Life Sciences Commons^™

Understanding Crx-Associated Retinopathies Using Animal Models, Nicholas Minh Abell Tran

All Theses and Dissertations (ETDs)

Cone-rod homeobox: CRX) protein is a "paired-like" homeodomain transcription factor that is essential for regulating rod and cone photoreceptor transcription. Mutations in human CRX are associated with the dominant retinopathies Retinitis Pigmentosa: RP), Cone-Rod Dystrophy: CoRD) and Leber Congenital Amaurosis: LCA), with variable severity. The goal of my dissertation project was to develop and characterize animal models to understand genetic mechanisms of phenotypic diversity in CRX-associated disease. Heterozygous Crx Knock-Out: KO) mice: "+/-") have normal vision as adults and fail to model the dominant human disease.

We generated two Crx Knock-IN: K-IN) mouse models: CrxE168d2: "E168d2") and CrxR90W: "R90W"), which …

Beef Cattle Body Temperature During Climatic Stress: A Genome-Wide Association Study, Jeremy T. Howard, Stephen D. Kachman, Warren M. Snelling, E. John Pollak, Daniel C. Ciobanu, Larry A. Kuehn, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Cattle are reared in diverse environments and collecting phenotypic body temperature (BT) measurements to characterize BT variation across diverse environments is difficult and expensive. To better understand the genetic basis of BT regulation, a genome-wide association study was conducted utilizing crossbred steers and heifers totaling 239 animals of unknown pedigree and breed fraction. During predicted extreme heat and cold stress events, hourly tympanic and vaginal BT devices were placed in steers and heifers, respect i v e l y. I n d i v i dua l s we r e genotyped with t h e BovineSNP50K_v2 assay and data …

Interaction-Based Discovery Of Functionally Important Genes In Cancers, Dario Ghersi, Mona Singh

Interdisciplinary Informatics Faculty Publications

A major challenge in cancer genomics is uncovering genes with an active role in tumorigenesis from a potentially large pool of mutated genes across patient samples. Here we focus on the interactions that proteins make with nucleic acids, small molecules, ions and peptides, and show that residues within proteins that are involved in these interactions are more frequently affected by mutations observed in large-scale cancer genomic data than are other residues. We leverage this observation to predict genes that play a functionally important role in cancers by introducing a computational pipeline (http://canbind.princeton.edu) for mapping large-scale cancer exome data …

The Diversity Of Quantitative Trait Loci In Yeast Sporulation Efficiency, Kimberly Lorenz

All Theses and Dissertations (ETDs)

A complex trait is one that exhibits continuous phenotypic variation due to genetic variation in many quantitative trait genes: QTGs). The ultimate goal of genetics is to relate genotype to phenotype; in the case of complex traits this requires a better understanding of what types of genes harbor causal natural variation, and what form the variation takes. Here I describe two experiments using the model complex trait of sporulation efficiency in the yeast Saccharomyces cerevisiae, one to specifically investigate how small effects contribute to a quantitative trait and the other to determine whether certain types of genes are more likely …

On The Origin Of Phenotypic Variation: Novel Technologies To Dissect Molecular Determinants Of Phenotype, Francesco Vallania

All Theses and Dissertations (ETDs)

This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of …

Integrating Human Omics Data To Prioritize Candidate Genes., Yong Chen, Xuebing Wu, Rui Jiang

Faculty Scholarship for the College of Science & Mathematics

BACKGROUND: The identification of genes involved in human complex diseases remains a great challenge in computational systems biology. Although methods have been developed to use disease phenotypic similarities with a protein-protein interaction network for the prioritization of candidate genes, other valuable omics data sources have been largely overlooked in these methods.

METHODS: With this understanding, we proposed a method called BRIDGE to prioritize candidate genes by integrating disease phenotypic similarities with such omics data as protein-protein interactions, gene sequence similarities, gene expression patterns, gene ontology annotations, and gene pathway memberships. BRIDGE utilizes a multiple regression model with lasso penalty to …

Identifying Potential Cancer Driver Genes By Genomic Data Integration., Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang

Faculty Scholarship for the College of Science & Mathematics

Cancer is a genomic disease associated with a plethora of gene mutations resulting in a loss of control over vital cellular functions. Among these mutated genes, driver genes are defined as being causally linked to oncogenesis, while passenger genes are thought to be irrelevant for cancer development. With increasing numbers of large-scale genomic datasets available, integrating these genomic data to identify driver genes from aberration regions of cancer genomes becomes an important goal of cancer genome analysis and investigations into mechanisms responsible for cancer development. A computational method, MAXDRIVER, is proposed here to identify potential driver genes on the basis …

The Empire Of Cancer: Gene Patents And Cancer Voices, Matthew Rimmer

Matthew Rimmer

In his book, The Emperor of All Maladies, Siddhartha Mukherjee writes a history of cancer — ‘It is a chronicle of an ancient disease — once a clandestine, “whispered-about” illness — that has metamorphosed into a lethal shape-shifting entity imbued with such penetrating metaphorical, medical, scientific, and political potency that cancer is often described as the defining plague of our generation’.Increasingly, an important theme in the history of cancer is the role of law, particularly in the field of intellectual property law. It is striking that a number of contemporary policy debates over intellectual property and public health have concerned …

Effects Of Excitation Pressure On Variegation And Global Gene Expression In Arabidopsis Thaliana, Rainer Bode

Electronic Thesis and Dissertation Repository

I assessed the effects of photosystem II excitation pressure on chloroplast biogenesis and leaf sectoring in the Arabidopsis thaliana variegated mutants im, spotty, var1, var2, chs5 and atd2. The plants were grown under varying degrees of excitation pressure induced by growth at increasing irradiance at different temperatures and the extent of variegation was quantified throughout the plant’s development. I found that the degree of variegation was positively correlated with excitation pressure, regardless of whether high light or low temperature was used to induce increased excitation pressure in all the mutants tested. This was irrespective of …

Role Of Carotenoid Cleavage Dioxygenases In Volatile Emissions And Insect Resistance In Arabidopsis, Shailu Lakshminarayan

Electronic Thesis and Dissertation Repository

In Arabidopsis thaliana, carotenoid degradation by enzymatic oxidative cleavage is catalyzed by nine CCD and NCED enzymes; this cleavage produces an array of terpenoid products that are collectively known as apocarotenoids, which include volatile and non-volatile compounds. Previous studies on CCD1 revealed that its overexpression in A. thaliana enhances β-ionone emission and reduces damage caused by flea beetles. In consideration of these findings, I generated CCD4 and CCD8 Arabidopsis overexpression lines. Further, I characterized these overexpression lines on the basis of their carotenoid content and their volatile profiles. Surprisingly, accumulation of key carotenoids in the leaves was observed in both …

Characterizing The Human Vaginal Microbiome Using High-Throughput Sequencing, Jean Megan E. Macklaim

Electronic Thesis and Dissertation Repository

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC).

Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition …

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 …

Mitochondrial Dna Variation In North Dakota Residents Of European Ancestry, Katelyn Kjelland

Undergraduate Theses and Senior Projects

Globally, many groups have been subject to studies of genetic variation and structure. However, studies of this sort rarely engage populations in the United States and are often limited to analysis of continental supergroups (European, African American, Hispanic, Native American) that cluster several ancestral origins of diverse genetic and cultural pasts. The aim of this study is to examine the degree of mtDNA variation in the residents of European ancestry living in North Dakota. This state, located in north-central United States, has been relatively recently settled by European migrants of distinct origins who originally formed isolated ethnic enclaves.

Analysis of …

Loss Of Vascular Endothelial Growth Factor A (Vegfa) Isoforms In The Testes Of Male Mice Causes Subfertility, Reduces Sperm Numbers, And Alters Expression Of Genes That Regulate Undifferentiated Spermatogonia, Ningxia Lu, Kevin M. De Avila, Debra T. Clopton, William E. Pohlmeier, Vanessa M. Brauer, Renee M. Mcfee, John S. Weber, Napoleone Ferrara, David W. Silversides, Andrea S. Cupp

Department of Animal Science: Faculty Publications

Vascular endothelial growth factor A (VEGFA) isoform treatment has been demonstrated to alter spermatogonial stem cell homeostasis. Therefore, we generated pDmrt1-Cre;Vegfa^−/− (knockout, KO) mice by crossing pDmrt1-Cre mice to floxed Vegfa mice to test whether loss of all VEGFA isoforms in Sertoli and germ cells would impair spermatogenesis. When first mated, KO males took 14 days longer to get control females pregnant (P < .02) and tended to take longer for all subsequent parturition intervals (9 days; P < .07). Heterozygous males sired fewer pups per litter (P < .03) and after the first litter took 10 days longer (P < .05) to impregnate females, suggesting a more progressive loss of fertility. Reproductive organs were collected from 6-month-old male mice. There were fewer sperm per tubule in the corpus epididymides (P < .001) and fewer ZBTB16-stained undifferentiated spermatogonia (P < .003) in the testes of KO males. Testicular mRNA abundance for Bcl2 (P < .02), Bcl2:Bax (P < .02), Neurog3 (P < .007), and Ret was greater (P = .0005), tended to be greater for Sin3a and tended to be reduced for total Foxo1 (P < .07) in KO males. Immunofluorescence for CD31 and VE-Cadherin showed no differences in testis vasculature; however, CD31-positive staining was evident in undifferentiated spermatogonia only in KO testes. Therefore, loss of VEGFA isoforms in Sertoli and germ cells alters genes necessary for long-term maintenance of undifferentiated spermatogonia, ultimately reducing sperm numbers and resulting in subfertility.

Atf3 Expression In The Corpus Luteum: Possible Role In Luteal Regression, Dagan Mao, Xiaoying Hou, Heather Talbott, Robert A. Cushman, Andrea S. Cupp, John S. Davis

Department of Animal Science: Faculty Publications

The present study investigated the induction and possible role of activating transcription factor 3 (ATF3) in the corpus luteum. Postpubertal cattle were treated at midcycle with prostaglandin F2α(PGF) for 0–4 hours. Luteal tissue was processed for immunohistochemistry, in situ hybridization, and isolation of protein and RNA. Ovaries were also collected from midluteal phase and first-trimester pregnant cows. Luteal cells were prepared and sorted by centrifugal elutriation to obtain purified small (SLCs) and large luteal cells (LLCs). Real-time PCR and in situ hybridization showed that ATF3 mRNA increased within 1 hour of PGF treatment in vivo. Western blot and immunohistochemistry demonstrated …

Genome-Wide And Differential Proteomic Analysis Of Hepatitis B Virus And Aflatoxin B1 Related Hepatocellular Carcinoma In Guangxi, China, Lu-Nan Qi, Le-Qun Qi, Yuan-Yuan Chen, Zhao-Hong Chen, Tao Bai, Bang-De Xiang, Xiao Qin, Kai-Yin Xiao, Min-Hao Peng, Zhi-Ming Liu, Tang-Wei Liu, Xue Qin, Shan Li, Ze-Guang Han, Zeng-Nan Mo, Regina M. Santella, Cheryl Winkler, Stephen J. O'Brien, Tao Peng

Biology Faculty Articles

Both hepatitis B virus (HBV) and aflatoxin B1 (AFB1) exposure can cause liver damage as well as increase the probability of hepatocellular carcinoma (HCC). To investigate the underlying genetic changes that may influence development of HCC associated with HBV infection and AFB1 exposure, HCC patients were subdivided into 4 groups depending upon HBV and AFB1 exposure status: (HBV(+)/AFB1(+), HBV(+)/AFB1(-), HBV(-)/AFB1(+), HBV(-)/AFB1(-)). Genetic abnormalities and protein expression profiles were analyzed by array-based comparative genomic hybridization and isobaric tagging for quantitation. A total of 573 chromosomal aberrations (CNAs) including 184 increased and 389 decreased were detected in our study population. Twenty-five recurrently …

Identification And Characterization Of Genetic Factors Involved In Candida-Bacterial Interactions, Sean J. Fox

Electronic Theses and Dissertations

Throughout existence, fungi and bacteria have long shared ecological niches and thus engage in numerous interactions to mutually enhance survival or antagonistically gain competitive advantages. Of importance to human health are those interactions that involve bacteria with the opportunistic fungi, Candida albicans. An important virulence factor of C. albicans is the ability to control morphology, which allows the transition between yeast, pseudohyphal, and hyphal phenotypes. Morphological control in C. albicans is governed by quorum sensing and the secreted autoregulatory molecule farnesol. Quorum sensing allows individual cells to sense the environment and respond as a group. Bacteria also use quorum …

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 …

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

Dissertations & 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 …

Evaluating The Influence Of Environmental Factors On The Rate Of Extra-Pair Matings In Tropical And Temperate Populations Of The House Wren (Troglodytes Aedon), Kaitlin Claire Mckenney

Theses and Dissertations

Considerable variation exists in the rate of extra-pair matings (EPMs) in birds. Environmental variability likely influences EPM rates within species, but the effects of local environmental factors on EPM rates are largely unpredictable. To determine whether broad-scale environmental factors might be better predictors of EPM rates within species, we quantified levels of extra-pair paternity in the house wren (Troglodytes aedon) in four populations spanning a range of latitude, elevation, and primary productivity (measured by actual evapotranspiration rates). Our results indicated an intermediate and variable level of EPM among populations (6 -31% extra-pair young) that was not significantly affected by 3 …

A Synthetic Biology Approach To Engineering New Anticancer Agents, Shane Robert Wesener

Theses and Dissertations

Histone deacetylase (HDAC) inhibitors are becoming increasingly valuable therapeutic agents in treatment of several types of malignancies. FK228 is a depsipeptde anticancer compound produced by Chromobacterium violaceum no. 968 through a nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) hybrid assembly line. In the present study, reconstitution of the biosynthetic pathway responsible for the production of FK228 revealed cross-talk between modular PKS and fatty acid synthase. This pathway contains two PKS modules on the DepBC enzymes that lack a functional acyltransferase (AT) domain, and no apparent AT-encoding gene exists within the gene cluster or its vicinity. We reported through heterologous expression of …

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, …

Phylogeographic Inference Of Insular Mule Deer (Odocoileus Hemionus) Divergence In North America's Desert Southwest, Ona Alminas

Theses and Dissertations

Though mule deer (Odocoileus hemionus) persist in robust populations throughout most of their North American distribution, nearly 60% of their historic range in México has declined due to habitat loss and unregulated hunting. Two of the six subspecies inhabiting México's deserts and Baja California peninsula are of conservation concern, occurring on land bridge islands in the Pacific Ocean (O. h. cerrosensis on Cedros Island: threatened) and in the Sea of Cortés (O. h. sheldoni on Tiburón Island: endangered). Focusing on the desert southwest (n=449 deer), we obtained 1,611 bp of mtDNA sequence (control region: 583 bp; cytochrome b gene: 1,028 …

Population Demographics And Genetic Structure Of Black Bears In Coastal Louisiana, Jesse Charles Troxler

Masters Theses

The range and abundance of the Louisiana black bear (Ursus americanus luteolus) were greatly diminished during the 20th century. This subspecies was reduced to 3 small, isolated subpopulations in Louisiana as bottomland hardwood habitat was converted to agriculture. These bears were listed as threatened by the U.S. Fish and Wildlife Service in 1992 and a recovery plan was published in 1995. Recovery requires estimates of population parameters to evaluate current population status and future viability. I conducted a mark-recapture study from 2010 to 2012 to estimate demographic parameters of the coastal population of Louisiana black bears. Because inbreeding …

Introducing A Novel Method For Genetic Analysis Of Autism Spectrum Disorder, Sepideh Nouri

Dissertations & Theses (Open Access)

Autism is a spectrum of neurological disorders that is characterized by repetitive and stereotyped behaviors, lack of social skills in verbal and non-verbal communications, and intellectual disability. Recent statistics shows that 1 out of every 88 children in the US is affected by autism.

In this thesis, I first review previous studies on genetic association analyses of autism spectrum disorder. A large number of these studies fall into two categories: Genome Wide Association Studies (GWAS) and sequencing studies. Although GWAS are able to identify multiple common risk variants associated with different diseases, these common variants explain only a small portion …

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 …

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 …

C-Rel Is A Transcriptional Target Of Mesoderm Inducer In Xenopus Like 1 (Mixl1), Aaron C. Raymond

Dissertations & Theses (Open Access)

MIXL1, an evolutionarily conserved, paired-type homeobox transcription factor induced by BMP4/TGFb signaling, is a critical regulator of embryonic and adult hematopoiesis. Several lines of evidence implicate MIXL1 in hematopoietic transformation: (i) Aberrant MIXL1 expression is seen in human CML ( Chronic Myelogenous Leukemia) in blast crisis, AML (Acute myelogenous leukemia), B cell lymphomas and pediatric ALL (Acute lymphocytic leukemia). (ii) Retroviral transduction of Mixl1 induces AML in murine models. Nonetheless, mechanisms underlying MIXL1 mediated proliferative, survival advantages are unknown.

The goal of my studies is to understand if and how aberrant MIXL1 expression contributes to leukemogenesis. As a first step, …

Development Of Liriodendron Est-Ssr Markers And Genetic Composition Of Two Liriodendron Tulipifera L. Orchards, Xinfu Zhang

All Theses

Liriodendron tulipifera L., commonly known as yellow-poplar, is a fast-growing hardwood tree species with great ecological and economic value and is native to eastern North America. Liriodendron occupies an important phylogenetic position as a basal angiosperm and has been used in studies of the evolution of flowering plants. Genomic resources, such as Expressed Sequence Taq (EST) databases and Bacterial Artificial Chromosome (BAC) libraries, have been developed for this species. However, no genetic map is available for Liriodendron, and very few molecular markers have been developed. In this study, a total of 119 informative genomic SSR markers suitable were identified for …

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 …