Biochemistry, Biophysics, and Structural Biology Commons^™

Studies On The Roles Of Atp In Nitrogenase Catalysis, Wei Wu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogenase is the enzyme that catalyzes the reduction of nitrogen to ammonia in a reaction requiring MgATP hydrolysis. Two component proteins of nitrogenase are the iron protein (Fe protein) and the molybdenum-iron protein (MoFe protein).

Nitrogenase contains two nucleotide binding sites. During catalysis, the Fe protein binds two MgATP first. The conformational changes induced upon MgATP binding allow the Fe protein to associate with the MoFe protein. After the formation of the Fe protein-MoFe protein complex, a single electron is transferred from the Fe protein to the MoFe protein, an event that is coupled to MgATP hydrolysis in the Fe …

Comparison Of The Mutant Frequency And Mutation Spectra Of Three Non-Genotoxic Carcinogens Oxazepam, Phenobarbital, And Wyeth 14,643 At The Λcii Locus In Big Blue Transgenic Mice, Vijaypreet K. Singh

Honors Capstones

No abstract provided.

Test Of Intron Predictions Reveals Novel Splice Sites, Alternatively Spliced Mrnas And New Introns In Meiotically Regulated Genes Of Yeast, Carrie Davis, Leslie Grate, Marc Spingola, Manuel Ares

Biology Department Faculty Works

Correct identification of all introns is necessary to discern the protein-coding potential of a eukaryotic genome. The existence of most of the spliceosomal introns predicted in the genome of Saccharomyces cerevisiae remains unsupported by molecular evidence. We tested the intron predictions for 87 introns predicted to be present in non-ribosomal protein genes, more than a third of all known or suspected introns in the yeast genome. Evidence supporting 61 of these predictions was obtained, 20 predicted intron sequences were not spliced and six predictions identified an intron-containing region but failed to specify the correct splice sites, yielding a successful prediction …

Method And Apparatus For Three-Dimensional Ultrasound Imaging Of Biopsy Needle, Syed Omar Ishrak, Mir Said Seyed-Bolorforosh, William Thomas Hatfield, Todd Michael Tillman, Brian Peter Geiser, Gregory R. Bashford, Michael Joseph Washburn

Biomedical Imaging and Biosignal Analysis Laboratory

A method and an apparatus for three-dimensional ultrasound imaging of a needle-like instrument, such as a biopsy needle, inserted in a human body. The instrument is visualized by transmitting ultrasound beams toward the instrument and then detecting the echo signals using a linear array of transducer elements. The problem of ultrasound being reflected from a biopsy needle in a direction away from the transducer array is solved by steering the transmitted ultrasound beams t increase the angle at which the beams impinge upon the biopsy needle. Ideally the ultrasound beams are perpendicular to the needle. This increases the system's sensitivity …

Molecular Evolution Of Insecticidal Spore-Forming Bacteria, John Pool

Honors Theses

Molecular methods are increasingly being used to determine the phylogeny of microorganisms. This research was intended to determine phylogenetic relationships for bacteria of the species Bacillus thuringiensis and other members of the Bacillus cereus group. Each strain was analyzed by its sasp-B gene sequence to determine its species classification and relation to other strains studied. Results of this study indicated that according to the sasp-B gene tree, the species Bacillus thuringiensis is a paraphyletic with respect to both Bacillus cereus and Bacillus anthracis. Some unexpected results and implications for species designations are also discussed.

Effect Of Chlamydia Trachomatis Infection And Subsequent Tnfa Secretion On Apoptosis In The Murine Genital Tract, Jean-Luc Perfettini, Toni Darville, Gabriel Gachelin, Philippe Souque, Michel Huerre, Alice Dautry-Varsat, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

The pathology observed during Chlamydia infection is due initially to localized tissue damage caused by the infection itself, followed by deleterious host inflammatory responses that lead to permanent scarring. We have recently reported that the infection byChlamydia in vitro results in apoptosis of epithelial cells and macrophages and that infected monocytes secrete the proinflammatory cytokine interleukin-1β. At the same time, proinflammatory cytokines such as tumor necrosis factor alpha (TNF-α) can also trigger apoptosis of susceptible cells. To study the possible relationship between Chlamydia trachomatis infection and apoptosis in vivo, we used the terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling technique to …

Characterization Of Human T-Cell Leukemia Virus 1 Reverse Transcriptase, Pinky Gundayao Agbuya

Theses and Dissertations in Biomedical Sciences

Human T-cell leukemia virus 1 (HTLV-1) is a type C human retrovirus which has been the causative agent of Adult T-cell leukemia. Replication of the retrovirus; requires a reverse transcriptase which converts the retroviral RNA into DNA which is later incorporated into the host's genome. Very little is known about the reverse transcriptase of HTLV-1. Researchers have attempted to purify HTLV-1 RT by isolating the enzyme from human cell lines. Because large amounts of protein could not be produced by this isolation method, the reverse transcriptase cannot be fully characterized. In this research, a recombinant protein expressed in E. coli …

Novel Function Of Phosphoinositide 3-Kinase In T Cell Ca2+ Signaling, Ao-Lin Hsu, Tsui-Ting Ching, Goutam Sen, Da-Sheng Wan, Subbarao Bondada, Kalwant S. Authi, Ching-Shih Chen

Pharmaceutical Sciences Faculty Publications

This study presents evidence that phosphoinositide (PI) 3-kinase is involved in T cell Ca²⁺ signaling via a phosphatidylinositol 3,4,5-trisphosphate PI(3,4,5)P₃-sensitive Ca²⁺entry pathway. First, exogenous PI(3,4,5)P₃ at concentrations close to its physiological levels induces Ca²⁺ influx in T cells, whereas PI(3,4)P₂, PI(4,5)P₂, and PI(3)P have no effect on [Ca²⁺]_i. This Ca²⁺ entry mechanism is cell type-specific as B cells and a number of cell lines examined do not respond to PI(3,4,5)P₃ stimulation. Second, inhibition of PI 3-kinase by wortmannin and by overexpression of the …

Multi-Pass Reflectron Time-Of-Flight Mass Spectrometer, Curtiss D. Hanson

Patents (University of Northern Iowa)

A novel design for a time-of-flight mass spectrometer capable of tandem mass spectrometry measurements with high resolution and high sensitivity using two variable reflectrons in a co-linear geometry. Variably switched reflectrons are oriented coaxially on opposing ends of the ion flight region allowing multiple passes of the ions along the flight region permitting high resolution, tandem mass spectrometry experiments to be performed. An electrostatic particle guide is incorporated to ensure high ion transmission efficiency in a multi-pass system. In addition to permitting the high transmission efficiency of ions, the EPG can be used in a bipolar pulsed mode to isolate …

Determining The Phylogenetic Relationships Among The Northern Pike (Esox Lucius), The Muskellunge (Esox Masquinongy), And The Silver Pike, Steven W. Foster

Theses, Dissertations and Capstones

Prioritization of taxa has become a necessity due to limited resources available for conservation. Conservation efforts are often concentrated on those threatened and endangered species with the highest taxonomic importance. The silver pike is a rare game fish, often accounting for less than 1% of a total pike population where it is found. Although silver pike are normally found in association with northern pike, they have distinct morphological characteristics and have not been shown to hybridize with the northern pike. Still, many fisheries biologists consider the silver pike to be a color variant of the northern pike, and to date …

Response Properties Of Tibial Campaniform Sensilla On The Cockroach Leg In Restrained Preparations And Freely Moving Animals, Angela L. Ridgel

Theses, Dissertations and Capstones

The ability to detect changes in forces is important for effective use of a leg in posture and locomotion. This thesis examines how forces are detected in the legs of cockroaches by tibial campaniform sensilla. Campaniform sensilla are mechanoreceptors that encode forces through ovoid cuticular caps embedded in the exoskeleton. The tibial sensilla are unique in that they consist of two subgroups with mutually perpendicular cap orientations.

We characterized the responses of the tibial receptors in restrained preparations by applying forces to the leg at controlled magnitudes and rates. The tibial sensilla, as a group, were sensitive to increasing and …

Crystal Structure Of Bis(7-Nitro-8-Quinolinolato)Copper(Ii), Cuc18h10o6n4 / M. Shoja, H. Gershon And D. D. Clarke Fordham University, Department Of Chemistry, Fordham Road, Bronx, Ny 10458, Usa, Massud Shoja, Herman Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

C1sHwCuN406, monoclinic, P121/cl (No. 14), a= 4.567(9) Å, b = 10.723(8) Å, c = 17.095(6) Å, ~ = 100.0(1)0 , v = 824.5 Å3 , Z = 2, Rgt(F) = 0.043, wRgt(F) = 0.067, T = 293 K

Synthesis Of 2-Acetamido-5,6-Dihalophenyl Acetates / Donald D. Clarke, Herman Gershon, And John J. Mcmahon Department Of Chemistry, Fordham University, Bronx, Ny 10458, Usa, Donald Dudley Clarke Phd, Herman Gershon, John J. Mcmahon

Chemistry Faculty Publications

2-Acetamido-5,6-dihalophenyl acetates were synthesized as intermediates for the preparation of 6, 7-dihalo-8-quinolinols via the Skraup procedure

The Influence Of Leptin On Metabolic Expenditure And Thermogenesis During Thyroid Hormone (T₃) Suppression In The Obese (Ob/Ob) Mouse, Brian Kimball Underhill

Theses Digitization Project

No abstract provided.

Effect Of Thyroid Hormone On Formation Of The Nsf Fusion Complex In Normal And Obese Diabetic (Db/Db) Mice, Felipe Barajas Galicia

Theses Digitization Project

No abstract provided.

N-Methyl-D-Aspartate Receptor Subunit Nr2b Is Widely Expressed Throughout The Rat Diencephalon: An Immunohistochemical Study, Arshad Khan, B. Stanley, Lisa Bozzetti, Christina Chin, Cyndi Stivers, Margarita Curras-Collazo

Selected Works Temporary Series

No abstract provided.

N-Methyl-D-Aspartate Receptor Subunit Nr2b Is Widely Expressed Throughout The Rat Diencephalon: An Immunohistochemical Study, Khan, B. Stanley, Lisa Bozzetti, Christina Chin, Cyndi Stivers, Margarita Curras-Collazo

Departmental Papers (Biology)

No abstract provided.

Melanocortin-1-Receptor (Mcr-1) Gene Polymorphisms Associated With The Chicken E Locus Alleles, Andrew Ellett

Inquiry: The University of Arkansas Undergraduate Research Journal

The melanocortin 1-receptor (MCl-R) gene has been associated with E locus phenotypes in chickens. Variant alleles of the E locus are important for accurate down color sexing and also for the inhibition of unwanted tissue pigmentation in broilers. PCR (polymerase chain reaction) based tests for various replacement substitutions found in the published E allele sequences gave unexpected results when tested against known alleles of the E locus. To resolve these issues and gain a better understanding of how replacement substitutions in the MCl-R gene are affecting E locus phenotypes, a number of accessions of the e+, eb, wheaten ( ewh …

The Holliday Junction In An Inverted Repeat Dna Sequence: Sequence Effects On The Structure Of Four-Way Junctions, Brandt F. Eichman, Jeff Vargason, Blaine H.M. Mooers, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 Å. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4° as a right-handed X. A sequence comparison with previous …

Eph Receptors And Ephrins, Masaru Nakamoto

Biology Faculty Publications

The Eph receptors are the largest known family of receptor tyrosine kinases. The Eph receptors and theirmembrane-attached ligands, ephrins, show diverse expression patterns during development. Recent studies havedemonstrated that Eph receptors and ephrins play important roles in many developmental processes, includingneuronal network formation, the patterning of the neural tube and the paraxial mesoderm, the guidance of cellmigration, and vascular formation. In the nervous system, Eph receptors and ephrins have been shown to act aspositional labels to establish topographic projections. They also play a key role in pathway ®nding by axons andneural crest cells. The crucial roles of Eph receptors and …

Absence Of Insect Juvenile Hormones In The American Dog Tick, Dermacentor Veriabilis (Say) (Acari: Ixodidae), And In Ornithodoros Parkeri Cooley (Acari: Argasidae), P. A. Neese, Daniel E. Sonenshine, V. L. Kallapur, C. S. Apperson, R. M. Roe

Biological Sciences Faculty Publications

Synganglia, salivary gland, midgut, ovary, fat body and muscle alone and in combination from the ixodid tick, Dermacentor variabilis (Say), or the argasid tick, Ornithodoros parkeri Cooley, were incubated in vitro in separate experiments with _L-[methyl-³H]methionine and farnesoic acid or with [1-¹⁴C]acetate. Life stages examined in D. variabilis were 3 and 72 h old (after ecdysis) unfed nymphs, partially fed nymphs (18 and 72 h after attachment to the host), fully engorged nymphs (2 d after detachment from host), 3 and 72 h old (after eclosion) unfed females, partially fed unmated females (12–168 …

Applications Of The Atomic Force Microscope Within The Fields Of Haematology And Cytogenetics, Margaret O'Reilly-Crowley

Theses

Atomic force microscopy [AFM] has become a rapidly developing interdisciplinary field of research in recent years. The technique, including instrumentation and specimen preparation methods, is now more sophisticated and its application has increased dramatically. The key advantage of AFM is in providing three-dimensional images of samples imaged. Both size and shape of samples imaged can be obtained allowing their subsequent quantification. Red blood cells [RBCs] and chromosomes were imaged in this work. A brief overview of the current status of biomedical AFM, has been presented in the review.

Measurement of mean cell volume [MCV] of immobilised red blood cells with …

Isovolumic Regulation In Nervous Tissue: A Novel Mechanism Of Cell Volume Regulation, O. Quesada, R. Franco, K. Hernandez-Fonseca, K. Tuz

School of Veterinary and Biomedical Sciences: Faculty Publications

Cell volume regulation is a property present in most animal cell lineages that allows them to recover their original volume after events of swelling or shrinkage. Such events can be caused by changes in external osmolarity or to osmotic gradients generated during normal cell functioning.4,6 The mechanism of cell volume regulation involves transmembrane fluxes of osmotically active solutes in the necessary direction to counteract the net gain or loss of intracellular water.9 The process through which cells recover their normal volume after swelling is named Regulatory Volume Decrease (RVD). This consists of the efflux of inorganic osmolytes, such as K …

Rbcs Suppressor Mutations Improve The Thermal Stability And Co2/O2 Specificity Of Rbcl-Mutant Ribulose-1,5-Bisphosphate Carboxylaseyoxygenase, Yu-Chan Du, Seokjoo Hong, Robert J. Spreitzer

Department of Biochemistry: Faculty Publications

In the green alga Chlamydomonas reinhardtii, a Leu²⁹⁰-to-Phe (L²⁹⁰F) substitution in the large subunit of ribulose-1,5-bisphosphate carboxylaseyoxygenase (Rubisco), which is coded by the chloroplast rbcL gene, was previously found to be suppressed by second-site Ala222-to-Thr and Val²⁶²-to-Leu substitutions. These substitutions complement the photosynthesis deficiency of the L290F mutant by restoring the decreased thermal stability, catalytic efficiency, and CO₂/O₂ specificity of the mutant enzyme back to wild-type values. Because residues 222, 262, and 290 interact with the loop between β strands A and B of the Rubisco small subunit, which is …

Multiple Factors Independently Regulate Hila And Invasion Gene Expression In Salmonella Enterica Serovar Typhimurium, Robin L. Lucas, C. Phoebe Lostroh, Concetta C. Dirusso, Michael P. Spector, Barry L. Wanner, Catherine A. Lee

Department of Biochemistry: Faculty Publications

HilA activates the expression of Salmonella enterica serovar Typhimurium invasion genes. To learn more

about regulation of hilA, we isolated Tn5 mutants exhibiting reduced hilA and/or invasion gene expression. In

addition to expected mutations, we identified Tn5 insertions in pstS, fadD, flhD, flhC, and fliA. Analysis of the

pstS mutant indicates that hilA and invasion genes are repressed by the response regulator PhoB in the absence

of the Pst high-affinity inorganic phosphate uptake system. This system is required for negative control of the

PhoR-PhoB two-component regulatory system, suggesting that hilA expression may …

Multiple Factors Independently Regulate Hila And Invasion Gene Expression In Salmonella Enterica Serovar Typhimurium, Robin L. Lucas, C. Phoebe Lostroh, Concetta C. Dirusso, Michael P. Spector, Barry L. Wanner, Catherine A. Lee

Department of Biochemistry: Faculty Publications

HilA activates the expression of Salmonella enterica serovar Typhimurium invasion genes. To learn more

about regulation of hilA, we isolated Tn5 mutants exhibiting reduced hilA and/or invasion gene expression. In

addition to expected mutations, we identified Tn5 insertions in pstS, fadD, flhD, flhC, and fliA. Analysis of the

pstS mutant indicates that hilA and invasion genes are repressed by the response regulator PhoB in the absence

of the Pst high-affinity inorganic phosphate uptake system. This system is required for negative control of the

PhoR-PhoB two-component regulatory system, suggesting that hilA expression may …

Two-Step Processing Of Human Frataxin By Mitochondrial Processing Peptidase, Patrizia Cavadini, Jiri Adamec, Franco Taroni, Oleksandr Gakh, Grazia Isaya

Department of Biochemistry: Faculty Publications

We showed previously that maturation of the human

frataxin precursor (p-fxn) involves two cleavages by the

mitochondrial processing peptidase (MPP). This observation

was not confirmed by another group, however,

who reported only one cleavage. Here, we demonstrate

conclusively that MPP cleaves p-fxn in two sequential

steps, yielding a 18,826-Da intermediate (i-fxn) and a

17,255-Da mature (m-fxn) form, the latter corresponding

to endogenous frataxin in human tissues. The two cleavages

occur between residues 41–42 and 55–56, and both

match the MPP consensus sequence RX ↓ (X/S). Recombinant

rat and yeast MPP catalyze the pài step 4 and 40 …

Job Compensation In The Biotechnology Core Laboratory, Debra A. Mcmillen, William M. Old, Janice L. Bleibaum, Charles M. Nicolet, Katheryn R. Resing, Gautam Sarath, Satya P. Yadav

Gautam Sarath Publications

The results of a poll of core facility professionals by the Association of Biomolecular Resource Facilities (ABRF) Survey Committee.

Urea Hydrolysis Using Immobilized Urease, Anita Arullan

Student Works (2000-2009)

An inexpensive carrier matrix. vermiculite was used for immobilizing urease. A cost effective and simple method of coupling was developed using vermiculite. Immobilization of urease on Amberlite MB-land Nylon-6 tube were also studied. Activities of free and immobilized urease were studied and compared: Among all methods used for immobilization of urease. the method of coupling the enzyme to vermiculite gave the highest retained activity of 82% (Method I) and 89% (Method 2) at pH 6.0 and 5.5 respectively. Urease immobilized by Method I retained 69% and 30% of its original activity and Method 2 (using glutaraldehyde as coupling agent) retained …

Biochemical Composition Of Particles And Dissolved Organic Matter Slong An Estuarine Gradient: Sources And Implications For Dom Reactivity, Antonio Mannino, H. Rodger Harvey

OES Faculty Publications

The chemical composition of high molecular weight dissolved organic matter (DOM) and particulate organic matter (POM) was examined along the salinity gradient of the Delaware Estuary. DOM was collected and fractionated by tangential-flow ultrafiltration into 1-30 kDa (HDOM; high molecular weight) and 30 kDa to 0.2 μm (VHDOM; very high molecular weight) and compared to particles collected in parallel. Polysaccharides comprised 12-43% of particulate organic carbon (POC), 30-56% of VHDOM carbon, and 7.5-19% of HDOM carbon. Hydrolyzable amino acids comprised 17-38% of POC, 5.4-12% of VHDOM carbon, and 1.5-4.2% of HDOM carbon. Only 7-43% of dissolved organic nitrogen in VHDOM …