Genetics and Genomics Commons^™

Functional Approach To Condition, Dustin J. Wilgers, Eileen A. Hebets

Eileen Hebets Publications

Animal signaling is commonly thought to be costly. Signaling costs can arise via a variety of avenues, including energy expenditure, predator attraction, and so on (reviews in Zuk and Kolluru, 1998; Kotiaho, 2001), and are predicted to increase with signal expression (e.g., size, amplitude, and intensity; Johnstone, 1997). Due to these costs, signaler condition, which is hypothesized to be a reflection of a signaler’s genetic quality, is expected to influence the level of signal expression one can afford (Zahavi, 1975), resulting in a positive correlation between signaler condition and signal expression – that is, condition-dependent signaling (Zahavi, 1977; West-Eberhard, 1979; …

Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, Jan E. Janecka, Simone S. E. Nielsen, Sidsel D. Andersen, Federico G. Hoffmann, Roy E. Weber, Trevor Anderson, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

Genetically based modifications of hemoglobin (Hb) function that increase blood–O₂ affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O₂ affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, …

Smoking Patterns Among Vcu Students, Jasmine Saini

UROP Posters

For some individuals, college can be a high risk time for the development of problems associated with alcohol use and other substances. The purpose of this study is to examine these initiation and use patterns as they relate to nicotine use among college students 18 years of age and older enrolled in Spit for Science: The VCU Student Survey. The Spit for Science research project evaluates how genetic and environmental factors contribute to substance use and emotional health among college students at VCU. This study uses data from the Spit for Science 2011 cohort (n=2007) to investigate smoking patterns among …

Functional Analysis Of The Ovarian Cancer Susceptibility Locus At 9p22.2 Reveals A Transcription Regulatory Network Mediated By Bnc2 In Ovarian Cells, Melissa Buckley

USF Tampa Graduate Theses and Dissertations

GWAS have identified several chromosomal loci associated with ovarian cancer risk. However, the mechanism underlying these associations remains elusive. We identify candidate functional Single Nucleotide Polymorphisms (SNPs) at the 9p22.2 ovarian cancer susceptibility locus, several of which map to transcriptional regulatory elements active in ovarian cells identified by FAIRE-seq (Formaldehyde assisted isolation of regulatory elements followed by sequencing) and ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) in relevant cell types. Reporter and electrophoretic mobility shift assays (EMSA) determined the extent to which candidate SNPs had allele specific effects. Chromosome conformation capture (3C) reveals a physical association between Basonuclin 2 (BNC2) and …

Epigenetic Regulation Of Nuclear Hormone Receptor Dax-1, Michael B. Heskett

Master's Theses

DAX-1 (NR0B1) is an orphan nuclear receptor that plays a key role in the development and maintenance of steroidogenic tissue in mammals. Dax-1 is also expressed in mouse embryonic stem (ES) cells and is required to maintain pluripotency. Duplication of the X-chromosome in the region containing the NR0B1 gene results in sex reversal, and mutations in NR0B1 cause adrenal hypoplasia congenita. DAX-1 has been observed to act as a corepressor of other nuclear receptors including androgen receptor (AR), estrogen receptor (ER), and steroidogenic factor 1 (SF-1). In addition to pluripotent ES cells, DAX-1 is primarily expressed in select tissues of …

Regulation Of Three Nitrogenase Gene Clusters In The Cyanobacterium Anabaena Variabilis Atcc 29413, Teresa Thiel, Brenda Pratte

Biology Department Faculty Works

The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environmental deficiency in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts are microxic cells that allow nitrogenase to function in a filament comprised primarily of vegetative cells that produce oxygen by photosynthesis. A. variabilis is unique among well-characterized cyanobacteria in that it has three nitrogenase gene clusters that encode different nitrogenases, which function under different environmental conditions. The nif1 genes encode a Mo-nitrogenase that functions only in heterocysts, …

Review Of "The Pku Paradox: A Short History Of A Genetic Disease" By D. B. Paul And J. P. Brosco, John B. Jenkins

Biology Faculty Works

No abstract provided.

The Conservation Genetics Of Two Emydid Turtles: Emydoidea Blandingii And Malaclemys Terrapin, Charlotte Lizana Petre

Master's Theses

Conservation of turtles is complicated by their sensitivity to habitat degradation and overexploitation. I used microsatellites and standard population genetic analyses to explore genetic diversity, population structure, paternity and demographic history in two emydid turtles that are currently experiencing threats to their survival. The Blanding’s turtle, Emydoidea blandingii, has experienced habitat fragmentation throughout its range, and this study focuses on a population in Massachusetts where hatchlings from one population are being translocated to establish a new population. I found evidence of multiple paternity within clutches and found no significant reduction in genetic diversity when comparing the source population and …

Genetic Structure Of Yellow Perch Populations In Coastal Areas Of Eastern Lake Michigan, Jessica N. Wesolek

Masters Theses

Genetic population substructure is often overlooked because of discontinuities between management and actual population structure as in the case of yellow perch, an ecologically and economically important indigenous fish species in the Laurentian Great Lakes. A knowledge gaps pertaining to the natural history of yellow perch relates to the biological connectivity between nearshore Lake Michigan and drowned river mouth (DRM) lakes, where it remains unclear whether resident yellow perch from Lake Michigan use DRM lakes for spawning or whether DRM lakes contribute to nearshore yellow perch populations in Lake Michigan. I used DNA fingerprinting (genotyping) to explore biological connectivity between …

Antibacterial Gene Transfer Across The Tree Of Life, Jason A. Metcalf, Lisa J. Funkhouser-Jones, Kristen A. Brileya, Anna-Louise Reysenbach, Seth R. Bordenstein

Biology Faculty Publications and Presentations

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, …

An Active Role For The Ribosome In Determining The Fate Of Oxidized Mrna, Carrie L. Simms, Benjamin H. Hudson, John W. Mosior, Ali S. Rangwala, Hani S. Zaher

Biology Faculty Research

Chemical damage to RNA affects its functional properties and thus may pose a significant hurdle to the translational apparatus; however, the effects of damaged mRNA on the speed and accuracy of the decoding process and their interplay with quality-control processes are not known. Here, we systematically explore the effects of oxidative damage on the decoding process using a well-defined bacterial in vitro translation system. We find that the oxidative lesion 8-oxoguanosine (8-oxoG) reduces the rate of peptide-bond formation by more than three orders of magnitude independent of its position within the codon. Interestingly, 8-oxoG had little effect on the fidelity …

A Comparison Of The Caulobacter Na1000 And K31 Genomes Reveals Extensive Genome Rearrangements And Differences In Metabolic Potential, Craig Stephens, Kurt Ash, Theta Brown, Tynetta Watford, Latia E. Scott, Bert Ely

Biology

The genus Caulobacter is found in a variety of habitats and is known for its abilityto thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 48Cwith a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) thatcode for 438 additional proteins. A comparison of the K31 and the Caulobactercrescentus NA1000 genomes revealed extensive rearrangements of gene order,suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed …

Fisheries Management Paper No.266 - Exmouth Gulf Prawn Managed Fishery Bycatch Action Plan 2014-2019. Version 1.0, Department Of Fisheries, Western Australia

Fisheries Management Papers

Bycatch is described as the part of the catch which is returned to the sea (usually referred to as non-retained or discarded) either because it has no commercial value or because legislative requirements preclude it being retained. Thus, this Bycatch Action Plan (BAP) includes unmarketable finfish and invertebrate species, along with endangered, threatened and protected (ETP) species, such as marine mammals, reptiles and some elasmobranchs.

It is Government policy to minimise bycatch in all commercial fisheries. This BAP details a program of actions to address bycatch issues in the Exmouth Gulf Prawn Managed Fishery (EGPMF), in accordance with the EGPMF …

Phylogenetic Analysis Of Algal Symbionts Associated With Four North American Amphibian Egg Masses, Eunsoo Kim, Yuan Lin, Ryan R. Kerney, Lili Blumenberg, Cory Bishop

Biology Faculty Publications

Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga “Oophila amblystomatis” (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these …

Intercellular Cooperation And Competition In Brain Cancers: Lessons From Drosophila And Human Studies, Indrayani Waghmare, Austin Roebke, Mutsuko Minata, Madhuri Kango-Singh, Ichiro Nakano

Biology Faculty Publications

Glioblastoma (GBM) is a primary brain cancer with an extremely poor prognosis. GBM tumors contain heterogeneous cellular components, including a small subpopulation of tumor cells termed glioma stem cells (GSCs). GSCs are characterized as chemotherapy- and radiotherapy-resistant cells with prominent tumorigenic ability. Studies in Drosophila cancer models demonstrated that interclonal cooperation and signaling from apoptotic clones provokes aggressive growth of neighboring tumorigenic clones, via compensatory proliferation or apoptosis induced proliferation. Mechanistically, these aggressive tumors depend on activation of Jun-N-terminal kinase (upstream of c-JUN), and Drosophila Wnt (Wg) in the apoptotic clones. Consistent with these nonmammalian studies, data from several mammalian …

Eight Legged Encounters, Eileen A. Hebets

Eileen Hebets Publications

This program was funded in part by a National Science Foundation grant (DRL–1241482 to EAH). Material was developed in collaboration with Marie- Claire Chelini, Jessie Rose Storz, Cody Storz, and Malcolm Rosenthal. Steven Schwartz, Jason Stafstrom, Kathy French, Priscilla Grew, and Judy Diamond were all extremely helpful in grant writing, facilitating the first live event, and/or discussions. Pawl Tisdale (artist) was phenomenal to work with on all aspects of the project!

TABLE OF CONTENTS

CLASSIFICATION & TAXONOMY STATIONS
I. WHAT IS AN ARTHROPOD? page 4 a. The goal of this station is to introduce the audience to some basic information …

Editorial Overview: Environmental Physiology: Insect Environmental Physiology, Brent J. Sinclair

Biology Publications

No abstract provided.

The Peopling Of The African Continent And The Diaspora Into The New World, Michael Campbell, Jibril Hirbo, Jeffrey Peter Townsend, Sarah Tishkoff

Department of Biology Faculty Publications

Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will …

Identification And Characterization Of Factors Involved In Dna Demethylation And Anti-Silencing In Arabidopsis, Zhaobo Lang

Open Access Dissertations

DNA methylation is a key epigenetic mark for transcriptional gene silencing in many eukaryotes. DNA methylation status can be dynamically controlled by methylation and active demethylation processes. Compared to the well-known mechanisms of DNA methylation, the mechanisms of DNA demethylation and its regulation are poorly understood. In order to better understand the DNA demethylation pathway, we developed two genetic screening systems in Arabidopsis to identify new components involved in the DNA demethylation. In the first system, which is based on 35S promoter driven SUC2 (sucrose transporter 2) transgene, a mutant (91-1) was isolated and map-based cloning identified the …

Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad

Open Access Dissertations

Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within …

An Rnai-Based Suppressor Screen Identifies Interactors Of The Myt1 Ortholog Of Caenorhabditis Elegans, Anna Allen, Jessica Nesmith, Andy Golden

Department of Biology Faculty Publications

Oocyte maturation in all species is controlled by a protein complex termed the maturation promoting factor (MPF). MPF is comprised of a cyclin-dependent kinase (CDK) and its partner cyclin, and is regulated by dueling regulatory phosphorylation events on the CDK. In Caenorhabditis elegans, the Wee1/Myt1 ortholog WEE-1.3 provides the inhibitory phosphorylations on CDK-1 that keep MPF inactive and halts meiosis. Prior work has shown that depletion of WEE-1.3 in C. elegans results in precocious oocyte maturation in vivo and a highly penetrant infertility phenotype. This study sought to further define the precocious maturation phenotype and to identify novel interactors with …

Multimodal Sensory Reliance In The Nocturnal Homing Of The Amblypygid Phrynus Pseudoparvulus (Class Arachnida, Order Amblypygi)?, Eileen A. Hebets, Alfonso Aceves-Aparicio, Samuel Aguilar-Argüello, Verner P. Bingman, Ignacio Escalante, Eben J. Gering, David R. Nelson, Jennifer Rivera, José Ángel Sánchez-Ruiz, Laura Segura-Hernández, Virginia Settepani, Daniel D. Wiegmann, Jay A. Stafstrom

Eileen Hebets Publications

Like many other nocturnal arthropods, the amblypygid Phrynus pseudoparvulus is capable of homing. The environment through which these predators navigate is a dense and heterogeneous tropical forest understory and the mechanism(s) underlying their putatively complex navigational abilities are presently unknown. This study explores the sensory inputs that might facilitate nocturnal navigation in the amblypygid P. pseudoparvulus. Specifically, we use sensory system manipulations in conjunction with field displacements to examine the potential involvement of multimodal—olfactory and visual—stimuli in P. pseudoparvulus’ homing behavior. In a first experiment, we deprived individuals of their olfactory capacity and displaced them to the opposite side of …

Investigating The Role Of Micrornas In The Response To Nitrogen Deprivation In The Green Alga Chlamydomonas Reinhardtii, Adam Voshall

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

Microalgae are gaining attention as a potential feedstock for the production of biodiesel, mainly derived from triacylglycerols (TAG). In many algae, TAG synthesis increases dramatically upon certain stresses but this is often accompanied by growth retardation. Rational improvements to strain productivity are limited by the scant knowledge on algal lipid metabolism and gene regulatory mechanisms. In this context, systems-level approaches aimed at understanding and modeling metabolic and regulatory networks may enable hypothesis-driven genetic engineering strategies. The green microalga Chlamydomonas reinhardtii accumulates significant amounts of TAGs under nutrient starvation and provides a genetically tractable model for manipulating biosynthetic pathways. In order …

Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator

Department of Biological Sciences Publications

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants …

Hla Class Ii Alleles In The Otomi Population Of The Mezquital Valley. A Genetic Approach To The History Of Interethnic Migrations In The Mexican Central Plateau, Ana Itzel Juárez-Martín, Blanca Zoila González-Sobrino, Ángel Eduardo Camarena Olvera, Ramcés Falfán-Valencia

Human Biology Open Access Pre-Prints

From a historic and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the making of the population dynamics of the Mexican Central Plateau. Due to their antiquity in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua.

This study analyzes the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intra-regional level historical perspective of the genetic relationships between the Otomi of the …

Long-Term Cre-Mediated Retrograde Tagging Of Neurons Using A Novel Recombinant Pseudorabies Virus, Hysell V. Oviedo, Hassasna K. Oyibo, Petr Znamenskiy, Lynn W. Enquist, Anthony M. Zador

Publications and Research

Brain regions contain diverse populations of neurons that project to different long-range targets. The study of these subpopulations in circuit function and behavior requires a toolkit to characterize and manipulate their activity in vivo. We have developed a novel set of reagents based on Pseudorabies Virus (PRV) for efficient and long-term genetic tagging of neurons based on their projection targets. By deleting IE180, the master transcriptional regulator in the PRV genome, we have produced a mutant virus capable of infection and transgene expression in neurons but unable to replicate in or spread from those neurons. IE180-null mutants showed no cytotoxicity, …

Phenotypic Robustness And The Assortativity Signature Of Human Transcription Factor Networks, Dov A. Pechenick, Joshua L. Payne, Jason H. Moore

Dartmouth Scholarship

Many developmental, physiological, and behavioral processes depend on the precise expression of genes in space and time. Such spatiotemporal gene expression phenotypes arise from the binding of sequence-specific transcription factors (TFs) to DNA, and from the regulation of nearby genes that such binding causes. These nearby genes may themselves encode TFs, giving rise to a transcription factor network (TFN), wherein nodes represent TFs and directed edges denote regulatory interactions between TFs. Computational studies have linked several topological properties of TFNs - such as their degree distribution - with the robustness of a TFN's gene expression phenotype to genetic and environmental …

Global Population-Specific Variation In Mirna Associated With Cancer Risk And Clinical Biomarkers, Renata Rawlings-Goss, Michael Campbell, Sarah Tishkoff

Department of Biology Faculty Publications

Background: MiRNA expression profiling is being actively investigated as a clinical biomarker and diagnostic tool to detect multiple cancer types and stages as well as other complex diseases. Initial investigations, however, have not comprehensively taken into account genetic variability affecting miRNA expression and/or function in populations of different ethnic backgrounds. Therefore, more complete surveys of miRNA genetic variability are needed to assess global patterns of miRNA variation within and between diverse human populations and their effect on clinically relevant miRNA genes.

Gene-Environment Interactions In Human Health: Case Studies And Strategies For Developing New Paradigms And Research Methodologies, Fatimah Linda Collier Jackson

Department of Biology Faculty Publications

THE SYNERGISTIC EFFECTS OF GENES AND THE ENVIRONMENT ON HEALTH ARE EXPLORED IN THREE CASE STUDIES: adult lactase persistence, autism spectrum disorders, and the metabolic syndrome, providing examples of the interactive complexities underlying these phenotypes. Since the phenotypes are the initial targets of evolutionary processes, understanding the specific environmental contexts of the genetic, epigenetic, and environmental changes associated with these phenotypes is essential in predicting their health implications. Robust databases must be developed on the local scale to deconstruct both the population substructure and the unique components of the environment that stimulate geographically specific changes in gene expression patterns. To …

Multiplex Ssr-Pcr Analysis Of Genetic Diversity And Redundancy In The Philippine Rice (Oryza Sativa L.) Germplasm Collection, Jamaica L. Delos Reyes, Vivian A. Panes, Dindo A. Tabanao, Gabriel O. Romero

Biology Faculty Publications

Rice germplasm conservation is vital to ensuring the availability of a rich gene pool for future varietal improvement programs. However, with limited resources for gene banking, there is a need to identify and prioritize unique accessions in the PhilRice gene bank for maximum resource utilization. A robust and unequivocal way to identify duplicates is through multiplex SSR-PCR DNA fingerprinting. The present study established the optimal concentrations and reaction conditions for the successful amplification of PCR products using a multiplex panel composed of rice simple sequence repeat (SSR) markers, namely RM312, RM316, RM514 and RM171. The panel was then used to …