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Influence On Proline Upon The Folding And Geometry Of A Model Transmembrane Peptide, Rachel Thomas

Inquiry: The University of Arkansas Undergraduate Research Journal

The orientations, geometries and lipid interactions of designed transmembrane (TM) peptides have attracted significant experimental and theoretical interest. Because the amino acid proline will introduce a known discontinuity into an alpha-helix, it is important to measure the extent of helix kinking caused by a single proline within an isolated TM helical domain. For this purpose, acetyl-GWWLALALAP10ALALALWWA-ethanolamide was synthesized, and pairs of deuterated alanines were included by using 60-100% deuterated fluorenylmethoxycarbonyl-L-alanine ifmoc-d4-L-Ala) at selected sequence positions. Solid-state deuterium fH) magnetic resonance spectra from oriented, hydrated samples (1140, peptide/lipid; using several lipids) reveal signals from many of the alanine backbone Ca deuterons …

Evolution Of Gene Structure In Multicellular Eukaryotes, Maria Hester

Inquiry: The University of Arkansas Undergraduate Research Journal

We investigated the patterns of intron conservation in eukaryotes for five different genes. The genes examined were ribosomal proteins L8, S14 and S17, along with elongation factor 2B and triose phosphate isomerase. Intron conservation for S14, S17, and triose phosphate isomerase was determined for 32 species representing the major branches of multicellular eukaryotes. For 25 conserved introns 16 were phase 0, five were phase 1, and four were phase 2. Triose phosphate isomerase had five of nine conserved introns shared between plants and animals, where S14 had one of nine and S17 had one of seven. However, there were two …

Loop Dynamics Of The Extracellular Domain Of Human Tissue Factor And Activation Of Factor Viia, Agnese S. Minazzo, Reuben C. Darlington, J. B. A. Ross

Chemistry and Biochemistry Faculty Publications

In the crystal structure of the complex between the soluble extracellular domain of tissue factor (sTF) and activesite- inhibited VIIa, residues 91 and 92 in the Pro⁷⁹-Pro⁹² loop of sTF interact with the catalytic domain of VIIa. It is not known, however, whether this loop has a role in allosteric activation of VIIa. Time-resolved fluorescence anisotropy measurements of probes covalently bound to sTF mutants E84C and T121C show that binding uninhibited Factor VIIa affects segmental motions in sTF. Glu⁸⁴ resides in the Pro⁷⁹-Pro⁹² loop, and Thr¹²¹ resides in the turn between the …

Emissions From Biomass Burning In The Yucatan, Robert J. Yokelson, J. D. Crounse, P. F. Decarlo, T. Karl, S. P. Urbanski, E. Atlas, T. Campos, Y. Shinozuka, V. Kasputin, A. D. Clarke, A. Weinheimer, D. J. Knapp, D. D. Montzka, J. Holloway, P. Weibring, F. Flocke, W. Zheng, D. Toohey, P. O. Wennberg, C. Wiedinmyer, L. Mauldin, A. Fried, D. Richter, J. Walega, J. L. Jimenez, K. Adachi, P. R. Buseck, S. R. Hall, R. Shetter

Chemistry and Biochemistry Faculty Publications

In March 2006 two instrumented aircraft made the first detailed field measurements of biomass burning (BB) emissions in the Northern Hemisphere tropics as part of the MILAGRO project. The aircraft were the National Center for Atmospheric Research C-130 and a University of Montana/US Forest Service Twin Otter. The initial emissions of up to 49 trace gas or particle species were measured from 20 deforestation and crop residue fires on the Yucatan peninsula. This included two trace gases useful as indicators of BB (HCN and acetonitrile) and several rarely, or never before, measured species: OH, peroxyacetic acid, propanoic acid, hydrogen peroxide, …

Biomass Burning And Urban Air Pollution Over The Central Mexican Plateau, J. D. Crounse, P. F. Decarlo, Donald R. Blake, L. K. Emmons, T. L. Campos, E. C. Apel, A. D. Clarke, A. J. Weinheimer, D. C. Mccabe, Robert J. Yokelson, J. L. Jimenez, P. O. Wennberg

Chemistry and Biochemistry Faculty Publications

Observations during the 2006 dry season of highly elevated concentrations of cyanides in the atmosphere above Mexico City (MC) and the surrounding plains demonstrate that biomass burning (BB) significantly impacted air quality in the region. We find that during the period of our measurements, fires contribute more than half of the organic aerosol mass and submicron aerosol scattering, and one third of the enhancement in benzene, reactive nitrogen, and carbon monoxide in the outflow from the plateau. The combination of biomass burning and anthropogenic emissions will affect ozone chemistry in the MC outflow.

Light-Induced Fos Expression In Intrinsically Photosensitive Retinal Ganglion Cells In Melanopsin Knockout (Opn4-/-) Mice, Gary E. Pickard, Scott B. Baver, Malcolm D. Ogilvie, Patricia J. Sollars

School of Veterinary and Biomedical Sciences: Faculty Publications

Retinal ganglion cells that express the photopigment melanopsin are intrinsically photosensitive (ipRGCs) and exhibit robust synaptically driven ON-responses to light, yet they will continue to depolarize in response to light when all synaptic input from rod and cone photoreceptors is removed. The light-evoked increase in firing of classical ganglion cells is determined by synaptic input from ON-bipolar cells in the proximal sublamina of the inner plexiform layer. OFF-bipolar cells synapse with ganglion cell dendrites in the distal sublamina of the inner plexiform layer. Of the several types of ipRGC that have been described, M1 ipRGCs send dendrites exclusively into the …

Synthesis Of 12-Hete Using Asymmetric Phase-Transfer Catalysis, Michael A. Christiansen, M. B. Andrus

Chemistry and Biochemistry Faculty Presentations

A new method of asymmetric phase-transfer-catalyzed alkylation is described. The synthetic utility of this method is demonstrated with the total syntheses of kurasoin A, kurasoin B, and S-naproxenTM, with current work toward S-equol. This methodology is currently being applied to an improved asymmetric total synthesis of the natural compound 12-S-HETE.

A Microrna Imparts Robustness Against Environmental Fluctuation During Development, Xin Li, Justin J. Cassidy, Catherine A. Reinke, Stephen Fischboeck, Richard W. Carthew

Faculty Publications

The microRNA miR-7 is perfectly conserved from annelids to humans, and yet some of the genes that it regulates in Drosophila are not regulated in mammals. We have explored the role of lineage restricted targets, using Drosophila , in order to better understand the evolutionary significance of microRNA-target relationships. From studies of two well characterized developmental regulatory networks, we find that miR-7 functions in several interlocking feedback and feedforward loops, and propose that its role in these networks is to buffer them against perturbation. To directly demonstrate this function for miR-7, we subjected the networks to temperature fluctuation and found …

Nerve, Muscle, Blood, Toil, Tears, And Sweat: England’S Pioneering Biophysicist, Soldier, And Statesman, Khan

Departmental Papers (Biology)

No abstract provided.

Mass Stranding Of Marine Birds Caused By A Surfactant-Producing Red Tide., David A. Jessup, Melissa A. Miller, John P. Ryan, Hannah M. Nevins, Heather A. Kerkering, Abdou Mekebri, David B. Crane, Tyler A. Johnson, Raphael M. Kudela

Natural Sciences and Mathematics | Faculty Scholarship

In November-December 2007 a widespread seabird mortality event occurred in Monterey Bay, California, USA, coincident with a massive red tide caused by the dinoflagellate Akashiwo sanguinea. Affected birds had a slimy yellow-green material on their feathers, which were saturated with water, and they were severely hypothermic. We determined that foam containing surfactant-like proteins, derived from organic matter of the red tide, coated their feathers and neutralized natural water repellency and insulation. No evidence of exposure to petroleum or other oils or biotoxins were found. This is the first documented case of its kind, but previous similar events may have gone …

Correlations Between Oxygen Affinity And Sequence Classifications Of Plant Hemoglobins, Benoit J. Smagghe, Julie A. Hoy, Ryan Percifield, Suman Kundu, Mark S. Hargrove, Gautam Sarath, Jean-Louis Hilbert, Richard A. Watts, Elizabeth S. Dennis, W. James Peacock, Sylvia Dewilde, Luc Moens, George C. Blouin, John S. Olson, Cyril A. Appleby

Gautam Sarath Publications

Plants express three phylogenetic classes of hemoglobins (Hb) based on sequence analyses. Class 1 and 2 Hbs are full-length globins with the classical eight helix Mb-like fold, whereas Class 3 plant Hbs resemble the truncated globins found in bacteria. With the exception of the specialized leghemoglobins, the physiological functions of these plant hemoglobins remain unknown. We have reviewed and, in some cases, measured new oxygen binding properties of a large number of Class 1 and 2 plant nonsymbiotic Hbs and leghemoglobins. We found that sequence classification correlates with distinct extents of hexacoordination with the distal histidine and markedly different overall …

A Multiple Species Approach To Biomass Production From Native Herbaceous Perennial Feedstocks, J. L. Gonzalez-Hernandez, Gautam Sarath, J. M. Stein, V. Owens, K. Gedye, A. Boe

Gautam Sarath Publications

Due to the rapid rate of worldwide consumption of nonrenewable fossil fuels, production of biofuels from cellulosic sources is receiving increased research emphasis. Here, we review the feasibility to produce lignocellulosic biomass on marginal lands that are not well-suited for conventional crop production. Large areas of these marginal lands are located in the central prairies of North America once dominated by tallgrass species. In this article, we review the existing literature, current work, and potential of two native species of the tallgrass prairie, prairie cordgrass (Spartina pectinata), and little bluestem (Schizachyrium scoparium) as candidates for commercial production of …

A Structure-Based Approach For Detection Of Thiol Oxidoreductases And Their Catalytic Redox-Active Cysteine Residues, Stefano M. Marino, Vadim N. Gladyshev

Vadim Gladyshev Publications

Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understanding of what distinguishes their catalytic redox Cys from other Cys functions. Herein, we characterized thiol oxidoreductases at a structural level and developed an algorithm that can recognize these enzymes by (i) analyzing amino acid and secondary structure …

Classification And Cluster Analysis Of Complex Time-Of-Flight Secondary Ion Mass Spectrometry For Biological Samples, Stephen E. Reichenbach, Xue Tian, Qingping Tao, Alex Henderson

School of Computing: Conference and Workshop Papers

Identifying and separating subtly different biological samples is one of the most critical tasks in biological analysis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is becoming a popular and important technique in the analysis of biological samples, because it can detect molecular information and characterize chemical composition. ToF-SIMS spectra of biological samples are enormously complex with large mass ranges and many peaks. As a result the classification and cluster analysis are challenging. This study presents a new classification algorithm, the most similar neighbor with a probability-based spectrum similarity measure (MSN- PSSM), which uses all the information in the entire ToF- SIMS …

In Vitro And In Vivo Anthelmintic Activity Of Terminalia Arjuna Bark, Hafiz Allah Bachaya, Zafar Iqbal, Muhammad Nisar Khan, Abdul Jabbar, Anwar Hassan Gilani, Islam-Ud Din

Department of Biological & Biomedical Sciences

The present study was carried out to evaluate the anthelmintic activity of Terminalia arjuna (Roxb.) bark locally used as an anthelmintic. Lethal median concentration (LC50 values) of methanolic extract of T. arjuna bark in egg hatch and larval development tests against Haemonchus contortus ova and larva were found to be 645.65 and 467.74 μg mL-1, respectively. Inadult motility assay, efficacy of the extract was evident by the mortality of H. contortus at different hours post exposure. Invivo results revealed maximum (87.3%) egg count percent reduction (ECR) in sheep treated with crude methanolic extract @ 3 g kg-1 body …

Erk Activation Requires Cam Kinases In Mcf-7 Breast Cancer Cells, John M. Schmitt, Ellen Abell

Faculty Publications - Department of Biological & Molecular Science

Abstract A key signaling pathway involved in regulating cell growth and proliferation throughout the body is the ERK signaling pathway. ERK is activated via numerous pathways including intracellular calcium release downstream of G-Protein Coupled Receptors (GPCRs). Carbachol, a GPCR-agonist, both increases intracellular calcium and ERK activation in MCF-7 cells. ERK activation and control of cell growth may act through the transcription factor Elk-1. Our goal was to elucidate the specific proteins and kinases upstream of ERK in MCF-7 cells treated with carbachol. Secondly, we wanted to investigate the potential involvement of Elk-1 downstream of ERK. Carbachol treatment of MCF-7 cells …

Cam Kinase Kinase Control Of Prostate Cancer Cell Survival, John M. Schmitt, Brendon Hart

Faculty Publications - Department of Biological & Molecular Science

Abstract AKT has been implicated in promoting cell survival within certain cells. Current research has shown that hormones that increase the concentration of intracellular calcium can activate AKT that in turn leads to cancer cell survival. Interestingly, LNCaP cells express the M3-subtype of GPCR's that may couple to increases in intracellular calcium and activation of the Ca2+/Calmodulin-dependent Protein Kinases (CaM Ks). Specifically CaM Kinase Kinase (CaM KK) phosphorylates its direct substrates CaM Kinase I, CaM Kinase IV, and AKT. AKT promotes cell survival through phosphorylation of its target BAD that prevents caspase activation. Our goals were to examine the mechanism …

Proteomic Analysis Of Endodontic Infections By Liquid Chromatography–Tandem Mass Spectrometry, R. Nandakumar, Nandakumar Madayiputhiya, A. F. Fouad

Department of Biochemistry: Faculty Publications

Introduction—Endodontic infections are very prevalent and have a polymicrobial etiology characterized by complex interrelationships between endodontic microorganisms and the host defenses. Proteomic analysis of endodontic infections can provide global insights into the invasion, pathogenicity mechanisms, and multifactorial interactions existing between root canal bacteria and the host in the initiation and progression of apical periodontitis. The purpose of this study was to apply proteomic techniques such as liquid chromatography–tandem mass spectrometry (LC–MS/ MS) for the identification of proteins of bacterial origin present in endodontic infections.

Methods—Endodontic specimens were aseptically obtained from seven patients with root canal infections. Protein mixtures were subjected …

Hyaluronidase Activity Of Human Hyal1 Requires Active Site Acidic And Tyrosine Residues, Ling Zhang, Alamelu G. Bharadwaj, Andrew Casper, Joel Barkley, Joseph J. Barycki, Melanie A. Simpson

Department of Biochemistry: Faculty Publications

Hyaluronidases are a family of endolytic glycoside hydrolases

that cleave the β1–4 linkage between N-acetylglucosamine and

glucuronic acid in hyaluronan polymers via a substrate-assisted

mechanism. In humans, turnover of hyaluronan by this enzyme

family is critical for normal extracellular matrix remodeling.

However, elevated expression of the Hyal1 isozyme accelerates

tumor growth and metastatic progression. In this study, we used

structural information, site-directed mutagenesis, and steady

state enzyme kinetics to probe molecular determinants of

human Hyal1 function. Mutagenesis of active site residues

Glu¹³¹ and Tyr²⁴⁷ to Gln and Phe, respectively, eliminated activity

at all hyaluronan concentrations (to 125 …

Mechanistic Details Of Glutathione Biosynthesis Revealed By Crystal Structures Of Saccharomyces Cerevisiae Glutamate Cysteine Ligase, Ekaterina I. Biterova, Joseph J. Barycki

Department of Biochemistry: Faculty Publications

Glutathione is a thiol-disulfide exchange peptide critical for

buffering oxidative or chemical stress, and an essential cofactor

in several biosynthesis and detoxification pathways. The ratelimiting

step in its de novo biosynthesis is catalyzed by glutamate

cysteine ligase, a broadly expressed enzyme for which limited

structural information is available in higher eukaryotic species.

Structural data are critical to the understanding of clinical glutathione

deficiency, as well as rational design of enzyme modulators

that could impact human disease progression. Here, we

have determined the structures of Saccharomyces cerevisiae glutamate

cysteine ligase (ScGCL) in the presence of glutamate and

MgCl2 (2.1 Å; R …

Functional Characterization Of A Higher Plant Sphingolipid Δ4-Desaturase: Defining The Role Of Sphingosine And Sphingosine-1-Phosphate In Arabidopsis, Louise V. Michaelson, Simone Zäuner, Jennifer E. Markham, Richard P. Haslam, Radhika Desikan, Sarah Mugford, Sandra Albrecht, Dirk Warnecke, Petra Sperling, E. Heinz, Johnathan A. Napier

Department of Biochemistry: Faculty Publications

The role of Δ4-unsaturated sphingolipid long-chain bases such as sphingosine was investigated in Arabidopsis (Arabidopsis thaliana). Identification and functional characterization of the sole Arabidopsis ortholog of the sphingolipid Δ4-desaturase was achieved by heterologous expression in Pichia pastoris. A P. pastoris mutant disrupted in the endogenous sphingolipid Δ4-desaturase gene was unable to synthesize glucosylceramides. Synthesis of glucosylceramides was restored by the expression of Arabidopsis gene At4g04930, and these sphingolipids were shown to contain Δ4-unsaturated long-chain bases, confirming that this open reading frame encodes the sphingolipid Δ4-desaturase. At4g04930 has a very restricted expression pattern, transcripts only being detected in …

Modulation Of The Heme Electronic Structure And Cystathionine Β-Synthase Activity By Second Coordination Sphere Ligands: The Role Of Heme Ligand Switching In Redox Regulation, Sangita Singh, Peter Madzelan, Jay Stasser, Colin L. Weeks, Donald F. Becker, Thomas G. Spiro, James Penner-Hahn, Ruma Banerjee

Department of Biochemistry: Faculty Publications

In humans, cystathionine β-synthase (CBS) is a hemeprotein, which catalyzes a pyridoxal phosphate (PLP)-dependent condensation reaction. Changes in the heme environment are communicated to the active site, which is ~20 Å away. In this study, we have examined the role of H67 and R266, which are in the second coordination sphere of the heme ligands, H65 and C52 respectively, in modulating the heme's electronic properties and in transmitting information between the heme and active sites. While the H67A mutation is comparable to wild-type CBS, interesting differences are revealed by mutations at the R266 site. The pathogenic mutant, R266K, is moderately …

Heme Regulation Of Human Cystathionine Β-Synthase Activity: Insights From Fluorescence And Raman Spectroscopy, Colin L. Weeks, Sangita Singh, Peter Madzelan, Ruma Banerjee, Thomas G. Spiro

Department of Biochemistry: Faculty Publications

Cystathionine β-synthase (CBS) plays a central role in cysteine metabolism, and malfunction of the enzyme leads to homocystinuria, a devastating metabolic disease. CBS contains a pyridoxal 5′- phosphate (PLP) cofactor which catalyzes the synthesis of cystathionine from homocysteine and serine. Mammalian forms of the enzyme also contain a heme group, which is not involved in catalysis. It may, however, play a regulatory role, since the enzyme is inhibited when CO or NO are bound to the heme. We have investigated the mechanism of this inhibition using fluorescence and resonance Raman spectroscopies. CO binding is found to induce a tautomeric shift …

Influence Of Irradiance And Iron On The Growth Of Colonial Phaeocystic Antarctica: Implications For Seasonal Bloom Dynamics In The Ross Sea, Antarctica, Nathan S. Garcia, Peter N. Sedwick, Giacomo R. Ditullio

OES Faculty Publications

Laboratory culture experiments were used to investigate the growth rate of colonial Phaeocystis anarctica as a function of irradiance and dissolved iron concentration. The experiments were conducted with a P. antarctica strain isolated from the southern Ross Sea, Antarctica, and made use of natural, low-iron (P. antarctica attained an average maximum cell-specific growth rate of 0.37 d^-1at an irradiance of 68 μE m^-2s^-1, above which growth rates decreased to 0.27 d^-1 at an irradiance of 314 μE m^-2s^-1. The dependence of growth rate on ambient dissolved iron concentration was …

Isothermal Titration Calorimetry Studies Of Protein-Mediated Interactions And Preliminary Structural Studies Of Tandem Pdz1-2 Domain Of Psd-95 Protein, Ana Jankovic

Wayne State University Dissertations

Protein-mediated interactions that involve multiple ligands in their binding mechanisms are critical for many cellular functions. The primary focus of this dissertation research was to investigate such interactions for two proteins, the PDZ domain and frataxin, involving peptide and metal binding ligands, respectively. The three component projects of this work comprised (1) thermodynamic analysis of PDZ domain binding using calorimetry; (2) X-ray crystallographic structural studies of a PDZ dual domain; and (3) thermodynamic analysis of frataxin binding to iron. The specific goal of the research conducted with the PDZ domains was to understand the mechanism of action of multiple/tandem protein …

Lipid Uptake And Metabolism In The Parasitic Protozoan Giardia Lamblia., Mayte Yichoy

Open Access Theses & Dissertations

Giardia lamblia is a protozoan parasite that causes various intestinal syndromes, and it is a common cause of water-borne illness worldwide, both in developed and developing countries. Giardia attaches to the mucosal epithelia of the duodenum below the bile duct, where it is exposed to bile salts and dietary lipids. G. lamblia is unable to synthesize lipids de novo and must therefore scavenge necessary lipids from its extracellular environment and remodel them as needed. However, the current lipidomic analysis (presented in this Dissertation) has revealed that while the Giardia lipidome is rich in phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), …

The Impact Of Environment On Virulence Of The Pathogenic Yeast Cryptococcus Gattii, Deborah Jean Springer

Legacy Theses & Dissertations (2009 - 2024)

Four serotypes of Cryptococcus are responsible for most human and animal infections. C. gattii , serotype B and C, are the primary the causative agent of cryptococcosis in immune competent individuals whilst, C. neoformans var. neoformans serotype D, and C. neoformans var. grubii serotype A are most prevalent in immunocompromised hosts world-wide. C. gattii is recognized as a species distinct from C. neoformans based on differences in clinical manifestations, morphology, biological characteristics, and environmental niche. We used the plant model Arabidopsis thaliana plants and plant derived substrates as a model to explore C. gattii interactions in its ecological niche. C. …

A Locus-Based Paradigm For Generating Systems Biological Inferences From Large Scale Functional Genomics Datasets, Ajish Dominic George

Legacy Theses & Dissertations (2009 - 2024)

Genomics data is growing at a exponential rate. The ability to integrate new results with existing knowledge about genomic biology is rapidly becoming the limiting factor as there no universal language with which to describe genomic functional elements. To integrate and compare new and existing genomic data, we define our basic functional unit of a genome to be a locus -- a set of positional coordinates along any genome with an arbitrary amount of functional annotations attached. The locus concept enables addressing genomic elements and annotations at any level of granularity from entire swaths of chromosomes to single base-positions. We …

Opportunism And Diversity In The Lifestyle Of A Group Ii Intron, Arthur R. Beauregard

Legacy Theses & Dissertations (2009 - 2024)

Group II introns are mobile retroelements. They invade the cognate intron-minus gene in an efficient process known as retrohoming. They can also retrotranspose to ectopic sites at low frequency. Retrohoming occurs by the intron RNA reverse-splicing into double-stranded DNA (dsDNA) through an endonuclease-dependent pathway. However, in retrotransposition in Lactoccocus lactis, the intron inserts predominantly into single-stranded DNA (ssDNA), in an endonuclease-independent manner. Unlike in L. lactis, in Escherichia coli the Ll.LtrB intron retrotransposes frequently into dsDNA, and the process is dependent on the endonuclease activity of the intron-encoded protein. Further, the endonuclease-dependent integrations preferentially occurred around the origin and terminus …

Role Of Cyp2a5 In Drug Metabolism, Chemical Toxicity, And Maintenance Of Steroid Hormone Homeostasis : Insights From Studies On A Novel Cyp2a5-Null Mouse Model, Xin Zhou

Legacy Theses & Dissertations (2009 - 2024)

The central hypothesis is that CYP2A5 plays an important role in the metabolism of xenobiotic substrates, and in the toxicity induced by over-exposure to drugs, as well as in the metabolism of endogenous compounds and regulation of steroid hormone homeostasis. The specific aims are: 1) to generate and characterize a Cyp2a5-null mouse; 2) to determine the role of CYP2A5 in the systemic clearance of nicotine and cotinine; and 3) to explore the mechanisms underlying the resistance of the lateral nasal gland (LNG) of male Cyp2g1-null/Cyp2a5-low mouse and Cyp2a5-null mouse to acetaminophen (AP) toxicity.