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Moler, James C.Optimizing Approaches for Sensitive, High Performance Clustering of Gene Expressions
Master of Science, Miami University, 2011, Computer Science and Systems Analysis
This thesis presents several new algorithmic approaches to the problem of clustering conventional ESTs and high throughput gene expression data, which are implemented in the software tool PEACE. The d2 algorithm for sequence comparison is improved and enhanced with a novel two-pass extension, and a minimum spanning tree-based algorithm is used to cluster ESTs, providing an efficient and accurate solution. Furthermore, in order to address the unique challenges of high throughput sequencing technologies such as 454, Illumina and SOLiD sequencing, an adaptive d2 algorithm is introduced to handle variations in fragment length. The resulting tool compares favorably with other leading tools in the literature, including WCD, CAP3, and TGICL, on both EST and next-generation sequencing (NGS) data.

Committee:

John Karro, PhD (Advisor); Dhananjai Rao, PhD (Committee Member); Mufit Ozden, PhD (Committee Member)

Subjects:

Bioinformatics; Computer Science

Keywords:

clustering gene expressions; EST

Held, Jeremy B.Assessment of Genetic Diversity and Relatedness in an Emerald Ash Borer-Resistant Green Ash Population
Bachelor of Science (BS), Ohio University, 2017, Environmental and Plant Biology
Populations of North American ash (Fraxinus sp.) are declining due to the introduction of emerald ash borer (EAB; Agrilus planipennis), a wood-boring beetle native to East Asia. At Oak Openings Preserve Metropark in northwest Ohio, a population of green ash (F. pennsylvanica) exists in which 99% of the trees have succumbed to emerald ash borer, but a small number of trees have remained healthy. These “lingering” ash may be closely related, thus sharing common alleles that may be contributing to EAB resistance. However, relatedness may also indicate an overall lack of genetic diversity in the lingering ash relative to the former intact population. To compare genetic diversity, 39 individuals were sampled from the lingering population as well as from 19 individuals that declined significantly or suffered above-ground mortality due to EAB infestation, but developed stump sprouts. This essentially creates a temporal sampling of the population, with the susceptible and lingering samples allowing estimation of the gene pool pre- and post-EAB arrival, respectively. Genotyping of trees at 12 EST-SSR loci revealed similar levels of allelic diversity and heterozygosity between the two groups. In addition, relatedness was not significantly higher among post-EAB trees (p>0.05), but a spatial autocorrelation analysis revealed that genetically similar trees were clustering close together in geographic space. These results suggest that green ash are buffering population loss and maintaining genetic diversity, probably through life history characteristics (e.g. dioecy, wind-pollination). Knowledge of the lingering ash’s genotypes will aid any breeding efforts undertaken by the US Forest Service to preserve ash on the North American landscape.

Committee:

Harvey Ballard (Advisor)

Subjects:

Conservation; Ecology; Genetics; Plant Biology

Keywords:

EAB; emerald ash borer; Agrilus planipennis; green ash; Fraxinus pennsylvanica; tree genetic diversity; relatedness; EST-SSRs

Jo, Young KiManagement of dollar spot and gray leaf spot on turfgrass
Doctor of Philosophy, The Ohio State University, 2005, Plant Pathology
Most diseases of turfgrass are caused by fungal and oomycete pathogens. My dissertation research focused on assessing fungicide sensitivities within Sclerotinia homoeocarpa (causal agent of dollar spot) and genetics of Pyricularia grisea (causal agent of gray leaf spot)-resistance in St. Augustinegrass. As with other intensively managed diseases, the heavy use of fungicides has led to the development of resistance in S. homoeocarpa to several classes of fungicides. The goal of my work was to develop in vitro fungicide sensitivity assays using single discriminatory concentrations for thiophanate-methyl, propiconazole and iprodione and to use these assays to determine the prevalence of fungicide insensitivities within S. homoeocarpa isolates recovered from golf courses throughout Ohio. Discriminatory concentrations for these fungicides were determined as thiophanate-methyl = 500 ug a.i./ml; propiconazole = 0.1 ug a.i./ml; and iprodione = 1 ug a.i./ml. Replicated field trials correlating results of in vitro assays with fungicide efficacy in the field were conducted in 2002 and 2003. When used to screen 192 S. homoeocarpa isolates from 55 golf courses throughout Ohio, the in vitro assays revealed that thiophanate-methyl and propiconazole insensitivity was prevalent (34 and 18 golf courses, respectively). The prevalence of iprodione insensitivity in S. homoeocarpa was low (1/55 golf courses). P. grisea causes blast in rice and gray leaf spot in turfgrass. Virulence assays performed in this study revealed that some P. grisea isolates collected from rice could also infect St. Augustinegrass. To determine whether similar genetic mechanisms are involved in mediating the P. grisea -resistance in these two hosts, a P. grisea -infected rice expressed sequence tag (EST) library was screened using cDNA from P. grisea -infected St. Augustinegrass. Reverse northern, web-based virtual northern and northern (RNA blot) approaches were used to identify 30 rice ESTs that were either induced or suppressed in St. Augustinegrass following infection by P. grisea . These ESTs were classified into six different putative function groups according to the NCBI database of Clusters of Orthologous Groups of proteins (COGs) and potentially involved in P. grisea -resistance in these two graminaceous hosts.

Committee:

Michael Boehm (Advisor)

Subjects:

Agriculture, Plant Pathology

Keywords:

fungicide; homoeocarpa; grisea; TURFGRASS; DOLLAR SPOT; EC50; EST

Shyshynova, InnaA Novel Approach to Identification of Diagnositc Markers in Prostate Cancer
Doctor of Philosophy, Case Western Reserve University, 2006, Biochemistry
Prostate cancer is the most common malignancy and second leading cause of cancer deaths in men. The effectiveness of its cure depends on a timely and accurate diagnosis of the disease as well as application of appropriate therapeutic strategies. We designed an integrated program aimed at identification of prospective marker genes based on their expression properties and applied it to prostate cancer analysis. Our strategy employs in silico expression profiling (an advanced version of human EST database mining) and microarray-based analysis of genes under negative regulation of tumor suppressor genes. A combined list of prospective candidate genes was assembled, which contained a number of known cancer markers, thus demonstrating feasibility of the methodology used. Expression profiles of other candidates were characterized in a large set of tumor cell lines and tumor samples using custom cDNA microarray hybridization, RT-PCR and Northern blots. KIAA1181, MAL2, MGC13170, and FLJ30428, our most promising candidates, were investigated by real-time PCR in prostate cancer and normal tissue samples. KIAA1181 and MAL2 were capable of distinguishing between cancerous and cancer-free prostate as effectively as PSA or PSMA. This approach, proven feasible by the present study, can now be extended to marker identification of virtually any cancer or disease.

Committee:

Andrei Gudkov (Advisor)

Subjects:

Biology, Molecular

Keywords:

prostate cancer marker; tumor suppressor gene; EST data mining; microarray hybridization; prostate specific antigen

Zhang, YuanMST Based Ab Initio Assembler of Expressed Sequence Tags
Master of Computer Science, Miami University, 2010, Computer Science and Systems Analysis
In the thesis we present a new algorithm for the assembly of ESTs based on a minimum spanning tree construction. By representing the EST input as a graph, quickly assigning edge weights with a new distance heuristic for detecting edge overlap, and calculating a minimum spanning tree, we find that we can use a quick transversal of this tree to accurately order the EST set, filter out extraneous ESTs, correct errors and infer the actual transcript sequence from which the set was generated. Implementing this into a software tool, we find that our tool gives us results better than CAP3, the leading EST assembly tool in the literature. In this paper we will explain the EST assembly problem, outline the assembly algorithm, and present a quantitative comparison against the results of CAP3.

Committee:

John Karro, PhD (Advisor); Mufit Ozden, PhD (Committee Member); Chun Liang, PhD (Committee Member)

Subjects:

Bioinformatics

Keywords:

EST assembly; assembler; minimum spanning tree

Torto, Gertrude AyerchooFunctional Genomics of Extracellular Proteins of Phytophthora Infestans
Doctor of Philosophy, The Ohio State University, 2002, Plant Pathology

Genomics offers new perspectives for the discovery of novel genes in the oomycetes, a unique group of eukaryotic microbes comprising saprophytes as well as pathogens of plants and animals. Among the oomycetes, the most devastating plant pathogen is the potato and tomato late blight pathogen Phytophthora infestans. Currently tens of thousands of expressed sequence tags (ESTs) are available for P. infestans. The challenge of the post-genomic era is to link a sequence to a phenotype (functional genomics) with as little experimental effort as possible. In the first study, we combined EST data mining with functional assays to identify extracellular effector proteins from P. infestans, which can manipulate plant molecular and cellular processes to induce defense or disease like responses. We developed the PexFinder algorithm for automated identification of Phytophthora extracellular proteins (Pex). Using a virus based high throughput functional assay to express Pex cDNAs in Nicotiana benthamiana and tomato, we identified two novel necrosis inducing effectors crn1 and crn2, which are members of large gene family. crn1 and crn2 were demonstrated to be expressed during P. infestans infection on tomato. In addition, crn2 induced defense related genes in tomato.

In a second study, we characterized a Pex cDNA, pipg1 which represents the first endopolygalacturonase (endoPG) described from P. infestans. Generally, endopolygalacturonases are plant cell wall degrading enzymes primarily found and characterized extensively in plants and fungi. We showed that pipg1 is a member of a gene family and is expressed in both preinfection and infection stages. Phylogenetic analyses showed an affinity of pipg1 to fungal endoPGs, a feature that contrasts with phylogenies obtained with ribosomal sequences or compiled mitochondrial and chromosomal genes.

In a third study, We generated ESTs from a cDNA library constructed from mRNA of Saprolegnia parasitica, an oomycete pathogen that causes saprolegniasis in fish. We performed preliminary comparisons of abundance of selected ESTs between S. parasitica and P. infestans and assessed the implications for S. parasitica. The long-term objective of this project is to develop genomic resources from diverse oomycete pathogens for comparative genomics.

Committee:

Sophien Kamoun (Advisor)

Keywords:

functional genomics; secreted proteins; PexFinder; Phytophthora infestans; Saprolegnia parasitica; endopolygalacturonase; EST; data mining; horizontal transfer; thiamine; Proteases

Schott, Jacob RyanThe Kafka Case: Constructing Kafka, Deconstructing the Self in French Letters
Doctor of Philosophy, The Ohio State University, 2010, French and Italian
This dissertation studies the presence and importance of Franz Kafka’s writing in French letters of the twentieth century. Though born in Prague and a speaker of German, Kafka’s work has been instrumental to many French thinkers, and I study three in particular: Marthe Robert, Maurice Blanchot, and Alain Robbe-Grillet. I analyze the critical writings of Robert and Blanchot, as they are two of the most comprehensive and prolific writer’s on Kafka. Their theoretical writings will in turn be used to read and reevaluate the novels Dans le labyrinthe by Robbe-Grillet and Aminadab by Blanchot. This project may be divided into three parts. The first part consists of two chapters and relies on the critical work of Marthe Robert. In her career, she wrote three books devoted entirely to Kafka, and a cycle of four books which reference his writing with great frequency. In her criticism, several themes reappear that treat genre, the conventions of the novel, and the dualities that writers face between living their life, and crafting their art. In the light of her critical oeuvre, the second chapter uses Robert’s insights to read two novels that belong to a Kafkaesque tradition. In Dans le labyrinthe and Aminadab, I examine genre, rhetoric, and the problematic nature of interpretation. The second part consists of two chapters that rely on the critical work of Maurice Blanchot. Though he never wrote an entire book-length study devoted to Kafka’s text, Blanchot has written many articles that are dependent on Kafka. He studies the language of literature, the problems of commentary and interpretation, and the unique positioning of the author, who, alienated from him or herself, experiences a movement from je to il. The survey of Blanchot’s critical work is used to reexamine Dans le labyrinthe and Aminadab, and to use the novels as illustrations for some of Blanchot’s abstract ideas. The third part of this dissertation treats questions of selfhood and subjectivity. Writers who have discussed Kafka also exhibit a common interest in questions of subjectivity. This thematic, which is present in the entire project, is discussed at length in the fifth chapter, with the aid of Claude Morali’s Qui est moi aujourd’hui? This chapter analyzes how the discourse of subjectivity is related to childhood, a theme common to Kafka and the three French writers whom I have chosen. I conclude by questioning whether childhood may be used as a metaphor to help frame the questions I have studied regarding reading, writing, and the interpretation of literature.

Committee:

Karlis Racevskis, PhD (Advisor); Jennifer Willging, PhD (Committee Member); Eugene Holland, PhD (Committee Member)

Subjects:

Comparative Literature; Language; Literature

Keywords:

Kafka; Blanchot; Robbe-Grillet, Marthe Robert; Aminadab; Dans le labyrinthe; Claude Morali; De Kafka a Kafka; L'Espace litteraire; L'entretien infini; Faux Pas; La part au feu; Thomas L'Obscur; qui est moi aujourd'hui?