Biochemistry Commons^™

Potential Regulation Of Deadly Water-Borne Shigella Bacteria Pathogenesis Through The Shigella Infection Protein Spa47, Jamie Kingsford

Research on Capitol Hill

• Shigella is a gram-negative, bacterial pathogen typically found in contaminated water sources.
• Each year, Shigella is responsible for over 90 million infections and 100,000 deaths stemming from symptoms of severe dysentery, fever, nausea and vomiting.
• A needle-like apparatus found on the surface of Shigella allows the bacterium to infect host cells.
• Each needle-apparatus has an associated ATPase, a protein that can hydrolyze ATP into ADP and P_i.
• The Shigella needle-apparatus ATPase Spa47 is predicted to provide the energy for infection.
• Spa47 has been shown to be essential for infection – without Spa47, no infection will occur.
• We were …

The Dual Regulatory Role Of Amino Acids Leu480 And Gln481 Of Prothrombin, Joesph R. Wiencek, Jamila Hirbawi, Vivien C. Yee, Michael Kalafatis

Chemistry Faculty Publications

Prothrombin (FII) is activated to α-thrombin (IIa) by prothrombinase. Prothrombinase is composed of a catalytic subunit, factor Xa (fXa), and a regulatory subunit, factor Va (fVa), assembled on a membrane surface in the presence of divalent metal ions. We constructed, expressed, and purified several mutated recombinant FII (rFII) molecules within the previously determined fVa-dependent binding site for fXa (amino acid region 473–487 of FII). rFII molecules bearing overlapping deletions within this significant region first established the minimal stretch of amino acids required for the fVa-dependent recognition exosite for fXa in prothrombinase within the amino acid sequence Ser⁴⁷⁸–Val^{479 …}

Membrane Glycerolipidome Of Soybean Root Hairs And Its Response To Nitrogen And Phosphate Availability, Fang Wei, Brian Fanella, Liang Guo, Xuemin Wang

Biology Department Faculty Works

Root hairs are tubular extensions of specific root epidermal cells important in plant nutrition and water absorption. To determine membrane glycerolipids in root hairs and roots may differ, as well as their respective response to nutrient availability, this study analyzed the membrane glycerolipid species in soybean root hairs and in roots stripped of root hairs, and their response to nitrogen (N) and phosphate (Pi) supplementation. The ratio of phospholipids to galactolipids was 1.5 fold higher in root hairs than in stripped roots. Under Pi deficiency, the ratio of phospholipids to galactolipids in stripped roots decreased with the greatest decrease found …

Kdac8 With High Basal Velocity Is Not Activated By N-Acetylthioureas, Tasha B. Toro, Subramanya Pingali, Thao P. Nguyen, Destane S. Garrett, Kyra A. Dodson, Kyara A. Nichols, Rashad A. Haynes, Florastina Payton-Stewart, Terry J. Watt

Faculty and Staff Publications

Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Recently, a series of N-acetylthioureas were synthesized and reported to enhance the activity of KDAC8 with a fluorogenic substrate. To determine if the activation was general, we synthesized three of the most potent N-acetylthioureas and measured their effect with peptide substrates and the fluorogenic substrate under multiple reaction conditions and utilizing two enzyme purification approaches. No activation was observed for any of the three N-acetylthioureas under any assayed conditions. Further characteriza- tion of KDAC8 kinetics with the fluorogenic substrate yielded a k cat /K M of 164 …

Interactions Of Two Large Antiviral Polyamides With The Long Control Region Of Hpv16., Elena Vasilieva, Jacquelyn Niederschulte, Yang Song, George Harris, Kevin Koeller, Puhong Liao, James Bashkin, Cynthia Dupureur

Chemistry & Biochemistry Faculty Works

No abstract provided.

Cannabinoid Receptor Interacting Protein Suppresses Agonist-Driven Cb1 Receptor Internalization And Regulates Receptor Replenishment In An Agonist-Biased Manner, Lawrence C. Blumes, Sandra Leone-Kabler, Deborah J. Luessen, Glenn S. Marrs, Erica Lyons, Caroline E. Bass, Rong Chen, Dana E. Selley, Allyn C. Howlett

Neurology Publications

Cannabinoid receptor interacting protein 1a (CRIP1a) is a CB1 receptor (CB1R) distal C-terminus-associated protein that modulates CB1R signaling via G proteins, and CB1R down-regulation but not desensitization (Blume et al. [2015] Cell Signal., 27, 716-726; Smith et al. [2015] Mol. Pharmacol., 87, 747-765). In this study, we determined the involvement of CRIP1a in CB1R plasma membrane trafficking. To follow the effects of agonists and antagonists on cell surface CB(1)Rs, we utilized the genetically homogeneous cloned neuronal cell line N18TG2, which endogenously expresses both CB1R and CRIP1a, and exhibits a well-characterized endocannabinoid signaling system. We developed stable CRIP1a-over-expressing and CRIP1a-siRNA-silenced knockdown …

C-Reactive Protein Interactions With Cellular Membranes And Supported Lipid Bilayers, Aml Abd Alhamed Alnaas

Electronic Theses and Dissertations

C-reactive protein (CRP) is a serum protein that binds to damaged membranes and initiates the complement immune response. Different forms of CRP are thought to alter how the body responds to inflammation and the degradation of foreign material. Despite knowing that a modified form of CRP(mCRP) binds to downstream protein binding partners better than the native pentameric form, the role of CRP conformation on lipid binding is yet unknown. In this work, three main assays were performed to characterize how conformation affects CRP-membrane interactions. The first assay utilized supported lipid bilayers that mimic the plasma membrane of apoptotic cells. The …

Source Apportionment Of Atmospheric Particulate Matter In Developing Countries Using Trace Elements And Stable Metal Isotope Ratios, Nitika Dewan

Electronic Theses and Dissertations

The work presented herein details the source apportionment of atmospheric particulate matter in developing countries (Kyrgyzstan in Central Asia, metropolitan cities in Northern India, and Shenzhen in China) using trace elements and stable metal isotope ratios. The first study focused on the development of a novel method for the concomitant separation of rare-earth elements in environmental samples of any geological origin. The separation procedure is based on three extraction chromatographic materials, referred to as Sr.Spec, TRU.Spec, and Ln.Spec. This triple column arrangement enables the simultaneous isolation of pure Sr and Nd fractions in less than one day and with great …

Water Soluble Cationic Porphyrin Sensor For Detection Of Hg2+, Pb2+, Cd2+, And Cu2+, Matibur Zamadar, Christopher Orr, Miranda Uherek

Faculty Publications

Here we report the sensing properties of the aqueous solution of meso-tetra(N-methyl-4-pyridyl)porphine tetrachloride (1) for simultaneous detection of toxic metal ions by using UV-vis spectroscopy. Cationic porphyrin 1 displayed different electronic absorptions in UV-vis region upon interacting with Hg2+, Pb2+, Cd2+, and Cu2+ ions in neutral water solution at room temperature. Quite interestingly, the porphyrin 1 showed that it can function as a single optical chemical sensor and/or metal ion receptor capable of detecting two or more toxic metal ions, particularly Hg2+, Pb2+, and Cd2+ ions coexisting in a water sample. Porphyrin 1 in an aqueous solution provides a unique …

Agricultural Fires In The Southeastern U.S. During Seac4Rs: Emissions Of Trace Gases And Particles And Evolution Of Ozone, Reactive Nitrogen, And Organic Aerosol, Xiaoxi Liu, Y. Zhang, L. G. Huey, R. J. Yokelson, Y. Wang, J. L. Jimenez, P. Campuzano-Jost, A. J. Beyersdorf, D. R. Blake, Y. Choi, J. M. St. Clair, J. D. Crounse, D. A. Day, G. S. Diskin, A. Ried, S. R. Hall, T. F. Hanisco, L. E. King, S. Meinardi, T. Mikoviny, B. B. Palm, J. Peischl, A. E. Perring, I. B. Pollack, T. B. Ryerson, G. Sachse, J. P. Schwarz, I. J. Simpson, D. J. Tanner, K. L. Thornhil, K. Ullmann, R. J. Weber, P. O. Wennberg

Chemistry and Biochemistry Faculty Publications

Emissions from 15 agricultural fires in the southeastern U.S. were measured from the NASA DC-8 research aircraft during the summer 2013 Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) campaign. This study reports a detailed set of emission factors (EFs) for 25 trace gases and 6 fine particle species. The chemical evolution of the primary emissions in seven plumes was examined in detail for ~1.2 h. A Lagrangian plume cross-section model was used to simulate the evolution of ozone (O3), reactive nitrogen species, and organic aerosol (OA). Observed EFs are generally consistent with previous …

Planning, Implementation, And Scientific Goals Of The Studies Of Emissions And Atmospheric Composition, Clouds And Climate Coupling By Regional Surveys (Seac4Rs) Field Mission, Owen B. Toon, Hal Maring, Jack Dibb, Richard Ferrare, Daniel J. Jacob, Eric J. Jensen, Z. Johnny Luo, Gerald G. Mace, Laura L. Pan, Lenny Pfister, Karen H. Rosenlof, Jens Redemann, Jeffrey S. Reid, Hanwant B. Singh, Anne M. Thompson, Robert Yokelson, Patrick Minnis, Gao Chen, Kenneth W. Jucks, Alex Pszenny

Chemistry and Biochemistry Faculty Publications

The Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) fieldmission based at Ellington Field, Texas, during August and September 2013 employed the most comprehensive airborne payload to date to investigate atmospheric composition over North America. The NASA ER-2, DC-8, and SPEC Inc. Learjet flew 57 science flights fromthe surface to 20 km. The ER-2 employed seven remote sensing instruments as a satellite surrogate and eight in situ instruments. The DC-8 employed 23 in situ and five remote sensing instruments for radiation, chemistry, and microphysics. The Learjet used 11 instruments to explore cloud microphysics. SEAC4RS …

Ice-Nucleating Particle Emissions From Biomass Combustion And The Potential Importance Of Soot Aerosol, E. J.T. Levin, G. R. Mcmeeking, P. J. Demott, C. S. Mccluskey, C. M. Carrico, S. Nakao, T. Jayarathne, E. A. Stone, C. E. Stockwell, R. J. Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Ice-nucleating particles (INPs) are required for initial ice crystal formation in clouds at temperatures warmer than about -36°C and thus play a crucial role in cloud and precipitation formation. Biomass burning has been found to be a source of INPs in previous studies and is also a major contributor to atmospheric black carbon (BC) concentrations. This study focuses on isolating the BC contribution to the INP population associated with biomass combustion. Emissions of condensation mode INPs from a number of globally relevant biomass fuels were measured at -30°C and above water saturation as fires progressed from ignition to extinguishment in …

Rapidly Evolving Ultrafine And Fine Mode Biomass Smoke Physical Properties: Comparing Laboratory And Field Results, Christian M. Carrico, Anthony J. Prenni, Sonia M. Kreidenweis, Ezra J.T. Levin, Christina S. Mccluskey, Paul J. Demott, Gavin R. Mcmeeking, Shunsuke Nakao, Chelsea Stockwell, Robert J. Yokelson

Chemistry and Biochemistry Faculty Publications

Combining field and laboratory results, we present biomass smoke physical properties. We report sub-0.56 µm diameter (Dp) particle sizing (fast mobility particle sizer, FMPS) plus light absorption and scattering at 870nm (photoacoustic extinctiometer). For Dp<200 >nm, the FMPS characterized sizing within ±20% compared to standards. As compared to the traditional scanning mobility particle sizer, the FMPS responded most accurately to single-mode polydispersions with mean Dp<200 >nm, which characterized the smoke sampled here. Smoke was measured from laboratory fresh emissions (seconds to hours old), the High Park Fire (hours to<1 >day), and from regional biomass burning (several days). During a High …

Genomic Signatures For Paclitaxel And Gemcitabine Resistance In Breast Cancer Derived By Machine Learning., Stephanie N Dorman, Katherina Baranova, Joan H M Knoll, Brad L Urquhart, Gabriella Mariani, Maria Luisa Carcangiu, Peter K Rogan

Biochemistry Publications

Increasingly, the effectiveness of adjuvant chemotherapy agents for breast cancer has been related to changes in the genomic profile of tumors. We investigated correspondence between growth inhibitory concentrations of paclitaxel and gemcitabine (GI50) and gene copy number, mutation, and expression first in breast cancer cell lines and then in patients. Genes encoding direct targets of these drugs, metabolizing enzymes, transporters, and those previously associated with chemoresistance to paclitaxel (n = 31 genes) or gemcitabine (n = 18) were analyzed. A multi-factorial, principal component analysis (MFA) indicated expression was the strongest indicator of sensitivity for paclitaxel, and copy number and expression …

Development Of Gamma-Modified Atp Analogs To Study Kinase-Catalyzed Phosphorylations, Ahmed Eid Fouda

Wayne State University Dissertations

Kinase-catalyzed protein phosphorylation is one of the most important post-translational modifications that controls cascades of biochemical reactions. Irregularities in phosphorylation result in many diseases, such as diabetes mellitus, Parkinsons, and cancer. The development of new methods to monitor kinase-catalyzed phosphorylation is needed to decipher details of normal and diseased cell signaling. The Pflum lab recently developed several -modified ATP analogs to study kinase catalyzed phosphorylation reactions. The -modified ATP analogs have different tags, such as biotin for substrate labeling or aryl-azide for kinase substrates identification. Unfortunately, use of -modified ATP analogs was limited to in vitro studies due to the …

Nitrogenase Femoco Investigated By Spatially Resolved Anomalous Dispersion Refinement, Thomas Spatzal, Julia Schlesier, Eva-Maria Burger, Daniel Sippel, Limei Zhang, Susana L.A. Andrade, Douglas C. Rees, Oliver Einsle

Department of Biochemistry: Faculty Publications

The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S 1⁄4 3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the …

A Critical Role Of Cxcr2 Pdz Motif-Mediated Interactions In Endothelial Progenitor Cell Homing And Angiogenesis, Yuning Hou

Wayne State University Dissertations

Bone marrow-derived endothelial progenitor cells (EPCs) participate in postnatal vascularization in response to growth factors, cytokines, and chemokines. Chemokine receptor CXCR2 and its cognate ligands are reported to mediate EPC recruitment and angiogenesis. CXCR2 possesses a consensus PSD-95/DlgA/ZO-1 (PDZ) motif at its carboxyl terminus. The PDZ motif has been reported to regulate cellular signaling and functions. Here we investigated the potential role of the PDZ motif in CXCR2-mediated EPC motility and angiogenesis. We have found that introducing exogenous CXCR2 C-terminus significantly attenuated in vitro EPC migration and angiogenic activities in response to CXCR2 ligands, as well as in vivo EPC …

The Development Of Peptide Ligands To Target H69 Rrna, Danielle Nicole Dremann

Wayne State University Dissertations

ABSTRACT

THE DEVELOPMENT OF PEPTIDE LIGANDS TO TARGET H69

by

DANIELLE NICOLE DREMANN

December 2015

Advisor: Prof. Christine S. Chow

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

In the development of peptide ligands to target H69, SPPS and ESI MS was used to determine if 1) peptides could bind to modified H69 and 2) if increased affinity for the target RNA could be enhanced with modification. An alanine and arginine scan was synthesized and tested for this determination. Selected peptides were then tested using biophysical techniques such as circular dichroism and isothermal titration calorimetry. An assay was also designed to …

Bacterial Forensics: Revolutionizing Biochemical Analysis, Caitlin Cain

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Eva Childrey is a junior forensic science and chemistry double major working in Dr. Eh- rhardt’s research laboratory at VCU. The main goal of the research conducted in this laboratory is to explore the lipid profiles of different bacterial species.

Students' Perception Of Educational Environment At Aga Khan University Medical College, Karachi, Pakistan, Rehana Rehman, Kulsoom Ghias, Syeda Sadia Fatima, Mehwish Hussain, Faiza Alam

Department of Biological & Biomedical Sciences

Objective: To assess educational environment in Aga Khan University Medical College (AKUMC) by Dundee Ready Educational Environmental Measure (DREEM) scale.
Methods: A cross-sectional survey of students at the AKUMC with simple random sampling was carried out from June 2014 till March 2015. Responses in five subscales were used to calculate DREEM scores.
Results: The average DREEM score was 125.77±16.8 with a reliability of 91.3%. With regards to subscales, on the 12-item students' perceptions of learning (PoL) subscale, the maximum score was 48; 11 items of students' perceptions of teachers (PoT) had a maximum score of 44; students' academic self-perceptions (ASP) …