Genetics and Genomics Commons^™

Identifying Three-Way Gene Interactions From Microarray Data Using Kolmogorov-Smirnov And Cross-Match Tests, Shubhashree Khadka

Graduate Theses and Dissertations

Human gene network is much more complex than just pairwise interaction among the genes. Zhang et al. [6] extracted microarray data from International Genomics Consortium (IGC), and presented the detection of three-way gene interactions in their paper using Fisher’s z-transformation test. Three-way gene interactions are closer than pairwise correlations in representing the complex gene structures. Additionally, it was more tractable than assessing four or more gene interactions. In this paper, we are simulating different models where Fisher’s test might not be as effective. Zhang et al.’s approach utilized Pearson’s correlation coefficients and involved detection of linear interactions only. Since gene …

The Dlk1-Meg3 Locus In Malignant Cells Of Proposed Primordial Germ Cell Origins., Zachariah Payne Sellers

Electronic Theses and Dissertations

Primordial germ cells (PGCs) are hypothesized to deposit hematopoietic stem cells (HSCs) along their migration route through the embryo during the early stages of embryogenesis. PGCs also undergo global chromatin remodeling, including the erasure and reestablishment of genomic imprints, during this migration. While PGCs do not spontaneously form teratomas, their malignant development into germ cell tumors (GCTs) in vivo is often accompanied by the retention of hypomethylation at the IGF2-H19 imprinting control differentially methylated region (DMR). Previous studies in bimaternal embryos determined that proper genomic imprinting at two paternally imprinted loci was necessary for their growth and development: Igf2-H19 and …

Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, Shatovisha Dey

Graduate Theses and Dissertations

These studies have investigated different candidate genomic regions for their contributions to ascites in broilers. Ascites syndrome is a manifestation of idiopathic pulmonary arteriole hypertension that concerns the poultry industry worldwide. Investigations have demonstrated the disease to be genetically regulated and to exhibit moderate to high heritabilities. Although previous studies have indicated a few chromosomes to be involved with ascites, no genes have been identified to date with direct links to the disease. This dissertation presents a collection of studies that determine the genomic and genetic interactions for regions on chromosome 2 and 9 for ascites phenotypes in broiler chickens. …

Comprehensive Assessments Of The Genetic Determinants In Salmonella Typhimurium For Fitness Under Host Stressors: Oxidative Stress And Iron Restriction, Sardar Abdullah

Graduate Theses and Dissertations

Salmonella is an intracellular pathogen that infects a wide range of hosts. The infected host utilizes reactive oxygen species (ROS) and iron-restriction to eliminate the pathogen. We used proteogenomics to determine the candidate genes and proteins that have a role in resistance of S. Typhimurium to H2O2. For Tn-seq, a highly saturated Tn5 library was grown in vitro under either 2.5 (H2O2L) or 3.5 mM H2O2 (H2O2H). We identified two sets of overlapping genes that are required for resistance of S. Typhimurium to H2O2L and H2O2H, and the results were validated via phenotypic evaluation of 50 selected mutants. The enriched …

Optimizing A Method For Simultaneous Recovery Of Proteins And Dna From Fingerprints, Steven Kranes

Student Theses

DNA testing on touched objects is a valuable tool in forensic investigations, but DNA is usually present in low amounts, causing poor STR typing results. For touch DNA evidence, there is a clear need for additional individualization, especially for highly probative samples. This could be achieved by testing genetically variable proteins. The goal of this project was to develop a DNA/protein co-extraction method to facilitate DNA and protein testing on the same evidence item. Existing DNA extraction methods were carefully adjusted to allow for downstream mass spectrometry analysis. Initial experiments on saliva and fingerprints placed on glass suggested that trypsin …

Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding, Jaeil Han

Dissertations and Theses (Open Access)

The RNA exosome is an essential 3’-5 ribonuclease that processes or degrades a variety of RNA species in eukaryotes. It is composed of nine structural cores and one catalytic subunit, Rrp44. Structural studies captured two different conformations of Rrp44, Rrp44^ch (channel) and Rrp44^da (direct-access). The Rrp44^ch appears to recruit RNA substrates from the central channel formed by the core subunits, while the substrate is directly recruited to Rrp44^da bypassing the central channel. Although in vivo function of the Rrp44^ch-exosome is extensively studied, the function or even the presence of the Rrp44^da-exosome in …

Anaplasma Phagocytophilum Infection Modulates Expression Of Megakaryocyte Cell Cycle Genes Through Phosphatidylinositol-3-Kinase Signaling, Supreet Khanal, Hameeda Sultana, John D. Catravas, Jason A. Carlyon, Girish Neelakanta

Biological Sciences Faculty Publications

Anaplasma phagocytophilum, the agent of human granulocytic anaplasmosis infects neutrophils and other cells from hematopoietic origin. Using human megakaryocytic cell line, MEG-01, we show that expression of cell cycle genes in these cells are altered upon A. phagocytophilum infection. Expression of several cell cycle genes in MEG-01 cells was significantly up regulated at early and then down regulated at later stages of A. phagocytophilum infection. Lactate dehydrogenase (LDH) assays revealed reduced cellular cytotoxicity in MEG-01 cells upon A. phagocytophilum infection. The levels of both PI3KCA (p110 alpha, catalytic subunit) and PI3KR1 (p85, regulatory subunit) of Class …

Ephrin Receptors, Aiy Interneuron Physiology, And Behavior, Tyler Hill

Master of Science in Integrative Biology Theses

In order to survive, an organism must be able to receive, integrate, and respond to sensory stimuli. However, the cellular basis of sensory perception and response is difficult to study in complex animals such as humans, and is therefore poorly understood. The nematode Caenorhabditis elegans is a relatively simple organism yet displays many distinct behaviors, making it an ideal system to understand the relationship between gene function, cell shape, cell physiology, and behavioral output. Much of the thermosensory and chemosensory information that the nematode receives from its sensory neurons is processed via a pair of interneurons called AIYL and AIYR. …

Transcriptional Regulation Of Kal-1 In The Nematode Caenorhabditis Elegans, Zachery E. Mielko

Master of Science in Integrative Biology Theses

X-linked Kallmann syndrome (KS) is a genetic disease that is caused by loss-of-function mutations in the human kal-1 gene. The disorder consists of a loss of sense-of-smell coupled with failure to undergo spontaneous puberty. At the cellular level, KS phenotypes are caused by olfactory neurons’ failure to properly migrate to the olfactory bulb. This also prevents gonadotropin-releasing hormone neuroendocrine cells from migrating to the pituitary, preventing the pulsatile release of sex hormones at puberty. While many kal-1 interacting proteins have been studied in model organisms, little is known about the regulatory mechanisms that control kal-1’s expression. Since a 5.27kb …

T-Dna-Genome Junctions Form Early After Infection And Are Influenced By The Chromatin State Of The Host Genome, Shay Shilo, Pooja Tripathi, Cathy Melamed Bessudo, Oren Tzfadia, Theodore R. Muth, Avraham A. Levy

Publications and Research

Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected. Analysis of the epigenetic landscape of previously isolated sites of T-DNA integration in …

Elucidating The Molecular Parameters And Mechanism Of Homology Searching During Meiosis In Neurospora Crassa, Nicholas Adam Rhoades

Theses and Dissertations

Integration of foreign DNA into a host genome is often detrimental to the host organism, as the DNA is often of viral or transposon origin. Many organisms have established DNA surveillance and genome integrity mechanisms to defend against these harmful DNA insertions. Neurospora crassa, a filamentous fungus belonging to the Ascomycota group, has several DNA defense mechanisms to combat foreign DNA integration to its genome. One such mechanism is Meiotic Silencing of Unpaired DNA (MSUD). During meiosis, this remarkable system can detect unpaired genes on homologous chromosomes during sexual reproduction and silence their expression throughout meiosis. In order for the …

Draft Genome Sequence Of Bacillus Altitudinis Ynp4-Tsu, Isolated From Yellowstone National Park, Joshua A. O'Hair, Hui Li, Santosh Thapa, Matthew Scholz, Suping Zhou

Agricultural and Environmental Sciences Faculty Research

Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU.

Effect Assessment Of Tio2 Nanoparticles Exposure On Medicago By Monitoring Morphophysiology, Charles Towey

Mahurin Honors College Capstone Experience/Thesis Projects

In recent years titanium dioxide nanoparticles (TiO₂NPs) have been ingredients in everything from paints to cosmetics, and even in some kinds of food. This growth in use has resulted in a substantial increase in the amount of titanium released into the environment, which could have detrimental effects on nearby plant and animal life. Currently, the number of studies conducted on the effects of TiO₂NPs is quite small, especially when it comes to edible crops. Because of this lack of research data, this study has been designed to assess the effect of TiO₂ NPs exposure on …

A Rapid Colorimetric Peptide Nucleic Acid Loop-Mediated Isothermal Amplification Assay For The Detection Of The Idh1 Mutation In Glioblastoma, Edward J. Raack

All NMU Master's Theses

The IDH1 mutation is an important diagnostic and prognostic biomarker used to characterize glioblastoma (GBM). Patients harboring the IDH1 mutation have improved overall survival following maximal resection. Knowledge of the IDH1 mutation status allows the surgeon to modify the surgical plan; however, no existing molecular test can provide this information intraoperatively. We designed a novel colorimetric peptide nucleic acid loop-mediated isothermal amplification (PNA-LAMP) method that rapidly detects the IDH1 R132H mutation in GBM. PNA-LAMP amplifies target DNA under isothermal conditions with high specificity and speed. The PNA prevents amplification of wild-type IDH1 DNA, while allowing amplification of the R132H variant …

Functional Analysis Of Microrna Pathway Genes In The Somatic Gonad And Germ Cells During Ovulation In C. Elegans, Carmela Rios

Dissertations (1934 -)

MicroRNAs (miRNAs) are post-­transcriptional regulators of gene expression that play critical roles in animal development and physiology, though functions for most miRNAs remain unknown. Worms with reduced miRNA biogenesis due to loss of Drosha or Pasha/DGCR8 activity are sterile and fail to ovulate, indicating that miRNAs are required for the process of oocyte maturation and ovulation. Starting with this penetrant sterile phenotype and using new strains created to perform tissue-­specific RNAi, we characterize the roles of the C. elegans Pasha, pash-­1, and two miRNA-­specific Argonautes, alg-­1 and alg-­2, in somatic gonad cells and in germ cells in the regulation of …

Analysis Of Population Structure In A California Newt (Taricha Torosa) Metapopulation, Jessica Vincent

Mahurin Honors College Capstone Experience/Thesis Projects

As anthropogenic influences take an ever-increasing toll on the environment, understanding how environmental change affects species is paramount. Concern regarding decline in amphibian populations has spurred research examining the effects of habitat change on the dynamics of populations at landscape levels. One important goal is to understand how gene flow among populations is affected by changes in habitat. Biologists need to consider the relationship between gene flow and habitat alterations so that movements among individual breeding ponds can be maintained over time, reducing risk of local extinction events. This study focuses on patterns of gene flow among thirteen populations of …

Naturally-Derived Molecular Ensembles In Medicine, Materials Science And Evolutionary Biology: An Interdisciplinary Study, Silvio Panettieri

Dissertations, Theses, and Capstone Projects

The first chapter will introduce the work carried out in collaboration with the Govind laboratory at CCNY. Our quest was set forth to investigate the intimate relationship lying between chronic inflammation and tumor development. For at least the last fifteen years much research has been conducted on this topic; yet, the level of complexity arising from exceedingly interwoven biochemical pathways in mammals has resulted in slow advancements in this field. This is why we resorted to a simple yet powerful immunogenetic model organism, the fruit fly Drosophila melanogaster, in combination with the administration of the most common anti-inflammatory drug, …

The Recycling Gtpase, Rab-10, Regulates Autophagy Flux In Caenorhabditis Elegans, Nicholas J. Palmisano

Dissertations, Theses, and Capstone Projects

Autophagy and endocytosis are two cellular pathways that are vital to cell growth and homeostasis. Autophagy is a dynamic and catabolic process involving the formation of a double-membrane vesicle called the autophagosome, which engulfs long-lived proteins and damaged organelles. Endocytosis involves the uptake of extracellular material into the cell through the formation of intracellular vesicles termed endosomes. Although both endocytosis and autophagy are interconnected processes, the extent to which endocytic proteins and/or compartments contribute to autophagy, and how these endocytic components do so, is still unknown. To improve our understanding of the connections that exist between autophagy and endocytosis, we …

Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan

Dissertations, Theses, and Capstone Projects

The body size of an organism can be a crucial determinant of access to nutrition, reproductive success and overall survival in the wild. However, how body size of an individual is determined is incompletely understood. Body size is a complex trait determined by multiple pathways and genes, making it difficult to understand the role of individual genes and pathways in determining overall size. In Caenorhabditis elegans, a homolog of Bone Morphogenetic Proteins (BMP) is a major regulator of body size; functional loss of DBL-1 leads to a small body size. Due to a drastic change in body size in dbl-1 …

Examination Of The Monoamine Oxidase A Gene Promoter On Motivation To Exercise And Levels Of Voluntary Physical Activity, Erin M. Kinney

Senior Theses

Purpose: The purpose of this study was to examine the genetic basis underlying voluntary exercise. Monoamine oxidase A (MAO-A) is an enzyme that acts on monoamine neurotransmitters, such as dopamine, to cause inactivation. There are several polymorphisms in the promoter region of the MAO-A gene, and these variations change transcriptional activity and the amount of MAO-A produced, leading to alterations in available dopamine levels. Interestingly, polymorphisms in MAO-A have been associated recently with physical activity level. This study sought to determine whether there is an association between motivation to exercise, levels of voluntary physical activity, and MAO-A gene polymorphisms.

Methods: …

The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle

Biology Faculty Publications

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment, and they are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either cooperative public goods or as traits that provide a competitive advantage. Here, we empirically tested the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that (i) PSL is not metabolically costly to produce; (ii) PSL provides populationlevel benefits in biofilms, for both growth and antibiotic …

The Population Genetics Of Morro Bay Eelgrass (Zostera Marina), Julia Gardner Harencar

Master's Theses

Seagrass populations are in decline worldwide. Zostera marina (eelgrass), one of California’s native seagrasses, is no exception to this trend. In the last 8 years, Morro Bay, California has lost 95% of its eelgrass. Eelgrass is an ecosystem engineer, providing important ecosystem services such as sediment stabilization, nutrient cycling, and nursery habitats for fish. The failure of recent restoration efforts necessitates a better understanding of the causes of eelgrass decline in this estuary. Previous research on eelgrass in California has demonstrated a link between population genetic diversity and eelgrass bed health, ecosystem functioning, and resilience to disturbance and extreme climatic …

The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter

Electronic Theses, Projects, and Dissertations

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency …

Rosa Hybrid Gene Gapc Is Mutated In The Presence Of The Rose Rosette Virus, William A. Beams, Eva L. Burelos, Charles C. Hundley, Landon R. Dame, Laura G. Sims, Jacob J. Adler

Kentucky Journal of Undergraduate Scholarship

Rose Rosette Disease (RRD) harms the global rose supply by modification of the growth and development in rose cultivar. RRD spreads via a negative-sense RNA plant virus transmitted by eriophyid mites. Importantly, there is no pre-existing knowledge about the biochemistry by which this virus debilitates roses. Here we implicate glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the major metabolic enzymes in plants, as a possible target of the virus. Genomic DNA of the cytosolic form of the protein encoded by GAPC was extracted from both virally-infected and non-infected samples of the Rosa hybrid cultivar Rosa Tropicana. The sequence results provided several distinct …

Identification Of The Potentiating Mutations And Synergistic Epistasis That Enabled The Evolution Of Inter-Species Cooperation, Sarah Douglas, Lon Chubiz, William Harcombe, Christopher Marx

Biology Department Faculty Works

Microbes often engage in cooperation through releasing biosynthetic compounds required by other species to grow. Given that production of costly biosynthetic metabolites is generally subjected to multiple layers of negative feedback, single mutations may frequently be insufficient to generate cooperative phenotypes. Synergistic epistatic interactions between multiple coordinated changes may thus often underlie the evolution of cooperation through overproduction of metabolites. To test the importance of synergistic mutations in cooperation we used an engineered bacterial consortium of an Escherichia coli methionine auxotroph and Salmonella enterica. S. enterica relies on carbon by-products from E. coli if lactose is the only carbon source. …

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf …

Characterization Of Neuronal Specific Responses To Induced Misfolded Protein Stress In Caenorhabditis Elegans, Claire Gormley

Senior Honors Projects, 2010-2019

Abstract

Misfolded protein stress has been associated with many types of disease,

including neurodegenerative disorders like Alzheimer’s, Parkinson’s and Huntington’s

disease. When a cell accumulates misfolded proteins in the endoplasmic reticulum,

misfolded protein stress occurs and the unfolded protein response (UPR) is triggered to

induce mechanisms that will allow the cell to either survive or undergo cell death. The

nascent polypeptide associated complex (NAC) is a co-translational chaperone and α/β

heterodimer that manages protein folding and localization, and protects against misfolded

protein stress; changes in NAC function have been linked to both neurodegeneration and

cancer. In these studies, I depleted …

Epigenetic Modifications Of Human Placenta Associated With Preterm Birth, Drissa Toure

Theses & Dissertations

Preterm birth is a complex multifactorial process. Despite the well-known role of the placenta in supporting the fetal development and maternal-fetal tolerance, the placental epigenetic modifications and preterm birth (PTB) remains poorly understood and under investigated. Various maternal and environment factors can influence epigenetic programming during fetal development to affect the functioning and structures of organs, including the placenta, which can lead to adverse pregnancy outcomes, including PTB. The understanding of the placental epigenetic alterations and maternal determinants associated with PTB are apparently indispensable for the development of actual diagnosis and methods of prevention and treatment of premature labor. The …

Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell

Theses and Dissertations

Ruffed lemur (Varecia spp.) color vision research was conducted using a multidisciplinary approach: psychophysics, genetic analysis, technology, and animal training. The behavioral manifestation of Varecia spp. trichromacy was shown using a touchscreen apparatus (SMARTA). Trichromats performed better than dichromats when discriminating red from green (G₂ = 78.10, p < 0.001).

Investigating The Genetic Basis For Hominoid Taillessness, Samantha M. Tickey-Mccrane, Holly Dunsworth, Johanna E. Wegener

Senior Honors Projects

Investigating the Genetic Basis for Hominoid Taillessness:

A Comparative Genetic Approach Across Ten Catarrhine Taxa

Samantha Tickey-McCrane1,2, Johanna E. Wegener2, and Holly Dunsworth1

Honors Thesis Abstract Written by Samantha Tickey-McCrane, Departments of Anthropology & Biology

Advisor: Dr. Holly Dunsworth, Department of Anthropology

How did hominoid tail loss occur? My goals are to test phylogenetic and adaptive hypotheses for tail length variation among macaques, and use those insights to reconstruct the evolution of hominoid taillessness. Further, I aim to ultimately uncover which candidate genes or pathways may be responsible for catarrhine tail loss, and what other traits may be affected by …