Digital Commons Network^™

Serdemetan Antagonizes The Mdm2-Hif1Α Axis Leading To Decreased Levels Of Glycolytic Enzymes, Jason Alexander Lehman, Paula M. Hauck, Jaimie M. Gendron, Christopher N. Batuello, Jacob A. Eitel, Allan Albig, Madhavi P. Kadakia, Lindsey D. Mayo

Biochemistry and Molecular Biology Faculty Publications

Serdemetan (JNJ-26854165), an antagonist to Mdm2, was anticipated to promote the activation of p53. While regulation of p53 by Mdm2 is important, Mdm2 also regulates numerous proteins involved in diverse cellular functions. We investigated if Serdemetan would alter the Mdm2-HIF1α axis and affect cell survival in human glioblastoma cells independently of p53. Treatment of cells with Serdemetan under hypoxia resulted in a decrease in HIF1α levels. HIF1α downstream targets, VEGF and the glycolytic enzymes (enolase, phosphoglycerate kinase1/2, and glucose transporter 1), were all decreased in response to Serdemetan. The involvement of Mdm2 in regulating gene expression of glycolytic enzymes raises …

Protein Similarity Networks Reveal Relationships Among Sequence, Structure, And Function Within The Cupin Superfamily, Richard Uberto, Ellen W. Moomaw

Faculty Articles

The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional …

Combining Orthogonal Trna/Synthatase Pair And Amber Codon Suppression To Genetically Encode Oxidative Damage In High Density Lipoproteins, Jaclyn Alatrash, Nicholas Gilliam, Alisha House, Valentin Gogonea

Undergraduate Research Posters 2013

Apolipoprotein A-I (apoA-I) is the main protein constituent of high density lipoprotein (HDL - the “good cholesterol”). Oxidatively damaged apoA-I has been isolated from circulating plasma and atherosclerosis plaque with the amino acid residue tryptophan 72 (W72) of apoA-I identified as a primary oxidation site. ApoA-I designed to include specific oxidized amino acids can be used to further investigate the role of site-specific oxidative damage in atherosclerosis. Genetic encoding of oxidized amino acids through orthogonal tRNA/aminoacyl-tRNA synthetase (aaRS) pairs offers a reliable method for producing site-specific oxidized proteins. Our project involves the generation of Saccharomyces tryptophan-RS mutants for recognition of …

Self-Assembled Dna Origami Templates For The Fabrication Of Electronic Nanostructures, Elisabeth Pound Gates

Theses and Dissertations

An important goal of nanoscience is the self-assembly of nanoscale building blocks into complex nanostructures. DNA is an important and versatile building block for nanostructures because of its small size, predictable base pairing, and numerous sequence possibilities. I use DNA origami to design and fold DNA into predesigned shapes, to assemble thin, branched DNA nanostructures as templates for nanoscale metal features. Using a PCR-based scaffold strand generation procedure, several wire-like nanostructures with varying scaffold lengths were assembled. In addition, more complex prototype circuit element structures were designed and assembled, demonstrating the utility of this technique in creating complex templates. My …

Transformations In Matter And Energy: Student Learning And Inquiry To Inform Teaching, Jenny Dauer

Discipline-Based Education Research Group Speaker Series

Learning progressions are descriptions of increasing levels of sophistication of student reasoning about a topic based on empirical evidence. Our learning progression framework about student explanations of carbon-transforming processes (e.g. photosynthesis, cellular respiration) describes how student’s interconnected and mutually supporting ideas and practices are deeply embedded in discourse at all levels of achievement. My research is in two areas: 1) applying the learning progression framework for student explanations of carbon-transforming processes to describe the most productive pathways for student learning, 2) extending the research to student reasoning during inquiry activities about carbon-transforming processes. One finding is that students who consistently …

Demonstration Of Crispr/Cas9/Sgrna-Mediated Targeted Gene Modification In Arabidopsis, Tobacco, Sorghum And Rice, Wen Zhi Jiang, Huanbin Zhou, Honghao Bi, Michael E. Fromm, Bing Yang, Donald P. Weeks

Department of Biochemistry: Faculty Publications

The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/ single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/ sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites …

Draft Genome Sequence Of A Mucoid Isolate Of Pseudomonas Aeruginosa Strain C7447m From A Patient With Cystic Fibrosis, Yeshi Yin, T. Ryan Withers, Shannon L. Johnson, Hongwei D. Yu

Biochemistry and Microbiology

Alginate overproduction by Pseudomonas aeruginosa, or mucoidy, plays an important role in the pathogenesis of chronic lung infections in cystic fibrosis (CF) patients. Here we report the draft genome sequence of a clinical isolate of mucoid P. aeruginosa strain C7447m from a CF patient with chronic lung infection.

Draft Genome Sequence Of A Stable Mucoid Strain Of Pseudomonas Aeruginosa Pao581 With A Muca25 Mutation, Yeshi Yin, T. Ryan Withers, John R. W. Govan, Shannon L. Johnson, Hongwei D. Yu

Biochemistry and Microbiology

A mutation in the mucA gene, which encodes a negative regulator of alginate production in Pseudomonas aeruginosa, is the main mechanism underlying the conversion to mucoidy in clinical isolates from patients with cystic fibrosis (CF). Here, we announce the draft genome sequence of the stable alginate-overproducing mucoid strain P. aeruginosa PAO581 with a mucA25 mutation, a derivative from the nonmucoid strains P. aeruginosa PAO381 and PAO1.

Shared Mycobacterium Avium Genotypes Observed Among Unlinked Clinical And Environmental Isolates, M. Ashworth Dirac, Kris M. Weigel, Mitchell A. Yakrus, Annie L. Becker, Hui-Ling Chen, Gina Fridley, Arthur Sikora, Cate Speake, Elizabeth D. Hilborn, Stacy Pfaller, Gerard A. Cangelosi

Chemistry and Physics Faculty Articles

Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-resolution PCR-based genotyping approach, large-sequence polymorphism (LSP)-mycobacterial interspersed repetitive unit–variable-number tandem repeat (MIRU-VNTR), was selected and used to analyze clinical and environmental isolates of M. avium from geographically diverse sources. Among 127 clinical isolates from seven locations in North America, South America, and Europe, 42 genotypes were observed. Among 12 of these genotypes, matches were seen in …

Computational Study Of The Cyclization Of 5-Hexenyl, 3-Oxa-5-Hexenyl And 4-Oxa-5-Hexenyl Radicals, Albert Matlin, Matthew C. Leyden

Faculty & Staff Scholarship

The intramolecular cyclization of 5-hexenyl radicals continues to be an important synthetic method for the construction of five-membered rings. The synthetic utility arises from the high degree of regioselectivity to give predominantly cyclopentyl products in high yield under mild conditions. Recently we reported product cyclization studies on 4-oxa perturbed 5-hexenyl radical. In this paper we report our results from a computational study (UB3LYP and UCCSD(T)) of the cyclization of a series of 5-hexenyl and 3- and 4-oxa-5-hexenyl radicals. Three highly conserved cyclization transitions states (exo-chair, exo-boat and endo-chair) were located for 10 acyclic radicals. Activation en-ergies …

Allosteric Mechanism Of Water Channel Gating By Ca2+–Calmodulin, Steve Reichow, Daniel M. Clemens, J. Alfredo Freites, Karin L. Németh-Cahalan, Matthias Heyden, Douglas J. Tobias, James E. Hall, Tamir Gonen

Chemistry Faculty Publications and Presentations

Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, our understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudo-atomic structure of full-length mammalian aquaporin-0 (AQP0, Bos Taurus) in complex with CaM using electron microscopy to understand how this signaling protein modulates water channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 …

The Creation Of Α2nc1 Transgenic Drosophila Melanogaster, Jordan Olberding

Mahurin Honors College Capstone Experience/Thesis Projects

The α2 isoform of collagen IV’s noncollagenous 1 domain (α2NC1 or canstatin) has shown promise as an anti-cancer molecule, possessing both angiostatic and pro-apoptotic properties. This work aims to further the knowledge of α2NC1 by conducting a truly in vivo study in which the Gal4-induced endogenous overexpression of α2NC1 in Drosophila melanogaster will be used to assess the effects of α2NC1 upon normal development as well as tumorigenesis. To this end, transgenic fly lines capable of overexpressing α2NC1 were created. Initial overexpression studies indicated no developmental phenotype was caused by abundance of α2NC1. However, future overexpression studies in which α2NC1 …

Chronic Cadmium Exposure Stimulates Sdf-1 Expression In An Erα Dependent Manner, Esmeralda Ponce, Natalie B. Aquino, Maggie Louie

Collected Faculty Scholarship

Cadmium is an omnipotent environmental contaminant associated with the development of breast cancer. Studies suggest that cadmium functions as an endocrine disruptor, mimicking the actions of estrogen in breast cancer cells and activating the receptor to promote cell growth. Although acute cadmium exposure is known to promote estrogen receptor-mediated gene expression associated with growth, the consequence of chronic cadmium exposure is unclear. Since heavy metals are known to bioaccumulate, it is necessary to understand the effects of prolonged cadmium exposure. This study aims to investigate the effects of chronic cadmium exposure on breast cancer progression. A MCF7 breast cancer cell …

Pitfalls With The Use Of Enhancement Ratios Or Normalized Excess Mixing Ratios Measured In Plumes To Characterize Pollution Sources And Aging, Robert J. Yokelson, Meinrat O. Andreae, S. K. Akagi

Chemistry and Biochemistry Faculty Publications

Normalized excess mixing ratios (NEMRs), also known as enhancement ratios, are a common way to characterize plumes of pollution in atmospheric research. As single-source pollutant plumes disperse in the atmosphere, they are diluted by mixing with the adjacent background air. Changes in the composition of this background air can cause large changes to the NEMR that is subsequently measured by remote-sensing, airborne, or ground-based instruments. This scenario is common when boundary layer plumes enter the free troposphere and could also impact long-range transport or plumes near the top of the troposphere. We provide a context for these issues and an …

Mscs-Like Mechanosensitive Channels In Plants And Microbes, Margaret E. Wilson, Grigory Maksaev, Elizabeth S. Haswell

Biology Faculty Research

The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. …

Bioengineered Lysozyme Reduces Bacterial Burden And Inflammation In A Murine Model Of Mucoid Pseudomonas Aeruginosa Lung Infection, Charlotte C. Teneback, Thomas C. Scanlon, Matthew J. Wargo, Jenna L. Bement, Karl E. Griswold, Laurie W. Leclair

Dartmouth Scholarship

The spread of drug-resistant bacterial pathogens is a growing global concern and has prompted an effort to explore potential adjuvant and alternative therapies derived from nature's repertoire of bactericidal proteins and peptides. In humans, the airway surface liquid layer is a rich source of antibiotics, and lysozyme represents one of the most abundant and effective antimicrobial components of airway secretions. Human lysozyme is active against both Gram-positive and Gram-negative bacteria, ac

Individual Interactions Of The B Subunits Within The Stator Of The Escherichia Coli Atp Synthase., Karsten Brandt, Sarah Maiwald, Brigitte Herkenhoff-Hesselmann, Kerstin Gnirss, Joerg-Christian Greie, Stanley D Dunn, Gabriele Deckers-Hebestreit

Biochemistry Publications

FOF1 ATP synthases are rotary nanomotors that couple proton translocation across biological membranes to the synthesis/hydrolysis of ATP. During catalysis, the peripheral stalk, composed of two b subunits and subunit δ in Escherichia coli, counteracts the torque generated by the rotation of the central stalk. Here we characterize individual interactions of the b subunits within the stator by use of monoclonal antibodies and nearest neighbor analyses via intersubunit disulfide bond formation. Antibody binding studies revealed that the C-terminal region of one of the two b subunits is principally involved in binding of subunit δ, while the other one is accessible …

Phosphorylation Of Calcineurin At A Novel Serine-Proline Rich Region Orchestrates Hyphal Growth And Virulence In Aspergillus Fumigatus, Praveen R. Juvvadi, Christopher Gehrke, Jarrod R. Fortwendel, Frédéric Lamoth, Erik J. Soderblom, Erik C. Cook, Michael A. Hast, Yohannes G. Asfaw, M. Arthur Moseley, Trevor P. Creamer, William J. Steinbach

Molecular and Cellular Biochemistry Faculty Publications

The fungus Aspergillus fumigatus is a leading infectious killer in immunocompromised patients. Calcineurin, a calmodulin (CaM)-dependent protein phosphatase comprised of calcineurin A (CnaA) and calcineurin B (CnaB) subunits, localizes at the hyphal tips and septa to direct A. fumigatus invasion and virulence. Here we identified a novel serine-proline rich region (SPRR) located between two conserved CnaA domains, the CnaB-binding helix and the CaM-binding domain, that is evolutionarily conserved and unique to filamentous fungi and also completely absent in human calcineurin. Phosphopeptide enrichment and tandem mass spectrometry revealed the phosphorylation of A. fumigatus CnaA in vivo at four clustered serine residues …

Biochemistry / Histone Protein Modification - Purdue University, Jake R. Carlson, Katherine Beavis

Data Curation Profiles Directory

The researcher is conducting research on the brain cells of drosophila larvae. Specifically, the goal is to sort nuclei from glial and neuronal cells from the brains of mutant and wild type drosophila larvae. She will do transcriptome and high throughput ChIP-seq analysis on the cell nuclei to examine the distribution of complexes that modify histones and how loss of those complexes affects transcription. The stages of her research involve a long period of methodology development, a shorter data collection period, and then data analysis. The lab notebook contains written documentation of all experiments and trials and links to data, …

A Supramolecular Strategy To Assemble Multifunctional Viral Nanoparticles, Limin Chen, Xia Zhao, Yuan Lin, Yubin Huang, Qian Wang

Faculty Publications

Using a one-pot approach driven by the supramolecular interaction between β-cyclodextrin and adamantyl moieties, multifunctional viral nanoparticles can be facilely formulated for biomedical applications.

Synthesis And Evaluation Of Thermally-Responsive Coatings Based Upon Diels–Alder Chemistry And Renewable Materials, Dahlia N. Amato, Gregory A. Strange, John P. Swanson, Anton D. Chavez, Suzanne E. Roy, Kim L. Varney, Craig A. Machado, Douglas V. Amato, Philip Costanzo

Chemistry and Biochemistry

A soybean based coating with thermally responsive Diels–Alder linkages has been prepared following an automotive 2-component formulation. The resulting coatings displayed the capability to be healed following physical deformation by a thermal stimulus, and such a material has significant potential for end users. Various curing agents were employed, and resulted in variation of scratch resistance and re-healablity. Different thermally responsive soybean resins were synthesized to have varying amounts reversible and nonreversible linkages when incorporated into the coating. Additionally, different isocyanates were added at differing ratios of NCO:OH in search of the optimum coating. It was found through the analysis of …

Acrylamide Reduction In Potato Chips By Selection Of Potato Variety Grown In Iran And Processing Conditions, S. Shojaee-Aliabadi, Hooshang Nikoopour, Farzad Kobarfard, Mahdi Parsapour, Maryam Moslehishad, Hassan Hassanabadi, Jesus Maria Frias, Maryam Hashemi, Ezzat Dahaghin

Articles

Background

Acrylamide as a possible carcinogen is known to form in heated carbohydrate-rich food such as potato chips. In this study, the effect of three potato varieties (Agria, Sante and Savalan) and two blanching conditions ((75˚C for 9 min and 83˚C for 2.5 min) on the concentration of precursors and acrylamide reduction in potato chips was investigated.

Results

Results revealed that potato variety and blanching time-temperature ere important parameters for acrylamide formation in potato chips. Acrylamide content in Sante variety potatoes, which contained the highest amount of reducing sugars, was found to be the highest (8825μg/kg). However, Savalan, containing …

Intra And Extracellular Functions Of Sphingosine-1-Phosphate In Sterile Inflammation., Jessie Yester

Theses and Dissertations

Sterile inflammation is a key component of a variety of diseases including, gout, arthritis, type 1 diabetes, Alzheimer’s disease and multiple sclerosis (MS). Sterile inflammation induces the recruitment of immune cells via chemokines, such as CCL5 and CXCL10. Expression of these chemokines is dependent on IRF-1. Recently the FDA has approved the use of a pro-drug, FTY720 that after phosphorylation becomes a S1P mimetic for the treatment of MS. This report describes two novel and opposing mechanisms of S1P action in sterile inflammation. First, intracellular S1P acts as a cofactor of cIAP2 that inducesIL-1-dependent K63-polyubiquitination of IRF-1, which leads to …

Identification Of Novel Gene Targets And Functions Of P21-Activated Kinase 1 During Dna Damage By Gene Expression Profiling, Mona Motwani, Da-Qiang Li, Anelia Horvath, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

P21-activated kinase 1 (PAK1), a serine/threonine protein kinase, modulates many cellular processes by phosphorylating its downstream substrates. In addition to its role in the cytoplasm, PAK1 also affects gene transcription due to its nuclear localization and association with chromatin. It is now recognized that PAK1 kinase activity and its nuclear translocation are rapidly stimulated by ionizing radiation (IR), and that PAK1 activation is a component of the DNA damage response. Owing to the role of PAK1 in the cell survival, its association with the chromatin, and now, stimulation by ionizing radiation, we hypothesize that PAK1 may be contributing to modulation …

Mechanism Of Ubiquitin Ligation And Lysine Prioritization By A Hect E3, Hari B. Kamadurai, Yu Qiu, Alan Deng, Joseph S. Harrison, Chris Macdonald, Marcelo Actis, Patrick Rodrigues, Darcie J. Miller, Judith Souphron, Steven M. Lewis, Igor Kurinov, Naoaki Fujii, Michal Hammel, Robert Piper, Brian Kuhlman, Brenda A. Schulman

College of the Pacific Faculty Articles

Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT …

Computational And Biochemical Approaches To Molecular Epidemiology, Michael Calhoun, Hannah Dysinger, David Hobbs, Ph.D., Katie Hailer, Ph.D.

2013 Undergraduate Research

Mining activity in Butte, Montana has taken place, or continues to take place, within the urban residence of Butte itself. This has led to urban areas with high concentrations of toxic metals such as arsenic, lead, copper, zinc, mercury and cadmium. Advances in protein study and gene sequencing has opened the possibility of finding molecular biomarkers whose presence, absence or morphological changes could indicate disease processes in populations exposed to environmental toxins. While in principle, biomarkers can be any chemicals or metabolites, as well as proteins and genes that are indicative of exposure to xenobiotics, this study seeks to identify …

A Study On The Regulation Of Amino Acids And Glucose Sensing Pathways In Saccharomyces Cerevisiae, Mengying Chiang

LSU New Orleans Theses and Dissertations

Nutrient availability regulates eukaryotic cell growth. This study focuses on two signaling pathways, involved in sensing amino acids and carbon sources, which allow cells to respond appropriately to their presence. The first part of this study shows that Ssy1, a plasma membrane localized sensor in the Ssy1-Ptr3-Ssy5 (SPS) amino acid sensing pathway, can detect 19 common L-amino acids with different potencies and affinities based on the physiochemical structure of amino acids. Substituents around alpha carbon are critical for amino acid sensing by Ssy1. Furthermore, a high concentration of cysteine is toxic to cells. Inactivation of SPS signaling confers resistance to …

Sarcoptes Scabiei Mites Modulate Gene Expression In Human Skin Equivalents, Marjorie S. Morgan, Larry G. Arlian, Michael P. Markey

Biochemistry and Molecular Biology Faculty Publications

The ectoparasitic mite, Sarcoptes scabiei that burrows in the epidermis of mammalian skin has a long co-evolution with its hosts. Phenotypic studies show that the mites have the ability to modulate cytokine secretion and expression of cell adhesion molecules in cells of the skin and other cells of the innate and adaptive immune systems that may assist the mites to survive in the skin. The purpose of this study was to identify genes in keratinocytes and fibroblasts in human skin equivalents (HSEs) that changed expression in response to the burrowing of live scabies mites. Overall, of the more than 25,800 …

Preservation Of Biosignature Molecules In Potential Sample Return Container Of The Mars 2020 Mission, Kimberly E. Lykens, Fei Chen Ph.D

STAR Program Research Presentations

Preservation of Biosignature Molecules in Potential Sample Return Container of the Mars 2020 Mission

Kimberly Lykens¹ and Fei Chen²

¹Wittenberg University, Springfield, Ohio 45501 ²Jet Propulsion Laboratory, Pasadena, California, 91109

One requirement for sustainable life on terrestrial planets includes the presence of organic polymers, compounds that are essential for major biological functions such as replication and catalysis. An identified goal of the Mars mission in the year 2020 is to implement a sample-return to identify and validate signs of life on Mars through the discovery of biosignature molecules in Martian core samples. Martian core samples recovered …

Evidence For A Novel Mechanism Of The Pak1 Interaction With The Rho-Gtpases Cdc42 And Rac, Yong Jae Shin, Eun Hye Kim, Adhiraj Roy, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

P21-activated kinase 1 (PAK1) is activated by binding to GTP-bound Rho GTPases Cdc42 and Rac via its CRIB domain. Here, we provide evidence that S79 in the CRIB domain of PAK1 is not directly involved in this binding but is crucial for PAK1 activation. S79A mutation reduces the binding affinity of PAK1 for the GTPases and inhibits autophosphorylation and kinase activity of PAK1. Thus, this mutation abrogates the ability of PAK1 to induce changes in cell morphology and motility and to promote malignant transformation of prostate epithelial cells. We also show that growth of the prostate cancer cell line PC3 …