Developing a bioinformatics framework for proteogenomics

In the last 15 years, since the human genome was first sequenced, genome sequencing and annotation have continued to improve. However, genome annotation has not kept up with the accelerating rate of genome sequencing and as a result there is now a large backlog of genomic data waiting to be interpreted both quickly and accurately. Through advances in proteomics a new field has emerged to help improve genome annotation, termed proteogenomics, which uses peptide mass spectrometry data, enabling the discovery of novel protein coding genes, as well as the refinement and validation of known and putative protein-coding genes. The annotation of genomes relies heavily on ab initio gene prediction programs and/or mapping of a range of RNA transcripts. Although this method provides insights into the gene content of genomes it is unable to distinguish protein-coding genes from putative non-coding RNA genes. This problem is further confounded by the fact that only 5% of the public protein sequence repository at UniProt/SwissProt has been curated and derived from actual protein evidence. This thesis contends that it is critically important to incorporate proteomics data into genome annotation pipelines to provide experimental protein-coding evidence. Although there have been major improvements in proteogenomics over the last decade there are still numerous challenges to overcome. These key challenges include the loss of sensitivity when using inflated search spaces of putative sequences, how best to interpret novel identifications and how best to control for false discoveries. This thesis addresses the existing gap between the use of genomic and proteomic sources for accurate genome annotation by applying a proteogenomics approach with a customised methodology. This new approach was applied within four case studies: a prokaryote bacterium; a monocotyledonous wheat plant; a dicotyledonous grape plant; and human. The key contributions of this thesis are: a new methodology for proteogenomics analysis; 145 suggested gene refinements in Bradyrhizobium diazoefficiens (nitrogen-fixing bacteria); 55 new gene predictions (57 protein isoforms) in Vitis vinifera (grape); 49 new gene predictions (52 protein isoforms) in Homo sapiens (human); and 67 new gene predictions (70 protein isoforms) in Triticum aestivum (bread wheat). Lastly, a number of possible improvements for the studies conducted in this thesis and proteogenomics as a whole have been identified and discussed

A Re-Analysis of the Role of Race in the Federal Death Penalty System

The death penalty, as the ultimate sanction, has always served as a source of great debate and remains one of the most controversial punishments meted out by the criminal justice system. Due to concerns of its administration and application, a moratorium on the death penalty was declared by the U.S. Supreme Court in Furman v. Georgia in 1972, and states were mandated by the Court to overhaul their respective death sentencing statutes in a manner that would conform to Court-approved standards under the U.S. Constitution. After the death penalty was reinstated in 1976, it was believed by many that the deficiencies cited in sentencing outcomes in capital cases four years earlier in Furman would either be eliminated or at least brought within constitutionally acceptable levels. Although there has been a wealth of empirical studies over the years at the state level, very few analyses have focused on how the death penalty is administered in the Federal system. In 2002, a study was funded to examine the potential influence of race in decisions by U.S. Attorney's Offices to seek or not seek the death penalty for defendants charged with death-eligible offenses under Federal law. Three independent research teams investigated whether charging outcomes could be explained by relevant legal factors such as the heinousness of the offense. However, unlike the wealth of death penalty research which has conducted such analyses using more traditional multivariate models to isolate the effect of race on charging and sentencing outcomes, the three research teams conducted alternate analyses to compare outcomes in white victim versus non-white victim cases. The purpose of the current study will be to examine the role of race on charging decisions made in the federal death penalty system. The final results suggest that capital cases involving white victims may have a higher risk of being charged with the death penalty than cases involving non-white victims

No evidence that the introduced parasite Orthione griffenis markham, 2004 causes sex change or differential mortality in the native mud shrimp, Upogebia pugettensis (Dana, 1852)

Dramatic, rapid, population declines of the native North American burrowing shrimp Upogebia pugettensis (Dana, 1852) are associated with intense infestations by the introduced Asian bopyrid isopod parasite, Orthione griffenis Markham, 2004. However, expected host weight losses with increasing parasite weights do not occur, even among apparently castrated females. The prevailing assumption that energetic losses cause host castration have thus remained open to question, and the mechanism(s) resulting in castration and consequent population declines of U. pugettensis have remained unclear. Proposed alternative explanations for these declines, which have been based on a dramatically greater prevalence of O. griffenis among U. pugettensis females, include parasite induced sex change, increased male mortality, and differential tidal exposure of sexes to settling O. griffenis larvae. We examined 508 O. griffenis infestations from 2,014 shrimp collected from 26 stations in 5 Oregon estuaries to test these alternative hypotheses. We expected greater infestation frequencies among females than among males and a close association of O. griffenis infestations with intersex shrimp in the overall population if feminization occurs. We also expected covariation in sex ratio with tide exposure if O. griffenis settlement is sex linked. Instead, we found an overall 1:1.07 sex ratio, a lack of association of intersex U. pugettensis with O. griffenis infestations, and an unchanging sex ratio with tidal exposure, precluding parasite induced sex change, male mortality, or tidal immersion effects on infestations. The most likely mechanism driving U. pugettensis declines thus remains castration due to host energetic losses. This energetic interaction is likely to be resolved quantitatively through controlled experiments and increasingly detailed field surveys over time

Lithium Salt Effects on Silicon Electrode Performance and Solid Electrolyte Interphase (SEI) Structure, Role of Solution Structure on SEI Formation

Silicon electrodes were cycled with electrolytes containing different salts to investigate the effect of salt on the electrochemical performance and SEI structure. Comparable capacity retention were observed for the 1.2 M LiPF6, LiTFSI and LiClO4 electrolytes in ethylene carbonate (EC):dimethyl carbonate (DEC), 1:1, but severe fading was observed for the 1.2 M LiBF4 electrolyte. The differential capacity plots and EIS analysis reveals that failure of the 1.2 M LiBF4 electrolyte is attributed to large surface resistance and increasing polarization upon cycling. However, when LiBF4 was added as an electrolyte additive (10% LiBF4 and 90% LiPF6), the capacity retention and Coulombic efficiency were improved. The SEI was analyzed by FTIR and XPS for each electrolyte. Both spectroscopic methods suggest that the main components of the SEI are lithium ethylene dicarbonate (LEDC) and Li2CO3 in the 1.2 M LiPF6, LiTFSI and LiClO4 electrolytes, while an inorganic-rich SEI, composed of LiF and borates, was generated for both the 1.2 M LiBF4 electrolyte and the 10% LiBF4 electrolyte. The chemical composition of the SEIs and corresponding electrochemical performance of the Si electrodes were strongly correlated with electrolyte solution structure

Hepatocellular adenoma in a European flatfish (Limanda limanda) : genetic alterations in laser-capture microdissected tissue and global transcriptomic approach

Liver tumours in flatfish have been diagnosed using histopathology for decades to monitor the impacts of marine pollution. Here we describe the application of specific gene (retinoblastoma, Rb) profiling in laser capture micro-dissected samples, and a suppression subtractive hybridization (SSH) approach to isolate differentially expressed genes in hepatocellular adenoma (HCA) samples from dab, Limanda limanda. The Rb profiles from apparently normal and HCA micro-dissected samples of fish from the North Sea showed no significant difference, and genotypic heterogeneity within defined histological phenotypes was observed. In the SSH, sequences associated with cell signalling, cell cycle, gene expression regulation, protein transport and protein degradation were isolated. These included up-regulation of arrestin domain containing 3 (arrdc3), Rac-1 and tribbles, and down-regulation of ankyrin repeat/sterile alpha-motif domain-containing protein 1B-like (ANKS1B-like), c-fos, CDKN1B and RhoA-like sequences, previously implicated in mammalian HCA. This study offers new candidates involved in fish liver tumour development

Fine mapping of variants associated with endometriosis in the WNT4 region on chromosome 1p36

Genome-wide association studies show strong evidence of association with endometriosis for markers on chromosome 1p36 spanning the potential candidate genes WNT4, CDC42 and LINC00339. WNT4 is involved in development of the uterus, and the expression of CDC42 and LINC00339 are altered in women with endometriosis. We conducted fine mapping to examine the role of coding variants in WNT4 and CDC42 and determine the key SNPs with strongest evidence of association in this region. We identified rare coding variants in WNT4 and CDC42 present only in endometriosis cases. The frequencies were low and cannot account for the common signal associated with increased risk of endometriosis. Genotypes for five common SNPs in the region of chromosome 1p36 show stronger association signals when compared with rs7521902 reported in published genome scans. Of these, three SNPs rs12404660, rs3820282, and rs55938609 were located in DNA sequences with potential functional roles including overlap with transcription factor binding sites for FOXA1, FOXA2, ESR1, and ESR2. Functional studies will be required to identify the gene or genes implicated in endometriosis risk

Task 2: ShARe/CLEF eHealth evaluation lab 2014

This paper reports on Task 2 of the 2014 ShARe/CLEF eHealth evaluation lab which extended Task 1 of the 2013 ShARe/CLEF eHealth evaluation lab by focusing on template lling of disorder attributes. The task was comprised of two subtasks: attribute normalization (task 2a) and cue identication (task 2b).We instructed participants to develop a system which either kept or updated a default attribute value for each task. Participant systems were evaluated against a blind reference standard of 133 discharge summaries using Accuracy (task 2a) and F-score (task 2b). In total, ten teams participated in task 2a, and three teams in task 2b. For task 2a and 2b, the HITACHI team systems (run 2) had the highest performances, with an overall average average accuracy of 0.868 and F1-score (strict) of 0.676, respectively