Biochemistry, Biophysics, and Structural Biology Commons^™

Serine Proteolytic Pathway Activation Reveals An Expanded Ensemble Of Wound Response Genes In Drosophila, Rachel A. Patterson, Michelle T. Juarez, Anita Hermann, Roman Sasik, Gary Hardiman, William Mcginnis

Publications and Research

After injury to the animal epidermis, a variety of genes are transcriptionally activated in nearby cells to regenerate the missing cells and facilitate barrier repair. The range and types of diffusible wound signals that are produced by damaged epidermis and function to activate repair genes during epidermal regeneration remains a subject of very active study in many animals. In Drosophila embryos, we have discovered that serine protease function is locally activated around wound sites, and is also required for localized activation of epidermal repair genes. The serine protease trypsin is sufficient to induce a striking global epidermal wound response without …

Mesobiliverdin Ixα Enhances Rat Pancreatic Islet Yield And Function, Taihei Ito, Dong Chen, Cheng-Wei Tom Chang, Takashi Kenmochi, Tomonori Saito, Satoshi Suzuki, Jon Y. Takemoto

Chemistry and Biochemistry Faculty Publications

The aims of this study were to produce mesobiliverdin IXα, an analog of anti-inflammatory biliverdin IXα, and to test its ability to enhance rat pancreatic islet yield for allograft transplantation into diabetic recipients. Mesobiliverdin IXα was synthesized from phycocyanobilin derived from cyanobacteria, and its identity and purity were analyzed by chromatographic and spectroscopic methods. Mesobiliverdin IXα was a substrate for human NADPH biliverdin reductase. Excised Lewis rat pancreata infused with mesobiliverdin IXα and biliverdin IXα-HCl (1–100 μM) yielded islet equivalents as high as 86.7 and 36.5%, respectively, above those from non-treated controls, and the islets showed a high degree of …

Divergent Protein Motifs Direct Ef-P Mediated Translational Regulation In Salmonella And Escherichia Coli, Steven J. Hersch, Mengchi Wang, S. Betty Zou, Kyung-Mee Moon, Leonard J. Foster, Michael Ibba, William Wiley Navarre

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is a universally conserved bacterial translation factor homologous to eukaryotic/archaeal initiation factor 5A. In Salmonella, deletion of the efp gene results in pleiotropic phenotypes, including increased susceptibility to numerous cellular stressors. Only a limited number of proteins are affected by the loss of EF-P, and it has recently been determined that EF-P plays a critical role in rescuing ribosomes stalled at PPP and PPG peptide sequences. Here we present an unbiased in vivo investigation of the specific targets of EF-P by employing stable isotope labeling of amino acids in cell culture (SILAC) to compare the …

Effects Of Beta Amyloid On The Dna Methylation Status Of An In Vitro Model Of Alzheimer’S Disease, Noor Taher

Senior Honors Theses

Available evidence points toward an epigenetic process in Alzheimer’s disease. This thesis describes the research that was done to investigate changes in DNA methylation using an in vitro model of the disease. Although the results indicated no global changes in methylation levels after treating differentiated IMR-32 cells with beta amyloid, there were several regions of the genome that changed their methylation status. Gene ontology studies revealed that these regions are associated with neuronal differentiation and cell fate genes, thus providing a possible model for the contribution of beta amyloid to the development of Alzheimer’s disease. This study provides incentive to …

Kinetics Of Atmospheric Reactions Of Biogenic Volatile Organic Compounds: Measurement Of The Rate Constant Ofthujone + Cl· At 296 K And Calculation Ofthe Equilibrium Constant For The Ho2ch2ch2o2· H2o Complex, Marie Coy Killian

Theses and Dissertations

Biogenic volatile organic compounds (VOCs) react with Cl and OH radicals and the resulting radicals combine with oxygen to form peroxy radicals RO2. Organic peroxy radicals can then react with NO to form NO2, a precursor of tropospheric ozone. The work presented here explored the initial reaction between Cl and thujone, a VOC emitted by Great Basin sagebrush. The rate constant for the reaction of thujone + Cl at 296 K was measured with the method of relative rates with FTIR for detection of reactants. LEDs were used to photolyze Cl2 to generate Cl in the reaction cell. Thujone was …

Determination Of Trace Metals, Volatile Organic Compounds, And Other Water Standards In Wmu Drinking Water, Tyler Walter

Honors Theses

The USEPA creates drinking water maximum contamination levels to support safety in all environments. Inductively coupled plasma-optical emission spectroscopy (ICP-OES), Watersafe® Drinking Water Test kits, and solid phase microextraction with gas chromatography were used to assess the safety of drinking water in three buildings (Davis Hall, the Chemistry Building, and the Dalton Center) on the campus of Western Michigan University. ICP-OES was used to determine the concentration of several trace metals (Cu, Zn, Fe, Mn, Ni, Pb, and As), Watersafe® Drinking Water Test kits were used to determine the concentration of common contaminants and conditions (E. coli, pesticides atrazine and …

Investigations Of Substrate Channeling In The Proline Oxidative Pathway, Nikhilesh Sanyal

Department of Biochemistry: Dissertations, Theses, and Student Research

In cell metabolism, substrate channeling is a phenomenon where the product of one reaction is transported to a second enzyme active site without equilibrating into bulk solvent. Chapter 1 reviews the rationale and evidence for substrate channeling with the specific example of proline metabolism. Oxidation of proline to glutamate is catalyzed in consecutive reactions by proline dehydrogenase (PRODH) and pyrroline-5-carboxylate dehydrogenase (P5CDH). The intermediate Δ¹-pyrroline-5-carboxylate reportedly tends to be labile and inhibitory towards several metabolic pathways.

One of the main objectives of this dissertation was to investigate substrate channeling between independent proline oxidative enzymes from Thermus thermophilus- …

Roman Religion, Medicine, And Disease, Stephanie Clark

Honors Theses

Medicine, as experienced in the Roman Empire, was rapidly evolving. Balancing the newly developed theories with the already-established religious belief sparked the beginning of medical secularization. There were separate worlds, that of science and medicine, and that of the every day public, that had to be bridged in a way that honored both traditions, yet kept their integrity. The development of science and medicine pioneered by Galen, a philosopher whose medical knowledge and theory guided practitioners for almost two millennia, hit levels of exploration and understanding in ancient Rome that warranted its basis as common medical theory. However, the world, …

Erratum: Characterizing The Biomolecular Interactions Between Insulin And G-Quadruplexdna (Biophysical Journal (2013) 104:2 (419a)), Nicole L. Michmerhuizen, Christine M. Timmer, Margaret Van Winkle, Kylin Hamann

University Faculty Publications and Creative Works

No abstract provided.

Erratum: Characterizing The Biomolecular Interactions Between Insulin And G-Quadruplexdna (Biophysical Journal (2013) 104:2 (419a)), Nicole L. Michmerhuizen, Christine M. Timmer, Margaret Van Winkle, Kylin Hamann

University Faculty Publications and Creative Works

No abstract provided.

Chemically Diverse Microtubule Stabilizing Agents Initiate Distinct Mitotic Defects And Dysregulated Expression Of Key Mitotic Kinases., Cristina C. Rohena, Jiangnan Peng, Tyler A. Johnson, Phillip Crews, Susan L. Mooberry

Natural Sciences and Mathematics | Faculty Scholarship

Microtubule stabilizers are some of the most successful drugs used in the treatment of adult solid tumors and yet the molecular events responsible for their antimitotic actions are not well defined. The mitotic events initiated by three structurally and biologically diverse microtubule stabilizers; taccalonolide AJ, laulimalide/fijianolide B and paclitaxel were studied. These microtubule stabilizers cause the formation of aberrant, but structurally distinct mitotic spindles leading to the hypothesis that they differentially affect mitotic signaling. Each microtubule stabilizer initiated different patterns of expression of key mitotic signaling proteins. Taccalonolide AJ causes centrosome separation and disjunction failure to a much greater extent …

Chemical Warfare Agents In Plants: Biodefensive Terpenes From Sagebrush, Belinda Stierman

College of Arts and Sciences Poster Presentations

To prevent being eaten, some plants create compounds that are toxic to herbivores, and herbivores respond by creating new ways to metabolize these toxins. For example, sagebrush produces bio-defensive terpenes to deter foraging by sage grouse. A recent investigation to characterize plant secondary metabolites (PSM's) in sagebrush resulted in a correlation between terpene concentration and nutritional content in local sagebrush to the habitat selection of sage grouse. This study identified many of the terpenes in sagebrush, but not all of them. A highly volatile and elusive terpene is suspected to be an important PSM that significantly affects sage grouse foraging. …

Chelation Therapy For The Management Of Diabetic Complications: A Hypothesis And A Proposal For Clinical Laboratory Assessment Of Metal Ion Homeostasis In Plasma, Norma Frizzell, John W. Baynes

Faculty Publications

No abstract provided.

Establishing The Learning Effect Of Repeated Wingate Anaerobic Tests, Erin Thompson, Natalie Schaeffer, Eric T. Jones, Malcom T. Whitehead

Undergraduate Research Conference

The Wingate anaerobic test (WAnT) is a recognized and well established tool used to measure power output, muscular endurance, and fatigue. While litreature involving WAnT is plentiful, research addressing training effects within WAnT is limited. Previous studies have addressed changes in power output during repeated trials, however, to our knowledge multiple repeated trials over time to establish optimal learned effect has not been addressed. Past published studies using WAnT have incoporated various familiarization trails to account for the learned impact on performance (1, 2, 4). If an optimal number were established to produce a learned response the validity of future …

Side Chain Requirements For Affinity And Specificity In D5, An Hiv-1 Antibody Derived From The Vh1-69 Germline Segment, Alex Stewart, Joseph S. Harrison, Lauren K. Regula, Jonathan R. Lai

College of the Pacific Faculty Articles

BACKGROUND: Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. A. Khan, Madeline M. Lopez-Munoz, Charles W. Kaspar, Kai F. Hung

Faculty Research & Creative Activity

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. Khan, Madeline Lopez-Munoz, Charles Kaspar, Kai Hung

Faculty Research & Creative Activity

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Heme Oxygnase-1 Produced By A Human Monocytic Cell Line (U-937) After Exposure To Brevetoxin (Pbtx-2), Carolyn Fisher, Catherine Walsh, Stephanie Legget

The Review: A Journal of Undergraduate Student Research

In lieu of an abstract, below is the first paragraph of the paper.

Harmful Algal Blooms (HABs) along the west coast of Florida are the result of a large proliferation of the dinoflagellate Karenia brevis. The harmful nature of these algal blooms is the result of potent neurotoxins, specifically referred to as brevetoxins, which are released from K. brevis. PbTx-2 is one of the most abundant brevetoxins during HABs of K brevis and results in extreme mortality of marine wildlife and health implications for humans such as Neurotoxic Shellfish Poisoning (NSP) and immunosuppression. The cellular response to PbTx-2 is not …

Rna Sequencing Of Cancer Reveals Novel Splicing Alterations, Jeyanthy Eswaran, Anelia Horvath, Sucheta Godbole, Sirigiri Divijendra Natha Reddy, Prakriti Mudvari, Kazufumi Ohshiro, Dinesh Cyanam, Sujit S. Nair, Suzanne A.W. Fuqua, Kornelia Polyak, Liliana D. Florea, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

Breast cancer transcriptome acquires a myriad of regulation changes, and splicing is critical for the cell to “tailor-make” specific functional transcripts. We systematically revealed splicing signatures of the three most common types of breast tumors using RNA sequencing: TNBC, non-TNBC and HER2-positive breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast. We …

Multiscale Modeling Of Enzyme-Catalyzed Methanol Production By Particulate Methane Monooxygenase, Katherine K. Bearden

Doctoral Dissertations

In this work, the conversion of methane to methanol by the particulate Methane Monooxygenase (pMMO) enzyme is investigated using a multi-scale modeling approach. This enzyme participates in carbon cycling and aids in the removal of harmful atmospheric methane, converting it to methanol. The interaction between pMMO and a neighboring enzyme that is present in the same organism is studied, and the unknown pMMO active site is elucidated and tested for methane oxidation towards the production of methanol.

Fundamental knowledge of pMMO's mechanism is not fully understood. Understanding how this enzyme works in nature will provide information towards designing efficient synthetic …

Treating Cancer With Heat: Hyperthermia As Promising Strategy To Enhance Apoptosis, Kanwal Ahmed, Syed Faisal Zaidi

Department of Biological & Biomedical Sciences

The fundamental idea and the effects of heat on cancer cells are well known. However, the results obtained in therapy by hyperthermia (HT) alone have been only partially satisfactory. Treatment at temperatures between .40 and 44 degrees C is cytotoxic for cells in an environment with a low oxygen partial pressure and low pH, conditions that are found specifically within tumour tissue, due to insufficient blood perfusion. Under such conditions radiotherapy is less effective, and systemically applied cytotoxic agents will reach such areas in lower concentrations than in well-perfused areas. Therefore, clinically, it is preferred to use hyperthermia in combination …

Adenovirus Type 5 Virions Asymmetrically Lose Icosahedral Structure At Low Phs Of Endosomes, Jennifer Marie Jarboe

Honors Theses

After receptor mediated endocytosis into an endosome, human Adenovirus Type 5 (Ad5) undergoes structural changes that allow the virus to release a viral protein, pVI, that lyses the endosome and releases the virus core into the cytosol, where it travels to the nucleus to insert its genome. Structural studies of Ad5 at a range of pHs typical of endosomes (7.5-4.5) using a transmission electron microscope show that Ad5 undergoes asymmetrical loss of proteins from vertex regions at the pH of the late endosome (pH5.15). Following further acidification, Ad5 ejects core material preferentially through one vertex—indicating an asymmetry at one vertex …

Thermodynamics Of Binding By Calmodulin Correlates With Target Peptide Α-Helical Propensity, Tori B. Dunlap, Jessime M. Kirk, Emily A. Pena, Meghan S. Yoder, Trevor P. Creamer

Center for Structural Biology Faculty Publications

In this work, we have examined contributions to the thermodynamics of calmodulin (CaM) binding from the intrinsic propensity for target peptides to adopt an α-helical conformation. CaM target sequences are thought to commonly reside in disordered regions within proteins. Using the ability of TFE to induce α-helical structure as a proxy, the six peptides studied range from having almost no propensity to adopt α-helical structure through to a very high propensity. This despite all six peptides having similar CaM-binding affinities. Our data indicate there is some correlation between the deduced propensities and the thermodynamics of CaM binding. This finding implies …

Hydroxylamine Acutely Activates Glucose Uptake In L929 Fibroblast Cells, Larry L. Louters, Jared P. Scripture, David P. Kuipers, Stephen M. Gunnink

University Faculty Publications and Creative Works

Nitroxyl (HNO) has a unique, but varied, set of biological properties including beneficial effects on cardiac contractility and stimulation of glucose uptake by GLUT1. These biological effects are largely initiated by HNO's reaction with cysteine residues of key proteins. The intracellular production of HNO has not yet been demonstrated, but the small molecule, hydroxylamine (HA), has been suggested as possible intracellular source. We examined the effects of this molecule on glucose uptake in L929 fibroblast cells. HA activates glucose uptake from 2 to 5-fold within two minutes. Prior treatment with thiol-active compounds, such as iodoacetamide (IA), cinnamaldehyde (CA), or phenylarsine …

The Inner Workings Of The Dna Copying Nanomachine : Kinetic Studies Of Dna Polymerase I From The Thermophilic Bacterium Rhodothermus Marinus, Emily P. Kornberg

Honors Theses

DNA polymerase I from Rhodothermus marinus is a high-fidelity DNA polymerase capable of operating at high temperatures and incorporating 2´,3´-dideoxynucleotides. The R. marinus DNA Polymerase I active site contains an unusual proline in the middle of a mobile “O helix.” This proline residue is hypothesized to decrease the relative free energy of a kinetic checkpoint termed the ajar conformation, and thereby slow the incorporation of incorrect nucleotides. We aim to test the accuracy of a newly developed nucleotide incorporation model, in which the enzyme allows the template to interact with the bound dNTP in the ajar conformation, whether correct or …

Trimethylsilyl Trifluoromethanesulfonate-Mediated Additions To Acetals, Nitrones, And Aminals, Chelsea Safran

Honors Theses

One-pot reactions were studied in order to develop procedures for the formation of important carbon-carbon and carbon-nitrogen bonds that are easily reproducible. In the presence of trimethylsilyl triflouromethanesulfonate (TMSOTf), Mukaiyama-aldol and aldol-like reactions occur in one-pot due to TMSOTf acting as a Lewis acid and silylating agent. A variety of reactions, including methoxyalkylation, were performed to form carbon-nitrogen bonds. Here, research involving TMSOTf-mediated additions to acetals, nitrones, and aminals will be discussed.

Bayesian Reconstruction Of P(R) Directly From Two-Dimensional Detector Images Via A Markov Chain Monte Carlo Method, Sudeshna Paul, Alan M. Friedman, Chris Bailey-Kellogg, Bruce Craig

Dartmouth Scholarship

The interatomic distance distribution, P(r), is a valuable tool for evaluating the structure of a molecule in solution and represents the maximum structural information that can be derived from solution scattering data without further assumptions. Most current instrumentation for scattering experiments (typically CCD detectors) generates a finely pixelated two-dimensional image. In contin­uation of the standard practice with earlier one-dimensional detectors, these images are typically reduced to a one-dimensional profile of scattering inten­sities, I(q), by circular averaging of the two-dimensional image. Indirect Fourier transformation methods are then used to reconstruct P(r) from …

Novel Architecture Of Costal Cartilage And Implications In Chest Wall Deformities, Anthony J. Asmar

Biological Sciences Theses & Dissertations

Costal cartilage is a type of hyaline cartilage that forms rod-like structures that connect the ribs to the sternum. Deformation of costal cartilage is observed in the chest wall deformities, pectus excavatum and pectus carinatum. Pectus excavatum involves a sternal displacement causing a depression of the chest while pectus carinatum causes a protrusion of the chest. As costal cartilage is not a widely studied tissue, this leaves little knowledge into possible factors involved in the pathogenesis of pectus deformities. Costal cartilage in these deformities has been described as being weakened and may implicate proteoglycans which play an important role in …

Polystyrene: A Potential Standard For Developing In Vitro Cellular Tracking Methods For Nanotoxicology, Jennifer Dorney

Doctoral

Nanotoxicology has emerged as a discipline of a result of the revolution of nanotechnology. While nanotoxicology is in its infancy, there is a lack of toxicological data for nanoparticles, naturally occurring or commercially produced. The need for information regarding mechanisms associated with nanoparticle uptake by biological cells, as well as internalisation and accumulation of nanoparticles once penetrating cell membranes, is imperative. This project will focus on the internalisation studies of surface modified polystyrene nanoparticles. An in vitro lung model consisting of A549 (ATCC No: CRL185), a carcinogenic lung epithelial cell line, was employed to investigate the biocompatibility of nano scaled …

Effects Of Synthetic Histone Deacetylase Inhibitors On 3t3l1 Preadipocyte Adipogenic Differentiation Potential, Vikramjeet Singh

Honors Capstones

No abstract provided.