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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
61

Characterization Of A Novel Vps26c-Retromer Complex And Its Interaction With An Endosomal Trafficking Pathway Regulated By The Snare Vti13 In Controlling Polarized Growth And Cell Wall Organization In Arabidopsis Thaliana

Ghosh Jha, Suryatapa 01 January 2018 (has links)
The endosomal trafficking system is a network of highly coordinated cellular pathways that control the growth and function of cells. The coordination of secretion and endocytosis in cells is one of the primary drivers of polarized growth, where new plasma membrane and cell wall components are deposited at the growing apex. In plants, one of the cell types exhibiting polarized growth are the root hairs. Root hairs are regulated extensions of epidermal cells called trichoblasts and are essential for anchorage, absorption of water and nutrients, and plant-microbe interactions. In this thesis, I characterize a previously undescribed protein involved in retromer function and endosomal trafficking pathways that regulate tip growth in root hairs of Arabidopsis thaliana. The large retromer complex functions in recycling receptors in endosomal trafficking pathways essential for diverse developmental programs including cell polarity, programmed cell death, and shoot gravitropism in the model plant, Arabidopsis thaliana. I have characterized VPS26C, a novel member of the large retromer complex, that is essential in maintaining root hair growth in Arabidopsis. We used Bimolecular Fluorescence Complementation (BiFC) analysis to demonstrate thatVPS26C interacts with previously characterized core retromer subunits VPS35A and VPS29. Genetic analysis also indicates that vps26c suppresses the root hair growth and cell wall organization phenotypes of a null mutant of the SNARE VTI13 that localizes to early endosomes and the vacuole membrane, indicating a crosstalk between the VPS26C-retromer and VTI13-dependent vesicular trafficking pathways. Phylogenetic analysis was used to show that VPS26C genes are present in most angiosperms but appear to be absent in monocot genomes. Moreover, using a genetic complementation assay, we have demonstrated that VPS26C shares deep conservation of biochemical function with its human ortholog (DSCR3/VPS26C). We also used an affinity purification-based proteomic analysis to identify proteins associated with VTI13 in young seedlings. Preliminary results suggest that a number of proteins linked to cell plate organization in plants are associated with the VTI13 proteome, emphasizing the potential role of this pathway in new cell wall biosynthesis/organization. Additionally, we have identified endoplasmic reticulum (ER)-body proteins, involved in plant defense response pathways, suggesting that either the VTI13 endosomal trafficking pathway is functioning in plant defense responses, or the ER-body proteins have additional independent function(s) in Arabidopsis roots that depend on VTI13. In summary, I have described a novel retromer complex essential for polarized growth in Arabidopsis. VPS26C is an ancient gene and shares sequence and functional homology between human and Arabidopsis. vps26c is a genetic suppressor of the vti13- dependent root hair growth and cell wall organization pathways. Proteomic analysis of VTI13 endosomes in young seedlings suggests that a number of proteins associated with cell plate formation are associated with VTI13 compartments, supporting the genetic analysis described here and serves as a starting point to further describe the role of this pathway in controlling polarized growth in plants.
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62

Cisco Science: Using Omics To Answer A Range Of Key Questions

Lachance, Hannah 01 January 2019 (has links)
Coregonines, including cisco (Coregonus artedi), kiyi (Coregonus kiyi), and bloater (Coregonus hoyi), are a focus for prey fish conservation and restoration efforts throughout the Laurentian Great Lakes. However, fundamental questions about coregonine ecology and genetics remain. For example, we know little about how the early life stages of coregonines respond to environmental change at either the genotypic or phenotypic level. We also have limited knowledge about how to identify different species at the larval stage and the genetic relationships among species, which makes the different species difficult to study at the larval stage. To increase the probability for success in restoration efforts, current and future research need to integrate traditional and novel approaches to better understand what leads to current and future coregonine successes. We used DNA and RNA omics tools, genomics and transcriptomics to boost our comprehension of current coregonine populations and to help understand how C. artedi may respond to environmental change. During the winter of 2017, we conducted a pilot experiment to evaluate how C. artedi eggs may respond to increased light exposure resulting from current and expected reductions in annual ice and snow cover due to global warming. We used transcriptomics to assess differences in gene expression between a continuous light and continuous dark treatment. Our results indicate that light is an environmental factor that could lead to earlier hatch dates, smaller yolk sacs, changes in mortality and differential gene expression in metabolic related and other functionally important genes. In 2018, we sampled larval coregonines in the Apostle Islands of Lake Superior each week from hatch in May until late July. We used genomic sequencing to genetically identify 197 larvae to species: C. artedi, C. hoyi, and C. kiyi. The larval demographic characteristics of each species was assessed and revealed that length ranges, growth rates, yolk sac condition, and effective population size varied among species. Larvae of all three species were found throughout the entirety of the Apostle Islands and the genetic diversity within each species appears high. The results from our pilot experiment and field observations help advance our understanding of the important early life stages of coregonines and how changes in light exposure or growth rates could affect their success or failure in a changing climate.
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63

The Evolution and Domestication Genetics of the Mango Genus, Mangifera (Anacardiaceae)

Warschefsky, Emily 27 April 2018 (has links)
Domesticated species are vital to global food security and have also been foundational to the formulation and advancement of evolutionary theory. My dissertation employs emerging molecular genomic tools to provide an evolutionary context for crop improvement. I begin by providing a contemporary perspective on two components of domestication biology that have long been used to improve crop production: wild relatives of crop species and grafted rootstocks. First, I propose a method to systematically introgress crop wild relative diversity into crop breeding programs. Then, I explore rootstocks, the lesser-known half of the perennial crop equation, documenting prevalence and diversity, cataloging rootstock traits under selection, and discussing recent advances in rootstock biology. Both crop wild relatives and rootstocks remain largely underutilized resources and hold great promise for agricultural innovation. While humans have domesticated thousands of plant species, research has largely focused on annual crops, to the exclusion of perennials. To improve our understanding of how tree species respond to domestication, I examine the evolution and domestication of one of the world’s most important perennial tropical fruit crops, the mango, Mangifera indica, and its wild and semi-domesticated relatives. I generated a dataset suitable for studying Mangifera across evolutionary time using double digest restriction site associated DNA sequencing (ddRADseq). I present a multilocus phylogeny that informs the classification of Mangifera and reveals, for the first time, the evolutionary relationships of wild, semi-domesticated, and domesticated species in the genus. Narrowing my focus to the intraspecific level, I examine how the introduction of M. indica into regions of the world impacted its genetic diversity. My results show M. indica maintained high levels of genetic diversity during its introduction into the Americas. However, the novel diversity I detect in Southeast Asian mango cultivars suggests that M. indica has a more complex domestication history than previously assumed. I also find evidence that M. indica hybridized with multiple congeners following its introduction into Southeast Asia, forming two hybrid lineages that may be maintained by clonal polyembryonic reproduction. Collectively, my research provides a comprehensive framework for understanding the evolution and domestication of a tropical tree crop of global economic importance.
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64

Association statistics under the PPL framework

Huang, Yungui 01 May 2011 (has links)
In this dissertation, the posterior probability of linkage (PPL) framework is extended to the analysis of case-control (CC) data and three new linkage disequilibrium (LD) statistics are introduced. These statistics measure the evidence for or against LD, rather than testing the null hypothesis of no LD, and they therefore avoid the need for multiple testing corrections. They are suitable not only for CC designs but also can be used in application to family data, ranging from trios to complex pedigrees, all under the same statistical framework, allowing for the unified analysis of these disparate data structures. They also provide the other core advantages of the PPL framework, including the use of sequential updating to accumulate LD evidence across potentially heterogeneous sets of subsets of data; parameterization in terms of a very general trait likelihood, which simultaneously considers dominant, recessive, and additive models; and a straightforward mechanism for modeling two-locus epistasis. Finally, being implemented within the PPL framework, the new statistics readily allow linkage information obtained from distinct data, to be incorporated into LD analyses in the form of a prior probability distribution. Performance of the proposed LD statistics is examined using simulated data. In addition, the effects of key modeling violations on performance are assessed. These statistics are also applied to a previously published type 1 diabetes (T1D) family dataset with a few candidate genes with previously reported weak associations, and another T1D CC dataset also previously published as a genome-wide association (GWA) study with some strong associations reported. The new LD statistics under the PPLD framework confirm most of the findings in the published work and also find some new SNPs suspected of being associated with T1D. Sequential updating between the family dataset and the CC dataset dramatically increased the association signal strength for a CTLA4 SNP genotyped in both studies. Linkage information gleaned from the family dataset is also combined into the LD analysis of the CC dataset to demonstrate the utility of this unique feature of the PPL framework, and specifically for the new LD statistics.
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65

Conditional linkage methods--searching for modifier genes in a large Amish pedigree with known Von Willebrand disease major gene modification

Abbott, Diana Lee 01 May 2009 (has links)
Von Willebrand Disease (VWD) is the most common bleeding disorder. In addition to known major genes, genetic modifiers, such as ABO blood group, affect quantitative outcome measures for VWD. The data consist of an 854-member Amish pedigree with established linkage of VWD to a locus within the Von Willebrand Factor (VWF) gene on chromosome 12. The DNA sequence of the causative mutation is known. Phenotypic information and genotypic data consisting of VWF mutation status and a genome screen of markers are available for 385 pedigree members. Genetic modifiers of the VWF mutation are investigated using known and new conditional linkage methods that search for modifier genes of a major gene with known mutation. The MCMC-based program LOKI was used to conduct multipoint linkage analysis of VWD outcome measures while controlling for the VWF mutation. Adjustment for the mutation did not eliminate the linkage signal on chromosome 12 in the same location as the VWF mutation. Evidence for QTLs was also found on six other chromosomes. Smod, a score statistic that detects evidence of a genetic modifier conditional on linkage to a major gene, was developed for sib pair data. To limit the modifier gene main effect, Smod was developed so that variance due to the modifier locus is bounded above by the variance of the interaction between major gene and modifier gene. The performance of Smod was compared to other published score statistics. Power to detect linkage to the modifier locus depended on major gene and modifier gene risk allele frequencies, relative contribution of the major gene main effect to the interaction effect, and the upper bound on the modifier gene main effect. The Amish pedigree was broken up into sib pair data and analyzed using Smod and other score statistics. Using these statistics, the strongest evidence for QTLs for VWD was also found on chromosome 12 in the region of the VWF mutation. Combined with the LOKI results, further analysis will help determine if intragenic modification is occurring or if linkage disequilibrium between the mutation and analyzed markers is driving results.
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66

Automated Discovery of Pedigrees and Their Structures in Collections of STR DNA Specimens Using a Link Discovery Tool

Haun, Alex Brian 01 May 2010 (has links)
In instances of mass fatality, such as plane crashes, natural disasters, or terrorist attacks, investigators may encounter hundreds or thousands of DNA specimens representing victims. For example, during the January 2010 Haiti earthquake, entire communities were destroyed, resulting in the loss of thousands of lives. With such a large number of victims the discovery of family pedigrees is possible, but often requires the manual application of analytical methods, which are tedious, time-consuming, and expensive. The method presented in this thesis allows for automated pedigree discovery by extending Link Discovery Tool (LDT), a graph visualization tool designed for discovering linkages in large criminal networks. The proposed algorithm takes advantage of spatial clustering of graphs of DNA specimens to discover pedigree structures in large collections of specimens, saving both time and money in the identification process.
67

The Torsion Angle of Random Walks

He, Mu 01 May 2013 (has links)
In this thesis, we study the expected mean of the torsion angle of an n-stepequilateral random walk in 3D. We consider the random walk is generated within a confining sphere or without a confining sphere: given three consecutive vectors →e1 , →e2 , and →e3 of the random walk then the vectors →e1 and →e2 define a plane and the vectors →e2 and →e3 define a second plane. The angle between the two planes is called the torsion angle of the three vectors. Algorithms are described to generate random walks which are used in a particular space (both without and with confinement). The torsion angle is expressed as a function of six variables for a random walk in both cases: without confinement and with confinement, respectively. Then we find the probability density functions of these six variables of a random walk and demonstrate an explicit integral expression for the expected mean torsion value. Finally, we conclude that the expected torsion angle obtained by the integral agrees with the numerical average torsion obtained by a simulation of random walks with confinement.
68

The Torsion Angle of Random Walks

He, Mu 01 May 2013 (has links)
In this thesis, we study the expected mean of the torsion angle of an n-stepequilateral random walk in 3D. We consider the random walk is generated within a confining sphere or without a confining sphere: given three consecutive vectors →e1 , →e2 , and →e3 of the random walk then the vectors →e1 and →e2 define a plane and the vectors →e2 and →e3 define a second plane. The angle between the two planes is called the torsion angle of the three vectors. Algorithms are described to generate random walks which are used in a particular space (both without and with confinement). The torsion angle is expressed as a function of six variables for a random walk in both cases: without confinement and with confinement, respectively. Then we find the probability density functions of these six variables of a random walk and demonstrate an explicit integral expression for the expected mean torsion value. Finally, we conclude that the expected torsion angle obtained by the integral agrees with the numerical average torsion obtained by a simulation of random walks with confinement.
69

Towards an Action Spectrum for Photoentrainment of the <i>Chlamydomonas ReinhardtII</i> Circadian Clock

Gaskill, Christa 01 December 2008 (has links)
No description available.
70

Cloning of "Animal Cryptochrome" cDNA from the Model Organism <i>CHLAMYDOMONAS REINHARDTII</i> for Functional Analysis of Its Protein Product

Silparasetty, Shobha Lavanya 01 December 2009 (has links)
reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases are involved in the repair of UV light-induced DNA damage using the energy of blue light. In order to determine, if the “animal cryptochrome” gene of C. reinhardtii actually encodes a 6-4 DNA photolyase rather than a photoreceptor, an experimental design was developed to test whether the protein product is able to rescue an E. coli mutant defective in its DNA photolyase gene. The design is as follows: In a first step, the coding region of the “animal cryptochrome” cDNA is cloned. In a second step, the cDNA is inserted in-frame into an E. coli expression vector. In a third step, the construct is transformed into an E. coli photolyase mutant, its expression induced, and the strain tested for better survival after UV light exposure. To accomplish the first step, the cloning of “animal cryptochrome” cDNA, total RNA was successfully extracted from C. reinhardtii 4 hrs into the light phase of a 12 h light/12 h dark cycle and reverse transcribed into cDNA using oligo(dT) primers. After initially unsuccessful attempts at amplifying animal cryptochrome from cDNA or genomic template with a variety of primers and conditions, a short fragment with the expected size of 186 bp was amplifiable with both templates. However, even this fragment was not reliably obtained in every PCR assay. Because of this difficulty, real-time PCR was finally performed in the presence of DMSO (Dimethylsulfoxide) and Betaine. These two adjuvants were reported to improve amplifications particularly for GC-rich templates. C. reinhardtii DNA is especially GC-rich with an average of 64% Gs and Cs. The improved conditions allowed the reliable amplification of the 186 bp fragment from genomic template. It also enabled the amplification of a larger fragment of 528 bp from the same template. The results suggest that a combination of 5% DMSO and 1M Betaine is optimal for the amplification of C. reinhardtii DNA and thus can serve as the basis for successful amplification of the entire 1788 bp coding region of the animal cryptochrome cDNA.
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