Biochemistry, Biophysics, and Structural Biology Commons^™

Development And Application Of Minimum Energy Crossing Point Software Suite For Organometallic Reactions, Justin Snyder, Daniel H. Ess

Journal of Undergraduate Research

Computational studies are critical to the field of organometallic chemistry since many highly reactive and unstable compounds cannot be isolated or observed experimentally. It is well-known that many organometallic reaction mechanisms involve spin intersystem crossing, e.g. singlet to triplet conversion. To estimate the rate of intersystem crossing it is useful to calculate electronic structures where spin states and their energies are degenerate, which is called a “minimum energy crossing point (MECP).” Prior to the completion of this project, there was only one working program that interfaced with the Gaussian 09 electronic structure package for the calculation of minimum energy which …

Inhibiting Translesion Dna Synthesis As An Approach To Combat Drug Resistance To Dna Damaging Agents, Jung-Suk Choi, Seol Kim, Edward Motea, Anthony J. Berdis

Chemistry Faculty Publications

Anti-cancer agents exert therapeutic effects by damaging DNA. Unfortunately, DNA polymerases can effectively replicate the formed DNA lesions to cause drug resistance and create more aggressive cancers. To understand this process at the cellular level, we developed an artificial nucleoside that visualizes the replication of damaged DNA to identify cells that acquire drug resistance through this mechanism. Visualization is achieved using "click" chemistry to covalently attach azide-containing fluorophores to the ethynyl group present on the nucleoside analog after its incorporation opposite damaged DNA. Flow cytometry and microscopy techniques demonstrate that the extent of nucleotide incorporation into genomic DNA is enhanced …

Il-18 Polymorphisms Contribute To Hepatitis B Virus-Related Cirrhosis And Hepatocellular Carcinoma Susceptibility In Chinese Population: A Case-Control Study., Zhi-Jun Dai, Xing-Han Liu, Meng Wang, Yan Guo, Wenge Zhu, Xiao Li, Shuai Lin, Tian Tian, Kang Liu, Yi Zheng, Peng Xu, Tianbo Jin, Xiaopeng Li

Biochemistry and Molecular Medicine Faculty Publications

IL-18 polymorphisms influence the transcriptional activity of the IL-18 gene and associated with various diseases. However, their relationships with hepatitis B virus-related liver diseases had not reached a consensus. So we conducted this case-control study with a view to clarifying the association. We included four groups: healthy controls, chronic hepatitis B virus (CHB) carriers, liver cirrhosis (LC) and hepatocellular carcinoma (HCC) groups with each group of 250 persons. Odd ratios (ORs) and 95% confidence intervals (95%CIs) with or without adjustment were calculated. Haplotype analysis was also performed. The results showed people carrying rs187238 CG genotype had a lower risk of …

Safety And Potential Efficacy Of Gemfibrozil As A Supportive Treatment For Children With Late Infantile Neuronal Ceroid Lipofuscinosis And Other Lipid Storage Disorders., Kyeongsoon Kim, Hynda K Kleinman, Hahn-Jun Lee, Kalipada Pahan

Biochemistry and Molecular Medicine Faculty Publications

Neuronal Ceroid Lipofuscinosis (NCL), also known as Batten disease, is a group of genetically distinct lysosomal disorders that mainly affect the central nervous system, resulting in progressive motor and cognitive decline primarily in children. Multiple distinct genes involved in the metabolism of lipids have been identified to date with various mutations in this family of diseases. There is no cure for these diseases but some new therapeutic approaches have been tested that offer more hope than the standard palliative care. Many of the therapeutic advances require invasive procedures but some progress in slowing the disease has been found and more …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Sivasai Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Selected Works Temporary Series

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Departmental Papers (Biology)

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

Quantifying The Efficiency Of Heterobimetallic Complexes, Ryjul Stokes, David Michaelis

Journal of Undergraduate Research

Transition metal catalysts have revolutionized the efficiency by which pharmaceuticals and other value added products are synthesized due to their unique ability to activate small molecules and drive the formation of new C-C and C-N bonds. In particular, the direct functionalization of olefins with transition metal catalysts is a powerful method of converting simple, cheap building blocks into more complex molecules. The challenge is that many ligands that control reaction selectivity often decrease the electrophilicity of the catalyst. Heterobimetallic complexes containing an early/late transition metal pair could provide a solution to this challenge by providing a new way to activate …

Microwave Promoted Iminyl Radical Cyclization, Aaron Kubosumi, Steven L. Castle

Journal of Undergraduate Research

Pyrrolidines and their derivatives are found in many biologically active compounds, such as Lipitor and Atorvastatin, which possess a wide variety of remarkable pharmaceutical properties. Therefore, the efficient synthesis of functionalized pyrrolidines is of great value to organic chemists. Multiple attempts have been made to synthesize compounds containing pyrrolidine ring systems. Walton 1 utilized radical cyclization, via microwave heating, to transform Ophenyl oximes with terminal alkenes to dihydropyrroles, compounds closely related to pyrrolidines. Similarly, Sammis 2 proposed a method involving radical cyclizations of azidederived aminyl radicals onto silyl enol ethers. Unfortunately, the method proposed by Sammis requires highly toxic and …

Interleukin-18 Polymorphism As An Inflammatory Index In Metabolic Syndrome: A Preliminary Study, Syeda Sadia Fatima, Zehra Jamil, Syed Hani Abidi, Daniyal Nadeem, Zara Bashir, Ahmed Ansari

Department of Biological & Biomedical Sciences

Aim: To assess circulatory levels of interleukin-18 (IL-18) and determine whether the presence of IL-18 promoter polymorphism influences metabolic syndrome phenotypes.
Methods: This study recruited one hundred and eighty individuals divided into three groups with sixty subjects each as: Normal weight (18.0-22.9 kg/m2), overweight (23.0-25.9 kg/m2) and obese (> 26.0 kg/m2) according to South Asian criteria of BMI. Fasting blood glucose (FBG), Lipid profile, insulin, IL-18 and tumor necrosis factor (TNF)alpha were measured using ELISA kits, whereas low density lipoprotein (LDL)-cholesterol, insulin resistance (HOMA-IR) and insulin sensitivity (QUICKI) were calculated. The body fat percentage (BF) was measured through bioelectrical impedance …

Determining The Structure Of The Bbbsome, Grant Ludlam, Barry Willardson

Journal of Undergraduate Research

Bardet-Biedl Syndrome (BBS) occurs when an eight-protein complex called the BBSome is improperly assembled and can no longer function. The BBSome is responsible for trafficking membrane proteins to cilia, a projection from the cell surface packed with receptors that allow the cell to sense its surroundings. Loss of BBSome function causes malformation of cilia and leads to vision loss, obesity, kidney disease and mental retardation.

The Total Synthesis Of Yaku’Mide A, Shi Luo, Steven Castle

Journal of Undergraduate Research

Yaku’amide A (YA) has potent toxicity against cancer cells (IC50 = 14 ng/ml against P388 murine leukemia cells). Ueoka et al.1 first reported the isolation of YA from a marine sponge in the East China Sea. They used spectroscopy and chemical degradations to analyze its structure. YA contains unique dehydroamino acids (See Figure 1). In the growth inhibition study, YA showed unique activity against 39 cancer cell lines, indicating a novel mode of action. The unusual structure of YA and its prominent biological activity has attracted research groups from around the world to address its synthesis.

Using Three Incommensurate Wave Components To Generate Terahertz Radiation, Jacob Bagley, Jeremy Johnson

Journal of Undergraduate Research

Electromagnetic radiation is a wave composed of an electric field and a magnetic field. Examples of electromagnetic radiation include visible light, ultraviolet light, Xrays, infrared light, microwaves, and more. Electromagnetic radiation is an indispensable tool for both controlling and studying matter and is applied to countless fields such as electronics manufacturing and medical imaging. Over the past two decades terahertz (THz) radiation, a form of electromagnetic radiation, has become an intense area of research. This surge in activity in due in part to technological advances in generating THz radiation, but is also due to the myriad of potential applications of …

Igf-1 Mediated Neurogenesis Involves A Novel Rit1/Akt/Sox2 Cascade, Sajad Mir, Weikang Cai, Shaun W. Carlson, Kathryn E. Saatman, Douglas A. Andres

Molecular and Cellular Biochemistry Faculty Publications

Insulin-like growth factor 1 (IGF-1) is known to have diverse effects on brain structure and function, including the promotion of stem cell proliferation and neurogenesis in the adult dentate gyrus. However, the intracellular pathways downstream of the IGF-1 receptor that contribute to these diverse physiological actions remain relatively uncharacterized. Here, we demonstrate that the Ras-related GTPase, RIT1, plays a critical role in IGF-1-dependent neurogenesis. Studies in hippocampal neuronal precursor cells (HNPCs) demonstrate that IGF-1 stimulates a RIT1-dependent increase in Sox2 levels, resulting in pro-neural gene expression and increased cellular proliferation. In this novel cascade, RIT1 stimulates Akt-dependent phosphorylation of …

Conserved Amino Acid Networks Modulate Discrete Functional Properties In An Enzyme Superfamily, Chitra Narayanan, Donald Gagne, Kimberly A. Reynolds, Nicolas Doucet

Advanced Science Research Center

In this work, we applied the sequence-based statistical coupling analysis approach to characterize conserved amino acid networks important for biochemical function in the pancreatic-type ribonuclease (ptRNase) superfamily. This superfamily-wide analysis indicates a decomposition of the RNase tertiary structure into spatially distributed yet physically connected networks of co-evolving amino acids, termed sectors. Comparison of this statistics-based description with new NMR experiments data shows that discrete amino acid networks, termed sectors, control the tuning of distinct functional properties in different enzyme homologs. Further, experimental characterization of evolutionarily distant sequences reveals that sequence variation at sector positions can distinguish homologs with a conserved …

Rnaseq Analysis Of The Drosophila Response To The Entomopathogenic Nematode Steinernema., Shruti Yadav, Sean Daugherty, Amol Carl Shetty, Ioannis Eleftherianos

Computational Biology Institute

Drosophila melanogaster is an outstanding model to study the molecular and functional basis of host-pathogen interactions. Currently, our knowledge of microbial infections in D. melanogaster is well understood; however, the response of flies to nematode infections is still in its infancy. Here, we have used the potent parasitic nematode Steinernema carpocapsae, which lives in mutualism with its endosymbiotic bacteria Xenorhabdus nematophila, to examine the transcriptomic basis of the interaction between D. melanogaster and entomopathogenic nematodes. We have employed next-generation RNA sequencing (RNAseq) to investigate the transcriptomic profile of D. melanogaster larvae in response to infection by S. carpocapsae symbiotic (carrying …

Exploring Cancer Metabolism Using Stable Isotope-Resolved Metabolomics (Sirm), Ronald C. Bruntz, Andrew N. Lane, Richard M. Higashi, Teresa W. -M. Fan

Center for Environmental and Systems Biochemistry Faculty Publications

Metabolic reprogramming is a hallmark of cancer. The changes in metabolism are adaptive to permit proliferation, survival, and eventually metastasis in a harsh environment. Stable isotope-resolved metabolomics (SIRM) is an approach that uses advanced approaches of NMR and mass spectrometry to analyze the fate of individual atoms from stable isotope-enriched precursors to products to deduce metabolic pathways and networks. The approach can be applied to a wide range of biological systems, including human subjects. This review focuses on the applications of SIRM to cancer metabolism and its use in understanding drug actions.

Mechanosensing Of Shear By Pseudomonas Aeruginosa Leads To Increased Levels Of The Cyclic-Di-Gmp Signal Initiating Biofilm Development, Christopher A. Rodesney, Brian Roman, Numa Dhamani, Benjamin J. Cooley, Ahmed Touhami, Vernita D. Gordon

Physics & Astronomy Faculty Publications

Biofilms are communities of sessile microbes that are phenotypically distinct from their genetically identical, free-swimming counterparts. Biofilms initiate when bacteria attach to a solid surface. Attachment triggers intracellular signaling to change gene expression from the planktonic to the biofilm phenotype. For Pseudomonas aeruginosa, it has long been known that intracellular levels of the signal cyclic-di-GMP increase upon surface adhesion and that this is required to begin biofilm development. However, what cue is sensed to notify bacteria that they are attached to the surface has not been known. Here, we show that mechanical shear acts as a cue for surface adhesion …

A Lipid Binding Structure And Functional Analysis Of Human Arv1, Jessie Lee Cunningham

Graduate School of Biomedical Sciences Theses and Dissertations

Metabolic Syndrome (MetS) is a combination of risk factors that can over time increase the probability of developing diseases, including cardiovascular disease, type 2 diabetes, non-alcoholic fatty liver disease (NAFLD), and non-alcoholic steatohepatitis (NASH). Acyl-coenzyme-A: cholesterol O-acyl transferase related enzyme required for viability-1, abbreviated as Arv1, is an evolutionarily conserved putative lipid binding protein. Several studies have implicated hArv1 as a critical regulator of lipid transport and trafficking.

Recent work using an Arv1 knock out (KO) mouse model have established a clear link between Arv1 function and the progression of MetS and NAFLD/NASH [unpublished data] [1]. Overall, studies show that …

Growth Trade-Offs Accompany The Emergence Of Glycolytic Metabolism In Shewanella Oneidensis Mr-1, Lon Chubiz, Christopher Marx

Biology Department Faculty Works

Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved when Shewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism of N-acetylglucosamine are the common basis for evolved glucose metabolism …

A Comparison Of Nucleosome Organization In Drosophila Cell Lines, Rebecca L. Martin, John Maiorano, Greg J. Beitel, John F. Marko, Graham Mcvicker, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry Faculty Publications

Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogastercell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism’s genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and then …

C/D-Box Snornas Form Methylating And Non-Methylating Ribonucleoprotein Complexes: Old Dogs Show New Tricks, Marina Falaleeva, Justin R. Welden, Marilyn J. Duncan, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

C/D box snoRNAs (SNORDs) are an abundantly expressed class of short, non‐coding RNAs that have been long known to perform 2′‐O‐methylation of rRNAs. However, approximately half of human SNORDs have no predictable rRNA targets, and numerous SNORDs have been associated with diseases that show no defects in rRNAs, among them Prader‐Willi syndrome, Duplication 15q syndrome and cancer. This apparent discrepancy has been addressed by recent studies showing that SNORDs can act to regulate pre‐mRNA alternative splicing, mRNA abundance, activate enzymes, and be processed into shorter ncRNAs resembling miRNAs and piRNAs. Furthermore, recent biochemical studies have shown that a given SNORD …

Current Status Of Helicobacter Pylori Association With Haematological And Cardiovascular Diseases: A Mini Review, Jibran Sualeh Muhammad, Syed Faisal Zaidi, Sheikh Abdul Saeed, Muhammad Ishaq

Department of Biological & Biomedical Sciences

Helicobacter pylori infection is considered the most commonly prevalent gastrointestinal pathogen where it manages to survive despite the hostile environment of human stomach, leading to various gastric diseases including gastric cancer. Due to the chronic inflammatory state induced by H. pylori and its interaction with host immune system have diverted researchers to investigate its correlation with systemic diseases outside of the gastrointestinal tract. This literature review was done to explore the association of H. pylori infection with haematological and cardiovascular diseases. We used medical subject heading (MeSH) terms "Helicobacter pylori" with "inflammation," "haematological diseases," "coronary heart diseases" or "vascular diseases" …

The Mechanistic Requirements Of Passive H+ Import Through The Na, K-Atpase, Kevin S. Stanley

Theses and Dissertations

This work focuses on the elucidation of the mechanism of passive proton import through the Na,K-ATPase. This enzyme uses the energy in ATP hydrolysis to exchange three intracellular Na+ for two extracellular K+ to maintain ion gradients within the cell, and while in the absence of physiological external Na+ and K+, the phosphorylated externally open (E2P) conformation passively imports protons, generating an inward current (IH). Chapter one reports on the effects of intracellular cations and nucleotides to shift the Na,K-ATPase into the E2P conformation. We identified that a combination of either internal Na+ and ATP or K+ and Pi. In …

Life Line June 2017, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

Research presented at Intl. Coral Reef Symposium - Mussels - South African Internship Experience - EHS Degree Coming - Otterbein Rock Garden - Nicaragua - Chris Shockley

A Novel Population Of Cardiovascular Progenitors Persist In Neonates As Mesendodermal Cells, Julia Kim

Loma Linda University Electronic Theses, Dissertations & Projects

The rise in mortality due to cardiovascular disease has increased the need to develop an efficient regenerative therapeutic for heart failure. Numerous cell-based therapies have been investigated for myocardial regeneration; however, an optimal progenitor has yet to be discovered. Identifying a resident cell population with enhanced ability to differentiate into multiple lineages would greatly contribute to the field of stem cell-based regenerative therapy. Evidence suggests that endogenous cardiovascular progenitor cells (CPCs) that have been isolated from the heart itself express ISL1, KDR, and MESP1, and are capable of differentiating into all major cardiac lineages. The earlier developmental stage at which …

Non-Thiolate Ligation Of Nickel By Nucleotide-Free Ureg Of Klebsiella Aerogenes, Vlad Martin-Diaconescu, Crisjoe A. Joseph, Jodi L. Boer, Scott B. Mulrooney

University Faculty Publications and Creative Works

Nickel-dependent ureases are activated by a multiprotein complex that includes the GTPase UreG. Prior studies showed that nucleotide-free UreG from Klebsiella aerogenes is monomeric and binds one nickel or zinc ion with near-equivalent affinity using an undefined binding site, whereas nucleotide-free UreG from Helicobacter pylori selectively binds one zinc ion per dimer via a universally conserved Cys-Pro-His motif in each protomer. Iodoacetamide-treated K. aerogenes UreG was nearly unaffected in nickel binding compared to non-treated sample, suggesting the absence of thiolate ligands to the metal. X-ray absorption spectroscopy of nickel-bound UreG showed the metal possessed four-coordinate geometry with all O/N donor …

Anthrax, Matrix Biology, And Angiogenesis: Capillary Morphogenesis Gene 2 Mediates Activity And Uptake Of Type Iv Collagen-Derived Anti-Angiogenic Peptides, Jordan Grant Finnell

Theses and Dissertations

Capillary Morphogenesis Gene 2 (CMG2) is a type I transmembrane, integrin-like receptor. It was originally identified as one of several genes upregulated during capillary formation. It was subsequently identified as one of two physiological anthrax toxin receptors, where CMG2 serves as a cell-surface receptor for anthrax toxin and mediates entry of the toxin into cells via clathrin-dependent endocytosis. Additionally, loss-of-function mutations in CMG2 cause the genetic disorder hyaline fibromatosis syndrome (HFS), where the core symptom is dysregulation of extracellular matrix homeostasis (ECM), including excessive accumulation of proteinaceous hyaline material; HFS clearly indicates that CMG2 plays an essential function in ECM …

Industrial Grade 2d Molybdenum Disulphide (Mos2): An In-Vitro Exploration Of The Impact On Cellular Uptake, Cytotoxicity, And Inflammation, Caroline Moore, Hugh Byrne, Jonathan N. Coleman, Yuri Volkov, Jennifer Mcintyre

Articles

The recent surge in graphene research, since its liquid phase monolayer isolation and characterization in 2004, has led to advancements which are accelerating the exploration of alternative 2D materials such as molybdenum disulphide (MoS2), whose unique physico-chemical properties can be exploited in applications ranging from cutting edge electronic devices to nanomedicine. However, to assess any potential impact on human health and the environment, the need to understand the bio-interaction of MoS2 at a cellular and sub-cellular level is critical. Notably, it is important to assess such potential impacts of materials which are produced by large scale production techniques, rather than …

Enzyme Encapsulation, Biosensing Endocrine Disrupting Chemicals, And Bio-Therapeutic Expression Platforms Using Cell-Free Protein Synthesis, Seung Ook Yang

Theses and Dissertations

Cell-free protein synthesis (CFPS) is a powerful protein expression platform where protein synthesis machinery is borrowed from living organisms. Target proteins are synthesized in a reaction tube together with cell extract, amino acids, energy source, and DNA. This reaction is versatile, and dynamic optimizations of the reaction conditions can be performed. The "œopen" nature of CFPS makes it a compelling candidate for many technologies and applications. This dissertation reports new and innovative applications of CFPS including 1) enzyme encapsulation in a virus-like particle, 2) detection of endocrine disrupting chemicals in the presence of blood and urine, and 3) expression of …

Investigation Into The Mechanism Of Ion Transport In Rio Negro Characiformes, Vineza D. Reduta

Undergraduate Honors Theses

Four fish species within the Characiform Order [(Rosy tetras (Hyphessobrycon rosaceus), Serpae tetras (Hyphessobrycon eques), Emperor tetras (Nematobrycon palmeri) and Penguin tetras (Thayeria obliqua)] are native to the ion-poor, acidic waters of the Rio Negro. In this paper, we focus on Wood’s revised Na⁺/NH₄⁺ exchange model to gain better insight into the mechanisms of ion transport within the Characids. We exposed each species to two experimental treatments: (i) 1mM ammonia (high external ammonia [HEA]), to test coupling of Na⁺ uptake and ammonia excretion, and (ii) 100μM Acetazolamide …