Genetics and Genomics Commons^™

Modeling Sporadic Tumor Formation Driven By Telomere Dysfunction In The Gastrointestinal Tract, Suzanne S. Chan

Dissertations and Theses (Open Access)

Colorectal cancer is a complex disease that is thought to arise when cells accumulate mutations that allow for uncontrolled growth. There are several recognized mechanisms for generating such mutations in sporadic colon cancer; one of which is chromosomal instability (CIN). One hypothesized driver of CIN in cancer is the improper repair of dysfunctional telomeres. Telomeres comprise the linear ends of chromosomes and play a dual role in cancer. Its length is maintained by the ribonucleoprotein, telomerase, which is not a normally expressed in somatic cells and as cells divide, telomeres continuously shorten. Critically shortened telomeres are considered dysfunctional as they …

Regulation Of Morphogenesis In Filamentous Fungi, Haoyu Si

School of Biological Sciences: Dissertations, Theses, and Student Research

One of the distinguishing features of fungal cells is their highly polarized model of growth. Both yeast cells and hyphal cells grow by cell surface expansion at specified cortical sites. Although the same general mechanisms are likely to be involved in controlling the establishment of hyphal polarity in budding yeast and filamentous fungi, it is noticeable that hyphal cells are organized in a fundamentally different manner to yeast dells. For example, hyphal cells organize formins, septins and actins at the division site while simultaneously retain the same machinery at the tip; whereas yeast cells undergo a transient period of isotropic …

Candidate Gene Studies In Patients With Autism Spectrum Disorder, Pamela Jackson

All Dissertations

Autism Spectrum Disorder is a grouping of disorders that range from the diagnosis of Asperger Syndrome to Autistic Disorder (formally known as autism). Attention Deficit Disorders and Pervasive Developmental Disorder-Not Otherwise Specified are also a part of this spectrum of disorders. Autism Spectrum Disorder affects one out of every 110 children and has a male to female ratio of 4:1. This has led to the need to identify genes that may be causative for this disorder.
Several genome-wide scans have been conducted and have identified locations in the human genome that may contain causative genes for Autism Spectrum Disorder. One …

Transcriptional Regulation Of The Shigella Flexneri Icsp Promoter: Silencing And Anti-Silencing By H-Ns And Virb, Dustin Harrison

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella species are gram-negative intracellular pathogens that cause bacillary dysentery in humans. Many genes required for virulence of Shigella are carried on a large 230 kb plasmid and many of these are under the transcriptional control of the histone-like nucleoid structuring protein (H-NS) and by the major virulence regulator VirB. At the non-permissive temperature of 30⁰C, H-NS represses transcription, while at 37⁰C VirB alleviates this repression. This mechanism of gene regulation has been coined "silencing/anti-silencing" and is commonly found in many important bacterial pathogens including Salmonella spp. and Yersinia spp. The icsP gene, encoded by the Shigella virulence plasmid, is …

The Larval Salivary Gland Of Drosophila Melangogaster: A Model System For Temporal And Spatial Steroid Hormone Regulation, Benjamin Constantino

UNLV Theses, Dissertations, Professional Papers, and Capstones

Drosophila melanogaster provides an ideal model organism to test genetic and molecular biological mechanisms within the context of a living animal. For over one hundred years Drosophila continues to produce a boundless extent of informative and important scientific data providing crucial insight into development, disease progression and genetic interactions. A century as a model organism allowed for the development of an abundance of unique genetic and molecular tools allowing researchers to tease apart cellular mechanisms with very little limitation. From the whole adult body to tissue function to molecular networks, if a biological question arises it most likely can be …

Selection For Increased Starvation Resistance Using Drosophila Melanogaster: Investigating Physiological And Life History Trait Responses To Starvation And Dietary Supplementation In The Context Of An Obese Phenotype, Tiffany Elisse Schwasinger-Schmidt

School of Biological Sciences: Dissertations, Theses, and Student Research

Artificial selection for starvation resistance provided insight into the relationships between evolved physiological and life history trait responses following exposure to biologically induced stress. Investigations of alterations to body composition, metabolic rate, movement, and life history traits including development time, female egg production, and longevity in response to brief periods of starvation were conducted on genetically based starvation-resistant and control lines of Drosophila melanogaster. Analysis of the starvation-resistant lines indicated increased energy storage with increased triglyceride deposition and conversion of carbohydrates to lipid, as identified by respiratory quotient values. Correlations between reductions in metabolic rates and movement in the starvation-resistant …

Genetic Polymorphisms Of Cyp2e1, Gstp1, Nqo1 And Mpo And The Risk Of Nasopharyngeal Carcinoma In A Han Chinese Population Of Southern China, Xiuchan Guo, Yi Zeng, Hong Deng, Jian Liao, Yuming Zheng, Ji Li, Bailey Kessing, Stephen J. O'Brien

Biology Faculty Articles

Background

Southern China is a major area for endemic nasopharyngeal carcinoma (NPC). Genetic factors as well as environmental factors play a role in development of NPC. To investigate the roles of previously described carcinogen metabolism gene variants for NPC susceptibility in a Han Chinese population, we conducted a case-control study in two independent study population groups afflicted with NPC in Guangdong and Guangxi Provinces of southern China.

Methods

Five single nucleotide polymorphisms (SNPs) of CYP2E1-rs2031920, CYP2E1-rs6413432, GSTP1-rs947894, MPO-rs2333227 and NQO1-rs1800566 were genotyped by PCR-based RFLP, sequencing and TaqMan assay in 358 NPC cases and 629 …

Quantitative Trait Loci For Agronomic And End-Use Quality Performance And The Effect Of Soilborne Wheat Mosaic Virus In A Hard Winter Wheat Population In Nebraska, Nicholas A. Crowley

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

To better understand agronomic and end-use quality in wheat (Triticum aestivum L.) we developed a population containing 154 F6:8 recombinant inbred lines (RILs) from the cross TAM107-R7/Arlin. The parental lines and RILs were phenotyped at six environments in Nebraska and differed for resistance to Wheat soilborne mosaic virus (WSBMV), morphological, agronomic, and end-use quality traits. Additionally, a 2300 cM genome-wide linkage map was created for quantitative trait loci (QTL) analysis. Based on our results across multiple environments, the best RILs could be used for cultivar improvement. The population and marker data are publicly available for interested researchers for future research. …

A Decision-Theory Approach To Interpretable Set Analysis For High-Dimensional Data, Simina Maria Boca, Hector C. Bravo, Brian Caffo, Jeffrey T. Leek, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

A ubiquitous problem in igh-dimensional analysis is the identification of pre-defined sets that are enriched for features showing an association of interest. In this situation, inference is performed on sets, not individual features. We propose an approach which focuses on estimating the fraction of non-null features in a set. We search for unions of disjoint sets (atoms), using as the loss function a weighted average of the number of false and missed discoveries. We prove that the solution is equivalent to thresholding the atomic false discovery rate and that our approach results in a more interpretable set analysis.

Rna Processing Of Nitrogenase Transcripts In The Cyanobacterium Anabaena Variabilis, Justin Ungerer, Brenda Pratte, Teresa Thiel

Biology Department Faculty Works

Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, …

Genes For High Altitudes, Jay F. Storz

Jay F. Storz Publications

Analyses of genomes from Tibetan populations reveal a signaling pathway that may account for high-altitude adaptation. Tibetans, who have lived at high altitudes for nearly 25,000 years, survive the low-oxygen environment through a low blood hemoglobin concentration.

Determining The Fate Of Hybridized Genomes In The Allopolyploid Brassica Napus, Tina Y. Wang

Master's Theses

Polyploidy is widely acknowledged as a widespread mechanism in the evolution and speciation of the majority of flowering plants. Allopolyploid forms through interspecific hybridization and whole genome duplication. While allopolyploids may display increased vigor relative to their progenitors, they can also face challenges to fertility following hybridization. Genetic changes in allopolyploids result from recombination between the hybridized subgenomes, which can influence phenotype and ultimately determine fitness of future generations. To study dynamic changes that follow allopolyploid formation, Brassica napus lineages were derived by hybridizing Brassica oleracea and Brassica rapa. Two lineages of B. napus were analyzed for genetic and phenotypic …

Identification Of Markers Associated With Sow Lifetime Productivity For Whole Genomic Selection, Daniel Ciobanu

Department of Animal Science: Faculty Publications

Sows are more productive today than ever before. However, concurrent with increased prolificacy, high sow death losses and replacement rates are serious economic and welfare issues facing producers. Reproductive failure is the most frequent reason for culling sows. Length of productive life is moderately heritable and has high variance; thus, substantial genetic variation is expected to exist in most populations. Genetic improvement in the swine industry occurs from selection in nucleus herds and is then transmitted through the breeding pyramid in the multiplication process. Thus, it is critical to identify selection methods that can be applied in nucleus herds that …

Improved Ibd Detection Using Incomplete Haplotype Information, Giulio Genovese, Gregory Leibon, Martin R. Pollak, Daniel N. Rockmore

Dartmouth Scholarship

The availability of high density genetic maps and genotyping platforms has transformed human genetic studies. The use of these platforms has enabled population-based genome-wide association studies. However, in inheritance-based studies, current methods do not take full advantage of the information present in such genotyping analyses. In this paper we describe an improved method for identifying genetic regions shared identical-by-descent (IBD) from recent common ancestors. This method improves existing methods by taking advantage of phase information even if it is less than fully accurate or missing. We present an analysis of how using phase information increases the accuracy of IBD detection …

Following Tetraploidy In Maize, A Short Deletion Mechanism Removed Genes Preferentially From One Of The Two Homeologs, Margaret R. Woodhouse, James C. Schnable, Brent S. Pedersen, Eric Lyons, Damon Lisch, Shabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homeologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity …

The Strength Of Statistical Evidence For Composite Hypotheses: Inference To The Best Explanation, David R. Bickel

COBRA Preprint Series

A general function to quantify the weight of evidence in a sample of data for one hypothesis over another is derived from the law of likelihood and from a statistical formalization of inference to the best explanation. For a fixed parameter of interest, the resulting weight of evidence that favors one composite hypothesis over another is the likelihood ratio using the parameter value consistent with each hypothesis that maximizes the likelihood function over the parameter of interest. Since the weight of evidence is generally only known up to a nuisance parameter, it is approximated by replacing the likelihood function with …

Constraint-Based Model Of Shewanella Oneidensis Mr-1 Metabolism: A Tool For Data Analysis And Hypothesis Generation, Grigoriy E. Pinchuk, Eric A. Hill, Oleg V. Geydebrekht, Jessica De Ingeniis, Xiaolin Zhang, Andrei Osterman, James H. Scott

Dartmouth Scholarship

Shewanellae are gram-negative facultatively anaerobic metal-reducing bacteria commonly found in chemically (i.e., redox) stratified environments. Occupying such niches requires the ability to rapidly acclimate to changes in electron donor/acceptor type and availability; hence, the ability to compete and thrive in such environments must ultimately be reflected in the organization and utilization of electron transfer networks, as well as central and peripheral carbon metabolism. To understand how Shewanella oneidensis MR-1 utilizes its resources, the metabolic network was reconstructed. The resulting network consists of 774 reactions, 783 genes, and 634 unique metabolites and contains biosynthesis pathways for all cell constituents. Using constraint-based …

An Initial Map Of Chromosomal Segmental Copy Number Variations In The Chicken, Xiaofei Wang, Samuel N. Nahashon, Tromondae K. Feaster, Ann L. Bohannon-Stewart, Nathaniel Adefope

Agricultural and Environmental Sciences Faculty Research

Background

Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory elements. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as a model for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosomal regions that segregate for important agricultural and disease phenotypes.

Results

Ninety six CNVs were identified in three lines of chickens (Cornish Rock broiler, Leghorn and Rhode Island …

A Functional Calcium-Transporting Atpase Encoded By Chlorella Viruses, Maria Cristina Bonza, Holger Martin, Ming Kang, Gentry L. Lewis, Timo Greiner, Sonia Giacometti, James L. Van Etten, Maria Ida De Michelis, Gerhard Thiel, Anna Moroni

James Van Etten Publications

Calcium-transporting ATPases (Ca²⁺ pumps) are major players in maintaining calcium homeostasis in the cell and have been detected in all cellular organisms. Here, we report the identification of two putative Ca²⁺ pumps, M535L and C785L, encoded by chlorella viruses MT325 and AR158, respectively, and the functional characterization of M535L. Phylogenetic and sequence analyses place the viral proteins in group IIB of P-type ATPases even though they lack a typical feature of this class, a calmodulin-binding domain. A Ca²⁺ pump gene is present in 45 of 47 viruses tested and is transcribed during virus infection. Complementation analysis of …

Identification Of An L-Rhamnose Synthetic Pathway In Two Nucleocytoplasmic Large Dna Viruses, Madhu Parakkottil Chothi, Garry A. Duncan, Andrea Armirotti, Chantal Abergel, James R. Gurnon, James L. Van Etten, Cinzia Bernardi, Gianluca Damonte, Michela Tonetti

James Van Etten Publications

Nucleocytoplasmic large DNA viruses (NCLDVs) are characterized by large genomes that often encode proteins not commonly found in viruses. Two species in this group are Acanthocystis turfacea chlorella virus 1 (ATCV-1) (family Phycodnaviridae, genus Chlorovirus) and Acanthamoeba polyphaga mimivirus (family Mimiviridae), commonly known as mimivirus. ATCV-1 and other chlorovirus members encode enzymes involved in the synthesis and glycosylation of their structural proteins. In this study, we identified and characterized three enzymes responsible for the synthesis of the sugar L-rhamnose: two UDP-D-glucose 4,6-dehydratases (UGDs) encoded by ATCV-1 and mimivirus and a bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase (UGER) from mimivirus. Phylogenetic …