Biochemistry, Biophysics, and Structural Biology Commons^™

Further Evidence That Geometries Of Fungicides And Pores In Fungal Wall Must Be Compatible To Show Bioavailability / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

Copper(II) biscomplexes of 3-bromo-6-chloro-8- quinolinol and 6-bromo-3-chloro-8-quinolinol were prepared, the long axes ofwhich were 16.8 A and 17.6 A respectively. The long axes of the pores in the walls of the test fungi were determined: A niger (15.0 A), A. oryzae (16.8 A), M verrucaria (17.4 A), T viride (15.0 A). M circinelloides (not determined), and T mentagrophytes (11 .4 A). When the long axis of the copper(II) complex was was shorter or equal to that of the pore, there was fungitoxicity. When the long axis of the complex was longer than that of the pore in the fungal wall …

Endothelial Cell Cortactin Coordinates Icam-1 Clustering And Actin Cytoskeleton Remodeling During Polymorphonuclear Leukocyte Adhesion And Transmigration, Jennifer Kowalski

Scholarship and Professional Work - LAS

Endothelial cell ICAM-1 interacts with leukocyte beta2 integrins to mediate adhesion and transmit outside-in signals that facilitate leukocyte transmigration. ICAM-1 redistribution and clustering appear necessary for leukocyte transmigration, but the mechanisms controlling ICAM-1 redistribution and clustering have not been identified. We recently reported that Src kinase phosphorylation of endothelial cortactin regulates polymorphonuclear cell (PMN) transmigration. In this study, we tested the hypotheses that the Src family kinase-cortactin pathway mediates association of ICAM-1 with the actin cytoskeleton and that this association is required for ICAM-1 clustering and leukocyte transmigration. Cross-linking ICAM-1 induced cytoskeletal remodeling and a decrease in ICAM-1 lateral mobility, …

Heparin Modulates The 99-Loop Of Factor Ixa: Effects On Reactivity With Isolated Kunitz-Type Inhibitor Domains, Pierre F. Neuenschwander, Stephen R. Williamson, Armen Nalian, Kimberly J. Baker-Deadmond

Faculty Publications

Reactivity of factor IXa with basic pancreatic trypsin inhibitor is enhanced by low molecular weight heparin (enoxaparin). Previous studies by us have suggested that this effect involves allosteric modulation of factor IXa. We examined the reactivity of factor IXa with several isolated Kunitz-type inhibitor domains: basic pancreatic trypsin inhibitor, the Kunitz inhibitor domain of protease Nexin-2, and the first two inhibitor domains of tissue factor pathway inhibitor. We find that enhancement of factor IXa reactivity by enoxaparin is greatest for basic pancreatic trypsin inhibitor (>10-fold), followed by the second tissue factor pathway inhibitor domain (1.7-fold) and the Kunitz inhibitor …

Differential Effects Of Sodium And Magnesium Sulfate On Water Consumption By Beef Cattle, A. S. Grout, D. M. Veira, D. M. Weary, M. A. G. Von Keyserlingk, D. Fraser

Biochemistry Collection

The existing guidelines for maximum sulfate (SO₄) in cattle drinking water are based on Na2SO₄, although many water sources contain greater concentrations of MgSO₄. Two experiments compared the effect of different SO₄ salts on water consumption and fecal DM of cattle. In Exp. 1, 8 yearling heifers (initial BW = 345 ± 8 kg; mean ± SD) were watered twice daily with tapwater or water containing Na₂SO₄ or MgSO₄ at target levels of 1,500, 3,000, or 4,500 mg of SO₄/L for 2-d treatment periods separated by 2 …

Characterization Of Vinyl Chloride Degrading Bacteria From A Serial Anaerobic-Aerobic Chloroethene Bioreactor, Fredrick Heath Damron

Theses, Dissertations and Capstones

Chloroethenes are among the most common groundwater contaminants in the United States. In anoxic groundwater, chloroethenes can be reduced to vinyl chloride (VC), a known carcinogen. The goal of this research was to characterize bacteria that could mineralize VC from a microbial community within a serial aerobic-anaerobic chloroethene bioreactor. Isolations for organisms capable of VC degradation were performed. The ability to degrade VC was first indicated by accumulation of chloride. Gas chromatography assay showed that VC was degraded in cultures capable of chloride accumulation. The epoxyalkane:coenzyme M transferase (EaCoMT) gene which codes for an enzyme previously shown to function in …

Novel Gene Therapeutic Approaches To Brain Cancer, Maria Castro, James Curtin, Gwendalyn King, Marianela Candolfi, Peter Czer, Sandra Sciascia, Kurt Kroeger, Tamer Fakhouri, Sarah Honig, William Kuoy, Terry Kang, Stephen Johnson, Pedro Lowenstein

Books/Book chapters

In the United States, approximately 17,000 people per year are diagnosed with brain tumors, the leading cause of death from cancers in children ages 1-15 year (1,2). Gliomas are the most prevalent type of brain tumors in adults, affecting 3.2/100,000 persons/yr in the United States (www.CBTRUS.org). In spite of advances in surgery, chemotherapy, and radiotherapy, the mean survival time of patients post-diagnosis remains approximately 9-12 months.

Direct Control Of Cell Cycle Gene Expression By Proto-Oncogene Product Actr, And Its Autoregulation Underlies Its Transforming Activity, Maggie C. Louie, Alexey S. Revenko, June X. Zou, Jennifer Yao, Hong-Wu Chen

Collected Faculty Scholarship

ACTR (also called AIB1 and SRC-3) was identified as a coactivator for nuclear receptors and is linked to multiple types of human cancer due to its frequent overexpression. However, the molecular mechanism of ACTR oncogenicity and its function independent of nuclear receptors remain to be defined. We demonstrate here that ACTR is required for both normal and malignant human cells to effectively enter S phase. RNA interference-mediated depletion and chromatin immunoprecipitation assays show that endogenous ACTR directly controls the expression of genes important for initiation of DNA replication, which include cdc6, cdc25A, MCM7, cyclin E, and Cdk2. Moreover, consistent with …

Coordinated Effects Of Distal Mutations On Environmentally Coupled Tunneling In Dihydrofolate Reductase, Lin Wang, Nina M. Goodey, Stephen J. Benkovic, Amnon Kohen

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

One of the most intriguing questions in modern enzymology is whether enzyme dynamics evolved to enhance the catalyzed chemical transformation. In this study, dihydrofolate reductase, a small monomeric protein that catalyzes a single C-H-C transfer, is used as a model system to address this question. Experimental and computational studies have proposed a dynamic network that includes two residues remote from the active site (G121 and M42). The current study compares the nature of the H-transfer step of the WT enzyme, two single mutants, and their double mutant. The contribution of quantum mechanical tunneling and enzyme dynamics to the H-transfer step …

Monosaccharide Interactions With Rh(Iii) Cis-Bipyridine Complexes, Sarah M. Lane

Undergraduate Review

No abstract provided.

A Phylogenomic Profile Of Globins, Serge N. Vinogradov, David Hoogewijs, Xavier Bailly, Raãºl Arredondo-Peter, Julian Gough, Sylvia Dewilde, Luc Moens, Jacques R. Vanfleteren

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FAD-binding domain and the gene-regulating globin coupled sensors, with variable C-terminal domains. The single-domain globins encompass sequences related to chimeric globins and «truncated» hemoglobins with a 2-over-2 instead of the canonical 3-over-3 α-helical fold.

Results

A census of globins in 26 archaeal, 245 bacterial and 49 eukaryote genomes was carried out. Only ~25% of archaea have globins, including globin coupled sensors, related single domain globins and 2-over-2 globins. From one to seven …

Microorganisms Pumping Iron: Anaerobic Microbial Iron Oxidation And Reduction, Karrie A. Weber, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Iron (Fe) has long been a recognized physiological requirement for life, yet for many microorganisms that persist in water, soils and sediments, its role extends well beyond that of a nutritional necessity. Fe(II) can function as an electron source for iron-oxidizing microorganisms under both oxic and anoxic conditions and Fe(III) can function as a terminal electron acceptor under anoxic conditions for iron-reducing microorganisms. Given that iron is the fourth most abundant element in the Earth’s crust, iron redox reactions have the potential to support substantial microbial populations in soil and sedimentary environments. As such, biological iron apportionment has been described …

Purification And Initial Biochemical Characterization Of Atp:Cob(I)Alamin Adenosyltransferase (Eutt) Enzyme Of Salmonella Enterica, Nicole R. Baun, Jorge C. Escalante-Semerena

Department of Biochemistry: Faculty Publications

ATP:cob(I)alamin adenosyltransferase (EutT) of Salmonella

enterica was overproduced and enriched to ~70% homogeneity,

and its basic kinetic parameters were determined. Abundant

amounts of EutT protein were produced, but all of it remained

insoluble. Soluble active EutT protein (~70% homogeneous) was

obtained after treatment with detergent. Under conditions in which

cobalamin (Cbl) was saturating, _Km(ATP) = 10 µM, k_cat = 0.03 s^-1,

and V_max = 54.5 nM min^-1. Similarly, under conditions in which

MgATPwas saturating,K_m(Cbl) = 4.1µM, k_cat = 0.06 s^-1, andV_max= …

Critical Evaluation Of The Claims Made By Pharmaceutical Companies In Drug Promotional Material In Pakistan, Dileep Kumar Rohra, Anwarul Hassan Gilani, Ismail Kamal Memon, Ghazala Perven, Muhammad Talha Khan, Hina Zafar, Rakesh Kumar

Department of Biological & Biomedical Sciences

Background: In Pakistan, there is no mechanism to monitor the drug promotional campaign by pharmaceutical industry despite the fact that there is enough evidence that irrational pharmacotherapy is increasingly encountered even in the developed countries due to unethical practices of pharmaceutical promotion. Objectives. To audit the drug promotional claims made by the pharmaceutical companies in Pakistan.
Methods: Drug promotional pamphlets and brochures containing claims for the drugs, which were circulated by the pharmaceuticalrepresentatives were collected from 122 general practitioners (GPs) from Karachi and Larkana cities of the Sindh Province. The claims were critically analyzed and audited with the help of …

[3120+1kbdel86kb]+[Pn1303k] Genotype In An Emirati Cystic Fibrosis Patient: Indication Of A Founder Mutation In Palestinian Arabs, Danish Saleheen, Philippe M. Frossard, Emmanuelle Girodon

Department of Biological & Biomedical Sciences

Cystic fibrosis (CF) is the most common life-limiting autosomal recessive disorder in Caucasian population. The disease was initially considered to be rare in Middle Eastern countries. 95% of CF in Emirati families is due to two mutations only--p.S549R(T > G) and p.F508del. We report here the case of a patient referred to CF and Respiratory Clinic at Tawam Hospital for cystic fibrosis transmembrane regulator (CFTR) gene screening to ascertain the diagnosis of CF, who was found to carry a unique genotype, signifying the importance of retrieving ancestral histories of patients with monogenic disorders.

Hiv-1 Subtype A Infection In A Community Of Intravenous Drug Users In Pakistan, Saeed Khan, Mohammad A. Rai, Mohammad R. Khanani, Muhammad N. Khan, Syed H. Ali

Department of Biological & Biomedical Sciences

Background: Data on the subtypes of HIV in a population help in predicting the potential foci of epidemic, tracking the routes of infection and following the patterns of the virus' genetic divergence. Globally, the most prevalent HIV infection is the HIV-1 subtype C. In Asia, predominant subtypes of HIV-1 are B, C, and CRF-01AE. During the last few years, HIV prevalence in Pakistan has taken the form of a concentrated epidemic in at least two high risk groups, namely, Intravenous Drug Users (IDUs) and Male Sex Workers (MSWs). Factors that have facilitated the proliferation of HIV infection include transmission through …

Fluorescent Analysis Of Translesion Dna Synthesis By Using A Novel, Non-Natural Nucleotide Analogue, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The replication of damaged DNA is a promutagenic process that can lead to disease development. This report evaluates the dynamics of nucleotide incorporation opposite an abasic site, a commonly formed DNA lesion, by using two fluorescent nucleotide analogues, 2-aminopurine deoxyribose triphosphate (2-APTP) and 5-phenylindole deoxyribose triphosphate (5-PhITP). In both cases, the kinetics of incorporation were compared by using a 32 P-radiolabel extension assay versus a fluorescence-quenching assay. Although 2-APTP is efficiently incorporated opposite a templating nucleobase (thymine), the kinetics for incorporation opposite an abasic site are significantly slower. The lower catalytic efficiency hinders its use as a probe to study …

Recent Developments Inthe Mechanistic Enzymology Of The Atp-Dependent Lon Protease From Escherichia Coli: Highlights From Kinetic Studies, Irene Lee, Anthony J. Berdis, Carolyn K. Suzuki

Chemistry Faculty Publications

Lon protease, also known as protease La, is one of the simplest ATP-dependent proteases that plays vital roles in maintaining cellular functions by selectively eliminating misfolded, damaged and certain short-lived regulatory proteins. Although Lon is a homo-oligomer, each subunit of Lon contains both an ATPase and a protease active site. This relatively simple architecture compared to other hetero-oligomeric ATP-dependent proteases such as the proteasome makes Lon a useful paradigm for studying the mechanism of ATP-dependent proteolysis. In this article, we survey some recent developments in the mechanistic characterization of Lon with an emphasis on the utilization of pre-steady-state enzyme kinetic …

Nanoelectropulse-Driven Membrane Perturbation And Small Molecule Permeabilization, P. Thomas Vernier, Yinghua Sun, Martin A. Gundersen

Bioelectrics Publications

Background
Nanosecond, megavolt-per-meter pulsed electric fields scramble membrane phospholipids, release intracellular calcium, and induce apoptosis. Flow cytometric and fluorescence microscopy evidence has associated phospholipid rearrangement directly with nanoelectropulse exposure and supports the hypothesis that the potential that develops across the lipid bilayer during an electric pulse drives phosphatidylserine (PS) externalization.

Results
In this work we extend observations of cells exposed to electric pulses with 30 ns and 7 ns durations to still narrower pulse widths, and we find that even 3 ns pulses are sufficient to produce responses similar to those reported previously. We show here that in contrast to …

Plasma Membrane Voltage Changes During Nanosecond Pulsed Electric Field Exposure, W. Frey, R. O. Price, P. F. Blackmore, R. P. Joshi, R. Nuccitelli, S. J. Beebe, K. H. Schoenbach, J. F. Kolb

Bioelectrics Publications

The change in the membrane potential of Jurkat cells in response to nanosecond pulsed electric fields was studied for pulses with a duration of 60 ns and maximum field strengths of similar to 100 kV/cm (100 V/cell diameter). Membranes of Jurkat cells were stained with a fast voltage-sensitive dye, ANNINE-6, which has a subnanosecond voltage response time. A temporal resolution of 5 ns was achieved by the excitation of this dye with a tunable laser pulse. The laser pulse was synchronized with the applied electric field to record images at times before, during, and after exposure. When exposing the Jurkat …

Sequential Processing Of A Mitochondrial Tandem Protein: Insights Into Protein Import In Schizosaccharomyces Pombe, Oleh Khalimonchuk, Martin Ott, Soledad Funes, Kai Ostermann, Gerhard Rödel, Johannes M. Herrmann

Department of Biochemistry: Faculty Publications

The sequencing of the genome of Schizosaccharomyces pombe revealed the presence of a number of genes encoding tandem proteins, some of which are mitochondrial components. One of these proteins (pre-Rsm22- Cox11) consists of a fusion of Rsm22, a component of the mitochondrial ribosome, and Cox11, a factor required for copper insertion into cytochrome oxidase. Since in Saccharomyces cerevisiae, Cox11 is physically attached to the mitochondrial ribosome, it was suggested that the tandem organization of Rsm22-Cox11 is used to covalently tie the mitochondrial ribosome to Cox11 in S. pombe. We report here that pre-Rsm22-Cox11 is matured in two subsequent …

A Characterization Of Subterranean Termites In Nebraska Using Micro-Morphological And Molecular Techniques, Timothy J. Husen, Shripat T. Kamble, Julie M. Stone

Department of Biochemistry: Faculty Publications

Recent studies have demonstrated a great potential for the use of molecular biology in Reticulitermes species identification and to study other aspects of termite biology. This study utilized micro-morphological identification and microsatellite Simple Sequence Length Polymorphic (SSLP) DNA genotyping to characterize subterranean termites collected from 73 locations across the state of Nebraska. Morphological characters of soldier termites from 30/73 collection sites revealed the presence of two species, Reticulitermes flavipes (Kollar) and R. tibialis Banks. Morphology of the gular plate ratio was used for species differentiation. Deoxyribonucelic acid (DNA) was extracted from termite workers (from all samples) and used as a …

The Effects Of Varying The Timing Of Inputs On A Neural Oscillator, Christina Ambrosio-Mouser, Farzan Nadim, Amitabha Bose

Publications and Research

The gastric mill network of the stomatogastric ganglion of the crab Cancer borealis is comprised of a set of neurons that require modulatory input from outside the stomatogastric ganglion and input from the pyloric network of the animal in order to oscillate. Here we study how the frequency of the gastric mill network is determined when it receives rhythmic input from two different sources but where the timing of these inputs may differ. We find that over a certain range of the time difference one of the two rhythmic inputs plays no role what so ever in determining the network …

Never Let Me Clone? Countering An Ethical Argument Against The Reproductive Cloning Of Humans, Yvette Pearson

Philosophy Faculty Publications

In the March 2006 issue of EMBO reports, Christof Tannert, a bioethicist at the Max Delbrück Research Centre in Berlin, Germany, presented a moral argument against human reproductive cloning on the basis of Immanuel Kant’s categorical imperative (Tannert, 2006). In this article, I address some problems with Tannert’s views and show that our concerns about this prospective procedure should prompt us to scrutinize carefully the conventional procreative practices and attitudes. Indeed, if we set aside objections that are grounded in genetic determinism, many of the offensive features of human cloning are identical to problems with procreation by more conventional means, …

2-Aminoethoxydiphenyl Borate As A Prototype Drug For A Group Of Structurally Related Calcium Channel Blockers In Human Platelets, Yuliya Dobrydneva, Christopher J. Abelt, Beth Dovel, Celina M. Thadigiri, Roy L. Williams, Peter F. Blackmore

Chemistry & Biochemistry Faculty Publications

We have synthesized a series of 2-aminoethoxydiphenyl borate (2-APB, 2,2-diphenyl-1,3,2-oxazaborolidine) analogs and tested their ability to inhibit thrombin-induced Ca²⁺ influx in human platelets. The analogs were either synthesized by adding various substituents to the oxazaborolidine ring (methyl, dimethyl, tert-butyl, phenyl, methyl phenyl, and pyridyl) or increasing the size of the oxazaborolidine ring to seven- and nine-membered rings. NMR analysis of the boron-containing analogs suggests that each of them exist as a ring structure through the formation of an N -> B coordinate bond (except for the hexyl analog). The possibility that these boron-containing compounds formed dimers was also …

Structural And Thermodynamic Parameters Associated With The Interaction Of Cobalt (Iii) Complexes And Duplex Dna, Jaime M. Ferreira

Seton Hall University Dissertations and Theses (ETDs)

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Role Of Mdm2 In Cell Growth Regulation, Rebecca Anne Frum

Theses and Dissertations

MDM2 has been shown to induce G0-Gl/S phase arrest. To determine the cell cycle step targeted by MDM2, flow cytometry was employed to detect induction of events during the G1-S phase transition in MDM2-arrested cells. MDM2 overexpression does not prevent expression of cyclin D, cyclin D-CDK mediated phosphorylation of Rb or cyclin E in normal, immortal or tumor-derived cells. However, MDM2 down-regulates cyclin A expression specifically in normal cells, which is associated with G1 arrest. The domain of MDM2 capable of this function is located within its N-terminal 58-109 amino acids. To down-regulate cyclin A, MDM2 requires a functional pl6/Brg …

Novel Cancer Therapeutics, The Generation Of Ros, And Cell Survival, Clint Mitchell

Theses and Dissertations

The impact of Ad.mda-7 on the survival of renal cell carcinoma lines (RCC), primary renal epithelial cells, glioblastoma multiforme lines (GBM), and primary rodent astrocytes is unknown. The present studies examine whether the GST fusion protein, GST-MDA-7, and the adenovirus, Ad.mda-7, altered the growth and survival of the A498 and UOK121N RCC lines or radiosensitized GBM, respectively. Due to previous findings that the RCC lines, but not primary renal epithelial cells, were resistant to type 5 adenoviral infection, we used purified GST-MDA-7 protein to show that GST-MDA-7, but not GST, caused a dose-dependent reduction in A498 and UOK121N proliferation but …

Potential Of Vibrational Spectroscopy In The Diagnosis Of Human Tumours., Eoghan O'Faolain

Doctoral

Just fewer than 20,000 people are annually diagnosed with some form of cancer in Ireland and one in three people are likely to contract some form of cancer by age 74. With the number of cases increasing at an annual rate of 2%, the early detection and treatment of cancer is becoming increasingly important. Both IR and Raman spectroscopy offer the potential for real time, quantitative detection of cancer and even precancer. This study investigates the potential of Raman and Fourier transform infrared, both benchtop and synchrotron spectroscopies for the detection of cervical cancer. The tissue was classified and its …

Intercellular Spreading Of Porphyromonas Gingivalis Infection In Primary Gingival Epithelial Cells, Özlem Yilmaz, Philippe Verbeke, Richard J. Lamont, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Porphyromonas gingivalis, an important periodontal pathogen, is an effective colonizer of oral tissues. The organism successfully invades, multiplies in, and survives for extended periods in primary gingival epithelial cells (GECs). It is unknown whether P. gingivalis resides in the cytoplasm of infected cells throughout the infection or can spread to adjacent cells over time. We developed a technique based on flow cytofluorometry and fluorescence microscopy to study propagation of the organism at different stages of infection of GECs. Results showed that P. gingivalis spreads cell to cell and that the amount of spreading increases gradually over time. There was a …

S-Adenosylmethionine Stabilizes Cystathionine Β-Synthase And Modulates Redox Capacity, Anna Prudova, Zachary Bauman, Aaron Braun, Victor Vitvitsky, Shelly C. Lu, Ruma Banerjee

Department of Biochemistry: Faculty Publications

The transsulfuration pathway converts homocysteine to cysteine and represents the metabolic link between antioxidant and methylation metabolism. The first and committing step in this pathway is catalyzed by cystathionine β-synthase (CBS), which is subject to complex regulation, including allosteric activation by the methyl donor, S-adenosylmethionine (AdoMet). In this study, we demonstrate that methionine restriction leads to a >10-fold decrease in CBS protein levels, and pulse proteolysis studies reveal that binding of AdoMet stabilizes the protein against degradation by ≈12 kcal/mol. These observations predict that under pathological conditions where AdoMet levels are diminished, CBS, and therefore glutathione levels, will be reduced. …