Purification And Initial Biochemical Characterization
Of Atp:Cob(I)Alamin Adenosyltransferase (Eutt)
Enzyme Of Salmonella Enterica,
2021
University of Nebraska-Lincoln
Purification And Initial Biochemical Characterization Of Atp:Cob(I)Alamin Adenosyltransferase (Eutt) Enzyme Of Salmonella Enterica, Nicole R. Buan, Jorge C. Escalante-Semerena
Department of Biochemistry: Faculty Publications
ATP:cob(I)alamin adenosyltransferase (EutT) of Salmonella enterica was overproduced and enriched to ~70% homogeneity, and its basic kinetic parameters were determined. Abundant amounts of EutT protein were produced, but all of it remained insoluble. Soluble active EutT protein (~70% homogeneous) was obtained after treatment with detergent. Under conditions in which cobalamin (Cbl) was saturating, Km(ATP) = 10 μM, kcat = 0.03 s–1, and Vmax = 54.5 nM min–1. Similarly, under conditions in which MgATPwas saturating,Km(Cbl)= 4.1μM, kcat = 0.06 s–1, andVmax …
The Simulation Experiment Description
Markup Language (Sed-Ml): Language
Specification For Level 1 Version 4,
2021
University of Washington
The Simulation Experiment Description Markup Language (Sed-Ml): Language Specification For Level 1 Version 4, Lucian P. Smith,, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson,, Herbert Sauro, Dagmar Waltemath, Matthias König
Department of Biochemistry: Faculty Publications
Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these …
Liquid And Semisolid Lubricant
Compositions , Methods Of Making , And Uses Thereof,
2021
Denton, TX
Liquid And Semisolid Lubricant Compositions , Methods Of Making , And Uses Thereof, Diana Berman, Kent Dean Chapman, Tervor Bradley Romsdahl, Edgar Benjamin Cahoon, Robert Earl Minto, Chunyu Zhang
Department of Biochemistry: Faculty Publications
Various liquid and semisolid lubricant compositions are provided, in particular lubricant compositions containing oil from the seeds of the Brassicaceae Orychophragmus violaceus, preferably those that have been esterified with one or more fatty acids such as palmitoleic acid, oleic acid, linoleic acid, lauric acid, palmitic acid, stearic acid, or a combination thereof. In various aspects, lubricant compositions are provided that include a petroleum or a synthetic base oil and about 40 % or less by weight of a liquid lubricant composition containing oil from the seeds of the Brassicaceae Orychophragmus violaceus preferably those that have been esterified with one …
Shift In Conformational Equilibrium Underlies The Oscillatory Phosphoryl Transfer Reaction In The Circadian Clock,
2021
Marshall University
Shift In Conformational Equilibrium Underlies The Oscillatory Phosphoryl Transfer Reaction In The Circadian Clock, Pyonghwa Kim, Neha Thati, Shreya Peshori, Hye-In Jang, Yongick Kim
Chemistry Faculty Research
Oscillatory phosphorylation/dephosphorylation can be commonly found in a biological system as a means of signal transduction though its pivotal presence in the workings of circadian clocks has drawn significant interest: for example in a significant portion of the physiology of Synechococcus elongatus PCC 7942. The biological oscillatory reaction in the cyanobacterial circadian clock can be visualized through its reconstitution in a test tube by mixing three proteins—KaiA, KaiB and KaiC—with adenosine triphosphate and magnesium ions. Surprisingly, the oscillatory phosphorylation/dephosphorylation of the hexameric KaiC takes place spontaneously and almost indefinitely in a test tube as long as ATP is present. This …
A Conserved Structural Role For The Walker-A Lysine In P-Loop Containing Kinases,
2021
CUNY City College
A Conserved Structural Role For The Walker-A Lysine In P-Loop Containing Kinases, Fatlum Hajredini, Ranajeet Ghose
Publications and Research
Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved “catalytic” lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg2+•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by …
Effects Of Exogenous Application Of Plant Growth Regulators (Snp And Ga3) On Phytoextraction By Switchgrass (Panicum Virgatum L.) Grown In Lead (Pb) Contaminated Soil,
2021
Kennesaw State University
Effects Of Exogenous Application Of Plant Growth Regulators (Snp And Ga3) On Phytoextraction By Switchgrass (Panicum Virgatum L.) Grown In Lead (Pb) Contaminated Soil, Adrianne Beavers, Marina Koether, Thomas C. Mcelroy, Sigurdur Greipsson
Faculty Articles
Soil lead (Pb) contamination is a major environmental and public health risk. Switch-grass (Panicum virgatum), a second-generation biofuel crop, is potentially useful for the long-term phytoremediation and phytoextraction of Pb contaminated soils. We evaluated the efficacy of a coor-dinated foliar application of plant growth regulators and soil fungicide and a chelator in order to optimize phytoextraction. Plants were grown in soil culture under controlled conditions. First, three exogenous nitric oxide (NO) donors were evaluated at multiple concentrations: (1) S-nitroso-N-acetylpenicillamine (SNAP); (2) sodium nitroprusside (SNP); and (3) S-nitrosoglutathione (GSNO). Second, the effect of SNP (0.5 µM) was examined further with the …
Analysis Of Single-Site Cysteine Mutation, I412c, In Human A Glycine Receptor States To Further Refine Structure And Allostery,
2021
University of Nebraska - Lincoln
Analysis Of Single-Site Cysteine Mutation, I412c, In Human A Glycine Receptor States To Further Refine Structure And Allostery, Leah Engquist
Honors Program: Senior Projects (Public)
The glycine receptor (GlyR) is the major inhibitory receptor in the brain and spinal cord. A member of the pentameric ligand gated ion channel superfamily, crystal structures are available but there are still unresolved areas, specifically the C-terminal tail and TM3-TM4 intracellular loop. Further refinement can provide deeper understanding of the molecular mechanism and allow the creation of novel therapeutics to modulate its function. We propose to insert a single cysteine mutation, I412C, into a Cys null background (C41S/C290A/C345S) to study non- conducting states (resting, desensitized) or with F207G/A288G mutations to study the open state. Purified, reconstituted GlyR is crosslinked …
Mitochondrial Contact Site And Cristae Organizing System (Micos) Machinery Supports Heme Biosynthesis By Enabling Optimal Performance Of Ferrochelatase,
2021
University of Nebraska–Lincoln
Mitochondrial Contact Site And Cristae Organizing System (Micos) Machinery Supports Heme Biosynthesis By Enabling Optimal Performance Of Ferrochelatase, Jonathan V. Dietz, Mathilda M. Willoughby, Robert B. Piel, Teresa A. Ross, Iryna Bohovych, Hannah G. Addis, Jennifer L. Fox, William N. Lanzilotta, Harry A. Dailey, James A. Wohlschlegel, Amit R. Reddi, Amy E. Medlock, Oleh Khalimonchuk
Department of Biochemistry: Faculty Publications
Heme is an essential cofactor required for a plethora of cellular processes in eukaryotes. In metazoans the heme biosynthetic pathway is typically partitioned between the cytosol and mitochondria, with the first and final steps taking place in the mitochondrion. The pathway has been extensively studied and its biosynthetic enzymes structurally characterized to varying extents. Nevertheless, understanding of the regulation of heme synthesis and factors that influence this process in metazoans remains incomplete. Therefore, we investigated the molecular organization as well as the physical and genetic interactions of the terminal pathway enzyme, ferrochelatase (Hem15), in the yeast Saccharomyces cerevisiae. Biochemical and …
Converging Technologies: Targeting The Hallmarks Of Cancer Using Ultrasound And Microbubbles,
2021
Technological University Dublin
Converging Technologies: Targeting The Hallmarks Of Cancer Using Ultrasound And Microbubbles, Janith Wanigasekara, Andressa Maria Aguiar De Carvalho, Patrick J. Cullen, Brijesh Tiwari, James F. Curtin
Articles
Various complex biological effects occur when ultrasonic compression waves travel through biological material. The myriad of biological outcomes instigated by ultrasound are evident when viewed through the lens of the hallmarks of cancer. Herein, we summarise the therapeutic potential of ultrasound, enhanced by microbubbles, for the treatment of cancer.
Fusion And Beyond: Satellite Cell Contributions To Loading-Induced Skeletal Muscle Adaptation,
2021
University of Arkansas, Fayetteville
Fusion And Beyond: Satellite Cell Contributions To Loading-Induced Skeletal Muscle Adaptation, Kevin A. Murach, Christopher S. Fry, Esther E. Dupont-Versteegden, John J. Mccarthy, Charlotte A. Peterson
Health, Human Performance and Recreation Faculty Publications and Presentations
Satellite cells support adult skeletal muscle fiber adaptations to loading in numerous ways. The fusion of satellite cells, driven by cell-autonomous and/or extrinsic factors, contributes new myonuclei to muscle fibers, associates with load-induced hypertrophy, and may support focal membrane damage repair and long-term myonuclear transcriptional output. Recent studies have also revealed that satellite cells communicate within their niche to mediate muscle remodeling in response to resistance exercise, regulating the activity of numerous cell types through various mechanisms such as secretory signaling and cell-cell contact. Muscular adaptation to resistance and endurance activity can be initiated and sustained for a period of …
Hiv-1 Transcription Elongation By Tat-Mediated Recruitment Of P-Tefb,
2021
University of Nebraska - Lincoln
Hiv-1 Transcription Elongation By Tat-Mediated Recruitment Of P-Tefb, Elizabeth Griggs
Honors Program: Senior Projects (Public)
Over 38.0 million people live with the human immunodeficiency virus (HIV) as of 462019. HIV hijacks the host's cellular machinery to replicate its viral DNA and transcribe the corresponding RNA. HIV-1 transcription relies on both cellular and viral transcription factors for proper regulation. The viral transcriptional activator Tat is a primary regulator. Transcription activation and elongation is controlled through the interaction of Tat with Positive Transcription Elongation Factor b (P-TEFb), a cellular transcriptional activator. The focus of this paper is 1) an in-depth understanding of the interaction between P-TEFb and Tat in HIV transcription, and 2) a review of recent …
Covid-19 In Silico Drug With Zingiber Officinale Natural Product Compound Library Targeting The Mpro Protein,
2021
Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta 13210, Indonesia
Covid-19 In Silico Drug With Zingiber Officinale Natural Product Compound Library Targeting The Mpro Protein, Renadya Maulani Wijaya, Muhammad Aldino Hafidzhah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit
Makara Journal of Science
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (Mpro) was generated from a protein sequence database, i.e., Protein Data Bank, …
Fe-Catalyzed Sulfide Oxidation In Hydrothermal Plumes Is A Source Of Reactive Oxygen Species To The Ocean,
2021
University of South Carolina
Fe-Catalyzed Sulfide Oxidation In Hydrothermal Plumes Is A Source Of Reactive Oxygen Species To The Ocean, Timothy J. Shaw, George W. Luther Iii, Richard Rosas, Véronique E. Oldham, Nicole R. Coffey, John L. Ferry, Dewamunnage M. C. Dias, Mustafa Yücel, Aubin Thibault De Chanvalon
Faculty Publications
Historically, the production of reactive oxygen species (ROS) in the ocean has been attributed to photochemical and biochemical reactions. However, hydrothermal vents emit globally significant inventories of reduced Fe and S species that should react rapidly with oxygen in bottom water and serve as a heretofore unmeasured source of ROS. Here, we show that the Fe-catalyzed oxidation of reduced sulfur species in hydrothermal vent plumes in the deep oceans supported the abiotic formation of ROS at concentrations 20 to 100 times higher than the average for photoproduced ROS in surface waters. ROS (measured as hydrogen peroxide) were determined in hydrothermal …
Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy,
2021
Emory University
Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not …
Small Studies, Big Decisions: The Role Of Pilot/Feasibility Studies In Incremental Science And Premature Scale-Up Of Behavioral Interventions,
2021
University of South Carolina
Small Studies, Big Decisions: The Role Of Pilot/Feasibility Studies In Incremental Science And Premature Scale-Up Of Behavioral Interventions, Michael William Beets, Lauren Von Klinggraeff, Robert G. Weaver, Bridget Ryan Armstrong, Sarah Burkart
Faculty Publications
Background: Careful consideration and planning are required to establish “sufficient” evidence to ensure an investment in a larger, more well-powered behavioral intervention trial is worthwhile. In the behavioral sciences, this process typically occurs where smaller-scale studies inform larger-scale trials. Believing that one can do the same things and expect the same outcomes in a larger-scale trial that were done in a smaller-scale preliminary study (i.e., pilot/feasibility) is wishful thinking, yet common practice. Starting small makes sense, but small studies come with big decisions that can influence the usefulness of the evidence designed to inform decisions about moving forward with a …
Targeting The Cdk6 Dependence Of Ph+ Acute Lymphoblastic Leukemia,
2021
Thomas Jefferson University
Targeting The Cdk6 Dependence Of Ph+ Acute Lymphoblastic Leukemia, Patrizia Porazzi, Marco De Dominici, Joseph Salvino, Bruno Calabretta
Department of Cancer Biology Faculty Papers
Ph+ ALL is a poor-prognosis leukemia subtype driven by the BCR-ABL1 oncogene, either the p190-or the p210-BCR/ABL isoform in a 70:30 ratio. Tyrosine Kinase inhibitors (TKIs) are the drugs of choice in the therapy of Ph+ ALL. In combination with standard chemotherapy, TKIs have markedly improved the outcome of Ph+ ALL, in particular if this treatment is followed by bone marrow transplantation. However, resistance to TKIs develops with high frequency, causing leukemia relapse that results in
Effects Of Copper Oxide (Cuo) And Zinc Oxide (Zno) Nano And Bulk Forms To Soil Fungal Community [Research Note],
2021
Bicol University College of Science Department of Biology, Legazpi City
Effects Of Copper Oxide (Cuo) And Zinc Oxide (Zno) Nano And Bulk Forms To Soil Fungal Community [Research Note], Jonathan Jaime Guerrero, Teresita Dalisay, Nolissa Organo, Ireneo Pangga
The Philippine Agricultural Scientist
The effects of copper oxide (CuO) and zinc oxide (ZnO) in bulk and nano forms on soil fungal community was determined. Lipa clay loam soil collected from the University of the Philippines Los Baños were placed in polypropylene bags and amended with 300 mg/L of CuO or ZnO in either forms. Colony-forming units (CFU) as well as average well color development (AWCD), functional richness and stress index were determined on day 1, 8 and 15 via indirect viable plate count method and community – level physiological profiling (CLPP). Fungal isolates from the same soil samples were likewise identified and tested …
Machine Learning And Solvation Theory For Drug Discovery,
2021
CUNY Graduate Center
Machine Learning And Solvation Theory For Drug Discovery, Lieyang Chen
Dissertations, Theses, and Capstone Projects
Drug discovery is a notoriously expensive and time-consuming process; hence, developing computational methods to facilitate the discovery process and lower the associated costs is a long-sought goal of computational chemists. Protein-ligand binding, which provides the physical and chemical basis for the mechanism of action of most drugs, occurs in an aqueous environment, and binding affinity is determined not only by atomic interactions between the protein and ligand but also by changes in their interactions with surrounding water molecules that occur upon binding. Thus, a quantitative understanding of the roles water molecules play in the protein-ligand binding process is an essential …
The Structural And Functional Role Of Photosensing In Rgs-Lov Proteins,
2021
CUNY Graduate Center
The Structural And Functional Role Of Photosensing In Rgs-Lov Proteins, Zaynab Jaber
Dissertations, Theses, and Capstone Projects
Light provides organisms with energy and spatiotemporal information. To survive and adapt, organisms have developed the ability to sense light to drive biochemical effects that underlie vision, entrainment of circadian rhythm, stress response, virulence, and many other important molecularly driven responses. Blue-light sensing Light-Oxygen-Voltage (LOV) domains are ubiquitous across multiple kingdoms of life and modulate various physiological events via diverse effector domains. Using a small molecule flavin chromophore, the LOV domain undergoes light-dependent structural changes leading to activation or repression of these catalytic and non-catalytic effectors. In silico analyses of high-throughput genomic sequencing data has led to the marked expansion …
The Role Of Estrogen Receptor Alpha In Regulating Messenger Rna 3’ End Processing And Controlling Gene Expression In Breast Cancer Cells,
2021
CUNY Graduate Center
The Role Of Estrogen Receptor Alpha In Regulating Messenger Rna 3’ End Processing And Controlling Gene Expression In Breast Cancer Cells, Sophia Varriano
Dissertations, Theses, and Capstone Projects
Estrogen signaling regulates various physiological processes within the female reproductive, cardiovascular, immune, and central nervous systems and is predominantly mediated by estrogen receptors (ER), ERα and ERβ. Transcriptional regulation by ERs has been widely studied, where activated ERs bind either directly to target genes through binding to estrogen response elements or indirectly through interacting with other proteins, resulting in changes in gene expression. However, the potential role of factors involved in the estrogen signaling pathway in posttranscriptional regulation has not been extensively documented. As 70-80% of breast cancers (BCs) are identified as ER(+), studying how these factors, particularly ERα, regulates …
