Biochemistry, Biophysics, and Structural Biology Commons^™

Classification Of Multi-Domain Glycoside Hydrolases To Aid In The Enzymatic Production Of Biofuels From Biomass, Emi Leonard, Gregg Beckham, Deanne Sammond, Michael Crowley

STAR Program Research Presentations

Biomass conversion to renewable biofuels provides an alternative to conventional fossil-fuel based transportation fuels and a means to reduce dependence on foreign oil. However, plant cell walls have evolved to be quite resistant to enzymatic deconstruction, a phenomenon generally termed biomass recalcitrance. As enzymes represent a substantial cost in biofuels production, there is significant impetus to understand and improve their efficiency in converting cell wall carbohydrates to fermentable sugars. Much research has been conducted on single "free" enzymes with one catalytic unit per protein and on the much larger, complexed "cellulosomes" with many tens of catalytic units per protein, but …

Understanding The Molecular Determinants Of Substrate And Inhibitor Specificities In The Carbapenemase Kpc-2: Exploring The Roles Of Arg220 And Glu276

Chemistry Faculty Publications

β-Lactamases are important antibiotic resistance determinants expressed by bacteria. By studying the mechanistic properties of β-lactamases, we can identify opportunities to circumvent resistance through the design of novel inhibitors. Comparative amino acid sequence analysis of class A β-lactamases reveals that many enzymes possess a localized positively charged residue (e.g., R220, R244, or R276) that is critical for interactions with β-lactams and β-lactamase inhibitors. To better understand the contribution of these residues to the catalytic process, we explored the roles of R220 and E276 in KPC-2, a class A β-lactamase that inactivates carbapenems and β-lactamase inhibitors. Our study reveals that substitutions …

Microrna-34a Modulates Mdm4 Expression Via A Target Site In The Open Reading Frame, Pooja Mandke, Nicholas Wyatt, Jillian Fraser, Benjamin Bates, Steven J. Berberich, Michael P. Markey

Biochemistry and Molecular Biology Faculty Publications

Background

MDM4, also called MDMX or HDMX in humans, is an important negative regulator of the p53 tumor suppressor. MDM4 is overexpressed in about 17% of all cancers and more frequently in some types, such as colon cancer or retinoblastoma. MDM4 is known to be post-translationally regulated by MDM2-mediated ubiquitination to decrease its protein levels in response to genotoxic stress, resulting in accumulation and activation of p53. At the transcriptional level, MDM4 gene regulation has been less clearly understood. We have reported that DNA damage triggers loss of MDM4 mRNA and a concurrent increase in p53 activity. These experiments attempt …

Inhibition Of Burkholderia Multivorans Adhesion To Lung Epithelial Cells By Bivalent Lactosides, Ciara Wight, Rosaria Leyden, Paul V. Murphy, Máire Callaghan, Trinidad Velasco-Torrijos, Siobhan Mcclean

Articles

Burkholderia cepacia complex (Bcc) is an opportunistic pathogen in cystic fibrosis patients which is inherently resistant to antimicrobial agents. The mechanisms of attachment and pathogenesis of Bcc, a group of 17 species, are poorly understood. The most commonly identified Bcc species in newly colonised patients, Burkholderia multivorans, continues to be acquired from the environment. Development of therapies which can prevent or reduce the risk of colonization on exposure to Bcc in the environment would be a better alternative to antimicrobial agents. Previously, it has been shown that Bcc strains bound to many glycolipid receptors on lung epithelia. Using a …

Amyloid-Beta42 Toxicity Reduction In Human Neuroblastoma Cells Using Cholera Toxin B Subunit-Myelin Basic Protein Expressed In Chloroplasts, Alexandra Ayache

HIM 1990-2015

Alzheimer's disease (AD) is an age progressive neurodegenerative brain disorder, affecting 37 million people worldwide. Cleavage of amyloid precursor protein by ?- and ?-secretase produces the amyloid-beta (A?) protein, which significantly contributes to AD pathogenesis. The A? aggregates, formed at the surface of neurons and intracellularly, cause neurotoxicity and decrease synaptic function. Inhibiting or degrading A? accumulation is a key goal for development of new AD treatments. Evidence shows that human Myelin Basic Protein (MBP) binds to and degrades A? thereby, preventing cytotoxicity. A potential method for oral drug delivery that will allow plant-derived bioencapsulated MBP to pass through intestinal …

Multiple Aspects Of Natural Killer Cell Expansion In Relevance To Immunotherapy For Hematologic Malignancies, Dominic Colosimo

HIM 1990-2015

Natural Killer (NK) cells are a subset of lymphocytes that regulate adaptive immune responses and utilize "missing self" recognition to activate anti-tumor and anti-viral cytotoxicity. Clinical research, as well as murine and ex vivo models, have shown that a variety of NK cell applications have proven useful as immunotherapeutic treatments for patients with hematologic malignancies. However, the selective expansion of NK cells to yield relevant amounts of these lymphocytes has been a major hurdle in the development of methods for clinical therapeutic use. Here, we demonstrate a novel ex vivo expansion method utilizing k562 leukemic cell lines and soluble cytokines …

The Real-Time Measurements Of Blood Nitric Oxide (No) And Hydrogen Peroxide (H2o2) Levels Under Acute Hyperglycemia, Michael Minni

PCOM Biomedical Studies Student Scholarship

Vascular endothelial dysfunction is one of the earliest recognizable events under hyperglycemic conditions. It is characterized by decreased endothelium-derived nitric oxide (NO) bioavailability and increased oxidative stress, such as superoxide and hydrogen peroxide (H₂O₂) overproduction. However, the real-time changes in blood NO and H₂O₂ levels under acute hyperglycemia have not been evaluated. In this study, acute hyperglycemia (200 mg/dl, 400 mg/dL, and 600 mg/dL) was induced by intravenous infusion of 20%, 30%, and 50% D-glucose respectively for 180 min. Infusion of saline or 30% L-glucose serve as controls. Blood NO or H_{2 …}

Leptospiral Hemolysins Induce Proinflammatory Cytokines Through Toll-Like Receptor 2-And 4-Mediated Jnk And Nf-Κb Signaling Pathways, Huan Wang, Yifei Hu, David M. Ojcius, X. Frank Yang, Chenglin Zhang, Shibiao Ding, Xu'ai Lin, Jie Yan

All Dugoni School of Dentistry Faculty Articles

Infection with pathogenic Leptospira species causes serious systemic inflammation in patients. Although a few leptospiral proinflammatory molecules have been identified, Leptospira likely encodes other unidentified strong inflammation stimulators. The pathogenic L. interrogans genome encodes numerous putative hemolysin genes. Since hemolysins from other bacteria can cause inflammatory reactions, we hypothesized that leptospiral hemolysins may function as proinflammatory stimulators that contribute to the strong inflammation associated with Leptospira infection.

Melanopsin Mediates Retrograde Visual Signaling In The Retina, Dao-Qi Zhang, Michael A. Belenky, Patricia J. Sollars, Gary E. Pickard, Douglas G. Mcmahon

School of Veterinary and Biomedical Sciences: Faculty Publications

The canonical flow of visual signals proceeds from outer to inner retina (photoreceptors→bipolar cells→ganglion cells). However, melanopsin-expressing ganglion cells are photosensitive and functional sustained light signaling to retinal dopaminergic interneurons persists in the absence of rods and cones. Here we show that the sustained-type light response of retinal dopamine neurons requires melanopsin and that the response is mediated by AMPA-type glutamate receptors, defining a retrograde retinal visual signaling pathway that fully reverses the usual flow of light signals in retinal circuits.

Regulation Of To Xin Synthesis By Clostridium Difficile, Charles Darkoh

Dissertations and Theses (Open Access)

Clostridium difficile is the leading definable cause of nosocomial diarrhea worldwide due to its virulence, multi-drug resistance, spore-forming ability, and environmental persistence. The incidence of C. difficile infection (CDI) has been increasing exponentially in the last decade. Virulent strains of C. difficile produce either toxin A and/or toxin B, which are essential for the pathogenesis of this bacterium. Current methods for diagnosing CDI are mostly qualitative tests that detect the bacterium, the toxins, or the toxin genes. These methods do not differentiate virulent C. difficile strains that produce active toxins from non-virulent strains that do not produce toxins or produce …

Part I - A Study Of The Formation Of Carbenes By Elimination Of Α-Bromosilanes And Application Toward The Synthesis Of Transition Metal Complexed Quinone Methide Analogs. Part Ii - Development Of Novel 7-Membered Ring Carbene Ligands For Palladium Catalyzed Cross Coupling Reactions., Christian Michael Loeschel

Graduate Theses and Dissertations

In part I, we wish to report our approaches toward transition metal complexed ortho-quinone methide analogs. ortho-Quinone Methides are a class of highly reactive compounds with a wide range of chemical and biological applications. Previously, a stable iron complexed benzannulated 5-membered ring quinone methide analog was reported by Allison and Neal27. Herein, we report our approaches to improve the reactivity of that system by removing benzannulation as well as changing the metal from iron to manganese and rhenium.

Furthermore, a methodological study on generating carbenes under mild conditions by elimination of α-halosilanes and its application towards metal complexed quinone methide …

Investigations Of Protein-Lipid Interactions In Model Membranes: Influence Of Aromatic Anchoring Residues And Buried Polar Residues, Nick Gleason

Graduate Theses and Dissertations

To investigate in detail the interactions between transmembrane proteins and the lipid bilayers in which they are constituted, designed model peptides with selective isotopic labels were synthesized and analyzed by means of solid-state deuterium NMR spectroscopy. Starting from the well-characterized model peptide GWALP23, acetyl-GGALW(LA)6LWLAGA-amide, several Trp to Tyr mutations were compared to evaluate their respective interfacial anchoring abilities. It was found that Tyr, substituted on either or both termini, can effectively anchor the transmembrane alpha-helix, which then adopts a similar transmembrane topology in a range of bilayer thicknesses. Nevertheless, a consistent ~10° shift in tilt direction (helix rotation) is observed …

Lignin Modification In Arabidopsis And Populus For Studies Of Gene Function And Improving Lignin Degradation, Yi Xu

All Dissertations

Lignin is one of the most abundant biopolymers in plants and plays an important role in plant structure and stress defense. Lignin is also considered to be a hallmark of vascular plants because of its crucial role in plant terrestrialization. However, lignin is an undesired component in the pulp and paper industry, bioethanol production, and forage digestibility. Thus, understanding the functions and the evolution of lignin biosynthesis genes can not only advance our knowledge of the evolution of land-adaptation for vascular plants but also help guide the effort to exploit the potential for genetic manipulation of lignin for desirable traits …

An Analysis Of The Redox Properties And Stability Of Chlamydomonas Reinhardtii Cytochrome F, Cytochrome C6, And Mutants Thereof, Nicole Lynn Vanderbush

Graduate Theses and Dissertations

This body of work presents mutagenesis studies conducted on two c-type cytochromes from Chlamydomonas reinhardtii. Cytochrome f, a unique c-type cytochrome, is investigated in regards to its redox potential, the dependence of the redox potential, and the thermal stability of the protein. The mutations made were Y1F, Y9F, Y160F, Y160L, R156L, and R156K. The residues that were mutated surround the heme. It was found that, relative to the wild-type, only the Y160L and R156 mutants showed any difference in midpoint potential at pH 7. Wild-type and mutants both had a midpoint potential that was dependent upon pH indicating that none …

A Genetic Analysis Of Bald Eagles In The Pacific Northwest: Retained Genetic Diversity Following A Large-Scale Population Bottleneck, Andrew Joseph Nadeau

Boise State University Theses and Dissertations

Bald eagle (Haliaeetus leucocephalus) populations in the continental United States experienced a dramatic population decline during the twentieth century. Populations across the species’ range have largely recovered, thanks in part to the ban of DDT, rapidly enacted conservation measures, and reintroduction efforts. Using six microsatellite loci, I tested the genetic variation of bald eagles across six states in the Pacific Northwest. Genetic analysis revealed that, despite undergoing a population-wide decline, the bald eagles in the locations sampled outside of Idaho did not exhibit the characteristics typically associated with a genetic bottleneck (i.e., a reduced number of alleles and …

Regulation Of Expression Of Enterohemolysin Toxin By The Global Repressor Hns And Characterization Of A New Class Of Protein Produced By Shiga Toxin-Producing Escherichia Coli, Miles T. Rogers

Dissertations

Shiga toxin-producing Escherichia coli (STEC) are worldwide pathogens causing an estimated 200,000 infections per year in the United States. Infections with STEC sometimes progress to kidney failure ending in death. Two studies presented below describe a novel virulence factor and mechanisms required for pathogenesis of STEC seropathotype 091 :H21.

First the novel protein, YghJ, was identified and found to be conserved amongst extraintestinal and diarrheal seropathotypes of E. coli with similar proteins carried by pathogens such as Vibrio cholerae. When the yghJ gene was disrupted creating a YghJ null mutant, the defect resulted in a significant growth deficiency in …

Spag16 Is A Bifunctional Gene Regulating Male Fertility, David R. Nagarkatti-Gude

Theses and Dissertations

SPAG16 is the murine orthologue of Chlamydomonas reinhardtii PF20, a protein known to be essential to the structure and function of the “9 + 2” axoneme. The “9 + 2” axoneme provides the cytoskeletal core of all eukaryotic motile cilia and flagella. In Chlamydomonas, the Pf20 gene encodes a single protein present in the central pair of the axoneme. Loss of Pf20 prevents central pair assembly and results in flagellar paralysis. The murine Spag16 gene encodes two proteins. While 71 kDa SPAG16L is found in all murine cells with motile cilia or flagella, 35 kDa SPAG16S transcript and protein are …

Characterizing The Interaction Between Ve-Ptp, Tie2 And Ve-Cadherin, Sharif Ossai Muhammad

Theses and Dissertations

Many signaling pathways have been shown to be involved in the formation of the vascular system. Among them are the endothelial specific receptor families such as VEGF, Ang/Tie, as well as other signaling pathways such as semaphorins, which are also involved, in axonal guidance. It is known that the interaction between receptor tyrosine kinase, Tie2, VE-Cadherin, and VE-PTP mediate endothelial cell quiescence and adhesion. However, the structural basis of these interactions is not well understood. The aim of our study is to characterize the binding interactions between these players. Another important part of our study is describing the cross-talk between …

Dietary Protein Influences Paracellular Calcium Transport: Two Molecular Targets, Belinda M. Kotler

Master's Theses

The effect of dietary protein on bone health remains controversial. We have shown that increasing dietary protein increases calcium absorption in both humans and rats with no change in bone resorption. We used a rat model in which dietary protein increases intestinal calcium absorption and whole body calcium retention, to explore the molecular basis for this effect. Female Sprague-Dawley rats were fed a low (5%) or high (40%) protein diet for 7 days. On day 7, duodenal mucosa was harvested and total RNA isolated. Microarray analyses using these RNA samples identified 208 genes whose expression was at least 1.5 fold …

Plant Lectin Can Target Receptors Containing Sialic Acid, Exemplified By Podoplanin, To Inhibit Transformed Cell Growth And Migration, Jhon Ochoa-Alvarez, Harini Krishnan, Yongquan Shen, Nimish Acharya, Min Han, Dean Mcnulty, Hitoki Hasegawa

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Cancer is a leading cause of death of men and women worldwide. Tumor cell motility contributes to metastatic invasion that causes the vast majority of cancer deaths. Extracellular receptors modified by α2,3-sialic acids that promote this motility can serve as ideal chemotherapeutic targets. For example, the extracellular domain of the mucin receptor podoplanin (PDPN) is highly O-glycosylated with α2,3-sialic acid linked to galactose. PDPN is activated by endogenous ligands to induce tumor cell motility and metastasis. Dietary lectins that target proteins containing α2,3-sialic acid inhibit tumor cell growth. However, anti-cancer lectins that have been examined thus far target receptors …