Biochemistry, Biophysics, and Structural Biology Commons^™

Glycation Of Lysozyme, Wisam Talib Joudah

Theses, Dissertations and Capstones

For this research project, I propose a method for the analysis of glycated lysozyme using Matrix Associated Laser Desorption / Ionization-Time of Flight Mass spectrometry (MALDI-TOF MS). Glycation or "Maillard reaction" is a non-enzymatic reaction that occurs between amino acid residues, usually primary and secondary amines, of proteins and the carbonyl group of reducing sugars to yield Schiff bases. The glycation mechanism occurs between the carbonyl group of the reducing sugars and a primary amine by nucleophilic addition, resulting in the formation of a Schiff base. The Schiff base can then rearrange into the more stable Amadori product which is …

Investigation Into The Biological Importance And Function Of Proinsulin C-Peptide, Christina L. Newsome

Theses, Dissertations and Capstones

The C-peptide of insulin was thought to be biologically inactive, but recent studies have shown that the C-peptide causes multiple molecular and physiological effects. Evidence has shown that C-peptide binds to a cell surface receptor, probably a G-protein coupled receptor, and that the COOH-terminal pentapeptide is essential for binding and constitutes an active site. For a further understanding of the detailed nature of the physiological effects of C-peptide, the receptor structure needs to be determined. We designed an affinity column using C-peptide to try and gain a better understanding of the biological effects by examining what proteins the affinity column …

Hcv Infection-Associated Hepatocellular Carcinoma In Humanized Mice., Zhao Wang, Ningbin Wu, Abeba Tesfaye, Stephen Feinstone, Ajit Kumar

Biochemistry and Molecular Medicine Faculty Publications

BACKGROUND AND AIMS: Hepatitis C virus (HCV) infection is a major risk factor for chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC). Our aim is to explore molecular changes that underlie HCV infection-associated HCC in a humanized mouse model, in order to identify markers of HCC progression.

METHODS: Liver proteins from human hepatocyte-engrafted and HCV-infected MUP-uPA/SCID/Bg mice were compared with either uninfected controls or HCV-infected but HCC-negative mice by Western blotting. MicroRNA markers of HCC positive or uninfected mouse liver were analyzed by RT-PCR.

RESULTS: We describe the depletion of tumor suppressor proteins and induction of oncoproteins and oncogenic microRNAs (oncomiRs) …

The Genus Cerion (Gastropoda: Cerionidae) In The Florida Keys., Yesha Shrestha, Herman H. Wirshing, M. G. Harasewych

Biochemistry and Molecular Medicine Faculty Publications

The systematic relationships and phylogeography of Cerion incanum, the only species of Cerion native to the Florida Keys, are reviewed based on partial sequences of the mitochondrial COI and 16S genes derived from 18 populations spanning the range of this species and including the type localities of all four described subspecies. Our samples included specimens of Cerion casablancae, a species introduced to Indian Key in 1912, and a population of C. incanum x C. casablancae hybrids descended from a population of C. casablancae introduced onto Bahia Honda Key in the same year. Molecular data did not support the partition of …

Atrial Fibrillation: Biophysics, Molecular Mechanisms, And Novel Therapies., Alexey V. Glukhov, Leonid V. Rosenshtraukh, Anamika Bhargava, Michele Miragoli, Bas J. D. Boukens

Anatomy and Regenerative Biology Faculty Publications

No abstract provided.

Extraordinary Diversity Of Immune Response Proteins Among Sea Urchins: Nickel-Isolated Sp185/333 Proteins Show Broad Variations In Size And Charge., Lauren S. Sherman, Catherine S. Schrankel, Kristy J. Brown, L. Courtney Smith

Pediatrics Faculty Publications

Effective protection against pathogens requires the host to produce a wide range of immune effector proteins. The Sp185/333 gene family, which is expressed by the California purple sea urchin Strongylocentrotus purpuratus in response to bacterial infection, encodes a highly diverse repertoire of anti-pathogen proteins. A subset of these proteins can be isolated by affinity to metal ions based on multiple histidines, resulting in one to four bands of unique molecular weight on standard Western blots, which vary depending on the individual sea urchin. Two dimensional gel electrophoresis (2DE) of nickel-isolated protein samples followed by Western blot was employed to detect …

Myocardium And Bmp Signaling Are Required For Endocardial Differentiation, Sharina Palencia-Desai, Megan S. Rost, Jennifer A. Schumancher, Quynh V. Ton, Michael P. Craig, Kristina Baltrunaite, Andrew L. Koenig, Jinhu Wang, Kenneth D. Poss, Neil C. Chi, Didier Y.R. Stainier

Biochemistry and Molecular Biology Faculty Publications

Endocardial and myocardial progenitors originate in distinct regions of the anterior lateral plate mesoderm and migrate to the midline where they coalesce to form the cardiac tube. Endocardial progenitors acquire a molecular identity distinct from other vascular endothelial cells and initiate expression of specific genes such as nfatc1. Yet the molecular pathways and tissue interactions involved in establishing endocardial identity are poorly understood. The endocardium develops in tight association with cardiomyocytes. To test for a potential role of the myocardium in endocardial morphogenesis, we used two different zebrafish models deficient in cardiomyocytes: the hand2 mutant and a myocardial-specific genetic …

Bacterial Expression Of Plant Pyruvate Kinase, Kristina Fuller

STAR Program Research Presentations

Pyruvate kinases serve an important role in regulating glycolysis pathways. Different pyruvate kinase isozymes can dictate which of several different products will be formed during the final step of glycolysis. Being able to reliably copy active pyruvate kinases (PK) would allow study of the different isozymes, with the goal of eventually creating plants that are more nutritionally beneficial for humans. This study focused on improving the protocol for replicating each of two isolated PK isozymes from the model plant Arabidopsis thaliana. Previous attempts had resulted in the PK denaturing and consequently precipitating out of solution and so we manipulated the …

Is There Pandemic Vitamin D Deficiency In The Black Population? A Review Of Evidence, Ria S. Roberts, Fafa Huberta Koudoro, Mark S. Elliott, Zhiyong Han

Biochemistry and Molecular Medicine Faculty Publications

Although 1,25-dihydroxyvitamin D [1,25(OH)2D] is the biologically active form of vitamin D, measurement of the total serum 25-hydroxyvitamin D [25(OH)D] level is the gold standard used to define vitamin D status. Currently, it is widely accepted that serum 25 (OH) D levels below 20 ng/ml defines vitamin D deficiency. According to this definition, there appears to be pandemic vitamin D deficiency in the Black population. However, there is no evidence of higher-thannormal rates of common complications and symptomology of true vitamin D deficiency in the Black population. What is going on? We researched the MEDLINE databases to find studies, from …

The Global Cancer Genomics Consortium's Symposium: New Era Of Molecular Medicine And Epigenetic Cancer Medicine - Cross Section Of Genomics And Epigenetics, Masakazu Toi, M. Radhakrishna Pillai, Sudeep Gupta, Rajendra Badwe, Maria Carmo-Fonseca, Luis Costa, Loius W.C. Chow, Stefan Knapp, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

The Global Cancer Genomics Consortium (GCGC) colleagues continue to function together as an interactive multidisciplinary team of cancer biologists and oncologists with interests in genomics and building a bidirectional bridge between cancer clinics and laboratories while taking advantage of shared resources among its member scientists. The GCGC includes member scientists from six institutions in Lisbon, United Kingdom, Japan, India and United States, and was formed in December 2010 for a period of five years. Driven by valuable lessons learned from the previous symposiums, the fourth GCGC Symposium focused on a cross section of genomic and epigenetic cancer medicine and it's …

Regulation Of Synaptogenesis By The Mirna Pathway And Fmr/P Bodies, Jacqueline Rochelle Furlong

Electronic Theses and Dissertations

Post-transcriptional regulation of mRNA is facilitated by different mechanisms, such as microRNA (miRNA) induced gene silencing or fragile X mental retardation protein (FMRP) mediated repression either independent of or acting through cytoplasmic RNA Processing bodies (P bodies). DPTP99A, Lar, and Wg have known functions during synaptogenesis and may be targets of miR-8. Here, we provide evidence that miR-8 regulates DPTP99A in vitro. Non-endogenous miR-8 expressed using an UAS driver regulates Lar. Endogenous miR-8 may regulate DPTP99A in vivo. Here we show that FMRP is capable of colocalizing with the P body components: DCP1, HPat, and Me31B, but not …

2015 Annual Report Department Of Biological Sciences, Ronald L. Frank, Chen Hou, Yue-Wern Huang, Adam R. Martin, Melanie R. Mormile, Dev Niyogi, Julie A. Semon, Katie S. Shannon, Matthew S. Thimgan, David J. Westenberg, Terry Wilson

Biological Sciences Faculty Research & Creative Works

No abstract provided.

Evaluation Of The Performance Of A Rural Municipal Wastewater Treatment Plant In Nacogdoches, East Texas (Usa) (Abstract), Kefa Karimu Onchoke, Michael Janusa, Salomey Asantewaa Sasu

Faculty Publications

The performance of a rural wastewater treatment facility, Nacogdoches Wastewater Treatment Plant

(NWWTP), in East Texas, USA, was assessed from January 2013 through June 2014. The elemental concentrations (Na, Mg, Ca, Ni, Pb, Mn, Cr, Mo, and Cu, Al, As, B, Ba, Ag, Cd, Fe, Hg, K, Se, Zn, Co, P, and S) were measured using inductively coupled plasma optical emission spectrometry. The anion concentrations (Br−, NO3- , NO2- , PO34-,F−, Cl−, and SO24−) were measured by ion chromatography. In general, the NWWTP was found efficient in removal to ≥ 96% for metals. The removal efficiency for anions was in …

Differential Protein Expression During Tail Regeneration Of Anolis Carolinensis, Victor Hong, Benjamin Thornton

Research in Biology

Some invertebrate and vertebrate species have the ability to regenerate a lost limb. The lizard species are unique in that they can autotomize their tails and regrow them back. In this study, the proteomic change occurring within the regenerating tail of Anolis carolinensis (Green anole) during 72 h period was examined. We ran 2-dimension electrophoresis to separate the proteins and utilized SameSpots software to find 6 different spots that had altered expression of protein. Within those spots, proteins involved in immunity, energetics, and protein folding and degradation were identified. The proteins that were up-regulated were transferrin, nucleotide-binding domain of the …

Current Advances In The Application Of Raman Spectroscopy For Molecular Diagnosis Of Cervical Cancer, Ines Martins Ramos, Alison Malkin, Fiona Lyng

Articles

Raman spectroscopy provides a unique biochemical fingerprint capable of identifying and characterizing the structure of molecules, cells and tissues. In cervical cancer, it is acknowledged as a promising biochemical tool due to its ability to detect pre-malignancy and early malignancy stages. This review summarizes the key research in the area and the evidence compiled is very encouraging for ongoing and further research. In addition to the diagnostic potential, promising results for HPV detection and monitoring treatment response suggest more than just a diagnosis prospective. A greater body of evidence is however necessary before Raman spectroscopy is fully validated for clinical …

Species Preference Of Viral Deubiquitinating Proteases Toward Isg15 Through Structural And Enzymatic Characterization, Michelle Kay Deaton

Electronic Theses and Dissertations

Proteases from the Ovarian Tumor domain (OTU) superfamily of deubiquitinating enzymes (DUBs) are expressed by a range of RNA viruses. Viral OTUs (vOTUs) are found in nairoviruses such as Crimean Congo Hemorrhagic Fever virus (CCHFV), Nairobi sheep disease virus (NSDV), the Erve virus (ERVEV), and the Dugbe virus (DUGV), as well as in the areterivirus Porcine Reproductive and Respiratory Syndrome virus (PRRSV), among others. vOTUs, which interfere with host innate immune response through editing of host Ub and Ub-like molecules such as interferon stimulated gene 15 (ISG15), have been identified as a potential virulence factor through their role in evading …

The Effects Of Molecular Chaperones On Tau Fibril Assembly, Ahmed Omran

Electronic Theses and Dissertations

The accumulation of microtubule-associated protein tau into fibrillar aggregates is the hallmark of Alzheimer’s disease and other neurodegenerative disorders, collectively referred to as tauopathies. Fibrils can propagate from one cell to the next and spread throughout the brain. However, a study shows that only small aggregates can be taken up by cultured neuronal cells. The mechanisms that lead to the breakage of fibrils into smaller fragments remain unknown. In yeast, the AAA+ chaperone HSP104 processes the reactivation of protein aggregates and is responsible for fragmentation of fibrils. This study focused on investigating the effects of molecular chaperones on tau fibrils …

Ph Dependence Of Cyanide And Imidazole Binding To The Heme Domains Of Sinorhizobium Meliloti And Bradyrhizobium Japonicum Fixl, Anil K. Bidwai, Angela J. Ahrendt, John S. Sullivan, Lidia B. Vitello, James E. Erman

Faculty Publications & Research

Equilibrium and kinetic properties of cyanide and imidazole binding to the heme domains of Sinorhizobium meliloti and Bradyrhizobium japonicum FixL (SmFixLH and BjFixLH) have been investigated between pH 5 and 11. K_D determinations were made at integral pH values, with the strongest binding at pH 9 for both ligands. K_D for the cyanide complexes of BjFixLH and SmFixLH is 0.15 ± 0.09 and 0.50 ± 0.20 μM, respectively, and 0.70 ± 0.01 mM for imido-BjFixLH. The association rate constants are pH dependent with maximum values of 443 ± 8 and 252 ± 61 …

Bacterial Death Results From Mutations Made In Translocation Peptide Of Leucyl-Trna Synthetase, Daniel M. Mcdonough, Layla N. Baykal, Mallory J. Banton, Rachel A. Hellmann-Whitaker

Bridges: A Journal of Student Research

The family of aminoacyl-tRNA synthetases (aaRSs) ensures the fidelity of translation through providing a pool of correctly aminoacylated tRNA products that become incorporated by the ribosome. Leucyl-tRNA synthetase (LeuRS) has two functionally separate domains, one is the aminoacylation domain and the other is the CP1 editing domain. LeuRS can aminoacylate noncognate amino acids, therefore it relies on the CP1 editing domain to hydrolyze misaminoacylated tRNA products before they are released from the enzyme. The LeuRS enzyme must undergo a structural transition state in its reaction cycle in order to translocate the 3' acceptor stem of tRNA 30 Å from the …

Bacterial Death Results From Mutations Made In Translocation Peptide Of Leucyl-Trna Synthetase, Daniel M. Mcdonough, Layla N. Baykal, Mallory J. Banton, Rachel A. Hellmann-Whitaker

Bridges: A Journal of Student Research

The family of aminoacyl-tRNA synthetases (aaRSs) ensures the fidelity of translation through providing a pool of correctly aminoacylated tRNA products that become incorporated by the ribosome. Leucyl-tRNA synthetase (LeuRS) has two functionally separate domains, one is the aminoacylation domain and the other is the CP1 editing domain. LeuRS can aminoacylate noncognate amino acids, therefore it relies on the CP1 editing domain to hydrolyze misaminoacylated tRNA products before they are released from the enzyme. The LeuRS enzyme must undergo a structural transition state in its reaction cycle in order to translocate the 3' acceptor stem of tRNA 30 Å from the …

Reversing Chromatin Accessibility Differences That Distinguish Homologous Mitotic Metaphase Chromosomes., Wahab A Khan, Peter K Rogan, Joan H M Knoll

Biochemistry Publications

BACKGROUND: Chromatin-modifying reagents that alter histone associating proteins, DNA conformation or its sequence are well established strategies for studying chromatin structure in interphase (G1, S, G2). Little is known about how these compounds act during metaphase. We assessed the effects of these reagents at genomic loci that show reproducible, non-random differences in accessibility to chromatin that distinguish homologous targets by single copy DNA probe fluorescence in situ hybridization (scFISH). By super-resolution 3-D structured illumination microscopy (3D-SIM) and other criteria, the differences correspond to 'differential accessibility' (DA) to these chromosomal regions. At these chromosomal loci, DA of the same homologous chromosome …

Validating A Method For Measuring Protein Domain And Lipid Binding Interactions Using Luciferase Fusion Proteins, Dezaray E. Thoen

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Dynamics Of Biopolymers On Nanomaterials Studied By Quasielastic Neutron Scattering And Mdsimulations, Gurpreet Dhindsa

Wayne State University Dissertations

Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, β-Casein and Inorganic Pyrophosphatase (IPPase).

RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and …

Platination Kinetics: Insight Into Rna-Cisplatin Interactions As A Probe For Rna Microenvironments, Gayani Dedduwa-Mudalige

Wayne State University Dissertations

RNAs are crucial for many cellular functions. Thus, studying ligand-RNA interactions and their dynamics in response to changes in the surrounding environment is important. In spite of the well-known DNA coordination, current research also indicates cisplatin binding to RNA. Kinetic studies of rRNA platination reactions are largely unexplored. This research was conducted to achieve two objectives. First, a broad kinetic study was carried out to investigate the cisplatin-rRNA interactions. The structure, function, and ligand interactions depend on RNA microenvironments. Second, the application of platination kinetics as a tool to interrogate RNA electrostatic environments was explored.

Three model rRNA hairpins from …

Scale Up Isolation Of Aaptamine For In Vivo Evaluation Indicates Its Neurobiological Activity Is Linked To The Delta Opioid Receptor, Nicole L. Mcintosh, Eptisam Lambu, Laura Millan-Lobo, Fei Li, Li He, Phillip Crews, Jennifer L. Whistler, Tyler Johnson

Student Research Posters

Opioid receptors belong to the large superfamily of seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). As a class, GPCRs are of fundamental physiological importance mediating the actions of the majority of known neurotransmitters and hormones. The Mu, Delta, and Kappa (MOP, DOP, KOP) opioid receptors are particularly intriguing members of this receptor family as they are the targets involved in many neurobiological diseases such as addiction, pain, stress, anxiety, and depression. Recently we discovered that the aaptamine class of marine sponge derived natural products exhibit selective agonist activity in vitro for the DOP versus MOP receptor. Our findings may explain …

Functional Transcranial Doppler Ultrasound For High Temporal Resolution Measurement Of Lateralization In Visual Memory And Visual Search Cognitive Tasks, B. Hage, M. Alwatban, E. Barney, M. Mills, M. Dodd, E. Truemper, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Functional transcranial Doppler ultrasound (fTCD) is a noninvasive sensing modality that measures blood flow velocities in cerebral arteries (CBFV) with high temporal resolution. Few studies have examined the relationship of CBFV change during visual search and visual memory cognitive tasks. Here a protocol to compare lateralization between these two similar tasks using fTCD is demonstrated. Thirteen healthy volunteers were shown visual scenes on a computer and performed visual search and visual memory tasks while CBFV in the bilateral middle cerebral arteries was monitored with fTCD. Each subject completed 40 trials, consisting of baseline, calibration, instruction, and task periods. Lateralization was …

The Significance Of Crispr/Cas9-Directed Cul3 Knockout On Human Colorectal Cancer Cells, Zoe A. Lautz

Departmental Honors Projects

Cancer, the second leading cause of death in the US, is caused by mutations in select genes that alter cellular function leading to uncontrolled proliferation. Understanding the specific genes that drive cancer can lead to the generation of novel cancer therapies. To identify novel genes that drive cancer in the colon (CRC), lungs, and ovaries in mice, Starr et al. employed a transposon-based insertional mutagenesis system. One of the genes identified, APC, is mutated in 70-80% of human CRCs. CUL3, suspected to be a general driver gene, was discovered in the lung cancer screen. CUL3 was analyzed for its role …

Tissue-Specific Splice Variants Of Hare/Stabilin-2 Are Expressed In Bone Marrow, Lymph Node, And Spleen, Amanda K. Hare, Edward N. Harris

Department of Biochemistry: Faculty Publications

The hyaluronan receptor for endocytosis (HARE), or Stabilin-2, is the mammalian endocytic clearance receptor for HA, heparin, advanced glycation end-products, acetylated and oxidized low-density lipoproteins and collagen N-terminal propeptides. This large 2551 amino acid receptor is encoded by a gene that covers over 180 kbp on human chromosome 12 and is predicted to be composed of 69 exons. Due to the expression profile of this gene and the number of exons it contains, we hypothesized that splice variants of stab2 are encoded in these tissues. In addition, a correlation between alternative splice variants and cancer progression has been shown in …

Hyaluronidase Hyal1 Increases Tumor Cell Proliferation And Motility Through Accelerated Vesicle Trafficking, Caitlin O Mcatee, Abigail R. Berkebile, Christian Elowsky, Teresa Fangman, Joseph J. Barycki, James K. Wahl Iii, Oleh Khalimonchuk, Naava Naslavsky, Steve Caplan, Melanie A. Simpson

Department of Biochemistry: Faculty Publications

Background: Hyal1 is a turnover enzyme for hyaluronan that accelerates metastatic cancer by increasing cell motility.

Results: Hyal1-overexpressing cells have a higher rate of endocytosis that impacts cargo internalization and recycling.

Conclusion: The higher rate of vesicle trafficking increases motility receptor function and nutrient uptake.

Significance: This novel mechanism implicates Hyal1 trafficking in multiple signaling events during tumor progression.

Advantages Of Distributed And Parallel Algorithms That Leverage Cloud Computing Platforms For Large-Scale Genome Assembly, Phil Kumari, Raja Mazumder, Vahan Simonyan, Konstantinos Krampis

Biochemistry and Molecular Medicine Faculty Publications

Background: The transition to Next Generation sequencing (NGS) sequencing technologies has had numerous applications in Plant, Microbial and Human genomics during the past decade. However, NGS sequencing trades high read throughput for shorter read length, increasing the difficulty for genome assembly. This research presents a comparison of traditional versus Cloud computing-based genome assembly software, using as examples the Velvet and Contrail assemblers and reads from the genome sequence of the zebrafish (Danio rerio) model organism.

Results: The first phase of the analysis involved a subset of the zebrafish data set (2X coverage) and best results were obtained using …