Biochemistry, Biophysics, and Structural Biology Commons^™

The Chondrocyte Channelome: A Novel Ion Channel Candidate In The Pathogenesis Of Pectus Deformities, Anthony J. Asmar

Biological Sciences Theses & Dissertations

Costal cartilage is a type of rod-like hyaline cartilage connecting the ribs to the sternum. The chest wall deformities pectus excavatum (PE) and pectus carinatum (PC) involve displacement of the sternum causing a depression or protrusion of the chest. There is little knowledge about costal cartilage and pectus deformities with much of its understanding based on assumptions from articular cartilage. Chondrocytes are subjected to a constantly changing environment with fluctuations in pH and osmolarity. Ion channels detect these changes and in turn regulate proliferation, differentiation, and extracellular matrix production. Using ion channel qPCR arrays, we produced expression profiles for normal, …

Biochemistry, Chavonda Mills, Shaundra Walker

Chemistry Grants Collections

This Grants Collection for Biochemistry was created under a Round Five ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

Biochemistry Lecture Notes, Chavonda Mills, Shaundra Walker

Chemistry Ancillary Materials

The following set of lecture notes are ancillary materials for Oregon State University's Biochemistry: Free for All.

This ancillary set was created under a Round Five ALG Textbook Transformation Grant. They are also available in an open-course format through LibGuides:

http://libguides.gcsu.edu/millsbiochem3510

Generating Enzyme And Radical‐Mediated Bisubstrates As Tools For Investigating Gcn5‐Related N‐Acetyltransferases, Cory T. Reidl, Karolina A. Majorek, Joseph Dang, David Tran, Kristen Jew, Melissa Law, Yasmine Payne, Wladek Minor, Daniel P. Becker, Misty L. Kuhn

Chemistry: Faculty Publications and Other Works

Gcn5‐related N‐acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor‐bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X‐ray induced radical‐mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely …

Perspective: The Physics, Diagnostics, And Applications Of Atmospheric Pressure Low Temperature Plasma Sources Used In Plasma Medicine, M. Laroussi

Electrical & Computer Engineering Faculty Publications

Low temperature plasmas have been used in various plasma processing applications for several decades. But it is only in the last thirty years or so that sources generating such plasmas at atmospheric pressure in reliable and stable ways have become more prevalent. First, in the late 1980s, the dielectric barrier discharge was used to generate relatively large volume diffuse plasmas at atmospheric pressure. Then, in the early 2000s, plasma jets that can launch cold plasma plumes in ambient air were developed. Extensive experimental and modeling work was carried out on both methods and much of the physics governing such sources …

An Approach To Identify Mycobacteriophage Diversity Prior To Dna Sequencing, Charles Gregory

Mahurin Honors College Capstone Experience/Thesis Projects

Over 6,869 Mycobacteriophages have been isolated and purified. Of these, 1,367 genomes have been sequenced at the DNA level and more are added each year through the SEA-PHAGES program. Sequenced mycobacteriophages are grouped into clusters based on a 50% or greater nucleotide identity. The number and breadth of these clusters represents the diversity present in the environment. Each year, as new phages are discovered by students in the SEA-PHAGES program, the question arises, “Which isolates should we sequence?” In order to sequence phages that represent the greatest possible diversity, and thus broaden under-represented clusters and identify new singletons, we need …

Investigating The Synergistic Effects Of Cisplatin And Two Curcuminoid Compounds On Cancer, Denis Hodzic

Mahurin Honors College Capstone Experience/Thesis Projects

Cisplatin is an anti-cancer drug effective against several cancers which can produce the serious side-effect of hearing loss. Curcumin, a natural plant compound, can increase the activity of cisplatin against cancer and counteract cisplatin’s effect against hearing. Because curcumin exhibits poor bioavailability, there is considerable interest in developing synthetic curcumin analogs (curcuminoids) that are more soluble and which retain anti-cancer activity and otoprotective function. This study investigated whether two curcuminoids, EF-24 and CLEFMA, increase the cytotoxic and ototoxic effects of cisplatin against the lung cancer cell line, A549, and the colorectal cancer cell line, Caco2. Cytotoxicity was measured by using …

The General Amino Acid Permease Gap1 Is Regulated Differentially By Torc1 Activation And Inhibition, Ray Bowman

D.U.Quark

How does cell signaling in response to extracellular stressors impact the trafficking of membrane proteins? In particular, the TORC1 complex plays a key role in this process and while some details of this system have reported, in a recent Journal of Biological Chemistry publication, Andre’s group has revealed new details of this pathway focusing on the general amino acid permease Gap1 as a model cargo. Andre et al. describe a novel and distinct pathway wherein ubiquitylation and downregulation of Gap1 is regulated not only by amino acid-induced activation of TORC1, but also by numerous sources of TORC1 inhibition and cellular …

Spatiotemporal Regulation Of Atg1 Kinase Activation In Selective Autophagy, Ning Sun

D.U.Quark

Autophagy is a potent intracellular degradation system and thus its activation requires exquisite regulation to maintain cellular homeostasis. Atg1, a serine-threonine protein kinase, is essential in both selective and non-selective autophagy. New findings suggest that in selective autophagy, Atg1 is activated at the vacuole by convergence of two independent recruitment pathways to prevent aberrant autophagy induction.

Hsp70 Conformational Plasticity Allows For Expansive Chaperone Role, Megan Bean

D.U.Quark

The Hsp70 system is an essential component of chaperone activity in many organisms. Hsp70 functions include: protein folding, aggregation prevention, trafficking, and enzyme regulation. Hsp70’s ability to bind such a vast array of substrates suggests wide range of conformational plasticity. By utilizing a single mode optical tweezers technique, Mashaghi1 et al., confirms previous theories Hsp70 binds and stabilizes extended peptide segments but also partially folded and near-native protein.

Plasmodium Falciparum 26s Proteasome Network: A Mystery Solved, Christina Grogan

D.U.Quark

One ofthe most devastating diseases thatthreatens the world population is malaria. The 26S proteasome complex of the malaria parasite Plasmodium falciparum, which was previously unknown, was characterized by the authors through an affinity purification protocol that isolated functional 26S proteasome complexes. This allowed for the identification of subunit composition and PfUSP14, a proteasomeassociated deubiquitinase. This new understanding presents a potential target to disrupt protein regulation in thequest for effective antimalarial strategies.

Autophagy Inhibition In Pain: Role Of A Microrna, Andrea Stevens

D.U.Quark

Neuropathic pain caused by peripheral nerve injury (PNI) leads to the activation and infiltration of microglial cells and to a neuroinflammatory-induced pain state. miRNAs and autophagy are two main factors and/or mechanisms which have the ability to alter the pain state. In this study, miR-195 was shown to be markedly increased after PNI and associated with the pain phenotype. In addition, inhibition of autophagy in vivo led to p62 accumulation, decreased production of LC3, and inhibition of ATG14.

Electronic Structure And Quassiclassical Dynamics Of [2+2] Tetrafluoroethylene Cycloaddition Reactions, Steven Jones, Daniel Ess

Journal of Undergraduate Research

Cycloaddition reactions are key reactions used to construct complex cyclic scaffolds (large networks of carbon atoms that can be used in catalysis, synthesis, etc.). While classical reactions that form 6-membered rings are well-known and generally have a one-step reaction mechanism, 4-member ring-forming reactions are much less used, but could be very valuable for the construction of cyclobutane structures.

Tetrafluoroethylene (TFE) is used on a large scale by Dow and other chemical companies to form hydrofluoro compounds such as teflon. The current understanding of the mechanism of cycloaddition reactions with TFE is limited. Standard hydrocarbon reactions proceed via a welldocumented, concerted …

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 …