Genetics and Genomics Commons^™

Evaluation And Integration Of Genetic Signature For Prediction Risk Of Nasopharyngeal Carcinoma In Southern China, Xiuchan Guo, Cheryl Winkler, Ji Li, Li Guan, Minzhong Tang, Jian Liao, Hong Deng, Guy De The, Yi Zeng, Stephen J. O'Brien

Biology Faculty Articles

Genetic factors, as well as environmental factors, play a role in development of nasopharyngeal carcinoma (NPC). A number of single nucleotide polymorphisms (SNPs) have been reported to be associated with NPC. To confirm these genetic associations with NPC, two independent case-control studies from Southern China comprising 1166 NPC cases and 2340 controls were conducted. Seven SNPs in ITGA9 at 3p21.3 and 9 SNPs within the 6p21.3 HLA region were genotyped. To explore the potential clinical application of these genetic markers in NPC, we further evaluate the predictive/diagnostic role of significant SNPs by calculating the area under the curve (AUC). Results …

Genetic Variation, Local Adaptation And Population Structure In North American Red Oak Species, Quercus Rubra L. And Q. Ellipsoidalis E. J. Hill, Jennifer F. Lind-Riehl

Dissertations, Master's Theses and Master's Reports - Open

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same …

Semantics In Support Of Biodiversity Knowledge Discovery: An Introduction To The Biological Collections Ontology And Related Ontologies, Ramona L. Walls, John Deck, Robert Guralnick, Steve Baskauf, Reed Beaman, Stanley Blum, Shaun Bowers

Computer Science Faculty Scholarship

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to …

Linking Molecular, Electrical And Anatomical Properties Of Human Epileptic Brain, Shruti Bagla

Wayne State University Dissertations

Epilepsy is a common neurological disorder of recurrent unprovoked seizures. It affects almost 1% of the world population. Although there is a wide range of anti-epileptic drugs (AEDs) available, they only treat the seizure symptoms and do not cure the disease itself. The poor role of AEDs can be attributed to the lack of knowledge of exact mechanisms and networks that produce epileptic activities in the neocortex. At present, the best cure for epilepsy is surgical removal of electrically localized epileptic brain tissue. Surgically removed brain tissue presents an excellent opportunity to discover the molecular and cellular basis of human …

Sex And Heterochromatin: An Investigation Of Sexual Dimorphism In Drosophila Melanogaster, Manasi S. Apte

Wayne State University Dissertations

Over 30% of Drosophila genome is assembled into heterochromatin. Heterochromatin is relatively gene poor, transcriptionally less active and remains condensed during interphase. Previous studies established that roX RNA and some of the Male Specific Lethal (MSL) proteins, all components of the dosage compensation complex, are required for full expression of autosomal heterochromatic genes in male flies but not in females. This was surprising since heterochromatin is generally not thought to be sexually dimorphic. The genetic basis for the regulation of sex-specific heterochromatin was completely unknown.

To determine if roX RNAs localize directly at the heterochromatic regions that they regulate, I …

Use Of Robust Multivariate Linear Mixed Models For Estimation Of Genetic Parameters For Carcass Traits In Beef Cattle, S. O. Peters, K. Kizilkaya, D. J. Garrick, R. L. Fernando, E. J. Pollak, R. Mark Enns, M. De Donato, O. O. Ajayi, I. G. Imumorin

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Assumptions of normality of residuals for carcass evaluation may make inferences vulnerable to the presence of outliers, but heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. We compare estimates of genetic parameters by fitting multivariate Normal (MN) or heavy-tail distributions (multivariate Student’s t and multivariate Slash, MSt and MS) for residuals in data of hot carcass weight (HCW), longissimus muscle area (REA) and 12th to 13th rib fat (FAT) traits in beef cattle using 2475 records from 2007 to 2008 from a large …

Genome-Wide Sequencing Of Small Rnas Reveals A Tissue-Specific Loss Of Conserved Microrna Families In Echinococcus Granulosus, Yun Bai, Zhuangzhi Zhang, Lei Jin, Hui Kang, Yongquiang Zhu, Lu Zhang, Xia Li, Fengshou Ma, Li Zhao, Et Al.

PCOM Scholarly Works

Background: MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown. Results: Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with …

Ribosome-Binding And Activity Of Release Factor 2 In The Presence Of L-Tryptophan, Nuzhat Majid

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Crispr-Cas Gene Engineering And The Characterization Of Cis-Regulatory Elements (Cres) In The Non-Coding Genome, Garrett Wilson

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Microgeographic Population Genetic Structure Of Baylisascaris Procyonis (Nematoda: Ascaroidae) In Western Michigan Indicates The Grand River Is A Barrier To Gene Flow, Christina A. Sarkissian, Douglas H. Graham

Student Summer Scholars Manuscripts

We developed eight polymorphic microsatellites from the parasitic nematode Baylisascaris procyonis. Amplification of these loci in a sample of 74 worms collected from 10 raccoons in Western Michigan revealed significant population structure. Bayesian clustering indicates two subpopulations, one on either side of the Grand River which bisects the region sampled. Estimates of F_ST, and results from AMOVA and isolation by distance, further corroborate a scenario whereby the river is acting as a barrier to gene flow, a rather unusual finding given the high vagility of raccoons and microgeographic scale of the analysis. We describe one possible mechanism …

Egonet: Identification Of Human Disease Ego-Network Modules, Rendong Yang, Yun Bai, Zhaohui Qin, Tianwei Yu

PCOM Scholarly Works

Background: Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed integrated analyses of microarray data and protein-protein interaction (PPI) networks to find diagnostic subnetwork markers. However, the neighborhood relationship among network member genes has not been fully considered by those methods, leaving many potential gene markers unidentified. The main idea of this study is to take full advantage of the biological observation that genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks.Results: …

Targeted Knockout Of Beclin-1 Reveals An Essential Function In Ovary And Testis, Thomas R. Gawriluk

Theses and Dissertations--Biology

An estimated 12% of couples worldwide are infertile. The contributing factor is approximately equal between men and women with nearly 25% diagnosed as idiopathic. Despite the increasing numbers of couples seeking assistance from infertility clinics, few molecular mechanisms have been identified for treatment. Autophagy is an evolutionarily conserved cellular process for bulk degradation and recycling of cytosolic components through the lysosome to maintain homeostasis. Several studies have observed increased levels of autophagy during ovarian folliculogenesis and gonadal steroidogenesis; however, no genetic studies to determine the significance of autophagy exist.

To investigate the function of autophagy in the ovary and testis, …

The Jak/Stat Pathway Is Reutilized In Drosophila Spermatogenesis, Lingfeng Tang

Theses and Dissertations--Biology

In the Drosophila testis, sperm are derived from germline stem cells (GSCs) which undergo a stereotyped pattern of divisions and differentiation. The somatic cells at the tip of the testis form the hub, which is the niche for both the somatic cyst stem cells (CySCs) and GSCs. The hub expresses Upd, a ligand for the JAK/STAT pathway that has roles in the maintenance of CySCs and GSCs. Male mutants of upd3, another ligand of the JAK/STAT pathway, become sterile much earlier than the wild-type, leading to the hypothesis that similar to upd, upd3 also promotes the self-renewal of …

Small Rna Expression During Programmed Rearragement Of A Vertebrate Genome, Joseph R. Herdy Iii

Theses and Dissertations--Biology

The sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangements (PGRs) during embryogenesis that results in the deletion of ~0.5 Gb of germline DNA from the somatic lineage. The underlying mechanism of these rearrangements remains largely unknown. miRNAs (microRNAs) and piRNAs (PIWI interacting RNAs) are two classes of small noncoding RNAs that play important roles in early vertebrate development, including differentiation of cell lineages, modulation of signaling pathways, and clearing of maternal transcripts. Here, I utilized next generation sequencing to determine the temporal expression of miRNAs, piRNAs, and other small noncoding RNAs during the first five days of lamprey …

Studies On Sensitivity Reduction In Solo And Mixture Treatments And Fungicide-Induced Mutagenesis In Monilinia Fructicola, Guido Schnabel, F. Chen, Sydney E. Everhart, W. C. Bridges, X. Liu

Department of Plant Pathology: Faculty Publications

Three fungicide-sensitive Monilinia fructicola isolates were exposed in weekly transfers of mycelia to a dose gradient of a DMI and a QoI fungicide (azoxystrobin) in solo or mixture treatments and fungicide sensitivity as well as genetic changes were assessed. Isolates showed a faster reduction in sensitivity (higher resistance factors) to azoxystrobin than to SYP-Z048; this process was slower in the mixture treatment. The decrease of fungicide sensitivity was not a heritable trait. Genomic mutagenesis at 8 of 15 microsatellite loci was evidenced in one of three isolates tested after exposure to azoxystrobin. These non-coding regions of the genome either showed …

Atx1/Atcompass And The H3k4me3 Marks: How Do They Activate Arabidopsis Genes?, Michael E. Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or “registers,” activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity …

Aba Signaling Is Necessary But Not Sufficient For Rd29b Transcriptional Memory During Successive Dehydration Stresses In Arabidopsis Thaliana, Laetitia Virlouvet, Yong Ding, Hiroaki Fujii, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Plants subjected to a prior dehydration stress were seen to have altered transcriptional responses during a subsequent dehydration stress for up to 5 days after the initial stress. The abscisic acid (ABA) inducible RD29B gene of Arabidopsis thaliana was strongly induced after the first stress and displayed transcriptional memory with transcript levels nine-fold higher during the second dehydration stress. These increased transcript levels were due to an increased rate of transcription and are associated with an altered chromatin template during the recovery interval between the dehydration stresses. Here we use a combination of promoter deletion/substitutions, mutants in the trans-acting …

Detection Of Predator Cues Alters Mating Tactics In Male Wolf Spiders, Dustin J. Wilgers, Daniel Wickwire, Eileen Hebets

Eileen Hebets Publications

Males of the wolf spider, Rabidosa punctulata, exhibit condition-dependent alternative mating tactics, whereby small, poor condition males engage in multimodal courtship while large, good condition males adopt a direct mount tactic that forgoes courtship. This study explores the possibility that tactic-specific costs can help explain this unintuitive pattern of mating tactic expression. Specifically, we hypothesize that courtship signaling is costly with respect to eavesdropping by predators and that males can alter their tactic expression based upon the perceived environmental predation risk. We test this by first examining the risk of predation associated with different mating tactics. We use a …

A Systems Biology Approach To Detect Eqtls Associated With Mirna And Mrna Co-Expression Networks In The Nucleus Accumbens Of Chronic Alcoholic Patients, Mohammed Mamdani

Theses and Dissertations

Alcohol Dependence (AD) is a chronic substance use disorder with moderate heritability (60%). Linkage and genome-wide association studies (GWAS) have implicated a number of loci; however, the molecular mechanisms underlying AD are unclear. Advances in systems biology allow genome-wide expression data to be integrated with genetic data to detect expression quantitative trait loci (eQTL), polymorphisms that regulate gene expression levels, influence phenotypes and are significantly enriched among validated genetic signals for many commonly studied traits including AD.

We integrated genome-wide mRNA and miRNA expression data with genotypic data from the nucleus accumbens (NAc), a major addiction-related brain region, of 36 …

Soil Microbial Community Distributions And Disease Suppressiveness In The Coastal Plain Of Georgia, Michael J. Sabula

College of Graduate Studies: Theses & Dissertations

This study compared the soil microbial communities of three vegetation types in the coastal plain of Georgia: 1. crop land actively in use for agricultural production, 2. transitional grassland in early stages of secondary succession, and 3. pristine unmanaged forest land. Microbial species diversity and quantities of microbial DNA were determined from each of these vegetation types at three separate locations near Statesboro, Georgia. Length heterogeneity PCR(LH-PCR) methods and subsequent analysis of fungal, bacterial, and metazoan communities by analysis of similarity (ANOSIM) revealed high within-group similarity by vegetation type, indicating land management intensity and vegetation cover is a strong determining …