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  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
    Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
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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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  • Dissert 1 Title
    GENETIC AND BIOCHEMICAL ANALYSIS OF ESSENTIAL ENZYMES IN TRIACYLGLYCEROL SYNTHESIS IN ARABIDOPSIS By KIMBERLY LYNN COTTON A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Molecular Plant Sciences DECEMBER 2015 © Copyright by KIMBERLY LYNN COTTON, 2015 All Rights Reserved To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of KIMBERLY LYNN COTTON find it satisfactory and recommend that it be accepted. ____________________________________________ John A. Browse, Ph.D., Chair _____________________________________________ Michael M. Neff, Ph.D. _____________________________________________ Thomas W. Okita, Ph.D. _____________________________________________ John J. Wyrick, Ph.D. ii ACKNOWLEDGMENTS To my PI John Browse, thank you for your support, guidance and patience over the years. To my committee, John Browse, Michael Neff, Thomas Okita, and John Wyrick, thank you for your insightful discussions and suggestions. To my collaborators Jay Shockey, Anushobha Regmi, Neil Adhikari, John Browse, and Phil Bates, thanks for the great work and great times. To Browse Lab members past and present, thanks for the help, guidance and wonderful memories. To the undergraduate students who have helped me over the years, thank you for all your help in making this project possible; and with a special thank you to Arlene, Tesa, Breana, and “no-longer-undergrads” David and Barbara Cotton for their particular dedication to this project. And finally, a huge thank you to my family and friends who have loved and supported me throughout this venture. Go Cougs! iii GENETIC AND BIOCHEMICAL ANALYSIS OF ESSENTIAL ENZYMES IN TRIACYLGLYCEROL SYNTHESIS IN ARABIDOPSIS Abstract by Kimberly Lynn Cotton, Ph.D.
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  • Crystal Structure of the Targeting Endonuclease of the Human LINE-1 Retrotransposon
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure, Vol. 12, 975–986, June, 2004, 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.str.2004.04.011 Crystal Structure of the Targeting Endonuclease of the Human LINE-1 Retrotransposon Oliver Weichenrieder,1,* Kostas Repanas,1 transcriptase. Depending on the DNA integration mech- and Anastassis Perrakis* anism, two classes of retrotransposons are distin- The Netherlands Cancer Institute guished. The first class contains long terminal repeat Department of Molecular Carcinogenesis-H2 (LTR) retrotransposons and retroviruses. These retroele- Plesmanlaan 121 ments use an integrase that recognizes the LTRs of the 1066 CX Amsterdam double-stranded DNA copy. The second, much larger, The Netherlands and more ancient class includes all non-LTR retro- transposons. Those are thought to integrate via target- primed reverse transcription (TPRT), a process in which Summary reverse transcription and integration are coupled (Eick- bush and Malik, 2002; Kazazian, 2004). An endonuclease The human L1 endonuclease (L1-EN) is encoded by that is part of the same polypeptide chain as the reverse the non-LTR retrotransposon LINE-1 (L1). L1 is re- transcriptase nicks the genomic DNA and hands over sponsible for more than 1.5 million retrotransposition the resulting ribose 3Ј-hydroxyl end as a primer for re- events in the history of the human genome, contribut- verse transcription of associated template RNA (Cost ing more than a quarter to human genomic DNA (L1 et al., 2002; Luan et al., 1993). and Alu elements). L1-EN is related to the well-under- Most non-LTR retrotransposons encode an endonu- stood human DNA repair endonuclease APE1, and its clease located N-terminally of the reverse transcriptase.
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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 [email protected]. 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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  • Enzymatic Encoding Methods for Efficient Synthesis Of
    (19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN,
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  • Restriction Endonucleases
    Molecular Biology Problem Solver: A Laboratory Guide. Edited by Alan S. Gerstein Copyright © 2001 by Wiley-Liss, Inc. ISBNs: 0-471-37972-7 (Paper); 0-471-22390-5 (Electronic) 9 Restriction Endonucleases Derek Robinson, Paul R. Walsh, and Joseph A. Bonventre Background Information . 226 Which Restriction Enzymes Are Commercially Available? . 226 Why Are Some Enzymes More Expensive Than Others? . 227 What Can You Do to Reduce the Cost of Working with Restriction Enzymes? . 228 If You Could Select among Several Restriction Enzymes for Your Application, What Criteria Should You Consider to Make the Most Appropriate Choice? . 229 What Are the General Properties of Restriction Endonucleases? . 232 What Insight Is Provided by a Restriction Enzyme’s Quality Control Data? . 233 How Stable Are Restriction Enzymes? . 236 How Stable Are Diluted Restriction Enzymes? . 236 Simple Digests . 236 How Should You Set up a Simple Restriction Digest? . 236 Is It Wise to Modify the Suggested Reaction Conditions? . 237 Complex Restriction Digestions . 239 How Can a Substrate Affect the Restriction Digest? . 239 Should You Alter the Reaction Volume and DNA Concentration? . 241 Double Digests: Simultaneous or Sequential? . 242 225 Genomic Digests . 244 When Preparing Genomic DNA for Southern Blotting, How Can You Determine If Complete Digestion Has Been Obtained? . 244 What Are Your Options If You Must Create Additional Rare or Unique Restriction Sites? . 247 Troubleshooting . 255 What Can Cause a Simple Restriction Digest to Fail? . 255 The Volume of Enzyme in the Vial Appears Very Low. Did Leakage Occur during Shipment? . 259 The Enzyme Shipment Sat on the Shipping Dock for Two Days.
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  • Control Engineering Perspective on Genome-Scale Metabolic Modeling
    Control Engineering Perspective on Genome-Scale Metabolic Modeling by Andrew Louis Damiani A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama December 12, 2015 Key words: Scheffersomyces stipitis, Flux Balance Analysis, Genome-scale metabolic models, System Identification Framework, Model Validation, Phenotype Phase Plane Analysis Copyright 2015 by Andrew Damiani Approved by Jin Wang, Chair, Associate Professor of Chemical Engineering Q. Peter He, Associate Professor of Chemical Engineering, Tuskegee University Thomas W. Jeffries, Professor of Bacteriology, Emeritus; University of Wisconsin-Madison Allan E. David, Assistant Professor of Chemical Engineering Yoon Y. Lee, Professor of Chemical Engineering Abstract Fossil fuels impart major problems on the global economy and have detrimental effects to the environment, which has caused a world-wide initiative of producing renewable fuels. Lignocellulosic bioethanol for renewable energy has recently gained attention, because it can overcome the limitations that first generation biofuels impose. Nonetheless, in order to have this process commercialized, the biological conversion of pentose sugars, mainly xylose, needs to be improved. Scheffersomyces stipitis has a physiology that makes it a valuable candidate for lignocellulosic bioethanol production, and lately has provided genes for designing recombinant Saccharomyces cerevisiae. In this study, a system biology approach was taken to understand the relationship of the genotype to phenotype, whereby genome-scale metabolic models (GSMMs) are used in conjunction with constraint-based modeling. The major restriction of GSMMs is having an accurate methodology for validation and evaluation. This is due to the size and complexity of the models.
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  • Cell-Type-Specific Cytokinin Distribution Within The
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Spiral - Imperial College Digital Repository The Plant Cell, Vol. 27: 1955–1967, July 2015, www.plantcell.org ã 2015 American Society of Plant Biologists. All rights reserved. Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root ApexOPEN Ioanna Antoniadi,a,b,1 Lenka Placková, c,1 Biljana Simonovik,a Karel Dolezal, c Colin Turnbull,b Karin Ljung,a,2 and Ondrej Novákc,2,3 a Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden b Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom c Laboratory of Growth Regulators and Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR and Faculty of Science of Palacký University, Slechtitelu˚ 27, CZ-78371 Olomouc, Czech Republic ORCID IDs: 0000-0001-9053-2788 (I.A.); 0000-0003-2537-4933 (L.P.); 0000-0002-0929-0791 (B.S.); 0000-0001-6635-1418 (C.T.); 0000-0003-2901-189X (K.L.); 0000-0003-3452-0154 (O.N.) Cytokinins (CKs) play a crucial role in many physiological and developmental processes at the levels of individual plant components (cells, tissues, and organs) and by coordinating activities across these parts. High-resolution measurements of intracellular CKs in different plant tissues can therefore provide insights into their metabolism and mode of action. Here, we applied fluorescence-activated cell sorting of green fluorescent protein (GFP)-marked cell types, combined with solid-phase microextraction and an ultra-high-sensitivity mass spectrometry (MS) method for analysis of CK biosynthesis and homeostasis at cellular resolution.
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  • Substrate Channel Flexibility in Pseudomonas Aeruginosa Murb Accommodates Two Distinct Substrates
    Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates Ming Wei Chen1,2, Bernhard Lohkamp1, Robert Schnell1, Julien Lescar2, Gunter Schneider1* 1 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden, 2 School of Biological Sciences, Nanyang Technological University, Singapore, Singapore Abstract Biosynthesis of UDP-N-acetylmuramic acid in bacteria is a committed step towards peptidoglycan production. In an NADPH- and FAD-dependent reaction, the UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) reduces UDP-N-acetylgluco- samine-enolpyruvate to UDP-N-acetylmuramic acid. We determined the three-dimensional structures of the ternary complex of Pseudomonas aeruginosa MurB with FAD and NADP+ in two crystal forms to resolutions of 2.2 and 2.1 A˚, respectively, to investigate the structural basis of the first half-reaction, hydride transfer from NADPH to FAD. The nicotinamide ring of NADP+ stacks against the si face of the isoalloxazine ring of FAD, suggesting an unusual mode of hydride transfer to flavin. Comparison with the structure of the Escherichia coli MurB complex with UDP-N- acetylglucosamine-enolpyruvate shows that both substrates share the binding site located between two lobes of the substrate-binding domain III, consistent with a ping pong mechanism with sequential substrate binding. The nicotinamide and the enolpyruvyl moieties are strikingly well-aligned upon superimposition, both positioned for hydride transfer to and from FAD. However, flexibility of the substrate channel allows the non-reactive parts of the two substrates to bind in different conformations. A potassium ion in the active site may assist in substrate orientation and binding. These structural models should help in structure-aided drug design against MurB, which is essential for cell wall biogenesis and hence bacterial survival.
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  • Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
    Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4)
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  • Construction of Prognostic Microrna Signature for Human Invasive Breast Cancer by Integrated Analysis
    Journal name: OncoTargets and Therapy Article Designation: Original Research Year: 2019 Volume: 12 OncoTargets and Therapy Dovepress Running head verso: Shi et al Running head recto: Shi et al open access to scientific and medical research DOI: 189265 Open Access Full Text Article ORIGINAL RESEARCH Construction of prognostic microRNA signature for human invasive breast cancer by integrated analysis This article was published in the following Dove Medical Press journal: OncoTargets and Therapy Wei Shi* Background: Despite the advances in early detection and treatment methods, breast cancer Fang Dong* still has a high mortality rate, even in those patients predicted to have a good prognosis. The Yujia Jiang purpose of this study is to identify a microRNA signature that could better predict prognosis in Linlin Lu breast cancer and add new insights to the current classification criteria. Changwen Wang Materials and methods: We downloaded microRNA sequencing data along with correspond- Jie Tan ing clinicopathological data from The Cancer Genome Atlas (TCGA). Of 1,098 breast cancer patients identified, 253 patients with fully characterized microRNA profiles were selected for Wen Yang analysis. A three-microRNA signature was generated in the training set. Subsequently, the per- Hui Guo formance of the signature was confirmed in a validation set. After construction of the signature, Jie Ming* we conducted additional experiments, including flow cytometry and the Cell Counting Kit-8 Tao Huang* assay, to illustrate the correlation of this microRNA signature with breast cancer cell cycle, Department of Breast and Thyroid apoptosis, and proliferation. Surgery, Union Hospital, Tongji Results: Three microRNAs (hsa-mir-31, hsa-mir-16-2, and hsa-mir-484) were identified to Medical College, Huazhong University of Science and Technology, Wuhan be significantly and independently correlated with patient prognosis, and performed with good 430022, China stability.
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