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Title: A FRAMEWORK FOR BIOLOGICAL DATA INTEGRATION AND FEATURE SELECTION IN LARGE DATA SETS
Creator: Gonzalez-Reymundez, Agustin
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The increasing volume of high-dimensional biological data (omics) has intensified the discovery of thousands of biomarkers across the different fundamental components of the cell (e.g., genome, transcriptome, proteome, epigenome) and allowed the characterization of complex phenotypes (e.g., metabolome, imaginome, phenome). However, the ability to integrate omics into informative results is constantly challenged by a seemingly ever-increasing volume of data. Furthermore, huge data sizes impose...
Show moreThe increasing volume of high-dimensional biological data (omics) has intensified the discovery of thousands of biomarkers across the different fundamental components of the cell (e.g., genome, transcriptome, proteome, epigenome) and allowed the characterization of complex phenotypes (e.g., metabolome, imaginome, phenome). However, the ability to integrate omics into informative results is constantly challenged by a seemingly ever-increasing volume of data. Furthermore, huge data sizes impose a tradeoff between how complex an omic integration algorithm can be and how much data it can handle (e.g., how fast can the algorithm be scaled to integrate large data sizes). In this dissertation, we explore statistical frameworks to face the challenges of modern omic data, including the integration of high-dimensional data of large sample sizes. We have developed a novel framework of competitive analytical performance compared with existing methods but suitable for omic data reaching biobank scales (i.e., hundreds of thousands of samples and variables). We implemented this method as an R package and showed its application on two traits of a complex molecular basis: cancer and regulation of energy intake and expenditure. In chapter one, we review the technologies and methods used to generate and integrate omic data. Chapter two describes our novel method and software of omic integration, shows examples in synthetic data, and evaluates its computational and analytical performance. Chapter three presents an application of our method to reveal a novel pan-cancer classification of tumors beyond the tissue of origin, regulated by distinct sets of molecular signatures. In chapter four, we present an application of our method to integrate phenomics data and identify patterns of energy balance regulated by genomic variation. Finally, in chapter five, we offer general conclusions to the entire thesis.
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Title: A cytogenetic investigation of sex expression in Spinacia
Creator: Bemis, William Putnam
Date: 1952
Collection: Electronic Theses & Dissertations

Title: A diallel analysis of bolt resistant germplasm in several Brassica species and the inheritance of lateral suppression and leaf number in broccoli (Brassica oleracea L. Italica group)
Creator: Keyes, Katherine A.
Date: 1987
Collection: Electronic Theses & Dissertations

Title: A genetic and morphological study of the diploid-tetraploid cross in the poinsettia, Euphoria pulcherrima Klotzsch
Creator: Milbocker, Daniel Clement
Date: 1966
Collection: Electronic Theses & Dissertations

Title: A genetic approach to understanding the evolutionary ecology of the family Hyaenidae
Creator: Califf, Katy J.
Date: 2013
Collection: Electronic Theses & Dissertations
Description: My dissertation combines molecular and behavioral data to examine the evolutionaryecology of the family Hyaenidae. More specifically, I focus on the evolution of adaptive geneticvariation in hyenas, the influence of this variation on fitness, and the genetic and ecologicalcauses and consequences of behavior. My dissertation consists of four chapters following theintroductory chapter. The first of these research chapters, Chapter 2, characterizes thediversity of three genes located within the...
Show moreMy dissertation combines molecular and behavioral data to examine the evolutionaryecology of the family Hyaenidae. More specifically, I focus on the evolution of adaptive geneticvariation in hyenas, the influence of this variation on fitness, and the genetic and ecologicalcauses and consequences of behavior. My dissertation consists of four chapters following theintroductory chapter. The first of these research chapters, Chapter 2, characterizes thediversity of three genes located within the major histocompatibility complex (MHC), and arecritical to the adaptive immune system. In addition to offering the first characterization ofthese loci in spotted (Crocuta crocuta) and striped (Hyaenidae hyaenidae) hyenas, this chapterdescribes the evolutionary history of alleles at each locus and documents the presence ofpositive selection acting to increase diversity at two out of three loci. The results of theseanalyses are consistent with the hypothesis that some shared selection pressure, rather thandiffering degrees of sociality, is the predominant force shaping MHC variation within the familyHyaenidae. Chapter 3 documents correlations between MHC variation and individual measuresof fitness in spotted hyenas, and suggest the importance of specific MHC alleles to longevityand immune system function. Chapter 4 investigates whether captive female spotted hyenasexhibit differences in their behavioral responses to odors originating from unknown males thatvary in degree of MHC similarity to the female. I found a significant correlation betweenaverage pairwise relatedness and time spent sniffing, such that females spent significantlylonger times investigating odors from males that were more closely related to them and frommales that were MHC-dissimilar to them. These data suggest that genetic variation mayinfluence hyena behavior, and that female spotted hyenas prefer the odor of males thatcontain dissimilar genotypes from them at functional (i.e. MHC) loci. Chapter Five presentsneutral microsatellite marker data from two populations of striped hyenas and examines howspace use and genetic relatedness are influenced by local population ecology. These datasuggest differences in the relationship between relatedness and space use between these twopopulations. Further, I show that the area occupied by the population inhabiting Shompole,Kenya has more than triple the ungulate (i.e. prey) density than does the area inhabited by theLaikipia, Kenya, population, whereas both populations exhibit the same hyena density. Femalehome range sizes in Shompole were significantly smaller in Shompole than in Laikipia,suggesting that the ecological differences in prey availability influence the amount of areaneeded by females to meet their food requirements.My dissertation utilizes both neutral and adaptive molecular marker data, incombination with behavioral data, as tools to address questions pertaining to the evolutionaryecology of hyenas. The results of my analyses demonstrate positive selection acting to increasevariation at functional loci, and show that this variation may indeed be integral to individualfitness in spotted hyenas. Further, I show that genetic variation may influence behavior inhyenas by affecting odor preference, and that hyenas may alter their space use patterns inresponse to local ecology. Overall, my dissertation offers molecular, behavioral, and ecologicaldata rarely available for large mammalian (non-model) species and contributes to the body ofknowledge regarding extant members of the family Hyaenidae.
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Title: A molecular genetic study of winter hardiness in canola (Brassica napus L.)
Creator: Song, Moontae
Date: 1994
Collection: Electronic Theses & Dissertations

Title: A nitrogen-responsive small peptide signaling mechanism modulates plant root system architecture
Creator: Lay-Pruitt, Katerina Sibala
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The plant root system changes dynamically in response to environmental cues. Plants utilize their root system for uptake of essential mineral nutrients that are heterogeneously distributed in the soil environment. Nutrient-dependent modulation of root system architecture (RSA) traits such as primary root growth, lateral root emergence, and the angles at which these roots grow allows for optimization of nutrient acquisition. Among signaling pathways by which plants may sense the availability...
Show moreThe plant root system changes dynamically in response to environmental cues. Plants utilize their root system for uptake of essential mineral nutrients that are heterogeneously distributed in the soil environment. Nutrient-dependent modulation of root system architecture (RSA) traits such as primary root growth, lateral root emergence, and the angles at which these roots grow allows for optimization of nutrient acquisition. Among signaling pathways by which plants may sense the availability of nutrients from the environment, small signaling peptide (SSP) pathways play important roles in optimizing root functions. These SSP pathways may further regulate molecular processes underlying RSA, such as the biosynthesis and transport of the major plant growth hormone, auxin. Characterization of these nutrient-responsive SSP pathways is thus of great importance and critical for understanding plant development in nutrient-poor environments. For my dissertation, I have identified and characterized a nitrogen (N)-responsive SSP pathway modulating root gravitropic response and lateral root development. Co-regulation of these RSA components by this module is proposed to prevent root outgrowth into N-poor regions and drive deeper root growth towards mobile nitrate (NO3-) resources stratified deeper in the soil profile. First, I show that a signaling pathway involving the CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) family of peptides and the CLAVATA1 (CLV1) receptor kinase, which is involved in N-dependent repression of lateral root emergence, also enhances root gravitropic response under N-limited conditions. Transcriptomic profiling of a clv1 mutant and CLE3 overexpressing lines identified Arabidopsis thaliana CENTRORADIALIS (ATC), a mobile protein previously characterized for its role in flowering regulation, as a downstream target of CLE-CLV1 signaling. Loss of ATC function significantly weakens root gravitropic response and has a moderate impact on lateral root emergence under low NO3- availability. ATC promoter activity and protein localization are also detected throughout the phloem and in the root columella cells, which are major centers for gravity sensing. Second, I demonstrate the relevance of ATC function on the molecular processes underlying root gravitropic response. While mutation in ATC does not impact gravity sensing via amyloplast sedimentation, it does inhibit the asymmetric transport of auxin needed for gravitropic bending. I determine that this occurs via the significant reduction of the PIN3 auxin efflux transporter in the vasculature and root tip of atc mutant lines. Lastly, I examine how the known roles of ATC in floral development could be implicated in root developmental processes. ATC binds to phosphatidic acid and phosphatidylserine, which is contrary to the binding capacity of its homolog FLOWERING LOCUS T (FT) to phosphatidylcholine and may contribute to its activity in N-limited environments. I also investigate the interaction of ATC and the transcription factor FD in the transcriptional regulation of PIN3. Although FD appears to have an impact on root gravitropic response, FD inhibits the expression of PIN3, suggesting potentially complex control of this gene via floral regulatory components. Taken together, the results presented in this dissertation contribute greatly to our understanding of how plant root architecture alters in response to N. These results can be further utilized in plant engineering strategies to regulate root growth in nutrient-limited soils.
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Title: AFLP, mtDNA, and microsatellite analysis of emerald ash borer population structure from Asia and North America
Creator: Bray, Alicia Marie
Date: 2009
Collection: Electronic Theses & Dissertations

Title: An investigation of the transcriptional dynamics during the Pseudoperonospora cubensis - Cucumis sativus interaction
Creator: Burkhardt, Alyssa Kay
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Downy mildew of cucumber (Cucumis sativus) is caused by the obligate oomycete, Pseudoperonospora cubensis, and the research described in the dissertation provides new insight on the transcriptional regulation within the pathogen through the mechanism of alternative splicing and investigates the transcriptional changes of the host genes within a resistant and susceptible interaction. Previously, the genome of cucumber and P. cubensis as well transcriptome of a compatible interaction between...
Show moreDowny mildew of cucumber (Cucumis sativus) is caused by the obligate oomycete, Pseudoperonospora cubensis, and the research described in the dissertation provides new insight on the transcriptional regulation within the pathogen through the mechanism of alternative splicing and investigates the transcriptional changes of the host genes within a resistant and susceptible interaction. Previously, the genome of cucumber and P. cubensis as well transcriptome of a compatible interaction between the plant and the pathogen were sequenced. In addition, one gene from P. cubensis was known to be alternatively spliced, but the breadth of alternative splicing across the transcriptome was unknown. Through the work described in this thesis, we investigated the breadth of alternative splicing across the entire transcriptome of P. cubensis over the time course of infection. We found P. cubensis genes are frequently spliced and have intron retention as the most common mechanism of alternative splicing with some evidence for the retention of the 5' or 3' end of the exon but no evidence for exon skipping. Furthermore, we found that alternative splicing occurred in genes encoding several types of proteins, including the effectors, which impact pathogenicity and virulence. In some cases, the frequency of alternative splicing was found to correlate with developmental stages of the pathogen and thus alternative splicing might play a role in regulating transcript abundance and availability during development.Advances in sequencing and bioinformatics also contributed to our work in advancing the knowledge of the transcriptomic changes in a resistant (PI 197088) or susceptible (Vlaspik) plant during an infection time course. Our work shows that while P. cubensis is able to enter the resistant plant leaf, it is not able to sporulate; in contrast, the pathogen is able to grow and sporulate in the susceptible host, Vlaspik. To investigate the transcriptional changes underlying resistance, we identified the differentially expressed genes between the resistant and susceptible plant lines over the time course of infection. We found that the resistant plant responded earlier to the pathogen, as demonstrated by a higher number of differentially expressed genes at earlier time points compared to the susceptible plant. In addition, we found changes in genes encoding proteins with functions in hormone-related processes, nutrition, and transportation that might indicate a role for some of these genes in initiating or responding to the resistance response in cucumber. Beyond identifying differentially expressed transcripts, we identified small RNAs in the host and pathogen, as small RNAs have a role in modifying gene expression. We found novel miRNAs in the pathogen and known and novel miRNA in the host and predicted potential targets for each miRNA within the cucumber transcriptome. Some of these miRNAs may have a role in mediating the response of the plant to the pathogen. In the future, work will be done to validate the roles of candidate resistance-associated genes and to validate the presence and role of miRNA in both the host and the pathogen. Some of this future work will involve incorporating other “omics” methods including metabolomics and proteomics in order to get a more complete understanding of the molecular changes in the plant during infection. Finally, strong candidates for resistance could be validated using the proposed in planta methods, which includes the development of transgenic cucumbers.
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Title: Analysis of genetic parameters for growth and carcass traits of Canadian Charolais cattle
Creator: Sexton, Dwight A. (Dwight Aaron)
Date: 1996
Collection: Electronic Theses & Dissertations

Title: Assessment of state-specific DNA methylation patterns to improve functional annotation of farm animal genomes
Creator: Corbett, Ryan James
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Over the past several decades, genetic advancements in the domestic pig (Sus scrofa) and other farm animal species have resulted in increased economic output and expanded use of these organisms as biomedical models to study human disease. However, limited functional annotation of the porcine genome—particularly in non-coding regulatory regions—hinders both identification of causal genes for complex traits and translational research capabilities. The Functional Annotation of Animal Genomes...
Show moreOver the past several decades, genetic advancements in the domestic pig (Sus scrofa) and other farm animal species have resulted in increased economic output and expanded use of these organisms as biomedical models to study human disease. However, limited functional annotation of the porcine genome—particularly in non-coding regulatory regions—hinders both identification of causal genes for complex traits and translational research capabilities. The Functional Annotation of Animal Genomes consortium seeks to map functional elements in domesticated animal genomes in part by performing sequencing assays to characterize the animal epigenome, as specific chromatin modifications have been shown to be predictive of regulatory regions. DNA methylation is the most ubiquitous epigenetic modification made to the DNA molecule, and in mammals occurs almost exclusively at cytosines in CpG dinucleotides. DNA methylation exerts regulatory effects through numerous mechanisms, including the occlusion of transcription factors at activating regulatory regions, and as such has been shown to play important roles in establishing spatiotemporal gene expression. Furthermore, differential methylation has been associated with genomic imprinting and stress-induced physiological changes in mammals. Assessment of DNA methylation in the pig and other farm animal species has thus far been limited in scope. In this dissertation, I have characterized state-specific DNA methylation patterns in farm animal genomes across a diverse collection of cell types, developmental stages, and environmental conditions, to enhance understanding of epigenetic gene regulation in livestock and poultry. First, I demonstrate that sorted porcine immune cells exhibit unique DNA methylation landscapes that are strongly correlated with local and distal gene expression as well as binding sites for transcription factors regulating immune cell-specific functions. The co-localization of immune cell differentially methylated regions with GWAS SNPs for immune-related traits supports the use of epigenomics assays to increase functional annotation of economically relevant genomic regions. Second, I show that development of four porcine fetal tissues (whole brain, liver, loin muscle, and placenta) is associated with increased differentiation of DNA methylation profiles that likely contributes to tissue-specific transcriptomes and transcription factor regulatory potential. I also report widespread allele-biased methylation in fetal tissues associated with breed-specific gene regulation as well as putative regions of genomic imprinting events. Third, I characterize associations between environmental stimuli and DNA methylation patterns in two studies. I show that piglet weaning correlates with changes in peripheral blood mononuclear cell DNA methylation, and that increased weaning stress is associated with increased methylation and decreased expression of T cell-enriched genes, suggesting a diminished adaptive immune response. Lastly, I assess the impact of broiler chick incubation parameters on cardiac DNA methylation and observe significant temperature-associated differential methylation of genes involved in heart morphogenesis. I identified differentially methylated and expressed genes between temperature treatments that may influence environment-driven differences in cardiovascular development. In conclusion, I have performed the most expansive survey of whole-genome DNA methylation in farm animal species to date and have identified thousands of putative regulatory elements influencing state-specific gene and phenotype expression. These data will be a valuable resource for future functional annotation efforts seeking to identify mechanistic links between genetic and phenotypic variation in animal species.
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Title: Biosynthesis of cyclic peptide natural products in mushrooms
Creator: Sgambelluri, Robert Michael
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "This work aims to describe cycloamanide biosynthesis and its capacity for cyclic peptide production, and to harness the pathway as a means to design and synthesize bioactive peptides and novel compounds."--From abstract.

Title: CNGB1 mutation in papillon dogs : the identification, characterization and cure
Creator: Winkler, Paige A.
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Progressive retinal atrophy (PRA) is an inherited retinal dystrophy that affects over 100 breeds of dogs. It is characterized by a bilateral retinal degeneration commonly resulting in blindness. Affected dogs typically present with loss of dim light vision, attenuation of retinal blood vessels and tapetal hyperreflectivity. The purpose of this study was to identify the underlying cause of PRA in Papillon dogs and to characterize the phenotype at the cellular and molecular levels. I identified...
Show moreProgressive retinal atrophy (PRA) is an inherited retinal dystrophy that affects over 100 breeds of dogs. It is characterized by a bilateral retinal degeneration commonly resulting in blindness. Affected dogs typically present with loss of dim light vision, attenuation of retinal blood vessels and tapetal hyperreflectivity. The purpose of this study was to identify the underlying cause of PRA in Papillon dogs and to characterize the phenotype at the cellular and molecular levels. I identified a mutation in the gene CNGB1 which accounts for 70% of the PRA in the Papillon dogs. The CNGB1 mutation involves a 6 base pair insertion and a 1 base pair deletion resulting in exon skipping and a premature stop codon cause by a frameshift. CNGB1 encodes the β-subunit of a cyclic nucleotide-gated ion (CNG) channel. CNGB1 has multiple splice variants expressed in rod photoreceptors, olfactory sensory neurons and other tissues. CNG channels are directly involved in rod phototransduction and olfactory transduction. The retinal phenotype of the CNGB1 affected dogs was characterized by in vivo and ex vivo analyses. Electroretinograms (ERGs) and behavioral vision testing were conducted to assess retinal function throughout the course of the disease. The CNGB1 affected dogs had decreased and abnormal rod function at the earliest age tested but cone function was preserved until 5.5 years of age. Histological analyses showed that the morphology of rod photoreceptors deteriorate slowly over the first ~1.5 years of life while cone photoreceptor morphology is preserved for longer.Adeno-associated viral (AAV) vector therapy was used to treat five CNGB1 affected dogs with a wild-type copy of canine CNGB1 cDNA. One eye was injected with a low titer (1x1012) of an AAV vector delivering CNGB1 cDNA, six eyes were injected with a higher titer (5x1012) and one eye was injected with a GFP-expressing construct as a vehicle and procedural control. All dogs treated with the AAV vector containing the wild-type copy of CNGB1 showed rescue of rod function that was maintained throughout the time course of the study (9 months).The CNGB1 affected dog olfactory phenotype was investigated using in vivo and ex vivo techniques. The olfactory epithelium and the olfactory bulbs were abnormal in the CNGB1 affected dogs when compared to control dogs. I developed a behavioral test that could assess olfactory function in the CNGB1 dogs. The CNGB1 affected dogs had decreased but not absent olfactory function. The detailed descriptions of the retinal and olfactory phenotypes, in addition to the successful gene replacement therapy trial, in the CNGB1 affected dogs have laid the ground work for future studies including working with clinicians to advance gene replacement therapy trials in human patients with mutations in the CNGB1 gene.
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Title: Carbon partitioning in engineered cyanobacterium for the study of feedback inhibition of photosynthesis
Creator: Abramson, Bradley William
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Cyanobacteria have promising potential to generate valuable compounds from light energy and atmospheric carbon dioxide (CO2). Many strains have been engineered to express pathways to generate a variety of products from pharmaceuticals to biofuels. Even with cyanobacteria’s high photosynthetic efficiencies most strains remain economically inviable. Many strains are grown in bioreactors where ample light and CO2 are provided, however, photosynthetic conversion of carbon and light to useful...
Show moreCyanobacteria have promising potential to generate valuable compounds from light energy and atmospheric carbon dioxide (CO2). Many strains have been engineered to express pathways to generate a variety of products from pharmaceuticals to biofuels. Even with cyanobacteria’s high photosynthetic efficiencies most strains remain economically inviable. Many strains are grown in bioreactors where ample light and CO2 are provided, however, photosynthetic conversion of carbon and light to useful compounds is limited. I propose photosynthesis is feedback limited, or sink limited, and the mechanisms of feedback inhibition can be alleviated in a Synechococcus elongatus PCC7942 strain engineered to export sucrose. By inducing expression of sucrose permease, in various salt conditions, the amount of sucrose can be tuned, which allowed us to measure a transient increase in the operating efficiency of PSII proportional to the rate of sucrose export. Concomitantly, an oxidized electron transport chain and lowered PSI acceptor side limitation were observed. These two photosynthetic parameters could be consequences of increased carbon fixation since the ratio of RbcL to PSII increases as well as greater accumulation of RbcS-GFP following sucrose export. These data suggest that sucrose export leads to greater carbon fixation and as a consequence increase light use efficiency within PSII. Furthermore, using this knowledge, we created strains that could partition carbon from growth and division to bioproduction and observed greater total and specific productivities for sucrose production. The ideas herein aid in the understanding of bioproduction strain inefficiencies and novel avenues for future genetic engineering for increased bioproduction.
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Title: Characterization of cyclic-GMP-AMP signaling and novel gene networks in the Vibrio Seventh Pandemic Islands of El Tor Vibrio cholerae
Creator: Severin, Geoffrey Blaine-Graessley
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Vibrio cholerae is the causative agent of the diarrheal disease cholera, for which there have been seven pandemics. The first six pandemics (1817-1923) have been attributed to strains of the classical biotype while the seventh pandemic (1961- current) is being perpetuated by circulating strains of the El Tor biotype. It is hypothesized that El Tor's acquisition of two unique genomic islands of unknown origins, Vibrio Seventh Pandemic Island 1 & 2 (VSP-1 & 2), potentiated its displacement of...
Show moreVibrio cholerae is the causative agent of the diarrheal disease cholera, for which there have been seven pandemics. The first six pandemics (1817-1923) have been attributed to strains of the classical biotype while the seventh pandemic (1961- current) is being perpetuated by circulating strains of the El Tor biotype. It is hypothesized that El Tor's acquisition of two unique genomic islands of unknown origins, Vibrio Seventh Pandemic Island 1 & 2 (VSP-1 & 2), potentiated its displacement of classical strains in both environmental and clinical reservoirs prior to the seventh pandemic. Despite their connection to the pandemic evolution of the El Tor biotype and the likelihood they encode a wealth of novel biological functions the majority of the 303036 ORFs in the VSP islands have remained uncharacterized. The works presented in the thesis represent examples of our collective efforts to understand the unique traits afforded to the El Tor biotype by the VSP islands. .In 2012, ten years after the initial discovery of the VSP islands, the cyclic di-nucleotide synthase DncV was identified in VSP-1 and shown to synthesize the novel second messenger cyclic-GMP-AMP (cGAMP). Despite this significant discovery, cGAMP remained an orphan second messenger in bacteria for six years. In Chapter 2, I present our identification of the first cGAMP signaling network in bacteria by connecting the synthesis of cGAMP to the allosteric activation of the VSP-1 encoded patatin-like phospholipase vc0178, now named CapV. This finding helped catalyze the revelation that homologous cyclic-dinucleotide signaling networks contribute to bacteriophage-immunity and are distributed widely across the bacterial phyla.dncV and capV represent just two of the 103031 ORFs encoded in VSP-1, therefore we hypothesized that cGAMP signaling may extend to include additional genes within the island. Bioinformatic analysis of VSP island genes performed in collaboration with the laboratory of Eva Top at the University of Idaho predicted that dncV was likely to share a biological pathway with the VSP-1 encoded putative deoxycytidylate deaminase vc0175, we have now named DcdV. In Chapter 3, I describe our ongoing efforts to understand the biological function of DcdV and the discovery of its novel negative regulator DifV.The work presented in this thesis has made fundamental contribution to understanding the pandemic evolution of the El Tor biotype and the utility homologous genes afford to their bacterial host while providing a roadmap for further exploration of the biological role of the VSP-1 and VSP-2 islands in pandemic V. cholerae.
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Title: Characterization of two large gene families in the sea lamprey
Creator: Chang, Steven
Date: 2013
Collection: Electronic Theses & Dissertations
Description: ABSTRACTCHARACTERIZATION OF TWO LARGE GENE FAMILIES IN THE SEA LAMPREYBySteven ChangThis dissertation employed molecular biology and bioinformatics to examine two large gene families in the sea lamprey, Petromyzon marinus. An integrative approach was used to define these gene families in order to ensure the validity of the size and members of each gene family. There are two chapters: Chapter 1 examines chemosensory gene expression in a specialized part of the olfactory system and Chapter 2...
Show moreABSTRACTCHARACTERIZATION OF TWO LARGE GENE FAMILIES IN THE SEA LAMPREYBySteven ChangThis dissertation employed molecular biology and bioinformatics to examine two large gene families in the sea lamprey, Petromyzon marinus. An integrative approach was used to define these gene families in order to ensure the validity of the size and members of each gene family. There are two chapters: Chapter 1 examines chemosensory gene expression in a specialized part of the olfactory system and Chapter 2 studies the expression of detoxification genes in the liver and gills in response to the lampricide, 3-trifluoromethyl-4-nitrophenol (TFM).CHEMORECEPTOR GENESFor this dissertation, I will restrict chemoreception to the detection of chemical signals in the nose (note: chemoreception includes taste), and is accomplished by detection of odorants in the environment by specialized sensory cells in the main olfactory epithelium (MOE). In certain tetrapods, a second sensory epithelium is also found in the nose, called the vomeronasal organ (VNO). Canonically, each epithelium represents the start of different olfactory pathways, which govern different behavioral responses. Each epithelium expresses different classes of chemoreceptor (CR) genes; the MOE expresses odorant receptors (ORs) and trace amine-associated receptors (TAARs), while the VNO expresses ORs, vomeronasal type-1 and type-2 receptors (V1Rs and V2Rs). The sea lamprey olfactory organ has one nostril and so has one nasal capsule, which is divided into two spatially distinct regions: the main olfactory epithelium (MOE) and the accessory olfactory organ (AOO). The MOE has been well studied in lampreys but the function of the AOO has eluded description for over 100 years. Based on other research and due to its proximity to the MOE, we hypothesized that the AOO represents an ancestral VNO. If this AOO is indeed an ancestral VNO, we expect a different connectivity to the central nervous system than from the MOE, and would expect expression of pheromone receptors (V1Rs and V2Rs). CR expression in the MOE and AOO of sea lamprey were examined. The differential expression of CR genes between the two epithelia was determined and the connectivity of the main and accessory epithelia was determined using neural tract tracing. Quantitative PCR confirmed and quantified the differential expression of specific genes in the main and accessory olfactory epithelia.CYTOCHROME P450 GENESThe second gene family to be explored is the cytochrome P450 family. P450 genes encode for steroidogenic or detoxification enzymes that are inducible by a substrate. As part of the strategy for controlling sea lamprey populations TFM is applied to streams. Very little is known at the molecular level of how TFM works to kill sea lamprey larvae, but based on responses by other organisms to xenobiotic substances, our hypothesis is that P450 genes are induced by exposure to TFM. P450 genes were predicted from the sea lamprey genome and larvae were exposed to TFM and gill and liver tissues were harvested over an 8-hour time course. Expression was confirmed using high-throughput sequencing and quantitative PCR. The immediate goal was to determine which P450 genes are induced by exposure to TFM. Alternatively, we generated a list of predicted Phase II detoxification enzymes in the event that P450 genes showed no difference in expression. The long-term goal is to use that knowledge to design more efficient and specific lampricides.
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Title: Characterizing gene expression changes and gene family evolution in the context of stress response in micro-algal species
Creator: Wu, Guangxi
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Algae are a large group of organisms that are of ecological and economical importance, as they play an important role in the food web and the biogeochemical cycle, and some of them are found to be suitable for biofuel production. Under stress conditions, they accumulate a large amount of storage lipid. However, the mechanistic details of this phenomenon are not yet well understood. Towards deciphering this phenomenon, I focused on characterizing gene expression changes and gene family...
Show moreAlgae are a large group of organisms that are of ecological and economical importance, as they play an important role in the food web and the biogeochemical cycle, and some of them are found to be suitable for biofuel production. Under stress conditions, they accumulate a large amount of storage lipid. However, the mechanistic details of this phenomenon are not yet well understood. Towards deciphering this phenomenon, I focused on characterizing gene expression changes and gene family evolution in the context of stress response in two micro-algal species. I first analyzed the global gene expression changes of the green alga model organism Chlamydomonas reinhardtii under normal and nitrogen deprived conditions. I found that global gene expression changes significantly under nitrogen deprivation; lipid metabolism was associated with up-regulated genes while DNA replication and photosynthesis were down-regulated. Second, I outlined global gene family evolution in the green algal lineage, particularly in the extent of duplicate retention and loss, and stress response evolution among duplicates. I found that stress responsive genes tend to be lineage-specifically retained and functional gains occur frequently in gene duplicates, shaping the stress response gene repertoire in a species-specific manner. Finally, I assembled and annotated the genome of the stramenopile Nannochloropsis oceanica CCMP1779, a phylogenetically distant species to C. reinhardtii considered for biofuel production. I found that N. oceanica responds similarly to nitrogen deprivation as C. reinhardtii, suggesting that general metabolic change is conserved across distantly related species. In addition, we compared the N. oceanica genome to Nannochloropsis gaditana to reveal its uniqueness in gene repertoire. We found that it is significantly different from N. gaditana and this might reflect physiological and biochemical differences. Overall, I reveal that though major metabolic changes under stress in micro-algae across diverse phylogeny are similar, the particular genes involved in stress response could be significantly different as they have been shaped by lineage-specific evolution. Thus, the species-specific mechanism in stress response cannot be deciphered by studying one model organism. Therefore, it would be beneficial to explore more micro-algal species, especially the ones considered for biofuel production, to discover their uniqueness in stress response towards identifying and engineering the ideal alga for biofuel production.
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Title: Component interaction in relation to mean expression of complex traits in a field bean cross
Creator: Duarte, Rodrigo Antonio
Date: 1961
Collection: Electronic Theses & Dissertations

Title: Composition of gut microbiota affects C. jejuni-mediated inflammation and autoimmunity in murine models
Creator: Brooks, Phillip Tremaine
Date: 2016
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni is the leading antecedent infection to the acute peripheral neuropathy Guillain-Barre Syndrome (GBS). GBS is debilitating, often causes paralysis, and can require several months or more for recovery. Most concerning is that GBS patients are frequently left with long-term neurologic disabilities. Because a vaccine for Campylobacter is lacking there are no viable approaches for preventing this form of GBS. Currently, therapeutic approaches for GBS include plasma exchange...
Show moreCampylobacter jejuni is the leading antecedent infection to the acute peripheral neuropathy Guillain-Barre Syndrome (GBS). GBS is debilitating, often causes paralysis, and can require several months or more for recovery. Most concerning is that GBS patients are frequently left with long-term neurologic disabilities. Because a vaccine for Campylobacter is lacking there are no viable approaches for preventing this form of GBS. Currently, therapeutic approaches for GBS include plasma exchange and intravenous immunoglobulin but they require specialized equipment, pose significant financial burden, and produce mixed results. These strategies lack a strong rationale because GBS is poorly defined mechanistically. While new working mouse models of GBS may lead to alternative therapies, confirmation of C. jejuni’s specific role in precipitating GBS and the mechanism(s) through which this occurs remain elusive. Thus far, evidence gathered from murine models demonstrates that multiple factors influence C. jejuni pathogenesis, including host genetics and C. jejuni genetics, particularly the genetic plasticity of this pathogen. Notably, the gut microbiota can modulate C. jejuni colonization- and colitis- resistance; however, its role in modulating C. jejuni-triggered autoimmunity remains unknown. The overarching goal of this study is to determine if the composition of gut microbiota affects C. jejuni-triggered autoimmunity in murine models. The chapters of this thesis present the following data addressing this goal; mice infected with antimicrobial resistant Campylobacter strains from Guillain-Barré syndrome patients produced severe colitis and type 2 autoimmune responses when their microbiota were depleted by antibiotics. Furthermore, we demonstrated that transplanted human fecal microbiota alters the immune response to Campylobacter jejuni infection in C57BL/6 mice, potentially increasing the risk of autoimmune sequelae. Finally, comparative genomic analysis of passaged C. jejuni populations revealed genetic variation in multidrug transporter genes cmeB and cmeR in Campylobacter jejuni populations from antibiotic treated mice. CmeR regulates expression of C. jejuni cell surface molecules, again potentially impacting the risk of autoimmune sequelae. Taken together, our results demonstrate that composition of gut microbiota is a critical determinant of inflammatory and autoimmune outcomes in C. jejuni murine models.
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Title: Conservation of the low temperature transcriptomes and CBF regulons between Solanum species and arabidopsis
Creator: Carvallo-Pinto, Marcela Alejandra
Date: 2009
Collection: Electronic Theses & Dissertations

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