Biochemistry, Biophysics, and Structural Biology Commons^™

Rescuing Acetylcholinesterase From Nerve Agent Inhibition: Protein Dynamics Driven Drug Discovery, Aiyana M. Emigh, Brian Bennion

STAR Program Research Presentations

Severe morbidity and mortality consequences result from irreversible inhibition of human acetylcholinesterase by organophosphates (OPs). Oxime-based reactivators are currently the only available treatments but lack efficacy in the central nervous system (CNS) where the most damage occurs. Computational docking and molecular dynamics (MD) simulations reveal complex structural barriers that may reduce oxime efficacy. These results may guide future drug designs of more effective countermeasures.

Genetic Regulation Of Mucoidy In Pseudomonas Aeruginosa, T. Ryan Withers

Theses, Dissertations and Capstones

Cystic fibrosis is a genetic disorder that results from mutations in the CF transmembrane conductance regulator gene. These mutations cause a disruption in the chloride transport in mucosal tissues causing the accumulation of dehydrated mucus, and a decrease in the mucocilliary removal of environmental pathogens within the lungs. Additionally, the accumulation of dehydrated mucus within the lungs provides a hospitable environment for various bacteria, including the Gram-negative opportunistic pathogen Pseudomonas aeruginosa. P. aeruginosa uses the overproduction of a surface polysaccharide called alginate to form a biofilm to evade the host’s immunological defenses. The overproduction of alginate, often referred to as …

Toward A Comprehensive Model Of Photosystem Ii Oxygen Evolving Complex Photoassembly, James Scott Board Ii

Theses, Dissertations and Capstones

Elucidating the mechanism of photoassembly of the oxygen-evolving complex (OEC) will lead to a better understanding of how nature catalyzes water oxidation. Although the temperature dependence of oxygen evolution has been described in the literature [1,2], we have performed a comprehensive study that covers Photosystem II (PSII) activity oxygen evolution in the presence and absence of 2,6-dichloro-1,4benzoquinone (DCBQ) from 5–45°C. In addition, we performed similar measurements for OEC photoassembly in the absence of DCBQ. PSIIenriched particles used for our measurements were prepared according to Berthold, Babcock, and Yocum[3], with modifications from Kolling, et al.[4] The oxygen-evolution of intact BBY particles …

Omega-3 Fatty Acids As Therapeutic Options For The Treatment Of B-Cell Chronic Lymphocytic Leukemia, Johannes Francois Fahrmann

Theses, Dissertations and Capstones

B-cell chronic lymphocytic leukemia (CLL) is the most common form of adult leukemia in the western world. CLL is often diagnosed in the asymptomatic (early-stage) stages. However, approximately 50% of these patients will progress to advanced, symptomatic disease and require therapy. Current treatment options are limited due to progressive drug resistance and severe drug-induced toxicities which are often too toxic for the elderly or those with co-morbidities. Therefore, a non-toxic therapeutic intervention that could slow the progression of asymptomatic CLL to symptomatic CLL or enhance the effects of actively used chemo-therapeutic drugs in patients who require therapy would be clinically …

A Comprehensive, Multi-Scale Dynamical Model Of Erbb Receptor Signal Transduction In Human Mammary Epithelial Cells, Tomas Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumy Naramura, Srikumar M. Raja, Vimla Band, Hamid Band, Jim A. Rogers

Biochemistry and Molecular Medicine Faculty Publications

The non-receptor tyrosine kinase Src and receptor tyrosine kinase epidermal growth factor receptor (EGFR/ErbB1) have been established as collaborators in cellular signaling and their combined dysregulation plays key roles in human cancers, including breast cancer. In part due to the complexity of the biochemical network associated with the regulation of these proteins as well as their cellular functions, the role of Src in EGFR regulation remains unclear. Herein we present a new comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. This model, constructed manually from published biochemical literature, consists of 245 nodes representing proteins …

Novel Insights Into Breast Cancer Genetic Variance Through Rna Sequencing, Anelia Horvath, Suresh B. Pakala, Prakriti Mudvari, Sirigiri Divijendra Natha Reddy, Kazufumi Ohshiro, Sandra Casimiro, Ricardo Pires, Suzanne A.W. Fuqua, Masakazu Toi, Luis Costa, Sujit S. Nair, Saraswati Sukumar, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

Using RNA sequencing of triple-negative breast cancer (TNBC), non-TBNC and HER2-positive breast cancer sub-types, here we report novel expressed variants, allelic prevalence and abundance, and coexpression with other variation, and splicing signatures. To reveal the most prevalent variant alleles, we overlaid our findings with cancer- and population-based datasets and validated a subset of novel variants of cancer-related genes: ESRP2, GBP1, TPP1, MAD2L1BP, GLUD2 and SLC30A8. As a proof-of-principle, we demonstrated that a rare substitution in the splicing coordinator ESRP2(R353Q) impairs its ability to bind to its substrate FGFR2 pre-mRNA. In addition, we describe novel SNPs and INDELs in …

Detection Of Viable Microorganisms Using Propidium Monoazide, Erik J. Mcfarland, Adrian Ponce Dr.

STAR Program Research Presentations

Propidium monoazide (PMA) is a molecular tool used to assess viability of microorganisms. Currently, PMA is thought to discern viability through membrane permeability; PMA enters only membrane compromised cells, irreversibly crosslinks to theirDNAand precipitates theDNAout of solution, preventing it from being amplified during polymerase chain reaction (PCR). Using PMA on a sample of live and dead microorganisms results in only theDNAof living organisms being amplified and identified. Therefore, a comparison ofPCRresults with and without PMA allows one to determine the live fraction and total population, respectively.

Current literature provides conflicting evidence as to the effectiveness of the technique. Our research …

Disocvering Ionic Liquid Resistant Genes, Bree Person, Douglass Higgins, Michael Thelen

STAR Program Research Presentations

: Plant biomass is a rich source of sugars that can be converted to biofuels by engineered microbes. However, because the lignocellulose in biomass is insoluble in aqueous conditions and recalcitrant to enzymatic degradation, thermochemical treatment is required to break apart the lignin and cellulose polymers before sugars can be released. The most effective chemicals for doing this are known as ionic liquids, which are salts that are molten at temperatures below 100° C. Although these solvents have many unique properties that are ideal for solubilizing lignocellulose, they have been found to inhibit the growth of bacterial strains used to …

Using Stable Isotope Analysis Of Zooplankton To Document Trophic And Biogeochemical Changes In The San Francisco Estuary, Steven C. Westbrook, Julien Moderan

STAR Program Research Presentations

Zooplankton represent a vital link between phytoplankton and fish, like the endangered Delta Smelt. Human interferences (nitrates from waste water, flow alteration, invasive species introduction…) have altered the structure of the San Francisco Estuary (SFE) ecosystem. We use stable isotope analysis to improve our knowledge of the planktonic food web in the SFE and gain insights into its evolution over the past decades. We use the ratios of certain isotopes (Nitrogen, Carbon, Sulfur, etc.) in different species of zooplankton to tell us what it is feeding on as well as the trophic level it feeds in. My research focused on …

Bone Morphogenetic Protein-7 Attenuates Inflammation And Apoptosis And Improves Cardiac Function In Diabetes, Princess Urbina

Electronic Theses and Dissertations

Bone Morphogenetic Protein-7 (BMP-7) belongs to the transforming growth factor-β (TGFβ) family of cytokines has is known to have potent anti-inflammatory properties. It has been used in patients to treat osteoporosis clinically and has been reported to treat diabetic nephropathy in murine models. Moreover, studies show that inflammation is up-regulated in patients with pre-diabetes (PD). We, therefore, hypothesize that the administration of BMP-7 will attenuate inflammation in the heart of Streptozotocin (STZ)-induced PD mice. In this study, we divided C57Bl/6 mice into three groups: CONTROL, PD, and PD+BMP-7. CONTROL mice received intraperitoneal (i.p.) injections of Sodium Citrate Buffer while PD …

Guilty Or Not Guilty: Can Dna Help Prove Guilt Or Innocence?, Suzanne Eckstein

The Science Journal of the Lander College of Arts and Sciences

Throughout our history, science was always on the front lines for discovery and exploration. Science is used as an investigative tool by the human race to figure out all the mysteries of the universe. The discovery of DNA was tremendous, providing each human being with their own unique genetic identity - no longer would an individual be genetically confused with another. DNA fingerprinting, in particular, has changed the world. In the 1980's the legal system began using DNA fingerprinting to help establish the guilt of an indicted criminal. DNA (besides for fingerprints) is the only way to confirm scientifically if …

Community Annotation And The Evolution Of Cooperation: How Patience Matters, Atin Basuchoudhary, Vahan Simoyan, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

We investigate why biologists fail to contribute to biological databases although almost all of them use these databases for research. We find, using evolutionary game theory and computer simulations, that (a) the initial distribution of contributors who are patient determines whether a culture of contribution will prevail or not (b) institutions (where institution means “a significant practice, relationship, or organization in a society or culture”) that incentivize patience and therefore limit free riding make contribution more likely and, (c) a stable institution, whether it incentivizes patience or not, will increase contribution. As a result we suggest there is a trade-off …

Glycosylation Of Cyclooxygenase-2 (Cox-2) Influences The Migratory Potential Of Cos-1 Cells, Julia Hand, Renee Dominguez, Miguel Regidor, Mary B. Sevigny

Natural Sciences and Mathematics | Faculty Research Posters

A cancer cell’s most threatening property is its ability to metastasize or detach from the primary tumor and migrate to other locations in the body. Previous studies have shown that overexpression of the enzyme cyclooxygenase-2 (COX-2) can increase the metastatic potential of several cell types. COX-2 is the rate-limiting enzyme in the prostanoid biosynthesis pathway, converting arachidonic acid to prostaglandin H2, an important signaling molecule in the body. Glycosylation of COX-2 at the amino acid site Asn580 occurs about 50% of the time, and this results in two forms of the enzyme with molecular weights 72 and 74kDa. The purpose …

Regulation Of Actin Dynamics During Drosophila Germband Extension, Ashley M. Motlong

Electronic Theses and Dissertations

Convergent extension is a process that occurs in the development of a wide variety of organisms, including gastrulation in the Drosophila embryo to begin to lay out the adult body plan. In fly embryos, this is known as germband extension and is mainly driven by cell intercalation or neighbor exchange by planar polarized cell-cell interface contraction to shorten the tissue along the dorsal-ventral axis. In this thesis, I show that interface contraction consists of phases of fast interface shortening and intervals of stable interface size. My data also suggests that regulation of F-actin aggregates at these shrinking interfaces is important …

X-Band Rapid-Scan Epr, Deborah Gale Mitchell

Electronic Theses and Dissertations

The advantages of rapid-scan EPR relative to CW and pulse techniques for samples with long longitudinal relaxation time T₁ (N_s⁰ defects in diamond, N@C₆₀, and amorphous hydrogenated silicon), heterogeneous samples (crystalline 1:1 α,γ-bisdiphenylene-β-phenylallyl (BDPA):benzene), lossy samples (aqueous nitroxyl radicals), and transient radicals (5-tert-butoxycarbonyl-5-methyl-1-pyrroline-N-oxide (BMPO)-superoxide adduct) were studied.

For samples with long relaxation times, CW (continuous wave) EPR is challenging due to power saturation and distortions from passage effects. In rapid-scan EPR, the field is swept through resonance in a time that is short relative to T₂. In rapid-scan EPR, the magnetic field is …

Cell Type Difference In Influenza A Viral Mrna Nuclear Export, Sean William Larsen

Theses Digitization Project

The focus of this thesis research was to clarify the role of host Nxf1 in influenza viral mRNA nuclear export. This study aims to define the nuclear mRNA export pathways of influenza viral mRNA. If viral mRNAs are discovered to utilize neither known mRNA nuclear export pathway this would indicate the mRNA exports via undefined mRNA nuclear export pathway. This might be an atypical pathway not utilized by many host mRNAs and thus might reveal novel antiviral target. 293T (Human embryonic kidney cells) and A549 (Human lung epithelial) cells were purchased from ATCC American Tissue Culture Collection.

Dopaminergic Modulation Of Glutamate Signaling In Caenorhabditis Elegans, Melvin Suman Baidya

Theses Digitization Project

This study investigates how DA (dopamine) modulates GLU (glutamate) signaling at the interneuron level of the C. elegans avoidance circuit in response to the noxious chemical 1-octanol. Many neural processes involved in addiction, exhibit cellular mechanisms using the neurotransmitters dopamine and glutamate along with their intracellular and genomic targets.

The Influence Of Ubiquitin-Related Modifier Protein Urm1 On Prion Formation, Jacob Beaver

Bridges: A Journal of Student Research

Prions are infectious proteins that are autocatalyzing (formed by altering a regular protein into the structurally different prion form), and are associated with many neurodegenerative diseases such as Alzheimer's, Parkinson's, Huntington's, and Bovine Spongiform encephalopathy (or Mad Cow disease). This experiment tested the effect of three different plasmids—pH317, pER62, and pMP46—on prion formation in both wild-type and Urm1 deletion mutants in the yeast Saccharomyces cerevisiae. The proposed hypothesis was over-expression of the Ure2 prion forming protein would increase the frequency of prion formation, as well as yield less sustainable prion amyloids (or prion aggregations) that are easier to cure. Another …

A Dft Study Of Vibrational Spectra And Mutagenicity Predictions Of Mononitrated Fluoranthenes [Abstract], Kefa Karimu Onchoke, Jorge Ojeda

Faculty Publications

No abstract provided.

Ammonium Sulfate Precipitation Combined With Liquid Chromatography Is Sufficient For Purification Of Bovine Serum Albumin That Is Suitable For Most Routine Laboratory Applications, Odutayo O. Odunuge, Alina Shazhko

Faculty Publications

The use of bovine serum albumin (BSA) in routine biochemical assays such as restriction enzyme digestion and immunodetection is plagued largely by two common contaminants, DNase and immunoglobulins G (IgGs). Acetylation of BSA to inactivate DNase limits its use as a protein standard due to interference with color development in assays such as Lowry’s. In spite of the availability of inexpensive BSA, its purification involves several cumbersome and time-consuming steps. In this work, we employed a modified strategy of ammonium sulfate precipitation coupled with liquid chromatography to purify BSA that is free of DNase and IgGs. Purified BSA tested negative …

Generation And Characterization Of Peptide Fusion Proteins, Brianna L. Probasco

Graduate School of Biomedical Sciences Theses and Dissertations

Pathogenic Th17 cells drive progression of many autoimmune diseases. Th17 cells develop from naïve T cells in the immune system after antigen-driven stimulation in a specific cytokine environment. Normally, T cells act to fight off infection, but when not properly controlled, they can cause disease. The cytokine interleukin-23 (IL-23) plays an essential role in the expansion of pathogenic Th17 cells. IL-23 is a heterodimeric protein, composed of a p19 alpha chain and a p40 beta chain. The p40 is also part of IL-12 and binds to the IL-12 receptor beta 1 (IL-12Rβ1) subunit. Thus, it follows that the IL-23 receptor …

Identification Of Potential Lead Antimalarial Compounds From Marine Microbial Extracts, Abigail Carbonell

HIM 1990-2015

Malaria, caused by the parasite Plasmodium falciparum, has a long history as a global health threat. The vector-borne disease causes millions of deaths yearly, especially in developing countries with tropical climates that facilitate transmission. Compounding the problem is the emergence of drug-resistant strains due to overuse of outdated treatments. New compounds with antiplasmodial activity are needed to be developed as effective drugs against malaria. The hypothesis for this project is that marine microorganisms have a high likelihood of yielding novel antiplasmodial chemotypes because of their high diversity, which has not yet been explored for antimalarial development. In this project, microbes …

Elucidating The Role Of Dopamine In The Avoidance Response Of Caenorhabditis Elegans Utilizing Microfluidics, Patricia Frances Turturro

Theses Digitization Project

This study looks at dopamine modulation of ASH neurons, which are part of the avoidance circuit of C. elegans, and their response to water soluble stimuli. Because nematodes such as Caenorhabditis elegans utilize dopamine at the molecular and cellular level in much the same way as mammals, they offer researchers a unique opportunity to study the mechanisms of dopamine signaling.

Role Of Resonance-Enhanced Multiphoton Excitation In High-Harmonic Generation Of N-2: A Time-Dependent Density-Functional-Theory Study, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

A minimum at similar to 39 eV is observed in the high-harmonic-generation spectra of N-2 for several laser intensities and frequencies. This minimum appears to be invariant for different molecular orientations. We reproduce this minimum for a set of laser parameters and orientations in time-dependent density-functional-theory calculations, which also render orientation-dependent maxima at 23-26 eV. Photon energies of these maxima overlap with ionization potentials of excited states observed in photoelectron spectra. Time profile analysis shows that these maxima are caused by resonance-enhanced multiphoton excitation. We propose a four-step mechanism, in which an additional excitation step is added to the well-accepted …

Coupling Field And Laboratory Measurements To Estimate The Emission Factors Of Identified And Unidentified Trace Gases For Prescribed Fires, Robert J. Yokelson, I. R. Burling, J. Gilman, C. Warneke, C. Stockwell, J. De Gouw, S. K. Akagi, S. P. Urbanski, P. Veres, J. M. Roberts, W. C. Kuster, J. Reardon, David W. T. Griffith, T. J. Johnson, S. Hosseini, J. W. Miller, D. R. Cocker Iii, H. Jung, D. R. Weise

Chemistry and Biochemistry Faculty Publications

An extensive program of experiments focused on biomass burning emissions began with a laboratory phase in which vegetative fuels commonly consumed in prescribed fires were collected in the southeastern and southwestern US and burned in a series of 71 fires at the US Forest Service Fire Sciences Laboratory in Missoula, Montana. The particulate matter (PM2.5) emissions were measured by gravimetric filter sampling with subsequent analysis for elemental carbon (EC), organic carbon (OC), and 38 elements. The trace gas emissions were measured by an open-path Fourier transform infrared (OP-FTIR) spectrometer, proton-transfer-reaction mass spectrometry (PTRMS), proton-transfer ion-trap mass spectrometry (PIT-MS), negative-ion proton-transfer …

Measurements Of Reactive Trace Gases And Variable O-3 Formation Rates In Some South Carolina Biomass Burning Plumes, S. K. Akagi, Robert J. Yokelson, I. R. Burling, S. Meinardi, Isobel J. Simpson, Donald R. Blake, G. R. Mcmeeking, A. Sullivan, T. Lee, S. Kreidenweis, S. P. Urbanski, J. Reardon, David W. T. Griffith, T. J. Johnson, D. R. Weise

Chemistry and Biochemistry Faculty Publications

In October-November 2011 we measured trace gas emission factors from seven prescribed fires in South Carolina (SC), US, using two Fourier transform infrared spectrometer (FTIR) systems and whole air sampling (WAS) into canisters followed by gas-chromatographic analysis. A total of 97 trace gas species were quantified from both airborne and ground-based sampling platforms, making this one of the most detailed field studies of fire emissions to date. The measurements include the first emission factors for a suite of monoterpenes produced by heating vegetative fuels during field fires. The first quantitative FTIR observations of limonene in smoke are reported along with …

Biophysical Approaches To Human Genetic Disease: Adsl Deficiency As A Model, Stephen P. Ray

Electronic Theses and Dissertations

Biophysical tools are becoming more useful in approaching human genetic disease. The pathogenic mechanisms behind many disorders have been attributed to protein loss of function or gain in toxic function. For example, changes in the protein Adenylosuccinate Lyase (ADSL) lead to ADSL deficiency, a disorder that causes symptoms ranging from epilepsy to expression of autistic features. Biophysics offers different tools to study intrinsic properties of proteins. We have applied such tools to study the enzyme kinetics and protein stability of ADSL and two mutations (R426H and R303C) to formulate better hypotheses regarding the pathogenic mechanism. Enzyme kinetic findings indicate a) …

Gender Differences In The Development Of Uremic Cardiomyopathy Following Partial Nephrectomy: Role Of Progesterone, Christopher A. Drummond, George Buddny, Steven T. Haller, Jiang Liu, Yanling Yan, Zijian Xie, Deepak Malhotra, Joseph I. Shapiro Md, Jiang Tian

Biochemistry and Microbiology

Gender difference has been suggested as a risk factor for developing cardiovascular and renal diseases in humans and experimental animals. As a major sex hormone, progesterone was reported to compete with cardiotonic steroid binding to Na/K-ATPase. Our previous publication demonstrated that cardiotonic steroids (e.g., marinobufagenin) play an important role in the development of experimental uremic cardiomyopathy. We also observed that the putative mineralocorticoid antagonists, spironolactone and its major metabolite canrenone, antagonize binding of cardiotonic steroids to Na/K-ATPase in a competitive manner and also ameliorate experimental uremic cardiomyopathy induced by partial nephrectomy. In the following studies, we noted that progesterone displayed …

Estrogen Receptor Α Regulates Erk In Mcf-7 Cells, John M. Schmitt, Angela J. Rofelty

Faculty Publications - Department of Biological & Molecular Science

Abstract Estrogen (E2) signaling significantly affects breast tumorigenesis by enhancing cell growth and preventing apoptosis. The actions of estrogen in MCF-7 breast cancer cells are mediated through a kinase pathway involving CaM KK, CaM KI, and ERK. Current research is examining the involvement of the Estrogen Receptor (ER) alpha (α) and beta (β) as well as G-Protein Coupled Receptor GPR30 in cell growth and proliferation. ERα is suggested to be responsible for ERK and perhaps CaM Kinase activation. Our goal was to evaluate if ERα, rather than GPR30 or ERβ, mediates CaM KI and ERK activation upon treatment of MCF-7 …

Histone Deacetylase 1: Mutagenesis And Small Molecule Studies, Magdalene Wambua

Wayne State University Dissertations

Histone deacetylase 1 (HDAC1) has been linked to cell growth and cell cycle regulation, which makes it a widely recognized target for anticancer drugs. The 14 Å channel of Class 1 HDAC isotypes has long being hypothesized to be the exit cavity for acetate following deacetylation. The amino acids lining this cavity are very similar among the HDAC isoforms, suggesting the role of the cavity is relevant to all HDACs proteins Importanly, HDAC1 selective inhibitors designed to fit the 14Å channel have been designed. To understand the importance of the 14Å channel to HDAC1 activity, we used an alanine scan …