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

Relatedness Of Haemophilus Parasuis Strains And Their Proteins' Possible Roles As Virulence Factors, Emilie Susanna Noel Zehr Jan 2008

Relatedness Of Haemophilus Parasuis Strains And Their Proteins' Possible Roles As Virulence Factors, Emilie Susanna Noel Zehr

Retrospective Theses and Dissertations

Haemophilus parasuis, the causative agent of Glasser's disease, is considered to be a remerging pathogen of swine in high-health status herds. Several molecular typing methods have been suggested as alternatives to serotyping, which failed to identify up to 30% of field isolates. This study compared random amplification of polymorphic DNA (RAPD) profiles and protein profiles of H. parasuis reference strains and field isolates as methods for identifying and grouping virulent and avirulent isolates. DNA and protein profiles of 15 reference strains and 31 field isolates of H. parasuis, analyzed with two computer-based similarity analyses, revealed unique and reproducible DNA ...


The Structure And Mechanism Of Saicar Synthetase, Nathaniel Daum Ginder Jan 2008

The Structure And Mechanism Of Saicar Synthetase, Nathaniel Daum Ginder

Retrospective Theses and Dissertations

SAICAR synthetase catalyzes the eighth step in bacterial de novo purine nucleotide biosynthesis: ATP + L-aspartate + CAIR → ADP + Pi + SAICAR Enzymes involved in nucleotide synthesis are common targets for chemotherapeutic and antimicrobial drugs. They work by reducing the rate of growth of rapidly proliferating cells, thus preventing tumor growth and microbial fecundity. L-Alanosine, an L-aspartate analogue that acts as a substrate for SAICAR synthetase, is a natural product with antiviral and antitumor activities. The product of the reaction is a potent inhibitor of adenylosuccinate synthetase and adenylosuccinate lyase and is responsible for L-alanosine toxicity. L-Alanosine may be effective as a chemotherapeutic ...


Understanding The Biological Activity Of Hypericum Species Through Metabolomics Studies, Matthew Lee Hillwig Jan 2008

Understanding The Biological Activity Of Hypericum Species Through Metabolomics Studies, Matthew Lee Hillwig

Retrospective Theses and Dissertations

The Hypericum genus contains plants which biosynthesize various polyketides with various known and unknown biological and medicinal activities. However, many Hypericum species have not been chemically or biochemically characterized. These species represent an opportunity for understanding chemical ecology and for new drug discovery research. Acyl-phloroglucinols are of particular interest since they are the most diverse class of specialized metabolites in Hypericum. We used analytical methods such as HPLC, LC-MS and 2-D NMR to screen Hypericum species for metabolite diversity. One species, H. gentianoides, was investigated further based on its historical use by Native Americans and its unique metabolite fingerprint. This ...


Functional Analysis Of Paralogous Genes In Acetyl Coenzyme A Metabolism, Joel D. Schmidt Jan 2008

Functional Analysis Of Paralogous Genes In Acetyl Coenzyme A Metabolism, Joel D. Schmidt

Retrospective Theses and Dissertations

No abstract provided.


Nutritional And Hormonal Modulation Of Diabetes-Perturbed Folate, Homocysteine, And Methyl Group Metabolism, Kristin M. Nieman Jan 2008

Nutritional And Hormonal Modulation Of Diabetes-Perturbed Folate, Homocysteine, And Methyl Group Metabolism, Kristin M. Nieman

Retrospective Theses and Dissertations

Folate, homocysteine, and methyl group metabolism mutually function to provide methyl groups for numerous biosynthetic- and modification-type reactions necessary for optimal health. Methyl groups from these pathways are utilized in the production of important compounds such as nucleic acids, protein, and phospholipids. Thus it is vital to understand the factors that both disrupt and maintain their delicate balance to prevent disease. Disruption of these metabolic pathways is associated with several pathologies including carcinogenesis, birth defects, and vascular disease. Moreover, the disruption of these metabolic pathways may be a link between chronic disease and complications of that disease. Both nutritional and ...


Use Of Fourier Transform Infrared (Ftir) Spectroscopy To Determine The Health-Promoting Index (Hpi) Of Cow's Milk, Wendy Leanne Thomas Jan 2008

Use Of Fourier Transform Infrared (Ftir) Spectroscopy To Determine The Health-Promoting Index (Hpi) Of Cow's Milk, Wendy Leanne Thomas

Retrospective Theses and Dissertations

Fourier transform infrared (FTIR) spectroscopy steadily has been gaining popularity for the analysis of milk components including total fat, protein, lactose, and ketones. To date, there have been few descriptions of the use of FTIR spectroscopy for the determination of milk fatty acid composition.;The first objective of this thesis was to develop a method utilizing FTIR spectroscopy for prediction of the health-promoting index (HPI) of milk. The HPI is known to affect the relative softness of butter (Bobe et al., 2003); so, this model could be used to predict which cows' milk could be designated for generation of niche ...


The Locations And Signaling Of H-Ras On Endosomes And Plasma Membrane, Xing Wang Jan 2008

The Locations And Signaling Of H-Ras On Endosomes And Plasma Membrane, Xing Wang

Retrospective Theses and Dissertations

No abstract provided.


Development Of An Rna Aptamer To Pd173955n Through Selex, Samir Mehanovic Jan 2008

Development Of An Rna Aptamer To Pd173955n Through Selex, Samir Mehanovic

Retrospective Theses and Dissertations

With all the technology available to us, the causes of cancers are still puzzling researchers all over the world. Everyday different approaches are being tested to help cure various cancers. With the development of molecular biology, we are able to understand cancer more at molecular level, which helps us look at different methods to treat cancer patients.;The molecular basis for leukemia cancers are understood to a level where we are able to design treatments that specifically target proteins responsible for the disease. One of those proteins is the Bcr-Abl tyrosine kinase which is mostly responsible for chronic myelogenous leukemia ...


Investigation Of Allosteric Regulation Of Porcine Fructose-1,6-Bisphosphatase, Jian Lu Jan 2007

Investigation Of Allosteric Regulation Of Porcine Fructose-1,6-Bisphosphatase, Jian Lu

Retrospective Theses and Dissertations

Porcine Fructose-1,6-bisphosphatase is a homotetramer with four identical subunits. It plays a central role in gluconeogenesis and is tightly regulated by metabolites fructose 2,6-bisphosphate (F26P2) and AMP. Loop 52-72, loop 182-194 and residues 7-11 of the N-terminal segment play important role in the mechanism of catalysis and allosteric inhibition by AMP by retaining a structural hydrophobic region. Disruption of the hydrophobic region will evidently affect the catalysis and regulation of FBPase. Mutation of Thr53 reduced the catalysis activity of FBPase, mutation of Thr194 eliminated inhibition of AMP due to its low affinity to the enzyme, while double mutation ...


Effects Of Dietary Conjugated Linoleic Acid On European Corn Borer Survival, Growth, Fatty Acid Composition, And Fecundity, Lindsey Gereszek Jan 2007

Effects Of Dietary Conjugated Linoleic Acid On European Corn Borer Survival, Growth, Fatty Acid Composition, And Fecundity, Lindsey Gereszek

Retrospective Theses and Dissertations

No abstract provided.


Crystallographic Analysis Of Parasponia Andersonii Hemoglobin, Andrea Savage Jan 2007

Crystallographic Analysis Of Parasponia Andersonii Hemoglobin, Andrea Savage

Retrospective Theses and Dissertations

The x-ray crystal structure of ferric Parasponia andersonii hemoglobin has been determined to 2.3 A resolution by molecular replacement with Rice hemoglobin 1 (rHb1). By means of absorbance spectroscopy, electrochemistry and x-ray crystallography, it has been revealed that depending on the oxidation state, the heme iron can exsist in either the pentacoordinate or hexacoordinate form. Pentacoordination of the heme iron is found primarily in the deoxy ferrous (2+) form, whereas the ferric (3+) form is exhibited predominantly in bis-histidine coordination. This is unique among known forms of hemoglobins. Furthermore, the crystallographic data has provided evidence which supports previous works ...


Biophysical Characterization Of The 117 Amino Acids Long N-Terminal Segment Of D-Raf (Isoform A), Oren Tchaicheeyan Jan 2007

Biophysical Characterization Of The 117 Amino Acids Long N-Terminal Segment Of D-Raf (Isoform A), Oren Tchaicheeyan

Retrospective Theses and Dissertations

Drosophila Raf (D-Raf) is an orthologue of Human B-Raf. D-Raf may have two splice variants, a short (Isoform A, I-A) and a long one (Isoform B, I-B). Protocols for over-expression (E. Coli) and purification of 117 amino acids (aa) N-terminal segment (NTS) of D-Raf protein (I-A), both WT and Mutant (T60E) were established. These protein constructs were also biophysically characterized. Thrombin cleavage conditions were optimized, as monitored by 5 amino acid NTS sequencing, mass spectroscopy and SDS-PAGE electrophoresis. An attempt to purify the 160 aa D-Raf (I-B) NTS failed. NMR characterization in a 700 MHz magnet employing three experiments (HSQC ...


Structural And Functional Studies On Membrane Fusion Proteins-Snares, Yibin Xu Jan 2007

Structural And Functional Studies On Membrane Fusion Proteins-Snares, Yibin Xu

Retrospective Theses and Dissertations

Membrane fusion is a ubiquitous and essential intracellular function. Membrane fusion is mediated by a protein superfamily known as N-ethymaleimide-sensitive fusion protein attachment protein receptors (SNAREs). From plant to mammal, there is a remarkable sequence similarity among the SNARE-family related to the conserved function of this family. The function of SNAREs has been proposed to be the key to membrane fusion as minimal fusion machinery. Depending on their distinct membrane distribution, SNAREs were classified into v (vesicle)-SNAREs and t (target)-SNAREs. It is widely believed that SNARE complex assembly by v- and t-SNAREs on opposite membranes offers the ultimate ...


Structural Study Of Yeast Snare Proteins On Membrane By Epr, Yinghui Zhang Jan 2007

Structural Study Of Yeast Snare Proteins On Membrane By Epr, Yinghui Zhang

Retrospective Theses and Dissertations

Membrane fusion is a basic biophysical process involved in cell's physiological activities. The value of studying the exocytosis of mammalian cells and yeast cells lies in that a highly conserved SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein super family mediates this process and is proposed to be the core protein machinery for the membrane. The SNARE proteins located on plasma membrane and vesicle membrane are assembled together to form a trans-SNARE bridging two separate membranes and initiating membrane.;My research centers on how SNARE assembly involved in yeast cells' exocytosis promotes membrane fusion between yeast vesicle and plasma ...


Advanced Detection And Separation Methods: Developments In Surface-Enhanced Raman Scattering Readout Immunoassays And Electrochemically Modulated Liquid Chromatography, Betsy Jean Yakes Jan 2007

Advanced Detection And Separation Methods: Developments In Surface-Enhanced Raman Scattering Readout Immunoassays And Electrochemically Modulated Liquid Chromatography, Betsy Jean Yakes

Retrospective Theses and Dissertations

This dissertation explores the use of novel detection methods for biological and chemical components commonly found in the environment. It encompasses two techniques: surface-enhanced Raman scattering (SERS) and electrochemically modulated liquid chromatography (EMLC).;Immunoassays using SERS as a readout tool have been developed in this laboratory and have shown low levels of detection (i.e., pico- to femtomolar and single binding event detection) for disease and biowarfare agents. This thesis seeks to further the performance of this platform for bacteria detection and explore strategies to increase the SERS response. Specifically, the first section of this dissertation focuses on the detection ...


Biophysical And Biochemical Characterization Of Hexacoordinate Hemoglobins, Benoit Joel Smagghe Jan 2007

Biophysical And Biochemical Characterization Of Hexacoordinate Hemoglobins, Benoit Joel Smagghe

Retrospective Theses and Dissertations

Within the hemoglobin (Hb) superfamily, an unusual group called hexacoordinate hemoglobin (hxHbs) whose members are found in all living organisms is the subject of exciting studies since their discovery. They are named "hexacoordinate" because of reversible coordination of the sixth coordination site of the heme iron by a histidine side chain located in the heme distal pocket. Interestingly, hxHbs share high degree of similarity in their primary sequence and a common globin fold indicating that they might share a common role and that endogenous coordination might be an important part of their not yet characterized physiological function. The characterization of ...


Allosteric Regulation Of Mammalian And Bacterial Fructose-1,6-Bisphosphatases, Justin Keith Hines Jan 2007

Allosteric Regulation Of Mammalian And Bacterial Fructose-1,6-Bisphosphatases, Justin Keith Hines

Retrospective Theses and Dissertations

Fructose-1,6-bisphosphatase (FBPase) is a critical regulatory enzyme in gluconeogenesis. In mammals, the enzyme is subject to metabolic regulation; the hormones insulin and glucagon reciprocally regulate the enzyme in the liver through the controlled production and degradation of the inhibitor fructose-2,6-bisphosphate (Fru-2,6-P2) and hence control hepatic glucose production. FBPase is nearly ubiquitous in living organisms and in the bacterium Escherichia coli , the homologous enzyme is imperative for growth on gluconeogenic substrates. How does this organism regulate FBPase without the use of exogenous hormones or Fru-2,6-P2? Investigations reported herein describe high resolution crystal structures of the enzyme from ...


Kinetic Studies Of Escherichia Coli And Human Saicar Synthetase, Daniel Joseph Binkowski Jan 2007

Kinetic Studies Of Escherichia Coli And Human Saicar Synthetase, Daniel Joseph Binkowski

Retrospective Theses and Dissertations

Phosphoribosyl-aminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) catalyzes the eighth step of de novo IMP biosynthesis in bacteria, and the seventh step in humans. The SAICAR synthetase reaction is analogous to that of adenylosuccinate synthetase (first committed step of AMP biosynthesis), using ATP to ligate 5-amino-imidazole-4-carboxy ribonucleotide and L-aspartate to produce 5-aminoimidazole-4(N-succinylcarboxamide) ribonucleotide (SAICAR). SAICAR synthetase and other enzymes of purine nucleotide biosynthesis are targets of natural products that impair cell growth. Prior to these studies, the kinetic mechanism of any SAICAR synthetase was unknown. Herein are reported the kinetic mechanisms of bacterial and human SAICAR synthetase activities, the structure of the ...


Investigating Reactions Catalyzed By Terpene Synthases In A Novel Model System, Paul Ross Wilderman Jan 2007

Investigating Reactions Catalyzed By Terpene Synthases In A Novel Model System, Paul Ross Wilderman

Retrospective Theses and Dissertations

Terpene synthases are a set of enzymes that initiate the biosynthetic production of the largest class of known natural products. However, not much is known about how these enzymes carry out their complex cyclization reactions to form polycyclic olefins from linear hydrocarbon diphosphates such as geranylgeranyl diphosphate.;Since rice is known to produce many diterpenoid natural products and the rice genome was recently published, sequence information for many putative diterpene synthases was available. This provided the basis for functional characterization of the diterpene synthases from rice (Oryza sativa ssp. Indica). An enzyme producing syn-pimaradiene was identified, followed by those producing ...


Methanobactin And The Membrane-Associated Methane Monooxygenase In Methanotrophy: A Tale Of Two Proteins, Dongwon Choi Jan 2007

Methanobactin And The Membrane-Associated Methane Monooxygenase In Methanotrophy: A Tale Of Two Proteins, Dongwon Choi

Retrospective Theses and Dissertations

No abstract provided.


Investigation Of The Peptide-Lipid Interactions Of A Beta-Hairpin Antimicrobial Peptide Using Solid-State Nmr, Rajeswari Mani Jan 2007

Investigation Of The Peptide-Lipid Interactions Of A Beta-Hairpin Antimicrobial Peptide Using Solid-State Nmr, Rajeswari Mani

Retrospective Theses and Dissertations

Solid-state NMR (SSNMR) has gained importance as a versatile tool to elucidate the structure and function of many chemical and biological molecules. In this thesis, we have used SSNMR to study the interactions of an antimicrobial peptide (AMP), Protegrin-1 (PG-1) with membranes of varying lipid composition. Based on our studies we have proposed a model for the mechanism of action of PG-1 with two different lipid membranes. PG-1 is a disulfide-linked beta-sheet peptide with broad-spectrum antimicrobial activities. Similar to many AMPs, it selectively disrupts the anionic membranes of microbial cells but leaves the cholesterol-rich zwitterionic mammalian cell membranes intact.;Studying ...


Cloning, Expression, Purification, And Characterization Of A Glycoside Hydrolase Family 44 Cellulase From Clostridium Acetobutylicum In Escherichia Coli, Taran Christopher Shilling Jan 2007

Cloning, Expression, Purification, And Characterization Of A Glycoside Hydrolase Family 44 Cellulase From Clostridium Acetobutylicum In Escherichia Coli, Taran Christopher Shilling

Retrospective Theses and Dissertations

Glycoside hydrolase family 44 (GH44) remains one of the smallest and least studied families of cellulases. The cellulosome of Clostridium acetobutylicum ATCC 824 contains the gene CAC0915, which codes for a putative extracellular GH44 catalytic domain with a C-terminal type I dockerin domain. The GH44 catalytic domain was synthesized with codon modifications, ligated into the expression vector pET--22b, and transformed into Escherichia coli BL21 (DE3). Expression during cell growth was induced by isopropyl-beta-D-thiogalactopyranoside and the recombinant protein, produced as a fusion protein containing a C-terminal His6-tag, and isolated from the harvested cells' cytoplasm after sonication. The enzyme has a mass ...


Biochemical Studies Of Mms6--A Biomineralization Protein, Lijun Wang Jan 2007

Biochemical Studies Of Mms6--A Biomineralization Protein, Lijun Wang

Retrospective Theses and Dissertations

Magnetotactic bacteria are aquatic prokaryotes that can move under the direction of a local geomagnetic field. The magnetosomes found in magnetotactic bacteria are arranged in a single chain or chains, which is the physics basis of magnetotaxis trait. It is believed that with the trait of magnetotaxis, magnetotactic bacteria can simplify their search for the optimal oxygen environments.;Mms6 is a magnetosome membrane-associated protein in Magnetospirillum magneticum strain AMB-1. It has 59 amino acids with a hydrophobic N-terminal and a hydrophilic C-terminal region. Magnetite nanoparticles with similar size and shape to bacterial magnetite can be synthesized in vitro in the ...


Characterization Of The Starch Branching Enzymes In Arabidopsis Thaliana, Qinglei Gan Jan 2007

Characterization Of The Starch Branching Enzymes In Arabidopsis Thaliana, Qinglei Gan

Retrospective Theses and Dissertations

The roles of three starch branching enzyme isoforms, BE1, BE2 and BE3, in Arabidopsis leaf starch metabolism were investigated by AtBE mutant analysis. We also determined the expression patterns of BEs in Arabidopsis by GUS staining and microarray experiments. The possible correlation of BE gene expression with other genes in the Arabidopsis genome was analyzed to identify putative genes that are functionally correlated with BEs. Motifs in the promoters of the Arabidopsis BE genes were identified to better understand their expression differences. BE2 and BE3 expression levels during a diurnal cycle were evaluated with isoform specific antibodies. Meantime, the in ...


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 ...


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 ...


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 ...


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.


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 ...


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 ...