Aquaculture Journals – Table of Contents April 2012
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Martian Crater Morphology
ANALYSIS OF THE DEPTH-DIAMETER RELATIONSHIP OF MARTIAN CRATERS A Capstone Experience Thesis Presented by Jared Howenstine Completion Date: May 2006 Approved By: Professor M. Darby Dyar, Astronomy Professor Christopher Condit, Geology Professor Judith Young, Astronomy Abstract Title: Analysis of the Depth-Diameter Relationship of Martian Craters Author: Jared Howenstine, Astronomy Approved By: Judith Young, Astronomy Approved By: M. Darby Dyar, Astronomy Approved By: Christopher Condit, Geology CE Type: Departmental Honors Project Using a gridded version of maritan topography with the computer program Gridview, this project studied the depth-diameter relationship of martian impact craters. The work encompasses 361 profiles of impacts with diameters larger than 15 kilometers and is a continuation of work that was started at the Lunar and Planetary Institute in Houston, Texas under the guidance of Dr. Walter S. Keifer. Using the most ‘pristine,’ or deepest craters in the data a depth-diameter relationship was determined: d = 0.610D 0.327 , where d is the depth of the crater and D is the diameter of the crater, both in kilometers. This relationship can then be used to estimate the theoretical depth of any impact radius, and therefore can be used to estimate the pristine shape of the crater. With a depth-diameter ratio for a particular crater, the measured depth can then be compared to this theoretical value and an estimate of the amount of material within the crater, or fill, can then be calculated. The data includes 140 named impact craters, 3 basins, and 218 other impacts. The named data encompasses all named impact structures of greater than 100 kilometers in diameter. -
Conformational Landscapes of Halohydrin Dehalogenases and Their Accessible Active Site Tunnels
catalysts Article Conformational Landscapes of Halohydrin Dehalogenases and Their Accessible Active Site Tunnels 1 1, , 1,2, Miquel Estévez-Gay , Javier Iglesias-Fernández * y and Sílvia Osuna * 1 CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain; [email protected] 2 ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain * Correspondence: [email protected] (J.I.-F.); [email protected] (S.O.) Present address: Nostrum Biodiscovery, Carrer de Baldiri Reixac, 10–12, 08028 Barcelona, Catalonia, Spain. y Received: 12 November 2020; Accepted: 28 November 2020; Published: 1 December 2020 Abstract: Halohydrin dehalogenases (HHDH) are industrially relevant biocatalysts exhibiting a promiscuous epoxide-ring opening reactivity in the presence of small nucleophiles, thus giving access to novel carbon–carbon, carbon–oxygen, carbon–nitrogen, and carbon–sulfur bonds. Recently, the repertoire of HHDH has been expanded, providing access to some novel HHDH subclasses exhibiting a broader epoxide substrate scope. In this work, we develop a computational approach based on the application of linear and non-linear dimensionality reduction techniques to long time-scale Molecular Dynamics (MD) simulations to study the HHDH conformational landscapes. We couple the analysis of the conformational landscapes to CAVER calculations to assess their impact on the active site tunnels and potential ability towards bulky epoxide ring opening reaction. Our study indicates that the analyzed HHDHs subclasses share a common breathing motion of the halide binding pocket, but present large deviations in the loops adjacent to the active site pocket and N-terminal regions. -
Molecular Basis of Two Novel Dehalogenating Activities in Bacteria
Molecular basis of two novel dehalogenating activities in bacteria Structure/function relationships in an evolutionary context 1 Foto’s omslag: Dinanda Lutikhedde, MFA Druk: Digital Printing Partners Utrecht bv The research presented in this work was performed in the protein crystallography group at the Laboratory of Biophysical Chemistry of the University of Groningen. This work was supported by The Netherlands Foundation of Chemical Research (CW) with financial aid from The Netherlands Foundation for Scientific Research (NWO). 2 RIJKSUNIVERSITEIT GRONINGEN Molecular basis of two novel dehalogenating activities in bacteria Structure/function relationships in an evolutionary context Proefschrift ter verkrijging van het doctoraat in de Wiskunde en Natuurwetenschappen aan de Rijksuniversiteit Groningen op gezag van de Rector Magnificus, dr. F. Zwarts, in het openbaar te verdedigen op vrijdag 30 januari 2004 om 14.15 uur door René Marcel de Jong geboren op 22 maart 1976 te Heerenveen 3 Promotor: Prof. dr. B. W. Dijkstra Beoordelingscommissie: Prof. dr. D. B. Janssen Prof. dr. A. E. Mark Prof. dr. J.B.F.N. Engberts 4 CONTENTS CHAPTER 1: GENERAL INTRODUCTION ..........................................................9 EVOLUTION IN THE MICROBIAL WORLD.................................................................................. 10 EVOLUTION AT THE MOLECULAR LEVEL................................................................................. 12 BACTERIAL DEHALOGENATING ACTIVITY TOWARDS ANTHROPOGENIC COMPOUNDS ................... 14 SCOPE -
Appendix I Lunar and Martian Nomenclature
APPENDIX I LUNAR AND MARTIAN NOMENCLATURE LUNAR AND MARTIAN NOMENCLATURE A large number of names of craters and other features on the Moon and Mars, were accepted by the IAU General Assemblies X (Moscow, 1958), XI (Berkeley, 1961), XII (Hamburg, 1964), XIV (Brighton, 1970), and XV (Sydney, 1973). The names were suggested by the appropriate IAU Commissions (16 and 17). In particular the Lunar names accepted at the XIVth and XVth General Assemblies were recommended by the 'Working Group on Lunar Nomenclature' under the Chairmanship of Dr D. H. Menzel. The Martian names were suggested by the 'Working Group on Martian Nomenclature' under the Chairmanship of Dr G. de Vaucouleurs. At the XVth General Assembly a new 'Working Group on Planetary System Nomenclature' was formed (Chairman: Dr P. M. Millman) comprising various Task Groups, one for each particular subject. For further references see: [AU Trans. X, 259-263, 1960; XIB, 236-238, 1962; Xlffi, 203-204, 1966; xnffi, 99-105, 1968; XIVB, 63, 129, 139, 1971; Space Sci. Rev. 12, 136-186, 1971. Because at the recent General Assemblies some small changes, or corrections, were made, the complete list of Lunar and Martian Topographic Features is published here. Table 1 Lunar Craters Abbe 58S,174E Balboa 19N,83W Abbot 6N,55E Baldet 54S, 151W Abel 34S,85E Balmer 20S,70E Abul Wafa 2N,ll7E Banachiewicz 5N,80E Adams 32S,69E Banting 26N,16E Aitken 17S,173E Barbier 248, 158E AI-Biruni 18N,93E Barnard 30S,86E Alden 24S, lllE Barringer 29S,151W Aldrin I.4N,22.1E Bartels 24N,90W Alekhin 68S,131W Becquerei -
In Pdf Format
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(12) United States Patent (10) Patent No.: US 7,381,538 B2 Reardon Et Al
US007381538B2 (12) United States Patent (10) Patent No.: US 7,381,538 B2 Reardon et al. (45) Date of Patent: Jun. 3, 2008 (54) OPTICAL BIOSENSOR WITH ENHANCED 6,060,327 A * 5/2000 Keen ..................... 204,403.14 ACTIVITY RETENTION FOR DETECTION 6,159,681 A 12/2000 Zebala .......................... 435/4 OF HALOGENATED ORGANIC COMPOUNDS OTHER PUBLICATIONS Derek W. Campbell, entitled “The Development of Biosensors for (75) Inventors: Kenneth F. Reardon, Fort Collins, CO the Detection of Halogenated Groundwater Contaminants,” avail (US); Neema Das, Murgeshpalya (IN) able from Morgan Library at the CSU in Fort Collins, Colorado, having been submitted by Derek W. Campbell in fulfillment of the (73) Assignee: Colorado State University Research requirements for the Degree of Master of Science at Colorado State Foundation (CSURF), Fort Collins, University, Spring 1998 (labeled “Attachment B” of applicants' CO (US) provisional app. filed Jun. 1, 2001 as containing general background technical information}. (*) Notice: Subject to any disclaimer, the term of this inst k Eyle A. PS SEE s past l S.s I listed under 35 12,alogenated 1998 by Reardonflydrocarbons, and Campbell, U.S. Appl. 7 pages No. (labeled,89U, “Attachment Illed Sep. M YW- (b) by ayS. C” of applicants’pp pprovisional app.pp filed Jun. 1, 2001 as containin9. general background technical information}. (21) Appl. No.: 10/478,822 Cord Müller. F. Schubert. T. Scheper,p "Multicomponentp fiberopticalp biosensor for use in hemodialysis monitoring.” Proc. SPIE vol. (22) PCT Filed: Jun. 1, 2002 2131, 555-562 Biomedical Fiber Optic Instrumentation(Jul 1994) {referenced as “Cord Müller, et al.” in applicants’ provisional app. -
PROGRAM SCHEDULE (Oral Presentations)
PROGRAM SCHEDULE (Oral Presentations) ID Title Session Time Room Date Speaker Authors 40SS - Passive control systems: Equivalent static analysis for structures with Giada Gasparini, Michele Palermo, Luca Landi, 2030 analysis methods and designing 10:30 - 10:45 Vitacura Room (1) Monday, January 9th Michele Palermo added viscous dampers Stefano Silvestri, Tomaso Trombetti procedures 40SS - Passive control systems: A General Design Method for Buildings with JUAN CARLOS DE LA 1187 analysis methods and designing 10:45 - 11:00 Vitacura Room (1) Monday, January 9th JUAN C. DE LA LLERA, JUAN J. BESA Energy Dissipation Devices LLERA procedures IMPORTANCE OF DUCTILE CONFINEMENT IN 40SS - Passive control systems: Horacio J. Nangullasmu- 3327 REINFORCED CONCRETE FRAMES WITH analysis methods and designing 11:00 - 11:15 Vitacura Room (1) Monday, January 9th Horacio Nangullasmu, Arturo Tena Hernandez STRUCTURAL FUSES procedures 40SS - Passive control systems: NEW SEISMIC RESPONSE CONTROL SYSTEM 1652 analysis methods and designing 11:15 - 11:30 Vitacura Room (1) Monday, January 9th Taiki SAITO Taiki SAITO, Satoshi DENNO, Toshio Maekawa USING BLOCK AND TACKLE procedures 40SS - Passive control systems: Eccentric Lever Arm Amplification System for 3870 analysis methods and designing 11:30 - 11:45 Vitacura Room (1) Monday, January 9th Jose Almazan Jose Almazan, Nicolas Tapia, Juan Baquero Frictional Energy Dissipation Devices procedures Experimental Study on the Seismic Performance 40SS - Passive control systems: 1223 of Four-Tower High-rise with an isolated -
Wo 2008/127291 A2
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date PCT (10) International Publication Number 23 October 2008 (23.10.2008) WO 2008/127291 A2 (51) International Patent Classification: Jeffrey, J. [US/US]; 106 Glenview Drive, Los Alamos, GOlN 33/53 (2006.01) GOlN 33/68 (2006.01) NM 87544 (US). HARRIS, Michael, N. [US/US]; 295 GOlN 21/76 (2006.01) GOlN 23/223 (2006.01) Kilby Avenue, Los Alamos, NM 87544 (US). BURRELL, Anthony, K. [NZ/US]; 2431 Canyon Glen, Los Alamos, (21) International Application Number: NM 87544 (US). PCT/US2007/021888 (74) Agents: COTTRELL, Bruce, H. et al.; Los Alamos (22) International Filing Date: 10 October 2007 (10.10.2007) National Laboratory, LGTP, MS A187, Los Alamos, NM 87545 (US). (25) Filing Language: English (81) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of national protection available): AE, AG, AL, AM, AT,AU, AZ, BA, BB, BG, BH, BR, BW, BY,BZ, CA, CH, (30) Priority Data: CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, 60/850,594 10 October 2006 (10.10.2006) US ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, (71) Applicants (for all designated States except US): LOS LR, LS, LT, LU, LY,MA, MD, ME, MG, MK, MN, MW, ALAMOS NATIONAL SECURITY,LLC [US/US]; Los MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PG, PH, PL, Alamos National Laboratory, Lc/ip, Ms A187, Los Alamos, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, NM 87545 (US). -
University of Groningen Biocatalytic Conversion of Epoxides De Vries, Erik
University of Groningen Biocatalytic conversion of epoxides de Vries, Erik; Janssen, DB Published in: Current Opinion in Biotechnology DOI: 10.1016/S0958-1669(03)00102-2 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2003 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): de Vries, E., & Janssen, DB. (2003). Biocatalytic conversion of epoxides. Current Opinion in Biotechnology, 14(4), 414-420. https://doi.org/10.1016/S0958-1669(03)00102-2 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. -
Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in The
1 Bioremediation 3.0: Engineering pollutant-removing bacteria 2 in the times of systemic biology 3 4 by 5 6 Pavel Dvořák1, Pablo I. Nikel2, Jiří Damborský3,4, Víctor de Lorenzo1# 7 8 1 Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 9 28049 Madrid, Spain 10 2 The Novo Nordisk Foundation Center for Biosustainability, 2800 Lyngby, Denmark 11 3 Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX 12 and Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 13 Brno, Czech Republic 14 4 International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 15 91 Brno, Czech Republic 16 17 # E-mail: [email protected], Tel.: +34 91-585 4536 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 1 1 2 3 4 Table of Contents 5 6 1. Introduction 7 2. Approaches and tools of systems biology and metabolic engineering for tailoring 8 biodegradation pathways 9 2.1 Step 1: Get to know the contaminant and find a suitable catabolic pathway 10 2.1.1 Databases 11 2.1.2 Pathway prediction systems and toxicity prediction algorithms 12 2.1.3 Detection and quantification of pathway building blocks 13 2.2 Step2: Select and get to know a suitable microbial host 14 2.2.1 Omic techniques in studies of bacterial degraders 15 2.3 Step 3: Build the pathway and optimize its performance in the context of host 16 metabolism 17 2.3.1 Computational tools for pathway and strain optimization 18 2.3.2 Experimental tools for pathway and strain optimization 19 2.3.3 Protein engineering to eliminate bottlenecks of biodegradation pathways 20 3. -
148240825.Pdf
University of Groningen Novel Dehalogenase Mechanism for 2,3-Dichloro-1-Propanol Utilization in Pseudomonas putida Strain MC4 Arif, Muhammad Ilan; Samin, Ghufrana; van Leeuwen, Jan G. E.; Oppentocht, Jantina; Janssen, Dick Published in: Applied and Environmental Microbiology DOI: 10.1128/AEM.00760-12 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2012 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Arif, M. I., Samin, G., van Leeuwen, J. G. E., Oppentocht, J., & Janssen, D. B. (2012). Novel Dehalogenase Mechanism for 2,3-Dichloro-1-Propanol Utilization in Pseudomonas putida Strain MC4. Applied and Environmental Microbiology, 78(17), 6128-6136. DOI: 10.1128/AEM.00760-12 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 11-02-2018 Novel Dehalogenase Mechanism for 2,3-Dichloro-1-Propanol Utilization in Pseudomonas putida Strain MC4 Muhammad Irfan Arif, Ghufrana Samin,* Jan G. -
Newsletter 61
Society News Editorial diatoms to infer past physical oceanographic processes and also investigated the effects that diatoms can have The outgoing editor on sediment fabric and opal preservation in marine This will be the final issue of the newsletter edited by sediments. If asked over a beer what she dislikes most me. Jenny Pike from Cardiff University takes over from about micropalaeontology Jenny would probably reply issue 62 and I wish her success for the future. In a “systematics and taxonomy” which she regards as an final vain attempt at injecting some news into the essential evil, closely followed by “hours of staring newsletter, this issue introduces a new column entitled down the microscope”!! Jenny is currently a Lecturer what the papers say that is intended to summarise in Marine Geoscience at Cardiff University teaching articles of interest to all facets of micropalaeontology. Introductory Micropalaeontology to second year The first column is definitely foram-centric, but this undergraduates. fairly reflects a group in which much exciting research By building on previous efforts to set up a of global interest is being undertaken. I am sure that specialist siliceous microfossil group in the BMS, Jenny, Jenny will be only too pleased to receive unsolicited together with John Gregory, has introduced the reviews of recently published papers that are of broad Silicofossil Group to the Society at the 1998 AGM. An interest to our membership. inaugural meeting was held in September 1999 and it Finally, I have a couple of books available for is hoped that this group will continue to be as success- review in the newsletter, if any of you fancy filling up ful as the other specialist groups.