Biochemistry, Biophysics, and Structural Biology Commons^™

Seastar: Systematic Evaluation Of Alternative Transcription Start Sites In Rna, Zhiyi Qin, Peter Stoilov, Xuegong Zhang, Yi Xing

Faculty & Staff Scholarship

Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5′ Untrans- lated Regions (5′UTRs) and N-terminal coding se- quences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to iden- tify the 5′ ends of transcripts. We developed a compu- tational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and com- pares alternative first exon usage across multiple bi- ological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified di- rectly by CAGE experiments and bear epigenetic hall- marks of active promoters. To …

Graphene Nanoplatelets-Sericin Surface-Modified Gum Alloy For Improved Biological Response, Valentina Mitran, Valentina Dinca, Raluca Ion, Vasile D. Cojocaru, Patricia Neacsu, Cerasela Zoica Dinu, Laurentiu Rusen, Simona Brajnicov, Anca Bonciu, Maria Dinescu, Doina Raducanu, Ioan Dan

Faculty & Staff Scholarship

In this study a “Gum Metal” titanium-based alloy, Ti-31.7Nb-6.21Zr-1.4Fe-0.16O, was synthesized by melting and characterized in order to evaluate its potential for biomedical applications. The results showed that the newly developed alloy presents a very high strength, high plasticity and a low Young's modulus relative to titanium alloys currently used in medicine. For further bone implant applications, the newly synthesized alloy was surface modified with graphene nanoplatelets (GNP), sericin (SS) and graphene nanoplatelets/sericine (GNP–SS) composite films via Matrix Assisted Pulsed Laser Evaporation (MAPLE) technique. The characterization of each specimen was monitored by scanning electron microscopy (SEM), atomic force microscopy (AFM), …

A Functional Signature Ontology (Fusion) Screen Detects An Ampk Inhibitor With Selective Toxicity Toward Human Colon Tumor Cells, Binita Das, Beth K. Neilsen, Kurt W. Fisher, Drew Gehring, Youcai Hu, Deanna J. Volle, Hyun Seok Kim, Jamie L. Mccall, David L. Kelly, John B. Macmillian, Michael A. White, Robert E. Lewis

Faculty & Staff Scholarship

AMPK is a serine threonine kinase composed of a heterotrimer of a catalytic, kinase-containing α and regulatory β and γ subunits. Here we show that individual AMPK subunit expression and requirement for survival varies across colon cancer cell lines. While AMPKα1 expression is relatively consistent across colon cancer cell lines, AMPKα1 depletion does not induce cell death. Conversely, AMPKα2 is expressed at variable levels in colon cancer cells. In high expressing SW480 and moderate expressing HCT116 colon cancer cells, siRNA-mediated depletion induces cell death. These data suggest that AMPK kinase inhibition may be a useful component of future therapeutic strategies. …

Farnesylation Of The Transducin G Protein Gamma Subunit Is A Prerequisite For Its Ciliary Targeting In Rod Photoreceptors, Celine Brooks, Joseph Murphy, Marycharmain Belcastro, Daniel Heller, Saravanan Kolandaivelu, Oleg Kisselev, Maxim Sokolov

Faculty & Staff Scholarship

Primary cilia are microtubule-based organelles, which protrude from the plasma membrane and receive a wide range of extracellular signals. Various cilia use G protein-coupled receptors (GPCRs) for the detection of these signals. For instance, vertebrate rod photoreceptors use their cilia (also called outer segments) as antennae detecting photons by GPCR rhodopsin. Rhodopsin recognizes incoming light and activates its G protein, transducin, which is composed of three subunits α, β, and γ. Similar to all G protein γ subunits, the transducin Gγ1 subunit undergoes C-terminal prenylation resulting in the addition of an isoprenoid farnesyl; however, the significance of this posttranslational modification …

Spontaneous Dna Damage To The Nuclear Genome Promotes Senescence, T Redox Imbalance And Aging, Andria R. Robinson, Matthew J. Yousefzadeh, Tania A. Rozgaja, Jin Wang, Xuesen Li, Jeremy S. Tilstra, Chelsea H. Feldman, Siobhan Q. Gregg, Caroline H. Johnson, Erin M. Skoda, Marie-Celine Frantz, Harris Bell-Temin, Hannah Pope-Varsalona, Aditi U. Gurkar, Luigi A. Nasto, Rena A.S. Robinson, Heike Fuhrmann-Stroissnigg, Jolanta Czerwinska, Sara J. Mcgowan, Nadiezhda Cantu-Madellin, Jamie B. Harris, Salony Maniar, Mark A. Ross, Christy E. Trussoni, Nicholas F. Larusso, Eugenia Cifuentes-Pagano, Patrick J. Pagano, Barbara Tudek, Nam V. Vo, Lora H. Rigatti, Patricia L. Opresko, Donna B. Stolz, Simon C. Watkins, Christin E. Burd, Claudette M. St, Croix, Gary Siuzdak, Nathan A. Yates, Paul D. Robbins, Yinsheng Wang, Peter Wipf, Eric E. Kelley, Laura J. Neidernhofer

Faculty & Staff Scholarship

Accumulation of senescent cells over time contributes to aging and age-related diseases. However, what drives senescence in vivo is not clear. Here we used a genetic approach to determine if spontaneous nuclear DNA damage is sufficient to initiate senescence in mammals. Ercc1-/Δ mice with reduced expression of ERCC1-XPF endonuclease have impaired capacity to repair the nuclear genome. Ercc1-/Δ mice accumulated spontaneous, oxidative DNA damage more rapidly than wild-type (WT) mice. As a consequence, senescent cells accumulated more rapidly in Ercc1-/Δ mice compared to repair-competent animals. However, the levels of DNA damage and senescent cells in Ercc1-/Δ mice never exceeded that …

Development Of Low Frequency Electron Paramagnetic Resonance Methods And Instrumentation For Biological Applications, Laura A. Buchanan

Electronic Theses and Dissertations

EPR is a powerful biophysical tool that can be used to measure tumor physiology. With the addition of magnetic field gradients, the spectral properties of paramagnetic species can be mapped. To facilitate EPR imaging, methods and instrumentation at frequencies between 250 MHz and 1 GHz were developed.

At low spin concentrations, the rapid scan background signal is often many times larger than the EPR signal of interest. To help remove the background contribution, a data acquisition procedure that takes advantage of a cross-loop resonator and bipolar power supplies was developed at 250 MHz. In this procedure, two scans are collected. …

Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman

Electronic Theses and Dissertations

Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using …

Brønsted Acid Catalyzed Carbon-Carbon Bond Forming Reactions, Jiangyue Miao

Electronic Theses and Dissertations

The focus of this research project lies in the development of new methodology in the field of Brønsted acid catalysis enabling rapid synthesis of medicinally relevant compounds. It is foreseen that small molecule sulfonic acids evaluated in this research project will unveil new asymmetric carbon carbon bond forming reactions between substrates hitherto unexplored with Brønsted acid catalysis. It has been established that strong Brønsted acids, such as phosphoric acids, are capable of mediating highly selective transformations operating through unique mechanistic manifolds.

Specific focus for the sulfonic acid catalysts was geared towards asymmetric coupling reactions with synthetically useful precursors such as …

Tau Aggregation, Conformational Selection, And Inhibition, Michael R. Holden

Electronic Theses and Dissertations

Tau fibrils are a pathological hallmark of over 20 neurodegenerative disorders, including Alzheimer's disease. There currently is no cure for these diseases and treatments are limited. Once Tau fibrils form in the brain, they propagate down neuronal networks, and this spreading is linked to disease progression. Studying the behavior and structure of Tau monomer and Tau aggregates therefore may give insight into methods by which the spread of Tau fibrils can be inhibited. The structures of the Tau fibrils from different diseases are thought to vary, partially giving rise to the different disease phenotypes. Tau natively binds to microtubules by …

Multilevel Structural Equation Modeling Of Students’ Dietary Intentions/Behaviors, Bmi, And The Healthfulness Of Convenience Stores, Tanya Horacek, Elif Dede Yildirim, Kendra Kattelmann, Carol Byrd-Bredbenner, Onikia Brown, Sarah Colby, Geoffrey Greene, Sharon Hoerr, Tandalayo Kidd, Mallory Koenings, Jesse Morrell, Melissa D. Olfert, Beatrice Phillips, Karla Shelnutt, Adrienne White

Faculty & Staff Scholarship

Background: When dietary behaviors are habitual, intentions are low, and environmental cues, such as the consumer food environment, might guide behavior. How might intentions to eat healthily and ultimately actual dietary behaviors, be influenced by the consumer food environment (including the availability and affordability of healthy foods) in convenience stores? This study will determine pathways between the healthfulness of convenience stores and college students’ dietary intentions/behaviors, and body mass index (BMI). Methods: Through multilevel structural equation modeling, a comparison was made of students’ healthful meal intentions (HMI); intake (fruits/vegetables, %kcal/fat, sugar-sweetened beverages (SSBs) and whole-grains); and measured BMI; as well …

Progress Toward The Synthesis Of Novel Bacterial Topoisomerase Inhibitors Derived From Fluoroquinolones. N-1 Amine Derivatives, Luke Burroughs, Joshua Kuperus, Evamarie Medendorp, Michael Barbachyn

Summer Research

Bacterial resistance to current antibiotics is a growing problem across the globe. The CDC reported that the estimated minimum illnesses caused by antibiotic resistance in the year 2013 was over 2 million, resulting in about 23,000 deaths in the U.S. 1 In 2014, the Obama administration released an executive order mandating that research be conducted to identify solutions to the bacterial resistance problem, especially in Gram-negative bacteria. One antibiotic series that has shown some promise are the fluoroquinolones. Fluoroquinolones have been on the market for years, with a current reference example being moxifloxacin. Fluoroquinolones (FQs) work by targeting DNA gyrase …

Scopoletin Excited-State Proton Transfer And Excited-State Pkₐ, Hunter T. Pham, Mark Muyskens

Summer Research

Scopoletin is suspected to undergo excited-state proton transfer (ESPT), resulting in fluorescent emission from the anionic structure except in very low pH. Excitation and emission spectra were collected in water of varying pH and were used to determine the pKₐ of ground-state and excited-state scopoletin to be 7.6 ± 0.2 and 1.7 ± 0.2 respectively. This agrees with literature’s calculated value for the ground state [3] and the literature excited-state value for a molecule of similar structure [6]. Spectra were then collected using tetrahydrofuran as a solvent to force neutral conditions and added sodium metal to force anionic conditions. These …

A Conceptual Framework For Understanding The Biogeochemistry Of Dry Riverbeds Through The Lens Of Soil Science, Maria Isabel Arce, Clara Mendoza, Maria Almagro, Nuria Catalan, Anna M. Romani, Eugenia Marti, R. Gomez, Susana Bernal, Arnaud Foulquier, Michael Mutz, Rafael Marce, Annamaria Zoppini, Giulia Gionchetta, Gabriele Weigelhofer, R. Del Campo, Christopher T. Robinson, Alan Gilmer, Martin Rulik, Obrador Biel, Oleksandra Shumilova, Sanja Zlatanovic, Shai Arnon, Petr Baldrian, Gabriel Andreas Singer, Thibault Datry, Nikolaos Th Skoulikidis, Britta Tietjen, Daniel Von Schiller

Articles

Intermittent rivers and ephemeral streams (IRES) encompass fluvial ecosystems that eventually stop flowing and run dry at some point in space and time. During the dry phase, channels of IRES consist mainly of dry riverbeds (DRBs), prevalent yet widely unexplored ecotones between dry and wet phases that can strongly influence the biogeochemistry of fluvial networks. DRBs are often overlooked because they do not strictly belong to either domain of soil or freshwater science. Due to this dual character of DRBs, we suggest that concepts and knowledge from soil science can be used to expand the understanding of IRES biogeochemistry. Based …

Four Hapten Spacer Sites Modulating Class Specificity: Nondirectional Multianalyte Immunoassay For 31 Β-Agonists And Analogues., Lanteng Wang, Wenmeng Jiang, Xing Shen, Xiangmei Li, Xin-An Huang, Zhenlin Xu, Yuanming Sun, Shun-Wan Chan, Lingwen Zeng, Eremin Sergei Alexandrovich, Hongtao Lei

Faculty of Science & Technology (THEi)

Immunoassay methods are important for monitoring β-agonists illegally used for reducing animal fat deposition in livestock. However, there is no simultaneous screening surveillance immunoassay for detecting various β-agonist chemicals that are possibly present in food. In this study, through the use of an R-(−)-salbutamol derivative as the immunizing hapten, an antibody recognizing 31 β-agonists and analogues was generated for the first time. Three-dimensional quantitative structure–activity relationship (3D QSAR) revealed that strong steric and hydrophobic fields around the hapten spacer near C-2, as well as a chirality at C-1′, dominantly modulated the class specificity of the raised antibody. However, a hapten …

Synthesis Of Trisubstitiuted Indolizines: Mechanistic Studies, Miles M. Mason, Leslie A. Nickerson, Emily E. Zerull, Carolyn E. Anderson

Summer Research

Indolizines are a versatile heterocyclic core, found frequently in pharmaceutical targets, for a wide variety of therapeutic areas, including: anti-bacterial1 and anti-tumor,2 in addition to targets against Alzheimer’s disease,3 asthma,4 erectile dysfunction,5 and inflammation related to respiratory or cardiovascular disease

Investigating The Effects Of Antibiotics Perturbation On Lactobacillus Species Metabolomics Profiles, Sophia Lee, Kundi Yang, Jiangjiang (Chris) Zhu

Summer Research

Our gut microbiota contains a vast array of cells that influence human physiology, metabolism, nutrition and immune function. Lactobacillus is a group of Gram-positive, lactic acid bacteria that is naturally present in the human gastrointestinal tract. Some species are probiotics that provide beneficial health effects to humans. Many studies have investigated and noted their various health benefits to their human host, including prevention of certain diseases such as colon cancer, breaking down of food, and absorption of nutrients. Maintaining the balance of our normal flora is essential - even small perturbations to the microbiota can have significant health effects. It …

Elucidating Genotype-Phenotype Relationships In Bcs1l Mutations, Kalina Reese, Shannon Stewart, Rachael Baker, Amy Wilstermann

Summer Research

• Establish a yeast model system for the study of BCS1L function.
• Develop assays to investigate differences in mitochondrial efficiency and electron transport chain functionality of BCS1L mutants.
• Connect hearing-loss associated BCS1L mutations to mitochondrial structure and function to better explain the clinical variation observed in patients with BCS1L mutations

Improving The Detection Limit Of Tau Aggregates For Use With Biological Samples, Emily Rickman Hager

Electronic Theses and Dissertations

The protein Tau is found in neurofibrillary tangles in Alzheimer's disease and over 20 other neurodegenerative diseases. An assay has been developed to detect minute amounts of fibrils from human brain tissue. This assay subjects brain tissue extract and recombinant Tau to several rounds of sonication and incubation. Incubation allows recombinant Tau to add itself to the ends of the existing fibrils in brain tissue extract. Sonication breaks the existing fibrils in the brain tissue extract offering more ends for Tau to add onto. Cycles of sonication and incubation have been shown to allow for amplification of Tau fibrils from …

Relationship Between Tdp-43 Toxicity And Aggregation In Saccharomyces Cerevisiae, Martin Anthony Aguilar

Electronic Theses and Dissertations

Protein aggregation and inclusion body formation are hallmarks of neurodegenerative diseases such as Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis (ALS). These neurodegenerative diseases share a common pathology in that all include accumulation of insoluble protein aggregates in the brain. TAR-DNA-binding protein (TDP-43) is the major component found in the pathological inclusions of two of these diseases, ALS and frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U). This thesis focuses upon the biophysical basis for TDP-43 aggregation in S. cerevisiae. Current in vitro evidence indicates that TDP-43 is a natively dimeric protein and that binding to RNA inhibits aggregation. Corresponding …

The Igf2/Igf1r/Nanog Signaling Pathway Regulates The Proliferation Of Acute Myeloid Leukemia Stem Cells., Dan-Dan Xu, Ying Wang, Peng-Jun Zhou, Shu-Rong Qin, Rong Zhang, Yi Zhang, +Several Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

Acute myeloid leukemia is an aggressive disease characterized by clonal proliferation and differentiation into immature hematopoietic cells of dysfunctional myeloid precursors. Accumulating evidence shows that CD34+CD38- leukemia stem cells (LSCs) are responsible for drug resistance, metastasis, and relapse of leukemia. In this study, we found that Nanog, a transcription factor in stem cells, is significantly overexpressed in CD34+ populations from patients with acute myeloid leukemia and in LSCs from leukemia cell lines. Our data demonstrate that the knockdown of Nanog inhibited proliferation and induced cell cycle arrest and cell apoptosis. Moreover, Nanog silencing suppressed the leukemogenesis of LSCs in mice. …