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

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 ...


Identification Of A Role For Janus Kinase2 (Jak2) In Skeletal Muscle Mitogenesis, Myogenesis, And Hypertrophy , Symantha Ann Anderson Jan 2005

Identification Of A Role For Janus Kinase2 (Jak2) In Skeletal Muscle Mitogenesis, Myogenesis, And Hypertrophy , Symantha Ann Anderson

Retrospective Theses and Dissertations

Skeletal muscle is a dynamic tissue with tight developmental control and the ability to significantly remodel in the postnatal animal. Understanding the molecular mechanisms underlying skeletal muscle development and postnatal growth is critical to potential therapeutic manipulation. Janus kinase2 (JAK2) is a tyrosine kinase critical for growth of numerous cell types and is causative in many cancers, including leukemia. In this study we sought to understand the role of the JAK/STAT signaling cascade in skeletal muscle. In particular, this research focused on the role of JAK2 in skeletal muscle mitogenesis, myogenesis, and hypertrophy. Little work has been done regarding ...


Translational Control Of Gene Expression Mediated By The 3' Untranslated Region Of Barley Yellow Dwarf Virus , Elizabeth Lynn Pettit Jan 2005

Translational Control Of Gene Expression Mediated By The 3' Untranslated Region Of Barley Yellow Dwarf Virus , Elizabeth Lynn Pettit

Retrospective Theses and Dissertations

The 869 nt 3' untranslated region (3' UTR) of Barley yellow dwarf luteovirus (BYDV) RNA facilitates cap-independent and poly(A) tail-independent translation. A 105 nt cap-independent translation element (BTE, or BYDV TE) within the 3' UTR was previously defined using wheat germ translation extracts (Guo et al., 2000), but additional 3' UTR sequence is required for translation in plant cells. One domain, nt 4918--5008, confers cap-independent translation in vivo in a discrete and strong manner. Some of this extra sequence places the BTE on a phylogenetically conserved, long double-stranded "stalk", making it more accessible to cellular translational machinery. Another sequence ...


Distance-Based Nmr Structure Determination And Refinement, Feng Cui Jan 2005

Distance-Based Nmr Structure Determination And Refinement, Feng Cui

Retrospective Theses and Dissertations

Protein structures play a pivotal role in understanding protein functions. X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) are two main experimental approaches for protein structure determination. The structures determined by NMR are not as accurate as those by X-ray crystallography in general, due to limited distance data (e.g. NOEs) that can be generated from NMR experiments. The NMR modeling algorithms are not well developed either, to produce high-quality structures with desired accuracy and efficiency. To address the NMR modeling issues, a so-called geometric build-up approach for NMR modeling has been developed, which remarkably reduces computing time in determining ...


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 ...


Understanding 16s Ribosomal Rna Conformational Changes During 30s Subunit Assembly , Kristi L. Holmes Jan 2005

Understanding 16s Ribosomal Rna Conformational Changes During 30s Subunit Assembly , Kristi L. Holmes

Retrospective Theses and Dissertations

The purpose of this course of study is to understand the conformational changes that occur in 16S rRNA during ribosomal assembly. The prokaryotic ribosome comprises two asymmetric subunits, the large (50S) and small (30S) subunits. The 30S subunit contains 16S rRNA and the small ribosomal proteins (S1--S21). Functional 30S ribosomal subunits can be reconstituted in vitro from purified components. Reconstitution performed at low temperatures results in a stall in 30S subunit assembly. This stall produces a R&barbelow;econstitution I&barbelow;ntermediate (RI) which sediments at 21S and contains 16S rRNA and a subset of small subunit proteins. In order for RI ...


Molecular And Chemical Characterization Of Genes Involved In Maize Cuticular Wax Biosynthesis , M. Ann D. N. Perera Jan 2005

Molecular And Chemical Characterization Of Genes Involved In Maize Cuticular Wax Biosynthesis , M. Ann D. N. Perera

Retrospective Theses and Dissertations

The primary surfaces of the arial parts of plants, and the surfaces of reproductive organs are covered by an extra cellular layer called the cuticle. The cuticle provides the foremost protection to the plant in order to adapt to the terrestrial environment. The cuticle composed of a biopolymer (cutin), which is embedded in a coating of cuticular waxes. Understanding the biochemical, genetic and physiological mechanisms for the biosynthesis of these cuticular waxes is relatively poor. This body of work has established methods for the chemical analysis of the cuticular waxes of maize plants. I have used these methods to chemically ...


Qtl Mapping And Gene Discovery In Perennial Ryegrass (Lolium Perenne L.) , Yanwen Xiong Jan 2005

Qtl Mapping And Gene Discovery In Perennial Ryegrass (Lolium Perenne L.) , Yanwen Xiong

Retrospective Theses and Dissertations

Perennial ryegrass (Lolium perenne L.) has been used extensively for both forage and turf in temperate regions. To understand the genetic basis of winter hardiness and forage quality and molecular basis of cold acclimation of ryegrass, we mapped quantitative trait loci (QTL) that control winter hardiness and forage quality by using an interspecific ryegrass population and identified a C&barbelow;-repeat (CRT)/dehydration-responsive element (DRE) b&barbelow;inding f&barbelow;actors (CBF)-like gene in perennial ryegrass. Winter hardiness related traits including fall growth (FG), freezing tolerance (FT), and winter survival (WS) were measured over two years. A total of twenty-six QTLs were ...


Identification Of Interface Residues Involved In Protein-Protein And Protein-Dna Interactions From Sequence Using Machine Learning Approaches , Changhui Yan Jan 2005

Identification Of Interface Residues Involved In Protein-Protein And Protein-Dna Interactions From Sequence Using Machine Learning Approaches , Changhui Yan

Retrospective Theses and Dissertations

Identification of interface residues involved in protein-protein and protein-DNA interactions is critical for understanding the functions of biological systems. Because identifying interface residues using experimental methods cannot catch up with the pace at which protein sequences are determined, computational methods that can identify interface residues are urgently needed. In this study, we apply machine-learning methods to identify interface residues with the focus on the methods using amino acid sequence information alone. We have developed classifiers for identification of the residues involved in protein-protein and protein-DNA interactions using a window of primary sequence as input. The classifiers were evaluated using both ...


Cell Envelope Constituents Of Pseudomonas Putida Contributing To Growth And Survival In Low-Water-Content Habitats , Martinus Franciscus Maria Van De Mortel Jan 2005

Cell Envelope Constituents Of Pseudomonas Putida Contributing To Growth And Survival In Low-Water-Content Habitats , Martinus Franciscus Maria Van De Mortel

Retrospective Theses and Dissertations

The ability of bacteria to respond to the ever changing environmental conditions they encounter requires the utilization of a broad range of colonization and survival strategies. One of the most important and probably least understood factors determining bacterial activity in terrestrial habitats is water availability. The goal of this dissertation research was to identify traits that contribute to maintaining a functional cell envelope when cells are dehydrated, which will help us to assess the scope of physiological changes necessary for growth in low-water-content habitats. The primary objective was to identify genes that are specifically regulated by dehydration (matric stress), and ...


Analysis Of A Nuclear Complex Of Proteins That Form A Spindle Matrix During Mitosis In Drosophila , Uttama Rath Jan 2005

Analysis Of A Nuclear Complex Of Proteins That Form A Spindle Matrix During Mitosis In Drosophila , Uttama Rath

Retrospective Theses and Dissertations

A spindle matrix is a macromolecular structure hypothesized to provide a stationary support or strut for the anchorage of motor proteins during force generation, microtubule sliding, and chromosome segregation in mitosis. Previous work in Drosophila has shown Skeletor, as the first putative molecular candidate of spindle matrix structure since it possesses many features consistent with the proposed spindle matrix structure.;We have identified two more putative spindle matrix candidate proteins, Chromator and Megator, using yeast two-hybrid interaction assay, cross-immunoprecipitation and immunocytochemistry. Chromator is a novel and essential chromodomain containing protein that interacts directly with Skeletor and extensively colocalizes with it ...


Subunits Of Highly Fluorescent Protein R-Phycoerythrin As Probes For Cell Imaging And Single-Molecule Detection , Dragan Isailovic Jan 2005

Subunits Of Highly Fluorescent Protein R-Phycoerythrin As Probes For Cell Imaging And Single-Molecule Detection , Dragan Isailovic

Retrospective Theses and Dissertations

R-phycoerythrin (R-PE) subunits and enzymatic digests were characterized by high-performance liquid chromatography (HPLC), capillary and gel electrophoresis, and HPLC-electrospray ionization mass spectrometry. Subunits were isolated from R-PE by HPLC and detected as single molecules by total internal reflection fluorescence microscopy (TIRFM). Favorable spectroscopic characteristics of R-PE subunits and digest peptides in the visible region of spectrum originate from phycoerythrobilin (PEB) and phycourobilin (PUB) chromophores. High absorption coefficients and fluorescence (even under denaturing conditions), broad excitation and emission fluorescence spectra, and low molecular weights make these molecules suitable for fluorescence labeling of biomolecules and cells.;Fluorescent proteins were further formed both ...


Analysis Of Hoxa5 Expression And Function In Development Of The Central Nervous System , Milan Joksimovic Jan 2005

Analysis Of Hoxa5 Expression And Function In Development Of The Central Nervous System , Milan Joksimovic

Retrospective Theses and Dissertations

The Hox genes encode transcription factors that are indispensable for proper spatio-temporal patterning of the vertebrate body axes. In mouse, Hoxa5 transcripts are differentially expressed in specific mesoderm-derived structures and in the most anterior domain of expression in the central nervous system (CNS). However, the functional significance of any pattern of protein-coding RNAs must be verified by correlating the presence of the protein(s) and RNAs. Here we describe the dynamic pattern of HOXA5 protein during mouse embryogenesis. The HOXA5 protein is detected as early as embryonic day (E) 9.0, and is found, as development proceeds, in several mesoderm-derived ...


Exploring Statistical Methods For Analysis Of Microarray Data , Tanzy Mae Tallapoosa Paz Love Jan 2005

Exploring Statistical Methods For Analysis Of Microarray Data , Tanzy Mae Tallapoosa Paz Love

Retrospective Theses and Dissertations

The expansion of molecular biology in recent years has created an increasing amount of data and interest in specific tools to analyze them. Much of these data come from a class of high-throughput technology that measures hundreds or thousands of variables at the same time. One such high-throughput technology currently in use is microarray technology. The three major objectives in expression analysis are data preprocessing, identifying differential expression, and grouping genes by common behavior. Extracting the useful information on gene expression from the available output is not trivial. The data collection process is quite noisy in that non-biological bias may ...


Probing Carbohydrate Biocatalysis Through The Use Of Electrospray Ionization Mass Spectrometry And Isothermal Titration Calorimetry , Corbin James Zea Jan 2005

Probing Carbohydrate Biocatalysis Through The Use Of Electrospray Ionization Mass Spectrometry And Isothermal Titration Calorimetry , Corbin James Zea

Retrospective Theses and Dissertations

Electrospray ionization mass spectrometry,(ESI-MS)-based assays have been newly developed to study three classes of enzymes (sugar nucleotidyltransferases, glycosyltransferases, and phosphorylases) from the three distinct families of life: archaea, eukaryotes, and prokaryotes. These three classes of enzymes play vital roles in carbohydrate storage, degradation and synthesis. The sugar nucleotidyltransferases from Escherichia coli and yeast that biosynthesize UDP-glucose and ADP-glucose respectively were studied using the first ESI-MS assay. Nonlinear regression of the kinetic data was comparable to those determined from the traditional UDP-glucose dehydrogenase coupled assay. This technique allowed us to determine that the yeast sugar nucleotidyltransferase has one binding ...


Sooty Blotch And Flyspeck On Apple: Expansion Of The Fungal Complex, Post-Harvest Removal And Heterogeneity Of Apple Canopy Wetness And Its Impact On The Outcome Of A Disease-Warning System , Jean Carlson Batzer Jan 2005

Sooty Blotch And Flyspeck On Apple: Expansion Of The Fungal Complex, Post-Harvest Removal And Heterogeneity Of Apple Canopy Wetness And Its Impact On The Outcome Of A Disease-Warning System , Jean Carlson Batzer

Retrospective Theses and Dissertations

Sooty blotch and flyspeck (SBFS) fungi blemish the cuticle of apples. Previous studies reported that the SBFS complex is comprised of four species. This is study surveyed the SBFS complex from nine orchards in four Midwestern states (USA). The LSU analyses of the rDNA inferred that 30 species were Dothideomycetes; one species was within the Pleosporales, 27 were within Dothideales, and two species could not be placed at the ordinal level. The LSU sequences of 17 Dothideales species clustered with LSU sequences of known species of Mycosphaerella. Post-harvest dips in commercial disinfestants were used to remove SBFS signs. Apples were ...


Real-Time Monitoring And Manipulation Of Single Bio-Molecules In Free Solution , Hung-Wing Li Jan 2005

Real-Time Monitoring And Manipulation Of Single Bio-Molecules In Free Solution , Hung-Wing Li

Retrospective Theses and Dissertations

The observation and manipulation of single biomolecules allow their dynamic behaviors to be studied to provide insight into molecular genetics, biochip assembly, biosensor design, DNA biophysics.;In a PDMS/glass microchannel, a nonuniform electroosmotic flow (EOF) was created. By using a scanning confocal fluorescence microscope and total internal-reflection fluorescence microscope (TIRFM), we demonstrated that negatively charged DNA molecules were focused by the nonuniform EOF into a thin layer at the glass surface. This phenomenon was applied to selectively detect target DNA molecules without requiring the separation of excessive probes and can be applied continuously to achieve high throughput.;A variable-angle-TIRFM ...


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 ...


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 ...


Genetic Profiling Of Mycoplasma Hyopneumoniae , Melissa L. Madsen Jan 2005

Genetic Profiling Of Mycoplasma Hyopneumoniae , Melissa L. Madsen

Retrospective Theses and Dissertations

A microarray was constructed and applied to transcriptional profiling and genetic variation studies of Mycoplasma hyopneumoniae. The genome sequence enabled the construction of the microarray to allow a global approach to understanding fundamental processes in M. hyopneumoniae . These studies focused on whether M. hyopneumoniae regulates its genes under different environmental conditions and if genetic changes can be correlated with virulence. The microarray consisted of 632 open reading frames represented by polymerase chain reaction products and were used in a two-color experimental design. Data were analyzed using a mixed linear statistical model. Unique features implemented in these studies included the printing ...