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Title: Nucleic acid metabolism in yeast
Creator: Bradford, Stuart William
Date: 1961
Collection: Electronic Theses & Dissertations

Title: QTL mapping of post-processing color retention and other traits in two black bean populations
Creator: Bornowski, Nolan M.
Date: 2018
Collection: Electronic Theses & Dissertations
Description: "When black beans are processed for consumption, they can lose their dark coloration due to the leaching of water-soluble pigments called anthocyanins. After hydrothermal processing, beans are commonly a faded brown color instead of the dark black color typical of the dry seed. The aim of this research was to develop mapping populations with different genetic sources of color retention in order to identify regions of the dry bean genome associated with canning quality traits. To this end, two...
Show more"When black beans are processed for consumption, they can lose their dark coloration due to the leaching of water-soluble pigments called anthocyanins. After hydrothermal processing, beans are commonly a faded brown color instead of the dark black color typical of the dry seed. The aim of this research was to develop mapping populations with different genetic sources of color retention in order to identify regions of the dry bean genome associated with canning quality traits. To this end, two half-sibling black bean recombinant inbred line (RIL) populations segregating for post-processing color retention were developed. These RIL populations were phenotyped for canning quality over two years and genotyped using the BARCBean6k_3 BeadChip. A novel phenotyping method using digital image analysis was shown to outperform current methods of quantitative color measurement. QTL for post-processing color retention were detected on six chromosomes, with QTL on Pv03, Pv08, and Pv11 being the most notable for their co-localization with QTL for quantitative measurements of color. In particular, QTL associated with color retention on Pv11 mapped to a very small physical interval and were consistent across years, populations, and phenotyping methodologies. Color retention QTL on Pv08 and Pv11 are good candidates for development of molecular markers that may be used in marker assisted selection (MAS) or early-generation screening to improve post-processing color retention in black beans."--Page ii.
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Title: GENOME BIOLOGY OF THE CULTIVATED POTATO, SOLANUM TUBEROSUM
Creator: Pham, Gina Mai
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Cultivated potato is a highly heterozygous, clonally propagated autotetraploid. These traits make it a difficult crop to study and make genetic improvements. In the following dissertation, I present studies that aim to improve our knowledge of genetic complexity in potato and potato breeding strategies. First, I show that several thousand genes in cultivated potato varieties show evidence of preferential allele expression, a characteristic not expected for autotetraploids. This trend was...
Show moreCultivated potato is a highly heterozygous, clonally propagated autotetraploid. These traits make it a difficult crop to study and make genetic improvements. In the following dissertation, I present studies that aim to improve our knowledge of genetic complexity in potato and potato breeding strategies. First, I show that several thousand genes in cultivated potato varieties show evidence of preferential allele expression, a characteristic not expected for autotetraploids. This trend was observed in evolutionarily conserved genes, suggesting that cultivated potato may have preferential expression of functional alleles. Cultivated potato also has excessive copy number variation. The results indicate that ~16-18,000 genes are copy number variable, and are evolutionarily recent and related to adaptation to biotic and abiotic stress. They are also lowly expressed, with only 528 genes showing correlation between copy number and gene expression. Second, a common method of genome reduction in potato, interspecific crossing, is explored to determine possible mechanisms by which genome elimination occurs and somaclonal variation which arises during the process. The results show that haploid inducer line, IVP101, produces <1% somatic translocation event frequency in the Superior dihaploid population studied. The translocation events occurred in regions of open chromatin, suggesting that they may be driven by transcription-coupled DNA repair. Finally, I present an improved potato genome assembly and annotation using a combination of long-read sequencing methods. The new assembly, DM v.5, is 727 Mb, of which 91% is contained in 12 chromosome-scale scaffolds. DM v.5 presents a new opportunity for studies in comparative genomics and potato biology.
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Title: Landscape genetics of black bears (Ursus americanus) in the Northern Lower Peninsula (NLP) of Michigan, USA
Creator: Draheim, Hope M.
Date: 2015
Collection: Electronic Theses & Dissertations
Description: My dissertation combines population genetics, landscape ecology and spatial statistics to examine connectivity and degree of gene flow in black bears (Ursus americanus). More specifically, I used the interdisciplinary approach of landscape genetics to address an array of questions, including identifying specific landscape features that impede or promote dispersal, identity source-sink dynamics, and inferring the effect of landscape change on connectivity of a large, highly harvested, isolated...
Show moreMy dissertation combines population genetics, landscape ecology and spatial statistics to examine connectivity and degree of gene flow in black bears (Ursus americanus). More specifically, I used the interdisciplinary approach of landscape genetics to address an array of questions, including identifying specific landscape features that impede or promote dispersal, identity source-sink dynamics, and inferring the effect of landscape change on connectivity of a large, highly harvested, isolated black bear population in the Northern Lower Peninsula (NLP) of Michigan. My dissertation consists of four chapters following the introductory chapter (Chapter 1). Chapter 2 evaluates the effects of timing and heterogeneity in collection methodology on our ability to draw inferences about the extent of gene flow in NLP black bears. This chapter shows black bears exhibit significant positive genetic spatial autocorrelation and results were concordant across seasons and years indicating the overall pattern of spatial genetic structure would be detected regardless of season, year, or collection methodology. Chapter 3 results indicate that two genetically distinct groups exist in the NLP, defined as a western and an eastern genetic cluster. In addition, I found land cover was the landscape feature most strongly correlated with genetic distance. Chapter 4 investigates the presence of source-sink dynamics in NLP black bear population. I found by asymmetric emigration and immigration, revealing black bears in the NLP is composed of source and sink areas. Further, I showed source strength was associated with black bear local harvest density (a proxy for bear density). Chapter five examines the influence of landscape change on spatial genetic structure over time. My times series analyses shows land cover was significantly correlated with gene flow; however, comparisons among sampling years revealed temporal variability in the predictive power and performance of landscape resistance models. I found the best model to explain temporal inconsistencies was land cover change over time.These data represents one of most comprehensive landscape genetic studies performed on a single black bear population. Our data enables managers to target regions or habitat types that are important for maintaining connectivity across anthropogenically-altered habitats. In addition, here I present two novel extensions of current landscape genetics analytical approaches that provide flexible frameworks for understanding connectivity and assessing impacts of future change landscape alternation which could be widely integrated into landscape genetics research and conservation planning at multiple spatial scales.
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Title: Reducing iron on a knife's edge - genomic and mechanistic studies of (hyper)thermophilic dissimilatory iron-reducing bacteria and archaea
Creator: Manzella, Michael P.
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Some members of the Bacteria and the Archaea have the rare ability to transfer electrons beyond the surface of their cells. This extracellular electron transfer permits the reduction of otherwise inaccessible electron acceptors such as insoluble Fe(III) oxides. The mechanisms that enable this ability have direct implications for geochemical cycles today and for life on early Earth. The physical settings present on early Earth, hot and influenced primarily by hydrothermal activity, can be...
Show moreSome members of the Bacteria and the Archaea have the rare ability to transfer electrons beyond the surface of their cells. This extracellular electron transfer permits the reduction of otherwise inaccessible electron acceptors such as insoluble Fe(III) oxides. The mechanisms that enable this ability have direct implications for geochemical cycles today and for life on early Earth. The physical settings present on early Earth, hot and influenced primarily by hydrothermal activity, can be found in rare sites on modern Earth. These sites most often surround deep-sea hydrothermal vents. Organisms present at these sites thrive, in most cases, absent of the sun’s influence. Instead of primary production from photosynthetic microorganisms, these communities rest on the shoulders of chemoautolithotrophic bacteria and archaea. Two of these organisms, the thermophilic bacterium Geothermobacter ehrlichii and the hyperthermophilic archaeon Geoglobus ahangari were selected to undergo genome and physiological characterization to determine how they interact with the abundant insoluble Fe(III) oxides found at hydrothermal vents. Both genomes were sequenced and, while only the genome of G. ahangari was complete, this permitted identification of critical components for iron respiration. In addition, mechanistic studies were performed on G. ahangari to elucidate a direct-contact mechanism of iron reduction. Finally, the extracellular filaments from these microorganisms were characterized and the more abundant filaments, in both organisms, were found to be conductive. These are the first examples of nanowires discovered outside of the mesophilic bacteria. In addition, the phylogenetic and geographic diversity between these isolates suggests that microbial nanowires are more widespread than previously thought.
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Title: Kernel-based nonparametric testing in high-dimensional data with applications to gene set analysis
Creator: He, Tao, Ph. D.
Date: 2015
Collection: Electronic Theses & Dissertations
Description: The ultimate goal of genome-wide association studies (GWAS) is understanding the underlying relationship between genetic variants and phenotype. While the heretability is largely missing in univariate analysis of traditional GWAS, it is believed that the joint analysis of variants, that are interactively functioning in a biological pathway (gene set), is more beneficial in detecting association signals. With the fast developing pace of sequencing techniques, more detailed human genome...
Show moreThe ultimate goal of genome-wide association studies (GWAS) is understanding the underlying relationship between genetic variants and phenotype. While the heretability is largely missing in univariate analysis of traditional GWAS, it is believed that the joint analysis of variants, that are interactively functioning in a biological pathway (gene set), is more beneficial in detecting association signals. With the fast developing pace of sequencing techniques, more detailed human genome variation will be observed and hence the dimension of variants in the pathway could be extremely high. To model the systematic mechanism and the potential nonlinear interactions among the variants, in this dissertation we propose to model the set effect though a flexible non-parametric function under the high-dimensional setup, which allows the dimension goes to infinity as the size goes to infinity.Chapter 2 considers testing a nonparametric function of high-dimensional variates in a reproducing kernel Hilbert space (RKHS), which is a function space generated by a positive definite or semidefinite kernel function. We propose a test statistic to test the nonparametric function under the high-dimensional setting. The asymptotic distributions of the test statistic are derived under the null hypothesis and a series of local alternative hypotheses, the explicit power formula under which are also provided. We also develop a novel kernel selection procedure to maximize the power of the proposed test, as well as a kernel regularization procedure to further improve power. Extensive simulation studies and a real data analysis were conducted to evaluate the performance of the proposed method.Chapter 3 is theoretical investigation on the statistical optimality of kernel-based test statistic under the high-dimensional setup, from the minimax point of view. In particularly, we consider a high-dimensional linear model as the initial study. Unlike the sparsity or independence assumptions existing in related literature, we discussed the minimax properties under a structure free setting. We characterize the boundary that separates the testable region from the non-testable region, and show the rate-optimality of the kernel-based test statistic, under certain conditions on the covariance matrix and the growing speed of dimension.Our work in Chapter 4 fills the blank of kernel-based test using multiple candidate kernels under the high dimensional setting. Firstly, we extend the test statistic proposed in Chapter 2 to an inclusive form that allows the adjustment of covariants. The asymptotic distribution of the new test statistic under the null hypothesis is then provided. Two practical and efficient strategies are developed to incorporate multiple kernel candidates into the testing procedures. Through comprehensive simulation studies we show that both strategies can calibrates the type I error rate and improve the power over the the poor choice of kernel candidate in the set. Particularly, the maximum method, one of the two strategies, is shown having potential to boost the power close to one using the best candidate kernel. An application to Thai baby birth weight data further demonstrates the merits of our proposed methods.
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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: 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: 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: Lipid trafficking and lipid breakdown in Chlamydomonas
Creator: Warakanont, Jaruswan
Date: 2015
Collection: Electronic Theses & Dissertations
Description: With their high photosynthetic efficiency and the ability to synthesize triacylglycerol (TAG), unicellular microalgae have an important ecological role, as well as value for production of triacylglycerol lipids that can be converted to biodiesel. The recent state of knowledge about microalgal lipid metabolism had been deduced from that of a model seed plant, Arabidopsis. However, recent studies have revealed that aspects of lipid metabolism differ between microalgae and Arabidopsis....
Show moreWith their high photosynthetic efficiency and the ability to synthesize triacylglycerol (TAG), unicellular microalgae have an important ecological role, as well as value for production of triacylglycerol lipids that can be converted to biodiesel. The recent state of knowledge about microalgal lipid metabolism had been deduced from that of a model seed plant, Arabidopsis. However, recent studies have revealed that aspects of lipid metabolism differ between microalgae and Arabidopsis. Investigating these differences was a cornerstone of this study, using Chlamydomonas, a representative of microalgae, and Arabidopsis. Two major approaches were undertaken: forward and reverse genetics. The forward genetic screening used insertional mutagenesis of Chlamydomonas and focused on a knockout mutation of a gene, which proved to be an orthologue of the Arabidopsis TRIGALACTOSYLDIACYLGLYCEROL 2 (TGD2). The tgd2 mutant exhibits increases in cellular concentrations of phosphatidic acid (PtdOH) and triacylglycerol (TAG); the latter contains signature fatty acids of monogalactosyldiacylglycerol (MGDG), pointing to its likely origin of synthesis. The mutant also experiences low viability in extended culture. Similar to AtTGD2, CrTGD2 is located in the chloroplast inner envelope membrane and binds PtdOH in vitro. Radioactive labeling experiments suggest that CrTGD2 functions in transferring a lipid precursor, presumably PtdOH, from the outer chloroplast envelope into the chloroplast. This study shows that, in contrast to prevailing assumptions, Chlamydomonas is able to import lipids from the endoplasmic reticulum (ER) to the chloroplast, and utilizes the eukaryotic pathway to synthesize galactoglycerolipids. The reverse genetics investigation focused on CrLIP4, a putative TAG lipase. CrLIP4 is an orthologue of a major Arabidopsis TAG lipase. Reverse transcription PCR revealed that the CrLIP4 transcript is reduced in abundance during N deprivation when TAG accumulates. Down-regulation of this gene through an artificial microRNA construct resulted in delayed TAG degradation. Expression of CrLIP4 in Escherichia coli alters the pattern of neutral lipids. Recombinant CrLIP4 exhibited TAG lipase activity. These results show that CrLIP4 has TAG lipase activity both in in vitro and in vivo. In summary, two Arabidopsis orthologues in Chlamydomonas were characterized through forward and reverse genetic approaches. The results elaborate and refine our understanding of Chlamydomonas lipid metabolism, and are likely relevant for other unicellular microalgae.
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Title: The response of symbiotic zooxanthellae (Symbiodinium spp.) diversity and gene expression to stress in geographically distinct reefs
Creator: Hauff Salas, Briana Patricia
Date: 2015
Collection: Electronic Theses & Dissertations
Description: The persistence of coral reefs in the Florida Keys reef tract is of concern as coral bleaching, due to increased ocean temperatures, and human-linked disease outbreaks have led to a reduction in coral cover of 40% since the 1980’s. Evidence suggests a variation in stress susceptibility of conspecific coral from inshore and offshore reefs in the Florida Keys. However, the mechanism behind the disparity in stress susceptibility is unknown. Variation in genetic composition of a coral’s symbiotic...
Show moreThe persistence of coral reefs in the Florida Keys reef tract is of concern as coral bleaching, due to increased ocean temperatures, and human-linked disease outbreaks have led to a reduction in coral cover of 40% since the 1980’s. Evidence suggests a variation in stress susceptibility of conspecific coral from inshore and offshore reefs in the Florida Keys. However, the mechanism behind the disparity in stress susceptibility is unknown. Variation in genetic composition of a coral’s symbiotic algae (Symbiodinium spp.; referred to as zooxanthellae) has been proposed as a mechanism to withstand stress. As such, I investigated zooxanthellae composition of Porites astreoides and Montastraea cavernosa from an inshore and offshore reef in the Lower Florida Keys to determine links to stress susceptibility. Additionally, I investigated variation in the expression of metabolically related genes in zooxanthellae of P. astreoides reciprocally transplanted between reefs, as well as exposed to elevated temperatures and disease. Chapter one examines changes in the dominant zooxanthellae subclade type in P. astreoides and M. cavernosa throughout a two-year reciprocal transplant study. The goal of this study was to determine if zooxanthellae subclade type could explain higher rates of bleaching in offshore reef coral, as well as assessing the possibility of acclimatization to different environments. Increased complexity and diversity was seen in the composition of zooxanthellae subclade types from coral collected at offshore reefs, compared to inshore reefs. As a result, offshore reef zooxanthellae displayed less stability, possibly explaining higher bleaching susceptibility. Additionally, zooxanthellae composition patterns were retained throughout the reciprocal transplant, demonstrating a lack of acclimatization. Chapter two examined site-specific variation in the expression of metabolically related genes in zooxanthellae from P. astreoides following the reciprocal transplant. Symbionts from offshore corals experienced significantly increased expression in PCNA, SCP2, G3PDH, PCP and psaE (p<0.05) compared to inshore symbionts, a pattern consistent with increased bleaching susceptibility. Significant differences in gene expression between zooxanthellae from inshore and offshore reef indicate functional variability and are likely a result of localized adaptation. Similar to results in chapter one, gene expression patterns from site of origin were retained throughout the reciprocal transplant, suggesting no acclimatization. Chapter three investigated variation in the response of the same zooxanthellae genes when P. astreoides was exposed to extreme temperatures and disease. Here disease was mimicked by the application of lipopolysaccharide from Serratia marcescens, the causative agent of acroporid serratosis. Gene expression did not differ in zooxanthellae from inshore and offshore reefs, nor as a consequence of extreme temperature or disease. Several factors may explain the lack of variation including zooxanthellae response to acute versus moderate stress, host protection and targeting of symbionts by S. marcescens. These results suggest that symbionts of P. astreoides may be locally adapted to chronic moderate stress, but respond similarly to acute extreme conditions.
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Title: Mechanisms mediating life history traits in the spotted hyena (Crocuta crocuta
Creator: Lewin, Nora Shannon
Date: 2017
Collection: Electronic Theses & Dissertations
Description: My dissertation focuses on understanding the mechanisms underpinning growth, reproduction, and survival in the spotted hyena. Following a general introductory chapter, my dissertation is composed of four independent research chapters. I begin with Chapter 2 in which my colleagues and I document a positive linear relationship between social dominance rank and telomere length. We also report significant variability in telomere length of high-ranking females among different social groups,...
Show moreMy dissertation focuses on understanding the mechanisms underpinning growth, reproduction, and survival in the spotted hyena. Following a general introductory chapter, my dissertation is composed of four independent research chapters. I begin with Chapter 2 in which my colleagues and I document a positive linear relationship between social dominance rank and telomere length. We also report significant variability in telomere length of high-ranking females among different social groups, suggesting that both social dominance rank and group membership influence this important biomarker of aging. In Chapter 3, we describe the role of juvenile concentrations of the hormone, insulin-like growth-factor -1 (IGF-1), in predicting trade-offs between early-life growth and later-life reproduction and survival among female hyenas. In Chapter 4, I explore IGF-1 as a potential mechanism of female-biased sexual size dimorphism by documenting sex-biased concentrations, sensitivities, and adaptive values of IGF-1 during the early postnatal period. Finally, in Chapter 5, I describe that age-related improvement and senescence in reproductive performance varies with social dominance rank among female hyenas. Cumulatively, my dissertation is an exploration of how physiological mechanisms may be used to understand social, physiological, and evolutionary forces operating in a free-living social carnivore. My work offers a unique contribution to the field of life-history evolution and furthers our understanding of the mechanisms that give rise to it.
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Title: The roles of C/EBPbeta and c-Jun in transcription of the gene encoding the murine progesterone receptor
Creator: Do, Han Ngoc
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Progesterone (P) and its receptor, the progesterone receptor (PR), are important for mammary gland development. Moreover, P/PR signaling also contributes to mammary tumorigenesis. Thus, studying the mechanism of PR expression is important in breast cancer research. C/EBPB-deficient mice and mice blocked for AP-1 activity show similar defects in mammary gland development as do PRB-deficient mice, especially during pregnancy, suggesting that these transcription factors might act in the same...
Show moreProgesterone (P) and its receptor, the progesterone receptor (PR), are important for mammary gland development. Moreover, P/PR signaling also contributes to mammary tumorigenesis. Thus, studying the mechanism of PR expression is important in breast cancer research. C/EBPB-deficient mice and mice blocked for AP-1 activity show similar defects in mammary gland development as do PRB-deficient mice, especially during pregnancy, suggesting that these transcription factors might act in the same pathway or may regulate overlapping sets of downstream target genes. An overall decrease in PR observed in sexually mature wild type mice fails to occur in C/EBPB-deficient mice, while no alterations in C/EBPB expression are observed in PR-deficient mice. Moreover, AP-1 has been found to regulate PR expression. These observations suggest that C/EBPB and AP-1 act upstream of PR. This leads us to study the possibility that C/EBPB and AP-1 are required for PR expression.We examined whether C/EBPB participated in the transcriptional regulation of PR expression in the mammary gland. Transient co-transfection of a PR promoter-reporter construct with expression vectors that individually express C/EBPB isoforms (LAP1, LAP2, or LIP) into a mouse mammary carcinoma cell line revealed that all C/EBPB isoforms, surprisingly including LIP (the shortest isoform lacking transactivation domains), can transactivate the PR promoter. Importantly, we found that LIP, in particular, robustly synergizes with an AP-1 member, c-Jun, to drive PR transcription. Consistent with significant roles for C/EBPB and c-Jun in PR expression, knockdown experiments showed that endogenous levels of C/EBPB and c-Jun expression were sufficient to drive the PR promoter-reporter. Additionally, overexpression of LIP elevated PR protein expression from the intact endogenous gene encoding PR. Furthermore, in vivo immunofluorescence studies showed that C/EBPB and PRA expression are mutually exclusive in the mammary epithelium, while PRB is only expressed in cells that express C/EBPB. This suggests an important role for C/EBPB in PRB expression during pregnancy. Then, we studied the mechanism by which LIP and c-Jun synergistically activate the PR promoter. We demonstrated in the reporter assay that the integrity of C/EBP- and AP-1-binding sites was required for the respective C/EBPB; and c-Jun activities on the PR promoter. Moreover, we showed in ChIP assay that efficient promoter occupancy of both LIP and c-Jun and their synergistic transactivation of the PR promoter required at least one C/EBP- and one AP-1-binding site. In addition, as indicating in the sequential ChIP assay, C/EBPB and c-Jun simultaneously occupied PR promoter. This leads us to propose a model where the synergy of C/EBPB and c-Jun in transactivation of the PR promoter is dependent on the two factors mutually stabilizing their recruitment to the PR promoter. Collectively, our data suggest a critical role for C/EBPB, particularly LIP, in PRB expression.
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Title: Molecular structure and physicochemical properties of starch isolated from Phaseolus vulgaris
Creator: Hooper, Sharon
Date: 2014
Collection: Electronic Theses & Dissertations
Description: The health benefits of legumes have been known for many years. They are considered to be a food staple in the diet of humans. Dry beans have been implicated in the prevention and management of type II diabetes mellitus and in the reduction of risks associated with colon cancer. Dry beans are good sources of complex carbohydrates, protein, dietary fiber, vitamins and minerals. However, use of the starch fraction of dry beans is limited due to the lack of molecular structure-functionality...
Show moreThe health benefits of legumes have been known for many years. They are considered to be a food staple in the diet of humans. Dry beans have been implicated in the prevention and management of type II diabetes mellitus and in the reduction of risks associated with colon cancer. Dry beans are good sources of complex carbohydrates, protein, dietary fiber, vitamins and minerals. However, use of the starch fraction of dry beans is limited due to the lack of molecular structure-functionality relationships. The specific objectives of this study were: (1) to determine and compare the physicochemical properties of starch isolated from six varieties of Phaseolus vulgaris, namely black bean, dark red kidney bean, light red kidney bean, navy bean, pinto bean and small red bean, (2) to determine and compare the digestibility, estimated glycemic index, and molecular weight distributions of isolated raw, canned and stovetop-cooked bean starches, (3) to investigate the effects of canning and a traditional cooking method (boiling) on the digestibility and molecular weight distributions of starch isolated from dried bean. The physicochemical characteristics of starches isolated from six varieties of Phaseolus vulgaris grown in Michigan were determined. Starch yield varied from 22.8% to 34.1% on a whole seed basis (~ 10% moisture content). The raw isolated bean starches exhibited high resistant starch contents ranging from 41.9% (light red kidney bean) to 55.7% (pinto bean), whilst total amylose content varied from 28.0% (pinto bean) to 29.8% (dark red kidney bean). Significant differences were observed for the gelatinization transition temperatures, pasting parameters, and resistant starch contents of the isolated dark red kidney and light red kidney bean starches when compared to isolated starch from black, navy, pinto and, small red beans. All isolated bean starches displayed the characteristic C-type X-ray diffraction pattern of legumes. The crystallinity and B-type starch polymorph contents ranged from 36.1% to 24.9% and 19.6% to 15.6% respectively. This study demonstrated that the chemical compositions of beans are different for different varieties, and thus the varieties exhibit different physicochemical properties. The weight average molecular weight distribution (Mw) of starches isolated from native, canned, and stovetop-cooked beans were analyzed using high-performance size exclusion chromatography with multi-angle laser light scattering and refractive index detectors (HPSEC-MALLS-RI). Results revealed that amylose of isolated native dark red kidney bean starch had the smallest Mw (1.0 x 106 g/mol), whereas isolated native pinto bean starch had the largest value of Mw (1.8 x 106 g/mol). The Mw values of amylopectin for isolated native bean starches ranged from 2.4 x 107 g/mol to 3.9 x 107 g/mol. Isolated canned and stovetop-cooked bean starches displayed a mono-modal Mw distribution, with a reduction in high molecular weight fractions, whereas isolated native bean starch Mw distribution was bi-modal. Results of in vitro á-amylase starch hydrolysis showed ranges of rapidly digestible starch (RDS) (1.95-2.71%), slowly digestible starch (SDS) (14.36-17.39%), and resistant starch (RS) (78.95-83.7%) among the tested isolated native Phaseolus vulgaris starches. However, RDS, SDS, and RS fractions in isolated canned bean starches ranged from 7.58-13.21%, 20.75-24.90%, and 63.17- 68.54%, respectively. Isolated stovetop-cooked bean starches yielded similar results: RDS, 7.37-10.61%; SDS, 22.55-26.84%; and RS, 62.55-68.59%). The hydrolysis indices (HI) and glycemic indices (GI) were marginally greater for isolated canned bean starches than for stovetop-cooked starches.
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Title: Sexual differentiation of the zebra finch neural song circuit
Creator: Beach, Linda Qi
Date: 2014
Collection: Electronic Theses & Dissertations
Description: The Australian zebra finch is an advantageous model for investigatingmechanisms regulating neural structure and behavior. Males and females exhibit remarkable differences in brain morphology and in the song behavior that they subserve. Thus, we can exploit these sexually dimorphic traits to begin to understand the factors that underlie development of the nervous system. While early studies implicated a critical role of estradiol (E2) in masculinizing both structure and function, Z-linked...
Show moreThe Australian zebra finch is an advantageous model for investigatingmechanisms regulating neural structure and behavior. Males and females exhibit remarkable differences in brain morphology and in the song behavior that they subserve. Thus, we can exploit these sexually dimorphic traits to begin to understand the factors that underlie development of the nervous system. While early studies implicated a critical role of estradiol (E2) in masculinizing both structure and function, Z-linked genes (males: ZZ; females: ZW) might also contribute. In the experiments conducted for this dissertation, I investigated the role of one Z-gene, tubulin specific chaperone protein A (TBCA) and its potential interactions with E2, in masculinizing the zebra finch song system. TBCA is one of several chaperone proteins involved in the formation of β-tubulin, and is critical for microtubule biosynthesis and integrity.I show that TBCA exhibits male-biased expression in the lateral magnocellularnucleus of the anterior nidopallium (LMAN). I also find that TBCA transcript and its protein product are developmentally regulated, such that this expression is higher in juveniles compared to adults. Further, TBCA is expressed in neurons that project to an efferent target, the robust nucleus of the arcopallium (RA). While the morphology of LMAN is not particularly different between the sexes, the projection from LMAN to RA is more robust in males, and this might influence masculine development of RA. Thus, TBCA is both temporally and spatially primed to influence sex-specific development.TBCA expression does not appear to be modulated by E2, as administration ofthis hormone did not influence TBCA mRNA quantity or stereological cell counts of TBCA+ cells in LMAN. However, treatment of males with the aromatase inhibitor, fadrozole, induced a hypermasculine phenotype in neural structures, including in the volume of LMAN, cell size in RA, and of the projection between these two regions.Finally, TBCA knockdown in LMAN in vivo demasculinized these samemorphological parameters in both males and females. Moreover, I did not detect an interaction between TBCA and E2 in facilitating masculine development, nor did I observe an additive effect of the two factors. Collectively, the present body of work represents an initial effort in determining the role of a Z-gene in the development of brain and behavior. The results here serve as an important platform from which wecan begin to explore the mechanisms regulating the observed effects, including those underlying cell survival and maintenance of neural projections.
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Title: Exploration of the genetic diversity of cultivated potato and its wild progenitors (Solanum sect. Petota) with insights into potato domestication and genome evolution
Creator: Hardigan, Michael Alan
Date: 2016
Collection: Electronic Theses & Dissertations
Description: "Cultivated potato (Solanum tuberosum L.) is a clonally propagated autotetraploid (2n=4x=48) with high potential for genetic improvement due to the expansive genetic diversity of its related germplasm. This diversity includes high levels of heterozygosity but also deleterious genetic load in cultivated clones, multiple groups of genetically distinct landrace sub-species, and over 100 related tuber-bearing species that can introduce heterosis and adaptation. To generate a better understanding...
Show more"Cultivated potato (Solanum tuberosum L.) is a clonally propagated autotetraploid (2n=4x=48) with high potential for genetic improvement due to the expansive genetic diversity of its related germplasm. This diversity includes high levels of heterozygosity but also deleterious genetic load in cultivated clones, multiple groups of genetically distinct landrace sub-species, and over 100 related tuber-bearing species that can introduce heterosis and adaptation. To generate a better understanding of the landscape of potato genetic diversity, studies were conducted to (1) explore the genetic relationships between tuber-bearing Solanum species, landraces, and cultivars, (2) investigate the role of structural variation in cultivated potato genome evolution and diversity, and (3) identify key loci that were selected during domestication of potato. Phylogenetic analysis of tuber-bearing Solanum species was examined in the first application of genome-wide nuclear single nucleotide polymorphism (SNP) markers with a diversity panel of potato species from the USDA Potato Gene Bank core collection. Genotyping a panel of 75 accessions representing 25 species and 213 cultivated tetraploid clones using 5,023 polymorphic SNPs supported previous taxonomic placement of wild potato germplasm, while reinforcing the theory of a Peruvian domestication origin for potato. Several genes involved in carbohydrate metabolism or with potential roles in tuber development were found to contain diverging allele frequencies in the wild and cultivated potato groups suggesting they may have been key loci involved in domestication. A comprehensive analysis of genomic variation (sequence and structural variation) using 30- 70x sequence coverage in a panel of 12 monoploid/doubled monoploid potatoes derived from primitive South American diploid landraces was performed. Extensive copy number variation (CNV) was found to impact over 30% of the potato genome and nearly 30% of genes, with widespread deletion affecting lowly expressed sequences, and enriched duplication within gene families that function in adaptation and environmental response. This study revealed CNV is equally relevant to sequence-level variation (SNPs, insertions/deletions) in its contribution to deleterious mutation load and gene evolution in the potato genome. The study also demonstrated that the extensive structural heterogeneity present in tetraploid genotypes is present in their diploid progenitors, and thus, is not the result of polyploidy alone. A diversity panel was sequenced at 8x to 16x coverage to enable genome-wide comparison of allele composition in 23 tetraploid potato cultivars, 20 wild species and 20 landrace progenitors. Analysis of selection signatures including FST, Tajima's D, reduced nucleotide diversity and allele frequency differences yielded a set of domestication candidate genes including several regulating carbohydrate pathways, glycoalkaloid biosynthesis and stress responses. Comparable levels of total sequence diversity were present in elite cultivars and South American landraces, yet significant genetic variance between landrace populations was repartitioned as single-clone heterozygosity in cultivars, confirming the hypothesis that elite varieties represent a highly heterozygous group lacking significant population structure. These findings may assist the ability of potato breeders to exploit key performance-related loci and heterosis in the future."--Pages ii-iii.
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Title: Hierarchical Bayes models for beef cattle genetic evaluation under extensive management conditions
Creator: Cardoso, Fernando Flores
Date: 2003
Collection: Electronic Theses & Dissertations

Title: The genetic control of self-incompatability in sweet and sour cherry
Creator: Hauck, Nathanael R.
Date: 2004
Collection: Electronic Theses & Dissertations

Title: USING THE REGULATION OF GA2-OXIDASE AS A MODEL TO UNDERSTAND GIBBERELLIN’S ROLES IN APPLE AND ARABIDOPSIS THALIANA
Creator: Zhang, Songwen
Date: 2021
Collection: Electronic Theses & Dissertations
Description: In the model plant Arabidopsis thaliana (Arabidopsis), where the gibberellin (GA) signaling pathway has been best studied, GAs promote flowering. However, in many woody perennial plants such as apple (Malus x domestica Borkh.), GAs generally have a repressive role in flowering. The genetic and molecular mechanisms of GA-mediated flowering repression in apple and other plants remain unknown. In this study, we carried out transcriptional profiling of apple shoot apices during the anticipated...
Show moreIn the model plant Arabidopsis thaliana (Arabidopsis), where the gibberellin (GA) signaling pathway has been best studied, GAs promote flowering. However, in many woody perennial plants such as apple (Malus x domestica Borkh.), GAs generally have a repressive role in flowering. The genetic and molecular mechanisms of GA-mediated flowering repression in apple and other plants remain unknown. In this study, we carried out transcriptional profiling of apple shoot apices during the anticipated period of floral induction and examined how gene regulation is influenced by exogenous GAs. GA treatment resulted in downregulation of a diversity of genes participating in GA biosynthesis, transport and reception, and strong upregulation of the GA catabolic GA2-ox (GA2-oxidase) genes, suggesting GA homeostasis is mediated at multiple levels in these tissues. We also observed rapid and strong upregulation of both of two copies of a gene previously observed to inhibit flowering in apple, MdTFL1 (TERMINAL FLOWER 1), offering a potential explanation for the flowering-inhibitory effects of GA in apple. These results provide a context for investigating factors that may transduce the GA signal in apple and contribute to a preliminary genetic framework for the repression of flowering by GAs in a woody perennial plant. GA2ox expression and the enzyme activity determines concentrations of specific GAs in the right structure at the right time and contributes to enabling GAs to execute their function precisely. In return, their expression is under tight regulation by GA. Taking advantage of this tight link between GA2ox and GA activity, we aimed to develop regulation of GA2ox as a model to evaluate GA activity and function in both apple and Arabidopsis with a focus on floral induction. Through analysis of high-quality apple genomes and our transcriptional datasets, we identified 16 canonical GA2ox-like genes in the apple genome, representing eight pairs of homoeologous genes. By analyzing their spatial and developmental expression, we found that at least half of the genes were expressed in all the structures studied. In addition, individual members of homoeologous pairs displayed both overlapping and distinct expression patterns, suggesting function redundance and divergency. Finally, we found that two pairs of homoeologous genes (MdGA2ox1A, -1B, -2A and -2B) may be responsible for regulating GA activity in the shoot apex during floral induction. These findings provide biological and evolutionary insights into GA biology in apple, particularly in floral induction. In Arabidopsis, where GA2ox has been relatively well studied, we developed a genetic tool kit comprising both CRISPR/Cas-induced, transgene-free single knockout mutants and transcriptional and translational GUS fusion lines for the seven canonical Arabidopsis GA2ox genes (AtGA2ox1-AtGA2ox8). Mutations in the loss-of-function mutants have presumably disrupted function of both two functional domains of the GA2ox proteins. By comparing GUS activity in the GUS fusion lines, we found that the transcribed region is required for appropriate expression for several genes. This tool kit can be used for a wide spectrum of GA biology.
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Title: GENERATION OF HT-B AND HT-B PLUS S-RNASE KNOCKOUT LINES TO UNDERSTAND SELF-COMPATIBILITY IN DIPLOID POTATO
Creator: Lee, Sarah
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Domesticated potato (Solanum tuberosum L.) is the world’s third most important food crop and is a food security crop according to the Food and Agriculture Organization of the United Nations. Currently, commercial potatoes are autotetraploid and mainly produced via asexual clonal propagation. The autotetraploid nature of most cultivated potatoes in combination with acute inbreeding depression when self-fertilized over multiple generations cause challenges in making advances with traditional...
Show moreDomesticated potato (Solanum tuberosum L.) is the world’s third most important food crop and is a food security crop according to the Food and Agriculture Organization of the United Nations. Currently, commercial potatoes are autotetraploid and mainly produced via asexual clonal propagation. The autotetraploid nature of most cultivated potatoes in combination with acute inbreeding depression when self-fertilized over multiple generations cause challenges in making advances with traditional breeding schemes. The benefits of moving potato to a diploid breeding model include a simplified breeding scheme, easier fixation of desirable alleles, and generation of inbred lines that may be used to generate F1 hybrids with heterotic potential. A major hinderance to self-compatibility originates from the gametophytic self-incompatibility (GSI) system in which the S-RNase and HT-B genes play a critical role. Utilizing CRISPR-Cas9 gene editing, HT-B and HT-B + S-RNase knockout (KO) lines were produced. HT-B KOs produced parthenocarpic fruit but remained self-incompatible. However, the S-RNase and HT-B double KOs were self-compatible. Self-compatibility was measured quantitatively using fruit set, fruit weight, and seed count. Fruit set varied across both self-incompatible and self-compatible lines, with no clear trend in statistical significance. Double KO lines consistently displayed higher fruit weight than incompatible lines. Seed count served as the best measure of self-compatibility, with S-RNase and HT-B double KO lines producing up to three times mean seed per fruit when compared to S-RNase only KOs from prior studies. The lines with the highest levels of self-compatibility will serve as useful additions in advancing potato breeding to the diploid level.
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