Biochemistry, Biophysics, and Structural Biology Commons^™

Examination Of The Role Of The Clamp-Loader And Atp Hydrolysis In The Formation Of The Bacteriophage T4 Polymerase Holoenzyme, Michael A. Trakselis, Anthony J. Berdis, Stephen J. Benkovic

Chemistry Faculty Publications

Transient kinetic analyses further support the role of the clamp-loader in bacteriophage T4 as a catalyst which loads the clamp onto DNA through the sequential hydrolysis of two molecules of ATP before and after addition of DNA. Additional rapid-quench and pulse-chase experiments have documented this stoichiometry. The events of ATP hydrolysis have been related to the opening/closing of the clamp protein through fluorescence resonance energy transfer (FRET). In the absence of a hydrolysable form of ATP, the distance across the subunit interface of the clamp does not increase as measured by intramolecular FRET, suggesting gp45 cannot be loaded onto DNA. …

Trace Gas Emissions From The Production And Use Of Domestic Biofuels In Zambia Measured By Open-Path Fourier Transform Infrared Spectroscopy, Isaac T. Bertschi, Robert J. Yokelson, Darold E. Ward, Ted J. Christian, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

[1] Domestic biomass fuels (biofuels) were recently estimated to be the second largest source of carbon emissions from global biomass burning. Wood and charcoal provide approximately 90% and 10% of domestic energy in tropical Africa. In September 2000, we used open-path Fourier transform infrared (OP-FTIR) spectroscopy to quantify 18 of the most abundant trace gases emitted by wood and charcoal cooking fires and an earthen charcoal-making kiln in Zambia. These are the first in situ measurements of an extensive suite of trace gases emitted by tropical biofuel burning. We report emission ratios (ER) and emission factors (EF) for (in order …

Phosphoproteomic Studies Of Smooth Muscle Contraction: Investigation Of Differential Phosphorylation In Relaxed/Contracted Rat Aortic Smooth Muscle Tissue Using Maldi-Tof Ms, Tonya M. Pekar

Theses, Dissertations and Capstones

Many human disorders are associated with the malfunction of smooth muscle tissue, or are related to the capabilities of its proper function—asthma, glaucoma, renal inefficiency, hypertension, and cardiovascular disease. Dysfunctional proteins are frequently implicated as the source of such disorders. As the second highest cause of death in the United States, the epidemic of cardiovascular disease makes the study of smooth muscle of utmost concern.

The capabilities of proteomics and mass spectrometry allow the entire proteome complement of a cell or tissue type to be analyzed at once. This investigation employs such techniques in an effort to better understand the …

Effect Of Dimethyl Sulfoxide And Dimethylformamide On The Stability Of 4-Halo-8quinolinols / Herman Gershon, Donald D. Clarke, And John J. Mcmahon Department Of Chemistry, Fordham University, Bronx, Ny 10458-9993, Usa New York Botanical Garden, Bronx, Ny 10458-9993, Usa, Herman Gershon, Donald Dudley Clarke Phd, John J. Mcmahon

Chemistry Faculty Publications

Polyhalo-8-quinolinols with chlorine or bromine in position 4 were not stable in DMSO or DMF. The degradation product from 4,5-dichloro-8-quinolinol was 5-chloro-4,8-quinolindiol and the major product from 4,5-dibromo-8-quinolinol was 3,5-dibromo-4,8-quinolindiol. 4,5,7-Trichloro- and 4,5,7-tribromo-8-quinolinols yielded similar hydrolytic products, and for the bromo compound, a rebrominated product in DMSO. In DMF rebrornination did not occur. In pyridine-d5 these reactions did not take place, indicating a special ability of DMSO and DMF to cause such hydrolysis at position 4 of 4-halo-8-quinolinols

Tetratricopeptide Repeat Motif-Mediated Hsc70-Msti1 Interaction Molecular Characterization Of The Critical Contacts For Successful Binding And Specificity*, Odutayo O. Odunuge, Judith A. Hornby, Chrisiane Bies, Richard Zimmermann, David J. Pugh, Gregory L. Blatch

Faculty Publications

Murine stress-inducible protein 1 (mSTI1) is a cochaperone that is homologous with the human Hsp70/ Hsp90-organizing protein (Hop). Guided by Hop structural data and sequence alignment analyses, we have used site-directed mutagenesis, co-precipitation assays, circular dichroism spectroscopy, steady-state fluorescence, and surface plasmon resonance spectroscopy to both qualitatively and quantitatively characterize the contacts necessary for the N-terminal tetratricopeptide repeat domain (TPR1) of mSTI1 to bind to heat shock cognate protein 70 (Hsc70) and to discriminate between Hsc70 and Hsp90. We have shown that substitutions in the first TPR motif of Lys8 or Asn12 did not affect binding of mSTI1 to Hsc70, …

Fluorescence Determination Of Tryptophan Side-Chain Accessibility And Dynamics In Triple-Helical Collagen-Like Peptides, K. V. Simon-Lukasik, A. V. Persikov, B. Brodsky, J. A. M. Ramshaw, William Laws, J. B. A. Ross, R. D. Ludescher

Chemistry and Biochemistry Faculty Publications

We report tryptophan fluorescence measurements of emission intensity, iodide quenching, and anisotropy that describe the environment and dynamics at X and Y sites in stable collagen-like peptides of sequence (Gly-X-Y)(n). About 90% of tryptophans at both sites have similar solvent exposed fluorescence properties and a lifetime of 8.5-9 ns. Analysis of anisotropy decays using an associative model indicates that these long lifetime populations undergo rapid depolarizing motion with a 0.5 ns correlation time; however, the extent of fast motion at the Y site is considerably less than the essentially unrestricted motion at the X site. About 10% of tryptophans at …

Constrained Analysis Of Fluorescence Anisotropy Decay: Application To Experimental Protein Dynamics, E. Feinstein, G. Deikus, E. Rusinova, E. L. Rachofsky, J. B. A. Ross, William Laws

Chemistry and Biochemistry Faculty Publications

Hydrodynamic properties as well as structural dynamics of proteins can be investigated by the well-established experimental method of fluorescence anisotropy decay. Successful use of this method depends on determination of the correct kinetic model, the extent of cross-correlation between parameters in the fitting function, and differences between the timescales; of the depolarizing motions and the fluorophore's fluorescence lifetime. We have tested the utility of an independently measured steady-state anisotropy value as a constraint during data analysis to reduce parameter cross correlation and to increase the timescales over which anisotropy decay parameters can be recovered accurately for two calcium-binding proteins. Mutant …

Methylene Tetrahydrofolate Reductase Gene And Coronary Artery Disease, M P. Iqbal, P M. Frossard

Department of Biological & Biomedical Sciences

Abstract is not provided by the author/publisher

Renal Cortical Necrosis: A Case Series Of Nine Patients & Review Of Literature, Syed Sohail Ali, Syed Zulfiqar Rizvi, Suhail Muzaffar, Aasim Ahmad, Akhtar Ali, Sheema H. Hassan

Department of Biological & Biomedical Sciences

Background: The purpose of this study is to review cases of renal cortical necrosis (RCN) which we came across during a period of five years, confirmed on needle biopsy specimens, with literature available so far.
Methods: All renal biopsy records between January 1996 to December 2001 at the Aga Khan University Hospital, Karachi, Pakistan were reviewed to identify patients with histologically proven renal cortical necrosis. Seven patients were also referred by the department of Nephrology, Lady Reading Hospital, Peshawar, Pakistan. Patients' medical records were reviewed for demographic, clinical, and follow up data.
Results: There were total of nine patients identified …

Rec12 (Spo11) Recominase Of Fission Yeast Promotes A Backup, Distributive Pathway For Chromosome Segregation In Meiosis I, Wallace D. Sharif, Mari K. Davidson, Wayne P. Wahls

Journal of the Arkansas Academy of Science

We studied the relationship between recombination and segregation in the fission yeast Schizosaccharomyces pombe. In meiosis, chromosomes undergo two rounds of segregation to produce haploid meiotic products. Crossover meiotic ecombination (chiasmata) promotes chromosome segregation during meiosis I; achiasmatic chromosomes often suffer on disjunction in meiosis I. Recl2 protein is a topoisomerase IIortholog that introduces double-strand DNA breaks that nitiate recombination. The red2 null (deletion) and active site (Y98F) mutants lack recombination and crossovers, and onsequently suffer meiosis I nondisjunction. However, null mutants chromosomes segregate to opposite poles more frequently than predicted. Thus, fission yeast has a backup, "distributive segregation" pathway …

Isovolumetric Regulation In Mammal Cells: Role Of Taurine, B. Ordaz, R. Franco, National University Of Mexico Tuz

School of Veterinary and Biomedical Sciences: Faculty Publications

The ability to regulate cell volume is an ancient conserved trait present in essentially all species through evolution. The maintenance of a constant cell volume is a homeostatic imperative in animal cells. Changes in cell water content affecting the concentration of intracellular messenger molecules impair the complex signaling network, crucial for cell functioning and intercellular communication. Although the renal homeostatic mechanisms exert a precise control of extracellular fluid osmolarity, this is challenged in a variety of pathological situations. The intracellular volume constancy is continuously compromised by the generation of local and transient osmotic microgradients, associated with nutrients uptake, secretion, cytoskeleton …

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies …

Historical Perspectives (Apoptosis), James Curtin, Thomas Cotter

Articles

Apoptosis is one of the most widely studied fields in biology and accounts for over 2% of all life science publications annually. It plays a fundamental role in development, and defects in the regulation of apoptosis are directly implicated in numerous well-known diseases including cancer, neurodegenerative disorders, tissue atrophy and auto-immune diseases. However, the field of apoptosis has humble beginnings and was neglected by biologists for much of its history. This chapter reviews the history of research in apoptosis and highlights key experiments that have contributed significantly to our current understanding of apoptosis. In addition, the topics covered in later …

Urer, The Transcriptional Activator Of The Proteus Mirabilis Urease Gene Cluster, Is Required For Urease Activity And Virulence In Experimental Urinary Tract Infections, Jonathan D. Dattelbaum, C. Virginia Lockatell, David E. Johnson, Harry L.T. Mobley

Chemistry Faculty Publications

Proteus mirabilis, a cause of complicated urinary tract infection, produces urease, an essential virulence factor for this species. UreR, a member of the AraC/XylS family of transcriptional regulators, positively activates expression of the ure gene cluster in the presence of urea. To specifically evaluate the contribution of UreR to urease activity and virulence in the urinary tract, a ureR mutation was introduced into P. mirabilis HI4320 by homologous recombination. The isogenic ureR::aphA mutant, deficient in UreR production, lacked measurable urease activity. Expression was not detected in the UreR-deficient strain by Western blotting with monoclonal antibodies raised against UreD. Urease …

Osmosensitive Taurine Release: Does Taurine Share The Same Efflux Pathway With Chloride And Other Amino Acid Osmolytes?, Rodrigo Franco

School of Veterinary and Biomedical Sciences: Faculty Publications

Swelling subsequent to hyposmotic conditions activates a process of volume regulation present in most cell types. This volume adjustment is accomplished by osmolyte translocation toward the extracellular space to reach a new osmotic equilibrium. Molecules involved in this homeostatic mechanism have been broadly classified into two categories: organic and inorganic osmolytes. Inorganic osmolytes comprise mainly the intracellular ions K⁺ and Cl^–. Cell swelling–induced activation of separate K⁺ and Cl^– channels has been described in most preparations. Organic osmolytes are grouped in three categories: amino acids, polyalcohols, and methylamines. These osmolytes, particularly taurine, are present in …

Role Of Activator Protein-1 In The Down-Regulation Of The Human Cyp2j2 Gene In Hypoxia, Nicole Y. Marden, Eva Fiala-Beer, Shi-Hua Xiang, Michael Murray

School of Veterinary and Biomedical Sciences: Faculty Publications

The cytochrome P450 (CYP) 2J2 arachidonic acid epoxygenase gene was down-regulated at a pre-translational level in human hepatoma-derived HepG2 cells incubated in a hypoxic environment; under these conditions, the expression of c-Jun and c-Fos mRNA and protein was increased. The 5′-upstream region of the CYP2J2 gene was isolated by amplification of a 2341 bp fragment and putative regulatory elements that resembled activator protein-1 (AP-1)-like sequences were identified. From transient transfection analysis, c-Jun was found to strongly activate a CYP2J2–luciferase reporter construct, but co-transfection with plasmids encoding c-Fos or c-Fos-related antigens, Fra-1 and -2, abrogated reporter activity. Using a series …

Mucosal Priming Of Simian Immunodeficiency Virus-Specific Cytotoxic T-Lymphocyte Responses In Rhesus Macaques By The Salmonella Type Iii Secretion Antigen Delivery System, David T. Evans, Li-Mei Chen, Jacqueline Gillis, Kuei-Chin Lin, Brian Harty, Gail P. Mazzara, Ruben O. Donis, Keith G. Mansfield, Jeffrey D. Lifson, Ronald C. Desrosiers, Jorge E. Galán, R. Paul Johnson

School of Veterinary and Biomedical Sciences: Faculty Publications

Nearly all human immunodeficiency virus (HIV) infections are acquired mucosally, and the gut-associated lymphoid tissues are important sites for early virus replication. Thus, vaccine strategies designed to prime virus-specific cytotoxic T lymphocyte (CTL) responses that home to mucosal compartments may be particularly effective at preventing or containing HIV infection. The Salmonella type III secretion system has been shown to be an effective approach for stimulating mucosal CTL responses in mice. We therefore tested ∆phoP-phoQ attenuated strains of Salmonella enterica serovar Typhimurium and S. enterica serovar Typhi expressing fragments of the simian immunodeficiency virus (SIV) Gag protein fused to the …

Method To Detect The Presence Of A Microorganism Or Agent In An Animal, David R. Smith, Laura L. Hungerford, Rodney A. Moxley, Susanne Hinkley, Terry Klopfenstein, Jeff Gray

School of Veterinary and Biomedical Sciences: Faculty Publications

The present invention provides a method to detect the presence of a microorganism or agent in an animal. The method encompasses placement of devices at various locations where the animal resides so as to induce the animal to initiate contact with the device. As a result of this contact, the animal deposits various microorganisms and agents on the device. The device is then tested for the presence of the particular microorganism or agent of interest.

A Phylogenetic Study Of Cytochrome B561 Proteins, Wim Verelst, Han H. Asard

Department of Biochemistry: Faculty Publications

Background: As an antioxidant and cofactor to numerous metabolic enzymes, ascorbate has an essential role in plants and animals. Cytochromes b561 constitute a class of intrinsic membrane proteins involved in ascorbate regeneration. Despite their importance in ascorbate metabolism, no evolutionary analysis has been presented so far on this newly described protein family. Results: Cytochromes b561 have been identified in a large number of phylogenetically distant species, but are absent in fungi and prokaryotes. Most species contain three or four cytochrome b561 paralogous proteins, and the encoding genes usually have four or five exons. At the protein level, sequence similarities are …

Functional Copper At The Acetyl-Coa Synthase Active Site, Javier Seravalli, Welwel Gu, Annie Tam, Erick Strauss, Stephen P. Cramer, Stephen W. Ragsdale

Department of Biochemistry: Faculty Publications

The bifunctional CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) plays a central role in the Wood–Ljungdahl pathway of autotrophic CO₂ fixation. A recent structure of the Moorella thermoacetica enzyme revealed that the ACS active site contains a [4Fe-4S] cluster bridged to a binuclear Cu-Ni site. Here, biochemical and x-ray absorption spectroscopic (XAS) evidence is presented that the copper ion at the M. thermoacetica ACS active site is essential. Depletion of copper correlates with reduction in ACS activity and in intensity of the ‘‘NiFeC’’ EPR signal without affecting either the activity or the EPR spectroscopic properties associated with CODH. In contrast, Zn content …

Transmembrane Movement Of Exogenous Long-Chain Fatty Acids: Proteins, Enzymes, And Vectorial Esterification, Paul N. Black, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

INTRODUCTION......................................................................................................................................................454

FATTY ACIDS AND BIOLOGICAL MEMBRANES.............................................................................................455

Fatty Acid Transport Defined ...............................................................................................................................456

MODEL SYSTEMS TO INVESTIGATE FATTY ACID TRANSPORT ..............................................................456

Genetic Foundations of Fatty Acid Transport....................................................................................................456

PROTEINS IMPLICATED IN FATTY ACID TRANSPORT ...............................................................................456

Fatty Acid Translocase..........................................................................................................................................457

Fatty Acid Binding Protein—Membrane Bound ................................................................................................457

Fatty Acid Transport Protein...............................................................................................................................458

The Long-Chain Fatty Acid Transport Protein FadL .......................................................................................458

Fatty Acyl-CoA Synthetase ...................................................................................................................................459

VECTORIAL ACYLATION: ONE MECHANISM OPERATIONAL IN FATTY ACID TRANSPORT...........460

THE BACTERIAL PARADIGM ...............................................................................................................................460

Energetics of Fatty Acid Transport in Gram-Negative Bacteria......................................................................460

The Fatty Acid Transporter FadL........................................................................................................................461

The Fatty Acyl-CoA Synthetase FadD..................................................................................................................461

Structural Considerations of FACS .....................................................................................................................462

FATTY ACID TRANSPORT AND ACTIVATION IN YEAST: …

The Many Faces Of Vitamin B12: Catalysis By Cobalamin-Dependent Enzymes, Ruma Banerjee, Stephen W. Ragsdale

Department of Biochemistry: Faculty Publications

Vitamin B₁₂ is a complex organometallic cofactor associated with three subfamilies of enzymes: the adenosylcobalamin-dependent isomerases, the methylcobalamin-dependent methyltransferases, and the dehalogenases. Different chemical aspects of the cofactor are exploited during catalysis by the isomerases and the methyltransferases. Thus, the cobalt-carbon bond ruptures homolytically in the isomerases, whereas it is cleaved heterolytically in the methyltransferases. The reaction mechanism of the dehalogenases, the most recently discovered class of B₁₂ enzymes, is poorly understood. Over the past decade our understanding of the reaction mechanisms of B₁₂ enzymes has been greatly enhanced by the availability of large amounts of enzyme …

Demographic Assessment Of The Blue Crab (Callinectes Sapidus) In Chesapeake Bay Using Extractable Lipofuscins As Age Markers, Se-Jong Ju, David H. Secor, H. Rodger Harvey

OES Faculty Publications

The blue crab (Callinectes sapidus) plays an important economic and ecological role in estuaries and coastal habitats from the Gulf of Mexico to the east coast of North America, but demographic assessments are limited by length-based methods. We applied an alternative aging method using biochemical measures of metabolic byproducts (lipofuscins) sequestered in the neural tissue of eyestalks to examine population age structure. From Chesapeake Bay, subsamples of animals collected from the 1998-99 (n-769) and 1999-2000 (n=367) winter dredge surveys were collected and lipofuscin was measured. Modal analysis of the lipofuscin index provided separation into three modes, whereas carapace-width …

Algal Composition And Abundance In The Neuston Surface Micro Layer From A Lake And Pond In Virginia (U.S.A.), Lubomira Burchardt, Harold G. Marshall

Biological Sciences Faculty Publications

A comparative study was conducted that characterized the algae within the neuston, ca 2 mm below the surface, and the algae in the water column from two freshwater habitats. There were significant differences in total algal abundance and the abundance of diatoms, cyanoprokaryotes, and chlorophytes between the neuston and water column algae of these two regions during each season and at both sites. The pond neuston was dominated by chlorophytes, with total algal abundance ranging seasonally from 0.6 to 59.6 x 10^-3 cells ml^-1 compared to water column algal concentrations of 4.1 to 40.4 x 10-3 cells ml-1. …

Comparative Serological And Molecular Analysis Of Group Viii Spiroplasma From Australia And North America, April Carmita Murphy

College of Graduate Studies: Theses & Dissertations (1964–2006)

Spiroplasma bacteria (Mollicutes: Spiroplasmataceae) are characterized by motility, helical morphology and are most frequently found in insect guts and phloem tubes of plants. Traditionally, Spiroplasma have been classified by serology. Recent work has generated 16S rDNA sequences that generally correlate with the serological findings. Although the serology and the 16S rDNA sequence analysis clearly classifies strains to the group level, they do not distinguish between strains within the same group. The goal of this project was to investigate the utility of the 16S-23S rDNA intergenic spacer region sequence as a means to distinguish these closely related strains.

We chose Group …

Mosquitoes, West Nile Virus, Attractants, Competition, Environmental Conditions, And Insecticide Resistance, Alan Bradley Wells

College of Graduate Studies: Theses & Dissertations (1964–2006)

The six main objectives of this project were: 1) test for levels of West Nile Virus in mosquitoes collected at a Fulton County Recreational Facility, 2) assay various mosquito oviposition attractants on West Nile virus positive female mosquitoes, 3) test effects of distance between mosquito infusion attractants, 4) determine effects of study site location, treatment, and competition distances on mosquito collections, 5) test for any correlation between environmental factors and mosquito abundance, and 6) measure levels of enzymatic insecticide resistance present in species of female mosquitoes that tested positive for the presence of West Nile Virus. Ofthe two species that …

Multiple Transporters Associated With Malaria Parasite Responses To Chloroquine And Quinine, Jianbing Mu, Michael T. Ferdig, Xiaorong Feng, Deirdre A. Joy, Junhui Duan, Tetsuya Furuya, G. Subramanian, L. Aravind, Roland A. Cooper, John C. Wootton, Momia Xiong, Xin-Zhuan Su

Biological Sciences Faculty Publications

Mutations and/or overexpression of various transporters are known to confer drug resistance in a variety of organisms. In the malaria parasite Plasmodium falciparum, a homologue of P-glycoprotein, PfMDR1, has been implicated in responses to chloroquine (CO), quinine (ON) and other drugs, and a putative transporter, PfCRT, was recently demonstrated to be the key molecule in CO resistance. However, other unknown molecules are probably involved, as different parasite clones carrying the same pfcrt and pfmdr1 alleles show a wide range of quantitative responses to CO and ON. Such molecules may contribute to increasing incidences of ON treatment failure, the molecular basis …

The Effects Of Student Manipulated Lewis Structure Models On Chemistry Achievement According To Cognitive Level, Kimberly M. Ross

Dissertations and Theses @ UNI

The purpose of this study was to determine if there was a correlation between teaching method or cognitive development and achievement in a unit on Lewis electron dot structures. Forty-six students were taught a unit on Lewis electron dot structures using the traditional paper and pencil method. Thirty-eight students were taught the same unit using a manipulative model instead of the traditional method. Both groups of students were given pre and post-tests on Lewis electron dot structures and their gains after instruction were measured. The Group Assessment of Logical Thinking measured student's cognitive level. Students were categorized as concrete, transitional …