clinical application of those candidate biomarkers in PCa screening and diagnosis. In addition, we review the specificity of the putative markers and existing challenges in the proteomics research of PCa.

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

    PubMed

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

    2014-01-01

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

  11. [Application of differential proteomics in mechanism research of acupuncture].

    PubMed

    Yu, Lin-na; Pei, Jian

    2011-08-01

    Proteomics, a new branch of science, has been used to study protein expressions on the molecular level with a dynamic perspective. Organisms under varying states may express different proteins, which results in the set-up of differential proteomics. Research methods of differential proteomics include the separation and identification of proteins. Differential proteomics has a rapid development in recent years. In the study of acupuncture, researchers have reached certain achievements using differential proteomics to investigate the mechanisms of acupuncture treatment for some diseases, including acute spinal cord injury, ischemic cerebrovascular disease, Parkinson's disease and neuralgia.

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

    SciTech Connect

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

    2014-10-10

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

  13. Analysis of the human saliva proteome.

    PubMed

    Amado, Francisco Manuel Lemos; Vitorino, Rui Miguel Pinheiro; Domingues, Pedro Miguel Dimas Neves; Lobo, Maria João Calheiros; Duarte, José Alberto Ramos

    2005-08-01

    Interest in the characterization of the salivary proteome has increased in the last few years. This review discusses the different techniques and methodologies applied to the separation and identification of salivary proteins. Nowadays, proteomic techniques are the state of the art for the analysis of biologic materials and saliva is no exception. 2D electrophoresis and tryptic digest analysis by mass spectrometry are the typical methodology, but new approaches using 2D liquid chromatography/mass spectrometry methods have already been introduced for saliva analysis. Due to their important physiologic role in the oral cavity, low-molecular-weight proteins and peptides are also included in this article and the methodologies discussed.

  14. Pollen cultivation and preparation for proteomic studies.

    PubMed

    Pertl-Obermeyer, Heidi; Obermeyer, Gerhard

    2014-01-01

    The quality of the collected experimental data very much depends on the quality of the biological starting material. Especially the proteome analysis of a highly dynamic system like the germinating and tube-growing pollen grain needs several precautions which allow an accurate and acceptable interpretation of the obtained results. Optimized protocols for pollen collection, storage, and in vitro culture as well as pollen organelle separations are described which help to obtain well-defined and reproducible experimental conditions for the subsequent proteomic analysis.

  15. Unraveling pancreatic islet biology by quantitative proteomics

    SciTech Connect

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

    2011-08-01

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

  16. Considerations about gastric cancer proteomics.

    PubMed

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

    2016-01-01

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

  17. Characterizing the successful student in general chemistry and physical science classes in terms of Jung's personality types as identified by the Myers-Briggs Type Indicator

    NASA Astrophysics Data System (ADS)

    Riley, Wayne David

    1998-11-01

    A student's success in a science class can depend upon previous experiences, motivation, and the level of interest in the subject. Since psychological type is intrinsic to a person's whole being, it can be influential upon the student's motivation and interests. Thus, a study of student psychological types versus the level of success in a class, as measured by a percentage, has potential to uncover certain personality characteristics which may be helpful to or which may hinder a student's learning environment. This study was initiated, using the Myers-Briggs Type Indicator, to evaluate any correlation between a student's personality type and his/her performance in a science class. A total of 1041 students from three classes: Chemistry 121/122, Chemistry 112, Physical Science 100, volunteered for the study. An analysis of variance (ANOVA) was used to determine the levels of significance among sixteen personality types' averages. The results reveal that for the Chemistry 1121/122 course, the average score of the INTJ personality type was 5.1 to 12.6 points higher than every other personality type. The ANOVA identifies 3 personality types with averages significantly below the INTJ at the p < 0.05 significance level. The ANOVA analysis for the Chemistry 112 course identified significances between student scores at p = 0.08. The significance level for the differences among scores for the Physical Science 100 course was determined at a level of p = 0.02. Significance levels for p < 0.05 and <0.01 were identified between several groups in this course. The data suggest, that although personality type may not predict a particular student's success in a science class, students with certain personality traits may be favored in a chemistry class due the structure of the instruction and the presentation of the subject matter.

  18. 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

  19. Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-02-01

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

  1. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

    PubMed Central

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

    2015-01-01

    Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

  2. PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics.

    PubMed

    Nebrich, Grit; Herrmann, Marion; Hartl, Daniela; Diedrich, Madeleine; Kreitler, Thomas; Wierling, Christoph; Klose, Joachim; Giavalisco, Patrick; Zabel, Claus; Mao, Lei

    2009-04-01

    In recent years proteomics became increasingly important to functional genomics. Although a large amount of data is generated by high throughput large-scale techniques, a connection of these mostly heterogeneous data from different analytical platforms and of different experiments is limited. Data mining procedures and algorithms are often insufficient to extract meaningful results from large datasets and therefore limit the exploitation of the generated biological information. In our proteomic core facility, which almost exclusively focuses on 2-DE/MS-based proteomics, we developed a proteomic database custom tailored to our needs aiming at connecting MS protein identification information to 2-DE derived protein expression profiles. The tools developed should not only enable an automatic evaluation of single experiments, but also link multiple 2-DE experiments with MS-data on different levels and thereby helping to create a comprehensive network of our proteomics data. Therefore the key feature of our "PROTEOMER" database is its high cross-referencing capacity, enabling integration of a wide range of experimental data. To illustrate the workflow and utility of the system, two practical examples are provided to demonstrate that proper data cross-referencing can transform information into biological knowledge.

  3. HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease

    SciTech Connect

    Diamond, Deborah L.; Proll, Sean; Jacobs, Jon M.; Chan, Eric Y.; Camp, David G.; Smith, Richard D.; Katze, Michael G.

    2006-08-01

    The wealth of human genome sequence information now available, coupled with technological advances in robotics, nanotechnology, mass spectrometry, and information systems, has given rise to a method of scientific inquiry known as functional genomics. By using these technologies to survey gene expression and protein production on a near global scale, the goal of functional genomics is to assign biological function to genes with currently unknown roles in physiology. This approach carries particular appeal in disease research, where it can uncover the function of previously unknown genes and molecular pathways that are directly involved in disease progression. With this knowledge may come improved diagnostic techniques, prognostic capabilities, and novel therapeutic approaches. In this regard, the continuing evolution of proteomic technologies has resulted in an increasingly greater impact of proteome studies in many areas of research and hepatology is no exception. Our laboratory has been extremely active in this area, applying both genomic and proteomic technologies to the analysis of virus-host interactions in several systems, including the study of hepatitis C virus (HCV) infection and HCV-associated liver disease. Since proteomic technologies are foreign to many hepatologists (and to almost everyone else), this article will provide an overview of proteomic methods and technologies and describe how they're being used to study liver function and disease. We use our studies of HCV infection and HCV-associated liver disease to present an operational framework for performing high throughput proteome analysis and extracting biologically meaningful information.

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

    PubMed Central

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

    2017-01-01

    The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components. We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange. PMID:27924013

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

    PubMed

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

    2017-01-04

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

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

    SciTech Connect

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

    2011-02-01

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

  7. Meeting Report: "Proteomics from Discovery to Function:" 6th Annual Meeting of Proteomics Society, India and International Conference-A Milestone for the Indian Proteomics Community.

    PubMed

    Gupta, Shabarni; Reddy, Panga Jaipal; Ray, Sandipan; Atak, Apurva; Gollapalli, Kishore; Jain, Rekha; Shah, Veenita Grover; Ghantasala, Saicharan; Kumar, Saurabh; Pandala, Narendra Goud; Phapale, Prasad; Pandey, Vishnu Kumar; Zingde, Surekha; Srivastava, Sanjeeva

    2015-06-01

    Proteomics is at the epicenter of post-genomics biotechnologies that are currently driving the next generation system science. Moreover, proteomics is a truly global science. The 6(th) Annual Meeting of Proteomics Society, India (PSI) and International Conference on "Proteomics from Discovery to Function" held from December 7-9, 2014, was a transformative endeavor for global proteomics, bringing together the luminaries in the field of proteomics for the very first time in India. This meeting report presents the lessons learned and the highlights of this international scientific conference that was comprised of nine thematic sessions, pre- and post-conference workshops, and an opportunity to cultivate enduring collaborations for proteomics science to benefit both India and global society. The conference had an unforgettable impression on the participants: for the first time, India hosted past and present President and Council members from the Human Proteome Organization (HUPO), along with eminent scientists and young scholars from India and abroad in the field of proteomics at such a large scale, a major highlight of this international event. In all, the PSI 2014 was a milestone conference that has firmly poised the Indian life sciences community as a leading contributor to post-genomics life sciences, thus cultivating crucial trans-generational capacity and inspiration by recognizing the emerging scholars and omics systems scientists who can think and conduct science from cell to society.

  8. Subcellular localization of the yeast proteome.

    PubMed

    Kumar, Anuj; Agarwal, Seema; Heyman, John A; Matson, Sandra; Heidtman, Matthew; Piccirillo, Stacy; Umansky, Lara; Drawid, Amar; Jansen, Ronald; Liu, Yang; Cheung, Kei-Hoi; Miller, Perry; Gerstein, Mark; Roeder, G Shirleen; Snyder, Michael

    2002-03-15

    Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any eukaryote. Using directed topoisomerase I-mediated cloning strategies and genome-wide transposon mutagenesis, we have epitope-tagged 60% of the Saccharomyces cerevisiae proteome. By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. Extrapolating these data through a computational algorithm employing Bayesian formalism, we define the yeast localizome (the subcellular distribution of all 6100 yeast proteins). We estimate the yeast proteome to encompass approximately 5100 soluble proteins and >1000 transmembrane proteins. Our results indicate that 47% of yeast proteins are cytoplasmic, 13% mitochondrial, 13% exocytic (including proteins of the endoplasmic reticulum and secretory vesicles), and 27% nuclear/nucleolar. A subset of nuclear proteins was further analyzed by immunolocalization using surface-spread preparations of meiotic chromosomes. Of these proteins, 38% were found associated with chromosomal DNA. As determined from phenotypic analyses of nuclear proteins, 34% are essential for spore viability--a percentage nearly twice as great as that observed for the proteome as a whole. In total, this study presents experimentally derived localization data for 955 proteins of previously unknown function: nearly half of all functionally uncharacterized proteins in yeast. To facilitate access to these data, we provide a searchable database featuring 2900 fluorescent micrographs at http://ygac.med.yale.edu.

  9. Subcellular localization of the yeast proteome

    PubMed Central

    Kumar, Anuj; Agarwal, Seema; Heyman, John A.; Matson, Sandra; Heidtman, Matthew; Piccirillo, Stacy; Umansky, Lara; Drawid, Amar; Jansen, Ronald; Liu, Yang; Cheung, Kei-Hoi; Miller, Perry; Gerstein, Mark; Roeder, G. Shirleen; Snyder, Michael

    2002-01-01

    Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any eukaryote. Using directed topoisomerase I-mediated cloning strategies and genome-wide transposon mutagenesis, we have epitope-tagged 60% of the Saccharomyces cerevisiae proteome. By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. Extrapolating these data through a computational algorithm employing Bayesian formalism, we define the yeast localizome (the subcellular distribution of all 6100 yeast proteins). We estimate the yeast proteome to encompass ∼5100 soluble proteins and >1000 transmembrane proteins. Our results indicate that 47% of yeast proteins are cytoplasmic, 13% mitochondrial, 13% exocytic (including proteins of the endoplasmic reticulum and secretory vesicles), and 27% nuclear/nucleolar. A subset of nuclear proteins was further analyzed by immunolocalization using surface-spread preparations of meiotic chromosomes. Of these proteins, 38% were found associated with chromosomal DNA. As determined from phenotypic analyses of nuclear proteins, 34% are essential for spore viability—a percentage nearly twice as great as that observed for the proteome as a whole. In total, this study presents experimentally derived localization data for 955 proteins of previously unknown function: nearly half of all functionally uncharacterized proteins in yeast. To facilitate access to these data, we provide a searchable database featuring 2900 fluorescent micrographs at http://ygac.med.yale.edu. PMID:11914276

  10. Role of Proteomics in Crop Stress Tolerance

    PubMed Central

    Ahmad, Parvaiz; Abdel Latef, Arafat A. H.; Rasool, Saiema; Akram, Nudrat A.; Ashraf, Muhammad; Gucel, Salih

    2016-01-01

    Plants often experience various biotic and abiotic stresses during their life cycle. The abiotic stresses include mainly drought, salt, temperature (low/high), flooding and nutritional deficiency/excess which hamper crop growth and yield to a great extent. In view of a projection 50% of the crop loss is attributable to abiotic stresses. However, abiotic stresses cause a myriad of changes in physiological, molecular and biochemical processes operating in plants. It is now widely reported that several proteins respond to these stresses at pre- and post-transcriptional and translational levels. By knowing the role of these stress inducible proteins, it would be easy to comprehensively expound the processes of stress tolerance in plants. The proteomics study offers a new approach to discover proteins and pathways associated with crop physiological and stress responses. Thus, studying the plants at proteomic levels could help understand the pathways involved in stress tolerance. Furthermore, improving the understanding of the identified key metabolic proteins involved in tolerance can be implemented into biotechnological applications, regarding recombinant/transgenic formation. Additionally, the investigation of identified metabolic processes ultimately supports the development of antistress strategies. In this review, we discussed the role of proteomics in crop stress tolerance. We also discussed different abiotic stresses and their effects on plants, particularly with reference to stress-induced expression of proteins, and how proteomics could act as vital biotechnological tools for improving stress tolerance in plants. PMID:27660631

  11. Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles.

    PubMed

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

    2015-01-01

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

  12. Proteomic Analysis of HIV-Infected Macrophages

    PubMed Central

    Colon, Krystal; Rivera, Linda; Rodriguez-Franco, Eillen; Toro-Nieves, Dianedis

    2010-01-01

    Mononuclear phagocytes (monocytes, macrophages, and microglia) play an important role in innate immunity against pathogens including HIV. These cells are also important viral reservoirs in the central nervous system and secrete inflammatory mediators and toxins that affect the tissue environment and function of surrounding cells. In the era of antiretroviral therapy, there are fewer of these inflammatory mediators. Proteomic approaches including surface enhancement laser desorption ionization, one- and two-dimensional difference in gel electrophoresis, and liquid chromatography tandem mass spectrometry have been used to uncover the proteins produced by in vitro HIV-infected monocytes, macrophages, and microglia. These approaches have advanced the understanding of novel mechanisms for HIV replication and neuronal damage. They have also been used in tissue macrophages that restrict HIV replication to understand the mechanisms of restriction for future therapies. In this review, we summarize the proteomic studies on HIV-infected mononuclear phagocytes and discuss other recent proteomic approaches that are starting to be applied to this field. As proteomic instruments and methods evolve to become more sensitive and quantitative, future studies are likely to identify more proteins that can be targeted for diagnosis or therapy and to uncover novel disease mechanisms. PMID:21153888

  13. Aluminum induced proteome changes in tomato cotyledons

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. The Rhesus Macaque (Macaca mulatta) Sperm Proteome*

    PubMed Central

    Skerget, Sheri; Rosenow, Matthew; Polpitiya, Ashoka; Petritis, Konstantinos; Dorus, Steve; Karr, Timothy L.

    2013-01-01

    Mass spectrometry based proteomics has facilitated sperm composition studies in several mammalian species but no studies have been undertaken in non-human primate species. Here we report the analysis of the 1247 proteins that comprise the Rhesus macaque (Macaca mulatta) sperm proteome (termed the MacSP). Comparative analysis with previously characterized mouse and human sperm proteomes reveals substantial levels of orthology (47% and 40% respectively) and widespread overlap of functional categories based on Gene Ontology analyses. Approximately 10% of macaque sperm genes (113/1247) are significantly under-expressed in the testis as compared with other tissues, which may reflect proteins specifically acquired during epididymal maturation. Phylogenetic and genomic analyses of three MacSP ADAMs (A-Disintegrin and Metalloprotease proteins), ADAM18-, 20- and 21-like, provides empirical support for sperm genes functioning in non-human primate taxa which have been subsequently lost in the lineages leading to humans. The MacSP contains proteasome proteins of the 20S core subunit, the 19S proteasome activator complex and an alternate proteasome activator PA200, raising the possibility that proteasome activity is present in mature sperm. Robust empirical characterization of the Rhesus sperm proteome should greatly expand the possibility for targeted molecular studies of spermatogenesis and fertilization in a commonly used model species for human infertility. PMID:23816990

  15. Shotgun proteome profile of Populus developing xylem.

    PubMed

    Kalluri, Udaya C; Hurst, Gregory B; Lankford, Patricia K; Ranjan, Priya; Pelletier, Dale A

    2009-11-01

    Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here, we report the application of shotgun MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP-like and CHB3-SWI/SNF-related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript-level expression and functional categorization of identified proteins. In addition to finding protein-level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.

  16. Shotgun proteome profile of Populus developing xylem

    SciTech Connect

    Kalluri, Udaya C; Hurst, Gregory {Greg} B; Lankford, Patricia K; Ranjan, Priya; Pelletier, Dale A

    2009-01-01

    Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here we report the application of shotgun tandem mass spectrometry profiling to the proteome of Populus developing xylem. Additionally, we mined public databases to obtain information in support of subcellular localization, transcript-level expression, and functional categorization of these proteins. Nearly 6000 different proteins were identified from the xylem proteome, with over 4400 proteins identified from one or more unique peptides. In addition to finding protein-level evidence of candidate wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, phenylalanine ammonia-lyase, and 4-coumarate:CoA ligase, several other potentially new candidate genes in the pathway were discovered. In order to identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factor and chromatin remodeling proteins were identified using this method, such as LIM and NAC domain transcription factors and CHB3-SWI/SNF-related proteins. Further application of these proteomics methods will enhance understanding not only of cell wall biosynthesis in system biology modeling, but also other plant developmental and physiological pathways.

  17. feature - Office of Cancer Clinical Proteomics Research

    Cancer.gov

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

  18. Proteomic analysis of mitochondria from Caenorhabditis elegans.

    PubMed

    Li, Jing; Cai, Tanxi; Wu, Peng; Cui, Ziyou; Chen, Xiulan; Hou, Junjie; Xie, Zhensheng; Xue, Peng; Shi, Linan; Liu, Pingsheng; Yates, John R; Yang, Fuquan

    2009-10-01

    Mitochondria play essential roles in cell physiological processes including energy production, metabolism, ion homeostasis, cell growth, aging and apoptosis. Proteomic strategies have been applied to the study of mitochondria since 1998; these studies have yielded decisive information about the diverse physiological functions of the organelle. As an ideal model biological system, the nematode Caenorhabditis elegans has been widely used in the study of several diseases, such as metabolic diseases and cancer. However, the mitochondrial proteome of C. elegans remains elusive. In this study, we purified mitochondria from C. elegans and performed a comprehensive proteomic analysis using the shotgun proteomic approach. A total of 1117 proteins have been identified with at least two unique peptides. Their physicochemical and functional characteristics, subcellular locations, related biological processes, and associations with human diseases, especially Parkinson's disease, are discussed. An orthology comparison was also performed between C. elegans and four other model organisms for a general depiction of the conservation of mitochondrial proteins during evolution. This study will provide new clues for understanding the role of mitochondria in the physiological and pathological processes of C. elegans.

  19. Urinary proteomic analysis of chronic allograft nephropathy

    PubMed Central

    O’Riordan, Edmond; Orlova, Tatyana N.; Mendelev, Natalia; Patschan, Daniel; Kemp, Rowena; Chander, Praveen N.; Hu, Rena; Hao, Gang; Gross, Steven S.; Iozzo, Renato V.; Delaney, Veronica; Goligorsky, Michael S.

    2015-01-01

    The pathogenesis of progressive renal allograft injury, which is termed chronic allograft nephropathy (CAN), remains obscure and is currently defined by histology. Prospective protocolbiopsy trials have demonstrated that clinical and standard laboratory tests are insufficiently sensitive indicators of the development and progression of CAN. The study aim was to determine if CAN could be characterized by urinary proteomic data and identify the proteins associated with disease. The urinary proteome of 75 renal transplant recipients and 20 healthy volunteers was analyzed using surface enhanced laser desorption and ionization MS. Patients could be classified into subgroups with normal histology and Banff CAN grades 2-3 with a sensitivity of 86% and a specificity of 92% by applying the classification algorithm Adaboost to urinary proteomic data. Several urinary proteins associated with advanced CAN were identified including α1-micro-globulin, β2-micro-globulin, prealbumin, and endorepellin, the antiangiogenic C-terminal fragment of perlecan. Increased urinary endorepellin was confirmed by ELISA and increased tissue expression of the endorepellin/perlecan ratio by immunofluoresence analysis of renal biopsies. In conclusion, analysis of urinary proteomic data has further characterized the more severe CAN grades and identified urinary endorepellin, as a potential biomarker of advanced CAN. PMID:21136903

  20. Proteomic Profiling of Rat Thyroarytenoid Muscle

    ERIC Educational Resources Information Center

    Welham, Nathan V.; Marriott, Gerard; Bless, Diane M.

    2006-01-01

    Purpose: Proteomic methodologies offer promise in elucidating the systemwide cellular and molecular processes that characterize normal and diseased thyroarytenoid (TA) muscle. This study examined methodological issues central to the application of 2-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2D SDS-PAGE) to the study of…

  1. Proteomics of Primary Cilia by Proximity Labeling

    PubMed Central

    Mick, David U.; Rodrigues, Rachel B.; Leib, Ryan D.; Adams, Christopher M.; Chien, Allis S.; Gygi, Steven P.; Nachury, Maxence V.

    2015-01-01

    SUMMARY While cilia are recognized as important signaling organelles, the extent of ciliary functions remains unknown because of difficulties in cataloguing proteins from mammalian primary cilia. We present a method that readily captures rapid snapshots of the ciliary proteome by selectively biotinylating ciliary proteins using a cilia-targeted proximity labeling enzyme (cilia-APEX). Besides identifying known ciliary proteins, cilia-APEX uncovered several ciliary signaling molecules. The kinases PKA, AMPK and LKB1 were validated as bona fide ciliary proteins and PKA was found to regulate Hedgehog signaling in primary cilia. Furthermore, proteomics profiling of Ift27/Bbs19 mutant cilia correctly detected BBSome accumulation inside Ift27−/− cilia and revealed that β-arrestin 2 and the viral receptor CAR are candidate cargoes of the BBSome. This work demonstrates that proximity labeling can be applied to proteomics of non-membrane-enclosed organelles and suggests that proteomics profiling of cilia will enable a rapid and powerful characterization of ciliopathies. PMID:26585297

  2. Functional proteomics within the genus Lactobacillus.

    PubMed

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

    2016-03-01

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

  3. The genomics and proteomics of biofilm formation

    PubMed Central

    Sauer, Karin

    2003-01-01

    Bacterial communities that are attached to a surface, so-called biofilms, and their inherent resistance to antimicrobial agents are a cause of many persistent and chronic bacterial infections. Recent genomic and proteomic studies have identified many of the genes and gene products differentially expressed during biofilm formation, revealing the complexity of this developmental process. PMID:12801407

  4. Proteomics and chronic inflammatory bowel diseases.

    PubMed

    Felley-Bosco, Emanuela; André, Muriel

    2004-01-01

    Inflammatory bowel diseases (IBD) are relatively frequent in developed countries. Physiopathological events involved in the etiology of IBDs include activation of immune, mesenchymal and epithelial cells. This review gives an overview of the currently applied proteomics technologies. It describes metabolic changes and goes into the approaches using this methodology to understand the molecular mechanisms implicated in the development of the disease.

  5. Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Proteomic analysis of inclusion body myositis.

    PubMed

    Li, Jie; Yin, Chunyue; Okamoto, Hiroaki; Jaffe, Howard; Oldfield, Edward H; Zhuang, Zhengping; Vortmeyer, Alexander O; Rushing, Elisabeth J

    2006-08-01

    Sporadic inclusion body myositis (IBM) is the most frequently acquired inflammatory myopathy of late adult life, yet its diagnostic criteria and pathogenesis remain poorly defined. Because effective treatment is lacking, research efforts have intensified to identify specific markers for this debilitating disorder. In this study, proteomic analysis of 4 cases of sporadic IBM was compared with 5 cases of inflammatory myopathy without clinicopathologic features of IBM to distinguish the IBM-specific proteome. Proteins were separated by 2-dimensional polyacrylamide gel electrophoresis and profiled by mass spectrometric sequencing. Expression of most proteins remained unchanged; however, 16 proteins were upregulated and 6 proteins were downregulated in IBM compared with cases of non-IBM inflammatory myopathy. These IBM-specific proteins included apolipoprotein A-I, amyloid beta precursor protein, and transthyretin, which have been associated with amyloidosis; superoxide dismutase, enolase, and various molecular chaperones indicate perturbations in detoxification, energy metabolism, and protein folding, respectively. The IBM-downregulated proteins mainly serve as carriers for muscle contraction and other normal muscle functions. We further applied Western blot and immunohistochemistry to verify the proteomic findings. This study validates proteomics as a powerful tool in the study of muscle disease and indicates a unique pattern of protein expression in IBM.

  7. Proteome Regulation during Olea europaea Fruit Development

    PubMed Central

    Bianco, Linda; Alagna, Fiammetta; Baldoni, Luciana; Finnie, Christine; Svensson, Birte; Perrotta, Gaetano

    2013-01-01

    Background Widespread in the Mediterranean basin, Olea europaea trees are gaining worldwide popularity for the nutritional and cancer-protective properties of the oil, mechanically extracted from ripe fruits. Fruit development is a physiological process with remarkable impact on the modulation of the biosynthesis of compounds affecting the quality of the drupes as well as the final composition of the olive oil. Proteomics offers the possibility to dig deeper into the major changes during fruit development, including the important phase of ripening, and to classify temporal patterns of protein accumulation occurring during these complex physiological processes. Methodology/Principal Findings In this work, we started monitoring the proteome variations associated with olive fruit development by using comparative proteomics coupled to mass spectrometry. Proteins extracted from drupes at three different developmental stages were separated on 2-DE and subjected to image analysis. 247 protein spots were revealed as differentially accumulated. Proteins were identified from a total of 121 spots and discussed in relation to olive drupe metabolic changes occurring during fruit development. In order to evaluate if changes observed at the protein level were consistent with changes of mRNAs, proteomic data produced in the present work were compared with transcriptomic data elaborated during previous studies. Conclusions/Significance This study identifies a number of proteins responsible for quality traits of cv. Coratina, with particular regard to proteins associated to the metabolism of fatty acids, phenolic and aroma compounds. Proteins involved in fruit photosynthesis have been also identified and their pivotal contribution in oleogenesis has been discussed. To date, this study represents the first characterization of the olive fruit proteome during development, providing new insights into fruit metabolism and oil accumulation process. PMID:23349718

  8. Characterization of protein complexes using targeted proteomics.

    PubMed

    Gomez, Yassel Ramos; Gallien, Sebastien; Huerta, Vivian; van Oostrum, Jan; Domon, Bruno; Gonzalez, Luis Javier

    2014-01-01

    Biological systems are not only controlled by the abundance of individual proteins, but also by the formation of complexes and the dynamics of protein-protein interactions. The identification of the components of protein complexes can be obtained by shotgun proteomics using affinity purification coupled to mass spectrometry. Such studies include the analyses of several samples and experimental controls in order to discriminate true specific interactions from unspecific interactions and contaminants. However, shotgun proteomics have limited quantification capabilities for low abundant proteins on large sample sets due to the undersampling and the stochastic precursor ion selection. In this context, targeted proteomics constitutes a powerful analytical tool to systematically detect and quantify peptides in multiple samples, for instance those obtained from affinity purification experiments. Hypothesis-driven strategies have mainly relied on the selected reaction monitoring (SRM) technique performed on triple quadrupole instruments, which enables highly selective and sensitive measurements of peptides, acting as surrogates of the pre-selected proteins, over a wide range of concentrations. More recently, novel quantitative methods based on high resolution instruments, such as the parallel reaction monitoring (PRM) technique implemented on the quadrupole-orbitrap instrument, have arisen and provided alternatives to perform quantitative analyses with enhanced selectivity.The application of targeted proteomics to protein-protein interaction experiments from plasma and other physiological fluid samples and the inclusion of parallel reaction monitoring (PRM), combined with other recent technology developments opens a vast area for clinical application of proteomics. It is anticipated that it will reveal valuable information about specific, individual, responses against drugs, exogenous proteins or pathogens.

  9. Proteomic analysis of zebrafish caudal fin regeneration.

    PubMed

    Saxena, Sandeep; Singh, Sachin K; Lakshmi, Mula G Meena; Meghah, Vuppalapaty; Bhatti, Bhawna; Swamy, Cherukuvada V Brahmendra; Sundaram, Curam S; Idris, Mohammed M

    2012-06-01

    The epimorphic regeneration of zebrafish caudal fin is rapid and complete. We have analyzed the biomechanism of zebrafish caudal fin regeneration at various time points based on differential proteomics approaches. The spectrum of proteome changes caused by regeneration were analyzed among controls (0 h) and 1, 12, 24, 48, and 72 h postamputation involving quantitative differential proteomics analysis based on two-dimensional gel electrophoresis matrix-assisted laser desorption/ionization and differential in-gel electrophoresis Orbitrap analysis. A total of 96 proteins were found differentially regulated between the control nonregenerating and regenerating tissues of different time points for having at least 1.5-fold changes. 90 proteins were identified as differentially regulated for regeneration based on differential in-gel electrophoresis analysis between the control and regenerating tissues. 35 proteins were characterized for its expression in all of the five regenerating time points against the control samples. The proteins identified and associated with regeneration were found to be directly allied with various molecular, biological, and cellular functions. Based on network pathway analysis, the identified proteome data set for regeneration was majorly associated in maintaining cellular structure and architecture. Also the proteins were found associated for the cytoskeleton remodeling pathway and cellular immune defense mechanism. The major proteins that were found differentially regulated during zebrafish caudal fin regeneration includes keratin and its 10 isoforms, cofilin 2, annexin a1, skeletal α1 actin, and structural proteins. Annexin A1 was found to be exclusively undergoing phosphorylation during regeneration. The obtained differential proteome and the direct association of the various proteins might lead to a new understanding of the regeneration mechanism.

  10. Biogeoscience from a Metallomic and Proteomic Perspective

    NASA Astrophysics Data System (ADS)

    Anbar, A. D.; Shock, E.

    2004-12-01

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

  11. Proteomic technologies for biomarker studies in psychiatry: advances and needs.

    PubMed

    Martins-de-Souza, Daniel; Guest, Paul C; Vanattou-Saifoudine, Natacha; Harris, Laura W; Bahn, Sabine

    2011-01-01

    In the postgenome era, proteomics has arisen as a promising tool for more complete comprehension of diseases and for biomarker discovery. Some of these objectives have already been partly achieved for illnesses such as cancer. In the case of psychiatric conditions, however, proteomic advances have had a less profound impact. Here, we outline the necessity of improving and applying proteomic methods for biomarker discovery and validation in the field of psychiatric disorders. While proteomic-based applications in neurosciences have increased in accuracy and sensitivity over the past 10 years, the development of orthogonal validation technologies has fallen behind. These issues are discussed along with the importance of integrating systems biology approaches and combining proteomics with other research approaches. The future development of such technologies may put proteomics closer to clinical applications in psychiatry.

  12. Proteomic developments in the analysis of formalin-fixed tissue.

    PubMed

    Gustafsson, Ove J R; Arentz, Georgia; Hoffmann, Peter

    2015-06-01

    Retrospective proteomic studies, including those which aim to elucidate the molecular mechanisms driving cancer, require the assembly and characterization of substantial patient tissue cohorts. The difficulty of maintaining and accessing native tissue archives has prompted the development of methods to access archives of formalin-fixed tissue. Formalin-fixed tissue archives, complete with patient meta data, have accumulated for decades, presenting an invaluable resource for these retrospective studies. This review presents the current knowledge concerning formalin-fixed tissue, with descriptions of the mechanisms of formalin fixation, protein extraction, top-down proteomics, bottom-up proteomics, quantitative proteomics, phospho- and glycoproteomics as well as imaging mass spectrometry. Particular attention has been given to the inclusion of proteomic investigations of archived tumour tissue. This article is part of a Special Issue entitled: Medical Proteomics.

  13. Evolution of complexity in the zebrafish synapse proteome.

    PubMed

    Bayés, Àlex; Collins, Mark O; Reig-Viader, Rita; Gou, Gemma; Goulding, David; Izquierdo, Abril; Choudhary, Jyoti S; Emes, Richard D; Grant, Seth G N

    2017-03-02

    The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characterization of the proteomes and ultrastructure of central synapses in zebrafish and analyse the importance of the TSGD. While the TSGD increases overall synapse proteome complexity, the postsynaptic density (PSD) proteome of zebrafish has lower complexity than mammals. A highly conserved set of ∼1,000 proteins is shared across vertebrates. PSD ultrastructural features are also conserved. Lineage-specific proteome differences indicate that vertebrate species evolved distinct synapse types and functions. The data sets are a resource for a wide range of studies and have important implications for the use of zebrafish in modelling human synaptic diseases.

  14. Evolution of complexity in the zebrafish synapse proteome

    PubMed Central

    Bayés, Àlex; Collins, Mark O.; Reig-Viader, Rita; Gou, Gemma; Goulding, David; Izquierdo, Abril; Choudhary, Jyoti S.; Emes, Richard D.; Grant, Seth G. N.

    2017-01-01

    The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characterization of the proteomes and ultrastructure of central synapses in zebrafish and analyse the importance of the TSGD. While the TSGD increases overall synapse proteome complexity, the postsynaptic density (PSD) proteome of zebrafish has lower complexity than mammals. A highly conserved set of ∼1,000 proteins is shared across vertebrates. PSD ultrastructural features are also conserved. Lineage-specific proteome differences indicate that vertebrate species evolved distinct synapse types and functions. The data sets are a resource for a wide range of studies and have important implications for the use of zebrafish in modelling human synaptic diseases. PMID:28252024

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

    PubMed

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

    2013-12-01

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

  16. Optimization of a protein extraction technique for fungal proteomics.

    PubMed

    Bhadauria, Vijai; Peng, You-Liang

    2010-10-01

    Protein extraction is a critical step in any proteomics study. Since most fungi possess a robust cell wall, efficient isolation of total proteins has become challenge to fungal proteomics. To circumvent this bottleneck of fungal proteomics, we standardized a protocol named as Mg/CHAPS extraction by comparing with an established method of protein extraction (Tris/EDTA extraction), using 2-DE and MALDI-TOF MS. Total mycelial proteins were isolated using both protocols from Magnaporthe grisea (causal agent of rice blast disease). Six hundred forty two proteins were resolved on two 2-DE gels corresponding to mycelial proteomes isolated by Mg/CHAPS and Tris/EDTA. Mycelial proteome extracted by Mg/CHAPS showed higher number protein spots than to Tris/EDTA. Quantitative analysis of mycelial proteome, histogram and MS analyses of a protein spot suggested that Mg/CHAPS extraction is more effective than the widely used protocol i.e. Tris/EDTA.

  17. Proteomics quality and standard: from a regulatory perspective.

    PubMed

    Gu, Qiang; Yu, Li-Rong

    2014-01-16

    Proteomics has emerged as a rapidly expanding field dealing with large-scale protein analyses. It is anticipated that proteomics data will be increasingly submitted to the U.S. Food and Drug Administration (FDA) for biomarker qualification or in conjunction with applications for the approval of drugs, medical devices, and other FDA-regulated consumer products. To date, however, no established guideline has been available regarding the generation, submission and assessment of the quality of proteomics data that will be reviewed by regulatory agencies for decision making. Therefore, this commentary is aimed at provoking some thoughts and debates towards developing a framework which can guide future proteomics data submission. The ultimate goal is to establish quality control standards for proteomics data generation and evaluation, and to prepare government agencies such as the FDA to meet future obligations utilizing proteomics data to support regulatory decision.

  18. The Path to Clinical Proteomics Research: Integration of Proteomics, Genomics, Clinical Laboratory and Regulatory Science

    PubMed Central

    Boja, Emily S.

    2011-01-01

    Better biomarkers are urgently needed to cancer detection, diagnosis, and prognosis. While the genomics community is making significant advances in understanding the molecular basis of disease, proteomics will delineate the functional units of a cell, proteins and their intricate interaction network and signaling pathways for the underlying disease. Great progress has been made to characterize thousands of proteins qualitatively and quantitatively in complex biological systems by utilizing multi-dimensional sample fractionation strategies, mass spectrometry and protein microarrays. Comparative/quantitative analysis of high-quality clinical biospecimen (e.g., tissue and biofluids) of human cancer proteome landscape has the potential to reveal protein/peptide biomarkers responsible for this disease by means of their altered levels of expression, post-translational modifications as well as different forms of protein variants. Despite technological advances in proteomics, major hurdles still exist in every step of the biomarker development pipeline. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) has taken a critical step to close the gap between biomarker discovery and qualification by introducing a pre-clinical "verification" stage in the pipeline, partnering with clinical laboratory organizations to develop and implement common standards, and developing regulatory science documents with the US Food and Drug Administration to educate the proteomics community on analytical evaluation requirements for multiplex assays in order to ensure the safety and effectiveness of these tests for their intended use. PMID:21474978

  19. The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science.

    PubMed

    Boja, Emily S; Rodriguez, Henry

    2011-04-01

    Better biomarkers are urgently needed to cancer detection, diagnosis, and prognosis. While the genomics community is making significant advances in understanding the molecular basis of disease, proteomics will delineate the functional units of a cell, proteins and their intricate interaction network and signaling pathways for the underlying disease. Great progress has been made to characterize thousands of proteins qualitatively and quantitatively in complex biological systems by utilizing multi-dimensional sample fractionation strategies, mass spectrometry and protein microarrays. Comparative/quantitative analysis of high-quality clinical biospecimen (e.g., tissue and biofluids) of human cancer proteome landscape has the potential to reveal protein/peptide biomarkers responsible for this disease by means of their altered levels of expression, post-translational modifications as well as different forms of protein variants. Despite technological advances in proteomics, major hurdles still exist in every step of the biomarker development pipeline. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) has taken a critical step to close the gap between biomarker discovery and qualification by introducing a pre-clinical "verification" stage in the pipeline, partnering with clinical laboratory organizations to develop and implement common standards, and developing regulatory science documents with the US Food and Drug Administration to educate the proteomics community on analytical evaluation requirements for multiplex assays in order to ensure the safety and effectiveness of these tests for their intended use.

  20. Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins.

    PubMed

    Omenn, Gilbert S

    2014-05-01

    This article addresses three inter-related subjects: the development of the Human Plasma Proteome Peptide Atlas, the launch of the Human Proteome Project, and the emergence of alternative splice variant transcripts and proteins as important features of evolution and pathogenesis. The current Plasma Peptide Atlas provides evidence on which peptides have been detected for every protein confidently identified in plasma; there are links to their spectra and their estimated abundance, facilitating the planning of targeted proteomics for biomarker studies. The Human Proteome Project (HPP) combines a chromosome-centric C-HPP with a biology and disease-driven B/D-HPP, upon a foundation of mass spectrometry, antibody, and knowledgebase resource pillars. The HPP aims to identify the approximately 7000 "missing proteins" and to characterize all proteins and their many isoforms. Success will enable the larger research community to utilize newly-available peptides, spectra, informative MS transitions, and databases for targeted analyses of priority proteins for each organ and disease. Among the isoforms of proteins, splice variants have the special feature of greatly enlarging protein diversity without enlarging the genome; evidence is accumulating of striking differential expression of splice variants in cancers. In this era of RNA-sequencing and advanced mass spectrometry, it is no longer sufficient to speak simply of increased or decreased expression of genes or proteins without carefully examining the splice variants in the protein mixture produced from each multi-exon gene. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.

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

    PubMed

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

    2016-08-01

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

  2. 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

  3. 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

  4. 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

  5. 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.

  6. Farm animal serum proteomics and impact on human health.

    PubMed

    Di Girolamo, Francesco; D'Amato, Alfonsina; Lante, Isabella; Signore, Fabrizio; Muraca, Marta; Putignani, Lorenza

    2014-09-01

    Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum proteomics in order to identify novel biomarkers for animal welfare, early diagnosis, prognosis and monitoring of infectious disease treatment, and develop new vaccines, aiming at determining the reciprocal benefits for humans and animals.

  7. Application of proteomics in phylogenetic and evolutionary studies.

    PubMed

    Navas, Alfonso; Albar, Juan Pablo

    2004-02-01

    There are few papers that deal specifically with evolutionary studies and proteomics. However, applying proteomics to these studies promises to open new perspectives apropos the construction of phylogenetic trees and the detection of evolutionary changes. Principles and methods of phylogenetic systematics could be used to compare and evaluate proteomes. This would permit the detection and characterization of specific proteins that have evolutionary value in defining monophyly, paraphyly, and polyphyly.

  8. Utility, limitations, and promise of proteomics in animal science.

    PubMed

    Lippolis, John D; Reinhardt, Timothy A

    2010-12-15

    Proteomics experiments have the ability to simultaneously identify and quantify thousands of proteins in one experiment. The use of this technology in veterinary/animal science is still in its infancy, yet it holds significant promise as a method for advancing veterinary/animal science research. Examples of current experimental designs and capabilities of proteomic technology and basic principles of mass spectrometry are discussed. In addition, challenges and limitations of proteomics are presented, stressing those that are unique to veterinary/animal sciences.

  9. Dissociation techniques in mass spectrometry-based proteomics.

    PubMed

    Jones, Andrew W; Cooper, Helen J

    2011-09-07

    The field of proteomics, the large-scale analysis of proteins, has undergone a huge expansion over the past decade. Mass spectrometry-based proteomics relies on the dissociation of peptide and/or protein ions to provide information on primary sequence and sites of post-translational modifications. Fragmentation techniques include collision-induced dissociation, electron capture dissociation and electron transfer dissociation. Here, we describe each of these techniques and their use in proteomics. The principles, advantages, limitations, and applications are discussed.

  10. Farm Animal Serum Proteomics and Impact on Human Health

    PubMed Central

    Girolamo, Francesco Di; D’Amato, Alfonsina; Lante, Isabella; Signore, Fabrizio; Muraca, Marta; Putignani, Lorenza

    2014-01-01

    Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum proteomics in order to identify novel biomarkers for animal welfare, early diagnosis, prognosis and monitoring of infectious disease treatment, and develop new vaccines, aiming at determining the reciprocal benefits for humans and animals. PMID:25257521

  11. Technical note: proteomic approaches to fundamental questions about neutrophil biology.

    PubMed

    McLeish, Kenneth R; Merchant, Michael L; Klein, Jon B; Ward, Richard A

    2013-10-01

    Proteomics is one of a group of technologies that generates high-throughput, large-scale datasets that can be used to understand cell or organ functions at a systems level. This review will focus on the application of proteomics to the understanding of neutrophil biology. The strengths and weaknesses of common proteomic methods and their application to neutrophils are reviewed, with the goal of evaluating whether the technology is ready to advance our understanding of neutrophil biology.

  12. Proteomic dissection of plant responses to various pathogens.

    PubMed

    Fang, Xianping; Chen, Jianping; Dai, Liangying; Ma, Huasheng; Zhang, Hengmu; Yang, Jian; Wang, Fang; Yan, Chengqi

    2015-05-01

    During their growth and development, plants are vulnerable to the effects of a variety of pathogens. Proteomics technology plays an important role in research studies of plant defense mechanisms by mining the expression changes of proteins in response to various biotic stresses. This review article provides a comprehensive overview of the latest developments in international proteomic research on plant biotic stress. It summarizes the methods commonly used in plant proteomic research to investigate biotic stress, analyze the protein responses of plants in adverse conditions, and reviews the applications of proteomics combined with transgenic technology in plant protection.

  13. Proteomics, biomarkers, and HIV‐1: A current perspective

    PubMed Central

    Donnelly, Maire Rose

    2015-01-01

    Despite more than three decades of extensive research, HIV‐1 infection although well controlled with cART, remains incurable. Multifactorial complexity of the viral life‐cycle poses great challenges in understanding molecular mechanisms underlying this infection and the development of biomarkers, which we hope will lead us to its eradication. For a more in‐depth understanding of how the virus interacts with host target cells, T cells and macrophages, proteomic profiling techniques that offer strategies to investigate the proteome in its entirety were employed. Here, we review proteomic studies related to HIV‐1 infection and discuss perspectives and limitations of proteomic and systems biology approaches in future studies. PMID:26033875

  14. Mathematical biodescriptors of proteomics maps: background and applications.

    PubMed

    Basak, Subhash C; Gute, Brian D

    2008-05-01

    This article reviews recent developments in the formulation and application of biodescriptors to characterize proteomics maps. Such biodescriptors can be derived by applying techniques from discrete mathematics (graph theory, linear algebra and information theory). This review focuses on the development of biodescriptors for proteomics maps derived from 2D gel electrophoresis. Preliminary results demonstrated that such descriptors have a reasonable ability to differentiate between proteomics patterns that result from exposure to closely related individual chemicals and complex mixtures, such as the jet fuel JP-8. Further research is required to evaluate the utility of these proteomics-based biodescriptors for drug discovery and predictive toxicology.

  15. Biomarker discovery in transplantation--proteomic adventure or mission impossible?

    PubMed

    Kienzl-Wagner, Katrin; Pratschke, Johann; Brandacher, Gerald

    2013-04-01

    Optimal management of transplanted organs requires specific and sensitive biomarkers for immunologic graft monitoring and subsequently patient tailored treatment. Proteomic science has emerged as an attractive tool in clinical biomarker research generating massive amounts of proteomic-driven data. However, critical interpretation of these data requires basic knowledge of proteomic principles and technology. This review provides an overview of proteomic approaches along with their advantages and limitations. Furthermore, this article summarizes the current status of biomarker achievements in the different areas of solid organ transplantation and discusses the hurdles that have precluded routine clinical application of these promising markers so far.

  16. Submitting proteomics data to PRIDE using PRIDE Converter.

    PubMed

    Barsnes, Harald; Vizcaíno, Juan Antonio; Reisinger, Florian; Eidhammer, Ingvar; Martens, Lennart

    2011-01-01

    With the continuously growing amount of proteomics data being produced, it has become increasingly important to make these data publicly available so that they can be audited, reanalyzed, and reused. More and more journals are also starting to request the deposition of MS data in publicly available repositories for submitted proteomics manuscripts. In this chapter we focus on one of the most commonly used proteomics data repositories, PRIDE (the PRoteomics IDEntifications database, http://www.ebi.ac.uk/pride), and demonstrate how a new graphical user interface tool called PRIDE Converter (http://pride-converter.googlecode.com) greatly simplifies the submission of data to PRIDE.

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

    PubMed

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

    2012-10-26

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

  18. ISPIDER Central: an integrated database web-server for proteomics.

    PubMed

    Siepen, Jennifer A; Belhajjame, Khalid; Selley, Julian N; Embury, Suzanne M; Paton, Norman W; Goble, Carole A; Oliver, Stephen G; Stevens, Robert; Zamboulis, Lucas; Martin, Nigel; Poulovassillis, Alexandra; Jones, Philip; Côté, Richard; Hermjakob, Henning; Pentony, Melissa M; Jones, David T; Orengo, Christine A; Hubbard, Simon J

    2008-07-01

    Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.

  19. ISPIDER Central: an integrated database web-server for proteomics

    PubMed Central

    Siepen, Jennifer A.; Belhajjame, Khalid; Selley, Julian N.; Embury, Suzanne M.; Paton, Norman W.; Goble, Carole A.; Oliver, Stephen G.; Stevens, Robert; Zamboulis, Lucas; Martin, Nigel; Poulovassillis, Alexandra; Jones, Philip; Côté, Richard; Hermjakob, Henning; Pentony, Melissa M.; Jones, David T.; Orengo, Christine A.; Hubbard, Simon J.

    2008-01-01

    Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics. PMID:18440977

  20. Molecular biology tools: proteomics techniques in biomarker discovery.

    PubMed

    Lottspeich, Friedrich; Kellermann, Josef; Keidel, Eva-Maria

    2010-01-01

    Despite worldwide efforts biomarker discovery by plasma proteomics was not successful so far. Several reasons for this failure are obvious. Mainly, proteome diversity is remarkable between different individuals and is caused by genetic, environmental and life style parameters. To recognize disease related proteins that could serve as potential biomarkers is only feasible by investigating a non realizable large number of patients. Furthermore, plasma proteomics comprises enormous technical hurdles for quantitative analysis. High reproducibility of blood sampling in clinical routine is hard to achieve. Quantitative proteome analysis has to struggle with the complexity of millions of protein species comprising typical plasma proteins, cellular leakage proteins and antibodies and concentration differences of more than 1011 between high and low abundant proteins. Therefore, no successful quantitative and comprehensive plasma proteome analysis is reported so far. A novel proteomics strategy is proposed for biomarker discovery in plasma. Instead of comparing the plasma proteome of different individuals it is recommended to analyze the proteomes of different time points of a single individual during the development of a disease. This strategy is realized by the use of plasma of the Bavarian Red Cross Blood Bank, were three million samples are stored under standardized conditions. To achieve reliable data the isotope coded protein labelling proteomics technology was used.

  1. The proteomes of the human eye, a highly compartmentalized organ

    PubMed Central

    Omenn, Gilbert S.

    2017-01-01

    Proteomics has now published a series of Dataset Briefs on the EyeOme from the HUPO Human Proteome Project with high-quality analyses of the proteomes of these compartments of the human eye: retina, iris, ciliary body, retinal pigment epithelium/choroid, retrobulbar optic nerve, and sclera, with 3436, 2929, 2867, 2755, 2711, and 1945 proteins, respectively. These proteomics resources represent a useful starting point for a broad range of research aimed at developing preventive and therapeutic interventions for the various causes of blindness. PMID:27860232

  2. Proliferating cell nuclear antigen: a proteomics view.

    PubMed

    Naryzhny, S N

    2008-11-01

    Proliferating cell nuclear antigen (PCNA), a cell cycle marker protein, is well known as a DNA sliding clamp for DNA polymerase delta and as an essential component for eukaryotic chromosomal DNA replication and repair. Due to its mobility inside nuclei, PCNA is dynamically presented in a soluble or chromatin-associated form. The heterogeneity and specific modifications of PCNA may reflect its multiple functions and the presence of many binding partners in the cell. The recent proteomics approaches applied to characterizing PCNA interactions revealed multiple PCNA partners with a wide spectrum of activity and unveiled the possible existence of new PCNA functions. Since more than 100 PCNA-interacting proteins and several PCNA modifications have already been reported, a proteomics point of view seems exactly suitable to better understand the role of PCNA in cellular functions.

  3. Applying proteomic technology to clinical virology.

    PubMed

    Mancone, C; Ciccosanti, F; Montaldo, C; Perdomo, A B; Piacentini, M; Alonzi, T; Fimia, G M; Tripodi, M

    2013-01-01

    Developing antiviral drugs, vaccines and diagnostic markers is still the most ambitious challenge in clinical virology. In the past few decades, data from high-throughput technologies have allowed for the rapid development of new antiviral therapeutic strategies, thus making a profound impact on translational research. Most of the current preclinical studies in virology are aimed at evaluating the dynamic composition and localization of the protein platforms involved in various host-virus interactions. Among the different possible approaches, mass spectrometry-based proteomics is increasingly being used to define the protein composition in subcellular compartments, quantify differential protein expression among samples, characterize protein complexes, and analyse protein post-translational modifications. Here, we review the current knowledge of the most useful proteomic approaches in the study of viral persistence and pathogenicity, with a particular focus on recent advances in hepatitis C research.

  4. Proteomics as a Tool for Understanding Schizophrenia

    PubMed Central

    2011-01-01

    Schizophrenia is likely to be a multifactorial disorder, consequence of alterations in gene and protein expression since the neurodevelopment that together to environmental factors will trigger the establishment of the disease. In the post-genomic era, proteomics has emerged as a promising strategy for revealing disease and treatment biomarkers as well as a tool for the comprehension of the mechanisms of schizophrenia pathobiology. Here, there is a discussion of the potential pathways and structures that are compromised in schizophrenia according to proteomic findings while studying five distinct brain regions of post-mortem tissue from schizophrenia patients and controls. Proteins involved in energy metabolism, calcium homeostasis, myelinization, and cytoskeleton have been recurrently found to be differentially expressed in schizophrenia brains. These findings may encourage new studies on the understanding of schizophrenia biochemical pathways and even new potential drug targets. PMID:23430140

  5. Redox proteomics in the mussel, Mytilus edulis.

    PubMed

    McDonagh, B; Tyther, R; Sheehan, D

    2006-07-01

    Pollutants (e.g. PAHs, metals) cause oxidative stress (OS) by forming reactive oxygen species. Redox proteomics provides a means for identifying protein-specific OS effects in Mytilus edulis. Groups of mussels were sampled from a clean site in Cork Harbour, Ireland and exposed to 1 mM H2O2 in holding tanks. Protein extracts of gill and digestive gland were separated by two dimensional electrophoresis and similar protein expression profiles were found. Effects of OS on disulphide bridge patterns were investigated in diagonal gels by separating proteins in non-reducing conditions followed by a second reducing dimension. Immunoprecipitation selected carbonylated and glutathionylated proteins. These methodologies can contribute to redox proteomic studies of pollutant responses in marine organisms.

  6. Sperm Proteome: What Is on the Horizon?

    PubMed

    Mohanty, Gayatri; Swain, Nirlipta; Samanta, Luna

    2015-06-01

    As the mammalian spermatozoa transcends from the testis to the end of the epididymal tubule, the functionally incompetent spermatozoa acquires its fertilizing capability. Molecular changes in the spermatozoa at the posttesticular level concern qualitative and quantitative modifications of proteins along with their sugar moieties and membranous lipids mostly associated with motility, egg binding, and penetration processes. Proteomic studies have identified numerous sperm-specific proteins, and recent reports have provided a further understanding of their function with respect to male fertility. High-throughput techniques such as mass spectrometry have shown drastic potential for the identification and study of sperm proteins. In fact, compelling evidence has provided that proteins are critically important in cellular remodeling event and that aberrant expression is associated with pronounced defects in sperm function. This review highlights the posttesticular functional transformation in the epididymis and female reproductive tract with due emphasis on proteomics.

  7. Proteomic Definitions of Mesenchymal Stem Cells

    PubMed Central

    Maurer, Martin H.

    2011-01-01

    Mesenchymal stem cells (MSCs) are pluripotent cells isolated from the bone marrow and various other organs. They are able to proliferate and self-renew, as well as to give rise to progeny of at least the osteogenic, chondrogenic, and adipogenic lineages. Despite this functional definition, MSCs can also be defined by their expression of a distinct set of cell surface markers. In the current paper, studies investigating the proteome of human MSCs are reviewed with the aim to identify common protein markers of MSCs. The proteomic analysis of MSCs revealed a distinct set of proteins representing the basic molecular inventory, including proteins for (i) cell surface markers, (ii) the responsiveness to growth factors, (iii) the reuse of developmental signaling cascades in adult stem cells, (iv) the interaction with molecules of the extracellular matrix, (v) the expression of genes regulating transcription and translation, (vi) the control of the cell number, and (vii) the protection against cellular stress. PMID:21437194

  8. Comprehensive data analysis of human ureter proteome

    PubMed Central

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

    2016-01-01

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

  9. Dynamics of subcellular proteomes during brain development.

    PubMed

    McClatchy, Daniel B; Liao, Lujian; Lee, Ji Hyoung; Park, Sung Kyu; Yates, John R

    2012-04-06

    Many neurological disorders are caused by perturbations during brain development, but these perturbations cannot be readily identified until there is comprehensive description of the development process. In this study, we performed mass spectrometry analysis of the synaptosomal and mitochondrial fractions from three rat brain regions at four postnatal time points. To quantitate our analysis, we employed (15)N labeled rat brains using a technique called SILAM (stable isotope labeling in mammals). We quantified 167429 peptides and identified over 5000 statistically significant changes during development including known disease-associated proteins. Global analysis revealed distinct trends between the synaptic and nonsynaptic mitochondrial proteomes and common protein networks between regions each consisting of a unique array of expression patterns. Finally, we identified novel regulators of neurodevelopment that possess the identical temporal pattern of known regulators of neurodevelopment. Overall, this study is the most comprehensive quantitative analysis of the developing brain proteome to date, providing an important resource for neurobiologists.

  10. Statistical Aspects in Proteomic Biomarker Discovery.

    PubMed

    Jung, Klaus

    2016-01-01

    In the pursuit of a personalized medicine, i.e., the individual treatment of a patient, many medical decision problems are desired to be supported by biomarkers that can help to make a diagnosis, prediction, or prognosis. Proteomic biomarkers are of special interest since they can not only be detected in tissue samples but can also often be easily detected in diverse body fluids. Statistical methods play an important role in the discovery and validation of proteomic biomarkers. They are necessary in the planning of experiments, in the processing of raw signals, and in the final data analysis. This review provides an overview on the most frequent experimental settings including sample size considerations, and focuses on exploratory data analysis and classifier development.

  11. Preparation and proteomic analysis of chloroplast ribosomes.

    PubMed

    Yamaguchi, Kenichi

    2011-01-01

    Proteomics of chloroplast ribosomes in spinach and Chlamydomonas revealed unique protein composition and structures of plastid ribosomes. These studies have suggested the presence of some ribosomal proteins unique to plastid ribosomes which may be involved in plastid-unique translation regulation. Considering the strong background of genetic analysis and molecular biology in Arabidopsis, the in-depth proteomic characterization of Arabidopsis plastid ribosomes would facilitate further understanding of plastid translation in higher plants. Here, I describe simple and rapid methods for the preparation of plastid ribosomes from Chlamydomonas and Arabidopsis using sucrose gradients. I also describe purity criteria and methods for yield estimation of the purified plastid ribosomes and subunits, methods for the preparation of plastid ribosomal proteins, as well as the identification of some Arabidopsis plastid ribosomal proteins by matrix-assisted laser desorption/ionization mass spectrometry.

  12. Leveraging Genomics Software to Improve Proteomics Results

    SciTech Connect

    Fodor, I K; Nelson, D O

    2005-09-06

    Rigorous data analysis techniques are essential in quantifying the differential expression of proteins in biological samples of interest. Statistical methods from the microarray literature were applied to the analysis of two-dimensional difference gel electrophoresis (2-D DIGE) proteomics experiments, in the context of technical variability studies involving human plasma. Protein expression measurements were corrected to account for observed intensity-dependent biases within gels, and normalized to mitigate observed gel to gel variations. The methods improved upon the results achieved using the best currently available 2-D DIGE proteomics software. The spot-wise protein variance was reduced by 10% and the number of apparently differentially expressed proteins was reduced by over 50%.

  13. Proteomics Development and Application for Bioforensics

    SciTech Connect

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

    2010-09-15

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

  14. Serum proteomics of glioma: methods and applications.

    PubMed

    Somasundaram, Kumaravel; Nijaguna, Mamatha B; Kumar, Durairaj Mohan

    2009-10-01

    The prognosis of patients with glioblastoma, the most malignant adult glial brain tumor, remains poor in spite of advances in treatment procedures, including surgical resection, irradiation and chemotherapy. Genetic heterogeneity of glioblastoma warrants extensive studies in order to gain a thorough understanding of the biology of this tumor. While there have been several studies of global transcript profiling of glioma with the identification of gene signatures for diagnosis and disease management, translation into clinics is yet to happen. Serum biomarkers have the potential to revolutionize the process of cancer diagnosis, grading, prognostication and treatment response monitoring. Besides having the advantage that serum can be obtained through a less invasive procedure, it contains molecules at an extraordinary dynamic range of ten orders of magnitude in terms of their concentrations. While the conventional methods, such as 2DE, have been in use for many years, the ability to identify the proteins through mass spectrometry techniques such as MALDI-TOF led to an explosion of interest in proteomics. Relatively new high-throughput proteomics methods such as SELDI-TOF and protein microarrays are expected to hasten the process of serum biomarker discovery. This review will highlight the recent advances in the proteomics platform in discovering serum biomarkers and the current status of glioma serum markers. We aim to provide the principles and potential of the latest proteomic approaches and their applications in the biomarker discovery process. Besides providing a comprehensive list of available serum biomarkers of glioma, we will also propose how these markers will revolutionize the clinical management of glioma patients.

  15. Proteomic analysis of human osteoarthritis synovial fluid

    PubMed Central

    2014-01-01

    Background Osteoarthritis is a chronic musculoskeletal disorder characterized mainly by progressive degradation of the hyaline cartilage. Patients with osteoarthritis often postpone seeking medical help, which results in the diagnosis being made at an advanced stage of cartilage destruction. Sustained efforts are needed to identify specific markers that might help in early diagnosis, monitoring disease progression and in improving therapeutic outcomes. We employed a multipronged proteomic approach, which included multiple fractionation strategies followed by high resolution mass spectrometry analysis to explore the proteome of synovial fluid obtained from osteoarthritis patients. In addition to the total proteome, we also enriched glycoproteins from synovial fluid using lectin affinity chromatography. Results We identified 677 proteins from synovial fluid of patients with osteoarthritis of which 545 proteins have not been previously reported. These novel proteins included ADAM-like decysin 1 (ADAMDEC1), alanyl (membrane) aminopeptidase (ANPEP), CD84, fibulin 1 (FBLN1), matrix remodelling associated 5 (MXRA5), secreted phosphoprotein 2 (SPP2) and spondin 2 (SPON2). We identified 300 proteins using lectin affinity chromatography, including the glycoproteins afamin (AFM), attractin (ATRN), fibrillin 1 (FBN1), transferrin (TF), tissue inhibitor of metalloproteinase 1 (TIMP1) and vasorin (VSN). Gene ontology analysis confirmed that a majority of the identified proteins were extracellular and are mostly involved in cell communication and signaling. We also confirmed the expression of ANPEP, dickkopf WNT signaling pathway inhibitor 3 (DKK3) and osteoglycin (OGN) by multiple reaction monitoring (MRM) analysis of osteoarthritis synovial fluid samples. Conclusions We present an in-depth analysis of the synovial fluid proteome from patients with osteoarthritis. We believe that the catalog of proteins generated in this study will further enhance our knowledge regarding the

  16. Proteomic Analysis of Prostate Cancer Field Effect

    DTIC Science & Technology

    2011-02-01

    fragile X mental retardation protein interacting protein 1 [Homo sapiens] alpha-2-macroglobulin precursor [Homo sapiens] filamin A, alpha isoform 1...Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT We have undertaken a novel proteomic approach to identify proteins ...in normal cells, to discover cancer altered protein that could be more abundant in serum or urine since they would come from both benign and cancer

  17. Genomics, proteomics, and genetics of leptospira.

    PubMed

    Picardeau, Mathieu

    2015-01-01

    Recent advances in molecular genetics, such as the ability to construct defined mutants, have allowed the study of virulence factors and more generally the biology in Leptospira. However, pathogenic leptospires remain much less easily transformable than the saprophyte L. biflexa and further development and improvement of genetic tools are required. Here, we review tools that have been used to genetically manipulate Leptospira. We also describe the major advances achieved in both genomics and postgenomics technologies, including transcriptomics and proteomics.

  18. Inside SMP proteomics: six years German Human Brain Proteome Project (HBPP) - a summary.

    PubMed

    Hamacher, Michael; Hardt, Tanja; van Hall, Andre; Stephan, Christian; Marcus, Katrin; Meyer, Helmut E

    2008-03-01

    In 2001, the German Federal Ministry of Education and Research (BMBF) initiated the National Genome Research Network (NGFN; www.ngfn.de) as a nation-wide multidisciplinary networking platform aiming at the analysis of common human diseases and aging. Within the NGFN the Human Brain Proteome Project (HBPP; www.smp-proteomics.de) focuses on the analysis of the human brain in health and disease. The concept is based on two consecutive steps: (i) Elaborating and establishing the necessary technology platforms. (ii) Application of the established technologies for research in Alzheimer's disease and Parkinson's disease. In the first funding period, HBPP1, running from 2001 to 2004, necessary technologies were established and optimized. In HBPP2, which started 2004 and will end in May 2008, the developed technologies are used for large-scale experiments, offering new links for disease related research and therapies. The following overview describes structure, aims and outcome of this unique German Brain Proteome Project.

  19. Characterizing the nuclear proteome of Paracoccidioides spp.

    PubMed

    Oliveira, Lucas Nojosa; Casaletti, Luciana; Báo, Sônia Nair; Borges, Clayton Luiz; de Sousa Lima, Patrícia; de Almeida Soares, Célia Maria

    2016-10-01

    Paracoccidioidomycosis is an endemic disease in Latin America, caused by thermo dimorphic fungi of the genus Paracoccidioides. Although previous proteome analyses of Paracoccidioides spp. have been carried out, the nuclear subproteome of this pathogen has not been described. In this way, we aimed to characterize the nuclear proteome of Paracoccidioides species, in the yeast form. For that, yeast cells were disrupted and submitted to cell fractionation. The purity of the nuclear fraction was confirmed by fluorescence and electron microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allowed the identification of 867 proteins. In order to support our enrichment method for nuclear proteins, bioinformatics analysis were applied that allowed the identification of 281 proteins with nuclear localization. The analysis revealed proteins related to DNA maintenance, gene expression, synthesis and processing of messenger and ribosomal RNAs, likewise proteins of nuclear-cytoplasmic traffic. It was also possible to detect some proteins that are poorly expressed, like transcription factors involved in important roles such as resistance to abiotic stress, sporulation, cellular growth and DNA and chromatin maintenance. This is the first descriptive nuclear proteome of Paracoccidioides spp. that can be useful as an important platform base for fungi-specific nuclear processes.

  20. Defining the extracellular matrix using proteomics

    PubMed Central

    Byron, Adam; Humphries, Jonathan D; Humphries, Martin J

    2013-01-01

    The cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology. PMID:23419153

  1. Proteomics: a biotechnology tool for crop improvement

    PubMed Central

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

    2013-01-01

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

  2. Erythrocyte and platelet proteomics in hematological disorders.

    PubMed

    Chakrabarti, Abhijit; Halder, Suchismita; Karmakar, Shilpita

    2016-04-01

    Erythrocytes undergo ineffective erythropoesis, hemolysis, and premature eryptosis in sickle cell disease and thalassemia. Abnormal hemoglobin variants associated with hemoglobinopathy lead to vesiculation, membrane instability, and loss of membrane asymmetry with exposal of phosphatidylserine. This potentiates thrombin generation resulting in activation of the coagulation cascade responsible for subclinical phenotypes. Platelet activation also results in the release of microparticles, which express and transfer functional receptors from platelet membrane, playing key roles in vascular reactivity and activation of intracellular signaling pathways. Over the last decade, proteomics had proven to be an important field of research in studies of blood and blood diseases. Blood cells and its fluidic components have been proven to be easy systems for studying differential expressions of proteins in hematological diseases encompassing hemoglobinopathies, different types of anemias, myeloproliferative disorders, and coagulopathies. Proteomic studies of erythrocytes and platelets reported from several groups have highlighted various factors that intersect the signaling networks in these anucleate systems. In this review, we have elaborated on the current scenario of anucleate blood cell proteomes in normal and diseased individuals and the cross-talk between the two major constituent cell types of circulating blood.

  3. Proteomic evaluation of sheep serum proteins

    PubMed Central

    2012-01-01

    Background The applications of proteomic strategies to ovine medicine remain limited. The definition of serum proteome may be a good tool to identify useful protein biomarkers for recognising sub-clinical conditions and overt disease in sheep. Findings from bovine species are often directly translated for use in ovine medicine. In order to characterize normal protein patterns and improve knowledge of molecular species-specific characteristics, we generated a two-dimensional reference map of sheep serum. The possible application of this approach was tested by analysing serum protein patterns in ewes with mild broncho-pulmonary disease, which is very common in sheep and in the peripartum period which is a stressful time, with a high incidence of infectious and parasitic diseases. Results This study generated the first reference 2-DE maps of sheep serum. Overall, 250 protein spots were analyzed, and 138 identified. Compared with healthy sheep, serum protein profiles of animals with rhino-tracheo-bronchitis showed a significant decrease in protein spots identified as transthyretin, apolipoprotein A1 and a significant increase in spots identified as haptoglobin, endopin 1b and alpha1B glycoprotein. In the peripartum period, haptoglobin, alpha-1-acid glycoprotein, apolipoprotein A1 levels rose, while transthyretin content dropped. Conclusions This study describes applications of proteomics in putative biomarker discovery for early diagnosis as well as for monitoring the physiological and metabolic situations critical for ovine welfare. PMID:22630135

  4. Oxidative proteome alterations during skeletal muscle ageing.

    PubMed

    Lourenço dos Santos, Sofia; Baraibar, Martin A; Lundberg, Staffan; Eeg-Olofsson, Orvar; Larsson, Lars; Friguet, Bertrand

    2015-08-01

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

  5. Proteomic identification of rainbow trout sperm proteins.

    PubMed

    Nynca, Joanna; Arnold, Georg J; Fröhlich, Thomas; Otte, Kathrin; Ciereszko, Andrzej

    2014-06-01

    Proteomics represents a powerful tool for the analysis of fish spermatozoa, since these cells are transcriptionally inactive. The aim of the present study was to generate an inventory of the most prominent rainbow trout sperm proteins by SDS-PAGE prefractionation combined with nano-LC-MS/MS based identification. This study provides the first in-depth analysis of the rainbow trout sperm proteome, with a total of 206 identified proteins. We found that rainbow trout spermatozoa are equipped with functionally diverse proteins related to energetic metabolism, signal transduction, protein turnover, transport, cytoskeleton, oxidative injuries, and stress and reproduction. The availability of a catalog of rainbow trout sperm proteins provides a crucial tool for the understanding of fundamental molecular processes in fish spermatozoa, for the ongoing development of novel markers of sperm quality and for the optimization of short- and long-term sperm preservation procedures. The MS data are available at ProteomeXchange with the dataset identifier PXD000355 and DOI 10.6019/PXD000355.

  6. Cell wall proteome of pathogenic fungi.

    PubMed

    Karkowska-Kuleta, Justyna; Kozik, Andrzej

    2015-01-01

    A fast development of a wide variety of proteomic techniques supported by mass spectrometry coupled with high performance liquid chromatography has been observed in recent years. It significantly contributes to the progress in research on the cell wall, very important part of the cells of pathogenic fungi. This complicated structure composed of different polysaccharides, proteins, lipids and melanin, plays a key role in interactions with the host during infection. Changes in the set of the surface-exposed proteins under different environmental conditions provide an effective way for pathogens to respond, adapt and survive in the new niches of infection. This work summarizes the current state of knowledge on proteins, studied both qualitatively and quantitatively, and found within the cell wall of fungal pathogens for humans, including Candida albicans, Candida glabrata, Aspergillus fumigatus, Cryptococcus neoformans and other medically important fungi. The described proteomic studies involved the isolation and fractionation of particular sets of proteins of interest with various techniques, often based on differences in their linkages to the polysaccharide scaffold. Furthermore, the proteinaceous contents of extracellular vesicles ("virulence bags") of C. albicans, C. neoformans, Histoplasma capsulatum and Paracoccidioides brasiliensis are compared, because their production can partially explain the problem of non-classical protein secretion by fungi. The role assigned to surface-exposed proteins in pathogenesis of fungal infections is enormously high, thus justifying the need for further investigation of cell wall proteomes.

  7. The broccoli (Brassica oleracea) phloem tissue proteome

    PubMed Central

    2013-01-01

    Background The transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloem. To better understand these processes a comprehensive understanding of the proteins involved is required. While a considerable amount of data has been obtained from proteomic analyses of phloem sap, this has mainly served to identify the soluble proteins that are translocated through the phloem network. Results In order to obtain more comprehensive proteomic data from phloem tissue we developed a simple dissection procedure to isolate phloem tissue from Brassica oleracea. The presence of a high density of phloem sieve elements was confirmed using light microscopy and fluorescently labeled sieve element-specific antibodies. To increase the depth of the proteomic analysis for membrane bound and associated proteins, soluble proteins were extracted first and subsequent extractions were carried out using two different detergents (SDS and CHAPSO). Across all three extractions almost four hundred proteins were identified and each extraction method added to the analysis demonstrating the utility of an approach combining several extraction protocols. Conclusions The phloem was found to be enriched in proteins associated with biotic and abiotic stress responses and structural proteins. Subsequent expression analysis identified a number of genes that appear to be expressed exclusively or at very high levels in phloem tissue, including genes that are known to express specifically in the phloem as well as novel phloem genes. PMID:24195484

  8. Plant-bacterium interactions analyzed by proteomics

    PubMed Central

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

    2013-01-01

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

  9. Proteomics: a biotechnology tool for crop improvement.

    PubMed

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

    2013-01-01

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

  10. Platelet proteome in healthy volunteers who smoke.

    PubMed

    Della Corte, Anna; Tamburrelli, Chiara; Crescente, Marilena; Giordano, Lucia; D'Imperio, Marco; Di Michele, Michela; Donati, Maria Benedetta; De Gaetano, Giovanni; Rotilio, Domenico; Cerletti, Chiara

    2012-01-01

    Smoking accelerates atherosclerosis and is a well-known risk factor for acute cardiovascular complications; however, the mechanisms of these effects have not been completely clarified. Recently developed proteomic approaches may offer new clues when combined with well-established functional tests. Platelet proteome of healthy smokers and non-smokers was resolved by two-dimensional difference gel electrophoresis, compared by Decyder software and identified by mass spectrometry analysis (nano-LC-MS/MS). In smokers, three proteins (Factor XIII-A subunit, platelet glycoprotein IIb and beta-actin) were significantly up-regulated, whereas WDR1 protein and chaperonine HSP60 were down-regulated. Furthermore, the highest scored network derived by Ingenuity Pathway Analysis using the modulated proteins as input showed the involvement of several proteins to be related to inflammation and apoptosis. Platelet function tests and the levels of markers of platelet and leukocyte activation were not different in smokers vs. non-smoker subjects. The platelet proteomic approach confirms that cigarette smoking triggers several inflammatory reactions and may help clarify some of the molecular mechanisms of smoke effect on cellular systems relevant for vascular integrity and human health.

  11. Quantitative proteomics of intracellular Porphyromonas gingivalis

    PubMed Central

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

    2009-01-01

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

  12. Monolithic columns in plant proteomics and metabolomics.

    PubMed

    Rigobello-Masini, Marilda; Penteado, José Carlos Pires; Masini, Jorge Cesar

    2013-03-01

    Since "omics" techniques emerged, plant studies, from biochemistry to ecology, have become more comprehensive. Plant proteomics and metabolomics enable the construction of databases that, with the help of genomics and informatics, show the data obtained as a system. Thus, all the constituents of the system can be seen with their interactions in both space and time. For instance, perturbations in a plant ecosystem as a consequence of application of herbicides or exposure to pollutants can be predicted by using information gathered from these databases. Analytical chemistry has been involved in this scientific evolution. Proteomics and metabolomics are emerging fields that require separation, identification, and quantification of proteins, peptides, and small molecules of metabolites in complex biological samples. The success of this work relies on efficient chromatographic and electrophoretic techniques, and on mass spectrometric detection. This paper reviews recent developments in the use of monolithic columns, focusing on their applications in "top-down" and "bottom-up" approaches, including their use as supports for immobilization of proteolytic enzymes and their use in two-dimensional and multidimensional chromatography. Whereas polymeric columns have been predominantly used for separation of proteins and polypeptides, silica-based monoliths have been more extensively used for separation of small molecules of metabolites. Representative applications in proteomics and in analysis of plant metabolites are given and summarized in tables.

  13. Proteome Analysis of Rheumatoid Arthritis Gut Mucosa.

    PubMed

    Bennike, Tue Bjerg; Ellingsen, Torkell; Glerup, Henning; Bonderup, Ole Kristian; Carlsen, Thomas Gelsing; Meyer, Michael Kruse; Bøgsted, Martin; Christiansen, Gunna; Birkelund, Svend; Andersen, Vibeke; Stensballe, Allan

    2017-01-06

    Rheumatoid arthritis (RA) is an inflammatory joint disease leading to cartilage damage and ultimately impaired joint function. To gain new insight into the systemic immune manifestations of RA, we characterized the colon mucosa proteome from 11 RA-patients and 10 healthy controls. The biopsies were extracted by colonoscopy and analyzed by label-free quantitative proteomics, enabling the quantitation of 5366 proteins. The abundance of dihydrofolate reductase (DHFR) was statistically significantly increased in RA-patient biopsies compared with controls and correlated with the administered dosage of methotrexate (MTX), the most frequently prescribed immunosuppressive drug for RA. Additionally, our data suggest that treatment with Leflunomide, a common alternative to MTX, increases DHFR. The findings were supported by immunohistochemistry with confocal microscopy, which furthermore demonstrated that DHFR was located in the cytosol of the intestinal epithelial and interstitial cells. Finally, we identified 223 citrullinated peptides from 121 proteins. Three of the peptides were unique to RA. The list of citrullinated proteins was enriched in extracellular and membrane proteins and included known targets of anticitrullinated protein antibodies (ACPAs). Our findings support that the colon mucosa could trigger the production of ACPAs, which could contribute to the onset of RA. The MS data have been deposited to ProteomeXchange with identifiers PXD001608 and PXD003082.

  14. Proteomics in the Study of Bacterial Keratitis

    PubMed Central

    Bouhenni, Rachida; Dunmire, Jeffrey; Rowe, Theresa; Bates, James

    2015-01-01

    Bacterial keratitis is a serious ocular infection that can cause severe visual loss if treatment is not initiated at an early stage. It is most commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, or Serratia species. Depending on the invading organism, bacterial keratitis can progress rapidly, leading to corneal destruction and potential blindness. Common risk factors for bacterial keratitis include contact lens wear, ocular trauma, ocular surface disease, ocular surgery, lid deformity, chronic use of topical steroids, contaminated ocular medications or solutions, and systemic immunosuppression. The pathogenesis of bacterial keratitis, which depends on the bacterium-host interaction and the virulence of the invading bacterium, is complicated and not completely understood. This review highlights some of the proteomic technologies that have been used to identify virulence factors and the host response to infections of bacterial keratitis in order to understand the disease process and develop improved methods of diagnosis and treatment. Although work in this field is not abundant, proteomic technologies have provided valuable information toward our current knowledge of bacterial keratitis. More studies using global proteomic approaches are warranted because it is an important tool to identify novel targets for intervention and prevention of corneal damage caused by these virulent microorganisms. PMID:28248282

  15. Proteomics in the Study of Bacterial Keratitis.

    PubMed

    Bouhenni, Rachida; Dunmire, Jeffrey; Rowe, Theresa; Bates, James

    2015-12-14

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

  16. Proteomic Contributions to Personalized Cancer Care*

    PubMed Central

    Koomen, John M.; Haura, Eric B.; Bepler, Gerold; Sutphen, Rebecca; Remily-Wood, Elizabeth R.; Benson, Kaaron; Hussein, Mohamad; Hazlehurst, Lori A.; Yeatman, Timothy J.; Hildreth, Lynne T.; Sellers, Thomas A.; Jacobsen, Paul B.; Fenstermacher, David A.; Dalton, William S.

    2008-01-01

    Cancer impacts each patient and family differently. Our current understanding of the disease is primarily limited to clinical hallmarks of cancer, but many specific molecular mechanisms remain elusive. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies that improve patient prognosis are not widely available for most cancers. Individualized care plans, also described as personalized medicine, still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics holds great promise in contributing to the prevention and cure of cancer because it provides unique tools for discovery of biomarkers and therapeutic targets. As such, proteomics can help translate basic science discoveries into the clinical practice of personalized medicine. Here we describe how biological mass spectrometry and proteome analysis interact with other major patient care and research initiatives and present vignettes illustrating efforts in discovery of diagnostic biomarkers for ovarian cancer, development of treatment strategies in lung cancer, and monitoring prognosis and relapse in multiple myeloma patients. PMID:18664563

  17. Recent advances in plant cell wall proteomics.

    PubMed

    Jamet, Elisabeth; Albenne, Cécile; Boudart, Georges; Irshad, Muhammad; Canut, Hervé; Pont-Lezica, Rafael

    2008-02-01

    The plant extracellular matrix contains typical polysaccharides such as cellulose, hemicelluloses, and pectins that interact to form dense interwoven networks. Plant cell walls play crucial roles during development and constitute the first barrier of defense against invading pathogens. Cell wall proteomics has greatly contributed to the description of the protein content of a compartment specific to plants. Around 400 cell wall proteins (CWPs) of Arabidopsis, representing about one fourth of its estimated cell wall proteome, have been described. The main points to note are that: (i) the diversity of enzymes acting on polysaccharides suggests a great plasticity of cell walls; (ii) CWPs such as proteases, polysaccharide hydrolytic enzymes, and lipases may contribute to the generation of signals; (iii) proteins of unknown functions were identified, suggesting new roles for cell walls. Recently, the characterization of PTMs such as N- and O-glycosylations improved our knowledge of CWP structure. The presence of many glycoside hydrolases and proteases suggests a complex regulation of CWPs involving various types of post-translational events. The first 3-D structures to be resolved gave clues about the interactions between CWPs, or between CWPs and polysaccharides. Future work should include: extracting and identifying CWPs still recalcitrant to proteomics, describing the cell wall interactome, improving quantification, and unraveling the roles of each of the CWPs.

  18. Cancer heterogeneity determined by functional proteomics.

    PubMed

    Szász, A Marcell; Győrffy, Balázs; Marko-Varga, György

    2016-08-26

    Current manuscript gives a synopsis of tumor heterogeneity related to patient samples analyzed by proteomics, protein expression analysis and imaging mass spectrometry. First, we discuss the pathophysiologocal background of cancer biology as a multifactorial and challenging diseases. Disease pathology forms the basis for protein target selection. Therefore, histopathological diagnostics and grading of tumors is highlighted. Pathology is the cornerstone of state-of-the-art diagnostics of tumors today both by establishing dignity and - when needed - describing molecular properties of the cancers. Drug development by the pharmaceutical industry utilizes proteomics studies to pinpoint the most relevant targets. Molecular studies profiling affinity-interactions of the protein(s) with targeted small drug molecules to reach efficacy and optimal patient safety are today requested by the FDA and other agencies for new drug development. An understading of basic mechanisms, controlling drug action and drug binding is central, as a new era of personalized medicine becomes an important milestone solution for the healthcare sector as well as the Pharma and Biotech industry. Development of further diagnostic, prognostic and predictive tests will aid current and future treatment of cancer patients. In the paper we present current status of Proteomics that we believe requires attention in order to collectively advance forward in the fight against cancer, addressing the burning opportunities and challenges.

  19. Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics.

    PubMed

    Arruda, Sandra Cristina Capaldi; Barbosa, Herbert de Sousa; Azevedo, Ricardo Antunes; Arruda, Marco Aurélio Zezzi

    2011-10-21

    The present review reports the principles, fundamentals and some applications of two-dimensional difference gel electrophoresis for analytical proteomics based on plant proteome analysis, also emphasizing some advantages of 2-D DIGE over 2-D PAGE techniques. Some fluorescent protein labeling reagents, methods of protein labeling, models of 2-D DIGE experiments, and some limitations of this technique are presented and discussed in terms of 2-D DIGE plant proteomes. Finally, some practical applications of this technique are pointed out, emphasizing its potentialities in plant proteomics.

  20. The human salivary proteome: a critical overview of the results obtained by different proteomic platforms.

    PubMed

    Castagnola, Massimo; Cabras, Tiziana; Iavarone, Federica; Fanali, Chiara; Nemolato, Sonia; Peluso, Giusy; Bosello, Silvia Laura; Faa, Gavino; Ferraccioli, Gianfranco; Messana, Irene

    2012-01-01

    The development of new separation techniques and different mass spectrometry instrumental devices, as well as the great availability of specific reactants, offers ample choice to scientists for carrying out high-throughput proteomic studies and being competitive in the field today. However, the different options available often do not provide comparable results, which can be linked to factors such as the strategy adopted, the nature of the sample and the instrumental availability. In this critical review, the results obtained so far in the study of human saliva by different proteomic approaches will be compared and discussed.

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

    SciTech Connect

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

    2013-10-03

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

  2. Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea.

    PubMed

    Hamacher, Michael; Stephan, Christian; Hardt, Tanja; Eisenacher, Martin; Henkel, Andreas; Wiltfang, Jens; Jimenez, Connie R; Park, Young Mok; Marcus, Katrin; Meyer, Helmut E

    2008-05-01

    What are the current approaches in brain proteomics? Can we combine different, but complementary study designs to obtain better results concerning brain diseases? What are the neuro-hotspots, especially in Korea? These were some of the questions the participants of the 8(th) HUPO Brain Proteome Project Workshop tried to answer prior to the 6(th) HUPO World Congress in Seoul, Korea. Around 100 scientists came together during the afternoon of 7 October, 2007, to discuss and to catch up on the latest results and strategies concerning Huntington's disease, glioblastoma and standardization.

  3. Edward Adrian Wilson (1872-1912): polar explorer and artist.

    PubMed

    Brown, Kevin

    2012-11-01

    Dr Edward Wilson was a polar explorer who accompanied Robert Falcon Scott (1868-1912) on his expeditions to Antarctica in 1900 and 1910. He went with Scott to the South Pole and died with him on the return journey in 1912. Although medically qualified, he is now remembered more as a naturalist and as a talented artist recording the Antarctic expeditions.

  4. For the relief of Mikael Adrian Christopher Figueroa Alvarez.

    THOMAS, 111th Congress

    Rep. Lofgren, Zoe [D-CA-16

    2009-02-13

    03/10/2009 Referred to the Subcommittee on Immigration, Citizenship, Refugees, Border Security, and International Law. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  5. Proteomics of Trypanosoma evansi Infection in Rodents

    PubMed Central

    Pallavi, Rani; Chakravarthy, Harshini; Chandran, Syama; Kumar, Rajender; Gupta, Ashok Kumar; Singh, Raj Kumar; Yadav, Suresh Chandra; Tatu, Utpal

    2010-01-01

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

  6. 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.

  7. Mass spectrometry-based proteomics: principles, perspectives, and challenges.

    PubMed

    Wiśniewski, Jacek R

    2008-10-01

    Mass spectrometry-based proteomics is a modern and rapidly developing methodology for qualitative and quantitative characterization of proteins and their posttranslational modification, subcellular localization, and interaction partners. It enables characterization of entire proteomes with unprecedented sensitivity and precision, providing platforms for identification of biomarkers and drug targets.

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

    Cancer.gov

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

  9. Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis.

    PubMed

    Bencharit, Sompop; Baxter, Sarah Schwartz; Carlson, Jim; Byrd, Warren C; Mayo, Mary Virginia; Border, Michael B; Kohltfarber, Heidi; Urrutia, Eugene; Howard-Williams, Escher L; Offenbacher, Steven; Wu, Michael C; Buse, John B

    2013-11-01

    Effective monitoring of glucose levels is necessary for patients to achieve greater control over their diabetes. However, only about a quarter of subjects with diabetes who requires close serum glucose monitoring, regularly check their serum glucose daily. One of the potential barriers to patient compliance is the blood sampling requirement. Saliva and its protein contents can be altered in subjects with diabetes, possibly due to changes in glycemic control. We propose here that salivary proteomes of subjects with diabetes may be different based on their glycemic control as reflected in A1C levels. A total of 153 subjects with type 1 or 2 diabetes were recruited. Subjects in each type of diabetes were divided into 5 groups based on their A1C levels; <7, 7-8, 8-9, 9-10, >10. To examine the global proteomic changes associated with A1C, the proteomic profiling of pooled saliva samples from each group was created using label-free quantitative proteomics. Similar proteomic analysis for individual subjects (N=4, for each group) were then applied to examine proteins that may be less abundant in pooled samples. Principle component analysis (PCA) and cluster analysis (p<0.01 and p<0.001) were used to define the proteomic differences. We, therefore, defined the salivary proteomic changes associated with A1C changes. This study demonstrates that differences exist between salivary proteomic profiles in subjects with diabetes based on the A1C levels.

  10. Proteomics of multiprotein complexes: answering fundamental questions in neuroscience.

    PubMed

    Grant, S G; Husi, H

    2001-10-01

    Proteomics tools offer new ways to analyse networks of proteins that control important neurobiological phenomena such as learning and memory. In this review, we discuss how a combined proteomic, pharmacological and genetic approach reveals that multiprotein complexes process neural information and encode memories. Simultaneous analysis of multiple proteins enables the development of new concepts and approaches for neuroscience research.

  11. The proteomic future: where mass spectrometry should be taking us

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A newcomer to the -omics era, proteomics is a broad, instrument-intensive research area that has advanced rapidly since its inception less than twenty years ago. Although the “wet-bench” aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techni...

  12. The Escherichia coli Proteome: Past, Present, and Future Prospects†

    PubMed Central

    Han, Mee-Jung; Lee, Sang Yup

    2006-01-01

    Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects. PMID:16760308

  13. Human Pituitary Adenoma Proteomics: New Progresses and Perspectives

    PubMed Central

    Zhan, Xianquan; Wang, Xiaowei; Cheng, Tingting

    2016-01-01

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

  14. Proteomic changes in chicken plasma induced by Salmonella typhimurium lipopolysaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lipopolysaccharides (LPS) are cell wall components of gram-negative bacteria that cause inflammation and sickness through genetic and proteomic activation. The objective of our study was to identify the proteomic changes in plasma associated with inflammation induced by LPS treatment. Five-week-old ...

  15. 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.

  16. Proteomics for Validation of Automated Gene Model Predictions

    SciTech Connect

    Zhou, Kemin; Panisko, Ellen A.; Magnuson, Jon K.; Baker, Scott E.; Grigoriev, Igor V.

    2008-02-14

    High-throughput liquid chromatography mass spectrometry (LC-MS)-based proteomic analysis has emerged as a powerful tool for functional annotation of genome sequences. These analyses complement the bioinformatic and experimental tools used for deriving, verifying, and functionally annotating models of genes and their transcripts. Furthermore, proteomics extends verification and functional annotation to the level of the translation product of the gene model.

  17. Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis

    PubMed Central

    Bencharit, Sompop; Baxter, Sarah Schwartz; Carlson, Jim; Byrd, Warren C.; Mayo, Mary Virginia; Border, Michael B.; Kohltfarber, Heidi; Urrutia, Eugene; Howard-Williams, Escher L.; Offenbacher, Steven; Wu, Michael C.; Buse, John B.

    2013-01-01

    Effective monitoring of glucose levels is necessary for patients to achieve greater control over their diabetes. However, only about a quarter of subjects with diabetes who requires close serum glucose monitoring, regularly check their serum glucose daily. One of the potential barriers to patient compliance is the blood sampling requirement. Saliva and its protein contents can be altered in subjects with diabetes, possibly due to changes in glycemic control. We propose here that salivary proteomes of subjects with diabetes may be different based on their glycemic control as reflected in A1C levels. A total of 153 subjects with type 1 or 2 diabetes were recruited. Subjects in each type of diabetes were divided into 5 groups based on their A1C levels; <7, 7–8, 8–9, 9–10, >10. To examine the global proteomic changes associated with A1C, the proteomic profiling of pooled saliva samples from each group was created using label-free quantitative proteomics. Similar proteomic analysis for individual subjects (N=4, for each group) were then applied to examine proteins that may be less abundant in pooled samples. Principle component analysis (PCA) and cluster analysis (p<0.01 and p<0.001) were used to define the proteomic differences. We, therefore, defined the salivary proteomic changes associated with A1C changes. This study demonstrates that differences exist between salivary proteomic profiles in subjects with diabetes based on the A1C levels. PMID:24056972

  18. Biospecimen Solicitation - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    A new 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. This procurement is being solicited for award by SAIC-F under its contract #HHSN261200800001E for Operations and Technical support at the Frederick National Laboratory for Cancer Research.

  19. Maintaining standardization: an update of the HUPO Brain Proteome Project.

    PubMed

    Hamacher, Michael; Stephan, Christian; Eisenacher, Martin; Hardt, Tanja; Marcus, Katrin; Meyer, Helmut E

    2008-04-01

    The Human Proteome Organisation was launched in February 2001 as a result of the need of an international proteomic forum to improve the understanding of human diseases. The initiative dealing with the brain is the Human Proteome Organisation Brain Proteome Project chaired in Germany and Korea. In order to estimate the existing approaches in brain proteomics, as well as to establish a standardized data reprocessing pipeline, pilot studies were initiated including both mouse and human samples. Data had to be submitted to a Data Collection Center for central re-processing and are now publicly accessible at the PRIDE database serving as reference data for future analysis. It became clear that heterogeneity, for example, different analysis strategies and data formats, are a real challenge when comparing results and when working in a consortium. Therefore, standardization, the organisation of data management and the synergistic effects of a consortium of collaborators are of outstanding importance to any big proteome analysis. The following manuscript will highlight these activities and aims of the Human Proteome Organisation Brain Proteome Project, summarizing its historical timeline and its two pilot studies.

  20. The role of targeted chemical proteomics in pharmacology

    PubMed Central

    Sutton, Chris W

    2012-01-01

    Traditionally, proteomics is the high-throughput characterization of the global complement of proteins in a biological system using cutting-edge technologies (robotics and mass spectrometry) and bioinformatics tools (Internet-based search engines and databases). As the field of proteomics has matured, a diverse range of strategies have evolved to answer specific problems. Chemical proteomics is one such direction that provides the means to enrich and detect less abundant proteins (the ‘hidden’ proteome) from complex mixtures of wide dynamic range (the ‘deep’ proteome). In pharmacology, chemical proteomics has been utilized to determine the specificity of drugs and their analogues, for anticipated known targets, only to discover other proteins that bind and could account for side effects observed in preclinical and clinical trials. As a consequence, chemical proteomics provides a valuable accessory in refinement of second- and third-generation drug design for treatment of many diseases. However, determining definitive affinity capture of proteins by a drug immobilized on soft gel chromatography matrices has highlighted some of the challenges that remain to be addressed. Examples of the different strategies that have emerged using well-established drugs against pharmaceutically important enzymes, such as protein kinases, metalloproteases, PDEs, cytochrome P450s, etc., indicate the potential opportunity to employ chemical proteomics as an early-stage screening approach in the identification of new targets. PMID:22074351

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

    PubMed Central

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

    2015-01-01

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

  2. 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

  3. Bead Based Proteome Enrichment Enhances Features of the Protein Elution Plate (PEP) for Functional Proteomic Profiling

    PubMed Central

    Wang, Xing; Davies, Michael; Roy, Swapan; Kuruc, Matthew

    2015-01-01

    A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separate complex proteomes from natural sources and analyze protein functions systematically. The technology takes advantage of the powerful resolution of two-dimensional gel electrophoresis (2-D Gels). The modification of electrophoretic conditions in combination with a high-resolution protein elution plate supports the recovery of functionally active proteins. As 2DE(2-Dimensional Electrophoresis) resolution can be limited by protein load, we investigated the use of bead based enrichment technologies, called AlbuVoid™ and KinaSorb™ to determine their effect on the proteomic features which can be generated from the PEP platform. Using a variety of substrates and enzyme activity assays, we report on the benefits of combining bead based enrichment to improve the signal report and the features generated for Hexokinase, Protein Kinase, Protease, and Alkaline Phosphatase activities. As a result, the PEP technology allows systematic analysis of large enzyme families and can build a comprehensive picture of protein function from a complex proteome, providing biological insights that could otherwise not be observed if only protein abundances were analyzed. PMID:28248280

  4. 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.

  5. 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.

  6. 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.

  7. Principles of proteomics and its applications in cancer.

    PubMed

    Chuthapisith, S; Layfield, R; Kerr, I D; Eremin, O

    2007-02-01

    During the past decade, genomic analyses have been introduced into cancer studies with variable success. It has become recognised, however, that genomic techniques in isolation are insufficient to study the complex pathways of carcinogenesis; this has led to the application of proteomic techniques, which allow for the reliable analysis of complex mixtures of proteins. This article reviews the basic principles of proteomics, methods currently used in proteomics including two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS), and the application of proteomics in cancer research. Currently, proteomic technology has been used in two main areas of cancer research: early diagnosis and treatment (included prediction of response to treatment and targeting novel cancer agents). The initial results from both in vitro and in vivo studies are impressive. These technologies, particularly when combined with genomic analyses, will provide valuable insights into the molecular basis of carcinogenesis and the development of more effective anti-cancer therapies.

  8. Quantitative proteomics using SILAC: Principles, applications, and developments.

    PubMed

    Chen, Xiulan; Wei, Shasha; Ji, Yanlong; Guo, Xiaojing; Yang, Fuquan

    2015-09-01

    SILAC is based on direct addition of selected stable isotope amino acids into the cell culture medium, allowing superior quantitative analysis of the cellular proteome compared to other labeling methods. The great advantages of SILAC lie in its straight-forward implementation, quantitative accuracy, and reproducibility over chemical labeling or label-free quantification strategies, favoring its adoption for proteomic research. SILAC has been widely applied to characterize the proteomic changes between different biological samples, to investigate dynamic changes of protein PTMs, to distinguish specific interacting proteins in interaction proteomic analysis, and to analyze protein turnover in the proteome-wide scale. The present review summarizes the principles of SILAC technology, its applications in biological research, and the present state of this technology.

  9. Proteomic approaches in biological and medical sciences: principles and applications.

    PubMed

    Conrotto, P; Souchelnytskyi, S

    2008-09-01

    After the first introduction of the concept of "proteome" more than 10 years ago, large-scale studies of protein expression, localization, activities and interactions have gained an exponential increase of interest, leading to extensive research and technology development. Proteomics is expansively applied in many areas, ranging from basic research, various disease and malignant tumors diagnostic and biomarker discovery to therapeutic applications. Several proteomics approaches have been developed for protein separation and identification, and for the characterization of protein function and structure. Two-dimensional gel electrophoresis, chromatography, capillary electrophoresis and mass spectrometry have become the most used proteomics methods. These techniques are also under constant development. This review provides an overview of the main techniques and their combinations, used in proteomics. The emphasis is made on description of advantages and disadvantages of each technique, to navigate in selection of the best application for solving a specific problem.

  10. Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks.

    PubMed

    Benevento, Marco; Tonge, Peter D; Puri, Mira C; Hussein, Samer M I; Cloonan, Nicole; Wood, David L; Grimmond, Sean M; Nagy, Andras; Munoz, Javier; Heck, Albert J R

    2014-12-10

    The ectopic expression of Oct4, Klf4, c-Myc and Sox2 (OKMS) transcription factors allows reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). The reprogramming process, which involves a complex network of molecular events, is not yet fully characterized. Here we perform a quantitative mass spectrometry-based analysis to probe in-depth dynamic proteome changes during somatic cell reprogramming. Our data reveal defined waves of proteome resetting, with the first wave occurring 48 h after the activation of the reprogramming transgenes and involving specific biological processes linked to the c-Myc transcriptional network. A second wave of proteome reorganization occurs in a later stage of reprogramming, where we characterize the proteome of two distinct pluripotent cellular populations. In addition, the overlay of our proteome resource with parallel generated -omics data is explored to identify post-transcriptionally regulated proteins involved in key steps during reprogramming.

  11. The proteomics of formalin-fixed wax-embedded tissue.

    PubMed

    Vincenti, David Cilia; Murray, Graeme I

    2013-04-01

    Proteomics, which is the global analysis of protein expression in cells and tissues, has emerged over the last ten to fifteen years as a key set of technologies to improve our understanding of disease processes and to identify new diagnostic, prognostic and predictive disease biomarkers. Whilst most proteomic studies have been conducted on fresh frozen tissue, the continuous improvements in technical procedures for protein extraction and separation, coupled with increasingly powerful bioinformatics, have provided the opportunity for proteomic analysis to be conducted on formalin-fixed wax-embedded tissue. This potential advance should allow proteomic analysis to be performed on the extensive archives of clinically annotated formalin fixed wax embedded tissue blocks stored in pathology departments worldwide. In this review the main techniques and their limitations involved in proteomic analysis of formalin fixed wax embedded tissue will be outlined and examples of their successful application will be indicated.

  12. Proteomic profiling predicts drug response to novel targeted anticancer therapeutics.

    PubMed

    Lin, Fan; Li, Zilin; Hua, Yunfen; Lim, Yoon Pin

    2016-01-01

    Most recently approved anti-cancer drugs by the US FDA are targeted therapeutic agents and this represents an important trend for future anticancer therapy. Unlike conventional chemotherapy that rarely considers individual differences, it is crucial for targeted therapies to identify the beneficial subgroup of patients for the treatment. Currently, genomics and transcriptomics are the major 'omic' analytics used in studies of drug response prediction. However, proteomic profiling excels both in its advantages of directly detecting an instantaneous dynamic of the whole proteome, which contains most current diagnostic markers and therapeutic targets. Moreover, proteomic profiling improves understanding of the mechanism for drug resistance and helps finding optimal combination therapy. This article reviews the recent success of applications of proteomic analytics in predicting the response to targeted anticancer therapeutics, and discusses the potential avenues and pitfalls of proteomic platforms and techniques used most in the field.

  13. Controlled vocabularies and ontologies in proteomics: Overview, principles and practice☆

    PubMed Central

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

    2014-01-01

    This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23429179

  14. 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.

  15. Human liver proteome project: plan, progress, and perspectives.

    PubMed

    He, Fuchu

    2005-12-01

    The Human Liver Proteome Project is the first initiative of the human proteome project for human organs/tissues and aims at writing a modern Prometheus myth. Its global scientific objectives are to reveal the "solar system" of the human liver proteome, expression profiles, modification profiles, a protein linkage (protein-protein interaction) map, and a proteome localization map, and to define an ORFeome, physiome, and pathome. Since it was first proposed in April 2002, the Human Liver Proteome Project has attracted more than 100 laboratories from all over the world. In the ensuing 3 years, we set up a management infrastructure, identified reference laboratories, confirmed standard operating procedures, initiated international research collaborations, and finally achieved the first set of expression profile data.

  16. Mass spectrometry based proteomics: existing capabilities and future directions

    PubMed Central

    Angel, Thomas E.; Aryal, Uma K.; Hengel, Shawna M.; Baker, Erin S.; Kelly, Ryan T.; Robinson, Errol W.; Smith, Richard D.

    2012-01-01

    Mass spectrometry (MS)-based proteomics is emerging as a broadly effective means for identification, characterization, and quantification of proteins that are integral components of the processes essential for life. Characterization of proteins at the proteome and sub-proteome (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects of biology. Emerging technologies such as ion mobility separations coupled with MS and microchip-based-proteome measurements combined with MS instrumentation and chromatographic separation techniques, such as nanoscale reversed phase liquid chromatography and capillary electrophoresis, show great promise for both broad undirected and targeted highly sensitive measurements. MS-based proteomics is increasingly contribute to our understanding of the dynamics, interactions, and roles that proteins and peptides play, advancing our understanding of biology on a systems wide level for a wide range of applications including investigations of microbial communities, bioremediation, and human health. PMID:22498958

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

    PubMed Central

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

    2016-01-01

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

  18. Determination of Serum Lost Goodwill Target Proteome in Patients with Severe Traumatic Brain Injury.

    PubMed

    Ji, Hongming; Hu, Changchen; Zhang, Gangli; Ren, Jinrui; Tan, Yihu; Sun, Wenxiao; Wang, Junwen; Li, Jun; Liu, Hongchao; Xie, Ruifan; Hao, Zhipeng; Guo, Dongsheng

    2015-01-01

    This study investigates the biokinetics of LGT proteome, a potential biomarker of severe TBI, in serum of severe TBI patients. The LGT proteome presents in the serum of severe TBI patients. The abundance diversity of LGT proteome is closely associated with pathologic condition of TBI patients. Serum LGT proteome may be used as a promising marker for evaluating severity of severe TBI.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-01

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