An automated proteomic data analysis workflow for mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be integrated and quantitatively analyzed. The Sequest™ search algorithm is a commonly used algorithm for identifying peptides and proteins from two dimensional liquid chromatography electrospray ionization tandem mass spectrometry (2-D LC ESI MS²) data. A number of proteomic pipelines that facilitate high throughput 'post data acquisition analysis' are described in the literature. However, these pipelines need to be updated to accommodate the rapidly evolving data analysis methods. Here, we describe a proteomic data analysis pipeline that specifically addresses two main issues pertinent to protein identification and differential expression analysis: 1) estimation of the probability of peptide and protein identifications and 2) non-parametric statistics for protein differential expression analysis. Our proteomic analysis workflow analyzes replicate datasets from a single experimental paradigm to generate a list of identified proteins with their probabilities and significant changes in protein expression using parametric and non-parametric statistics.</p> <p>Results</p> <p>The input for our workflow is Bioworks™ 3.2 Sequest (or a later version, including cluster) output in XML format. We use a decoy database approach to assign probability to peptide identifications. The user has the option to select "quality thresholds" on peptide identifications based on the P value. We also estimate probability for protein identification. Proteins identified with peptides at a user-specified threshold value from biological experiments are grouped as either control or treatment for further analysis in ProtQuant. ProtQuant utilizes a parametric (ANOVA) method, for calculating differences in protein expression based on the quantitative measure ΣXcorr. Alternatively ProtQuant output can be further processed using non-parametric Monte-Carlo resampling statistics to calculate P values for differential expression. Correction for multiple testing of ANOVA and resampling P values is done using Benjamini and Hochberg's method. The results of these statistical analyses are then combined into a single output file containing a comprehensive protein list with probabilities and differential expression analysis, associated P values, and resampling statistics.</p> <p>Conclusion</p> <p>For biologists carrying out proteomics by mass spectrometry, our workflow facilitates automated, easy to use analyses of Bioworks (3.2 or later versions) data. All the methods used in the workflow are peer-reviewed and as such the results of our workflow are compliant with proteomic data submission guidelines to public proteomic data repositories including PRIDE. Our workflow is a necessary intermediate step that is required to link proteomics data to biological knowledge for generating testable hypotheses.</p

Partnering to develop resilience in health professionals and faculty through mindfulness-based education

Given the pressures that exist in our health care system, health care professionals often are under significant stress to provide both quality clinical care to patients and quality teaching to their learners. We present an innovative program to develop faculty and health professional  skills in reflective practice and resilience, which strengthen participants' ability to act as effective clinicians, educators, role models, and leaders. The basis of the curriculum  rests in the neuroscience of mindfulness  and its applications. This program was enabled through a unique partnership between acute care hospitals (Hamilton Health Sciences and St Joseph's Healthcare Hamilton), Family Health Teams (McMaster Family Health Team and Hamilton Family Health Team) and the McMaster Faculty of Health Sciences Program for Faculty Development (PFD), with additional funding support in 2013 from the Ontario Ministry of Health and Long Term Care (MOH-LTC). Data from 2013 course participants (validated measurement  tools and qualitative feedback) was analyzed to evaluate the effectiveness of this initiative. This poster outlines the journey of this work and a summary of the data gathered to inform further education.

Phenomenology of Mixed Modulus-Anomaly Mediation in Fluxed String Compactifications and Brane Models

In some string compactifications, for instance the recently proposed KKLT set-up, light moduli are stabilized by nonperturbative effects at supersymmetric AdS vacuum which is lifted to a dS vacuum by supersymmetry breaking uplifting potential. In such models, soft supersymmetry breaking terms are determined by a specific mixed modulus-anomaly mediation in which the two mediations typically give comparable contributions to soft parameters. Similar pattern of soft terms can arise also in brane models to stabilize the radion by nonperturbative effects. We examine some phenomenological consequences of this mixed modulus-anomaly mediation, including the pattern of low energy sparticle spectrum and the possibility of electroweak symmetry breaking. It is noted that adding the anomaly-mediated contributions at $M_{GUT}$ amounts to replacing the messenger scale of the modulus mediation by a mirage messenger scale $(m_{3/2}/M_{Pl})^{\alpha/2}M_{GUT}$ where $\alpha=m_{3/2}/[M_0\ln(M_{Pl}/m_{3/2})]$ for $M_0$ denoting the modulus-mediated contribution to the gaugino mass at $M_{GUT}$. The minimal KKLT set-up predicts $\alpha=1$. As a consequence, for $\alpha={\cal O}(1)$, the model can lead to a highly distinctive pattern of sparticle masses at TeV scale, particularly when $\alpha= 2$.Comment: 20 pages, 15 figures, some notations are changed, typos are corrected and discussions on the CP phase from $\mu$ and B are adde

Serially coupling hydrophobic interaction and reversed-phase chromatography with simultaneous gradients provides greater coverage of the metabolome

The serial coupling of a reversed-phase liquid chromatography (RPLC) column to a hydrophilic interaction liquid chromatography (HILIC) column has been developed in recent years for the detection of polar and nonpolar metabolites. TCA intermediates, bile acid standards and numerous polar and non-polar metabolites extracted from beer were analysed using a combined RPLC/HILIC method. Non-polar metabolites were retained by the RPLC column. Polar metabolites not retained by the RPLC column were retained and separated by the HILIC column. The results from this study validate this simple yet powerful metabolomics approach

'The heart of what we do': policies on teaching, learning and assessment in the learning and skills sector

One of the stated aims of government policy in England is to put teaching, training,and learning at the heart of the learning and skills system. This paper provides a critical review of policies on teaching, learning and assessment in the learning and skills sector over the past five years. It draws upon data collected and analysed in the early stages of an ESRC-funded Teaching and Learning Research Programme project. Using evidence from policy sources, we argue that despite policy rhetoric about devolution of responsibility to the 'front line', the dominant 'images' that government has of putting teaching, learning and assessment at the heart of the Learning and Skills Sector involves a narrow concept of learning and skills; an idealisation of learner agency lacking an appreciation of the pivotal role of the learner/tutor relationship and a top-down view of change in which central government agencies are relied on to secure education standards

Prospectus, September 21, 1977

ONLY 830.1 NIGHT STUDENTS? PARKLAND NIGHT CLASSES: GOING, GOING, GOING…; Activity Day today: music, food, games; Insurance for Parkland students now available; Parkland Events; Stoeber tops Jones for Stu-Go Vice-Prexy slot; Blue Angels at Willard Airport; Editorial: Who cares for people?; Scholarships are given to area persons; Counseling Service provided: each college division; Parkland news in brief; What to do with a bad case of ivy? Maybe Jack Frost can help; Holograms: three-D images or \u27miracles\u27; 100,000 children hurt each year; SSU invites students to Career Day; U. of I. to burn liquid radioactive wastes; Early books, manuscripts on display in U. of I. Library Rare Book Room; Home health care to be topic at CHI program; Animation Festival at T-Bird will end today; \u27Jazz, Blues and Langston Hughes\u27 to be topic of talk; Young are growing older, old are living longer; Classifieds; Women spikers trample Kankakee; Saskatoon Buzzsaws cut Al \u27Albino\u27 Catfish; Gymnasium: Tennis courts installed; LaBadie pleased with Cross Country team\u27s performance; Sigma Omega participate in walk; New rules this week: Mike O\u27Neill 12 for 12, wins Fast Freddy No. 2; Parkland golfers gracious hosts, finish at bottom in own tournament; Tennis anyone?; Maupin refractures ankle bone, sophomore\u27s status uncertain; Fishbein frys Cobras, first defeat of year; Fast Freddy Football Forecasthttps://spark.parkland.edu/prospectus_1977/1012/thumbnail.jp

Chickspress: a resource for chicken gene expression

High-throughput sequencing and proteomics technologies are markedly increasing the amount of RNA and peptide data that are available to researchers, which are typically made publicly available via data repositories such as the NCBI Sequence Read Archive and proteome archives, respectively. These data sets contain valuable information about when and where gene products are expressed, but this information is not readily obtainable from archived data sets. Here we report Chickspress (http://geneatlas.arl.arizona.edu), the first publicly available gene expression resource for chicken tissues. Since there is no single source of chicken gene models, Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and Ensembl gene prediction pipelines, researchers can, for the first time, easily compare gene models from each of these prediction workflows to available experimental data for these products. We use Chickspress data to show the differences between these gene annotation pipelines. Chickspress also provides rapid search, visualization and download capacity for chicken gene sets based upon tissue type, developmental stage and experiment type. This first Chickspress release contains 161 gene expression data sets, including expression of mRNAs, miRNAs, proteins and peptides. We provide several examples demonstrating how researchers may use this resource.National Institutes of Health [R24 GM079326]; US Department of Agriculture National Institute of Food and Agriculture [2011-67015-30332]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Athletics & Recreation Master Plan Sub‐Committee Final Report

In 2000 the Athletics & Recreation Department at UMass Boston Implemented a five year strategic plan that would more realistically align sports sponsorship with available financial and facility resources. We reduced the number of sports sponsored from 20 to 14 maintaining 7 sports for women and 7 sports for men. The only sports maintained without a facility were Men’s baseball and Cross Country Track. We eliminated football, swimming and indoor & outdoor track and field for men and women. Since 2005 The Athletics & Recreation Department has been focused on University wide transition and planning efforts. In that period we have experienced three changes in the Chancellors office, two changes in Athletics Director Position and our operation has moved from a university department to a university division. We have engaged in university‐wide strategic planning and master planning while redefining the role of athletics within the campus community. This four year process of transition & planning has been at the same time taxing and invigorating while allowing the Division of Athletics & Recreation, Special Programs & Projects to emerge as a university service entity supportive of the primary mission of the university. The division has engaged in areas of the university heretofore out of its purview. It has established internal and external partnerships that are transformative and beneficial to the entire community. This report focuses on facilities that will allow for the established partnerships to flourish, that will uphold the new standards for high quality facilities that have been implemented over the last four years on our campus and most importantly this report addresses in a comprehensive way a vision for athletics & recreation at UMass Boston that will put us in the fore front of those institutions that offer athletics & recreation for the purpose of the health and both physical and mental wellness of students, faculty and staff. It does begin with a pride of place

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction.

BACKGROUND: The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian visceral fat hardly expresses leptin, the key adipokine in mammals. Therefore, to assess the endocrine role of adipose tissue in birds, we compared the transcriptome and proteome between two metabolically different types of chickens, broilers and layers, bred towards efficient meat and egg production, respectively. RESULTS: Broilers and layer hens, grown up to sexual maturation under free-feeding conditions, differed 4.0-fold in weight and 1.6-fold in ovarian-follicle counts, yet the relative accumulation of visceral fat was comparable. RNA-seq and mass-spectrometry (MS) analyses of visceral fat revealed differentially expressed genes between broilers and layers, 1106 at the mRNA level (FDR ≤ 0.05), and 203 at the protein level (P ≤ 0.05). In broilers, Ingenuity Pathway Analysis revealed activation of the PTEN-pathway, and in layers increased response to external signals. The expression pattern of genes encoding fat-secreted proteins in broilers and layers was characterized in the RNA-seq and MS data, as well as by qPCR on visceral fat under free feeding and 24 h-feed deprivation. This characterization was expanded using available RNA-seq data of tissues from red junglefowl, and of visceral fat from broilers of different types. These comparisons revealed expression of new adipokines and secreted proteins (LCAT, LECT2, SERPINE2, SFTP1, ZP1, ZP3, APOV1, VTG1 and VTG2) at the mRNA and/or protein levels, with dynamic gene expression patterns in the selected chicken lines (except for ZP1; FDR/P ≤ 0.05) and feed deprivation (NAMPT, SFTPA1 and ZP3) (P ≤ 0.05). In contrast, some of the most prominent adipokines in mammals, leptin, TNF, IFNG, and IL6 were expressed at a low level (FPKM/RPKM< 1) and did not show differential mRNA expression neither between broiler and layer lines nor between fed vs. feed-deprived chickens. CONCLUSIONS: Our study revealed that RNA and protein expression in visceral fat changes with selective breeding, suggesting endocrine roles of visceral fat in the selected phenotypes. In comparison to gene expression in visceral fat of mammals, our findings points to a more direct cross talk of the chicken visceral fat with the reproductive system and lower involvement in the regulation of appetite, inflammation and insulin resistance.The study was supported by the Israel Academy of Sciences grants no. 876/ 14 and 1294/17, and Chief Scientist of the Israeli Ministry of Agriculture 0469/14 (to MFE and ES)

Intervention and revision: Expertise and interaction in text mediation

Many EAL (English as an Additional Language) scholars enlist text mediators’ support when faced with the challenges of writing for international publication. However, the contributions these individuals are able to make in improving scientific manuscripts remains unclear, especially when language professionals such as English teachers do this work. In this article, we explore this topic by examining how three mediators employed their very different expertise and brought different processes to bear on the same discussion section of a medical manuscript written by a novice scholar in China. We find that successfully mediated texts are often the result of an interplay between the mediator’s expertise and the relationship between the participants. Our findings contradict those of previous studies that question the role of English teachers in this process and have the potential to inform both text mediation practices and revision studies