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Articles 1 - 19 of 19

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

Structural And Biochemical Insight Into The Inositol Polyphosphate 4-Phosphatase Family Of Proteins , Colin Tucker Shearn Jan 2004

Structural And Biochemical Insight Into The Inositol Polyphosphate 4-Phosphatase Family Of Proteins , Colin Tucker Shearn

Retrospective Theses and Dissertations

Inositol polyphosphate 4-phosphatases (IP4Ps) are lipid phosphatases that remove the 4-position phosphate from the lipid second messenger phosphatidylinositol 3,4-bis-phosphate converting it to phosphatidylinositol 3-phosphate. There are 2 families of IP4P's that are 37% homologous to each other denoted type I and type II. Previously, several different isoforms of both type I and type II IP4P had been identified. These include the beta-spliceoforms of both type I and II that contained a hydrophobic tail instead of a hydrophilic tail and a novel deletion spliceoform found in brain tissue that is approximately 1kDa smaller than type Ialpha called type Ialpha2 ...


Mesoporous Silica Nanomaterials For Applications In Catalysis, Sensing, Drug Delivery And Gene Transfection , Daniela Rodica Radu Jan 2004

Mesoporous Silica Nanomaterials For Applications In Catalysis, Sensing, Drug Delivery And Gene Transfection , Daniela Rodica Radu

Retrospective Theses and Dissertations

The central theme of this dissertation is represented by the versatility of mesoporous silica nanomaterials in various applications such as catalysis and bio-applications, with main focus on biological applications of Mesoporous Silica Nanospheres (MSN). The metamorphosis that we impose to these materials from catalysis to sensing and to drug and gene delivery is detailed in this dissertation. First, we developed a synthetic method that can fine tune the amount of chemically accessible organic functional groups on the pores surface of MSN by exploiting electrostatic and size matching between the cationic alkylammonium head group of the CTAB surfactant and various anionic ...


Multifunctional Mesoporous Silica Nanospheres For Biosensor, Stimuli-Responsive Controlled-Release Drug Delivery Carriers And Gene Transfection Vectors , Cheng-Yu Lai Jan 2004

Multifunctional Mesoporous Silica Nanospheres For Biosensor, Stimuli-Responsive Controlled-Release Drug Delivery Carriers And Gene Transfection Vectors , Cheng-Yu Lai

Retrospective Theses and Dissertations

Structurally well-defined mesoporous silica materials with tunable pore size and narrow pore-size distribution have attracted much attention for their potential applications in sensing, drug delivery and gene transfer. A series of mesoporous silica nanosphere-based (MSN) nano-devices were synthesized and utilized for the aforementioned applications.;For sensing application, we provide a first example in utilization of a multi-functionalized mesoporous silica material to selectively detect dopamine. A second application, rooted in this work, is the selective detection of amino-containing neurotransmitters under physiological condition.;The drug delivery applications have been built around a controlled release drug delivery device. In the original conception, the ...


Investigation Of Microcin 24 For Applications In Food Safety, Mechanism Of Resistance And Effect On Activity After Site-Directed Mutagenesis , Timothy Steven Frana Jan 2004

Investigation Of Microcin 24 For Applications In Food Safety, Mechanism Of Resistance And Effect On Activity After Site-Directed Mutagenesis , Timothy Steven Frana

Retrospective Theses and Dissertations

Microcin 24 is an antimicrobial peptide produced by Escherichia coli with activity against Salmonella typhimurium. In this study microcin 24 was investigated for its potential use in food safety, resistance development, and structure-activity relationship following site-directed mutagenesis. An attempt was made to produce microcin 24 from lactic acid bacteria by substituting the natural, dedicated leader peptide microcin-producing gene with a signal leader from divergicin A, which accesses the general secretion pathway. RNA sequences could be recovered from Carnobacterium divergens harboring an expression vector with the fusion construct, but no microcin activity could be detected. Concurrently, development and mechanism of resistance ...


A Threading Approach To Protein Structure Prediction: Studies On Tnf-Like Molecules, Rev Proteins, And Protein Kinases , Yungok Ihm Jan 2004

A Threading Approach To Protein Structure Prediction: Studies On Tnf-Like Molecules, Rev Proteins, And Protein Kinases , Yungok Ihm

Retrospective Theses and Dissertations

The main focus of this dissertation is the application of the threading approach to specific biological problems. The threading scheme developed in our group targets incorporating important structural features necessary for detecting structural similarity between the target sequence and the template structure. This enables us to use our threading method to solve problems for which sequence-based methods are not very much useful. We applied our threading method to predict the three-dimensional structures of lentivirus (EIAV, HIV-1, FIV, SIV) Rev proteins. Predicted structures of Rev proteins suggest that they share a structural similarity among themselves (four-helix bundle). Also, the threading approach ...


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 ...


Escherichia Coli 30s Ribosomal Subunit Assembly: A Novel Role For The Dnak Chaperone System , Jennifer Anne Maki Jan 2004

Escherichia Coli 30s Ribosomal Subunit Assembly: A Novel Role For The Dnak Chaperone System , Jennifer Anne Maki

Retrospective Theses and Dissertations

The prokaryotic ribosome is a 2.5 MDa particle comprised of two asymmetric subunits, the large (50S) and small (30S) subunits. The large subunit contains two RNAs (5S and 23S) in addition to thirty-four proteins. The small subunit consists of one RNA (16S rRNA) and twenty-one proteins. Although the crystal structure has been solved, much remains to be revealed concerning the assembly of this macromolecular structure. Our laboratory is focused on the assembly of the small subunit. In vitro assembly of this structure was achieved in the late 1960's and early 1970's. At low temperature when 16S rRNA ...


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 ...


The Essential Jil-1 Kinase Regulates Histone H3 Phosphorylation And Maintains Chromatin Structure In Drosophila , Weiguo Zhang Jan 2004

The Essential Jil-1 Kinase Regulates Histone H3 Phosphorylation And Maintains Chromatin Structure In Drosophila , Weiguo Zhang

Retrospective Theses and Dissertations

JIL-1 encodes a chromatin-associated tandem serine/threonine kinase in Drosophila melanogaster. JIL-1 predominantly associates with interbands on polytene chromosomes. It appears at higher levels on the X chromosome than on autosomes in males, and distributes about equally on all chromosomes in females. In addition, in males JIL-1 overlaps with the MSL (for male specific lethal) complex that specifically associates with the male X chromosome on which expression of most genes are upregulated.;We isolated JIL-1 mutants by inducing imprecise excision of an EP element inserted in JIL-1. We found that JIL-1 is required for viability of both females and males ...


Expression Analysis Of Maize Opaque2 Mutants And Glu-1dx5 Transgenic Corn , Hongwu Jia Jan 2004

Expression Analysis Of Maize Opaque2 Mutants And Glu-1dx5 Transgenic Corn , Hongwu Jia

Retrospective Theses and Dissertations

The maize (Zea mays L.) opaque2 (o2) mutant has high lysine content, but soft and starchy kernels. We confirm that Lys content, kernel density, and reduction of zein proteins in o2 mutants are genetic-background dependent. Microarray analysis was carried out by pooling the same amount of mRNA from eight o2 lines to probe the maize Unigene cDNA chip to understand the o2 main effects. 202 genes identified as differentially expressed fit our definition of main effect genes. Comparative analysis of the expression profiles of two additional inbred lines shows that B46WT/B46 o2 with the most extreme phenotype has the ...


Gene Regulation Of Rna Viruses With Uncapped And Non-Polyadenylated Genomic Rna , Ruizhong Shen Jan 2004

Gene Regulation Of Rna Viruses With Uncapped And Non-Polyadenylated Genomic Rna , Ruizhong Shen

Retrospective Theses and Dissertations

New roles of RNAs as regulators of gene expression have emerged and expanded in recent years. However, gene regulation by viral RNA in trans is less noted and not well understood. Barley yellow dwarf virus (BYDV) is a positive sense RNA virus with a single genomic RNA (gRNA). As it replicates it generates three subgenomic RNAs (sgRNA). Data in this dissertation show that BYDV sgRNA2 serves as a regulatory RNA to control viral gene expression. In vitro and In vivo, BYDV sgRNA2 inhibits translation of gRNA, but has less or little effect on translation of sgRNA1, respectively. These data support ...


Protein-Protein Interaction And Electron Transfer: Case Of Cytochrome F And Cytochrome C6 , Tijana Žarković Grove Jan 2004

Protein-Protein Interaction And Electron Transfer: Case Of Cytochrome F And Cytochrome C6 , Tijana Žarković Grove

Retrospective Theses and Dissertations

We used photo-induced reaction as a tool to look to explore dynamics of the protein-protein interaction between cytochrome f and cytochrome c6 from C. reinhardtii. In our studies of electron transfer between 3Zncyt c6 and cyt f(III) we discovered two distinct intracomplex processes corresponding to electron transfer within diprotein complexes termed persistent and transient. The overall reaction remained biphasic and the rate constants for both processes were invariant to the change of ionic strength within the studied interval. The docking of these proteins is due to strong hydrophobic interaction slightly augmented by weak electrostatic attraction. We used covalent cross-linking ...


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 ...


Insights Into The Working Of P-Rex2: An Inositol Polyphosphate 4-Phosphatase Domain Containing Guanine Nucleotide Exchange Factor , Raji Elizabeth Joseph Jan 2004

Insights Into The Working Of P-Rex2: An Inositol Polyphosphate 4-Phosphatase Domain Containing Guanine Nucleotide Exchange Factor , Raji Elizabeth Joseph

Retrospective Theses and Dissertations

Inositol polyphosphate 4-phosphatases (IP4Ps) are enzymes that catalyze the hydrolysis of the 4-position phosphate of phosphatidylinositol 3,4-bisphosphate to form phosphatidylinositol 3-phosphate. Database searches for proteins similar to IP4Ps led to the identification of two novel proteins: P-Rex1 and P-Rex2. These proteins, in addition to sharing similarity with IP4Ps, had a Dbl homology (DH) domain followed by a pleckstrin homology (PH) domain, a characteristic feature of the Dbl family of guanine nucleotide exchange factors (GEFs). P-Rex1 was recently isolated from neutrophils, where it plays a key role in stimulating the neutrophil oxidative burst by activating Rac, a component of the ...


Assembly Of The 30s Ribosomal Subunit: S15 As The Probe , Indumathi Jagannathan Jan 2004

Assembly Of The 30s Ribosomal Subunit: S15 As The Probe , Indumathi Jagannathan

Retrospective Theses and Dissertations

The aim of this study is to dissect molecular events that occur during the assembly of 30S subunit of the E. coli ribosome. The 30S ribosomal subunit is made up of 16S ribosomal RNA (rRNA) and 21 proteins (S1--S21). Crystal structure of the 30S subunit has answered longstanding questions on the three-dimensional organization of its constituents. However, this view does not expose the nature of interesting cooperative movements and conformational changes that occur during the formation of this macromolecular complex. Hence, biochemical and genetic efforts are required to understand these rearrangements.;In this study, we have employed directed hydroxyl radical ...


Molecular And Functional Analysis Of Drosophila Hillarin And Its Leech Homolog , Yun Ji Jan 2004

Molecular And Functional Analysis Of Drosophila Hillarin And Its Leech Homolog , Yun Ji

Retrospective Theses and Dissertations

This thesis describes the molecular and functional analysis of the leech Hillarin and its Drosophila homolog D-hil. Leech Hillarin was identified by screening a leech expression library with the mAb Lan3-15, which specifically labels the axon hillock region of leech neurons. Database searches revealed that leech Hillarin has a number of potential homologs in a variety of organisms such as yeast, cyanobacterium, fly, nematode, mouse and human and that these proteins share two novel protein domains, the W180 domain and the H domain. The W180 domain is enriched with tryptophans whereas the H domain shares high number of invariant residues ...


Site-Directed Mutagenesis In Photosystem I Complex: Functional Analysis Of P700 , Maria Pantelidou Jan 2004

Site-Directed Mutagenesis In Photosystem I Complex: Functional Analysis Of P700 , Maria Pantelidou

Retrospective Theses and Dissertations

Photosynthesis is the process by which plants and cyanobacteria convert light to chemical energy. Photosystem I and photosystem II are the two photosynthetic reaction centers that perform light-driven electron transport across thylakoid membranes. Using photon energy, photosystem I oxidizes plastocyanin, transfers the electron through a series of cofactors, and finally reduces ferredoxin. Photosystem I, consists of 12 or more proteins, 96 chlorophyll alpha molecules, 22 beta-carotenes, two phylloquinones, two lipid molecules, and three iron-sulfur clusters. PsaA and PsaB, the largest subunits, surround the electron transfer chain cofactors with a two-fold symmetry. These cofactors are: P700, the primary electron donor chlorophylls ...


Structural And Molecular Analysis Of Leech Neuronal Proteins, Calsensin And Filamin , Deepa V. Venkitaramani Jan 2004

Structural And Molecular Analysis Of Leech Neuronal Proteins, Calsensin And Filamin , Deepa V. Venkitaramani

Retrospective Theses and Dissertations

This thesis describes the structural and molecular analysis of two leech neuronal proteins, Calsensin and Filamin. Calsensin is an EF-hand calcium-binding protein expressed by a subset of peripheral sensory neurons which fasciculate into a single tract in the leech central nervous system. Calsensin is a 9 kD protein with two EF-hand calcium-binding motifs. Calsensin can multimerize via disulfide bridge formation involving the two cysteine residues in vitro. Furthermore, Calsensin shows differential gel migration depending on the presence or absence of calcium suggesting a conformational change upon calcium binding. Using multidimensional NMR spectroscopy we have determined the solution structure and backbone ...


Functional Interactions Among Starch Biosynthetic Enzymes , Seungtaek Kim Jan 2004

Functional Interactions Among Starch Biosynthetic Enzymes , Seungtaek Kim

Retrospective Theses and Dissertations

Understanding the starch biosynthetic mechanism is often hampered by the existence of many isoforms of the involved enzymes as well as numerous pleiotropic effects of mutations affecting these enzymes. This dissertation investigated interactions among starch biosynthetic enzymes, focusing on both physical association of the proteins and functional interactions in a transgenic in vivo system. Specific protein-protein interactions among the starch biosynthetic enzymes that were indicated by yeast two-hybrid experiments were confirmed directly by affinity chromatography. The functional significance of such interactions, specifically between starch synthase and starch branching enzyme, was studied using heterologous expression in the yeast Saccharomyces cerevisiae. A ...