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Articles 1 - 28 of 28

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

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 ...


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 ...


Phenotypic, Biochemical, And Molecular Diversity In Coriander (Coriandrum Sativum L) Germplasm, Pedro Antonio López Jan 2006

Phenotypic, Biochemical, And Molecular Diversity In Coriander (Coriandrum Sativum L) Germplasm, Pedro Antonio López

Retrospective Theses and Dissertations

A study was conducted to assess phenotypic, biochemical, and molecular diversity in coriander accessions from the North Central Regional Plant Introduction Station, in Ames, IA; initially, 139 accessions were characterized for phenological and morphological traits and for fatty-acid composition. A second year of data was collected on those traits from 60 accessions. Fruit essential-oil content and composition were determined, along with a headspace analysis from leaves and an analysis of amplified fragment length polymorphisms (AFLPs). Basic statistics and Pearson correlations were estimated. Matrices of geographical distances (GD), modified Rogers' (MD) distances for molecular data, and Euclidean distances for phenotypic (PD ...


A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne Jan 2006

A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne

Retrospective Theses and Dissertations

We propose a penalty-function method for constrained molecular dynamic simulation by defining a quadratic penalty function for the constraints. The simulation with such a method can be done by using a conventional, unconstrained solver only with the penalty parameter increased in an appropriate manner as the simulation proceeds. More specifically, we scale the constraints with their force constants when forming the penalty terms. The resulting force function can then be viewed as a smooth continuation of the original force field as the penalty parameter increases. The penalty function method is easy to implement and costs less than a Lagrange multiplier ...


Characterization And Interactions Of Tbx2 , Christian Nephi Paxton Jan 2006

Characterization And Interactions Of Tbx2 , Christian Nephi Paxton

Retrospective Theses and Dissertations

T-box (Tbx) proteins are dynamically expressed throughout embryogenesis and appear to have significant roles in a number of developmental processes. The T-box family is characterized by a highly conserved DNA binding domain. Over twenty mammalian T-box proteins have been identified, many of which have the demonstrated ability to regulate transcription. Both activators and repressors of gene transcription have been described within this family, but how their functions are performed is largely unknown;Tbx2 is a powerful transcriptional repressor with functional roles identified in cardiogenesis and limb development. However the functional domain(s) of Tbx2 are poorly characterized. Tbx2 contains a ...


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 ...


Molecular And Genetic Characterization Of A Biotin Biosynthetic Gene In Arabidopsis Encoding Both 7,8-Diaminopelargonic Acid Aminotransferase And Dethiobiotin Synthetase , Elve Chen Jan 2006

Molecular And Genetic Characterization Of A Biotin Biosynthetic Gene In Arabidopsis Encoding Both 7,8-Diaminopelargonic Acid Aminotransferase And Dethiobiotin Synthetase , Elve Chen

Retrospective Theses and Dissertations

Biotin is an essential enzyme cofactor required for different metabolic processes. Plants are a major source of biotin, however, the genes and the protein products of biotin biosynthetic pathway are not fully characterized. We have molecularly characterized the genetically defined Arabidopsis bio1 locus as encoding 7,8-diaminopelargonic acid (DAPA) aminotransferase. Molecular and genetic analysis revealed that the full length BIO1 cDNA is capable of producing a fusion protein that catalyzes not only DAPA aminotransferase, but also dethiobiotin synthetase (BIO3) which is another enzymatic step in the biotin biosynthetic pathway. We refer to this fusion-gene as BIO3/BIO1. This bifunctional enzyme ...


Recognition And Signal Transduction In The Expression Of Phytophthora Resistance In Soybean [Glycine Max (L) Merr] , Hongyu Gao Jan 2006

Recognition And Signal Transduction In The Expression Of Phytophthora Resistance In Soybean [Glycine Max (L) Merr] , Hongyu Gao

Retrospective Theses and Dissertations

Phytophthora sojae, a hemibiotrophic oomycete, is the causal pathogen of stem and root rot disease of soybean (Glycine max [L.] Merr). The annual soybean yield loss suffered from this disease is valued at about 300 million dollars. A series of single Rps genes protect soybean from the root and stem rot disease. In the last two decades Rps1-k has been the most stable and widely used Phytophthora resistance gene in the major soybean-producing regions of the United States;Two classes of CC-NB-LRR-type Rps1-k genes were isolated from the Rps1-k locus. Representative members from each gene class were expressed in transgenic ...


Chemical Reagents In The Study Of Biomolecules , Laura-Mirela Dutcă Jan 2006

Chemical Reagents In The Study Of Biomolecules , Laura-Mirela Dutcă

Retrospective Theses and Dissertations

Chemical reagents are an important tool in the study of biological systems. In this thesis some applications of chemical reagents in the study of biomolecules are presented. Selective cleavage of proteins is a common procedure in many biochemical applications ranging from standard protein sequencing to novel methods in proteomics and bioengineering. Pt(II) complexes are synthetic proteases, with the same selectivity as cyanogen bromide, they cleave at the C-terminus of methionine residues. Pt(II) reagent has several advantages over cyanogen bromide. For example, cyanogen bromide irreversibly converts methionine residues to serine lactone in 70% formic acid, while Pt(II) reagents ...


Cloning, Expression, And Characterization Of A Recombinant Bifunctional Protein -- Porcine Air Carboxylase And Saicar Synthetase , Xin Gao Jan 2006

Cloning, Expression, And Characterization Of A Recombinant Bifunctional Protein -- Porcine Air Carboxylase And Saicar Synthetase , Xin Gao

Retrospective Theses and Dissertations

The conversion of aminoimidazole ribonucleotide (AIR) to carboxyaminoimidazole ribonucleotide (CAIR) by phosphoribosylaminoimidazole carboxylase (AIR carboxylase) and the conversion of conversion of ATP, L-aspartate and CAIR to 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP and phosphate by phosphoribosylaminoimidazolesuccinocarboxamide synthetase (SAICAR synthetase) represent the 7th and 8th steps respectively of de novo purine nucleotide biosynthesis. For the vertebrate enzyme system, AIR carboxylase and SAICAR synthetase are combined in a bifunctional protein encoded by a single gene. Here, a porcine gene encoding AIR carboxylase/SAICAR synthetase was cloned and expressed in Escherichia coli. The native molecular weight of the purified recombinant protein infers an octameric ...


Identification Of Stbel5 Rna As A Long-Distance Mobile Signal In Short-Day Facilitated Tuber Formation , Yueyue Yu Jan 2006

Identification Of Stbel5 Rna As A Long-Distance Mobile Signal In Short-Day Facilitated Tuber Formation , Yueyue Yu

Retrospective Theses and Dissertations

In potato, the BEL1-like transcription factor, StBEL5 and its protein partner POTH1, regulate tuber formation by mediating hormone levels in the stolon tip. Heterografting experiments show that StBEL5 mRNA can move across the graft union to localize in stolon tips and enhance tuber formation. Over-expression of StBEL5 full-length transcripts including the untranslated regions (UTRs) endows transgenic lines with the capacity to overcome the long-day inhibitory effects on tuber formation.;In this study, the precise localization of endogenous StBEL5 mRNA and other gene specific transcripts in the vascular tissues were determined by laser microdissection coupled to laser pressure catapulting (LMPC) and ...


Release Of Human Brain Hexokinase From The Mitochondrial Membrane , David Andrew Skaff Jan 2006

Release Of Human Brain Hexokinase From The Mitochondrial Membrane , David Andrew Skaff

Retrospective Theses and Dissertations

Type I hexokinase (HKI) is the pacemaker of glycolysis in the brain and red blood cell. Recent work has tied hexokinase association with the mitochondrial membrane to the prevention of apoptosis. With increased hexokinase activity and expression in tumor cells, the importance in understanding the release of HKI from the membrane has become extremely important. Glucose 6-phosphate and nucleotides have been shown to effectively release HKI from the membrane; however, the mechanisms by which these molecules can induce release have never been studied;Expressed recombinant HKI protein was lacking the N-terminus that is required for binding to the mitochondrial membrane ...


Structural And Functional Studies On Snares-Mediated Membrane Fusion , Yong Chen Jan 2006

Structural And Functional Studies On Snares-Mediated Membrane Fusion , Yong Chen

Retrospective Theses and Dissertations

Membrane fusion is an essential biological process for vesicle trafficking in eukaryotic cells. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of proteins that have been recognized as key components of protein complexes that drive membrane fusion. The SNARE proteins localized in opposite membranes form a SNARE complex, which bridges the two membranes into close proximity and promotes fusion. Despite considerable sequence divergence among SNARE proteins, this fusion machinery is conserved structurally, mechanistically and evolutionally from yeast to human;Site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) are well established techniques to study the structures of membrane ...


Structural Characterization Of Ligand Binding In Hexacoordinate Hemoglobins , Julie Anne Hoy Jan 2006

Structural Characterization Of Ligand Binding In Hexacoordinate Hemoglobins , Julie Anne Hoy

Retrospective Theses and Dissertations

Hemoglobins are ancient proteins that predate the divergence of prokaryotes and eukaryotes. Although the most thoroughly studied hemoglobins are mammalian oxygen transporters, it has become clear that this function is a recent evolutionary advancement coinciding with the "oxygen revolution" and the development of multicellular organisms. Hemoglobins capable of oxygen transport are highly specialized structurally to maintain pentacoordination of the heme and appropriate ligand rate and equilibrium constants, while preventing autooxidation due to bound oxygen. Their predecessors however, adopt a more energetically favorable hexacoordinate conformation that precludes oxygen transport;Despite the fact that hexacoordinate hemoglobins are ubiquitous in biological organisms, little ...


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 ...


Synthesis Of Tetrasubstituted Olefins And Aryl Ketones Via Carbopalladation Of Alkynes And Nitriles , Chengxiang Zhou Jan 2006

Synthesis Of Tetrasubstituted Olefins And Aryl Ketones Via Carbopalladation Of Alkynes And Nitriles , Chengxiang Zhou

Retrospective Theses and Dissertations

Palladium-catalyzed reactions are versatile methods for carbon-carbon bond formation due to their generality and ability to tolerate a wide range of important organic functional groups. Developing novel Palladium-catalyzed reactions has therefore been of great interest to synthetic chemists for years;The regio- and stereoselective synthesis of tetrasubstituted olefins is a long-pursuing challenge for synthetic chemists. A multi-component reaction route is ideal to generate various tetrasubstituted olefins in a very concise manner and should be highly desirable for applications in combinatorial chemistry. A highly efficient, regio- and stereoselective route to tetrasubstituted olefins has been developed by the Pd-catalyzed three-component reaction of ...


Enhancement Of Plant Performance And Biochemical Constituents In Field And Hairy Root Production Of Echinacea , Fredy Rolando Romero Orellana Jan 2006

Enhancement Of Plant Performance And Biochemical Constituents In Field And Hairy Root Production Of Echinacea , Fredy Rolando Romero Orellana

Retrospective Theses and Dissertations

Echinacea is a commercially important source of natural products and phytopharmaceuticals. Echinacea products currently constitute a significant portion of the rapidly growing, multi-billion dollar natural products market. This popularity has led to the expansion of commercial cultivation of Echinacea and the need to find alternative methods to meet the increasing demands of the phytopharmaceutical market. Two methods of producing biochemical constituents in commercial use include extraction from field-grown plants and in vitro hairy root production;Echinacea seeds in the wild typically show a high degree of dormancy. In order to enhance Echinacea seed germination for field production, alternative methods to ...


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 ...


Signaling Capabilities Of A Novel H-Ras Mutant From The Golgi Apparatus , Daniel R. Zamzow Jan 2006

Signaling Capabilities Of A Novel H-Ras Mutant From The Golgi Apparatus , Daniel R. Zamzow

Retrospective Theses and Dissertations

The paradigm that H-Ras needs to be attached to the plasma membrane to signal has been put into question in the last decade. New insights into H-Ras signaling point to a biological requirement for signaling from endomembranes.;This thesis will demonstrate the abilities of a unique H-Ras mutant that accumulates on the Golgi.


A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld Jan 2006

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld

Retrospective Theses and Dissertations

This dissertation presents a modular software pipeline that searches collections of RNA sequences for novel RNA motifs. In this case the motifs incorporate elements of primary and secondary structure. The motif search pipeline breaks up sets of RNA sequences into shortened segments of RNA primary sequence. The shortened segments are then folded to obtain low energy secondary structures. The distance estimation module of the pipeline then calculates distances between the folded bricks, and then analyzes the resulting distance matrices for patterns;An initial implementation of the pipeline is applied to synthetic and biological data sets. This implementation introduces a new ...


Studies Of Intermediates In Snare-Induced Membrane Fusion , Fan Zhang Jan 2006

Studies Of Intermediates In Snare-Induced Membrane Fusion , Fan Zhang

Retrospective Theses and Dissertations

The purpose of this course of study is to understand the intermediates during SNAREs assembly and the membrane fusion mediated by SNAREs. SNAREs have been proposed to be the minimal machinery for the membrane fusion. According to the location distribution, SNAREs can be classified as either v-(vesicles) or t-(target) SNAREs. The assembly of three SNARE components from the opposing membranes into the ternary complex is believed to provide the ultimate driving force for merging the separate bilayers into a continuous entity. Before this step the t-SNAREs associate as the binary complex on the target membrane to serve as ...


An Examination Of Hexacoordinate Hemoglobins Using The Techniques Of Biochemistry, Biophysics And Molecular Biology , James Thomas Trent Iii Jan 2006

An Examination Of Hexacoordinate Hemoglobins Using The Techniques Of Biochemistry, Biophysics And Molecular Biology , James Thomas Trent Iii

Retrospective Theses and Dissertations

Hexacoordinate hemoglobins are found in a truly diverse array of organisms, ranging from cyanobacteria to humans. The prevalence of these proteins in nature coupled with very high sequence identity between species homologues suggests they have a role vital to life. The high sequence identity also implies that hxHb structural features, including the hexacoordination phenomenon, are critical aspects of the physiological function. A detailed understanding of the ligand binding behavior of these proteins will not only facilitate efforts towards discovering their physiological role(s), but will also help explain how hxHbs perform their function. This dissertation consists of four published papers ...


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 ...


Genetic And Molecular Analysis Of Starch Synthases Functions In Maize And Arabidopsis , Xiaoli Zhang Jan 2006

Genetic And Molecular Analysis Of Starch Synthases Functions In Maize And Arabidopsis , Xiaoli Zhang

Retrospective Theses and Dissertations

Understanding the specific functions played by individual starch synthase isoforms in maize and Arabidopsis will provide important evidence for how highly organized starch structure is made. Starch synthases (SS) catalyze the transfer of the glucosyl moiety from ADP-Glc to the terminus of a growing alpha-(1, 4)-linked glucan linear chain. At least five classes of SSs are identified in higher species, referred to as GBSS, SSI, SSII, SSIII, and SSIVN. They have high similarity in the catalytic and starch-binding domains of the C-termini but differ at their N-termini. All of these enzymes are highly conserved in plant kingdom, which ...


Development Of Aptamer Based Targeted Reversibly Attenuated Probes , Xiangyu Cong Jan 2006

Development Of Aptamer Based Targeted Reversibly Attenuated Probes , Xiangyu Cong

Retrospective Theses and Dissertations

The targeted reversely attenuated probe (TRAP) is an aptamer-based biosensor in which the aptamer activity can be regulated by a specific nucleic acid sequence such as an mRNA. The TRAP has the potential of being developed for imaging gene expression in vivo. The central portion of the TRAP, between the aptamer and the attenuator, is complementary to a target nucleic acid, such as an mRNA, which is referred to as a regulatory nucleic acid (regDNA);I developed 8att-cmRas20 and 9att-cmRas15 ATP DNA TRAPs with regDNA-dependent aptamer activity. The results suggested that, as well as inhibiting the aptamer, the attenuator also ...


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 ...


Molecular Genetic Analyses Of Oilseed Brassica Germplasm: Determination Of Life Forms And Germplasm Management Strategies By Using Microsatellite Markers And Flowering Locus-C (Flc1 And Flc3) Gene Sequences , Von Mark V. Cruz Jan 2006

Molecular Genetic Analyses Of Oilseed Brassica Germplasm: Determination Of Life Forms And Germplasm Management Strategies By Using Microsatellite Markers And Flowering Locus-C (Flc1 And Flc3) Gene Sequences , Von Mark V. Cruz

Retrospective Theses and Dissertations

Molecular markers were utilized in conjunction with phenological and morphological information, and statistical methods for diversity analyses to address plant genetic resource conservation issues. The objectives of this study have been categorized into two sets. The first set pertains to exploratory surveys of genetic variation using molecular markers and DNA sequences to determine if microsatellite markers or variation in two copies of the FLOWERING LOCUS C gene (FLC1 and FLC3) can be used in determining life forms of fifty representative accessions of Brassica napus. The second set of objectives addresses good genebank practices and includes: characterization of flowering time of ...


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 ...