Master of Science (MS), Wright State University, 2018, Biochemistry and Molecular Biology

Microsatellites repeat sequences are prone to forming non-canonical DNA structures and mutations. These areas of the genome can undergo expansions and contractions and are responsible for a variety of inherited neurological and neuromuscular disorders. Hairpin structures formed by trinucleotide repeats can lead to replication fork stalling, and fork collapse causing DNA double strand breaks. Various mechanisms are involved in processing microsatellites including mismatch repair, base excision repair, and crossover junction endonuclease cleavage. These processes, which are supposed to protect the genome, could also be the culprits which are causing mutations. In order to test and study this hypothesis, the use of a two color marker gene assay to detect DNA double strand breaks at trinucleotide repeats, was used to detect replication fork stalling, and collapse in presence or absence of replication stress. An important mechanism for the restart of a stalled replication fork involves crossover junction endonucleases, which cleave obstacles that prevent passage of the replication fork. This process is led by MUS81 and its associates EME1 and EME2, which form complexes to process these secondary structures allowing the replication fork to progress. My results indicate distinct roles for MUS81-EME1 and MUS81-EME2 complexes in the maintenance of genome stability.

Committee: Michael Leffak Ph.D. (Advisor); Michael Markey Ph.D. (Committee Member); Weiwen Long Ph.D. (Committee Member) Subjects: Biochemistry; Molecular Biology

Doctor of Philosophy (PhD), Wright State University, 2024, Biomedical Sciences PhD

Microsatellites are tandem repeats of short nucleotide sequences. These repeats are inherently unstable and can pose obstacles to replication process leading to double-strand breaks (DSBs). When unrepaired, these breaks can threaten genomic integrity leading to various neurological and developmental diseases. Alternatively, these replication-induced breaks are repaired via a highly mutagenic mechanism known as break-induced replication (BIR). My project specifically focuses on the trinucleotide repeats of CAG units capable of forming hairpin structures that stall the replication fork, eventually causing its collapse. Expansions in CAG repeats have been implicated in Huntington's disease and Myotonic Dystrophy Type I. To study instability caused by this repeat, we are using an engineered HeLa cell line with a dual fluorescent reporter construct harboring a repeat of 102 CAG units in the lagging strand template adjacent to a c-myc origin of replication. This will allow us to use flow cytometry, inverse PCR, and sequencing to study the effects of these repeats on replication and chromosomal instability at the single DNA molecule level by monitoring subsequent recombination, mutations and template switches generated from the BIR repair mechanism. We find that the repair of these replication-induced breaks leads to levels of DNA mutagenesis 100-1,000 fold over wildtype levels including insertions, deletions, base substitutions and the formation of extrachromosomal circular DNAs (eccDNAs). Extrachromosomal DNA circles (eccDNA) contain repetitive elements, and we want to investigate the role of CAG trinucleotide repeats in eccDNA formation. We find that the patterns of mutagenesis, recombination, and the generation of extrachromosomal DNA circles (eccDNA) resemble those found in human tumor DNA. We will also investigate the role of various v repair proteins in the DNA damage response and elucidate the possible roles of these proteins in BIR. To this end we explore three (open full item for complete abstract)

Committee: Michael Leffak Ph.D. (Advisor); Kwang-Jin Cho Ph.D. (Committee Member); Michael P. Markey Ph.D. (Committee Member); Michael Kemp Ph.D. (Committee Member); Quan Zhong Ph.D. (Committee Member) Subjects: Biomedical Research

MS, Kent State University, 2023, College of Arts and Sciences / Department of Biological Sciences

Eastern redcedar (Juniperus virginiana L. var. virginiana) is a native species currently invading open areas and grasslands outside of its original range in the United States. I studied the eastern redcedar's (ERC) invasion patterns in the Lakeside Daisy State Nature Preserve (LDSNP), a short grass prairie located on the Marblehead Peninsula in Ohio, examining the changes in the genetic diversity and structure of the encroaching population. I investigated the relative importance of long-distance dispersal vs. diffusion in the invasion of this short grass prairie by ERC. I used eight microsatellite marker loci and a database of single nucleotide polymorphisms to infer gene flow from external sources vs. within-population recruitment. I found that the older trees in this preserve were less than fifty-years-old, indicating that the population was established between 1970 and 1980. When I grouped trees into five age categories of 10-year increments, we found that the allelic diversity, as indicated by the average number of alleles per locus, increased as the age of the trees decreased. Principal Coordinate Analysis showed two distinct groups of trees in the LDSNP that I investigated further using soil type. Analysis of the population structure of the ERC trees using ADMIXTURE revealed three ancestral clusters in the ERC populations. All ancestral clusters are present in all age groups, suggesting that there is continual input of genetic information from the ancestral clusters. Overall, my findings indicate that ERC encroachment of the LDSNP results from multiple and reiterated gene flow events from the edge of the range through animal-mediated seed dispersal at short and intermediate distances.

Committee: Oscar Rocha (Advisor); David Ward (Committee Member); Sangeet Lamichhaney (Committee Member) Subjects: Bioinformatics; Conservation; Genetics; Natural Resource Management; Plant Biology; Plant Sciences; Range Management

Doctor of Philosophy (PhD), Wright State University, 2023, Biomedical Sciences PhD

Faithful DNA replication is essential to maintain genomic integrity. Compromises in this process are among the prime causes of cancer and other genetic disorders. Among several factors that can interfere with error-free DNA replication, the formation of non-B DNA structures by microsatellite sequences is critical. Microsatellites are 1-9 bp long tandem repetitive regions that can form secondary structures like hairpins, triplex, Gquadruplex etc. and undergo expansions due to replication fork stalling to cause several diseases. Hairpin forming microsatellites have been shown to induce DNA DSBs and lead to genetic instability and mutagenesis. The goal of this study is to understand the effects on genome stability of triplex and G quadruplex secondary structures formed by the homopurine-homopyrimidine (Pu/Py)88 microsatellite sequence. We hypothesize that this sequence can induce microsatellite instability, genetic instability, and mutagenesis through break induced replication (BIR). Our study shows that the (Pu/Py)88 sequence generates DNA DSBs, is unstable in a replication polarity dependent manner and shows a high frequency of mutagenesis. The pattern of mutagenesis suggests that BIR may function to repair replication- dependent DNA DSBs. To investigate whether triplex or G quadruplex structures are responsible for this instability, we generated cell lines that can specifically form either of these structures. Our data shows that both structures are unstable, but the G quadruplexes are more deleterious between the two. To determine other reasons leading to mutagenesis we studied the ability of triplex and G quadruplexes to form extrachromosomal DNA (eccDNA). Our data reveals that the non-B DNA structures can generate eccDNA which cause elevated mutagenesis and gross chromosomal rearrangements. Since our data suggests BIR functioning in the cells for DNA repair, we focused on understanding the role of fork remodeling proteins that operate in BI (open full item for complete abstract)

Committee: Michael Leffak Ph.D. (Advisor); Courtney Sulentic Ph.D. (Committee Member); Michael Kemp Ph.D. (Committee Member); Weiwen Long Ph.D. (Committee Member); Yong-jie Xu Ph.D. (Committee Member) Subjects: Biochemistry; Molecular Biology

Master of Science (MS), Wright State University, 2022, Biochemistry and Molecular Biology

We have previously documented our evidence of genetic instabilities at the (Pu/Py)78 and (ATTCT)47 sequences and our reasoning for identifying break-induced replication (BIR) as the mode of repair responsible for the mutations in the DNA flanking the unstable inserts. Now, as our lab investigates the protein mechanisms at play in the BIR pathway taking place at these sites, we are also expanding our knowledge of how this mechanism extends into the pathways responsible for forming extrachromosomal circular DNA (eccDNA) molecules. We have documented the phenomena posed as the driving factors for eccDNA formation in our systems containing (Pu/Py)78 and (ATTCT)47. Therefore, in this defense, we worked to uncover how STN1, COPS2, Pol and, generally, BIR function to produce eccDNAs in mammalian cells containing these unstable DNA sequences using inverse PCR (iPCR) to detect circular DNAs being generated in the genomic contents of these cells before and after knockdown of the proteins of interest.

Committee: Michael Leffak Ph.D. (Advisor); Kwang-Jin Cho Ph.D. (Committee Member); Weiwen Long Ph.D. (Committee Member) Subjects: Biochemistry; Molecular Biology

Master of Science (MS), Ohio University, 2021, Environmental Studies (Voinovich)

The state of Ohio is currently assessing the merits of opening a harvest season on Lynx rufus following their removal from the state threatened species list in 2014. Bobcats were extirpated from Ohio by 1850 but have naturally recolonized in the 21st century. Prior research has uncovered two genetically distinct subpopulations in the state with one occurring in the eastern region, and one in the southern. In assessing the current state of L. rufus in Ohio, genetic analysis will paint a better picture regarding genetic admixture of the two subpopulations. We additionally analyze demographic biases in road mortality in order to quantify the effect on population growth trends in the state. In the subsequent decades following L. rufus reestablishment in the state, abundance is increasing as indicated by increase of verified sightings. Refining previous population assessments, we determined that the formerly distinct subpopulations have now thoroughly admixed. Analysis of road mortality specimens demonstrates a bias towards males and dispersal-aged individuals, leading to lower actual recruitment than expected. Based on life tables, road mortality does lead to a reduction in net reproductive rate, though this reduction does not appear to be significant.

Committee: Nancy Stevens (Committee Chair); Stephen Spear (Committee Member); Viorel Popescu (Committee Member); Geoff Dabelko (Committee Member) Subjects: Ecology; Environmental Studies

Doctor of Philosophy, The Ohio State University, 2021, Biomedical Sciences

Cancers begin through acquisition of genomic alterations in normal cells, leading to uncontrolled cell division. However, cancer cells continue to accumulate alterations throughout the disease course. Therefore cancer in a patient is a continually changing entity subject to microevolution. This leads to tumor heterogeneity, or genetic diversity within a cancer case. Heterogeneity significantly complicates cancer diagnosis and treatment, as different cancer cells in the same patient may behave and respond differently. Current research and clinical paradigms of cancer inspect the disease at one or a few fixed time points, for instance at a patient's oncologist visits. Furthermore, most clinical and research assays of cancer in patients analyze only the small subsets of cancer cells obtained through singular biopsies. Through studying mutation and heterogeneity, we can formulate models of cancer as the dynamic process that it is, and explore the temporal and spatial gaps in between the currently studied snapshots of cancer. In this work, we first investigate microsatellite instability (MSI), a prolific mutational pattern present in subsets of human cancers. We introduce a new software algorithm, MANTIS, which uses next-generation sequencing data to quantify the accumulation of MSI rather than its mere presence or absence. Applying this to a large cohort of 11,139 cancers from 39 types, we identify MSI in 3.8% of cases, including adrenocortical carcinoma where MSI had not previously been characterized. These findings have direct clinical applicability, as tumors with MSI are frequently sensitive to checkpoint inhibitor immunotherapy. Our analysis of such a diverse cohort highlights the potential of large-scale sequencing to identify and characterize rare phenotypes which may benefit subsets of patients. Another means to assess changes in tumor heterogeneity over time is through subclonal modeling. Subclones provide a theoretical framework to approximate tumor hete (open full item for complete abstract)

Committee: Sameek Roychowdhury MD, PhD (Advisor); Robert Baiocchi MD, PhD (Committee Member); Lang Li PhD (Committee Member); Ewy Mathé PhD (Committee Member); Lianbo Yu PhD (Committee Member) Subjects: Bioinformatics; Biomedical Research; Genetics; Oncology

Doctor of Philosophy, The Ohio State University, 2018, Biomedical Sciences

Objective: Ewing Sarcoma is a pediatric bone malignancy initiated by a t(11;22) chromosomal translocation that produces the EWS/FLI oncoprotein. EWS/FLI transcriptionally activates and represses its target genes to mediate oncogenic reprogramming. Expression of its up-regulated targets correlates with EWS/FLI binding to associated GGAA-microsatellites, which show length polymorphisms. These microsatellite polymorphisms may critically affect EWS/FLI-responsiveness of key gene targets. For example, NR0B1 is necessary for EWS/FLI mediated oncogenic transformation, and we found a “sweet-spot” of 20-26 repeat length as optimal for EWS/FLI mediated transcriptional activity at NR0B1 through clinical observations and in vitro studies. The mechanism underlying this optimal length, however, is unknown. Methods: We explored the stoichiometry and binding affinity of EWS/FLI for different GGAA-repeat lengths through biochemical studies, including fluorescence polarization, ChIP-seq, and RNA-seq, combined with bioinformatics analysis. Additionally, use of EWS/FLI deletion constructs has been critical for elucidating the particular binding behavior of EWS/FLI at different microsatellite repeat lengths. Luciferase reporter assays, anchorage-independent growth and proliferation assays, as well as CRISPR technology have extended our findings to the in vivo setting. Finally, microscopy studies including use of confocal and transmission electron microscopy (TEM) have contributed visual characterization of the specific biochemical mechanisms we are investigating. Results: CRISPR-mediated deletion of the NR0B1 GGAA-microsatellite in Ewing sarcoma cells provided our field with the first in vivo evidence for the necessity of EWS/FLI binding at GGAA-microsatellites for anchorage dependent growth. Our biochemical studies, using recombinant ¿22 (a version of EWS/FLI containing only the FLI portion) demonstrate a stoichiometry of one monomer binding every two consecutive GGAA-repeats on (open full item for complete abstract)

Committee: Stephen Lessnick (Advisor); Michael Freitas (Committee Chair); Dennis Guttridge (Committee Member); Charles Bell (Committee Member) Subjects: Biomedical Research

Doctor of Philosophy, The Ohio State University, 2014, Horticulture and Crop Science

The genus Phlox is a staple of gardens worldwide that includes species admired for beauty and versatility in gardens, constructed landscapes, containers, and as cut flowers. Extensive breeding and selection has occurred in three primary species: Phlox drummondii, P. paniculata, and P. subulata, but the genus includes other species with ornamental value. Phlox L. (Polemoniaceae) includes approximately 65 species primarily endemic to North America; 20-23 species occur in the eastern U.S. and 40-45 in the west. The eastern species are a polymorphic group organized into 6 subsections that include the three main cultivated species and up to 20 related, rarely cultivated species. Thus, the species diversity of Phlox has barely been applied for ornamental use. The widespread availability of diverse germplasm can contribute not only to new cultivated forms but also to a greater understanding of species diversity and relationships. Such interest has made Phlox a priority genus for conservation at the Ornamental Plant Germplasm Center. This work describes the development, partial characterization, and manipulation of Phlox germplasm. Phlox germplasm collection development began in 2010 with an effort to collect all eastern species from natural populations throughout their native ranges; 187 accessions were collected from wild populations of 22 eastern species during a series of expeditions. Another 166 accessions were of cultivated origin; these were used for comparison to wild-collected material. The 353 accessions represent the most comprehensive germplasm collection of Phlox to date. This germplasm was first characterized by estimation of genome size using flow cytometry and ploidy estimates by chromosome counts. Genome size was surveyed in 287 accessions; 165 accessions were of wild origin and the rest were cultivars. Most accessions were diploid, but genome size was variable; both tetraploid and hexaploid populations were found in a species where it had n (open full item for complete abstract)

Committee: Pablo Jourdan (Advisor); Mark Bennett (Committee Member); David Francis (Committee Member); John Freudenstein (Committee Member) Subjects: Horticulture

Master of Environmental Science, Miami University, 2014, Environmental Sciences

Social behaviours serve many functions including conflict resolution and stabilizing group dynamics. Relatives may engage in more affiliative behaviours and be in frequent close proximity with each other. The distribution of food can increase intragroup competition and agonistic behaviours. I examined the influence of relatedness and food distribution on the social behaviour and proximity between free-roaming cats in a colony. To determine relatedness, individuals were genotyped at ten polymorphic microsatellite loci. Food was manipulated in dispersed and clumped treatments. Data included affiliative, agonistic and investigatory behaviours and the frequency of times cats were within 1 meter proximity to conspecifics. I compared behaviour/proximity data to relatedness data for each food treatment. Relatedness did not influence behaviour or proximity between conspecifics. Although food distribution did not influence behaviour or proximity between individuals within the entire colony, agonistic behaviours were influenced by the distribution of food at the subgroup level.

Committee: Nancy Solomon (Advisor); Thomas Crist (Committee Member); Brian Keane (Committee Member); Ann Rypstra (Committee Member) Subjects: Animals; Biology; Ecology; Genetics; Zoology

Doctor of Philosophy, The Ohio State University, 2013, Evolution, Ecology and Organismal Biology

The genus Viola is a large and diverse group of flowering plants. The objectives of this study were to develop and explore new morphological and molecular tools with horticultural and systematic applications. Chapter 1 employed digital image analysis software, Tomato Analyzer, for flower morphology analysis of a 127 accession collection of sect. Melanium violets ("pansy group"). Seventy-seven traits associated with shape, size, and color were scored separately as categorical or continuous variables. The qualitative analysis was favored, capturing more of the variation and receiving higher bootstrap support in cluster analysis dendrograms. Cluster and ordination analyses indicated that the presence of blotch was the primary grouping factor, and secondarily, measures of color and shape (e.g., petal width). Uniformity across accessions of some hybrid morphotypes (e.g., "white with blotch") led to tight clustering across analyses. There were no significant correlations between clustering patterns and accessions' originating country or parent company, as had been previously reported. Chapter 2 builds on the morphological analysis described in Chapter 1 by utilizing sequence-related amplified polymorphism (SRAP) markers to further characterize the collection of Melanium violets. Here, SRAP fragments indicated no significant differences between the horticultural classes of violets, though more were generated from species types than hybrid types of the same ploidy. Bayesian analysis suggested distinctive structure clusters within the collection, but was obscured by high levels of admixture. Some color forms (white, white with blotch, yellow with blotch, and orange) tended to cluster strongly together. Correlation analysis of morphological and molecular datasets, as well as analysis of a combined dataset, underscored the conclusion that some genetic lines could be generalized by blotch presence and flower color. The relationship between these data may help in (open full item for complete abstract)

Committee: Andrea Wolfe (Advisor); Pablo Jourdan (Committee Member); Laura Kubatko (Committee Member); Harvey Ballard (Committee Member) Subjects: Conservation; Horticulture; Plant Sciences

Master of Science, Miami University, 2013, Zoology

The biological importance of the unit of subspecies has been long debated. Much of the dispute revolves around criteria used to identify subspecies. Historically, taxonomic classifications were constructed using morphological traits. However, established phylogenies based on morphological data may not resemble those constructed using molecular data. Early work divided the prairie vole (Microtus ochrogaster) into 7 subspecies using morphological characteristics, but a morphometric analysis of three subspecies showed no consistent differences among them. I tested the hypothesis that M. ochrogaster subspecies delimitation based on molecular data will be congruent with the current subspecies classification based on morphology. Microsatellite data from the 7 subspecies suggested ~90% of molecular variation was within subspecies. A cluster analysis indicated there were two genetic groups, which do not correspond to existing subspecies or geography. My molecular data failed to support the current subspecific classifications and suggest they may need to be reevaluated using integrative taxonomy.

Committee: Nancy Solomon PhD (Advisor); Brian Keane PhD (Committee Member); David Berg PhD (Committee Member); Richard Moore PhD (Committee Member) Subjects: Animals; Biology; Evolution and Development; Genetics; Systematic; Zoology

PhD, University of Cincinnati, 2010, Arts and Sciences: Biological Sciences

Biological invasions have received considerable attention because of the increasing frequency with which they occur and the damage they can inflict on ecosystems. However, invasions are ideal study systems not only because of the insight they provide about management and preservation of biodiversity, but also because they can be used to answer a variety of ecological and evolutionary questions. In this series of studies I used the invasions of tropical geckos in urban habitats to address questions about range expansion and species replacement during invasion of an occupied niche. I used both the invasion of A-clones and replacement of B-clones of Lepidodactylus lugubris in Hawaii and the invasion of Hemidactylus mabouia and replacement of H. garnotii in Florida as models to test hypotheses about the process of range expansion and species replacement. To test hypotheses about the mechanisms and consequences of range expansion at multiple spatial scales, I developed 12 novel microsatellite markers in H. mabouia and used them to determine patterns of gene flow at both a very fine scale (tens of meters) and at a very large scale (statewide). To test hypotheses about species replacement, I used both laboratory studies and field studies to document mechanisms and timing of species replacement during invasion. In L. lugubris, I used controlled laboratory experiments to determine the behavioral mechanisms underlying the advantage of A-clones in the human environment. In H. mabouia, I used field census data from many locations in Florida to determine the rate at which H. garnotii was displaced during invasion. I found that dispersal was limited at a very fine spatial scale in H. mabouia, and that population structure arises at the leading edge of range expansion but erodes as the populations approach migration-drift equilibrium. I also demonstrated that human-mediated dispersal at the statewide scale plays a role in the rapid range expansion of H. mabouia. These findings dem (open full item for complete abstract)

Committee: Kenneth Petren PhD (Committee Chair); Eric Maurer PhD (Committee Member); Stephen Matter PhD (Committee Member); Michal Polak PhD (Committee Member); George Uetz PhD (Committee Member); Gisela Garcia-Ramos PhD (Committee Member) Subjects: Ecology

MS, University of Cincinnati, 2010, Arts and Sciences: Biological Sciences

Gene flow among adjacent populations of two different species and their putative hybrids has implications for allelic variation in all three groups, which could affect the evolution of breeding systems in some plant species. In the case of interspecific hybridization between two Schiedea species, both woody shrubs in the mountains of Maui, the genetic relationship between putative hybrids and the parental populations is largely unknown. The two species possess different breeding systems: Schiedea salicaria is gynodioecious while Schiedea menziesii is hermaphroditic, although some females have been detected in greenhouse-grown progeny of S. menziesii. We suspect there is an open pathway for gene flow through which the male sterility allele found in S. salicaria could possibly be passed to S. menziesii through a natural hybrid zone. To detect discernable maternal gene flow, chloroplast microsatellite markers were developed at five loci to genetically characterize populations of the two species and the putative hybrids. Thirteen different haplotypes were observed across the five loci. Each haplotype was observed in only one of the three groups, suggesting strong sub-population structure with no recent maternal gene flow. The genetic patterns observed give indication of unidirectional pollination allowing for the possibility of nuclear gene flow through the pollen to pass along the male sterility allele.

Committee: Theresa Culley PhD (Committee Chair); Steven Rogstad PhD (Committee Member); John Darling PhD (Committee Member) Subjects: Botany

MS, University of Cincinnati, 2010, Arts and Sciences : Biological Sciences

Invasive populations undergo changes in genetic diversity during colonization and range expansion, which may influence adaptive ability and ultimately invasion success. Yet, surprisingly few studies have shown evidence of genetic bottlenecks expected for an invasive species. Ten individuals of the Common Wall Lizard (Podarcis muralis) from northern Italy were released in Cincinnati, Ohio during the early 1950's and has since spread to surrounding areas, reaching densities of 1500 individuals/acre where there is suitable habitat. Though this lizard has become a well established invasive in the Cincinnati region, little work has been done to quantify changes in Podarcis muralis genetic diversity during small scale range expansion. In this study, I compared genetic variation at eight microsatellite loci in the Cincinnati population to two contemporary European populations. The results show that a significant loss in genetic diversity occurred in the Cincinnati population indicating a past genetic bottleneck. Genetic bottlenecks subsequent to the initial colonization bottleneck were also detected in all but two of the seventeen subpopulations in the study. High levels of population differentiation were also found, even at small distances, which indicate minimal levels of gene flow between subpopulations. These results show that range expansion in the Cincinnati population does not occur through simple diffusion alone. Reports from citizen scientists indicate that accidental or intentional human introductions may be more common than previously thought in Cincinnati Podarcis muralis. Despite a severe genetic bottleneck, Podarcis muralis is thriving in its introduced range possibly due to an apparent lack of selective pressures. Few native lizards are present within the urban/suburban areas where they are found, there is an abundance of suitable habitat, and Cincinnati has a similar climate to northern Italy. Podarcis muralis should be closely monitored because they have t (open full item for complete abstract)

Committee: Kenneth Petren PhD (Committee Chair); Stephen Matter PhD (Committee Member); Eric Maurer PhD (Committee Member) Subjects: Ecology

PhD, University of Cincinnati, 2008, Arts and Sciences : Biological Sciences

Pyrus calleryana is an emerging invasive species that appears to have had a recent and rapid increase in the rate of population spread. The species is a very popular ornamental tree, with as many as 29 different cultivated varieties. The species was originally thought to be of little invasive potential due to its genetically-controlled self-incompatibility mechanism and clonal propagation methods, so that cultivars were essentially clones of the same source tree. Virtually unknown as an invasive ten years ago, naturalized populations have since been identified in 26 states. Genetic analyses show that cultivars are highly genetically structured and are polymorphic at the self-incompatibility locus. Invasive trees were also highly admixed hybrid progeny of these different cultivars. In cross-pollination experiments, all cultivars were capable of freely crossing, indicating all are functionally different at the self-incompatibility locus. Measures of reproductive and establishment ability were used to compare different cultivars and hybrid types in terms of an advantage in contribution to invasive populations. All groups were found to be highly fecund, have low mortality, and have high biomass accumulation. Invasive trees also produced greater numbers of seeds than cultivated individuals, indicating that invasive populations may have an increasing rate of spread due to high reproductive output. Cultivated populations, therefore, appear to be the source for invasive populations, and invasive populations are self-sustaining and composed of highly productive individuals. In the case of the Callery pear, availability of multiple cultivar types and widespread horticultural use seems to have allowed the species to not only naturalize, but also increase reproductive output.

Committee: Theresa Culley PhD (Committee Chair); Kenneth Petren PhD (Committee Member); Steven Rogstad PhD (Committee Member); Jodi Shann PhD (Committee Member); Sarena Selbo MS (Committee Member) Subjects: Botany; Ecology; Genetics

PhD, University of Cincinnati, 2006, Medicine : Molecular Genetics, Biochemistry, and Microbiology

Multicellular organisms are mosaic in nature because of genetic alterations that occur in somatic cells. There are many factors that can contribute to the formation of such alterations including aberrant DNA repair, environmental insults, epigenetic modification, errors in DNA replication and errors in chromosome duplication/segregation. To further the study of the distributions, frequencies and rates at which some alterations can occur, mouse reporter models were implemented. The Tg(aA-G11PLAP) transgenic mutation reporter mouse harbors an allele (G11 PLAP ) that is rendered incapable of producing its functional enzyme because of a reading frame shift caused by an insertion of 11 G:C basepairs. Spontaneous deletion of one G:C basepair from this mononucleotide repeat restores gene function, and cells with PLAP activity can be detected histochemically. G11 PLAP mice enable mutant cells to be visualized in situ and were used to study variation during early development, in the germline, under oxidative stress and in solid tumors. To study LOH in diverse cell types in the body another reporter model was implemented. Mice that carry two different fluorescent protein genes as alleles of a locus were generated to address this issue because LOH would change a cell's phenotype from bichrome to monochrome. As a step in assessing the utility of this approach, we derived MEF and ES cell lines from mice that carried two different fluorescent protein genes as alleles at the chromosome 6 locus, ROSA26. FACS showed that the vast majority of cells in each line expressed the two marker proteins at similar levels, but populations exhibited extrinsic and intrinsic noise with respect to expression. In addition, cells with a monochrome phenotype were frequent (10-4). In ES cells, all monochrome events were accompanied by allele loss. Mitotic recombination appeared to be the major cause, although UPD also appeared to have contributed to LOH. These cells provided a novel assay for studying (open full item for complete abstract)

Committee: James Stringer (Advisor) Subjects:

Master of Science, University of Toledo, 2011, Biology (Ecology)

The population genetic structure of three of the largest walleye spawning groups in Lake Erie is tested for consistency over time and space spanning 14 years, based on nine high-resolution nuclear DNA microsatellite loci. Previous genetic studies focused on a one-time genetic “snapshot”, with an earlier study by our laboratory finding that the genetic structure of three Lake Erie spawning groups along the southern shore - Maumee River, Sandusky River, and Van Buren Bay reefs - appeared similar in 2003, whereas most other spawning groups across Lake Erie were genetically distinctive. The present study analyzes the stability of genetic similarity patterns within and among 726 walleye spawning at these three sites across years and age cohorts in 1995, 1998, 2003, 2007, and 2008. Genetic patterns are evaluated using pairwise FST analog and contingency tests, AMOVA partitioning, and Bayesian assignment tests. Results reveal overall year-to-year consistency in genetic structure of walleye spawning at the three sites, with some annual variation in the Van Buren Bay reef group. Greater genetic divergence from the other groups is detected in the Van Buren Bay spawning group, which reflects greater geographic separation. Walleye spawning in the Sandusky and Maumee Rivers are genetically distinguishable from each other when data from all years are combined, which suggests possible sample size effect (i.e., annual sample sizes likely were not large enough to detect their genetic differentiation). No significant differences occur among age cohorts, between the sexes, or among sampling dates within spawning runs. Results demonstrate the importance of sampling over several years of walleye spawning runs in order to resolve fine-scale genetic relationships within an open lake system.

Committee: Carol Stepien PhD (Committee Chair); William Sigler PhD (Committee Member); Patrick Kocovsky PhD (Committee Member) Subjects: Biology; Conservation; Ecology; Environmental Science; Genetics; Natural Resource Management

Bachelor of Science (BS), Ohio University, 2010, Biological Sciences

The muskellunge (Esox masquinongy) is an important recreational fish species native to the northern and eastern United States. The species has a long history of stocking and hatchery propagation. In order for the best management practices to be implemented, the genetic variation and structure within and among stocks must be understood. Currently, muskellunge are classified into three subspecies corresponding to major drainages, but these designations are disputed. In this study, the genetic stock structure of muskellunge was investigated at two scales: at the species level and at the local population level for Ohio's muskellunge stock. Using mitochondrial DNA (mtDNA) sequence variation, I examined the range-wide intraspecific phylogeographic patterns of muskellunge. Using three nuclear microsatellite loci, I assessed local stock structure of hatchery and natural populations in Ohio. Very little mtDNA sequence variation and a lack of genetic structure among populations from throughout the range do not support the subspecies designations. Further, the widespread distribution of two similar haplotypes suggests recent dispersal from a single glacial refugium. High levels of microsatellite variation within and between Ohio populations identified significant stock structuring among populations. Recent bottleneck events do not appear to have reduced genetic diversity in the sampled populations. Based on my data, Ohio contains at least five genetic stocks that should be maintained as separate management units.

Committee: Matthew White (Advisor) Subjects: Biology; Genetics

Doctor of Philosophy, The Ohio State University, 2005, Statistics

As more and more dense, yet cost-effective, genetic maps become increasingly available, the focus of linkage analysis is shifting from testing for linkage signals to sufficiently localizing putative disease loci before fine mapping begins. Currently, there exists only a limited number of methods that provide confidence regions for the locations of trait loci. Among them is the confidence set inference (CSI) procedure based on the mean IBD sharing statistic for data from affected sib-pair studies described by Lin (2002) that deduces such regions with known lower bound on their coverage. Although this method has many attractive features, including avoidance of multiplicity adjustment for the number of markers scanned, its formulation poses some restrictions that limit its usefulness on practical applications. First, it assumes that all markers are 100% polymorphic, so that the IBD state at each of them is inferred unequivocally, an assumption rarely met in reality. Second, when the genetic map available is sparse, it tends to produce intervals that overcover the trait locus. Finally, its application requires knowledge of the IBD sharing distribution at the trait locus by an affected sib-pair. These probabilities are estimated using population disease characteristics that can be obtained through epidemiological studies with reasonable accuracy. However, there is a number of issues that renders this method of estimating the IBD distribution impractical. We propose several extensions that address some of the limitations of the CSI approach. First, we extend it to accommodate markers with incomplete polymorphism, thereby increasing its practical value. Next, we modify it so that it tests each location on the genome for its possibility to be the trait locus. This way, we obtain regions with known exact coverage probability, rather than placing a lower bound on it. Finally, a two-step application of the CSI approach promises to avoid using population disease characteristics (open full item for complete abstract)

Committee: Shili Lin (Advisor) Subjects: