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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.


Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot 2017 The University of Western Ontario

Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot

Electronic Thesis and Dissertation Repository

Despite the use of the host for dispersal by most parasite species, the extremely loose relationship typical between highly mobile hosts and generalist ectoparasites may lead to very different gene flow patterns between the two, leading in turn to different spatial genetic structure, and potentially different demographic history. I examined how similar gene flow patterns are between Cimex adjunctus, a generalist ectoparasite of bats present throughout North America, and two of its key bat hosts. I first analyzed the continent-scale genetic structure and demographic history of C. adjunctus and compared it to that of two of its hosts, the little ...


Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small Rna Profiling: A Multiple Protocol Study Across Multiple Laboratories, Maria D. Giraldez, Kahraman Tanriverdi, Jane E. Freedman, Muneesh Tewari 2017 University of Michigan

Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small Rna Profiling: A Multiple Protocol Study Across Multiple Laboratories, Maria D. Giraldez, Kahraman Tanriverdi, Jane E. Freedman, Muneesh Tewari

University of Massachusetts Medical School Faculty Publications

Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation ...


Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh 2017 University of Massachusetts Medical School

Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh

GSBS Dissertations and Theses

Chromatin packages eukaryotic genomes via a hierarchical series of folding steps, encrypting multiple layers of epigenetic information, which are capable of regulating nuclear transactions in response to complex signals in environment. Besides the 1-dimensinal chromatin landscape such as nucleosome positioning and histone modifications, little is known about the secondary chromatin structures and their functional consequences related to transcriptional regulation and DNA replication. The family of chromosomal conformation capture (3C) assays has revolutionized our understanding of large-scale chromosome folding with the ability to measure relative interaction probability between genomic loci in vivo. However, the suboptimal resolution of the typical 3C techniques ...


Mrna Decay Pathways Use Translation Fidelity And Competing Decapping Complexes For Substrate Selection, Alper Celik 2017 University of Massachusetts Medical School

Mrna Decay Pathways Use Translation Fidelity And Competing Decapping Complexes For Substrate Selection, Alper Celik

GSBS Dissertations and Theses

mRNA decay is an important step in gene regulation, environmental responsiveness, and mRNA quality control. One such quality control pathway, Nonsense-mediated mRNA Decay (NMD), targets transcripts whose translation terminates prematurely. However, the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. The vast majority of NMD-regulated transcripts are normal-looking protein-coding mRNAs. Our bioinformatics analyses reveal that this set of NMD-regulated transcripts generally have lower translational efficiency, lower average codon optimality scores, and higher ratios of ...


Guideseq: A Bioconductor Package To Analyze Guide-Seq Datasets For Crispr-Cas Nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, Scot A. Wolfe 2017 University of Massachusetts Medical School

Guideseq: A Bioconductor Package To Analyze Guide-Seq Datasets For Crispr-Cas Nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, Scot A. Wolfe

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing ...


Genome Sequence Of Diabrotica Virgifera Virgifera Virus 2, A Novel Small Rna Virus Of The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning 2017 Iowa State University

Genome Sequence Of Diabrotica Virgifera Virgifera Virus 2, A Novel Small Rna Virus Of The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning

Entomology Publications

The genome of a novel small RNA virus, tentatively named Diabrotica virgifera virgifera virus 2 (DvvV2), was identified in the western corn rootworm, Diabrotica virgifera virgifera LeConte, through transcriptome sequencing and confirmed by reverse transcription-PCR. Here, we report the near-complete nucleotide sequence and the genome organization of DvvV2.


Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron 2017 Bowdoin College

Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron

Honors Projects

Hybrid zones and their dynamics are important in the understanding of the genetic basis of reproductive isolation and speciation. This study seeks to investigate the hybridization dynamics of a Scarus hybrid swarm within the Tropical Eastern Pacific (TEP) that includes four phenotypically distinct species: S. perrico, S. ghobban, S. rubroviolaceus, and S. compressus. Genetic and population structure analyses of four nuclear loci and a mitochondrial locus revealed that one of the four species, S. compressus, was the result of two different hybrid crosses: S. perricoS. rubroviolaceus and S. perricoS. ghobban. A NewHybrids model indicated that most of the ...


Adolescent Perspectives On Genetic Testing For Adult Onset Conditions, Olivia D’Accordo, Erin Davidson, Christina Miller, Yael Weinstein 2017 Sarah Lawrence College

Adolescent Perspectives On Genetic Testing For Adult Onset Conditions, Olivia D’Accordo, Erin Davidson, Christina Miller, Yael Weinstein

Human Genetics Theses and Capstones

The American Society of Human Genetics (ASHG) recommends that testing for adult onset conditions be deferred until adulthood because of the potential for psychological harm combined with lack of medical utility. ASHG’s 2016 DNA Day Essay Contest asked 9- 12th graders to defend or refute this position. 1241 essays were submitted. 572 students defended ASHG’s position statement, while 554 argued against. Essays that addressed Alzheimer’s disease (AD) and BRCA-related Hereditary Breast and Ovarian Cancer syndrome were qualitatively analyzed for themes related to the argued position. 64.4% of students argued for deferred testing of AD, and 46 ...


Non-Coding Rnas Identify The Intrinsic Molecular Subtypes Of Muscle-Invasive Bladder Cancer, Andrea E. Ochoa 2017 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Non-Coding Rnas Identify The Intrinsic Molecular Subtypes Of Muscle-Invasive Bladder Cancer, Andrea E. Ochoa

UT GSBS Dissertations and Theses (Open Access)

NON-CODING RNAS IDENTIFY THE INTRINSIC MOLECULAR SUBTYPES OF MUSCLE-INVASIVE BLADDER CANCER

Andrea Elizabeth Ochoa, B.S.

Advisory Professors: David J. McConkey, Ph.D. and Joya Chandra, Ph.D.

There has been a recent explosion of genomics data in muscle-invasive bladder cancer (MIBC) to better understand the underlying biology of the disease that leads to the high amount of heterogeneity that is seen clinically. These studies have identified relatively stable intrinsic molecular subtypes of MIBC that show similarities to the basal and luminal subtypes of breast cancer. However, previous studies have primarily focused on protein-coding genes or DNA mutations/alterations.

There ...


Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney 2017 University of Tennessee, Knoxville

Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney

Doctoral Dissertations

The family Russulaceae is an iconic family of mushroom-forming Basidiomycetes both because of their importance as edible mushrooms in many parts of the world and their species richness in both temperate and tropical forested biomes. While much mycological research has been focused on this group, recent systematic and ecological research has failed to develop a comprehensive or cohesive organization by which to understand the evolutionary relationships, patterns of diversification, or functional importance of the group. Recently, interest in ectomycorrhizal fungi (EmF), of which Russulaceae is a key lineage, has greatly increased due to the recognition of the importance of EmF ...


Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), Khemraj B.C. 2017 University of Southern Mississippi

Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), Khemraj B.C.

Dissertations

Amblyomma maculatum (Gulf coast tick) ticks are prevalent across the Atlantic to Gulf Coast region of United States. These ticks are recognized vectors of Rickettsia parkeri, a spotted fever group of Rickettsia (SFGR) known to cause American boutonneuse fever associated with fever and eschar rashes localized to the site of bites. We hypothesized that Rickettsia parkeri colonization and proliferation in the tick vector involve pathogen-symbiont dynamics and tick-pathogen interactions, which influence rickettsial transmission to the victims after tick bites. The rickettsial infection is maintained across the tick life cycle for many generations due to transovarial and transstadial transmission of the ...


Genome Sequence Of A Novel Positive-Sense, Single-Stranded Rna Virus Isolated From Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning 2017 Iowa State University

Genome Sequence Of A Novel Positive-Sense, Single-Stranded Rna Virus Isolated From Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning

Entomology Publications

The genome sequence of a novel small RNA virus was assembled from the transcriptome of the western corn rootworm, Diabrotica virgifera virgifera. The assembled genome has 13,182 nucleotides with a 3′ polyadenylated tail. Two open reading frames are predicted to encode polyproteins of 2,838 and 1,073 amino acids.


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 ...


Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, Jialu Li 2017 The University of Texas MD ANderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, Jialu Li

UT GSBS Dissertations and Theses (Open Access)

My dissertation is focused on quantitative methodology development and application for two important topics in translational and clinical cancer research.

The first topic was motivated by the challenge of applying transcriptome sequencing (RNA-seq) to formalin-fixation and paraffin-embedding (FFPE) tumor samples for reliable diagnostic development. We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. To comprehensively evaluate the FFPE RNA-seq data quality for expression profiling, we developed multiple computational methods for assessment, such as the uniformity and continuity ...


A Novel Method For Quantifying Spatial Patterns In Plants, Logan H. George 2017 College of William and Mary

A Novel Method For Quantifying Spatial Patterns In Plants, Logan H. George

Undergraduate Honors Theses

Color patterns are found in a plethora of organisms, from vertebrates to flowering plants. While many studies have examined the mechanisms that produce these diverse patterns in animals, little research has investigated the mechanisms by which plants create color patterns. The conclusions drawn from animal studies may not accurately translate to plants due to early divergence in the evolution of life. Characterization of plant patterning mechanisms would have widespread impacts on developmental and evolutionary biology. To unravel the mystery behind pattern formation, we suggest an experimental framework to understand pattern evolution and development at a phenotypic, genotypic, and quantitative level ...


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 ...


Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan 2017 Portland State University

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also ...


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 ...


Crispr/Cas System, Mother Nature’S Gift For Genomic Engineering, Alexander Jones, Yijing Chen 2017 Kent State University

Crispr/Cas System, Mother Nature’S Gift For Genomic Engineering, Alexander Jones, Yijing Chen

Student Showcase for Research, Scholarship & Creativity

Genomic engineering is direct manipulation of an organism’s genome (DNA) to alter its characteristics. It enables scientists to

• Study gene functions

• Model human diseases

• Correct mutations in diseased cells and tissues

• Control infectious diseases • Increase crop production…

The Challenge

• Most multicellular organisms’ genomes are vast. For example, each human cell contains ~ 6 billion base- pairs of DNA!

• It’s extremely time-consuming and expensive to generate precise and targeted modifications in complex genomes using conventional tools


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