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  • I HIGH MASS ACCURACY COUPLED to SPATIALLY-DIRECTED
    HIGH MASS ACCURACY COUPLED TO SPATIALLY-DIRECTED PROTEOMICS FOR IMPROVED PROTEIN IDENTIFICATIONS IN IMAGING MASS SPECTROMETRY EXPERIMENTS By David Geoffrey Rizzo Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry August, 2016 Nashville, Tennessee Approved: Richard M. Caprioli, Ph.D. Kevin L. Schey, Ph.D. John A. McLean, Ph.D. Michael P. Stone, Ph.D. i Copyright © 2016 by David Geoffrey Rizzo All Rights Reserved ii This work is dedicated to my family and friends, who have shown nothing but support for me in all of life’s endeavors. iii ACKNOWLEDGEMENTS “As we express our gratitude, we must never forget that the highest appreciation is not to utter words, but to live by them.” - John F. Kennedy – There are many people I must thank for showing kindness, encouragement, and support for me during my tenure as a graduate student. First and foremost, I would like to thank my research advisor, Richard Caprioli, for providing both ample resources and guidance that allowed me to grow as a scientist. Our discussions about my research and science in general have helped me become a much more focused and discerning analytical chemist. I must also thank my Ph.D. committee members, Drs. Kevin Schey, John McLean, and Michael Stone, who have brought valuable insight into my research and provided direction along the way. My undergraduate advisor, Dr. Facundo Fernández, encouraged me to begin research in his lab and introduced me to the world of mass spectrometry.
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  • In the Field of Clinical Examination, the Measurement of Creatine
    J. Clin. Biochem. Nutr., 3, 17-25, 1987 Bacterial Glucokinase as an Enzymic Reagent of Good Stability for Measurement of Creatine Kinase Activity Hitoshi KONDO, * Takanari SHIRAISHI, Masao KAGEYAMA, Kazuhiko NAGATA, and Kosuke TOMITA Research and Development Center, UNITIKA Ltd., Uji 611, Japan (Received January 10, 1987) Summary An enzymic reagent, that has long-term stability even in the liquid state, was successfully employed for the measurement of serum creatine kinase (CK, EC 2.7.3.2) activity. The enzyme used was the thermostable glucokinase (GlcK, EC 2.7.1.2) obtained from the thermo- phile Bacillus stearothermophilus. The reagent was found to be stable in solution for about one month at 6•Ž and for about one week at 30•Ž. This substitution of glucokinase for the hexokinase of the most commonly used hexokinase-glucose-6-phosphate dehydrogenase (HK-G6PDH) method results in a remarkable improvement of the method. The CK activity measured by the GlcK-G6PDH method was linear up to about 2,000 U/ liter at 37•Ž. The GlcK-G6PDH method was found to give a satisfactory precision and reproducibility (coefficient of variation less than 2.17%). Over a wide range of CK activity, an excellent agreement was obtained between the GlcK-G6PDH and the HK-G6PDH methods. Furthermore several coexistents and anticoagulants were found to have little effect on the measured value of CK activity by the GlcK-G6PDH method. Key Words: creatine kinase activity, glucokinase, improved stability of reagent, creatine kinase determination, thermostable enzyme In the field of clinical examination, the measurement of creatine kinase (CK, ATP : creatine phosphotransferase, EC 2.7.3.2) activity in serum is one of the important examinations usually employed for diagnosis of cardiac diseases such as myocardial infarction or muscular diseases such as progressive muscular dystrophy.
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  • Peroxidase Activity As an Indicator of the Iron Deficiency in Banana
    IndianJ Plant Physiol., Vol. 5, No.4, (N.S.) pp. 389-391 (Oct.-Dec., 2000) SHORT COMMUNICATION PEROXIDASE ACTIVITY AS AN INDICATOR OF THE IRON DEFICIENCY IN BANANA K. BALAKRISHNAN Department ofCrop Physiology, Horticultural College and Research Institute, Periyakulam - 625 604 Received on 30 Sept., 1998, Revised on 30 Nov., 2000 Effect oflime induced iron chlorosis on enzyme activities was studied in Banana cv. Rasthali. Iron content decreased progressively as the intensity of chlorosis increased. Iron content had positive correlation with catalase, peroxidase, acid phosphatase, polyphenol oxidase and nitrate reductase. Among the enzymes, the activityofperoxidasehad highest positivesignificant(r=997**) associationwith Fecontent. Hence, peroxidase activity could serve as a diagnostic tool to indentify the Fe deficiency/Fe status in Banana. Key words: Banana, chlorosis, iron, peroxidase Among the micrountrients, Fe deficiency is the most ofgreenness in sixmonths old crop. This leafwas used for widespread in ourcountry(Takkar, 1996). Iron deficiency all the physiological analysis viz chlorophyll (Yoshida et is very common in calcareous soils and hence termed as al., 1976) chlorophyllase (Almela et al., 1990), catalase, lime induced iron chlorosis. In a normal green plant 60% peroxidase and polyphenol oxidase (Kar and Mishra, ofall leafiron is present in the chlorophyIl and hence any 1976), acid phosphatase (Parida and Mishra, 1980) and reduction in Fe contentcauses chlorosis (Chen and Barak, nitrate reductase (Klepperetal., 1973). The Fe content of 1982). Iron deficiency in plant not only causes chlorosis the plant sample was estimated using atomic absorption because of its involvement in chlorophyll synthesis, but spectrophotometry. Data were subjected to simple also reduces the activity ofcertain enzymes viz., catalase correlation co-efficient.
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  • Phosphatidylinositol-3-Kinase in Tomato (Solanum Lycopersicum. L) Fruit and Its Role in Ethylene Signal Transduction and Senescence
    Phosphatidylinositol-3-Kinase in Tomato (Solanum lycopersicum. L) Fruit and Its Role in Ethylene Signal Transduction and Senescence by Mohd Sabri Pak Dek A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Mohd Sabri Pak Dek,June, 2015 ABSTRACT PHOSPHATIDYLINOSITOL-3-KINASE IN TOMATO (SOLANUM LYCOPERSICUM. L) FRUIT AND ITS ROLE IN ETHYLENE SIGNAL TRANSDUCTION AND SENESCENCE Mohd Sabri Pak Dek Co-Advisors: University of Guelph, 2015 Professor G. Paliyath Professor J. Subramanian The ripening process is initiated by ethylene through a signal transduction cascade leads to the expression of ripening-related genes and catabolism of membrane, cell wall, and storage components. One of the minor components in membrane phospholipids is phosphatidylinositol (PI). Phosphatidylinositol-3-kinase (PIK) is an enzyme that phosphorylates PI at the 3-OH position of inositol head group to produce phosphatidylinositol 3-phosphate (PI3P). Phosphorylation of PI may be an early event in the ethylene signal transduction pathway that generates negatively charged domains on the plasma membrane. PI3P domains may potentially serve as a docking site for phospholipase D (PLD) after ethylene stimulation. It is hypothesized that ethylene stimulation may activate PI3K resulting in enhanced level of phosphorylated phosphatidylinositol. However, the properties and function of PI3K is not well understood in plants. In the present study, the effect of PI3K inhibition during tomato fruit ripening was evaluated. This study demonstrated that PI3K activity is required for normal ripening process of the fruit. Inhibition of PI3K activity using wortmannin significantly reduced tomato ripening process.
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  • Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis
    Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact libcompass@vcu.edu. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing
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  • Structure-Function Analysis of the Catalytic Domain of the Histidine Kinase Chea
    Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 1997 Structure-Function Analysis of the Catalytic Domain of the Histidine Kinase Chea Dolph David Ellefson Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Microbiology Commons Recommended Citation Ellefson, Dolph David, "Structure-Function Analysis of the Catalytic Domain of the Histidine Kinase Chea" (1997). Dissertations. 3425. https://ecommons.luc.edu/luc_diss/3425 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact ecommons@luc.edu. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 1997 Dolph David Ellefson LOYOLA UNIVERSITY MEDICAL CENTER LIBRARY LOYOLA UNIVERSITY OF CHICAGO STRUCTURE-FUNCTION ANALYSIS OF THE CATALYTIC DOMAIN OF THE HISTIDINE KINASE CHEA A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF MICROBIOLOGY AND IMMUNOLOGY BY DOLPH DAVID ELLEFSON CHICAGO, ILLINOIS MAY, 1997 Copyright by Dolph David Ellefson, 1997 All Rights Reserved ii ACKNOWLEDGEMENTS I would like to thank my director, Dr. Alan J. Wolfe, for his support, advice, and encouragment during the many years in his laboratory. In his laboratory, I was given a rare opportunity to explore a new arena of science and interact with a field of gifted researchers who I would not known otherwise. I would also like to thank the members of my committee, Ors.
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  • Large XPF-Dependent Deletions Following Misrepair of a DNA Double Strand Break Are Prevented by the RNA:DNA Helicase Senataxin
    www.nature.com/scientificreports OPEN Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented Received: 26 October 2017 Accepted: 9 February 2018 by the RNA:DNA helicase Published: xx xx xxxx Senataxin Julien Brustel1, Zuzanna Kozik1, Natalia Gromak2, Velibor Savic3,4 & Steve M. M. Sweet1,5 Deletions and chromosome re-arrangements are common features of cancer cells. We have established a new two-component system reporting on epigenetic silencing or deletion of an actively transcribed gene adjacent to a double-strand break (DSB). Unexpectedly, we fnd that a targeted DSB results in a minority (<10%) misrepair event of kilobase deletions encompassing the DSB site and transcribed gene. Deletions are reduced upon RNaseH1 over-expression and increased after knockdown of the DNA:RNA helicase Senataxin, implicating a role for DNA:RNA hybrids. We further demonstrate that the majority of these large deletions are dependent on the 3′ fap endonuclease XPF. DNA:RNA hybrids were detected by DNA:RNA immunoprecipitation in our system after DSB generation. These hybrids were reduced by RNaseH1 over-expression and increased by Senataxin knock-down, consistent with a role in deletions. Overall, these data are consistent with DNA:RNA hybrid generation at the site of a DSB, mis-processing of which results in genome instability in the form of large deletions. DNA is the target of numerous genotoxic attacks that result in diferent types of damage. DNA double-strand breaks (DSBs) occur at low frequency, compared with single-strand breaks and other forms of DNA damage1, however DSBs pose the risk of translocations and deletions and their repair is therefore essential to cell integrity.
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  • Labeled in Thecourse of Glycolysis, Since Phosphoglycerate Kinase
    THE STATE OF MAGNESIUM IN CELLS AS ESTIMATED FROM THE ADENYLATE KINASE EQUILIBRIUM* BY TRWIN A. RoSE THE INSTITUTE FOR CANCER RESEARCH, PHILADELPHIA Communicated by Thomas F. Anderson, August 30, 1968 Magnesium functions in many enzymatic reactions as a cofactor and in com- plex with nucleotides acting as substrates. Numerous examples of a possible regulatory role of Mg can be cited from studies with isolated enzymes,'- and it is known that Mg affects the structural integrity of macromolecules such as trans- fer RNA" and functional elements such as ribosomes.'0 The major problem in translating this information on isolated preparations to the functioning cell is the difficulty in determining the distribution of Mg and the nucleotides among the free and complexed forms that function in the region of the cell for which this information is desired. Nanningall based an attempt to calculate the free Mg2+ and Ca2+ ion concentrations of frog muscle on the total content of these metals and of the principal known ligands (adenosine 5'-triphosphate (ATP), creatine-P, and myosin) and the dissociation constants of the complexes. However, this method suffers from the necessity of evaluating the contribution of all ligands as well as from the assumption that all the known ligands are contributing their full complexing capacity. During studies concerned with the control of glycolysis in red cells and the control of the phosphoglycerate kinase step in particular, it became important to determine the fractions of the cell's ATP and adenosine 5'-diphosphate (ADP) that were present as Mg complexes. Just as the problem of determining the distribution of protonated and dissociated forms of an acid can be solved from a knowledge of pH and pKa of the acid, so it would be possible to determine the liganded and free forms of all rapidly established Mg complexes from a knowledge of Mg2+ ion concentration and the appropriate dissociation constants.
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  • Phosphate Steering by Flap Endonuclease 1 Promotes 50-flap Specificity and Incision to Prevent Genome Instability
    ARTICLE Received 18 Jan 2017 | Accepted 5 May 2017 | Published 27 Jun 2017 DOI: 10.1038/ncomms15855 OPEN Phosphate steering by Flap Endonuclease 1 promotes 50-flap specificity and incision to prevent genome instability Susan E. Tsutakawa1,*, Mark J. Thompson2,*, Andrew S. Arvai3,*, Alexander J. Neil4,*, Steven J. Shaw2, Sana I. Algasaier2, Jane C. Kim4, L. David Finger2, Emma Jardine2, Victoria J.B. Gotham2, Altaf H. Sarker5, Mai Z. Her1, Fahad Rashid6, Samir M. Hamdan6, Sergei M. Mirkin4, Jane A. Grasby2 & John A. Tainer1,7 DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 50-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 50-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 50polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 50-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 50-flap specificity and catalysis, preventing genomic instability. 1 Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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  • Mapping Active Site Residues in Glutamate-5-Kinase. the Substrate Glutamate and the Feed-Back Inhibitor Proline Bind at Overlapping Sites
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 580 (2006) 6247–6253 Mapping active site residues in glutamate-5-kinase. The substrate glutamate and the feed-back inhibitor proline bind at overlapping sites Isabel Pe´rez-Arellanoa, Vicente Rubiob, Javier Cerveraa,* a Centro de Investigacio´n Prı´ncipe Felipe, Avda. Autopista del Saler, 16, Valencia 46013, Spain b Instituto de Biomedicina de Valencia (IBV-CSIC), Jaime Roig 11, Valencia 46010, Spain Received 22 August 2006; revised 10 October 2006; accepted 12 October 2006 Available online 20 October 2006 Edited by Stuart Ferguson (a domain named after pseudo uridine synthases and archaeo- Abstract Glutamate-5-kinase (G5K) catalyzes the controlling first step of proline biosynthesis. Substrate binding, catalysis sine-specific transglycosylases) domain [10]. AAK domains and feed-back inhibition by proline are functions of the N-termi- bind ATP and a phosphorylatable acidic substrate, and make nal 260-residue domain of G5K. We study here the impact on a phosphoric anhydride [11]. The function of the PUA domain these functions of 14 site-directed mutations affecting 9 residues (a domain characteristically found in some RNA-modifying of Escherichia coli G5K, chosen on the basis of the structure of enzymes) [12] is not known. By deleting the PUA domain of the bisubstrate complex of the homologous enzyme acetylgluta- E. coli G5K we showed [10] that the isolated AAK domain, mate kinase (NAGK). The results support the predicted roles as the complete enzyme, forms tetramers, catalyzes the reac- of K10, K217 and T169 in catalysis and ATP binding and of tion and is feed-back inhibited by proline.
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  • Negative Regulation of Diacylglycerol Kinase &Theta
    Cell Death and Differentiation (2010) 17, 1059–1068 & 2010 Macmillan Publishers Limited All rights reserved 1350-9047/10 $32.00 www.nature.com/cdd Negative regulation of diacylglycerol kinase h mediates adenosine-dependent hepatocyte preconditioning G Baldanzi1,5, E Alchera2,5, C Imarisio2, M Gaggianesi1, C Dal Ponte2, M Nitti3, C Domenicotti3, WJ van Blitterswijk4, E Albano2, A Graziani1,5 and R Carini*,2,5 In liver ischemic preconditioning (IP), stimulation of adenosine A2a receptors (A2aR) prevents ischemia/reperfusion injury by promoting diacylglycerol-mediated activation of protein kinase C (PKC). By concerting diacylglycerol to phosphatidic acid, diacylglycerol kinases (DGKs) act as terminator of diacylglycerol signalling. This study investigates the role of DGK in the development of hepatocyte IP. DGK activity and cell viability were evaluated in isolated rat hepatocytes preconditioned by 10 min hypoxia followed by 10 min re-oxygenation or by the treatment with the A2aR agonist, CGS21680, and subsequently exposed to prolonged hypoxia. We observed that after IP or A2aR activation, a decrease in DGK activity was associated with the onset of hepatocyte tolerance to hypoxia. CGS21680-induced stimulation of A2aR specifically inhibited DGK isoform h by activating RhoA–GTPase. Consistently, both siRNA-mediated downregulation of DGK h and hepatocyte pretreatment with the DGK inhibitor R59949 induced cell tolerance to hypoxia. The pharmacological inhibition of DGK was associated with the diacylglycerol- dependent activation of PKC d and e and of their downstream target p38 MAPK. In conclusion, we unveil a novel signalling pathway contributing to the onset of hepatocyte preconditioning, which through RhoA–GTPase, couples A2aR to the downregulation of DGK.
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  • Yeast Genome Gazetteer P35-65
    gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal
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