Computational Strategies for Proteogenomics Analyses

Proteogenomics is an area of proteomics concerning the detection of novel peptides and peptide variants nominated by genomics and transcriptomics experiments. While the term primarily refers to studies utilizing a customized protein database derived from select sequencing experiments, proteogenomics methods can also be applied in the quest for identifying previously unobserved, or missing, proteins in a reference protein database. The identification of novel peptides is difficult and results can be dominated by false positives if conventional computational and statistical approaches for shotgun proteomics are directly applied without consideration of the challenges involved in proteogenomics analyses. In this dissertation, I systematically distill the sources of false positives in peptide identification and present potential remedies, including computational strategies that are necessary to make these approaches feasible for large datasets. In the first part, I analyze high scoring decoys, which are false identifications with high assigned confidences, using multiple peptide identification strategies to understand how they are generated and develop strategies for reducing false positives. I also demonstrate that modified peptides can cause violations in the target-decoy assumptions, which is a cornerstone for error rate estimation in shotgun proteomics, leading to potential underestimation in the number of false positives. Second, I address computational bottlenecks in proteogenomics workflows through the development of two database search engines: EGADS and MSFragger. EGADS aims to address issues relating to the large sequence space involved in proteogenomics studies by using graphical processing units to accelerate both in-silico digestion and similarity scoring. MSFragger implements a novel fragment ion index and searching algorithm that vastly speeds up spectra similarity calculations. For the identification of modified peptides using the open search strategy, MSFragger is over 150X faster than conventional database search tools. Finally, I will discuss refinements to the open search strategy for detecting modified peptides and tools for improved collation and annotation. Using the speed afforded by MSFragger, I perform open searching on several large-scale proteomics experiments, identifying modified peptides on an unprecedented scale and demonstrating its utility in diverse proteomics applications. The ability to rapidly and comprehensively identify modified peptides allows for the reduction of false positives in proteogenomics. It also has implications in discovery proteomics by allowing for the detection of both common and rare (including novel) biological modifications that are often not considered in large scale proteomics experiments. The ability to account for all chemically modified peptides may also improve protein abundance estimates in quantitative proteomics.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/138581/1/andykong_1.pd

Introduction to customized occupational safety and health website and its effectiveness in improving psychosocial safety climate (PSC) among police officers

Introduction: The prevalence of stress among Malaysian police is high in which 38.8% polices have severe stress related to work resources and workplace environment. Psychosocial safety climate is one of the indicators that can be used to avoid psychosocial health problems. Objective: This study was conducted to determine the risk factors of psychosocial safety climate and to measure the effectiveness of a customised safety website in improving the safety climate. Methodology: This study involved 105 police officers who were randomly selected from nine different departments in PDRM Bukit Aman. A survey adapted from previous study was used to determine the psychosocial safety climate levels among respondents. Then, occupational safety website was introduced to the respondents and being used for two weeks. Lastly, post survey was done to see the difference of psychosocial safety climate before and after the use of the website. Results and Discussion: Findings showed that team psychological safety (r=0.381, p=<0.001) and physical safety climate (r=0.657, p=<0.001) were significantly associated with psychosocial safety climate level. The means before (36.095 ± 5.6202) and after (37.742 ± 4.7069) the introduction of occupational safety website was good. Still, there was a significant improvement of psychosocial safety climate level after the introduction of occupational safety website. Conclusion: This study showed that psychosocial safety climate level in an organization can be improved by introducing an informative website specific for police

Applicability of variability response function for geotechnical risk assessment

This paper explores the use of variability response function (VRF) for risk assessment of geotechnical system under spatially variable soil properties, where the properties exhibit a range of possible autocorrelation characteristics. VRF only requires a single set of analysis, but traditional Monte Carlo simulation (MCS) requires separate sets of analyses. VRF can be estimated through a simple regression procedure, which does not require random field simulation. In a footing displacement analysis, the reliability assessments by VRF match well with those of MCS, when the soil property has relatively low variance.The work presented this paper is financially supported by the Research Grants Council of the Hong Kong Special Administrative Region Government (Project No. 15212418)

Chronic social defeat stress shifts peripheral circadian clocks in male mice in a tissue-specific and time-of-day dependent fashion

Uncontrollable stress is linked to the development of many diseases, some of which are associated with disrupted daily rhythms in physiology and behavior. While available data indicate that the master circadian pacemaker in the suprachiasmatic nucleus (SCN) is unaffected by stress, accumulating evidence suggest that circadian oscillators in peripheral tissues and organs can be shifted by a variety of stressors and stress hormones. In the present study, we examined effects of acute and chronic social defeat stress in mice and addressed the question of whether effects of uncontrollable stress on peripheral clocks are tissue specific and depend on time of day of stress exposure. We used mice that carry a luciferase reporter gene fused to the circadian clock gene Period2 (PER2::LUC) to examine daily rhythms of PER2 expression in various peripheral tissues. Mice were exposed to social defeat stress in the early (ZT13-14) or late (ZT21-22) dark phase, either once (acute stress) or repeatedly on 10 consecutive days (chronic stress). One hour after the last stressor, tissue samples from liver, lung, kidney, and white adipose tissue (WAT) were collected. Social defeat stress caused a phase delay of several hours in the rhythm of PER2 expression in lung and kidney, but this delay was stronger after chronic than after acute stress. Moreover, shifts only occurred after stress in the late dark phase, not in the early dark phase. PER2 rhythms in liver and WAT were not significantly shifted by social defeat, suggesting a different response of various peripheral clocks to stress. This study indicates that uncontrollable social defeat stress is capable of shifting peripheral clocks in a time of day dependent and tissue specific manner. These shifts in peripheral clocks were smaller or absent after a single stress exposure and may therefore be the consequence of a cumulative chronic stress effect

6U MeV CubeSat Mission: A low-cost approach towards gamma-ray astronomy

The low-energy gamma-ray (0.1-30 MeV) sky has been poorly observed since the decommissioning of the COMPTEL instrument on board the Compton Gamma-ray Observer (CGRO) satellite in 2000. The study of photons from this energy band (the MeV "gap") is, however, crucial to answer many unsolved questions in high-energy and multi-messenger astrophysics. Although several MeV gamma-ray missions have been proposed (e.g. AMEGO, e-ASTROGAM), these are mostly in the planning phase, and their launch is not expected until the next decade, at the earliest. Recently, there has been a proliferation of CubeSat missions proposed as "pathfinder" alternatives due to their low cost and faster cycles of implementation. Indeed, a MeV CubeSat for gamma-ray astronomy can be a suitable demonstrator for future, larger-scale MeV payloads. In this paper, a gamma-ray payload design with a silicon tracker and CsI calorimeter is proposed. We report the results of simulations to assess the performance of this payload possibility and compare these with other previous gamma-ray instruments.Comment: Submitted in Journal of Astronomical Telescopes, Instruments, and Systems(SPIE). Manuscript# 23097G. 31 pages and 7 figure

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

Abstract Background Protein-RNA interactions are integral components of nearly every aspect of biology, including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. Results Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTRs) covering 72% of protein-coding transcripts encoded in the genome, confirming 3' UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3' UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression. Conclusions Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo.http://deepblue.lib.umich.edu/bitstream/2027.42/112318/1/13059_2012_Article_3050.pd

Mammalian systems biotechnology: An integrative framework for combining in silico modeling and multi-Omics datasets in different CHO parental cell lines

The increasing availability of multi-omics data from Chinese hamster ovary (CHO) cell cultures entails both opportunity and challenges toward next generation cell culture engineering. Herein, we present a comprehensive and integrative framework to systematically combine trancriptome, proteome, metabolome and glycome datasets in conjunction with a genome-scale metabolic model of CHO cells. We then apply the framework to compare and contrast the metabolic characteristics of the three commonly used parental cell lines (CHO-K1, CHO-DUKXB11 and CHO-DG44) so that “global” attributes of the parental hosts (e.g. growth related characteristics, glycosylation patterns, etc.) could be highlighted (Figure 1). The unique characteristics of the adherent against the suspension cell lines reveal that the latter are in an oxidative stress and that they differentially express genes/proteins associated with the lipid biosynthetic process. The unique transcriptomic and proteomic signatures of the different suspension cell lines, more relevant in an industrial context than the adherent, reflect the known historic divergence of the cell lines, i.e. the very different nature of the -DG44 cell line than the other two. Genes/proteins related with the purine nucleotide biosynthetic process (as expected, due to the Dhfr gene copy number differences), epigenetic regulation and programmed cell death present the major expression differences between the three parental cell lines. As far as the host N-glycome for each of the cell lines is concerned, it reveals similar profiles. Nevertheless, the cell lines present several differences in the expression of N-glycosylation related genes (e.g.Man2a1 and Fut8 are differentially expressed for -DG44 and Mgat4a for the -DXB11 cell line) and the pools of nucleotide sugar donors (-K1 presents higher UDP-Glc / UDP-Gal and CMP-sialic acid pools than -DG44; while -DG44 higher GDP-Fuc pools). Growth profiles of the various cell lines were also assessed and our results demonstrate that -K1 cells present significantly higher growth rate than the other two cell lines in suspension culture. Interestingly, adherent cells present a significantly faster growth profile than suspension cells that we attribute to the different media used for the two culture formats, i.e. to the presence of serum for adherent cells. The integrative framework also involves the use of the genome-scale metabolic model as a scaffold to map the multiomics datasets. Such an analysis allows us to readily pinpoint the heterogeneity in cellular metabolism between the multiple conditions and/or cell lines tested, as well as their correlations. Moreover, the correlation analysis of transcriptome and proteome for a given cell line revealed the plausible regulatory intracellular events that can be targeted for genetic engineering to achieve the enhanced productivity and quality of recombinant proteins in the context of bioprocessing. Interestingly, we identified many differences in the reactions associated with the N-glycan processing pathways for the various parental cell lines analyzed, which may be associated with different glycosylation capacity. Further investigation at the glycomics level may validate our hypothesis that choice of CHO hosts should be product-specific. It is expected that our results can serve as the golden standard for the comprehensive comparison of the various CHO cell lines used worldwide

Quantitative High-Speed Laryngoscopic Analysis of Vocal Fold Vibration in Fatigued Voice of Young Karaoke Singers

Summary: Purpose. The present study aimed to determine whether there were physiological differences in the vocal fold vibration between nonfatigued and fatigued voices using high-speed laryngoscopic imaging and quantitative analysis. Methods. Twenty participants aged from 18 to 23 years (mean, 21.2 years; standard deviation, 1.3 years) with normal voice were recruited to participate in an extended singing task. Vocal fatigue was induced using a singing task. Highspeed laryngoscopic image recordings of /i/ phonation were taken before and after the singing task. The laryngoscopic images were semiautomatically analyzed with the quantitative high-speed video processing program to extract indices related to the anteroposterior dimension (length), transverse dimension (width), and the speed of opening and closing. Results. Significant reduction in the glottal length-to-width ratio index was found after vocal fatigue. Physiologically, this indicated either a significantly shorter (anteroposteriorly) or a wider (transversely) glottis after vocal fatigue. Conclusion. The high-speed imaging technique using quantitative analysis has the potential for early identification of vocally fatigued voice

Reconceptualising the relationship between the creative economy and the city: Learning from the financial crisis

This paper uses the financial crisis as an opportunity to examine a number of key questions about the relationship of the creative economy and the city. We argue that weak conceptualisation of the nature of the relationship between the creative economy and the city, as well as a lack of clarity about what the creative economy is, has subverted debates about this important topic. This paper comprises four major sections: the first introduces the field of the creative economy, the second section seeks to clarify what exactly we mean by the term financial crisis; here we highlight the multifaceted character of the financial crisis and is variable impacts across the field of the creative economy. The third part outlines the range and diversity of the actually existing relations between the creative economy and the city. In the fourth section we reflect upon the earlier argument to consider what we can learn about the impacts (actual and expected) of the financial crisis on the creative economy and the city, and additionally to reflect upon what this might indicate about the changing and perhaps transformed relationship between the creative economy and the city in the last quarter century