Genetics and Genomics Commons^™

Development Of A Genetic Modification System In Clostridium Scatologenes Atcc 25775 For Generation Of Mutants, Prasanna Tamarapu Parthasarathy

Masters Theses & Specialist Projects

3-Methyl indole (3-MI) is a malodorant in food and animal waste and Clostridium scatologenes ATCC 25775 is the model organism for the study of 3-MI production. 3-MI is an anaerobic degradation product of L-tryptophan and can cause pulmonary disorders and death in cattle and goats. To elucidate the 3-MI biosynthesis pathway and the underlying genes, it is necessary to develop a system to allow genetic modification in Clostridium scatologenes ATCC 25775. Bacteriophages and transposons are useful tools to achieve this goal. Isolation of Clostridium scatologenes ATCC 25775 bacteriophage was attempted by prophage induction and enrichments using environmental sources. To induce …

Appearance Based Stage Recognition Of Drosophila Embryos, Gopi Chand Nutakki

Masters Theses & Specialist Projects

Stages in Drosophila development denote the time after fertilization at which certain specific events occur in the developmental cycle. Stage information of a host embryo, as well as spatial information of a gene expression region is indispensable input for the discovery of the pattern of gene-gene interaction. Manual labeling of stages is becoming a bottleneck under the circumstance of high throughput embryo images. Automatic recognition based on the appearances of embryos is becoming a more desirable scheme. This problem, however, is very challenging due to severe variations of illumination and gene expressions. In this research thesis, we propose an appearance …

Analysis Of The Clear Plaque Phenotype Of The Bacteriophage Hk75, Phani Chandrika Kunapuli

Masters Theses & Specialist Projects

The growth of bacteriophage HK75 is inhibited by specific mutations in the zinc binding domain of the host RNA polymerase beta prime subunit. It shares this rare property with bacteriophage HK022 and other phages that use RNA mediated antitermination to promote early gene expression. Recent genomic analysis of HK75 and HK022 has confirmed the relatedness of these two phages and place HK75 in the lambdoid family of bacteriophages. Lambdoid phages are temperate and can adopt a lytic or lysogenic lifestyle upon infection of a suitable host. However, HK75 only forms clear plaques and thus appears to be defective in its …

Phenotypic And Genetic Characterization Of Wildland Collections Of Western And Searls Prairie Clovers For Rangeland Revegetation In The Western Usa, Kishor Bhattarai

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Western prairie clover [Dalea ornata (Douglas ex Hook.) Eaton & J. Wright] is a perennial legume that occurs in the northern Great Basin, Snake River Basin, and southern Columbia Plateau, whereas Searls prairie clover [Dalea searlsiae (A. Gray) Barneby], also a perennial legume, occurs in the southern Great Basin and surrounding areas. Understanding the genetic and ecotypic variation of these prairie clovers is a prerequisite for developing populations suitable for rangeland revegetation in the western USA. DNA sequences of internal transcribed spacer (ITS/5.8S) and trnK/matK were used to study the phylogeny of these species. The species were distinguished …

Environmental Influence On Brain, Behavior, And Gene Expression In Drosophila, Xia Wang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Brain development and behavior are sensitive to environmental stimuli. To gain an understanding of how and to what extent environmental variations, particularly with regard to thermal stress and sensory input, affect brain development, function, and genomic activity, in this dissertation, three interrelated studies were conducted in Drosophila melanogaster.

The first study examined the effects of ecologically-relevant hyperthermia stress on development of the Drosophila mushroom body (MB), a conserved sensory integration and associative center in the insect brain. A daily hyperthermic episode throughout larval and pupal development was shown to severely disrupt MB anatomy by reducing intrinsic Kenyon cell neuron …

Discrete Diffusion Models To Study The Effects Of Mg2+ Concentration On The Phopq Signal Transduction System, Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. Das, Chaoyang Zhang

Faculty Publications

Background: The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes at multiple scales. This modeling method requires techniques that maintain a reasonable accuracy of the biological process and also reduces the computational overhead. This objective motivates the use of new methods that can transform the problem from energy and affinity based modeling to information theory based modeling. To achieve this, we transform all dynamics within the cell into a random event time, which is specified through an information domain …

A New Approach To Construct Pathway Connected Networks And Its Application In Dose Responsive Gene Expression Profiles Of Rat Liver Regulated By 2,4dnt, Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S. Wilbanks, Barbara Lynn Escalon, Edward J. Perkins, Jake Y. Chen

Faculty Publications

Background: Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and other organisms. However the mechanism of 2,4DNT induced toxicity is still unclear. Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported.

Results: Microarray analyses were conducted using liver tissue of rats collected 24h after exposure to a single oral gavage with one of five concentrations of 2,4DNT. We observed …

Characterizing And Treating The Neuropathology Of Tuberous Sclerosis Complex In The Mouse, Sharon W. Way

Dissertations and Theses (Open Access)

Tuberous sclerosis complex (TSC) is a multisystem, autosomal dominant disorder affecting approximately 1 in 6000 births. Developmental brain abnormalities cause substantial morbidity and mortality and often lead to neurological disease including epilepsy, cognitive disabilities, and autism. TSC is caused by inactivating mutations in either TSC1 or TSC2, whose protein products are known inhibitors of mTORC1, an important kinase regulating translation and cell growth. Nonetheless, neither the pathophysiology of the neurological manifestations of TSC nor the extent of mTORC1 involvement in the development of these lesions is known. Murine models would greatly advance the study of this debilitating disorder. This thesis …

Rmi1 Is Essential For Early Embryonic Development And Attenuation Of Tumor Development, Haoyi Chen

Dissertations and Theses (Open Access)

RMI1 (BLM-Associated Protein 75 or Blap75) is highly conserved from yeast to human. Previous studies have shown that hRMI1 is required for BLM/TopoIIIα/RMI1 complex stability and function. However, in vivo functions of RMI1 remain elusive. To address this question, I generated RMI1 knockout mice by homologous replacement targeting. While RMI1+/- mice showed no obvious phenotype, deletion of both RMI1 alleles leads to early embryonic lethality before implantation. I then generated RMI1/p53 double knockout mice. After ionizing radiation treatment at 4Gy, RMI1/p53 double-heterzygous mice showed shortened tumor latency and aggressive tumor types when comparing with wild type, RMI1+/- and p53+/- control …

Toxicogenomics Analysis Of Non-Model Transcriptomes Using Next-Generation Sequencing And Microarray, Arun Rawat

Dissertations

With the advent of next generation technologies like Roche/454 Life Sciences that require low cost and less time for sequencing will help in providing a workable draft of non-model species genomes. Availability of high throughput microarray technologies for gene expression profiling provides low-cost tools for investigation of highly-integrated responses to various stimuli. These advancements along with bioinformatics processing have led to an increasing number of non-model species having well-annotated transcriptomes. The project focuses on the life cycle of development, functional annotation, and utilization of genomic tools for the avian wildlife species to determine the molecular impacts of exposure to munitions …

Elucidating Functional Roles For Myogenin In Adult Skeletal Muscle Metabolism, Exercise Capacity, And Regeneration, Jesse Flynn

Dissertations and Theses (Open Access)

The four basic helix-loop-helix myogenic transcription factors, myogenin, Myf5, MRF4, and MyoD are critical for embryonic skeletal muscle development. Myogenin is necessary for the terminal differentiation of myoblasts into myofibers during embryogenesis, but little is known about the roles played by myogenin in adult skeletal muscle function and metabolism. Furthermore, while metabolism is a well-studied physiological process, how it is regulated at the transcriptional level remains poorly understood. In this study, my aim was to determine the function of myogenin in adult skeletal muscle metabolism, exercise capacity, and regeneration. To investigate this, I utilized a mouse strain harboring the Myogflox …

Characterization Of The Agrobacterium Tumefaciens Virb2 Pilin Of The Virb/D4 Type Iv Secretion System, Jennifer Kerr

Dissertations and Theses (Open Access)

The Agrobacterium tumefaciens VirB/D4 type IV secretion system (T4SS) delivers oncogenic T-DNA and effector proteins to susceptible plant cells. This leads to the formation of tumors termed Crown Galls. The VirB/D4 T4SS is comprised of 12 subunits (VirB1 to VirB11 and VirD4), which assemble to form two structures, a secretion channel spanning the cell envelope and a T-pilus extending from the cell surface. In A. tumefaciens, the VirB2 pilin subunit is required for assembly of the secretion channel and is the main subunit of the T-pilus. The focus of this thesis is to define key reactions associated with the T4SS …

Agrobacterium Virb10 Contributions To Type Iv Substrate Secretion, T-Pilus Biogenesis, And Outer Membrane Pore Formation, Isaac Garza

Dissertations and Theses (Open Access)

The VirB/D4 type IV secretion system (T4SS) of Agrobacterium tumefaciens functions to transfer substrates to infected plant cells through assembly of a translocation channel and a surface structure termed a T-pilus. This thesis is focused on identifying contributions of VirB10 to substrate transfer and T-pilus formation through a mutational analysis. VirB10 is a bitopic protein with several domains, including a: (i) cytoplasmic N-terminus, (ii) single transmembrane (TM) α-helix, (iii) proline-rich region (PRR), and (iv) large C-terminal modified β-barrel. I introduced cysteine insertion and substitution mutations throughout the length of VirB10 in order to: (i) test a predicted transmembrane topology, (ii) …

The Genetics Of Metal Uptake In Caulobacter Crescentus: Characterization Of Regulators And Identification Of Receptors, Leah Howell

All Dissertations

Caulobacter crescentus is an oligotrophic, Gram negative bacterium with a dimorphic lifecycle. It is a model system for cell cycle regulation and cellular development. Since C. crescentus resides primarily in freshwater, this microorganism can also serve as a model system for nutrient uptake by oligotrophic freshwater species. This study focused on TonB-dependent receptors and metal-dependent regulators in C. crescentus.
To maintain appropriate levels of iron within the cell, bacteria have evolved mechanisms to control iron uptake, storage, and use. In microbes, there are two protein families possessing members that accomplish this: Fur and Rrf2. In the C. crescentus genome, there …

Transcriptional Regulation Of Shigella Virulence Plasmid-Encoded Genes By Virb And Crp, Christopher Thomas Hensley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella flexneri is a species of Gram-negative intracellular pathogens that causes bacillary dysentery in humans. Shigella relies on the precise transcriptional regulation of virulence genes, encoded by a large virulence plasmid, for invasion and infection of human colonic epithelial cells. The transcription of most identified virulence genes are regulated through a cascade controlled by the primary regulator of virulence genes, VirF, and the global transcriptional regulator, VirB. Currently, few studies have addressed how individual Shigella virulence genes are precisely regulated for optimal expression during specific stages of pathogenesis and within the constraints of the regulatory cascade. This work addresses how …

Reconstructing Species Responses To Past Climatic Changes Using Niche Modeling And Genetic Data, Tereza Jezkova

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glacial – interglacial cycles have a pronounced impact on species distributions and genetic structure. Many species shift their distributions to lower latitudes and altitudes during the colder glacial periods and expand northwards and up the elevation during warmer interglacial periods. Some species however are capable of adapting to changing environment which allows them to persist in place despite climatic changes. I explored how climatic changes after the last glacial maximum (LGM) effected two species inhabiting the deserts of western North America: one mammal (Chisel-toothed Kangaroo Rat, Dipodomys microps) and one reptile (Desert Horned Lizard, Phrynosoma platyrhinos). I used …

Excision Dynamics Of Vibrio Pathogenicity Island-2 From Vibrio Cholerae: Role Of A Recombination Directionality Factor Vefa, Salvador Almagro-Moreno, Michael G. Napolitano, E. Fidelma Boyd

Dartmouth Scholarship

Vibrio Pathogenicity Island-2 (VPI-2) is a 57 kb region present in choleragenic V. cholerae isolates that is required for growth on sialic acid as a sole carbon source. V. cholerae non-O1/O139 pathogenic strains also contain VPI-2, which in addition to sialic acid catabolism genes also encodes a type 3 secretion system in these strains. VPI-2 integrates into chromosome 1 at a tRNA-serine site and encodes an integrase intV2 (VC1758) that belongs to the tyrosine recombinase family. ntV2 is required for VPI-2 excision from chromosome 1, which occurs at very low levels, and formation of a non-replicative circular intermediate.

A Bayesian Shared Component Model For Genetic Association Studies, Juan J. Abellan, Carlos Abellan, Juan R. Gonzalez

COBRA Preprint Series

We present a novel approach to address genome association studies between single nucleotide polymorphisms (SNPs) and disease. We propose a Bayesian shared component model to tease out the genotype information that is common to cases and controls from the one that is specific to cases only. This allows to detect the SNPs that show the strongest association with the disease. The model can be applied to case-control studies with more than one disease. In fact, we illustrate the use of this model with a dataset of 23,418 SNPs from a case-control study by The Welcome Trust Case Control Consortium (2007) …

Minimum Description Length And Empirical Bayes Methods Of Identifying Snps Associated With Disease, Ye Yang, David R. Bickel

COBRA Preprint Series

The goal of determining which of hundreds of thousands of SNPs are associated with disease poses one of the most challenging multiple testing problems. Using the empirical Bayes approach, the local false discovery rate (LFDR) estimated using popular semiparametric models has enjoyed success in simultaneous inference. However, the estimated LFDR can be biased because the semiparametric approach tends to overestimate the proportion of the non-associated single nucleotide polymorphisms (SNPs). One of the negative consequences is that, like conventional p-values, such LFDR estimates cannot quantify the amount of information in the data that favors the null hypothesis of no disease-association.

We …

Micrornas Reveal The Interrelationships Of Hagfish, Lampreys, And Gnathostomes And The Nature Of The Ancestral Vertebrate, Alysha M. Heimberg, Richard Cowper-Sal{Middle Dot}Lari, Marie Semon, Philip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more …

Computational Biology, Harvey Greenberg, Allen Holder

Mathematical Sciences Technical Reports (MSTR)

Computational biology is an interdisciplinary field that applies the techniques of computer science, applied mathematics, and statistics to address biological questions. OR is also interdisciplinary and applies the same mathematical and computational sciences, but to decision-making problems. Both focus on developing mathematical models and designing algorithms to solve them. Models in computational biology vary in their biological domain and can range from the interactions of genes and proteins to the relationships among organisms and species.

Identifying Functional Relationships Within Sets Of Co-Expressed Genes By Combining Upstream Regulatory Motif Analysis And Gene Expression Information, Viktor Martyanov, Robert H. Gross

Dartmouth Scholarship

Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to generate functionally coherent and biologically meaningful subclusters of genes. Specifically, the approach clusters co-expressed genes on the basis of similar content and distributions of predicted statistically significant sequence motifs in their upstream regions.

Genomic Tools Development For Aquilegia: Construction Of A Bac-Based Physical Map, Guang-Chen Fang, Barbara P. Blackmon, David C. Henry, Margaret E. Staton, Christopher Saski, Scott A. Hodges, Jeff P. Tomkins, Hong Luo

Publications

The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun …

Tips For New Horse Owners, Kathleen P. Anderson, Cushman

Department of Animal Science: Faculty Publications

Pleasure horses for personal and recreational use representthe largest category of horse ownership in the United States, with about 2 million people owning such horses. Whether a person already owns a horse or is considering the initial purchase of a horse, this NebGuide will help answer many questions asked by new horse owners.

Horses can be kept at a person’s own place or boarded at a commercial stable. Keeping a horse on a person’s acreage provides more management control, saves time and expenses, and can reduce the risk of injuries and disease. Most importantly, it allows fuller enjoyment and greater …

Genetic Introgression And The Survival Of Florida Panther Kittens, Jeffrey A. Hostetler, David P. Onorato, James D. Nichols, Warren E. Johnson, Melody E. Roelke, Stephen J. O'Brien, Deborah Jansen, Madan K. Oli

Biology Faculty Articles

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were …

Structure And Reactivity Of Hexacoordinate Hemoglobins, Smita Kakar, Federico G. Hoffmann, Jay F. Storz, Marian Fabian, Mark S. Hargrove

Jay F. Storz Publications

The heme prosthetic group in hemoglobins is most often attached to the globin through coordination of either one or two histidine side chains. Those proteins with one histidine coordinating the heme iron are called “pentacoordinate” hemoglobins, a group represented by red blood cell hemoglobin and most other oxygen transporters. Those with two histidines are called “hexacoordinate hemoglobins”, which have broad representation among eukaryotes. Coordination of the second histidine in hexacoordinate Hbs is reversible, allowing for binding of exogenous ligands like oxygen, carbon monoxide, and nitric oxide. Research over the past several years has produced a fairly detailed picture of the …

Evolutionary Rates And Gene Dispensability Associate With Replication Timing In The Archaeon Sulfolobus Islandicus, Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher, Vaughn S. Cooper

Molecular, Cellular & Biomedical Sciences

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog …

Complement Factor H-Related Proteins Cfhr2 And Cfhr5 Represent Novel Ligands For The Infection-Associated Crasp Proteins Of Borrelia Burgdorferi, Corinna Siegel, Teresia Hallström, Christine Skerka, Hannes Eberhardt, Barbara Uzonyi, Tobias Beckhaus, Michael Karas, Reinhard Wallich, Brian Stevenson, Peter F. Zipfel, Peter Kraiczy

Microbiology, Immunology, and Molecular Genetics Faculty Publications

BACKGROUND: One virulence property of Borrelia burgdorferi is its resistance to innate immunity, in particular to complement-mediated killing. Serum-resistant B. burgdorferi express up to five distinct complement regulator-acquiring surface proteins (CRASP) which interact with complement regulator factor H (CFH) and factor H-like protein 1 (FHL1) or factor H-related protein 1 (CFHR1). In the present study we elucidate the role of the infection-associated CRASP-3 and CRASP-5 protein to serve as ligands for additional complement regulatory proteins as well as for complement resistance of B. burgdorferi.

METHODOLOGY/PRINCIPAL FINDINGS: To elucidate whether CRASP-5 and CRASP-3 interact with various human proteins, both borrelial proteins …

Dynamic Evolution Of Precise Regulatory Encodings Creates The Clustered Site Signature Of Enhancers, Justin Crocker, Nathan Potter, Albert Erives

Dartmouth Scholarship

Concentration gradients of morphogenic proteins pattern the embryonic axes of Drosophila by activating different genes at different concentrations. The neurogenic ectoderm enhancers (NEEs) activate different genes at different threshold levels of the Dorsal (Dl) morphogen, which patterns the dorsal/ventral axis. NEEs share a unique arrangement of highly constrained DNA-binding sites for Dl, Twist (Twi), Snail (Sna) and Suppressor of Hairless (Su(H)), and encode the threshold variable in the precise length of DNA that separates one well-defined Dl element from a Twi element. However, NEEs also possess dense clusters of variant Dl sites. Here, we show that these increasingly variant sites …

Genomic Variation And Adaptation In Africa: Implications For Human Evolutionary History And Disease, Michael Campbell

Department of Biology Faculty Publications

Africa contains the greatest levels of human genetic variation and is the source of the worldwide range expansion of all modern humans. However, relatively little is known about genomic variation in ethnically diverse African populations.