Genetics and Genomics Commons^™

Phosphorylation Impairs Dicer1 Function To Accelerate Aging And Tumorigenesis In Vivo, Neeraj Aryal

Dissertations and Theses (Open Access)

Altered DICER1 protein levels are associated with developmental disorders, infertility, macular degenerative blindness, aging, and cancer in humans. Recently, post-translational regulation of Dicer1 via phosphorylation has been described in C. elegans. Oscillation of Dicer1 phosphorylation to regulate its activity is essential for germ cell development and embryogenesis in worms. These observations led us to posit that Dicer1 protein levels and activity are under tight regulation for normal mammalian homeostasis. To test whether phosphorylation of Dicer1 regulates its activity in mammals, I generated phospho-mimetic knock-in mouse models by replacing Serines 1712 and 1836 with Aspartic acids individually or together (dual …

Trim24 As An Oncogene In The Mammary Gland, Aundrietta Duncan

Dissertations and Theses (Open Access)

Despite the many advances made in breast cancer research and treatments, breast cancer remains one of the deadliest diseases plaguing women worldwide. While many findings on genetic mutations and their role in predisposing people to breast cancer have been uncovered, we are just beginning to understand the extent to which epigenetic regulators promote tumorigenic phenotypes, metastasis, and chemotherapeutic resistance. Moreover, new experimental tools offer the ability to address questions we were previously unable to assess. My project takes advantage of a new mouse model to understand the role of a proto-oncogenic, transcriptional co-regulator, TRIM24, in mammary gland development and disease. …

Identification And Utility Of Dna In Exosomes, Paul Kurywchak

Dissertations and Theses (Open Access)

Cancer-associated mortality has been declining for two decades but remains a significant public health problem, especially when patients initially present with advanced disease. Early detection methods have improved survival rates but remain unavailable for a majority of cancers due to a lack of sensitive biomarkers or numerous limitations associated with current diagnosis strategies. Approaches to develop “liquid biopsies” by detecting tumor cells or DNA in the blood have led to several breakthroughs and create the potential for non-invasive, routine assessment of diseases status. However, these biomarkers are rare and currently difficult to isolate, especially in the early stages of disease. …

The Regulation Of Dna Methylation In Mammalian Development And Cancer, Nicolas Veland

Dissertations and Theses (Open Access)

DNA methylation is an essential epigenetic modification in mammals, as it plays important regulatory roles in multiple biological processes, such as gene transcription, maintenance of chromosomal structure and genomic stability, genomic imprinting, retrotransposon silencing, and X-chromosome inactivation. Dysregulation of DNA methylation is associated with various human diseases. For example, cancer cells usually show global hypomethylation and regional hypermenthylation, which have been implicated in genomic instability and tumor suppressor silencing, respectively. Although great progress has been made in elucidating the biological functions of DNA methylation over the last several decades, how DNA methylation patterns and levels are regulated and dysregulated is …

Multivalency Regulates Activity In An Intrinsically Disordered Transcription Factor, Sarah Clark, Janette B. Myers, Ashleigh King, Radovan Fiala, Jiri Novacek, Grant Pearce, Steve L. Reichow, Elisar J. Barbar

Chemistry Faculty Publications and Presentations

The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference …

Polymorphisms Of Bovine Hsp90 And Their Implications In Beef Cattle Productivity, Glynn G. Smith

Animal Science Undergraduate Honors Theses

Production of beef cattle represents a $60 billion industry in the United States (USDA, 2015). The American beef cattle industry loses an estimated $370 million annually due to heat stress (St-Pierre, 2003). As of 2003, this was equal to nearly 99 million pounds of beef lost (USDA, 2015). The average American consumed roughly 65 pounds of beef in 2003; this means that the 99 million pounds of beef lost to heat stress would have been enough to feed approximately 1.5 million Americans for an entire year (Barclay, 2012).

Evolutionary Conservation Of Midline Repulsion By Robo Family Receptors In Flies And Mice, Allison Loy

Biological Sciences Undergraduate Honors Theses

As the nervous system develops in animal embryos, neuronal axons are guided to their synaptic targets by extra cellular cues that signal through axon guidance receptors expressed on the surface of the axon. In animals with bilateral symmetry, one of the important decisions made by nearly every axon in the embryonic nervous system is whether to stay on its own side of the body, or to cross the midline and connect to cells on the opposite side. The Roundabout (Robo) family is an evolutionarily conserved group of axon guidance receptors that regulate midline crossing in a wide range of animal …

Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan

Graduate Theses and Dissertations

Genome-wide association studies (GWASs) have received an increasing attention to understand genotype-phenotype relationships. The Bayesian network has been proposed as a powerful tool for modeling single-nucleotide polymorphism (SNP)-trait associations due to its advantage in addressing the high computational complex and high dimensional problems. Most current works learn the interactions among genotypes and phenotypes from the raw genotype data. However, due to the privacy issue, genotype information is sensitive and should be handled by complying with specific restrictions. In this work, we aim to build Bayesian networks from publicly released GWAS statistics to explicitly reveal the conditional dependency between SNPs and …

Genetic Analysis Of Deep Phenotyping Projects In Common Disorders, Elliot S. Gershon, Godfrey Pearlson, Matcheri S. Keshavan, Carol Tamminga, Ney Alliey Rodriguez

School of Medicine Publications

Several studies of complex psychotic disorders with large numbers of neurobiological phenotypes are currently under way, in living patients and controls, and on assemblies of brain specimens. Genetic analyses of such data typically present challenges, because of the choice of underlying hypotheses on genetic architecture of the studied disorders and phenotypes, large numbers of phenotypes, the appropriate multiple testing corrections, limited numbers of subjects, imputations required on missing phenotypes and genotypes, and the cross-disciplinary nature of the phenotype measures. Advances in genotype and phenotype imputation, and in genome-wide association (GWAS) methods, are useful in dealing with these challenges. As compared …

Genotype-Specific Insertion Of Cytotoxic Genetic Elements Into Cancer Cells, Ryan Englander

University Scholar Projects

The new gene editing system CRISPR/Cas9, composed of a complex composed of a guide RNA and the Cas9 endonuclease, promises to revolutionize biological research and potentially allow clinicians to directly modify patient DNA in vivo. While its applications in the treatment of genetic diseases and in modifying immune cells for immunotherapy are currently being explored, CRISPR/Cas9’s potential utility as a modular system for targeting tumor-specific mutated sequences has not as of yet been explored. While CRISPR/Cas9 is specific enough to target small insertions and deletions or gross chromosomal rearrangements, it is not specific enough to reliably restrict editing to …

Ketogenic Diet Enhances Neurovascular Function With Altered Gut Microbiome In Young Healthy Mice, David Ma, Amy C. Wang, Ishita Parikh, Stefan J. Green, Jared D. Hoffman, George Chlipala, M. Paul Murphy, Brent S. Sokola, Björn Bauer, Anika M. S. Hartz, Ai-Ling Lin

Sanders-Brown Center on Aging Faculty Publications

Neurovascular integrity, including cerebral blood flow (CBF) and blood-brain barrier (BBB) function, plays a major role in determining cognitive capability. Recent studies suggest that neurovascular integrity could be regulated by the gut microbiome. The purpose of the study was to identify if ketogenic diet (KD) intervention would alter gut microbiome and enhance neurovascular functions, and thus reduce risk for neurodegeneration in young healthy mice (12–14 weeks old). Here we show that with 16 weeks of KD, mice had significant increases in CBF and P-glycoprotein transports on BBB to facilitate clearance of amyloid-beta, a hallmark of Alzheimer’s disease (AD). These neurovascular …

Analysis Of Environmental Dna Methods For The Detection Of Small Stream Fishes, Taylor Kristen Lee

Student Theses and Dissertations

Analysis of environmental DNA (eDNA) represents a promising new tool geared toward assisting species detection, though there is still much to learn about its utility and robustness. The main objective of this study was to use eDNA with several other applied techniques to determine the presence of the federally threated Leopard Darter, Percina pantherina, within two tributaries of the Little River in Arkansas. Traditional field sampling failed to detect P. pantherina, and putative contamination prevented confident eDNA detection. My second objective used a spike experiment strategy to test the ability of the eDNA method to reliably detect low levels of …

Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez

Computational Biology Institute

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. …

Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks

Yale Day of Data

Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.

Author Correction: A Population-Specific Reference Panel Empowers Genetic Studies Of Anabaptist Populations., Liping Hou, Rachel L Kember, Jared C Roach, Jeffrey R O'Connell, David W Craig, Maja Bucan, William K Scott, Margaret Pericak-Vance, Jonathan L Haines, Michael H Crawford, Alan R Shuldiner, Francis J Mcmahon

Articles, Abstracts, and Reports

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Asas-Ssr Triennnial Reproduction Symposium: Looking Back And Moving Forward—How Reproductive Physiology Has Evolved: Fetal Origins Of Impaired Muscle Growth And Metabolic Dysfunction: Lessons From The Heat-Stressed Pregnant Ewe, Dustin T. Yates, Jessica Lynn Petersen, Ty B. Schmidt, Caitlin N. Cadaret, Taylor L. Barnes, Robert J. Posont, Kristin A. Beede

Department of Animal Science: Faculty Publications

Intrauterine growth restriction (IUGR) is the second leading cause of perinatal mortality and predisposes offspring to metabolic disorders at all stages of life. Muscle-centric fetal adaptations reduce growth and yield metabolic parsimony, beneficial for IUGR fetal survival but detrimental to metabolic health after birth. Epidemiological studies have reported that IUGRborn children experience greater prevalence of insulin resistance and obesity, which progresses to diabetes, hypertension, and other metabolic disorders in adulthood that reduce quality of life. Similar adaptive programming in livestock results in decreased birth weights, reduced and inefficient growth, decreased carcass merit, and substantially greater mortality rates prior to maturation. …

Effect Of Mutation Of Cvn7 Conservon Genes Sco6796 And Sco6798 Of Streptomyces Coelicolor., Caroline Fulmer

Undergraduate Distinction Papers

Abstract

Streptomyces coelicolor is a gram-positive Actinobacterium. It is a filamentous soil organism that performs complex multicellular development. Its physiological and morphological differentiation produces active secondary metabolite antibiotics that have pharmaceutical applications. Studies of S. coelicolor show that cyclic di-GMP proteins regulate physiological and morphological development. S. coelicolor has 13 copies of an operon that are collectively named “conservon” because they are highly conserved. The operons are named cvn1-13 and genes in each operon are denoted cvnA-D. RNA-Seq data of a cyclic di-GMP phosphodiesterase double mutant showed differential expression between wild type and many of the operons in the …

Identifying Rmda Protein Interactions In Streptomyces Using A Bacterial Two-Hybrid System, Rachel Nguyen

Undergraduate Distinction Papers

Streptomyces is a genus of the phylum actinobacteria most commonly found as soil bacteria and used as a major source of antibiotics. RmdA and RmdB are phosphodiesterases that break down the ubiquitous second messenger cyclic-di-GMP which determines colony morphology and development of Streptomyces. The objective of this research is to identify whether RmdA will have interactions with itself using the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) System. Each gene was fused into one of two BACTH vectors that encode a different domain of a single protein (T18 and T25) and then cotransformed into the BACTH indicator strain. The transformants were …

The Identification And Characterization Of A Putative Chromosome Segregation Gene In Streptomyces Coelicolor, Sean Kirk

Undergraduate Distinction Papers

Streptomyces coelicolor is a soil bacterium that is a model for bacterial development. It is a filamentous, sporulating bacterium known to produce many medically utilized antibiotics. The goal of this research was to examine several developmental mutants and characterize novel genes of interest. Previously generated random transposon insertion mutants were analyzed using visual and microscopic phenotyping. Mutants of interest were further pursued and each transposon disruption site was identified by Inverse PCR and DNA sequencing. One of the novel genes is suspected to be involved in DNA segregation and codes for a putative membrane protein. Staining with propidium iodide was …

Threshold-Dependent Repression Of Spl Gene Expression By Mir156/Mir157 Controls Vegetative Phase Change In Arabidopsis Thaliana, Jia He, Mingli Xu, Matthew R. Willmann, Kevin Mccormick, Tieqiang Hu, Li Yang, Colby G. Starker, Daniel F. Voytas, Blake C. Meyers, R. Scott Poethig

Faculty Publications

Vegetative phase change is regulated by a decrease in the abundance of the miRNAs, miR156 and miR157, and the resulting increase in the expression of their targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. To determine how miR156/miR157 specify the quantitative and qualitative changes in leaf morphology that occur during vegetative phase change, we measured their abundance in successive leaves and characterized the phenotype of mutations in different MIR156 and MIR157 genes. miR156/miR157 decline rapidly between leaf 1&2 and leaf 3 and decrease more slowly after this point. The amount of miR156/miR157 in leaves 1&2 greatly exceeds the …

Metabolic And Inflammatory Biomarkers Are Associated With Epigenetic Aging Acceleration Estimates In The Goldn Study, Marguerite R. Irvin, Stella Aslibekyan, Anh Do, Degui Zhi, Bertha Hidalgo, Steven A. Claas, Vinodh Srinivasasainagendra, Steve Horvath, Hemant K. Tiwari, Devin M. Absher, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

Background: Recently, epigenetic age acceleration-or older epigenetic age in comparison to chronological age-has been robustly associated with mortality and various morbidities. However, accelerated epigenetic aging has not been widely investigated in relation to inflammatory or metabolic markers, including postprandial lipids.

Methods: We estimated measures of epigenetic age acceleration in 830 Caucasian participants from the Genetics Of Lipid Lowering Drugs and diet Network (GOLDN) considering two epigenetic age calculations based on differing sets of 5′-Cytosine-phosphate-guanine-3′ genomic site, derived from the Horvath and Hannum DNA methylation age calculators, respectively. GOLDN participants underwent a standardized high-fat meal challenge after fasting for at least …

Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao

Theses

The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …

The Ecology And Feeding Behavior Of Mosquitoes In The Galapagos Islands, Samoa S. Asigau

Dissertations

Mosquitoes remain important vectors in transmitting wildlife diseases. This dissertation aims to understand the role that mosquitoes play in transmitting wildlife diseases such as avian malaria, a protozoan parasite belonging to the genus Plasmodium. Using data from wild-caught mosquitoes captured in multiple years and across multiple islands on the Galapagos Archipelago, we describe distributional patterns of mosquitoes, their range limits and assess whether there exists a disease-free refuge as occurs in Hawaii. We show that altitudinal ranges for disease transmission of avian malaria may not be bounded by a stable disease-free refuge, since mosquitoes are found at all elevations, …

Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen

Mahurin Honors College Capstone Experience/Thesis Projects

RNA polymerase is the central enzyme in all gene expression. The rpoCY75N mutation in the zinc-binding domain of the β’ subunit of E. coli RNA polymerase blocks a unique RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022 and its relatives. Here, we describe the characterization of mutant phage, orc0368, which overcomes the rpoCY75N mutation. The orc0368 genome varies from the wild type phage genome by 4 single base pair mutations. Three of these mutations were not characterized because they occur in intergenic regions but the fourth was chosen for study because of its location between a series …

Changes In Myoblast Responsiveness To Tnfα And Il-6 Contribute To Decreased Skeletal Muscle Mass In Intrauterine Growth Restricted Fetal Sheep, Robert J. Posont, Kristin A. Beede, Sean W. Limesand, Dustin T. Yates

Department of Animal Science: Faculty Publications

Intrauterine growth restriction (IUGR) is a leading cause of perinatal morbidity and mortality (Alisi et al., 2011). Skeletal muscle growth is disproportionately reduced in IUGR fetuses and offspring (Padoan et al. 2004; Yates et al. 2014). These individuals present with reduced muscle mass and increased risk for metabolic disorders at all stages of life (Godfrey and Barker, 2000; Yates et al. 2016.). Muscle growth requires proliferation, differentiation, and fusion of myoblasts (muscle stem cells) to form muscle fibers early in gestation and to increase myonuclear content of existing fibers during late gestation and after birth (Yates et al., 2014). These …

Impaired Muscle Stem Cell Function In Cows With High Concentrations Of Androstenedione In Their Follicular Fluid, Taylor L. Barnes, Kiristen A. Beede, Elena M. Merrick, Caitlin N. Cadaret, Andrea S. Cupp, Dustin T. Yates

Department of Animal Science: Faculty Publications

It is unclear whether androstenedione (A4) increases muscle mass and strength similar to testosterone or whether it produces primarily catabolic effects on muscle-like estrogen (Rasmussen et al., 2000). Summers et al. (2014) observed two populations of cows that exhibit either high (>40 ng/mL; High A4) or low (<20 ng/mL; Low A4) concentrations of A4 within the fluid of the dominant follicle just prior to ovulation. High A4 cows had decreased reproductive rates and shorter times before falling out of the herd, but those that did produce calves weaned them ~10-kg heavier than their low A4 counterparts (Summers et al., 2014). It appears that the difference in weights is due to faster growing and more efficient skeletal muscle. High A4 cows share many characteristics with women suffering from polycystic ovary syndrome (PCOS), whose high levels of circulating androgens are associated with changes in body composition (Kirchengast and Huber, 2001).

Generating And Repairing Genetically Programmed Dna Breaks During Immunoglobulin Class Switch Recombination, Laura Nicolas, Montserrat Cols, Jee Eun Choi, Jayanta Chaudhuri

Publications and Research

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig …

Testing Viability Of Oligonucleotide Primers On Microsatellite Markers Amplified By Polymerase Chain Reaction On Dermacentor Variabilis Samples From The Bulloch County Region Of Georgia, Usa, Danielle Souza

Honors College Theses

Dermacentor variabilis, more commonly known as the wood tick, or the American dog tick, can be found all over North America. D. variabilis is a common tick in Bulloch county, Georgia, USA, and little is known about the population structure of this population of the species. Microsatellite markers are able to locate sections of the genome and can aid in estimating relatedness among individuals in a population. Six different oligonucleotide primer pairs were published for D. variabilis, however, published and non-published works indicated that not all of those primer pairs were working equally well for PCR. This study is …

A Genome-Wide Association Study Of Red-Blood Cell Fatty Acids And Ratios Incorporating Dietary Covariates: Framingham Heart Study Offspring Cohort, Anya Kalsbeek, Jenna Veenstra, Jason Westra, Craig Disselkoen, Kristin Koch, Katelyn A. Mckenzie, Jacob O'Bott, Jason Vander Woude, Karen Fischer, Greg C. Shearer, William S. Harris, Nathan L. Tintle

Faculty Work Comprehensive List

Recent analyses have suggested a strong heritable component to circulating fatty acid (FA) levels; however, only a limited number of genes have been identified which associate with FA levels. In order to expand upon a previous genome wide association study done on participants in the Framingham Heart Study Offspring Cohort and FA levels, we used data from 2,400 of these individuals for whom red blood cell FA profiles, dietary information and genotypes are available, and then conducted a genome-wide evaluation of potential genetic variants associated with 22 FAs and 15 FA ratios, after adjusting for relevant dietary covariates. Our analysis …

Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng

Biology Faculty Articles

Hepatocellular carcinoma (HCC) is the most frequent malignancy of the liver. Transforming growth factor beta 1 (TGFB1) and marker of proliferation Ki-67 (MKI67) regulate cell proliferation, differentiation, and growth. The association between MKI67 and TGFB1 expression and its clinical implications in HCC remain unknown. Methods: Public databases were used to analyze TGFB1 and MKI67 expression in different pathologic grades/stages and tissue types of HCC. The association between MKI67 and TGFB1 expression was explored using pathway analysis and in a HepG2 cell line treated with TGFB1. Survival analysis was performed to evaluate the prognostic value of TGFB1 and MKI67 expression in …