Biochemistry Commons^™

Pdip46 (Dna Polymerase Delta Interacting Protein 46) Is An Activating Factor For Human Dna Polymerase Delta, Xiaoxiao Wang, Sufang Zhang, Rong Zheng, Fu Yue, Szu Hua Sharon Lin, Amal Rahmeh, Ernest Y C Lee, Zhongtao Zhang, Marietta Y W T Lee

NYMC Faculty Publications

PDIP46 (SKAR, POLDIP3) was discovered through its interaction with the p50 subunit of human DNA polymerase δ (Pol δ). Its functions in DNA replication are unknown. PDIP46 associates with Pol δ in cell extracts both by immunochemical and protein separation methods, as well as by ChIP analyses. PDIP46 also interacts with PCNA via multiple copies of a novel PCNA binding motif, the APIMs (AlkB homologue-2 PCNA-Interacting Motif). Sites for both p50 and PCNA binding were mapped to the N-terminal region containing the APIMs. Functional assays for the effects of PDIP46 on Pol δ activity on singly primed ssM13 DNA templates …

Stabilin-1 And Stabilin-2 Are Specific Receptors For The Cellular Internalization Of Phosphorothioate-Modified Antisense Oligonucleotides (Asos) In The Liver, Colton M. Miller, Aaron J. Donnerr, Emma E. Blank, Andrew W. Egger, Brianna M. Kellar, Michael E. Østergaard, Punit P. Seth, Edward N. Harris

Department of Biochemistry: Faculty Publications

Phosphorothioate (PS)-modified antisense oligonucleotides (ASOs) have been extensively investigated over the past three decades as pharmacological and therapeutic agents. One second generation ASO, Kynamro^TM, was recently approved by the FDA for the treatment of homozygous familial hypercholesterolemia and over 35 second generation PS ASOs are at various stages of clinical development. In this report, we show that the Stabilin class of scavenger receptors, which were not previously thought to bind DNA, do bind and internalize PS ASOs. With the use of primary cells from mouse and rat livers and recombinant cell lines each expressing Stabilin-1 and each isoform …

Learning Approaches And Performance Of Medical Students, Rehana Rehman, Khalid Ahmed, Rabiya Rehan, Farheen Hassan, Fatima Syed

Department of Biological & Biomedical Sciences

Objective: To identify the best assessment method for medical students with different learning approaches.
Methods: The cross-sectional questionnaire-based study was conducted at Bahria University Medical and Dental College, Karachi, from March 2010 to April 2011, and comprised first year medical students. The questionnaire was tailored from the Approaches and Study Skills Inventory for Students on a five-point scale Deep approach, Surface apathetic approach and Strategic approach were assessed through relevant sub-scales. Response to questions was summed for the subscales and main scales for a learning approach. Mean scores for aggregate marks obtained by multiple choice questions, short answer questions, problem-based …

The Interaction Between Eukaryotic Translation Initiation Factor Eif4g And 3’ Cap Independent Translation Element Of Barley Yellow Dwarf Virus Is Affected By Multiple Initiation Factors, Pei Zhao

Dissertations, Theses, and Capstone Projects

Barley Yellow Dwarf Virus (BYDV) lacks a 5’ (7-methyl guanosine) cap as well as a 3’poly A tail. Like many plant viruses, BYDV contains a cap independent translation element (CITE) in the 3’ untranslated region of the viral mRNA. BTE (Barley Yellow Dwarf Virus like cap-independent translation element) is one of the well characterized CITEs. BTE mediated translation primarily depends on eukaryotic initiation factor eIF4G. BTE binds to eIF4G; however, the details of BTE initiated translation are still unclear. Three eIF4G deletion mutants with different domain organization were used to investigate BTE interaction with eIF4G: eIF4G601-1196 is the eIF4G fragment …

Messenger Rna Transport And Translation Regulated By The 3' Utrs Of Dendritic Mrnas And Abnormal Alternative Splicing Of Neuroligin1 In The Fmr1 Ko Mouse Hippocampus, Tianhui Zhu

Dissertations, Theses, and Capstone Projects

Fragile X Syndrome (FXS) is one of the most commonly inherited mental retardations. It is caused by the loss of functional fragile X mental retardation protein (FMRP). Loss of functional FMRP is the most widespread single-gene cause of autism. The most prominent phenotype of FXS patients is an IQ ranging from 20 to 70. FMRP is an RNA binding protein, widely expressed in almost all tissues and highly expressed in brain. As a RNA binding protein, 85-90 % of FMRP in the brain is associated with polyribosomes. Approximately 4 % of total mRNA is associated with FMRP, which functions in …

Decorin As A Multivalent Therapeutic Agent Against Cancer., Thomas Neill, Liliana Schaefer, Renato V. Iozzo

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Decorin is a prototypical small leucine-rich proteoglycan that epitomizes the multifunctional nature of this critical gene family. Soluble decorin engages multiple receptor tyrosine kinases within the target-rich environment of the tumor stroma and tumor parenchyma. Upon receptor binding, decorin initiates signaling pathways within endothelial cells downstream of VEGFR2 that ultimately culminate in a Peg3/Beclin 1/LC3-dependent autophagic program. Concomitant with autophagic induction, decorin blunts capillary morphogenesis and endothelial cell migration, thereby significantly compromising tumor angiogenesis. In parallel within the tumor proper, decorin binds multiple RTKs with high affinity, including Met, for a multitude of oncosuppressive functions including growth inhibition, tumor cell …

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 …

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.

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 …

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 …

Towards Structural Determination Of Human Α1-Glycine Receptor Allostery, Rathna Jyothi Veeramachaneni

Electronic Theses and Dissertations

Recent advances in technology have led to the determination of numerous notable structures of membrane proteins. While they provide valuable information about the structure of membrane proteins these studies often provide static images with potentially limited dynamics, and structural determination often requires truncation of flexible regions, and often utilizes bacterial homologs given the need for stable, heterologous overexpression. In order to better understand allostery at a molecular level, state-dependent crosslinking studies coupled with multidimensional mass spectrometry (MS) were conducted on glycine receptor (GlyR) stabilized in different allosteric states. Predominant allosteric states were stabilized using wild type or mutated receptor in …

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 …