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Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, Amy Cochran 2017 University of Michigan-Ann Arbor

Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, Amy Cochran

Biology and Medicine Through Mathematics Conference

No abstract provided.


Denoising Tandem Mass Spectrometry Data, Felix Offei 2017 East Tennessee State Universtiy

Denoising Tandem Mass Spectrometry Data, Felix Offei

Electronic Theses and Dissertations

Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of ...


Systematic Analysis Of Whole Exome Sequencing Determines Ret G691s Polymorphism As Germline Variant In Melanoma, Brent J. Smith Jr, Jennifer D. Hintzsche, Carol M. Amato, Aik-Choon Tan, Keith R. Wells, Allison J. Applegate, Rita T. Gonzalez, Jodie R. Barr, William A. Robinson 2017 Marshall University Joan C. Edwards School of Medicine

Systematic Analysis Of Whole Exome Sequencing Determines Ret G691s Polymorphism As Germline Variant In Melanoma, Brent J. Smith Jr, Jennifer D. Hintzsche, Carol M. Amato, Aik-Choon Tan, Keith R. Wells, Allison J. Applegate, Rita T. Gonzalez, Jodie R. Barr, William A. Robinson

Marshall Journal of Medicine

Abstract

The RET proto-oncogene encodes a receptor tyrosine kinase that is activated by glial cell derived neutrotrophic factor (GDNF). Previous studies have found that a single nucleotide polymorphism (SNP), RETp (G691S), in the juxtamembrane domain enhances the signaling pathway and promotes tumor growth by GDNF in pancreatic and thyroid cancer in addition to melanoma. It is uncertain however whether this SNP is a germline variant or somatic mutation. A prior study reported that the RETp variant was a germline SNP in desmoplastic and non-desmoplastic melanomas. In the present study, we examined both melanoma tissue samples and matching peripheral blood DNA ...


Hippocampal Epigenetic Changes In A Mouse Model Of Fetal Alcohol Spectrum Disorders, Eric J. Chater-Diehl 2017 The University of Western Ontario

Hippocampal Epigenetic Changes In A Mouse Model Of Fetal Alcohol Spectrum Disorders, Eric J. Chater-Diehl

Electronic Thesis and Dissertation Repository

Fetal alcohol spectrum disorders (FASD) refers to the neurological, developmental, and behavioural abnormalities arising from in utero ethanol exposure. These abnormities included attention deficit, anxiety, and learning and memory impairment persisting into adulthood. The molecular mechanisms of such persistent behavioural changes remain unknown and are an area of intense research. In this thesis, mice were exposed to ethanol during the third trimester equivalent, the peak of synaptic development. Following this exposure, genome-wide epigenetic and gene expression and changes in the hippocampus were assessed in adult (70 day old) mice.

In the first experiment, genome-wide trimethylation of histone H3 at histone ...


Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez 2017 Georgia State University

Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez

Georgia State Undergraduate Research Conference

No abstract provided.


Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley 2017 Santa Clara University

Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley

Biology

Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on ...


P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith 2017 Western University

P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith

Western Research Forum

Background: Mitochondria genomes vary from 11 Mb to 6 kb, while plastids can vary from 1 Mb to 30 kb. Non-coding DNA accounts for most of this size variation, but the mechanistic and evolutionary reasons for that are still unknown. Next generation sequencing has generated unprecedented amounts of genomic and transcriptomic data that can be used for organelle genome evolution studies. However, most of these data is used only for the study of cell nucleus. Therefore, I decided to use these untapped data source to investigate the transcription of organelle genomes in plastid-bearing protists.

Methods: I mapped the transcriptomes over ...


Messenger Rna And Microrna Transcriptomic Signatures Of Cardiometabolic Risk Factors, David D. McManus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J. Munson, Martin G. Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane Freedman, Daniel Levy 2017 University of Massachusetts Medical School

Messenger Rna And Microrna Transcriptomic Signatures Of Cardiometabolic Risk Factors, David D. Mcmanus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J. Munson, Martin G. Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane Freedman, Daniel Levy

UMass Center for Clinical and Translational Science Supported Publications

BACKGROUND: Cardiometabolic (CM) risk factors are heritable and cluster in individuals. We hypothesized that CM risk factors are associated with multiple shared and unique mRNA and microRNA (miRNA) signatures. We examined associations of mRNA and miRNA levels with 6 CM traits: body mass index, HDL-cholesterol and triglycerides, fasting glucose, and systolic and diastolic blood pressures through cross-sectional analysis of 2812 Framingham Heart Study who had whole blood collection for RNA isolation for mRNA and miRNA expression studies and who consented to genetic research. We excluded participants taking medication for hypertension, dyslipidemia, or diabetes. We measured mRNA (n = 17,318; using ...


Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke 2017 The University of Western Ontario

Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke

Electronic Thesis and Dissertation Repository

In situ STAR (Self-sustaining Treatment for Active Remediation) is an emerging remediation technology which uses smouldering combustion to destroy nonaqueous phase liquid (NAPL) contamination in the subsurface. Since STAR smouldering travels through contaminated soils slowly (~0.5 to 5 m/day) and subjects them to high temperatures (400–1000°C), it is expected that this technology will thoroughly dry and sterilize the zones which it treats. Further, soils surrounding the treatment zone which are not smouldered will be heated, although not smouldered, by virtue of their proximity to STAR, impacting microbial communities within them. Therefore, the objectives of this work ...


Estimating The Probability Of Clonal Relatedness Of Pairs Of Tumors In Cancer Patients, Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, Colin B. Begg 2017 Memorial Sloan-Kettering Cancer Center

Estimating The Probability Of Clonal Relatedness Of Pairs Of Tumors In Cancer Patients, Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, Colin B. Begg

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

Next generation sequencing panels are being used increasingly in cancer research to study tumor evolution. A specific statistical challenge is to compare the mutational profiles in different tumors from a patient to determine the strength of evidence that the tumors are clonally related, i.e. derived from a single, founder clonal cell. The presence of identical mutations in each tumor provides evidence of clonal relatedness, although the strength of evidence from a match is related to how commonly the mutation is seen in the tumor type under investigation. This evidence must be weighed against the evidence in favor of independent ...


Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao 2017 Yale University

Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao

Yale Day of Data

The dropping costs and rising popularity of next-generation sequencing has introduced the possibility of personalizing medical treatments and screening for genetic diseases. Still, the clinical community’s understanding remains incomplete, with limited consensus on the proper interpretation for many genetic variants. Thus, the standard procedure when returning sequencing results has been to report findings only in genes related to the diagnostic indication, and not incidental findings in other genes. To balance the threat of false positives with the medical benefits of true findings, the American College on Medical Genetics and Genomics (ACMG) recommends an exception: that clinical sequencing laboratories seek ...


Detecting Discordance Enrichment Among A Series Of Two-Sample Genome-Wide Expression Data Sets, Yinglei Lai, Fanni Zhang, Tapan Nayak, Reza Modarres, Norman H. Lee, Timothy A. McCaffrey 2017 George Washington University

Detecting Discordance Enrichment Among A Series Of Two-Sample Genome-Wide Expression Data Sets, Yinglei Lai, Fanni Zhang, Tapan Nayak, Reza Modarres, Norman H. Lee, Timothy A. Mccaffrey

Epidemiology and Biostatistics Faculty Publications

Background

With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene set enrichment analysis have been frequently conducted. Integrative analysis can be conducted when multiple data sets are available. In practice, discordant molecular behaviors among a series of data sets can be of biological and clinical interest.

Methods

In this study, a statistical method is proposed for detecting discordance gene set enrichment. Our method is based on a two-level multivariate normal mixture model. It is statistically efficient with linearly increased parameter space when ...


Serine Biosynthesis And Glycine Biosynthesis/Degradation: Mrub_0173 Is Orthologous To E. Coli B2913 (Sera); Mrub_0125 Is Orthologous To E. Coli B4388 (Serb); Mrub_2910 Is Orthologous To E. Coli B2551 (Glya)., Megan M. Janssen, Dr. Lori R. Scott 2017 Augustana College, Rock Island Illinois

Serine Biosynthesis And Glycine Biosynthesis/Degradation: Mrub_0173 Is Orthologous To E. Coli B2913 (Sera); Mrub_0125 Is Orthologous To E. Coli B4388 (Serb); Mrub_2910 Is Orthologous To E. Coli B2551 (Glya)., Megan M. Janssen, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0173, Mrub_0125, and Mrub_ 2910. We predict that Mrub_0173 encodes the enzyme phosphoglycerate dehydrogenase (DNA coordinates 152982 ... 154347), which is the 1st step of the serine biosynthesis pathway (KEGG map number 00680). It catalyzes the conversion of NAD+ + 3-phospho-D-glycerate → NADH H+ + 3-phospho-hydroxypyruvate. The E. coli K12 MG1655 ortholog is predicted to be b2913, which has the gene identifier serA ...


Mrub_0860, Mrub_0701 And Mrub_2285 Are Orthologous To E. Coli B2892, B2562 And B3863 Within The Recfor Pathway For Homologous Recombination, Bailey Englund, Dr. Lori Scott 2017 Augustana College, Rock Island Illinois

Mrub_0860, Mrub_0701 And Mrub_2285 Are Orthologous To E. Coli B2892, B2562 And B3863 Within The Recfor Pathway For Homologous Recombination, Bailey Englund, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tool associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict the gene function. We investigated the biological function of the genes Mrub_0860, Mrub_0701,and Mrub_2285. We predicted that Mrub_0860 (DNA coordinates 842934..844868 on the forward strand) encodes for the enzyme single-stranded DNA-specific exonuclease, which is in the first step of homologous recombination via the RecFOR pathway (KEGG map number 03440). The E. coli K12 MG1655 ortholog is predicted to be b2892, which has the gene identifier RecJ. It is ...


Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, Nicholas M. Orslini, Dr. Lori R. Scott 2017 Augustana College, Rock Island Illinois

Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, Nicholas M. Orslini, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2642, Mrub_1054, and Mrub_1059.

We predict that Mrub_2642 encodes the enzyme methionine adenosyltransferase (DNA coordinates [2677251…2678426] on the reverse strand), the first step of the methionine degradation pathway (KEGG map number 00270). Methionine adenosyltransferase catalyzes the conversion of the substrates, ATP, L-methionine, and water, to yield the products S-adenosyl-L-methionine (SAM), inorganic phosphate, and diphosphate. Mrub_1054 encodes adenosylhomocysteine nucleosidase (DNA ...


Mrub_1873, Mrub_1872, Mrub_1871 Genes Are Predicted Orthologs Of The B2285, B2284, And B2283 Genes Respectively, Found In Escherichia Coli Coding For Nadh Ubiquinone Oxidoreductase Complex Subunits E, F, And G., Hannah Lohmeier, Dr. Lori R. Scott 2017 Augustana College, Rock Island Illinois

Mrub_1873, Mrub_1872, Mrub_1871 Genes Are Predicted Orthologs Of The B2285, B2284, And B2283 Genes Respectively, Found In Escherichia Coli Coding For Nadh Ubiquinone Oxidoreductase Complex Subunits E, F, And G., Hannah Lohmeier, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1873, Mrub_1872, and Mrub_1871.We predict that Mrub_1873 (DNA coordinates 1933743..1934309 on the reverse strand), Mrub_1872 (DNA coordinates 1932430..1933746 on the reverse strand), and Mrub_1871 (DNA coordinates 1930055..1932421 on the reverse strand) are subunits of the NADH ubiquinone oxidoreductase complex (00190). The complex catalyzes both the transfer of protons across the cytoplasmic membrane and the transfer of ...


Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan 2016 University of Southern Mississippi

Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan

Dissertations

The mitochondria are responsible for the bulk of energy production in eukaryotes. They possess their own genome that works in conjunction with the nuclear genome to accomplish the extraordinarily important task of energy conversion. When species hybridize there will be a mismatch in evolutionary histories between these two genomes. The deleterious interactions of these genomes have been studied in great detail (i.e. hybrid breakdown). However, little work has been conducted to understand the population genetic, and morphological consequences of wide-ranging replacement. The Fundulus notatus complex is comprised of 3 species: F. notatus, F. olivaceus, and F. euryzonus. Within the ...


Investigating The Functional Role Of Tick Antioxidants In Hematophagy And Vector Competence, Deepak Kumar 2016 University of Southern Mississippi

Investigating The Functional Role Of Tick Antioxidants In Hematophagy And Vector Competence, Deepak Kumar

Dissertations

Ticks are obligate hematophagous arthropods and harbor several pathogens which transmit various diseases to humans and their domesticated animals. Host blood- digestion in a tick midgut (MG) generates several reactive oxygen species (ROS), which are extremely toxic to essential macromolecules (e.g. DNA, proteins, and lipids) within the cell, resulting in high oxidative stress. Thus, this dissertation focuses on the questions of how tick homeostasis responds to high oxidative stress, and how ticks and their harbored pathogens survive the high surge of oxidative stress during blood digestion. We are specifically interested in the tick-pathogen, Rickettsia parkeri (R. parkeri, Rp), harbored ...


Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate 2016 University of California, San Francisco

Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate

Biology Faculty Publications and Presentations

Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the hosts ...


Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti 2016 Loyola University Chicago

Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from ...


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