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Articles 1 - 16 of 16

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

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 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 ...


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 ...


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 ...


Functional Analysis Of The Crinkly4 Gene Family In Arabidopsis Thaliana And Viviparous1 Promoter In Zea Mays , Xueyuan Cao Jan 2005

Functional Analysis Of The Crinkly4 Gene Family In Arabidopsis Thaliana And Viviparous1 Promoter In Zea Mays , Xueyuan Cao

Retrospective Theses and Dissertations

The cereal endosperm is an excellent system to study cell differentiation and fate specification. The aleurone of maize is one cell layer and requires continuous positional cues to specify and maintain its identity. A genetic hierarchy is implicated in this process. CRINKLY4 ( Cr4), a receptor-like kinase, belongs to cell fate-specifying genes and is required to specify aleurone cell identity. Viviparous1 ( Vp1), a B3 domain-containing transcription factor, functions late in development to regulate the expression of C1 in aleurone cells. It also plays an important regulatory role in late embryogenesis and seed maturation with abscisic acid (ABA).;The Arabidopsis genome encodes ...


The Mechanism Of Var2 Leaf Variegation , Fei Yu Jan 2005

The Mechanism Of Var2 Leaf Variegation , Fei Yu

Retrospective Theses and Dissertations

The Arabidopsis f&barbelow;ilamentation t&barbelow;emperature s&barbelow;ensitive (FtsH) metalloprotease gene family comprises 12 members (AtFtH1-AtFtsH12 ), including three pairs of closely related genes that are targeted to chloroplasts (AtFtsH2 and AtFtsH8; AtFtsH1 and AtFtsH5; and AtFtsH7 and AtFtsH9). Mutations in AtFtsH5 ( var1) and AtFtsH2 (var2) give rise to variegated plants with green- and white-sectored leaves. Cells in the green sectors contain morphologically normal chloroplasts, whereas cells in the white sectors are blocked in chloroplast biogenesis. A major question is how chloroplasts arise in cells that have a mutant genotype. We have found by two-dimensional (2-D) green gel and gel filtration ...


Co2 Concentrating Mechanism And Signal Transduction Pathway Associated With Limiting Co2 Acclimation In Chlamydomonas Reinhardtii , Yingjun Wang Jan 2005

Co2 Concentrating Mechanism And Signal Transduction Pathway Associated With Limiting Co2 Acclimation In Chlamydomonas Reinhardtii , Yingjun Wang

Retrospective Theses and Dissertations

Many aquatic photosynthetic organisms exhibit a variety of acclimation responses to limiting CO2 availability, including induction of CO2 concentrating mechanisms (CCMs), which represent adaptations to environments with changing and, at times, limiting CO2 availability. Although the characteristics and regulation of limiting CO2 acclimation, including the CCM, in the green alga Chlamydomonas reinhardtii have been well demonstrated by physiological and biochemical studies, much less information is available at the molecular level with regard to the components involved in the CCM and other parts of the limiting CO2 acclimation response. We have applied insertional mutagenesis and genetic approaches in an effort to ...


Genome-Wide Analysis Of Splicing Related Genes And Alternative Splicing In Plants , Bing-Bing Wang Jan 2005

Genome-Wide Analysis Of Splicing Related Genes And Alternative Splicing In Plants , Bing-Bing Wang

Retrospective Theses and Dissertations

The phenomenon of pre-mRNA splicing in eukaryotes has been mostly studied in mammalian and yeast systems. The splicing machinery in plants is thought to be largely conserved relative to animal and fungal organisms. This thesis encompasses systematic studies of splicing-related genes and alternative splicing (AS) in plants. A total of 74 snRNA genes and 395 genes encoding splicing related proteins were identified in Arabidopsis, including the previously elusive U4atac snRNA gene. About 50% of the splicing related genes are duplicated in plants. The duplication ratios for splicing regulators are even higher, indicating that the splicing mechanism is generally conserved among ...


Investigation Of The Molecular Mechanism Of Fertility Restoration In Texas Cytoplasm Maize , David Stewart Skibbe Jan 2004

Investigation Of The Molecular Mechanism Of Fertility Restoration In Texas Cytoplasm Maize , David Stewart Skibbe

Retrospective Theses and Dissertations

Cytoplasmic male sterility (cms) is a maternally inherited inability to produce viable pollen. In Texas (T)-cytoplasm maize, the combined action of two restorer of fertility genes, rfl and rfla , can overcome the male sterile phenotype. Previous research established rf2a encodes a mitochondrial aldehyde dehydrogenase (ALDH) with broad substrate specificity. This broad substrate specificity complicates determining the molecular mechanism of rf2a-mediated fertility restoration. In response, a combination of transgenic, biochemical, reverse genetic, and genomic approaches were utilized. Three additional functional maize ALDH genes (rf2b, rf2c, and rf2d) with differing substrate specificities were identified. Each ALDH gene was characterized via in ...


The Central Role Of Acetyl-Coa In Plant Metabolism, As Examined Through Studies Of Atp Citrate Lyase And The Bio1 Mutant Of Arabidopsis , Elizabeth K. Winters Jan 2004

The Central Role Of Acetyl-Coa In Plant Metabolism, As Examined Through Studies Of Atp Citrate Lyase And The Bio1 Mutant Of Arabidopsis , Elizabeth K. Winters

Retrospective Theses and Dissertations

The acetyl-CoA/biotin network encompasses acetyl-CoA generation and utilization, biotin synthesis, recovery, and transport, and myriad metabolic processes requiring biotin-containing enzymes. To expand understanding of this network and its control, plants with altered levels of ACL (ATP citrate lyase) and BIO1 (adenosylmethionine-8-amino-7-oxononanoate synthase) were examined.;An inducible promoter provides a powerful method to test the effects of altered expression of specific genes. The synthetic GVG promoter, reported to be sterol-inducible in Arabidopsis thaliana, was inducible in Glycine max (soybean) when used to control the GUS reporter gene, or the ACLA or ACLB genes. It showed the same unique pattern in ...


Computational And Molecular Analysis Of Myb Gene Family, Cizhong Jiang Jan 2004

Computational And Molecular Analysis Of Myb Gene Family, Cizhong Jiang

Retrospective Theses and Dissertations

Myb proteins are defined by a highly conserved DNA-specific binding domain termed Myb, which is composed of approximately 50 amino acids with constantly spaced tryptophan residues. Multiple copies of Myb domains often exist as tandem repeats within a single protein. There are up to four tandem Myb repeats present in Myb proteins identified to date (termed R0R1R2R3 hereafter).;In our study, we collected additional Myb genes, and performed a series of phylogenetic analyses to explore the evolutionary origin of Myb genes. The results suggest that the Myb gene family originated from an ancient one Myb-box gene. One and two intragenic ...


Herpes Virus Icp47 And Us11 Suppression Of Ctl Activity Adapted For Use In Gene Therapy , Thomas Joseph Radosevich Jan 2003

Herpes Virus Icp47 And Us11 Suppression Of Ctl Activity Adapted For Use In Gene Therapy , Thomas Joseph Radosevich

Retrospective Theses and Dissertations

A major stumbling block encountered in gene therapy clinical trials has been the rapid destruction of the therapeutic product by the host's immune response. The goal of this work is to diminish the host Cytotoxic T Lymphocyte (CTL) response to gene therapy transgenes and transduced cells by incorporating immunosuppression genes into gene therapy vectors. The processing and presentation of antigens through the class I Major Histocompatibility Complex (class I MHC) pathway is known to be an early response to viral infection. Disruption of the class I MHC pathway results in a decrease of the CD8+ CTL response and prolongs ...