Genetics and Genomics Commons^™

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 …

Understanding The Chemical Gymnastics Of Enzyme-Catalyzed 1’-1 And 1’-3 Triterpene Linkages, Stephen A. Bell

Theses and Dissertations--Plant and Soil Sciences

Squalene synthase (SS) is an essential enzyme in eukaryotic systems responsible for an important branch point in isoprenoid metabolism that leads to sterol formation. The mechanistic complexity of SS has made it a difficult enzyme to study. The green alga Botryococcus braunii race B possesses several squalene synthase-like (SSL) enzymes that afford a unique opportunity to study the complex mechanism of triterpene biosynthesis. SSL-1 catalyzes presqualene diphosphate (PSPP) formation, which can either be converted to squalene by SSL-2 or botryococcene by SSL-3. A rationally designed mutant study of B. braunii squalene synthase (BbSS) and SSL-3 was conducted to understand structure-function …

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 …

Snd1 Mediated Downregulation Of Ptpn23 In Hcc, Nidhi Jariwala

Theses and Dissertations

SND1 MEDIATED DOWNREGULATION OF PTPN23 IN HEPATOCELLULAR CARCINOMA

By Nidhi Jariwala, MS

A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University, 2014.

ADVISOR: Dr. Devanand Sarkar

Associate Professor, Department of Human and Molecular Genetics Blick Scholar Associate Scientific Director, Cancer Therapeutics VCU Institute of Molecular Medicine Massey Cancer Center

ABSTRACT

Staphyloccocal nuclease domain containing protein 1 (SND1) is identified as an oncogene in multiple cancers, including hepatocellular carcinoma (HCC). SND1 regulates gene expression at transcriptional as well as post-transcriptional level and mediates molecular pathways that culminate into carcinogenesis. SND1 …

Investigating The Role Of The Synaptic Transcriptome In Ethanol-Responsive Behaviors, Megan A. O'Brien

Theses and Dissertations

Alcoholism is a complex neurological disorder characterized by loss of control in limiting intake, compulsion to seek and imbibe ethanol, and chronic craving and relapse. It is suggested that the characteristic behaviors associated with the escalation of drug use are caused by long-term molecular adaptations precipitated by the drug’s continual administration. These lasting activity-dependent changes that underlie addiction-associated behavior are thought, in part, to depend on new protein synthesis and remodeling at the synapses. It is well established that mRNA can be transported to neuronal distal processes, where it can undergo localized translation that is regulated in a spatially restricted …

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 …

Cell- And Virus-Mediated Regulation Of The Barrier-To-Autointegration Factor’S Phosphorylation State Controls Its Dna Binding, Dimerization, Subcellular Localization, And Antipoxviral Activity, Augusta Jamin, April Wicklund, Matthew S. Wiebe

Nebraska Center for Virology: Faculty Publications

Barrier-to-autointegration factor (BAF) is a DNA binding protein with multiple cellular functions, including the ability to act as a potent defense against vaccinia virus infection. This antiviral function involves BAF’s ability to condense double-stranded DNA and subsequently prevent viral DNA replication. In recent years, it has become increasingly evident that dynamic phosphorylation involving the vaccinia virus B1 kinase and cellular enzymes is likely a key regulator of multiple BAF functions; however, the precise mechanisms are poorly understood. Here we analyzed how phosphorylation impacts BAF’s DNA binding, subcellular localization, dimerization, and antipoxviral activity through the characterization of BAF phosphomimetic and unphosphorylatable …

Characterization Of A Dual-Tropic Human Immunodeficiency Virus (Hiv-1) Strain Derived From The Prototypical X4 Isolate Hxbc2, Shi-Hua Xiang, Beatriz Pacheco, Dane Bowder, Wen Yuan, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

Human immunodeficiency virus type 1 (HIV-1) coreceptor usage and tropism can be modulated by the V3 loop sequence of the gp120 exterior envelope glycoprotein. For coreceptors, R5 viruses use CCR5, X4 viruses use CXCR4, and dual-tropic (R5X4) viruses use either CCR5 or CXCR4. To understand the requirements for dual tropism, we derived and analyzed a dual-tropic variant of an X4 virus. Changes in the V3 base, which allow gp120 to interact with the tyrosine-sulfated CCR5 N-terminus, and deletion of residues 310/311 in the V3 tip were necessary for efficient CCR5 binding and utilization. Thus, both sets of V3 changes allowed …

Live Siv Vaccine Correlate Of Protection: Immune Complex-Inhibitory Fc Receptor Interactions That Reduce Target Cell Availability, Anthony J. Smith, Stephen W. Wietgrefe, Liang Shang, Cavan S. Reilly, Peter J. Southern, Katherine E. Perkey, Lijie Duan, Heinz Kohler, Sybille Muller, James Robinson, John V. Carlis, Qingsheng Li, R. Paul Johnson, Ashley T. Haase

Nebraska Center for Virology: Faculty Publications

Principles to guide design of an effective vaccine against HIV are greatly needed, particularly to

protect women in the pandemic’s epicentre in Africa. We have been seeking these principles by

identifying correlates of the robust protection associated with SIV_mac239Δnef vaccination in the

SIV-rhesus macaque animal model of HIV-1 transmission to women. We have identified one

correlate of SIV_mac239Δnef protection against vaginal challenge as a resident mucosal system for

SIV-gp41 trimer antibody production and neonatal Fc receptor (FcRn)-mediated concentration of

these antibodies on the path of virus entry to inhibit establishment of infected founder populations

at the …

Review Of Epidemiology And Transmission Of Kaposi’S Sarcoma-Associated Herpesvirus, Veenu Minhas, Charles Wood

Nebraska Center for Virology: Faculty Publications

This review summarizes the current knowledge pertaining to Kaposi sarcoma-associated herpesvirus (KSHV) epidemiology and transmission. Since the identification of KSHV twenty years ago, it is now known to be associated with Kaposi’s sarcoma (KS), primary effusion lymphoma, and multicentric Castleman’s disease. Many studies have been conducted to understand its epidemiology and pathogenesis and their results clearly show that the worldwide distribution of KSHV is uneven. Some geographical areas, such as sub-Saharan Africa, the Mediterranean region and the Xinjiang region of China, are endemic areas, but Western Europe and United States have a low prevalence in the general population. This makes …

Seroprevalence Of Human Herpesvirus 8 And Hepatitis C Virus Among Drug Users In Shanghai, China, Tiejun Zhang, Ying Liu, Yuyan Zhang, Jun Wang, Veenu Minhas, Charles Wood, Na He

Nebraska Center for Virology: Faculty Publications

To elucidate and compare the seroprevalence of human herpesvirus 8 (HHV8) and hepatitis C virus (HCV) among Chinese drug users, a cross-sectional study of 441 participants, was conducted in Shanghai, China, from 2012 through 2013. Seventy-seven (17.5%) participants were found to be positive for HHV8 antibodies, while 271 (61.5%) participants were positive for HCV. No significant association between HHV8 seropositivity and drug use characteristics, sexual behaviors, HCV, or syphilis was observed. In contrast, a statistically significant association between HCV seropositivity and injected drug history (OR, 2.18, 95% CI 1.41–3.37) was detected, whereas no statistically significant association between HCV seropositivity and …

Vaccines Within Vaccines: The Use Of Adenovirus Types 4 And 7 As Influenza Vaccine Vectors, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

adenovirus Types 4 and 7 (ad4 and ad7) are associated with acute respiratory distress (aRD). In order to prevent wide- spread ad-associated aRD (ad-aRD) the United states military immunizes new recruits using a safe and effective lyophi- lized wildtype ad4 and ad7 delivered orally in an enteric-coated capsule. We cloned ad4 and ad7 and modified them to express either a GFP-Luciferase (GFPLuc) fusion gene or a centralized influenza H1 hemagglutinin (Ha1-con). BaLB/c mice were injected with GFPLuc expressing viruses intramuscularly (i.m.) and intranasally (i.n.). ad4 induced significantly higher luciferase expression levels as compared with ad7 by both routes. ad7 transduction …

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 …

Global Changes In Mineral Transporters In Tetraploid Switchgrasses (Panicum Virgatum L.), Nathan A. Palmer, Aaron J. Saathoff, Brian M. Waters, Teresa Donze, Tiffany M. Heng-Moss, Paul Twigg, Christian M. Tobias, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass (Panicum virgatum L) is a perennial, C4 grass with great potential as a biofuel crop. An in-depth understanding of the mechanisms that control mineral uptake, distribution, and remobilization will benefit sustainable production. Nutrients are mobilized from aerial portions to below-ground crowns and rhizomes as a natural accompaniment to above-ground senescence post seed-set. Mineral uptake and remobilization is dependent on transporters, however, little if any information is available about the specific transporters that are needed and how their relative expression changes over a growing season.Using well-defined classes of mineral transporters, we identified 520 genes belonging to 40 different transporter …

Switchgrass (Panicum Virgatum L) Flag Leaf Transcriptomes Reveal Molecular Signatures Of Leaf Development, Senescence, And Mineral Dynamics, Nathan A. Palmer, Teresa Donze-Reiner, David Horvath, Tiffany Heng-Moss, Brian M. Waters, Christian M. Tobias, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function in specific stages of leaf development. Here, we characterized gene expression in flag leaves over their development. By merging changes in leaf chlorophyll and the expression of genes for chlorophyll biosynthesis and degradation, a four-phase molecular roadmap for switchgrass flag leaf ontogeny was developed. Genes associated with early leaf development were up-regulated in phase 1. Phase 2 leaves had …

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 …

Nocturnal Homing In The Tropical Amblypygid Phrynus Pseudoparvulus (Class Arachnida, Order Amblypygi), Eileen Hebets, E.J. Gering, Verner P. Bingman, Daniel D. Wiegmann

Eileen Hebets Publications

Arthropods are renowned for their navigational capabilities, with numerous examples known from insects and crustaceans. Early studies of amblypygids (Class Arachnida, Order Amblypygi) also suggest complex nocturnal navigation, despite their apparent lack of visual adaptations to the low-light conditions of a tropical understory. In a series of two studies, we use the tropical amblypygid, Phrynus pseudoparvulus, to assess their nocturnal homing ability. Our first experiment displaced and tracked resident and nonresident individuals. Resident individuals, displaced up to 4.5 m from their home refuges and released onto their home tree, were more likely to return to their previously occupied refuge than …

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 …

Construction Of A Live-Attenuated Hiv-1 Vaccine Through Genetic Code Expansion, Nanxi Wang, Yue Li, Wei Niu, Ming Sun, Ronald Cerny, Qingsheng Li, Jiantao Guo

Qingsheng Li Publications

A safe and effective vaccine against human immunodeficiency virus type 1 (HIV-1) is urgently needed to combat the worldwide AIDS pandemic, but still remains elusive. The fact that uncontrolled replication of an attenuated vaccine can lead to regaining of its virulence creates safety concerns precluding many vaccines from clinical application. We introduce a novel approach to control HIV-1 replication, which entails the manipulation of essential HIV-1 protein biosynthesis through unnatural amino acid (UAA*)-mediated suppression of genome-encoded blank codon. We successfully demonstrate that HIV-1 replication can be precisely turned on and off in vitro.

Includes supporting information.

Heritable Health: An Exploration Of Parental Epigenetics And Their Impact On Individual And Public Health, Brittany F. Hayes 14

Honor Scholar Theses

None