Genetics and Genomics Commons^™

Chemical Synthesis Of Sensitive Dna, Komal Chillar

Dissertations, Master's Theses and Master's Reports

Over the past decades, researchers have tried various chemical methods to synthesize modified oligodeoxynucleotides (ODNs, i.e. short segments of DNAs). Traditional ODN synthesis methods require strong basic, and nucleophilic conditions for the deprotection and cleavage of the ODN from the solid support. However, the sensitive ODNs containing labile functionalities are vulnerable to such harsh conditions. Sensitive ODNs have a wide range of applications in research and pharmaceuticals. To synthesize sensitive ODNs, researchers devised different strategies but no practical methods have been developed. To overcome these challenges, we developed alkyl Dim alkyl Dmoc technology. This innovative technology uses weakly basic and …

Statistical Methods For Gene Selection And Genetic Association Studies, Xuewei Cao

Dissertations, Master's Theses and Master's Reports

This dissertation includes five Chapters. A brief description of each chapter is organized as follows.

In Chapter One, we propose a signed bipartite genotype and phenotype network (GPN) by linking phenotypes and genotypes based on the statistical associations. It provides a new insight to investigate the genetic architecture among multiple correlated phenotypes and explore where phenotypes might be related at a higher level of cellular and organismal organization. We show that multiple phenotypes association studies by considering the proposed network are improved by incorporating the genetic information into the phenotype clustering.

In Chapter Two, we first illustrate the proposed GPN …

Statistical Methods For Gwas And The Impact Of Diabetic Medication Adherence On Healthcare Costs, Meida Wang

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. In Chapter One, we develop a computationally efficient clustering linear combination approach to jointly analyze multiple phenotypes for GWAS. In this paper, based on the existing CLC method and ACAT strategy, we develop the ceCLC method to test association between multiple phenotypes and a genetic variant. In Chapter Two, we develop a novel method called sCLC for association studies of multiple phenotypes and a genetic variant based on GWAS summary statistics. Simulation results show that sCLC can control Type I error rates well and has the highest power in most scenarios. In Chapter Three, we …

Sequencing Antisense Transcriptome Of Populus Through Antisense/Sense Transcript Pair Enrichment, Emma V. Burke

Dissertations, Master's Theses and Master's Reports

Past transcriptome research on plants focused primarily on protein coding genes, and only recently researchers began looking into the non-protein coding regions that may play significant roles in gene regulation. Antisense RNA transcripts that are found naturally in the cell share complementary sequence with sense transcripts and have been shown to regulate expression of their sense counterparts. Since antisense RNA has been largely under-studied and difficult to sequence because of their low relative abundance, new methods are needed to target antisense RNA for efficient genome-wide profiling. To address this gap in methods to efficiently and cost effectively enrich antisense RNA …

White-Tailed Deer In A Winter-Wonderland: Long-Term Deer Yard Use And Methodological Considerations For Ungulate Fecal Dna Metabarcoding, Melanie A. Ottino

Dissertations, Master's Theses and Master's Reports

Northern white-tailed deer (Odocoileus virginianus) mitigate the increased energetic costs of severe winter conditions through obligate migration to densely congregated areas with abundant conifer cover, a behavior referred to as yarding. “Deer yards” in the Western Upper Peninsula (UP) of Michigan are principally located within the reduced snowpack and increased ambient temperature microclimates of densely canopied eastern hemlock (Tsuga canadensis) stands, but specific drivers of long-term site fidelity and utilization are largely uncharacterized. As an important game species of high economic and cultural value and a keystone herbivore with critical impact of plant community composition and structure, identifying winter yarding …

Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer, Zayne Knuth

Dissertations, Master's Theses and Master's Reports

Cancer testis genes are common targets for the development of immunotherapy for cancer treatment. Ovarian cancer is one of the leading causes of death in women cancer patients. Cancer testis genes play a role in tumorigenesis, but it is not clear how these genes are activated. This study utilized differential expression analysis between The Cancer Genome Atlas (TCGA) ovarian cancer data, Genotype-Tissue Expression (GTEx) non-cancerous ovary and testis data, and cell line data to identify a list of cancer testis genes that have a novel expression profile. To identify ovarian cancer testis genes, we obtained normal ovary tissue data and …

Characterizing Drought Adaptations, Phenotypic Plasticity, And Fixed Gene Expression Patterns Within Quercus, James K. Rauschendorfer

Dissertations, Master's Theses and Master's Reports

This dissertation was written on topics related to the genus Quercus with a primary focus on Quercus ellipsoidalis (northern pin oak) and Quercus rubra (northern red oak). Within this dissertation are chapters related to the setup of experimental common gardens within the Ford and Kellogg experimental forest, a literature review describing drought adaptations of Quercus sect. Lobatae (red oak group), identification of transcription factors within the Q. robur (English oak) and Q. rubra genomes, a study comparing leaf trait phenotypic plasticity of Q. ellipsoidalis and Q. rubra, and an RNA-seq experiment studying ecological speciation between Q. ellipsoidalis and Q. …

Construction And Analysis Of Genetic Regulatory Networks With Rna-Seq Data From Arabidopsis Thaliana, Tessa Kriz

Dissertations, Master's Theses and Master's Reports

Reconstruction of gene regulatory networks (GRNs) is a fundamental aspect of genetic engineering and provides a deeper understanding of the biological processes of an organism. Two methods were implemented to reconstruct the gene regulatory networks of Arabidopsis thaliana under two treatments: methyl jasmonate (MeJa) and salicylic acid (SA). The Joint Reconstruction of multiple Gene Regulatory Networks (JRmGRN) method was utilized to construct a joint network for identifying hub genes common to both conditions in addition to networks specific to each condition. The Differential Network Analysis with False Discover Rate Control method constructed a network of connections unique to only one …

The Effect Of Nutrition On Longevity And Fertility In Diverse Drosophila: A Tor-Mediated Process, Tessa E. Steenwinkel

Dissertations, Master's Theses and Master's Reports

Nutrition and growth are strongly linked, but not much is known about how nutrition leads to growth. To understand the connection between nutrition through diet, growth and/or proliferation, we need to study the phenotypes resulting from the activation and inhibition of central metabolic pathways. Here I use the model organism Drosophila melanogaster (D. mel.) and three non-model Drosophila species with different dietary needs, Drosophila guttifera (D. gut.), Drosophila deflecta (D. def.), and Drosophila tripunctata (D. tri.), to study the effects of dietary amino acid availability in these diverse flies on fecundity and …

Functional Genetic Approaches To Provide Evidence For The Role Of Toolkit Genes In The Evolution Of Complex Color Patterns In Drosophila Guttifera, Mujeeb Olushola Shittu

Dissertations, Master's Theses and Master's Reports

Toolkit genes are set of genes that orchestrate the development of basic body plan of animals, and they are highly conserved in all animals. The co-option of the toolkit genes into the pigmentation pathway has led to the evolution of novel species. This study focuses on understanding how the complex color patterns in animals develop by using the Drosophila species in the quinaria group as models. We developed an mRNA in situ hybridization (ISH) protocol, which allowed us to study gene expression patterns in the abdomen of developing pupae of non-model Drosophila species (Chapter 2). Through ISH, we found that …

Applications Of Machine Learning In Microbial Forensics, Ryan B. Ghannam

Dissertations, Master's Theses and Master's Reports

Microbial ecosystems are complex, with hundreds of members interacting with each other and the environment. The intricate and hidden behaviors underlying these interactions make research questions challenging – but can be better understood through machine learning. However, most machine learning that is used in microbiome work is a black box form of investigation, where accurate predictions can be made, but the inner logic behind what is driving prediction is hidden behind nontransparent layers of complexity.

Accordingly, the goal of this dissertation is to provide an interpretable and in-depth machine learning approach to investigate microbial biogeography and to use micro-organisms as …

Metagenomic Identification And Classification Of The Mercury-Methylating Gene Hgca In Response To Water Table And Plant Functional Group Manipulations In Peat Soil, Madeline Peterson

Dissertations, Master's Theses and Master's Reports

Methyl-mercury (MeHg) is a potent neurotoxin that threatens the health of humans and wildlife alike. Climate warming threatens to shift regional precipitation and climate regimes in peatland environments, which could destabilize northern peatlands and accelerate both Hg release from soil and MeHg production. Peatlands are among the leading hotspots for MeHg, yet little is known about the community composition or functional relationship of mercury-methylating microbes in response to varying environmental conditions. The recognized mercury-methylating genes responsible for this activity are the obligatory gene pair hgcA and hgcB. Metagenomic data from the full-factorial peatland mesocosm experiment PEATcosm was obtained to …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

Role Of Microrna-483 In Pancreatic Β-Cells, Jackson Waugh

Dissertations, Master's Theses and Master's Reports

Insulin is an essential hormone produced by β-cells in the pancreas. The release of insulin is tightly regulated in healthy people in order to control blood sugar level in our body. However, people with Type 2 Diabetes have insufficient insulin secretion from pancreatic β-cells, leaving to high blood sugar (hyperglycemia) and β-cell failure. microRNAs (miRNAs or miR) are newly discovered small regulatory molecules and have emerged as important regulator of cell growth, differentiation, and organ function. Altered miRNA function has been implicated in the pathogenesis of a variety of human disease, including diabetes. In this report, we focus on dissecting …

Monitoring Mammal Community Shifts Across Silvicultural Treatments Utilizing Camera Traps And The Development Of Invertebrate- Derived Dna In Hardwood Forests Of North America, Shallen Gurtler

Dissertations, Master's Theses and Master's Reports

Mammal distribution and diversity is quickly changing as humans modify the landscape. In particular, silviculture, which is the practice of controlling the growth, structure, and quality of forests to meet the needs of society and the landowner, influences the habitat usage of mammals. Utilizing camera traps, I monitored shifts in mammal communities across different silviculture treatments in the northern hardwood forests of the Great Lakes region in North America. I assessed the community composition across six canopy treatments and three understory treatments with a total of 2,018 active camera trap nights with 3,321 detections over the course of 147 days. …

Application Of Short Tandem Target Mimic (Sttm) Technique For Functional Analysis Of Micro-Rna396 In Transgenic Poplar Trees, Surattana Boonsai

Dissertations, Master's Theses and Master's Reports

Short Tandem Target Mimic (STTM) is a commonly technique used for functional studies of a number of genes in several plant model systems. However, very little is known about application of STTM technique in tree species. In this study, STTM was applied to knock down microRNA396 (miR396) in transgenic poplar trees for the first time. STTM396 expression resulted in dramatic decrease in miR396 expression levels leading to taller plants with larger leaves and larger leaf cell size. Additionally, an expression analysis of growth regulating factor genes (GRFs) that are members of miR396 target gene family showed up-regulation of GRF07 gene …

Impact Of Industrial Biocides On Bacterial Isolates From Hydraulic Fracturing Produced Water, Waad Ahmed Aljohani

Dissertations, Master's Theses and Master's Reports

Biocides are antimicrobial compounds that are designed to kill diverse groups of microbes in an untargeted fashion. Glutaraldehyde and DBNPA are commonly used to manage microbial growth in different industries. It is possible that biocide use may result in the development of bacterial resistance. However, resistance to DBNPA is believed to be limited under normal use conditions. We isolated a number of bacteria from produced water from a hydraulically fractured site in West Texas. We then tested the ability of these isolates to resist Glutaraldehyde and DBNPA. In this study, we found that these isolates have varying resistance to these …

The Impact Of Household Biocides And Antibiotics On Aquatic Microbial Community Composition, Abdulaziz Saud M Alrashdi

Dissertations, Master's Theses and Master's Reports

Triclosan (TCS) is antimicrobial agent that is used in a lot of consumer products, including toothpaste, liquid and bar soap, and cosmetics. TCS has been found in many lakes and rivers in the United States. However, The Food and Drug Administration (FDA) banned TCS recently and it will no longer be used in household products. Despite the recent ban, TCS is known to persist in the environment and may have long-term impacts. We conducted an experiment on using fresh water from three locations Houghton, Green Bay and the Huron Mountains. Our goals in the study is to assess the impact …

Development And Characterization Of Histidine-Tagged Hpv16 L2 And Ms2-Arginine-Tagged Recombinant Proteins For Downstream Processes, Tahiyat Alothaim

Dissertations, Master's Theses and Master's Reports

Human papillomaviruses (HPVs) are the most common sexually transmitted infections. Persistent infection with HPV can lead to anogenital cancers including head and neck cancers. Three prophylactic vaccines have been approved to prevent against some types of HPV infection. However, the vaccines are HPV-type specific and protect mostly against the HPV types included in the vaccines. To offer broader protection against more HPV types, studies in the field are developing candidate vaccines targeting a conserved minor capsid protein, L2. Nevertheless, reagents for developing and assessing L2 vaccines are limited. For example, antibodies to assess the antigenicity of some L2 epitopes are …

Blossomsttm Hub – An Online Tool For Designing Sttm Vectors And Visualizing Phenotypic Changes Of Sttm Transgenic Lines, Avinash Subramanian

Dissertations, Master's Theses and Master's Reports

Small RNAs including microRNAs (miRNAs) and short interfering RNAs (siRNAs) are widely present in plants. They are transcribed from non-coding small RNA genes and then play as regulators to modulate the levels of messenger RNAs (mRNAs) of protein-coding genes via sequence pairings. This is because a paired complementary double sequence helix structure can trigger mRNA degradation or interfere with mRNA translation. Short Tandem Target Mimic (STTM) is a recently developed technology that can be used to produce a complementary sequence to a miRNA and destroy it or reduce the expression level of this miRNA via the formation of paired double-strand …

Investigating Mirna Functions In Arabidopsis By Short Tandem Target Mimic (Sttm), Yiyou Gu

Dissertations, Master's Theses and Master's Reports

MicroRNA (miRNAs) and other endogenous small RNAs play important role in regulating gene expression in eukaryotes. Till now, several techniques have been developed for miRNA function analysis. Because of the characteristic of miRNAs, the most applicable method for miRNA function research is blocking the whole miRNA family specifically. Here, we report an artificial non-coding transcript termed Short Tandem Target Mimic (STTM) for blocking miRNA activity in Arabidopsis thaliana. The STTM composed of two miRNA target sites with three nucleotides bulge in the miRNA cleavage site, the two-miRNA targets separated by spacer linker. We used this technique blocking several important endogenous …

Feasibility & Discovery Using Fox System To Generate Gain-Of-Function Mutations With Hybrid Poplars, James Rauschendorfer

Dissertations, Master's Theses and Master's Reports

The Full-length complementary DNA OvereXpression (FOX) system is an approach to generating gain-of-function (GF) plants predominantly used for studying Arabidopsis. This approach inserts T-DNAs containing random full-length complementary DNA (fl-cDNA) with upstream promoter and downstream terminator into the host plant genome. Studies using this method report the success generating overexpression populations with high mutation rates. We choose to investigate the feasibility and effectiveness of this method using poplars. We suspected using a succulent xylem specific fl-cDNAs library would enrich the transformant poplars with mutants affected in traits specific to woody tissue development. We observed a characteristically high mutation rate …

Characterization Of Genic Microsatellite Markers (Est-Ssrs) In The Endangered Oak Species Quercus Georgiana M.A.Curtis, Priyanka Dipak Kadav

Dissertations, Master's Theses and Master's Reports

Quercus is important ecologically and economically because it provides food and habitat for wildlife, wood and paper products for humans. Oaks are endangered due to various factors like shifting climates, habitat loss, drought, pathogens and genetic swamping. Quercus georgiana (M.A. Curtis) is an endangered and restricted oak species which is remaining only in the southeastern part of the US. Efforts are required to conserve this endangered species from extinction. Conservation of this species can be done through these methods: ex-situ conservation (arboretum and botanical garden) and in-situ conservation strategies which protect the species in its natural habitat. For this conservation …

Development Of Gene-Based Microsatellite Markers In Acer Saccharum Marsh., Monica Harmon

Dissertations, Master's Theses and Master's Reports

Sugar maple (Acer saccharum Marsh) is an important ecological and economic resource. Despite its significance, there are few molecular genetic resources available to date. This study used previously developed EST libraries generated for sugar maple and other hardwood species to develop and characterize EST-SSRs in sugar maple and test their transferability to other Acer species. Out of 58 markers tested, 22 showed amplification in the expected size range. From these, 16 polymorphic markers were selected to test transferability and 13 of these showed amplification in at least one other Acer species.

Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

The Mechanisms Of Α-Amanitin Resistance In The Fruit Fly Drosophila Melanogaster, Chelsea L. Mitchell

Dissertations, Master's Theses and Master's Reports

Insect pesticide resistance has become a costly problem in the US. To make things more problematic, resistance to one pesticide is often associated with cross-resistance to other toxins, including pesticides that have not yet even been developed. In this study, we investigated a possible type of cross-resistance in the model fruit fly Drosophila melanogaster, some stocks of which are resistant to the very potent mushroom toxin α-amanitin. Because α-amanitin is solely produced by mushrooms, and because D. melanogaster does not feed on mushrooms in nature, the fruit flies should not be resistant to this toxin. In order to understand …