Biochemistry, Biophysics, and Structural Biology Commons^™

Epidemiological Ins And Outs Of Helicobacter Pylori: A Review, Jibran Sualeh Muhammad, Syed Faisal Zaidi, Toshiro Sugiyama

Department of Biological & Biomedical Sciences

Helicobacter pylori infection is now recognised as a worldwide problem. It is the most common cause of chronic gastritis, and is strongly linked to peptic ulcer disease and gastric cancer. A comprehensive understanding of epidemiological ins and outs of H. pylori infection is very important in solving the patho-physiological enigma and might help in leading towards better management and prognosis of infection. This article presents a review of the literature on the epidemiology of H. pylori infection from 2006 to 2011. The authors used Medical Subject Heading (MeSH) terms 'Helicobacter' with 'epidemiology,' 'transmission' or 'risk factor' to search PubMed database. …

Endogenous Inhibitor Proteins That Connect Ser/Thr Kinases And Phosphatases In Cell Signaling., Masumi Eto, David L Brautigan

Department of Molecular Physiology and Biophysics Faculty Papers

Protein phosphatase activity acts as a primary determinant of the extent and duration of phosphorylation of cellular proteins in response to physiological stimuli. Ser/Thr protein phosphatase-1 (PP1) belongs to the PPP superfamily, and is associated with regulatory subunits that confer substrate specificity, allosteric regulation, and subcellular compartmentalization. In addition, all eukaryotic cells contain multiple heat-stable proteins that originally were thought to inhibit phosphatase catalytic subunits released from the regulatory subunits, as a fail-safe mechanism. However, discovery of C-kinase-activated PP1 inhibitor, Mr of 17 kDa (CPI-17) required fresh thinking about the endogenous inhibitors as specific regulators of particular phosphatase complexes, acting …

Effect Of Egf-Receptor Tyrosine Kinase Inhibitor On Rab5 Function During Endocytosis, Ivan Jozic, Samar C. Saliba, M. Alejandro Barbieri

Biology Faculty Articles

Tyrosine autophosphorylation within the cytoplasmic tail of EGF-receptor is a key event, which in turn recruits several factors including Shc, Grb2 and Rin1 that are essential activities for receptor-mediated endocytosis and signaling. In this study, we demonstrated that treatment with AG1478, an EGF-receptor kinase inhibitor, blocked the formation of Rab5-positive endosomes as well as the activation of Rab5 upon addition of EGF. We also found that EGF-receptor catalytically inactive mutant failed to activate Rab5 upon EGF stimulation. Additionally, endosomal co-localization of Rab5 and EGF-receptor was inhibited by AG1478. Interestingly, AG1478 inhibitor did not block the formation of enlarged Rab5-positive endosomes …

Taking Aim At The Start Of Translation, Medha Raina, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

No abstract provided.

Role Of Sequence And Structure Of The Hendra Fusion Protein Fusion Peptide In Membrane Fusion, Everett Clinton Smith, Sonia M. Gregory, Lukas K. Tamm, Trevor P. Creamer, Rebecca Ellis Dutch

Molecular and Cellular Biochemistry Faculty Publications

Viral fusion proteins are intriguing molecular machines that undergo drastic conformational changes to facilitate virus-cell membrane fusion. During fusion a hydrophobic region of the protein, termed the fusion peptide (FP), is inserted into the target host cell membrane, with subsequent conformational changes culminating in membrane merger. Class I fusion proteins contain FPs between 20 and 30 amino acids in length that are highly conserved within viral families but not between. To examine the sequence dependence of the Hendra virus (HeV) fusion (F) protein FP, the first eight amino acids were mutated first as double, then single, alanine mutants. Mutation of …

Sex Determination In Beetles: Production Of All Male Progeny By Parental Rnai Knockdown Of Transformer, Jayendra Nath Shukla, Subba Reddy Palli

Entomology Faculty Publications

Sex in insects is determined by a cascade of regulators ultimately controlling sex-specific splicing of a transcription factor, Doublesex (Dsx). We recently identified homolog of dsx in the red flour beetle, Tribolium castaneum (Tcdsx). Here, we report on the identification and characterization of a regulator of Tcdsx splicing in T. castaneum. Two male-specific and one female-specific isoforms of T. castaneum transformer (Tctra) were identified. RNA interference-aided knockdown of Tctra in pupa or adults caused a change in sex from females to males by diverting the splicing of Tcdsx pre-mRNA to male-specific isoform. All the pupa and adults developed from Tctra …

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben Michael Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biological Sciences Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are “lemon” or “spindle”-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …

Small-Molecule Inhibition Of Brdt For Male Contraception., Martin M. Matzuk, Michael R. Mckeown, Panagis Filippakopoulos, Qinglei Li, Lang Ma, Julio E. Agno, Madeline E. Lemieux, Sarah Picaud, Richard M. Yu, Jun Qi, Stefan Knapp, James E. Bradner

Biochemistry and Molecular Medicine Faculty Publications

A pharmacologic approach to male contraception remains a longstanding challenge in medicine. Toward this objective, we explored the spermatogenic effects of a selective small-molecule inhibitor (JQ1) of the bromodomain and extraterminal (BET) subfamily of epigenetic reader proteins. Here, we report potent inhibition of the testis-specific member BRDT, which is essential for chromatin remodeling during spermatogenesis. Biochemical and crystallographic studies confirm that occupancy of the BRDT acetyl-lysine binding pocket by JQ1 prevents recognition of acetylated histone H4. Treatment of mice with JQ1 reduced seminiferous tubule area, testis size, and spermatozoa number and motility without affecting hormone levels. Although JQ1-treated males mate …

Biochemical Evaluation Of Srh Analogs As Potential Luxs Inhibitors, Richa Gupta

Master's Theses

Quorum sensing in bacteria is a process of cell-to-cell communication facilitated by small molecules called autoinducers. Interspecies quorum sensing is facilitated by the autoinducer AI-2. The enzyme LuxS catalyzes the formation of AI-2 from S-ribosyl homocysteine (SRH) in a wide variety of bacterial species. Inhibition of LuxS would therefore inhibit interspecies quorum sensing. The goal of this project is to establish biochemical assays for the evaluation of small molecules as potential LuxS inhibitors. The first assay is a conventional colorimetric assay that utilizes Ellman’s reagent to quantify the homocysteine byproduct of DPD production by LuxS. For this assay purified …

Green Tea Extract Protects Against Fibrogenesis Associated With Nonalcoholic Fatty Liver Disease In Diet-Induced Obese Rats, Allyson M. Bower

Master's Theses

No abstract provided.

Breast Tumour Initiating Cell Fate Is Regulated By Microenvironmental Cues From An Extracellular Matrix, Sharmistha Saha, Pang-Kuo Lo, Xinrui Duan, Hexin Chen, Qian Wang

Faculty Publications

Cancer stem cells, also known as tumour-initiating cells (TICs), are identified as highly tumorigenic population within tumours and hypothesized to be main regulators in tumour growth, metastasis and relapse. Evidence also suggests that a tumour microenvironment plays a critical role in the development and progression of cancer, by constantly modulating cell–matrix interactions. Scientists have tried to characterize and identify the TIC population but the actual combination of extracellular components in deciphering the fate of TICs has not been explored. The basic unanswered question is the phenotypic stability of this TIC population in a tissue extracellular matrix setting. The in vivo …

Gas Phase Characterization Of Supramolecules Using Cross-Sectional Areas By Fticr And Sustained Off-Resonance Irradiation Collision Induced Dissociation Techniques In A Fourier Transform Ion Cyclotron Resonance Mass Spectrometer, Fan Yang

Theses and Dissertations

In my dissertation, I use a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR-MS) to investigate supramolecules. Cross-sectional areas by Fourier transform ICR (CRAFTI), a novel technique for measurements of collision cross sections by FTICR, is demonstrated for the first time. The CRAFTI method measures the total "dephasing cross section" for removal of the ions from the coherent packet in the FTICR cell, including contributions not only from momentum transfer but also from reactive collisions including those leading to collisional dissociation. Experimental CRAFTI collision cross sections correlate linearly with theoretically computed results and with results obtained using ion mobility measurements. …

Flow Valve Diagnostics For Label-Free, Quantitative Biomarker Detection: Device Fabrication, Surface Modification, And Testing, Danielle Scarlet Mansfield

Theses and Dissertations

Diseases are often diagnosed by detection of disease-specific biomarkers in fluid samples. However, many state-of-the-art detection methods require a lab with complex machinery, trained operators, and/or lengthy analysis time. In contrast, point-of-care (POC) devices are brought to the patient's location, they are easy to use, and results are obtained almost immediately. Many current POC devices are too difficult to be used without a skilled assistant, and although many are able to detect analytes above a threshold value, they give little or no quantitative information. This work presents the development of polymer-based microfluidic devices capable of sensing and quantifying biomarkers in …

Synthesis And Biological Evaluation Of Various Derivatives Of A Broad-Spectrum Anticancer Nucleoside, Jadd R. Shelton

Theses and Dissertations

Recently the Peterson lab discovered a promising anticancer adenosine derivative-- 2´,3´-bis-O-tert-butyldimethylsilyl-5´-deoxy-5´-[N-(methylcarbamoyl)amino]-N6-(N-phenylcarbamoyl)adenosine. This compound showed selective toxicity against human colon cancer cells in vitro with LC50's = 6--10 µM. It was hypothesized that the lead compound exerted its cytotoxic effects by interacting with a protein kinase. A systematic Structure Activity Relationship (SAR) was undertaken in an attempt to increase the kinase-binding affinity of the lead compound. Many regions of the lead compound were examined: the N6-phenyl urea moiety, the 5´-N-methyl urea group, the 2´,3´-bis-O-TBS groups, the nucleobase, and the ribose sugar. Results of these studies produced some promising new derivatives. In …

Interactome-Wide Analysis Identifies End-Binding Protein 1 As A Crucial Component For The Speck-Like Particle Formation Of Activated Absence In Melanoma 2 (Aim2) Inflammasomes, Li-Jie Wang, Chia-Wei Hsu, Chiu-Chin Chen, Ying Liang, Lih-Chyang Chen, David M. Ojcius, Ngan-Ming Tsang, Chuen Hsueh, Chih-Ching Wu, Yu-Sun Chang

All Dugoni School of Dentistry Faculty Articles

Inflammasomes are cytoplasmic receptors that can recognize intracellular pathogens or danger signals and are critical for interleukin 1β production. Although several key components of inflammasome activation have been identified, there has not been a systematic analysis of the protein components found in the stimulated complex. In this study, we used the isobaric tags for relative and absolute quantification approach to systemically analyze the interactomes of the NLRP3, AIM2, and RIG-I inflammasomes in nasopharyngeal carcinoma cells treated with specific stimuli of these interactomes (H2O2, poly (dA:dT), and EBV noncoding RNA, respectively). We identified a number of proteins that appeared to be …

Sorafenib Enhances Pemetrexed-Induced Cytotoxicity Through And Autophagy-Dependent Mechanism In Cancer Cells, Bareford Mary

Theses and Dissertations

Acquired cellular resistance to traditional chemotherapeutics is a common obstacle in the treatment of most cancer cell types. This resistance occurs as a result of changes in the underlying molecular mechanisms of disease progression. The development of novel chemotherapeutic approaches designed to enhance the efficacy of protypical anti-cancer drugs is important in order to overcome this issue. Such approaches will aid in understanding the biomolecular phenomena responsible for drug resistance and disease progression. Combining signaling pathway inhibitors has become an effective strategy for enhancing tumor cell death by targeting multiple pathways known to regulate cell survival. Pemetrexed, an FDA-approved anti-folate …

Physiologically-Based Pharmacokinetic Modeling Of Acetaminophen Metabolism And Toxicity, David M. Ng, Ali Navid

STAR Program Research Presentations

Acetaminophen is a common analgesic and antipyretic. Metabolism of acetaminophen and acetaminophen-induced liver necrosis are predicted using physiologically-based pharmacokinetic (PBPK) modeling. Pharmacokinetic means the model determines where the drug is distributed in the body over time. Physiologically-based means the anatomy and physiology of the human body is reflected in the structure and functioning of the model. Acetaminophen is usually safe and effective when taken as recommended, but consumption at higher levels may lead to liver damage. Additionally, other factors such as alcoholic liver disease, smoking, and malnutrition affect the maximum safe dose of acetaminophen.

Using Stable Isotope Analysis To Study Zooplankton Trophic Ecology In San Francisco Estuary, Steven C. Westbrook, Julien Moderan, Wim Kimmerer

STAR Program Research Presentations

Zooplankton biomasses in estuaries are often high and represent an important food source for fish, like theendangered Delta Smelt. Human interferences (nitrates from crops, freshwater 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. Every living thing has a specific isotopic signature. For example, in the plankton we study exists Carbon 13 and Carbon 12. Carbon 13 is different only because it has one extra neutron, …

Quantification And In Vitro Analysis Of Nanolipoproteins (Nlps) Containing Adjuvants, Purna Venkataraman, Craig Blanchette, Nicholas O. Fischer

STAR Program Research Presentations

Nanolipoprotein particles (NLPs) self-assemble into nanoscale structures that can be used as vaccines or drug delivery agents. Due to the nature of the NLPs, a variety of immune stimulating compounds or adjuvants can be readily incorporated into NLPs: a characteristic difficult to engineer into most other nanoscale platforms. In light of this, a method for quantifying the amount adjuvant actually incorporated into NLPs is a question of high importance. Through the use of reverse phase High-Performance Liquid Chromatography (HPLC) and an Evaporative Light Scattering Detector (ELSD), standard curves can be constructed by analyzing mixtures of NLP components of known concentration, …

Analyzing Environmental Microbes For Genomic Regions Promoting Ionic Liquid Tolerance In E. Coli, Ann Nguyen, Alison Richins, Thomas Rüegg, Steven Singer, Michael Thelen

STAR Program Research Presentations

Ionic liquids (ILs) are promising as solvents to increase the efficiency of biofuel production; however, ILs are toxic to microbes used in the fermentation of liquid fuels. To engineer IL resistant biofuel hosts, environmental bacteria were screened for tolerance, and these were used to create gene libraries to test in E. coli. Future characterization of these libraries using molecular techniques will be used to identify genes that contribute IL-tolerance to transformed microbes.

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 …}

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 …

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 …

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.