Genetics and Genomics Commons^™

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.

Fusarium Head Blight Resistance And Agronomic Performance In Soft Red Winter Wheat Populations, Daniela Sarti Dvorjak

Theses and Dissertations--Plant and Soil Sciences

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schwein.(Petch)], is recognized as one of the most destructive diseases of wheat (Triticum aestivum L. and T. durum L.) and barley (Hordeum vulgare L.) worldwide. Breeding for FHB resistance must be accompanied by selection for desirable agronomic traits. Donor parents with two FHB resistance quantitative trait loci (QTL) Fhb1 (chromosome 3BS) and QFhs.nau-2DL (chromosome 2DL) were crossed to four adapted SRW wheat lines to generate backcross and forward cross progeny. F₂ individuals were genotyped and assigned to 4 different groups according to presence/ absence of …

Acquired Epigenetic And Chromosomal Changes In Women Treated For Breast Cancer, Noran Aboalela

Theses and Dissertations

Improved survival for women receiving chemotherapy for breast cancer (BC) has been accompanied by the development/persistence of psychoneurological symptoms (PNS) that compromise their quality of life. The biological basis for these PNS is unknown, but could reflect the acquisition of soma-wide chromosomal/epigenetic alterations. An important first step in testing this hypothesis is to determine if somatic genetic/epigenetic changes arise and persist following treatment. To answer this question we longitudinally studied 71 women (ages 23-71) with early-stage BC and collected measures before chemotherapy (baseline), and 4 weeks (mid-chemo); six months (during radiation therapy for a subset of women); and one year …

H3k27me3 And H3k4me3 Chromatin Environment At Super-Induced Dehydration Stress Memory Genes Of Arabidopsis Thaliana, Ning Liu, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Pre-exposure to a stress may alter the plant’s cellular, biochemical, and/or transcriptional responses during future encounters as a “memory” from the previous stress. Genes increasing transcription in response to a first dehydration stress, but producing much higher transcript levels in a subsequent stress, represent the super-induced “transcription memory” genes in Arabidopsis thaliana. The chromatin environment (histone H3 tri-methylations of Lys 4 and Lys 27, H3K4me3, and H3K27me3) studied at five dehydration stress memory genes revealed existence of distinct memory-response subclasses that responded differently to CLF deficiency and displayed different transcriptional activities during the watered recovery periods. Among the most …

Transcriptional Regulation Of Neurogenic Atrophy-Induced Gene Expression By Muscle Ring Finger-1 And Myogenic Regulatory Factors, Theodore Olson

UNF Graduate Theses and Dissertations

Skeletal muscle wasting is a consequence of numerous physiological conditions, including denervation, corticosteroid treatment, immobilization, and aging. The E3 ubiquitin ligases, MuRF1 and MAFbx, are induced under nearly all atrophy conditions and are believed to play a key role in protein degradation in atrophying muscle. However, the preliminary data described in this study provides new evidence that MuRF1 may also act as a transcriptional modulator of atrophy-induced gene activity, including the regulation of MAFbx and MuRF1 expression. To characterize the transcriptional regulation of MuRF1 and MAFbx, reporter gene constructs containing fragments of the proximal promoter regions of these genes were …

A Small Subset Of Fruitless Subesophageal Neurons Modulate Early Courtship In Drosophila, David Tran, Geoffrey Meissner, Rachael French, Bruce Baker

Faculty Publications, Biological Sciences

We show that a small subset of two to six subesophageal neurons, expressing the male products of the male courtship master regulator gene products fruitlessMale (fruM), are required in the early stages of the Drosophila melanogaster male courtship behavioral program. Loss of fruM expression or inhibition of synaptic transmission in these fruM(+) neurons results in delayed courtship initiation and a failure to progress to copulation primarily under visually-deficient conditions. We identify a fruM-dependent sexually dimorphic arborization in the tritocerebrum made by two of these neurons. Furthermore, these SOG neurons extend descending projections to the thorax and abdominal ganglia. These anatomical …

Lineage-Specific Transcriptional Profiles Of Symbiodinium Spp. Unaltered By Heat Stress In A Coral Host, Daniel J. Barshis, Jason T. Ladner, Thomas A. Oliver, Stephen R. Palumbi

Biological Sciences Faculty Publications

Dinoflagellates of the genus Symbiodinium form an endosymbiosis with reef building corals, in which photosynthetically derived nutrients comprise the majority of the coral energy budget. An extraordinary amount of functional and genetic diversity is contained within the coral-associated Symbiodinium, with some phylotypes (i.e., genotypic groupings), conferring enhanced stress tolerance to host corals. Recent advances in DNA sequencing technologies have enabled transcriptome-wide profiling of the stress response of the cnidarian coral host; however, a comprehensive understanding of the molecular response to stress of coral-associated Symbiodinium, as well as differences among physiologically susceptible and tolerant types, remains largely unexplored. Here, …

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 …

Endogenous Ros Levels In C. Elegans Under Exogenous Stress Support Revision Of Oxidative Stress Theory Of Life-History Tradeoffs, Samson W. Smith, Leigh C. Latta Iv, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals.

Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with …

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.

The Prevalence And Effect Of Wolbachia Infection On The Brown Widow Spider (Latrodectus Geometricus), Brittany Dane' Arrington

College of Graduate Studies: Theses & Dissertations

Wolbachia was recently identified in the Brown Widow Spider (Latrodectus geometricus). This symbiont has not previously been found in this genus, therefore the consequences on the host’s population dynamics are unknown. The frequency of endosymbiont infection can provide insight into the population dynamics of the host as this bacteria is known to alter host life history. In my 1^st chapter I determine the prevalence of Wolbachia pipentis infection in in the Brown Widow Spider (Latrodectus geometricus) from five locations in the Southeastern United States. Infection frequency differed significantly among sampling locations, ranging from 20% to …

Genetic Sex Conditions And Redefining Sex, Jayce O'Shields

Student Scholarship

Western culture has a tendency to value binaries and discreet categories that separate its social structure and provide a sense of order and organization. The value placed on binaries and categories may be advantageous in some aspects, but when it starts to infringe upon the legal and medical rights of individuals not easily placed in either binary category, it can become less advantageous.

A baby is usually classified as either male or female shortly after birth, and all future legal, social, and economic actions and rights of that individual are more or less decided according to this classification. A problem …

Single Nucleotide Polymorphisms Linked To Essential Hypertension In Kasigau, Kenya, Julia Carol Freeman

Masters Theses & Specialist Projects

Hypertension, or high blood pressure (BP), is an ever-growing epidemic in the developing world. Understanding the genetics behind essential hypertension (EH), or hypertension with no known cause, is especially important. In this study, three single nucleotide polymorphisms (SNPs) known to be linked to an increase in susceptibility to EH were quantified from a cohort of Kenyans living in the Kasigau region. The SNPs are located in three genes that are part of the renin angiotensin system, the primary regulatory pathway in humans controlling BP. They include: AGT (rs699), AGTR1 (rs5186), and HSD11β2 (rs5479). Overall, by using a fluorescent-based RT-PCR technique, …

Electrotransfer Of Single-Stranded Or Double-Stranded Dna Induces Complete Regression Of Palpable B16.F10 Mouse Melanomas, Loree Heller, Vesba Todorovic, Maja Cemazar

Bioelectrics Publications

Enhanced tumor delivery of plasmid DNA with electric pulses in vivo has been confirmed in many preclinical models. Intratumor electrotransfer of plasmids encoding therapeutic molecules has reached Phase II clinical trials. In multiple preclinical studies, a reduction in tumor growth, increased survival or complete tumor regression have been observed in control groups in which vector or backbone plasmid DNA electrotransfer was performed. This study explores factors that could produce this antitumor effect. The specific electrotransfer pulse protocol employed significantly potentiated the regression. Tumor regression was observed after delivery of single-stranded or double-stranded DNA with or without CpG motifs in both …

Determining Parentage And The Effects Of Relatedness On Play Partner Preference In Belding's Ground Squirrels, Jessica Weidenbach

Master's Theses

I investigated 1) multiple paternity in Belding’s ground squirrels (Urocitellus beldingi) and 2) social partner preferences in juvenile U. beldingi. Prior work with blood allozymes demonstrated multiple paternity in U. beldingi litters. I evaluated paternity using microsatellite DNA analysis, which is more accurate than examining blood allozymes. My results indicate that multiple paternity in U. beldingi is more extensive than previously shown, occurring in about 90% of litters with more than one juvenile, and averaging 2.95 fathers in multiply sired litters. I also evaluated the hypothesis that play and other social behavior promotes bonding among juvenile female …

Sex Determination Using Discriminant Function Analysis In Hispanic Children And Adolescents: A Lateral Cephalometric Study, Alyssa E. Sprowl

UNLV Theses, Dissertations, Professional Papers, and Capstones

Lateral cephalometric radiographs have been used for years to help diagnose skeletal and dental patterns in Orthodontics. Within the last decade, these radiographs have caught the interest of the department of Anthropology for the identification of gender within the adult and adolescent population. Numerous publications have been made but failed to identify sexual dimorphism in the pre-adolescent population. 303 lateral cephalograms of pre and post Latino adolescence age ranging from 6.5 to 17.9 years old were obtained from University of Nevada, Las Vegas (UNLV) digital database. 25 variables were identified and plotted with all linear and angular measurements transferred into …

The Role Of Histone H3 And H4 In Centromere Function And Genome Integrity, Payel Chaudhuri

Graduate Theses and Dissertations

Histone H2A plays an important role in chromosomal segregation among parent and daughter cells during mitosis. While it is established that this histone is important in maintaining chromosome number in cell, further work is carried out to explore the role of other histones like H3 and H4 for similar effects. A systematic study is initiated by screening a library based on mutation of different amino acid residues in these histones. This detailed screening identified specific regions within H3 and H4, which are critically important for centromeric function. These histones residing near the DNA entry/exit region of nucleosome effects the functionality …

Therapeutic Efficacy Of P53 Restoration In Mdm2-Overexpressing Tumors, Qin Li

Dissertations and Theses (Open Access)

The TP53 tumor suppressor is the most mutated gene in human cancers. Recent studies using genetically modified mouse models have shown that restoring the expression of wild-type p53 has led to tumor growth suppression in various types of tumors lacking p53. Other mechanisms, e.g. upregulation of Mdm2 levels, exist in tumors to inactivate the p53 pathway. Mdm2, an E3 ubiquitin-ligase that targets p53 for proteasomal degradation, is present at high levels in many tumors with wild-type p53. In this study, we probed the effects of restoring p53 activity in Mdm2-overexpressing tumors genetically using animal models. Here we demonstrated high levels …

The Roles Of Phenotypic Plasticity And Genotypic Specialization In High Altitude Adaptation, Danielle M. Tufts

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

In vertebrates living at high altitude, arterial hypoxemia may be ameliorated by reversible changes in the oxygen-carrying capacity of the blood (regulated by erythropoiesis) and/or changes in blood–oxygen affinity (regulated by allosteric effectors of hemoglobin function). These hematological traits often differ between taxa that are native to different elevational zones, but it is often unknown whether the observed physiological differences reflect fixed, genetically based differences or environmentally induced acclimatization responses (phenotypic plasticity). Here, we report measurements of hematological traits related to blood–O₂ transport in populations of deer mice (Peromyscus maniculatus) that are native to high- and low-altitude …

An Intergenic Region Shared By At4g35985 And At4g35987 In Arabidopsis Thaliana Is A Tissue Specific And Stress Inducible Bidirectional Promoter Analyzed In Transgenic Arabidopsis And Tobacco Plants, Joydeep Banerjee, Dipak K. Sahoo, Nrisingha Dey, Robert Houtz, Indu B. Maiti

Kentucky Tobacco Research and Development Center Faculty Publications

On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and …

Reflections On The Cost Of "Low-Cost" Whole Genome Sequencing: Framing The Health Policy Debate, Timothy Caulfield, Jim Evans, Amy Mcguire, Christopher Mccabe, Tania M. Bubela, Robert Cook-Deegan, Jennifer Fishman, Stuart Hogarth, Fiona A. Miller, Vardit Ravitsky

Office of the Provost

The cost of whole genome sequencing is dropping rapidly. There has been a great deal of enthusiasm about the potential for this technological advance to transform clinical care. Given the interest and significant investment in genomics, this seems an ideal time to consider what the evidence tells us about potential benefits and harms, particularly in the context of health care policy. The scale and pace of adoption of this powerful new technology should be driven by clinical need, clinical evidence, and a commitment to put patients at the centre of health care policy.

Novel Neuroprotective Function Of Apical-Basal Polarity Genecrumbs In Amyloid Beta 42 (Aβ42) Mediated Neurodegeneration, Andrew Steffensmeier, Meghana Tare, Oorvashi Roy Puli, Rohan Modi, Jaison Nainaparampil, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Alzheimer's disease (AD, OMIM: 104300), a progressive neurodegenerative disorder with no cure to date, is caused by the generation of amyloid-beta-42 (Aβ42) aggregates that trigger neuronal cell death by unknown mechanism(s). We have developed a transgenic Drosophilaeye model where misexpression of human Aβ42 results in AD-like neuropathology in the neural retina. We have identified an apical-basal polarity gene crumbs (crb) as a genetic modifier of Aβ42-mediated-neuropathology. Misexpression of Aβ42 caused upregulation of Crb expression, whereas downregulation of Crb either by RNAi or null allele approach rescued the Aβ42-mediated-neurodegeneration. Co-expression of full length Crb with Aβ42 increased severity of Aβ42-mediated-neurodegeneration, …

Homeotic Gene Teashirt (Tsh) Has A Neuroprotective Function In Amyloid-Beta 42 Mediated Neurodegeneration, Michael T. Moran, Meghana Tare, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Background: Alzheimer's disease (AD) is a debilitating age related progressive neurodegenerative disorder characterized by the loss of cognition, and eventual death of the affected individual. One of the major causes of AD is the accumulation of Amyloid-beta 42 (Aβ42) polypeptides formed by the improper cleavage of amyloid precursor protein (APP) in the brain. These plaques disrupt normal cellular processes through oxidative stress and aberrant signaling resulting in the loss of synaptic activity and death of the neurons. However, the detailed genetic mechanism(s) responsible for this neurodegeneration still remain elusive.

Methodology/Principal Findings: We have generated a transgenic Drosophila eye model where …

Identification Of Set1 Target Genes, William Beyer, Scott D. Briggs

The Summer Undergraduate Research Fellowship (SURF) Symposium

The Set1 complex, a histone methyltransferase complex found in S. cerevisiae (budding yeast), is the only histone methyltransferase responsible for catalyzing methylation of histone H3 at Lysine 4. It possesses homologues in other species, humans included. While yeast only have the Set1 complex, the human homologues of the yeast Set1 complex include mixed-lineage leukemia family (MLL1-4), Set1 A, Set1 B, among others. MLL1-4 has been shown to play a role in transcription, cell type specification, and the development of leukemia. One application of characterizing the role of a protein is that the information gained can provide insight into the function …

Forward Genetic Screen Of Trichomes For Discovery Of Cytoskeleton-Based Mutants, Adam M. Fessenden, Samuel Belteton, Daniel B. Szymanski

The Summer Undergraduate Research Fellowship (SURF) Symposium

Understanding plant cell development and what genes influence cell growth can lead to breakthroughs in beneficial areas such as bioremediation, agricultural production, and biofuels. However, information on many of the genes that control plant cell growth is either unknown or severely limited. Further research to fully comprehend the genetic pathways within the cells will enable the genetic engineering of plants to further benefit society. One approach is the combined use of a forward genetic screen, sophisticated growth analysis, and gene identification. Using Arabidopsis thaliana trichomes, leaf hairs, as a model system, the mutagenized population of thousands of plants was screened …

Saccharomyces Cerevisiae Cdc7 Homology In Drosophila Melanogaster, Marcus R. Hosler, Robert E. Stephenson, Vikki M. Weake

The Summer Undergraduate Research Fellowship (SURF) Symposium

Saccharomyces cerevisiae Dbf4(Dumbbell former 4) and Cdc7(Cell Division Cycle 7) form a complex that phosphorylates Mcm2 (Minichromosome maintenance 2) to initiate DNA replication. Cdc7 is a target for cancer research because there is a Cdc7 ortholog in humans that is necessary for DNA replication and cell survival. Our goal is to characterise a putative Cdc7 homolog in Drosophila melanogaster (dCdc7). We have previously shown that expression of the known Drosophila Dbf4 ortholog, Chiffon, and dCdc7 can rescue yeast cells deficient in active Cdc7. Our hypothesis is that the dCdc7 is activated by Chiffon to phosphorylate MCM2. To test this hypothesis, …

Resolution By Unassisted Top3 Points To Template Switch Recombination Intermediates During Dna Replication, M. Rebecca Glineburg, Alejandro Chavez, Vishesh Agrawal, Steven J. Brill, F. Brad Johnson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The evolutionarily conserved Sgs1/Top3/Rmi1 (STR) complex plays vital roles in DNA replication and repair. One crucial activity of the complex is dissolution of toxic X-shaped recombination intermediates that accumulate during replication of damaged DNA. However, despite several years of study the nature of these X-shaped molecules remains debated. Here we use genetic approaches and two-dimensional gel electrophoresis of genomic DNA to show that Top3, unassisted by Sgs1 and Rmi1, has modest capacities to provide resistance to MMS and to resolve recombination-dependent X-shaped molecules. The X-shaped molecules have structural properties consistent with hemicatenane-related template switch recombination intermediates (Rec-Xs) but not Holliday …

Notchless Interacts With Multiple Signaling Pathways During Mouse Peri-Implantation Development, Chiao-Ling Lo

Open Access Dissertations

During peri-implantation, the embryo transitions from a suspension environment in the fallopian tubes to an adherent system within the uterus. Successful transition requires maternal and fetal signaling cascades that establish maternal-fetal boundaries. Failure is common, as ~ 25% of all human pregnancies terminate during these steps. A large-scale mutation study in mice produced two mutants (l11Jus1 and l11Jus4) that are excellent models of this transition. l11Jus1 and l11Jus4 contain missense mutations in the Notchless homolog 1 (Drosophila) (Nle1) gene. NLE1 is thought to signal via the canonical NOTCH pathway in vertebrates. Although in invertebrates and lower vertebrates, NOTCH signaling directs …

Natural Genetic Variation Affecting Calcium Homeostasis, Rebecca Anna Replogle

Open Access Dissertations

Calcium (Ca) is essential for multiple functions within the body including skeletal health. The level of Ca in the serum is tightly regulated. During periods of habitual low Ca intake, the body senses a decrease in serum Ca and increases renal conversion of 25 hydroxyvitamin D (25(OH)D) to 1,25 dihydroxyvitamin D (1,25(OH)2D). 1,25(OH)2D acts through the vitamin D receptor (VDR) to increase intestinal Ca absorption, renal Ca reabsorption and skeletal Ca resorption. Efficient intestinal Ca absorption, especially during periods of low Ca intake, is critical for protecting bone mass. Ca absorption and its primary regulator, 1,25(OH)2D, are affected by both …

The Genetic Architecture Of Juvenile Migration In Rainbow Trout (Oncorhynchus Mykiss), Benjamin Charles Hecht

Open Access Dissertations

Animal migrations play a critical role in the health and balance of ecological systems and in the evolution and diversification of species, and this is perhaps best displayed amongst salmonid fishes (salmon, trout, and char) who exhibit variation in the propensity to migrate both within and among species. Rainbow and steelhead trout (Oncorhynchus mykiss), members of the salmonid family of fishes, capture this variation throughout their native range. Some populations and ecotypes will remain resident in freshwater habitats throughout their life history; while others have the ability to embark on tremendous marine migrations. Those that migrate undergo a suite of …