Biology Commons^™

Dissecting The Interaction Between P53 And Trim24, Aundrietta D. Duncan

Dissertations and Theses (Open Access)

Dissecting the Interaction of p53 and TRIM24

Aundrietta DeVan Duncan

Supervisory Professor, Michelle Barton, Ph.D.

p53, the “guardian of the genome”, plays an important role in multiple biological processes including cell cycle, angiogenesis, DNA repair and apoptosis. Because it is mutated in over 50% of cancers, p53 has been widely studied in established cancer cell lines. However, little is known about the function of p53 in a normal cell. We focused on characterizing p53 in normal cells and during differentiation. Our lab recently identified a novel binding partner of p53, Tripartite Motif 24 protein (TRIM24). TRIM24 is a member of …

Upregulation Of Reactive Oxygen Species During The Retrovirus Life Cycle And Their Roles In A Mutant Of Moloney Murine Leukemia Virus, Ts1-Mediated Neurodegeneration, Soo Jin Kim

Dissertations and Theses (Open Access)

Viral invasion of the central nervous system (CNS) and development of neurological symptoms is a characteristic of many retroviruses. The mechanism by which retrovirus infection causes neurological dysfunction has yet to be fully elucidated. Given the complexity of the retrovirus-mediated neuropathogenesis, studies using small animal models are extremely valuable. Our laboratory has used a mutant moloney murine leukemia retrovirus, ts1-mediated neurodegneration. We hypothesize that astrocytes play an important role in ts1-induced neurodegeneration since they are retroviral reservoirs and supporting cells for neurons. It has been shown that ts1 is able to infect astrocytes in vivo and in …

A Cell Biological Determination Of Integrator Subunit Localization, Sarah B. May

Dissertations and Theses (Open Access)

Uridine-rich small nuclear (U snRNAs), with the exception of the U6 snRNA, are RNA polymerase II (RNAPII) transcripts. The mechanism of 3’ cleavage of snRNAs has been unknown until recently. This area was greatly advanced when 12 of the Integrator complex subunits (IntS) were purified in 2005 through their interaction with the C-terminal domain (CTD) of the large subunit (RpbI) of RNAPII. Subsequently, our lab performed a genome-wide RNAi screen that identified two more members of the complex that we have termed IntS13 and IntS14. We have determined that IntS9 and 11 mediate the 3’ cleavage of snRNAs, but the …

Study Of Rest As A Negative Regulator Of P16ink4a, Monica B. Gireud

Dissertations and Theses (Open Access)

STUDY OF REST AS A NEGATIVE REGULATOR OF P16^INK4A

Monica Gireud, B.S.

Thesis Advisor: Vidya Gopalakrishnan, Ph.D.

The RE1 Silencing Transcription Factor (REST) is a negative regulator of neuronal differentiation. It is expressed ubiquitously in early embryos, but downregulated in neural progenitors concomitant with onset of neuronal differentiation in these cells. REST has been widely studied as a negative regulator of neuronal differentiation genes. Our recent work identified a novel role for REST in control of cell proliferation. However, the underlying molecular mechanism(s) are not known and is a focus of the current thesis project. Here, we provide evidence …

Lipid Metabolism In Trypanosoma Brucei: Molecular Characterization Of Fatty Acid Synthesis And Uptake, Patrick Vigueira

All Dissertations

My doctoral studies focused on the fatty acid metabolism of the deadly protozoan parasite, Trypanosoma brucei. Fatty acid metabolism in T. brucei can be broadly divided into two pathways, synthesis and uptake. In Chapters 2-4 I describe experiments investigating the parasite's fatty acid synthesis pathway. Chapter 2 contains the initial characterization of acetyl-CoA carboxylase (ACC) in T. brucei. Knockdown of TbACC by RNA interference (RNAi) reduced parasite virulence in a mouse model, suggesting that TbACC has the potential to be utilized as a drug target. Chapters 3 and 4 explore the effects of two known ACC inhibitors, the …

Repression Of Multiple Cyp2d Genes In Mouse Using A Single Sirna Construct, Omaima Elraghy

All Theses

The CYP2D subfamily is the second most important subfamily of hepatic drug metabolizing CYPs. In mouse, there are nine CYP2D subfamily members, while humans have only one highly polymorphic CYP2D member, CYP2D6. siRNA was used to repress the expression of multiple isoforms of mouse CYP2D in primary mouse hepatocytes with one siRNA construct. Successful knockdown of CYP function by RNAi may allow for further study of CYP2D function. Q-PCR demonstrated that male CD-1 mouse primary hepatocytes express Cyp2d10, Cyp2d11, Cyp2d22, and Cyp2d26; however the male specific and growth hormone-dependent, Cyp2d9, was not detected. Four different siRNAs were designed; Cyp2d-KD1 and …

Monitoring Atrazine-Degrading And Atrazine-Tolerant Bacterial Populations In Lower Rio Grande Valley Agricultural Canals Using Quantitative-Pcr And Internal Atza Primers, Ibdanelo Cortez

Theses and Dissertations - UTB/UTPA

The research hypothesis was that atrazine-degrading bacteria would be detectable during the planting and rainy seasons with their populations dissipating during non-planting and dry seasons in 2010-2011. Atrazine concentration was detected in March, May, June and August for all canals with June having the highest average concentration of 0.77ppb. Gene atzA abundance was detected from June through August with July samples having the highest gene abundance of 250.6 (pg). Tolerant bacterial densities were detectable from March through June. Atrazine concentration and population abundance were not statistically different during planting and non-planting, rainy and dry seasons, although there was a trend …

Role Of Porcine Reproductive And Respiratory Syndrome Virus Non-Structural Protein 1 In Viral Replications And Pathogenesis, Lalit Kumar Beura

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious agent of significant concern to the global swine industry. PRRSV infection of pigs is initiated by a long viremia after which the virus enters in an extended persistent phase of 3-4 months that ultimately is resolved by the immune system. The delayed and weak host adaptive response is responsible for the protracted convalescence period. An initial sub-optimal innate immune response is postulated to be the reason behind such meager adaptive immune response. A major focus of the studies undertaken in this dissertation was to identify the viral non-structural proteins (nsps) …

Phylogenetic Analysis Of Serine Proteases From Russell's Viper (Daboia Russelli Siamensis) And Agkistrodon Piscivorus Leucostoma Venom, Pattadon Sukkapan, Ying Jia, Issarang Nuchprayoon, John C. Pérez

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Serine proteases are widely found in snake venoms. They have variety of functions including contributions to hemostasis. In this study, five serine proteases were cloned and characterized from two different cDNA libraries: factor V activator (RVV-V), alpha fibrinogenase (RVAF) and beta fibrinogenase (RVBF) from Russell's viper (Daboia russelli siamensis), and plasminogen activator (APL-PA) and protein C activator (APL-C) from Agkistrodon piscivorus leucostoma. The snake venom serine proteases were clustered in phylogenetic tree according to their functions. KA/KS values suggested that accelerated evolution has occurred in the mature protein coding regions in cDNAs of snake venom …

Nr1l: A Novel Nuclear Receptor Group Activated By Juvenile Hormone Analogs, Yangchun Li

All Theses

Annotation of the Daphnia pulex nuclear receptors revealed a novel group of three receptors designated NR1L, and named HR97a/b/g because of their similarity to the HR96 receptors involved in xenobiotic detection. We cloned and sequenced the three receptors from a related species often used in aquatic toxicology studies, Daphnia magna, and then analyzed their genomic structure and conducted phylogenetic studies. Phylogenetic studies confirmed that the HR97s do form a distinct group with HR97g being the precursor of HR97a and b. They also confirmed that the HR97 receptors are related to the HR96 (NR1J) receptors, and the VDR/CAR/PXR (NR1I) group. Mining …

Going All The Way: Phylogeography And Trans-Pacific Divergence Genetics Of Nucella Lima, Lisa Cox

All Theses

Fluctuating climate over the last 2 million years (MY) has repeatedly caused latitudinal shifts in species distributions, fueling the hypothesis that the glacial-interglacial dynamics of the Pleistocene could have driven regional genetic differentiation and potentially speciation. For species whose distributions spanned the entire North Pacific, regional extinction of northern populations during cooler glacial periods may have resulted in isolation and genetic differentiation of eastern and western populations. To test this hypothesis, I gathered genetic data from a rocky shore intertidal gastropod, Nucella lima, whose current (i.e. warm interglacial) distribution spans the entire North Pacific. Mitochondrial DNA sequences are genetically structured …

Heterogeneity, Control, Social Infrastructure, And Possibilities Of Participation: Their Interplay In Modern Understandings Of Heredity And In Interpretation Of Science, Peter J. Taylor

Working Papers on Science in a Changing World

This working paper is a prospectus for research, writing, and engagement. It consists of vignettes, sketches of lines of inquiry, and proposals for engagement, all of which concern modern understandings of heredity and development over the life course as well as the social interpretation of science. The various items address a range of areas of science and of its interpretation: heritability studies, the social uses of genetic information, gene-by-environment interaction, personalized medicine, IQ paradoxes, racial group membership, biobanks, and life events and difficulties research. Fresh perspectives in these areas are opened up by examining the ways that research and application …

Morphology, Material And Vibratory Properties Of The Swimbladder In The Carp, Cyprinus Carpio, Yasha Mohajer

Theses and Dissertations

The carp Cyprinus carpio has a two-chambered swimbladder and excellent hearing. I explored the hypothesis that the anterior chamber, which connects to Weberian ossicles, is adapted for hearing by testing both chambers for material properties. I also determined displacement and auditory responses to mechanical strikes. Wall stress is higher in the posterior, strain in the anterior and modulus lower in the anterior chamber. Strikes increase pressure followed by a variable rebound that rapidly decays. Displacement and sound amplitude increase with hammer force, and amplitude is similar in both chambers for within chamber strikes but lower across chambers. Normalized for equivalent …

Bridging The Marine-Terrestrial Disconnect To Improve Marine Coastal Zone Science And Management, Benjamin I. Ruttenberg, Elise F. Granek

Biological Sciences

Coastal zone ecosystems sit between larger terrestrial and marine environments and, therefore, are strongly affected by processes occurring in both systems. Marine coastal zone systems provide a range of benefits to humans, and yet many have been significantly degraded as a result of direct and indirect human impacts. Management efforts have been hampered by disconnects both between management and scientific research and across linked marine–terrestrial systems. Management jurisdictions often start or end at the shoreline, and multiple agencies at different levels of government often have overlapping or conflicting management goals or priorities, or suffer from a lack of knowledge or …

Expression And Function Of The Dna Damage Protein Umud Of Acinetobacter Baylyi, And Its Predicted Cleavage And Nucleophilic Activator Residue Mutants In Escherichia Coli, Sabal Adhikari

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science & Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Sabal Adhikari on July 28, 2011.

A Rice Plastidial Nucleotide Sugar Epimerase Is Involved In Galactolipid Biosynthesis And Improves Photosynthetic Efficiency, Chunlai Li, Yiqin Wang, Linchuan Liu, Yingchun Hu, Fengxia Zhang, Sod Mergen, Guodong Wang, Michael Schläppi, Chengcai Chu

Biological Sciences Faculty Research and Publications

Photosynthesis is the final determinator for crop yield. To gain insight into genes controlling photosynthetic capacity, we selected from our large T-DNA mutant population a rice stunted growth mutant with decreased carbon assimilate and yield production named photoassimilate defective1 (phd1). Molecular and biochemical analyses revealed that PHD1 encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. The chloroplast localization of PHD1 was confirmed by immunoblots, immunocytochemistry, and UGE activity in isolated chloroplasts, which was approximately 50% lower in the phd1-1 mutant than in the wild type. In addition, the amounts of …

Na/K-Atpase Mimetic Pnaktide Peptide Inhibits The Growth Of Human Cancer Cells, Zhichuan Li, Zhongbing Zhang, Joe X. Xie, Xin Li, Jiang Tian, Ting Cai, Hongaun Cui, Hanfei Ding, Joseph I. Shapiro Md, Zijian Xie

Biochemistry and Microbiology

Cells contain a large pool of non-pumping Na/K-ATPase that participates in signal transduction. Here, we show that the expression of α1 Na/K-ATPase is significantly reduced in human prostate carcinoma as well as in several human cancer cell lines. This down-regulation impairs the ability of Na/K-ATPase to regulate Src-related signaling processes. Supplement of pNaKtide, a peptide derived from α1 Na/K-ATPase, reduces activities of Src and Src effectors. Consequently, these treatments stimulate apoptosis and inhibit growth in cultures of human cancer cells. Moreover, administration of pNaKtide inhibits angiogenesis and growth of tumor xenograft. Thus, the new findings demonstrate the in vivo effectiveness …

Alterations In The Transciptome And Antibiotic Susceptibility Of Staphylococcus Aureus Grown In The Presence Of Diclofenac, James T. Riordan, Joanne M. Dupre, Stephanie A. Cantore-Matyi, Atul Kumar-Singh, Yang Song, Shahrear Zaman, Sonia Horan, Nada S. Helal, Vijayaraj Nagarajan, Mohamed O. Elasri, Brian J. Wilkinson, John E. Gustafson

Faculty Publications

Background

Diclofenac is a non-steroidal anti-inflammatory drug (NSAID) which has been shown to increase the susceptibility of various bacteria to antimicrobials and demonstrated to have broad antimicrobial activity. This study describes transcriptome alterations in S. aureus strain COL grown with diclofenac and characterizes the effects of this NSAID on antibiotic susceptibility in laboratory, clinical and diclofenac reduced-susceptibility (Dc^RS) S. aureus strains.

Methods

Transcriptional alterations in response to growth with diclofenac were measured using S. aureus gene expression microarrays and quantitative real-time PCR. Antimicrobial susceptibility was determined by agar diffusion MICs and gradient plate analysis. Ciprofloxacin accumulation was measured …

Novel Methodology For Assessing Phytoplankton Response To Pco2 Enrichment In Fresh And Saltwater, Susan B. Gifford

Theses and Dissertations

Atmospheric CO2 emissions are on the rise and are expected to reach 780 parts per million by the year 2100. Research investigating the impacts of increasing CO2 is a relatively new field and the response of phytoplankton communities is largely unknown, especially in coastal and freshwater ecosystems where no CO2 manipulation studies have completed. The present study attempts to encourage uniformity in methods utilized in CO2 perturbation studies and identifies changes in phytoplankton abundance in freshwater (James River) and coastal ocean (Atlantic, Cape Hatteras) sites. A novel bubbling method to manipulate pCO2 was compared with the classic method of acid …

Computerized Analysis Of Biomarkers In Diagnosis Of Breast Cancer, Jie Li ^, Wei Qian, Jianying Zhang *

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Survival, Breeding Frequency, And Migratory Orientation In The Jefferson Salamander, Ambystoma Jeffersonianum, Stephen P. De Lisle, Kristine L. Grayson

Biology Faculty Publications

Accurate estimates of demographic parameters, such as survival and breeding frequency, are necessary for the conservation and management of animal populations. Additionally, life-history data are required for gaining an empirical understanding of the ecology of natural populations. We monitored a population of Jefferson Salamanders (Ambystoma jeffersonianum) breeding in a permanent mountain-top pond at the southern limit of this species’ geographic range in Virginia over four years. We used closed multistate mark-recapture models with Pollock's robust design to estimate the demographic parameters of this population. Additionally, we used point-of-capture data to compare the orientation of migrations into and out …

Investigation Of Pre- And Post-Zygotic Reproductive Barriers Between Two Host-Plant Complex Races Of The Parasitic Wasp Cotesia Congregata (Say) [Hymenoptera: Braconidae], Justin Bredlau

Theses and Dissertations

Investigations of host-associated differentiation of parasitoids have largely focused on the degree of molecular genetic differentiation, but a true test of species status must examine the mating patterns of differentiated populations to determine if they can interbreed in the wild and produce viable offspring. We examined possible mechanisms of isolation between two genetically distinct host-plant complex races of the braconid, Cotesia congregata, originating from hosts on tobacco and catalpa. We compared male responses to female pheromones, elements of male acoustic courtship signals, and breeding success between the two races. Males responded to pheromones from both sources and male courtship signals …

Caenorhabditis Briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility And The Evolution Of Recombination, Joseph A. Ross, Daniel C. Koboldt, Julia E. Staisch, Helen M. Chamberlin, Bhagwati P. Gupta, Raymond D. Miller, Scott Everet Baird, Eric S. Haag

Biological Sciences Faculty Publications

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by …

Cellular Expression Of Smarca4 (Brg1)-Regulated Genes In Zebrafish Retinas, Monica R. Hensley, Farida Emran, Sylvia Bonilla, Liyun Zhang, Wenxuan Zhong, Paul Grosu, John E. Dowling, Yuk Fai Leung

Department of Biological Sciences Faculty Publications

Background

In a recent genomic study, Leung et al. used a factorial microarray analysis to identify Smarca4 (Brg1)-regulated genes in micro-dissected zebrafish retinas. Two hundred and fifty nine genes were grouped in three-way ANOVA models which carried the most specific retinal change. To validate the microarray results and to elucidate cellular expression patterns of the significant genes for further characterization, 32 known genes were randomly selected from this group. In situ hybridization of these genes was performed on the same types of samples (wild-type (WT) and smarca4^a50/a50 (yng) mutant) at the same stages (36 and 52 hours …

Diversity, Loss, And Gain Of Malaria Parasites In A Globally Invasive Bird, Alfonso Marzal, Robert Ricklefs, Gediminas Valkiunas, Tamer Albayrak, Elena Arriero, Camille Bonneaud, Gábor Czirják, John Ewen, Olof Hellgren, Dita Hořáková, Tatjana Iezhova, Henrik Jensen, Asta Križanauskienė, Marcos Lima, Florentino De Lope, Eyðfinn Magnussen, Lynn Martin, Anders Møller, Vaidas Palinauskas, Péter Pap, Javier Pérez-Tris, Ravinder Sehgal, Manuel Soler, Eszter Szöllősi, Helena Westerdahl, Pavel Zetindjiev, Staffan Bensch

Biology Department Faculty Works

Invasive species can displace natives, and thus identifying the traits that make aliens successful is crucial for predicting and preventing biodiversity loss. Pathogens may play an important role in the invasive process, facilitating colonization of their hosts in new continents and islands. According to the Novel Weapon Hypothesis, colonizers may out-compete local native species by bringing with them novel pathogens to which native species are not adapted. In contrast, the Enemy Release Hypothesis suggests that flourishing colonizers are successful because they have left their pathogens behind. To assess the role of avian malaria and related haemosporidian parasites in the global …

An Invasive Species Reduces Aquatic Insect Flux To Terrestrial Food Webs, Steven S. Merkley

Theses and Dissertations

Although it is well documented how introduced species can negatively affect native species, we only poorly understand how they may alter ecosystem functions. We investigated how an invasive fish affected the flux of aquatic insects to terrestrial food webs using mesocosms in a desert spring ecosystem. We compared aquatic insect emergence between alternative community states with monocultures and polycultures of two native species of fish, least chub (Iotichthys phlegethontis) and Utah chub (Gila atraria) plus, introduced western mosquitofish (Gambusia affinis). We tested three hypotheses: (1) aquatic insect biomass will be greater than terrestrial insect …

Changes In Life History Within An Individual's Lifetime, Eric J. Billman

Theses and Dissertations

A central goal of life history theory is to understand the selective factors that generate the diversity of reproductive patterns observed in nature. Within lifetime changes in reproductive investment will determine an organism's fitness; however, this area of life history theory has received less attention than comparisons among population that characterize life history traits as a single population mean. Reproductive allocation can be affected by multiple cues; the integration of these cues across an organism's lifetime generates the diversity in life history strategies observed in nature. Life history studies should examine the interacting effects of multiple cues on life history …

Evolving Hard Problems: Generating Human Genetics Datasets With A Complex Etiology, Daniel S Himmelstein, Casey S Greene, Jason H Moore

Dartmouth Scholarship

BackgroundA goal of human genetics is to discover genetic factors that influence individuals' susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacting components instead of single component failures. This greatly complicates both the task of selecting informative genetic variants and the task of modeling interactions between them. We and others have previously developed algorithms to detect and model the relationships between these genetic factors and disease. Previously these methods have been evaluated with datasets simulated according to pre-defined genetic models.

Exome-Wide Dna Capture And Next Generation Sequencing In Domestic And Wild Species, Albano Beja-Pereira, Shanyuan Chen, Theodore F. Cosart, Gordon Luikart, Sarah B. Ng, Jay Shendure

Biological Sciences Faculty Publications

Our understanding of the molecular, genetic basis of adaptations and phenotypic differentiation among individuals will advance quickly thanks to new molecular techniques. This understanding is crucial given that accelerating environmental change and human population growth are increasingly threatening natural populations of fish and wildlife as well as increasing demands for agricultural production in domesticated species. This makes it urgent in many wild and domestic species to investigate the genetic basis of fitness, adaptation, and disease resistance [1], and to discover adaptive genes and speciation genes, i.e., the "loci of evolution" [2].

Biomedical Thrillers: Fiction Based In Fact, Or Just Fiction?, Emily F. Schmitt Lavin

Biology Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.