Genetics Commons^™

The Role Of Liver-Specific Transcription Factor Hnf4 In Reprogramming Of Fibroblasts, Mary Odubote

Masters Theses

The mammalian liver, a vital organ with complex functions, relies on a network of transcription factors to regulate gene expression. Fusion of hepatoma cells with fibroblasts often leads to gene extinction, silencing approximately 400 liver-enriched genes, including critical transcription factors such as HNF4. Previous studies revealed that ectopic expression of HNF4 in fibroblasts failed to prevent the extinction of SERPINA1, a liver-specific gene, upon subsequent fusion with hepatoma cells. Here, we sought to investigate the extent to which ectopic expression of HNF4 can reprogram fibroblast cells and prevent gene extinction in hybrid cells.

Using whole-genome expression analysis, we compared RAT1 …

Genetic Structure Of Urban White-Tailed Deer In West Michigan, Jacob David Brand

Masters Theses

In urban areas, green spaces are used by humans and wildlife. The proximity between them can lead to both positive and negative interactions, which can make managing urban wildlife difficult. Managers are challenged due to conflicts between wildlife population sizes that can be naturally supported versus those that are socially tolerable. White-tailed deer (Odocoileus virginianus) thrive in urban environments because their habitat requirements are met within green spaces and backyard vegetation. Matrilineal groups of urban white-tailed deer live within the same areas, at times forming high densities that can lead to the spread of diseases or environmental pests, including hemlock …

Pedigree And Molecular Assessment Of Relatedness In A Captive Chimpanzee Population, Francesca Golus

Masters Theses

As a crucial component of biodiversity, genetic diversity contributes to variability among individuals, allowing populations of endangered species to be resilient in the face of changing environmental conditions. Zoological institutions have become a cornerstone of conservation efforts and a refuge for endangered species given threats imposed on wild populations by climate change, habitat fragmentation and degradation, and overexploitation. Chimpanzees (Pan troglodytes) are an endangered species experiencing drastic population decline in the wild, yet are common residents in zoos and wildlife sanctuaries. To sustain long-term, genetically viable populations of species of concern, zoos use studbooks and paternity testing to …

A Genome Wide Survey Of The Insertion Sequences In Halanaerobium Hydrogeniformans, A Haloalkaliphilic Anaerobic Bacterium, Kody Austin Bassett

Masters Theses

"Insertion sequences (IS) are the smallest prokaryotic transposable elements. These mobile genes are highly diverse in size and structure, making them difficult to study. The transposition activity of insertion sequences has a significant role in evolution by enabling genomic plasticity via genome rearrangements. Insertion sequences are largely uncharacterized and thus methods to improve the ability to accurately identify, annotate, and infer genomic impact of insertion sequences is limited. A sequential set of methods using readily available genomic and bioinformatic tools was developed to accurately identify insertion sequences. This method was used to perform an entire genome survey of Halanaerobium hydrogeniformans …

Characterization Of Chromosomal Translocations In A Group Of Killifish Species By Using Genome-Wide High-Density Snp Mapping Approach, Naznin Sultana Remex

Masters Theses

"The role of chromosomal rearrangements in reproductive isolation and introgression between species is poorly understood. In heterozygous form, rearrangements may directly interrupt meiotic progression leading to partial sterility/subfertility (underdominance) or may suppress local meiotic segregation (recombination suppression). Such unbalanced meiotic segregation may also result in reproductive isolation and play roles as a driving force of speciation. The objective of this study was to gain insight into the pattern of chromosomal rearrangements in two closely related killifish species in the genus Fundulus (F. notatus, and F. olivaceus) by constructing genetic linkage maps using high-resolution single nucleotide polymorphism (SNP) …

A Pipeline For Exogenous Gene Expression And Biomass Analysis In Plants, Bijay Bisunke

Masters Theses

Biological pretreatment of biomass is typically required for the production of liquid biofuels, which are viable alternatives to traditional fossil fuels. While traditional thermomechanical pretreatments are effective at helping to deconstruct lignocellulose, they are often expensive and tend to generate environmentally dangerous waste materials. An alternative to traditional pretreatment strategies is biological pretreatment, which has focused on lignocellulose-degrading organisms, such as white-rot fungi. While direct pretreatment of biomass with white-rot fungi has shown great promise, directly expressing functional white-rot fungi genes in plants (i.e. in planta expression) has the potential to be even more efficient because the biomass itself …

The Transcriptional Response Of Trametes Versicolor To Growth On Maple Chips And Miscanthus Straw, Maha Alanazi

Masters Theses

This thesis research explored the transcriptional response of Trametes versicolor, a white-rot fungus, in response to fundamentally different types of lignocellulosic biomass (miscanthus and maple) and rich medium (malt extract agar). After five weeks of growth by the fungus on the biomass, the fungal RNA was extracted from three biological replicates per biomass type and mRNA was sequenced (approximately 30 million reads per sample). The reads were processed using ArrayStar to covert to RPKM and annotated using JGI's T. versicolor GO annotation file along with NCBI's BLAST. Comparisons were made between average gene expression of the fungus grown on …

Family-Based Association Studies Of Autism In Boys Via Facial-Feature Clusters, Luke Andrew Settles

Masters Theses

"Autism spectrum disorder (ASD) refers to a set of developmental disorders with varied attributes. Due to its substantial heterogeneity in terms of behavioral and clinical phenotypes, it is challenging to discern the genetic biomarkers behind ASD, even though the disease is known to be genetic in nature. This serves as a motivation to detect relationships between single nucleotide polymorphisms (SNPs) and a causal autism disease susceptibility locus (DSL) within more homogeneous subgroups. Recently, clinically meaningful subclassifications of ASD have been discovered utilizing facial features of prepubescent boys. Therefore, through the employment of data from 44 prepubertal Caucasian boys with ASD …

Scalable Parallelization Of A Markov Coalescent Genealogy Sampler, Philip E. Davis

Masters Theses

Coalescent genealogy samplers are effective tools for the study of population genetics. They are used to estimate the historical parameters of a population based upon the sampling of present-day genetic information. A popular approach employs Markov chain Monte Carlo (MCMC) methods. While effective, these methods are very computationally intensive, often taking weeks to run. Although attempts have been made to leverage parallelism in an effort to reduce runtimes, they have not resulted in scalable solutions. Due to the inherently sequential nature of MCMC methods, their performance has suffered diminishing returns when applied to large-scale computing clusters. In the interests of …

Genetic Structure And Diversity Of Channel Catfish (Ictalurus Punctatus) In Three Large Midwestern Rivers, Vaclav Alexei Sotola

Masters Theses

Little information is available regarding the genetic structure and diversity of sportfishes in large rivers, which can be vital to continuing the sustainable exploitation of these fisheries. Additionally, impoundments often have vast impacts on riverine systems. These impacts include altering the flow regime, changing the nutrient load, and preventing migratory fish from reaching their spawning grounds. If fishes are prevented from reaching their spawning grounds, their genetic diversity and structuring could begin to change relative to historic measures, potentially decreasing their fitness and ability to survive. I screened microsatellite loci to assess the genetic population structure and diversity of channel …

Characterization Of Insertion Sequence Is605 In Halanaerobium Hydrogeniformans, Michael C. Sadler

Masters Theses

"Insertion sequences are the smallest prokaryotic transposable elements. These genes play a significant evolutionary role by promoting genome plasticity. Insertion sequences are highly diverse elements that have largely been uncharacterized. As such, the ability to accurately identify, annotate, and infer genomic impact of insertion sequences is lacking. The study of new insertion sequences contributes knowledge to their annotation and evolution. Halanaerobium hydrogeniformans is a unique organism with an abnormally high number of insertion sequences. A family of insertion sequences, IS200/605, showed several interesting distinctions from other elements in the genome, including severe open reading frame degradation, and was characterized in …

Low-Head Dams On Habitat, Fish Functional Guilds And Genetic Structuring In A Midwestern River System, Shannon Cassandra Frary Smith

Masters Theses

The natural flow regime of the majority of rivers in the United States has been altered by anthropogenic structures. This loss of connectivity plays a strong role in shaping river ecosystems by altering physical habitat characteristics and shaping fish community assemblages. Although the impacts of large dams on river systems are well documented and often easy to observe, there are fewer studies on the effects of smaller low-head dams. Additionally, the influences of low-head dams on the genetic structuring of small-bodied riverine fishes have yet to be fully explored. I assessed the effects of two low-head dams on the Vermilion …

Genetic Structure Of Yellow Perch Populations In Coastal Areas Of Eastern Lake Michigan, Jessica N. Wesolek

Masters Theses

Genetic population substructure is often overlooked because of discontinuities between management and actual population structure as in the case of yellow perch, an ecologically and economically important indigenous fish species in the Laurentian Great Lakes. A knowledge gaps pertaining to the natural history of yellow perch relates to the biological connectivity between nearshore Lake Michigan and drowned river mouth (DRM) lakes, where it remains unclear whether resident yellow perch from Lake Michigan use DRM lakes for spawning or whether DRM lakes contribute to nearshore yellow perch populations in Lake Michigan. I used DNA fingerprinting (genotyping) to explore biological connectivity between …

Studies On Enzyme Functional Evolution In The Sabath Multigene Family Using Phylogenetic And Biochemical Approaches, Ruiqi Huang

Masters Theses

Gene duplication is believed to be the major source for providing genetic materials for the innovation and diversification of protein functions; natural selection and/or neutral drift then works on these genetic materials to guide their evolutionary directions. Here, I used the salicylic acid/benzoic acid/theobromine (SABATH) multigene family to study how natural selection acted on duplicated genes to prompt functional diversification. Members in this family methylate plant secondary metabolites by transferring the methyl group from S-adenosyl-L-methionine (SAM) to the carboxyl group or ring nitrogen of the substrates. In the Apocynaceae and Solanaceae lineage of this family, I documented three putative gene …

Comparisons Of Genetic Variance And Physiological Responses In Two Populations Of Western Mosquitofish, Gambusia Affinis, Brett Egger

Masters Theses

The study was conducted to determine the effects of lowered genetic variance in the Western mosquitofish (Gambusia affinis) on the physiological parameters of critical thermal maximum and minimum pH. Mosquitofish were obtained from two small central Illinois ponds, Lost Pond and Shadow Pond, by seines and dip nets. Once caught, fish were returned to the laboratory and acclimated for a minimum of five days at a temperature of 27°C and a pH of 8.25. At the beginning of each experimental run, fish were subjected to the physiological experiments for determination of critical thermal maximum and minimum pH, and then measured …

Strain Differences And Mutagen Treatment Influence Lectin Binding To Mouse Germ Cells, Marilyn Schmalz Holm

Masters Theses

Carbohydrate moieties on mouse germ cell surfaces were characterized by investigating the binding of FITC-labeled lectins to sperm and testis cells. Differences in lectin binding between different mouse strains, including T/t mice, were found. However, there was no evidence for the involvement of sialic acid or L-fucose in the T/t locus antigens. Antiserum to the t⁰, t⁶ haplotype was equally reactive to both ICR and T/t mouse testis cells in both immunofluorescence and cytotoxicity assays. Trypsinization of testis cells increased binding of soybean agglutinin and decreased binding of wheat germ agglutinin.

A method was developed for flow …

A Cytogenetic Study Of Xx/Xy Chimerism And Other Anomalies Of Bos Taurus In A Sampled Dairy Herd, Ferne M. Rogers

Masters Theses

The establishment of normal chromosomal patterns for a wide range of plants and animals has led to the recognition of abnormalities as well as their relationship to phenotypic irregularities. Research dealing with the expression of human karyotype is of prime interest; but, closely rivaling that is the genetic study of domestic animals which are of economic importance to man.

One observed anomaly which has come under scrutiny by cytogeneticists is that of the female member of a heterogeneous bovine twin pair, the freemartin. This is a sterile animal with internal morphology showing varying degrees of intersex. Cytogenetic studies reveal XX/XY …

Relationship Of Chemical Structure And Mutagenic Activity Of Streptozotocin And Its Analogs, Riaz-Ul Islam Zuberi

Masters Theses

No abstract provided.

N-Methyl-N’-Nitro-N-Nitrosoguanidine Induced Dominant And Recessive Mutations In Zea Mays, Frank Charles Janca

Masters Theses

No abstract provided.

The Gene Frequencies Of Ten Different Alleles In Man As Determined By The Hardy-Weinberg Equilibrium, Elizabeth Suzanne Shaw

Masters Theses

No abstract provided.

The Cytogenetics Of The Salivary Gland Chromosomes Of Three Wild Type Strains Of Drosophila Melanogaster, Rosemary Ann Harris

Masters Theses

This investigation involves the cytogenetics of three strains of field-collected, wild-type Illinois Drosophila melanogaster. These three strains were collected from Charleston, Channahon, and Olney, Illinois, in 1967.

The purpose of this study was to compare cytogenetically these three strains and to determine if there exists differences among them. First, the chromosomes themselves were studied for the purpose of identifying the four chromosomes of D. melanogaster by their characteristic banding patterns. Then, the chromosomes of the three strains were examined for chromosomal aberrations, principally inversions. The cytogenetics of the chromosomes of the three strains were then compared and contrasted.

Photographs …

Cytophotometric Determinations Of Dna In Karyotypes From Human Leukocyte Cultures Of Ten Males And Ten Females, Nancy Sue Whittaker

Masters Theses

No abstract provided.

Competition And Natural Selection Among Laboratory And Naturally Occurring Populations Of Drosophila Melanogaster, John M. Connor

Masters Theses

No abstract provided.

A Review Of The Status Of The Teaching Of Genetics And Evolution In High School Biology Courses With Suggestions For Improving The Teaching Of These Subjects, Carl Jay Bajema

Masters Theses

Introduction

It is the purpose of this thesis to: (1) discuss the place of genetics and evolution in high school biology courses; (2) specify the objectives that should be attained in teaching genetics and evolution; (3) discuss the current status of the teaching of genetics and evolution in high school biology courses; (4) suggest means of overcoming the three problems which have resulted in the poor teaching of genetics and evolution on the high school level -- first, the problem of religious opposition to the teaching of evolution; second, the problem of a lack of knowledge on the part of …