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Repair Of Endonuclease- And Transposon-Induced Dna Double Strand Breaks By Host Factors In Arabidopsis , Zhuying Li Jan 2006

Repair Of Endonuclease- And Transposon-Induced Dna Double Strand Breaks By Host Factors In Arabidopsis , Zhuying Li

Retrospective Theses and Dissertations

The maize Ac/Ds transposable elements are members of the hAT transposon family. Ac/Ds transpose in diverse species and via a mechanism similar to that involved in V(D)J recombination. Here, we studied the repair of Ds transposition-induced hairpins by host factors in Arabidopsis. The results indicate that AtKu could position hairpin-opening to sites close to the hairpin apex. In the absence of AtMre11 or AtKu70, repair junctions have a higher frequency of small deletions (3-10bp) and larger deletions (11-50bp), respectively. Comparison of the repair of I-SceI- and Ds-induced DSB indicates that Ac transposase could influence Ds-induced DSB ...


The Paleopolyploid Nature Of The Soybean Genome: Duplicate Gene Identification, Regional Sequence Characterization And Expression Studies , Jessica Ann Schlueter Jan 2006

The Paleopolyploid Nature Of The Soybean Genome: Duplicate Gene Identification, Regional Sequence Characterization And Expression Studies , Jessica Ann Schlueter

Retrospective Theses and Dissertations

The paleopolyploid nature of the soybean genome was investigated through bioinformatic analysis of ESTs, sequencing of homeologous BAC clones and functional analysis of retained duplicate genes. From ESTs, 294 soybean contig pairs were identified representing retained transcribed duplicate genes. Clustering of synonymous distances between each gene pair identified two mixtures of normal distributions corresponding to two rounds of genome duplication approximately 14.5 and 45 million years ago. Ratios of nonsynonymous to synonymous distances showed that most duplicate gene pairs are under purifying selection. Pearson correlation coefficients of EST-based expression patterns between duplicate pairs illustrated both retain expression and uncorrelated ...


Function Of Autophagy In Development And Abiotic Stress Tolerance In Arabidopsis Thaliana , Yan Xiong Jan 2006

Function Of Autophagy In Development And Abiotic Stress Tolerance In Arabidopsis Thaliana , Yan Xiong

Retrospective Theses and Dissertations

Autophagy is a process in which cytoplasmic components are degraded in the vacuole. It occurs when organisms are subjected to environmental stress conditions or during certain stages of development. Upon induction of autophagy, a portion of cytoplasm is surrounded by a double membrane structure to form an autophagosome. The outer membrane of the autophagosome then fuses with the vacuole and the inner membrane and its contents are degraded by vacuolar hydrolases. The morphological characteristics of autophagy have been observed in plants for decades and several autophagy defective mutants have been isolated recently; however, little is known about the molecular mechanism ...


Controlled Integration Of The Ty5 Retrotransposon In Saccharomyces Ceverisiae [I.E. Cerevisiae] , Junbiao Dai Jan 2006

Controlled Integration Of The Ty5 Retrotransposon In Saccharomyces Ceverisiae [I.E. Cerevisiae] , Junbiao Dai

Retrospective Theses and Dissertations

One essential step in the life cycle of retroelements is the stable integration of a copy of retroelement cDNA into the host genome. Random integration is potentially hazardous and could have deleterious genetic effects to the host. Therefore, elements and their hosts have coevolved mechanisms to regulate retroelement integration. In the budding yeast Saccharomyces cerevisiae, the Ty5 retrotransposon preferentially integrates into domains of heterochromatin. Targeting to these locations is determined by interactions between an amino acid sequence motif at the C-terminus of Ty5 integrase (the targeting domain) and the heterochromatin protein Sir4p. New Ty5 integration hotspots are created when Sir4p ...


The Mechanism Of Arabidopsis Immutans Variegation , Aigen Fu Jan 2006

The Mechanism Of Arabidopsis Immutans Variegation , Aigen Fu

Retrospective Theses and Dissertations

The Arabidopsis immutans (im) is variegated with green sectors and white sectors containing defective plastids due to a nuclear gene mutation. IM is a plastid terminal oxidase (PTOX) sharing similarity with mitochondrial alternative oxidase (AOX). In order to better understand IM's biological roles and variegation mechanism of im, I characterized im plants at different levels;A structural model of IM, in which the diiron reaction center is composed of two conserved histidine and four glutamate residues, was tested by mutagenesis in vitro and in planta. It that these six conserved residues were found essential for IM activity and do ...


Studies Of Hypoxia Response And Regulation Of Hypoxia-Inducible Factor Hif-1 In Caenorhabditis Elegans , Chuan Shen Jan 2006

Studies Of Hypoxia Response And Regulation Of Hypoxia-Inducible Factor Hif-1 In Caenorhabditis Elegans , Chuan Shen

Retrospective Theses and Dissertations

All aerobic organisms require molecular oxygen to generate metabolic energy for normal growth and survival. During evolution, multi-cellular organisms have developed and refined complex networks for adaptation to hypoxic environments at both systemic and cellular levels. Adaptation to hypoxia largely results from changes in the activity and expression of key proteins. These include proteins involved in increasing oxygen delivery to hypoxic tissues and proteins that facilitate glycolysis for anaerobic metabolism. The mammalian transcription factor hypoxia-inducible factor (HIF) is a master regulator of oxygen homeostasis. More than 100 target genes of HIF mediate broad systemic and local responses to hypoxia, including ...


Bayesian Recombination Detection Modeling And Application, Fang Fang Jan 2006

Bayesian Recombination Detection Modeling And Application, Fang Fang

Retrospective Theses and Dissertations

As a key evolutionary process, recombination shapes the genetic structure of virus populations. The increased availability of virus sequences provides a chance to study virus recombination through molecular data. Many statistical methods have been developed, and a lot of the methods are phylogenetic-based. My research focuses on recombination modeling and data analysis;I first apply an existing phylogenetic-base method, Bayesian dual change-point model (DMCP), to investigate the role of representative data types for recombination study. We conclude that consensus sequences are an all-around robust representative of virus genotypes. Using consensus data we study recombination of all full-length hepatitis B virus ...


The Analysis Of Global Gene Expression Related To Starch, Lipid And Protein Composition , Ling Li Jan 2006

The Analysis Of Global Gene Expression Related To Starch, Lipid And Protein Composition , Ling Li

Retrospective Theses and Dissertations

This dissertation provides a greater understanding of starch metabolism and its regulation by using mutants altered in starch accumulation, together with a combination of approaches such as global gene profiling, promoter::GUS/GFP analyses, and genetics;Starch debranching enzymes are critical for starch accumulation. The temporal and spatial co-expression of ISA1 and ISA2 is consistent with previous evidence that they co-function as a protein complex (ISA1/ISA2) for starch synthesis. The extensive temporal and spatial co-expression of ISA2 and ISA3 suggests they might also form a protein complex, taking part in starch metabolism. ISA3 protein is localized in leaf chloroplast ...


Plant Genome Informatics: Evaluation And Analysis Of Genomic Dna Features Involved In The Transcriptional Processing Of Protein Coding Genes , Shannon Dwayne Schlueter Jan 2006

Plant Genome Informatics: Evaluation And Analysis Of Genomic Dna Features Involved In The Transcriptional Processing Of Protein Coding Genes , Shannon Dwayne Schlueter

Retrospective Theses and Dissertations

As biological data collection methods have become more cost effective and less time consuming, the necessity for computational tools to store, manage, and analyze this data has led to the creation of a broad field of research. Bioinformatics, while firmly rooted in the technology of information management, is now a mainstream component in the majority of scientific investigations. With the vast majority of effort in bioinformatics being applied to research on vertebrate species, researchers in the plant sciences have often been left with less than satisfactory tools. The research presented in this dissertation was done in an effort to advance ...


Functional Characterization Of The Rad51 Genes In Zea Mays And Their Roles In Mu Transposition , Jin Li Jan 2006

Functional Characterization Of The Rad51 Genes In Zea Mays And Their Roles In Mu Transposition , Jin Li

Retrospective Theses and Dissertations

In Saccharomyces cerevisiae, Rad51p plays a central role in homologous recombination and DNA repair. Double mutants of the two Zea mays L. rad51 homologs are viable, but male sterile and have ~22% of normal seed set. Light microscopic analyses of male meiosis in these plants reveal: many chromosomes are unpaired at diakinesis and over 33% of quartets carry cells that either lack a nucleolus or have two nucleoli, indicating that non-disjunction occurs at both meiotic divisions. FISH analysis shows that 70% pachytene cells have paired 5S rDNA loci. Thus, maize RAD51 is required for efficient chromosome pairing and proper chromosome ...


Neuronal Functions Of Ahr-1, The Caenorhabditis Elegans Homolog Of The Aryl Hydrocarbon Receptor , Hongtao Qin Jan 2006

Neuronal Functions Of Ahr-1, The Caenorhabditis Elegans Homolog Of The Aryl Hydrocarbon Receptor , Hongtao Qin

Retrospective Theses and Dissertations

The mammalian aryl hydrocarbon receptor (AHR) mediates the toxic effects of dioxins and related compounds. Toxicological and genetic studies have shown that AHR regulates important development events and physiological functions. Interestingly, AHR homologs are found in most metazoans, and studies of AHR regulation and function in invertebrate model systems may provide insight to the ancient functions of AHR. In this thesis, I analyze the endogenous functions of the ahr-1 gene in the nematode Caenorhabditis elegans. ahr-1:GFP is expressed in a subset of neurons. ahr-1 regulates the development of diverse neuronal cell types, including the AVM and PLM touch receptor ...


From Pathway To Regulon In Arabidopsis, Wiesława Izabela Mentzen Jan 2006

From Pathway To Regulon In Arabidopsis, Wiesława Izabela Mentzen

Retrospective Theses and Dissertations

Combined bioinformatic approaches, using genomic and transcriptomic data, are applied to investigate the fatty acid biosynthesis pathway, at the molecular level, and in the context of the system biology of Arabidopsis. Fatty acids are essential components of all known bacterial and eukaryotic cells with critical role in cells as energy reserves and the metabolic precursors for biological membranes. The pathway for fatty acid synthesis seems to be conserved across all living systems. Acetyl-CoA carboxylase, a member of a superfamily of biotin-dependent enzymes, catalyzes the first committed step of the fatty acid biosynthesis pathway. Phylogenetic study exposed complex and intertwined evolutionary ...


The Roles Of Aldehyde Dehydrogenases (Aldhs) In Acetyl-Coa Biosynthesis And Root Elongation In Arabidopsis , Yanling Wei Jan 2006

The Roles Of Aldehyde Dehydrogenases (Aldhs) In Acetyl-Coa Biosynthesis And Root Elongation In Arabidopsis , Yanling Wei

Retrospective Theses and Dissertations

Aldehyde dehydrogenases (ALDHs, EC 1.2.1) oxidize aldehydes into carboxylic acids, and thus are important in regulating the level of toxic aldehydes. ALDHs from eukaryotes were classified into more than 20 families. In mammals Family 2 ALDHs detoxify acetaldehyde and a similar function has been suggested in plants. Specifically, it has been hypothesized that plant Family 2 ALDHs oxidize acetaldehyde generated via ethanolic fermentation and produce acetate for acetyl-CoA biosynthesis through acetyl-CoA synthetase (ACS) in plastids, similar to the yeast pathway termed the "pyruvate dehydrogenase (PDH) bypass". Arabidopsis. thaliana contains three Family 2 ALDHs, two of which are mitochondrial ...