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King RA, Schreiner PR, Crawford TD. Structure of [18]Annulene Revisited: Challenges for Computing Benzenoid Systems. J Phys Chem A 2024; 128:1098-1108. [PMID: 38306465 PMCID: PMC10875677 DOI: 10.1021/acs.jpca.3c07797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/04/2024]
Abstract
For cyclic conjugated structures, erratic computational results have been obtained with Hartree-Fock (HF) molecular orbital (MO) methods as well as density functional theory (DFT) with large HF-exchange contributions. In this work, the reasons for this unreliability are explored. Extensive computations on [18]annulene and related compounds highlight the pitfalls to be avoided and the due diligence required for such computational investigations. In particular, a careful examination of the MO singlet-stability eigenvalues is recommended. The appearance of negative eigenvalues is not (necessarily) problematic, but near-zero (positive or negative) eigenvalues can lead to dramatic errors in vibrational frequencies and related properties. DFT approaches with a lower HF admixture generally appear more robust in this regard for the description of benzenoid structures, although they may exaggerate the tendency toward planarity and C-C bond-equalization. For the iconic [18]annulene, the results support a nonplanar equilibrium structure. The density-fitted frozen natural orbital coupled-cluster singles and doubles with perturbative triples [DF-FNO CCSD(T)] method of electron correlation with an aug-pVQZ/aug-pVTZ basis set places the C2 global minimum 1.1 kcal mol-1 below the D6h stationary point.
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Affiliation(s)
- Rollin A. King
- Department
of Chemistry, Bethel University, St. Paul, Minnesota 55112, United States
| | - Peter R. Schreiner
- Institute
of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - T. Daniel Crawford
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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2
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Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, Hurtado AG, Kraus P, Kruse H, Lee SJR, Misiewicz JP, Naden LN, Ramezanghorbani F, Scheurer M, Schriber JB, Simmonett AC, Steinmetzer J, Wagner JR, Ward L, Welborn M, Altarawy D, Anwar J, Chodera JD, Dreuw A, Kulik HJ, Liu F, Martínez TJ, Matthews DA, Schaefer HF, Šponer J, Turney JM, Wang LP, De Silva N, King RA, Stanton JF, Gordon MS, Windus TL, Sherrill CD, Burns LA. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. J Chem Phys 2021; 155:204801. [PMID: 34852489 DOI: 10.1063/5.0059356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
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Affiliation(s)
- Daniel G A Smith
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | | | - Zachary L Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Jiyoung Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Taylor A Barnes
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Carlos H Borca
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - David L Dotson
- Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Alexander G Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Michael F Herbst
- Applied and Computational Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - Jan Hermann
- FU Berlin, Department of Mathematics and Computer Science, 14195 Berlin, Germany
| | - Colton B Hicks
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joshua T Horton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Adrian G Hurtado
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-5250, USA
| | - Peter Kraus
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth 6845, WA, Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | | | - Jonathon P Misiewicz
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Levi N Naden
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | | | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jeffrey B Schriber
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health-National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Johannes Steinmetzer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Jeffrey R Wagner
- Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Logan Ward
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Matthew Welborn
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Doaa Altarawy
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Fang Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Todd J Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Devin A Matthews
- The Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California Davis, Davis, California 95616, USA
| | - Nuwan De Silva
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, USA
| | - John F Stanton
- Quantum Theory Project, The University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Theresa L Windus
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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3
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Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, Schriber JB, Xie Y, Glick ZL, Sirianni DA, O’Brien JS, Waldrop JM, Kumar A, Hohenstein EG, Pritchard BP, Brooks BR, Schaefer HF, Sokolov AY, Patkowski K, DePrince AE, Bozkaya U, King RA, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.4: Open-source software for high-throughput quantum chemistry. J Chem Phys 2020; 152:184108. [PMID: 32414239 PMCID: PMC7228781 DOI: 10.1063/5.0006002] [Citation(s) in RCA: 301] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
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Affiliation(s)
| | - Lori A. Burns
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew C. Simmonett
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Robert M. Parrish
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Matthew C. Schieber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | | | - Peter Kraus
- School of Molecular and Life Sciences, Curtin
University, Kent St., Bentley, Perth, Western Australia 6102,
Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of
Sciences, Královopolská 135, 612 65 Brno, Czech
Republic
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical
and Computational Chemistry, UiT, The Arctic University of Norway, N-9037
Tromsø, Norway
| | - Asem Alenaizan
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew M. James
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Susi Lehtola
- Department of Chemistry, University of
Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki,
Finland
| | - Jonathon P. Misiewicz
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific
Computing, Heidelberg University, D-69120 Heidelberg,
Germany
| | - Robert A. Shaw
- ARC Centre of Excellence in Exciton Science,
School of Science, RMIT University, Melbourne, VIC 3000,
Australia
| | - Jeffrey B. Schriber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Yi Xie
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Zachary L. Glick
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Dominic A. Sirianni
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Joseph Senan O’Brien
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Jonathan M. Waldrop
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - Ashutosh Kumar
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Edward G. Hohenstein
- SLAC National Accelerator Laboratory, Stanford
PULSE Institute, Menlo Park, California 94025,
USA
| | | | - Bernard R. Brooks
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and Biochemistry, The
Ohio State University, Columbus, Ohio 43210, USA
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry,
Florida State University, Tallahassee, Florida 32306-4390,
USA
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe
University, Ankara 06800, Turkey
| | - Rollin A. King
- Department of Chemistry, Bethel
University, St. Paul, Minnesota 55112, USA
| | | | - Justin M. Turney
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | | | - C. David Sherrill
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
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4
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Schutt KA, King RA, Tiede C, Jankowski V, John V, Trehan A, Simmons K, Ponnambalam S, Fishwick CWG, McPherson MJ, Tomlinson DC, Ajjan RA. 5068A novel methodology to improve prolonged clot lysis in diabetes. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.5068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- K A Schutt
- RWTH University Hospital Aachen, Internal Medicine I, Cardiology, Pulmonology & Vascular Medicine, Aachen, Germany
| | - R A King
- University of Leeds, Leeds Institute for Cardiovascular and Metabolic Medicine, Leeds, United Kingdom
| | - C Tiede
- University of Leeds, Bioscreening Technology Group in the School of Molecular and Cellular Biology, Leeds, United Kingdom
| | - V Jankowski
- RWTH Aachen University, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | - V John
- University of Leeds, Leeds Institute for Cardiovascular and Metabolic Medicine, Leeds, United Kingdom
| | - A Trehan
- University of Leeds, Leeds Institute for Cardiovascular and Metabolic Medicine, Leeds, United Kingdom
| | - K Simmons
- University of Leeds, School of Chemistry, Leeds, United Kingdom
| | - S Ponnambalam
- University of Leeds, School of Molecular & Cellular Biology, Leeds, United Kingdom
| | - C W G Fishwick
- University of Leeds, School of Chemistry, Leeds, United Kingdom
| | - M J McPherson
- University of Leeds, Bioscreening Technology Group in the School of Molecular and Cellular Biology, Leeds, United Kingdom
| | - D C Tomlinson
- University of Leeds, Bioscreening Technology Group in the School of Molecular and Cellular Biology, Leeds, United Kingdom
| | - R A Ajjan
- University of Leeds, Leeds Institute for Cardiovascular and Metabolic Medicine, Leeds, United Kingdom
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5
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Smith DGA, Burns LA, Sirianni DA, Nascimento DR, Kumar A, James AM, Schriber JB, Zhang T, Zhang B, Abbott AS, Berquist EJ, Lechner MH, Cunha LA, Heide AG, Waldrop JM, Takeshita TY, Alenaizan A, Neuhauser D, King RA, Simmonett AC, Turney JM, Schaefer HF, Evangelista FA, DePrince AE, Crawford TD, Patkowski K, Sherrill CD. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development. J Chem Theory Comput 2018; 14:3504-3511. [DOI: 10.1021/acs.jctc.8b00286] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel G. A. Smith
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Lori A. Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Dominic A. Sirianni
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Daniel R. Nascimento
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Andrew M. James
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jeffrey B. Schriber
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Tianyuan Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Boyi Zhang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Adam S. Abbott
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Eric J. Berquist
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marvin H. Lechner
- Department of Chemistry, Technical University of Munich, 80333 Munich, Germany
| | - Leonardo A. Cunha
- The Technical Institute of Aeronautics, São José dos Campos, 12228-900, Brazil
| | - Alexander G. Heide
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, United States
| | - Jonathan M. Waldrop
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Tyler Y. Takeshita
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Daniel Neuhauser
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Rollin A. King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, United States
| | - Andrew C. Simmonett
- National Institutes of Health - National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Justin M. Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - T. Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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6
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Ikediashi C, Paris JR, King RA, Beaumont WRC, Ibbotson A, Stevens JR. Atlantic salmon Salmo salar in the chalk streams of England are genetically unique. J Fish Biol 2018; 92:621-641. [PMID: 29385651 DOI: 10.1111/jfb.13538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/14/2017] [Indexed: 06/07/2023]
Abstract
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.
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Affiliation(s)
- C Ikediashi
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - J R Paris
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - R A King
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - W R C Beaumont
- Salmon & Trout Research Centre, Game & Wildlife Conservation Trust (GWCT), East Stoke, Wareham, Dorset BH20 6BB, U.K
| | - A Ibbotson
- Salmon & Trout Research Centre, Game & Wildlife Conservation Trust (GWCT), East Stoke, Wareham, Dorset BH20 6BB, U.K
| | - J R Stevens
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
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7
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Parrish RM, Burns LA, Smith DGA, Simmonett AC, DePrince AE, Hohenstein EG, Bozkaya U, Sokolov AY, Di Remigio R, Richard RM, Gonthier JF, James AM, McAlexander HR, Kumar A, Saitow M, Wang X, Pritchard BP, Verma P, Schaefer HF, Patkowski K, King RA, Valeev EF, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. J Chem Theory Comput 2017; 13:3185-3197. [PMID: 28489372 PMCID: PMC7495355 DOI: 10.1021/acs.jctc.7b00174] [Citation(s) in RCA: 742] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Daniel G A Smith
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Andrew C Simmonett
- National Institutes of Health , National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - A Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306-4390, United States
| | - Edward G Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University , Ankara 06800, Turkey
| | - Alexander Yu Sokolov
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Ryan M Richard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Jérôme F Gonthier
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Andrew M James
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Harley R McAlexander
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Masaaki Saitow
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University , 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Xiao Wang
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Benjamin P Pritchard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Prakash Verma
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| | - Rollin A King
- Department of Chemistry, Bethel University , St. Paul, Minnesota 55112, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | | | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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8
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Carson BE, Parker TM, Hohenstein EG, Brizius GL, Komorner W, King RA, Collard DM, Sherrill CD. Competition Between π-π and C-H/π Interactions: A Comparison of the Structural and Electronic Properties of Alkoxy-Substituted 1,8-Bis((propyloxyphenyl)ethynyl)naphthalenes. Chemistry 2015; 21:19168-75. [PMID: 26568396 DOI: 10.1002/chem.201502363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 11/11/2022]
Abstract
The structural and electronic consequences of π-π and C-H/π interactions in two alkoxy-substituted 1,8-bis- ((propyloxyphenyl)ethynyl)naphthalenes are explored by using X-ray crystallography and electronic structure computations. The crystal structure of analogue 4, bearing an alkoxy side chain in the 4-position of each of the phenyl rings, adopts a π-stacked geometry, whereas analogue 8, bearing alkoxy groups at both the 2- and the 5-positions of each ring, has a geometry in which the rings are splayed away from a π-stacked arrangement. Symmetry-adapted perturbation theory analysis was performed on the two analogues to evaluate the interactions between the phenylethynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π-stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing π-π interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti-alignment of C-O bond dipoles, and two C-H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π-π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, unstacked arrangement.
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Affiliation(s)
- Bradley E Carson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452
| | - Trent M Parker
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452.,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA)
| | - Edward G Hohenstein
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452.,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA)
| | - Glen L Brizius
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452
| | - Whitney Komorner
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, MN 55112 (USA)
| | - David M Collard
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452.
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452. .,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA). .,School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332 (USA).
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9
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Carlson RK, Lee RA, Assam JH, King RA, Nagel ML. Free-radical copolymerisation of acrylamides, acrylates, and α-olefins. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1015641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Rachel A. Lee
- Department of Chemistry, Bethel University, St. Paul, MN, USA
| | - Jed H. Assam
- Department of Chemistry, Bethel University, St. Paul, MN, USA
| | - Rollin A. King
- Department of Chemistry, Bethel University, St. Paul, MN, USA
| | - Megan L. Nagel
- Department of Chemistry, Penn State Greater Allegheny, McKeesport, PA, USA
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10
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King RA, Symondson WOC, Thomas RJ. Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas. Bull Entomol Res 2015; 105:261-272. [PMID: 25572526 DOI: 10.1017/s0007485314000935] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.
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Affiliation(s)
- R A King
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| | - W O C Symondson
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| | - R J Thomas
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
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11
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Shao Y, Gan Z, Epifanovsky E, Gilbert AT, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X, Ghosh D, Goldey M, Horn PR, Jacobson LD, Kaliman I, Khaliullin RZ, Kuś T, Landau A, Liu J, Proynov EI, Rhee YM, Richard RM, Rohrdanz MA, Steele RP, Sundstrom EJ, Woodcock HL, Zimmerman PM, Zuev D, Albrecht B, Alguire E, Austin B, Beran GJO, Bernard YA, Berquist E, Brandhorst K, Bravaya KB, Brown ST, Casanova D, Chang CM, Chen Y, Chien SH, Closser KD, Crittenden DL, Diedenhofen M, DiStasio RA, Do H, Dutoi AD, Edgar RG, Fatehi S, Fusti-Molnar L, Ghysels A, Golubeva-Zadorozhnaya A, Gomes J, Hanson-Heine MW, Harbach PH, Hauser AW, Hohenstein EG, Holden ZC, Jagau TC, Ji H, Kaduk B, Khistyaev K, Kim J, Kim J, King RA, Klunzinger P, Kosenkov D, Kowalczyk T, Krauter CM, Lao KU, Laurent AD, Lawler KV, Levchenko SV, Lin CY, Liu F, Livshits E, Lochan RC, Luenser A, Manohar P, Manzer SF, Mao SP, Mardirossian N, Marenich AV, Maurer SA, Mayhall NJ, Neuscamman E, Oana CM, Olivares-Amaya R, O’Neill DP, Parkhill JA, Perrine TM, Peverati R, Prociuk A, Rehn DR, Rosta E, Russ NJ, Sharada SM, Sharma S, Small DW, Sodt A, Stein T, Stück D, Su YC, Thom AJ, Tsuchimochi T, Vanovschi V, Vogt L, Vydrov O, Wang T, Watson MA, Wenzel J, White A, Williams CF, Yang J, Yeganeh S, Yost SR, You ZQ, Zhang IY, Zhang X, Zhao Y, Brooks BR, Chan GK, Chipman DM, Cramer CJ, Goddard WA, Gordon MS, Hehre WJ, Klamt A, Schaefer HF, Schmidt MW, Sherrill CD, Truhlar DG, Warshel A, Xu X, Aspuru-Guzik A, Baer R, Bell AT, Besley NA, Chai JD, Dreuw A, Dunietz BD, Furlani TR, Gwaltney SR, Hsu CP, Jung Y, Kong J, Lambrecht DS, Liang W, Ochsenfeld C, Rassolov VA, Slipchenko LV, Subotnik JE, Van Voorhis T, Herbert JM, Krylov AI, Gill PM, Head-Gordon M. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol Phys 2014. [DOI: 10.1080/00268976.2014.952696] [Citation(s) in RCA: 1769] [Impact Index Per Article: 176.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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12
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Moreno-Ripoll R, Gabarra R, Symondson WOC, King RA, Agustí N. Trophic relationships between predators, whiteflies and their parasitoids in tomato greenhouses: a molecular approach. Bull Entomol Res 2012; 102:415-423. [PMID: 22314013 DOI: 10.1017/s0007485311000836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The whiteflies Bemisia tabaci Gennadius and Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) are two of the main pests in tomato crops. Their biological control in Mediterranean IPM systems is based on the predators Macrolophus pygmaeus (Rambur) and Nesidiocoris tenuis Reuter (Hemiptera: Miridae), as well as on the parasitoids Eretmocerus mundus (Mercet) and Encarsia pergandiella Howard (Hymenoptera: Aphelinidae). These natural enemies may interact with each other and their joint use could interfere with the biological control of those whitefly pests. Analysis of predator-prey interactions under field conditions is therefore essential in order to optimize whitefly control. Species-specific polymerase chain reaction (PCR)-primers were designed to detect DNA fragments of these whiteflies and parasitoids within both predator species in tomato greenhouses. We demonstrated that both predators feed on both whitefly species, as well as on both parasitoids under greenhouse conditions. Prey molecular detection was possible where prey abundance was very low or even where predation was not observed under a microscope. Whitefly DNA detection was positively correlated with adult whitefly abundance in the crop. However, a significant relationship was not observed between parasitoid DNA detection and the abundance of parasitoid pupae, even though the predation rate on parasitoids was high. This unidirectional intraguild predation (predators on parasitoids) could potentially reduce their combined impact on their joint prey/host. Prey molecular detection provided improved detection of prey consumption in greenhouse crops, as well as the possibility to identify which prey species were consumed by each predator species present in the greenhouse, offering a blueprint with wider applicability to other food webs.
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Affiliation(s)
- R Moreno-Ripoll
- IRTA, Entomology, Ctra. de Cabrils, Km. 2, E-08348 Cabrils, Barcelona, Spain
| | - R Gabarra
- IRTA, Entomology, Ctra. de Cabrils, Km. 2, E-08348 Cabrils, Barcelona, Spain
| | - W O C Symondson
- Cardiff School of Biosciences, Biomedical Sciences Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - R A King
- Cardiff School of Biosciences, Biomedical Sciences Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - N Agustí
- IRTA, Entomology, Ctra. de Cabrils, Km. 2, E-08348 Cabrils, Barcelona, Spain
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13
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King RA, Davey JS, Bell JR, Read DS, Bohan DA, Symondson WOC. Suction sampling as a significant source of error in molecular analysis of predator diets. Bull Entomol Res 2012; 102:261-266. [PMID: 22040612 DOI: 10.1017/s0007485311000575] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The molecular detection of predation is a fast growing field, allowing highly specific and sensitive detection of prey DNA within the gut contents or faeces of a predator. Like all molecular methods, this technique is prone to potential sources of error that can result in both false positive and false negative results. Here, we test the hypothesis that the use of suction samplers to collect predators from the field for later molecular analysis of predation will lead to high numbers of false positive results. We show that, contrary to previous published work, the use of suction samplers resulted in previously starved predators testing positive for aphid and collembolan DNA, either as a results of ectopic contamination or active predation in the collecting cup/bag. The contradictory evidence for false positive results, across different sampling protocols, sampling devices and different predator-prey systems, highlights the need for experimentation prior to mass field collections of predators to find techniques that minimise the risk of false positives.
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Affiliation(s)
- R A King
- Cardiff School of Biosciences, Cardiff University, UK.
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14
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Abrams KM, Guzik MT, Cooper SJB, Humphreys WF, King RA, Cho JL, Austin AD. What lies beneath: molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea). Mol Phylogenet Evol 2012; 64:130-44. [PMID: 22465443 DOI: 10.1016/j.ympev.2012.03.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/27/2012] [Accepted: 03/18/2012] [Indexed: 11/19/2022]
Abstract
The crustacean family Parabathynellidae is an ancient and significant faunal component of subterranean ecosystems. Molecular data were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species diversity of this group within Australia. We also used the resultant phylogenetic framework, in combination with an ancestral state reconstruction (ASR) analysis, to explore the evolution of two key morphological characters (number of segments of the first and second antennae), previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ASR approach also allowed an assessment of whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Sequence data from the mtDNA COI and nDNA 18S rRNA genes were obtained from 32 parabathynellid species (100% of described genera and ~25% of described species) from key groundwater regions across Australia. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. Additionally, ancestral state reconstruction analysis provided evidence for multiple cases of convergent evolution for the two morphological characters evaluated, suggesting that caution needs to be shown when using these characters for elucidating phylogenetic relationships, particularly when there are few morphological characters available for reconstructing relationships. The ancestral state analysis contradicted the conventional view of parabathynellid evolution, which assumes that more simplified taxa (i.e. those with fewer-segmented appendages and setae) are derived and more complex taxa are primitive.
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Affiliation(s)
- K M Abrams
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, The University of Adelaide, SA 5005, Australia.
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Hatteland BA, Symondson WOC, King RA, Skage M, Schander C, Solhøy T. Molecular analysis of predation by carabid beetles (Carabidae) on the invasive Iberian slug Arion lusitanicus. Bull Entomol Res 2011; 101:675-686. [PMID: 21342604 DOI: 10.1017/s0007485311000034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The invasive Iberian slug, Arion lusitanicus, is spreading through Europe and poses a major threat to horticulture and agriculture. Natural enemies, capable of killing A. lusitanicus, may be important to our understanding of its population dynamics in recently invaded regions. We used polymerase chain reaction (PCR) to study predation on A. lusitanicus by carabid beetles in the field. A first multiplex PCR was developed, incorporating species-specific primers, and optimised in order to amplify parts of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of large Arion slugs, including A. lusitanicus from the gut contents of the predators. A second multiplex PCR, targeting 12S rRNA mtDNA, detected predation on smaller Arion species and the field slug Deroceras reticulatum. Feeding trials were conducted to measure the effects of digestion time on amplicon detectability. The median detection times (the time at which 50% of samples tested positive) for A. lusitanicus and D. reticulatum DNA in the foreguts of Carabus nemoralis were 22 h and 20 h, respectively. Beetle activity-densities were monitored using pitfall traps, and slug densities were estimated using quadrats. Predation rates on slugs in the field by C. nemoralis in spring ranged from 16-39% (beetles positive for slug DNA) and were density dependent, with numbers of beetles testing positive being positively correlated with densities of the respective slug species. Carabus nemoralis was shown to be a potentially important predator of the alien A. lusitanicus in spring and may contribute to conservation biological control.
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Affiliation(s)
- B A Hatteland
- Department of Biology, University of Bergen, Norway.
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Turney JM, Simmonett AC, Parrish RM, Hohenstein EG, Evangelista FA, Fermann JT, Mintz BJ, Burns LA, Wilke JJ, Abrams ML, Russ NJ, Leininger ML, Janssen CL, Seidl ET, Allen WD, Schaefer HF, King RA, Valeev EF, Sherrill CD, Crawford TD. Psi4: an open-source ab initio
electronic structure program. WIREs Comput Mol Sci 2011. [DOI: 10.1002/wcms.93] [Citation(s) in RCA: 637] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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17
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Wesolowski SS, Valeev EF, King RA, Baranovski V, Schaefer HF. The not-so-peculiar case of calcium oxide: a weakness in atomic natural orbital basis sets for calcium. Mol Phys 2010. [DOI: 10.1080/00268970050080582] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Mach TJ, King RA, Crawford TD. A Coupled Cluster Benchmark Study of the Electronic Spectrum of the Allyl Radical†. J Phys Chem A 2010; 114:8852-7. [DOI: 10.1021/jp102292x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fortenberry RC, King RA, Stanton JF, Crawford TD. A benchmark study of the vertical electronic spectra of the linear chain radicals C2H and C4H. J Chem Phys 2010; 132:144303. [DOI: 10.1063/1.3376073] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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21
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Andre J, King RA, Stürzenbaum SR, Kille P, Hodson ME, Morgan AJ. Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape. Environ Pollut 2010; 158:883-890. [PMID: 19818541 DOI: 10.1016/j.envpol.2009.09.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 05/28/2023]
Abstract
A Pb-mine site situated on acidic soil, but comprising of Ca-enriched islands around derelict buildings was used to study the spatial pattern of genetic diversity in Lumbricus rubellus. Two distinct genetic lineages ('A' and 'B'), differentiated at both the mitochondrial (mtDNA COII) and nuclear level (AFLPs) were revealed with a mean inter-lineage mtDNA sequence divergence of approximately 13%, indicative of a cryptic species complex. AFLP analysis indicates that lineage A individuals within one central 'ecological island' site are uniquely clustered, with little genetic overlap with lineage A individuals at the two peripheral sites. FTIR microspectroscopy of Pb-sequestering chloragocytes revealed different phosphate profiles in residents of adjacent acidic and calcareous islands. Bioinformatics found over-representation of Ca pathway genes in EST(Pb) libraries. Subsequent sequencing of a Ca-transport gene, SERCA, revealed mutations in the protein's cytosolic domain. We recommend the mandatory genotyping of all individuals prior to field-based ecotoxicological assays, particularly those using discriminating genomic technologies.
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Affiliation(s)
- J Andre
- Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3TL, UK.
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22
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King RA, Oetting WS. Molecular basis of type IA (tyrosinase negative) oculocutaneous albinism. Pigment Cell Res 2008; Suppl 2:249-53. [PMID: 1409426 DOI: 10.1111/j.1600-0749.1990.tb00380.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Type IA (Tyrosinase negative) oculocutaneous albinism (OCA) is produced by mutations of the tyrosinase gene. We have found a total of 13 different mutations associated with type IA OCA. Analysis of the distribution of the 9 missense mutations shows that most of these mutations cluster in three areas of the gene. All but one of these mutations involve amino acids that are conserved between the mouse and human. Two clusters involve the copper A and copper B binding sites, and could disrupt the metal ion-protein interaction necessary for enzyme function. The third cluster is in exon I and could represent an important functional domain of the enzyme such as the tyrosine binding site. The deletion or insertion frameshift mutations are distributed throughout the coding region and do not appear to cluster. We conclude that a diverse number of mutations are responsible for type IA OCA and many individuals are compound heterozygotes for mutations responsible for this genetic disease (Table 3).
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Affiliation(s)
- R A King
- Department of Medicine, University of Minnesota, Minneapolis 55455
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Affiliation(s)
- D Townsend
- Department of Medicine, University of Minnesota, Minneapolis 55455
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Affiliation(s)
- Rollin A. King
- Bethel University, 3900 Bethel Drive, St. Paul, Minnesota 55112
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Harvey PS, King RA, Summers CS. Foveal depression and albinism. Ophthalmology 2008; 115:756; author reply 756-7. [PMID: 18387418 DOI: 10.1016/j.ophtha.2007.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022] Open
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Abstract
Molecular analysis of predation, through polymerase chain reaction amplification of prey remains within the faeces or digestive systems of predators, is a rapidly growing field, impeded by a lack of readily accessible advice on best practice. Here, we review the techniques used to date and provide guidelines accessible to those new to this field or from a different molecular biology background. Optimization begins with field collection, sample preservation, predator dissection and DNA extraction techniques, all designed to ensure good quality, uncontaminated DNA from semidigested samples. The advantages of nuclear vs. mitochondrial DNA as primer targets are reviewed, along with choice of genes and advice on primer design to maximize specificity and detection periods following ingestion of the prey by the predators. Primer and assay optimization are discussed, including cross-amplification tests and calibratory feeding experiments. Once primers have been made, the screening of field samples must guard against (through appropriate controls) cross contamination. Multiplex polymerase chain reactions provide a means of screening for many different species simultaneously. We discuss visualization of amplicons on gels, with and without incorporation of fluorescent primers. In more specialized areas, we examine the utility of temperature and denaturing gradient gel electrophoresis to examine responses of predators to prey diversity, and review the potential of quantitative polymerase chain reaction systems to quantify predation. Alternative routes by which prey DNA might get into the guts of a predator (scavenging, secondary predation) are highlighted. We look ahead to new technologies, including microarrays and pyrosequencing, which might one day be applied to this field.
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Affiliation(s)
- R A King
- Cardiff School of Biosciences, Biomedical Sciences Building, Cardiff University, Museum Avenue, Cardiff CF10 3US, UK
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Crawford TD, Sherrill CD, Valeev EF, Fermann JT, King RA, Leininger ML, Brown ST, Janssen CL, Seidl ET, Kenny JP, Allen WD. PSI3: an open-source Ab Initio electronic structure package. J Comput Chem 2007. [PMID: 17420978 DOI: 10.1002/jcc.20573)] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.
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Affiliation(s)
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061
| | - Justin T Fermann
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01002
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112
| | | | - Shawn T Brown
- Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213
| | | | - Edward T Seidl
- Lawrence Livermore National Laboratories, Livermore, California 94550
| | - Joseph P Kenny
- Sandia National Laboratories, Livermore, California 94551
| | - Wesley D Allen
- Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
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Crawford TD, Sherrill CD, Valeev EF, Fermann JT, King RA, Leininger ML, Brown ST, Janssen CL, Seidl ET, Kenny JP, Allen WD. PSI3: An open-source Ab Initio
electronic structure package. J Comput Chem 2007; 28:1610-1616. [PMID: 17420978 DOI: 10.1002/jcc.20573] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.
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Affiliation(s)
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061
| | - Justin T Fermann
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01002
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112
| | | | - Shawn T Brown
- Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213
| | | | - Edward T Seidl
- Lawrence Livermore National Laboratories, Livermore, California 94550
| | - Joseph P Kenny
- Sandia National Laboratories, Livermore, California 94551
| | - Wesley D Allen
- Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
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Crawford TD, Abrams ML, King RA, Lane JR, Schofield DP, Kjaergaard HG. The lowest A′2 excited state of the water-hydroxyl complex. J Chem Phys 2006; 125:204302. [PMID: 17144695 DOI: 10.1063/1.2388260] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Vertical and adiabatic excitation energies of the lowest (2)A(') excited state in the water-hydroxyl complex have been determined using coupled cluster, multireference configuration interaction, multireference perturbation theory, and density-functional methods. A significant redshift of about 0.4 eV in the vertical excitation energy of the complex compared to that of the hydroxyl radical monomer is found with the coupled cluster calculations validating previous results. Electronic excitation leads to a structure with near-equal sharing of the hydroxyl hydrogen by both oxygen atoms and a concomitantly large redshift of the adiabatic excitation energy of approximately 1 eV relative to the vertical excitation energy. The combination of redshifts ensures that the electronic transition in the complex lies well outside the equivalent excitation in the hydroxyl radical monomer. The complex is approximately five times more strongly bound in the excited state than in the ground state.
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Abstract
We report an extension of the coupled cluster iterative-triples model, CC3, to excited states of open-shell molecules, including radicals. We define the method for both spin-unrestricted Hartree-Fock (UHF) and spin-restricted open-shell Hartree-Fock (ROHF) reference determinants and discuss its efficient implementation in the PSI3 program package. The program is streamlined to use at most O(N(7)) computational steps and avoids storage of the triple-excitation amplitudes for both the ground- and excited-state calculations. The excitation-energy program makes use of a Lowdin projection formalism (comparable to that of earlier implementations) that allows computational reduction of the Davidson algorithm to only the single- and double-excitation space, but limits the calculation to only one excited state at a time. However, a root-following algorithm may be used to compute energies for multiple states of the same symmetry. Benchmark applications of the new methods to the lowest valence (2)B(1) state of the allyl radical, low-lying states of the CH and CO(+) diatomics, and the nitromethyl radical show substantial improvement over ROHF- and UHF-based CCSD excitation energies for states with strong double-excitation character or cases suffering from significant spin contamination. For the allyl radical, CC3 adiabatic excitation energies differ from experiment by less than 0.02 eV, while for the (2)Sigma(+) state of CH, significant errors of more than 0.4 eV remain.
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Rosario-Campos MC, Miguel EC, Quatrano S, Chacon P, Ferrao Y, Findley D, Katsovich L, Scahill L, King RA, Woody SR, Tolin D, Hollander E, Kano Y, Leckman JF. The Dimensional Yale-Brown Obsessive-Compulsive Scale (DY-BOCS): an instrument for assessing obsessive-compulsive symptom dimensions. Mol Psychiatry 2006; 11:495-504. [PMID: 16432526 DOI: 10.1038/sj.mp.4001798] [Citation(s) in RCA: 299] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Obsessive-compulsive disorder (OCD) encompasses a broad range of symptoms representing multiple domains. This complex phenotype can be summarized using a few consistent and temporally stable symptom dimensions. The objective of this study was to assess the psychometric properties of the Dimensional Yale-Brown Obsessive-Compulsive Scale (DY-BOCS). This scale measures the presence and severity of obsessive-compulsive (OC) symptoms within six distinct dimensions that combine thematically related obsessions and compulsions. The DY-BOCS includes portions to be used as a self-report instrument and portions to be used by expert raters, including global ratings of OC symptom severity and overall impairment. We assessed 137 patients with a Diagnostic and Statistical Manual-IV diagnosis of OCD, aged 6-69 years, from sites in the USA, Canada and Brazil. Estimates of the reliability and validity of both the expert and self-report versions of the DY-BOCS were calculated and stratified according to age (pediatric vs. adult subjects). The internal consistency of each of the six symptom dimensions and the global severity score were excellent. The inter-rater agreement was also excellent for all component scores. Self-report and expert ratings were highly intercorrelated. The global DY-BOCS score was highly correlated with the total Yale-Brown Obsessive-Compulsive Scale score (Pearson r = 0.82, P<0.0001). Severity scores for individual symptom dimensions were largely independent of one another, only modestly correlated with the global ratings, and were also differentially related to ratings of depression, anxiety and tic severity. No major differences were observed when the results were stratified by age. These results indicate that the DY-BOCS is a reliable and valid instrument for assessing multiple aspects of OCD symptom severity in natural history, neuroimaging, treatment response and genetic studies when administered by expert clinicians or their highly trained staff.
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Affiliation(s)
- M C Rosario-Campos
- Department of Psychiatry, University of São Paulo Medical School, São Paulo, Brazil
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Affiliation(s)
- R A King
- Department of Chemical Engineering, University of Manchester Institute of Science and Technology
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Zalsman G, Anderson GM, Peskin M, Frisch A, King RA, Vekslerchik M, Sommerfeld E, Michaelovsky E, Sher L, Weizman A, Apter A. Relationships between serotonin transporter promoter polymorphism, platelet serotonin transporter binding and clinical phenotype in suicidal and non-suicidal adolescent inpatients. J Neural Transm (Vienna) 2005; 112:309-15. [PMID: 15657646 DOI: 10.1007/s00702-004-0244-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Accepted: 10/16/2004] [Indexed: 11/29/2022]
Abstract
Relationships between the serotonin transporter promoter polymorphism (5-HTTLPR), platelet serotonin transporter (SERT) binding and clinical phenotype were examined in 32 suicidal and 28 non-suicidal Ashkenazi Israeli adolescent psychiatric inpatients. The 5-HTTLPR polymorphism was not associated with transporter binding or with suicidality or other clinical phenotypes. However, in the suicidal group, a significant positive correlation between platelet SERT density and anger scores (n=32, r=.40; p=.027) and a negative correlation between platelet count and trait anxiety (n=32, r=-.42; p=.034) were observed.
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Affiliation(s)
- G Zalsman
- Adolescent Inpatient Department and Research Unit, Geha Mental Health Center, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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DeYonker NJ, Li S, Yamaguchi Y, Schaefer HF, Crawford TD, King RA, Peterson KA. Application of equation-of-motion coupled-cluster methods to low-lying singlet and triplet electronic states of HBO and BOH. J Chem Phys 2005; 122:234316. [PMID: 16008450 DOI: 10.1063/1.1927078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The equilibrium structures and physical properties of the X (1)sigma(+) linear electronic states, linear excited singlet and triplet electronic states of hydroboron monoxide (HBO) (A (1)sigma(-), B (1)delta, a (3)sigma(+), and b (3)delta) and boron hydroxide (BOH) (A (1)sigma(+), B (1)Pi, and b (3)Pi), and their bent counterparts (HBO a (3)A('), b (3)A("), A (1)A("), B (1)A(') and BOH X (1)A('), b (3)A('), c (3)A("), A (1)A('), B (1)A('), C (1)A(")) are investigated using excited electronic state ab initio equation-of-motion coupled-cluster (EOM-CC) methods. A new implementation of open-shell EOM-CC including iterative partial triple excitations (EOM-CC3) was tested. Coupled-cluster wave functions with single and double excitations (CCSD), single, double, and iterative partial triple excitations (CC3), and single, double, and full triple excitations (CCSDT) are employed with the correlation-consistent quadruple and quintuple zeta basis sets. The linear HBO X (1)sigma(+) state is predicted to lie 48.3 kcal mol(-1) (2.09 eV) lower in energy than the BOH X (1)sigma(+) linear stationary point at the CCSDT level of theory. The CCSDT BOH barrier to linearity is predicted to lie 3.7 kcal mol(-1) (0.16 eV). With a harmonic zero-point vibrational energy correction, the HBO X (1)sigma(+)-BOH X (1)A(') energy difference is 45.2 kcal mol(-1) (1.96 eV). The lowest triplet excited electronic state of HBO, a (3)A('), has a predicted excitation energy (T(e)) of 115 kcal mol(-1) (4.97 eV) from the HBO ground state minimum, while the lowest-bound BOH excited electronic state, b (3)A('), has a T(e) of 70.2 kcal mol(-1) (3.04 eV) with respect to BOH X (1)A('). The T(e) values predicted for the lowest singlet excited states are A (1)A(")<--X (1)sigma(+)=139 kcal mol(-1) (6.01 eV) for HBO and A (1)A(')<--X (1)A(')=102 kcal mol(-1) (4.42 eV) for BOH. Also for BOH, the triplet vertical transition energies are b (3)A(')<--X (1)A(')=71.4 kcal mol(-1) (3.10 eV) and c (3)A(")<--X (1)A(')=87.2 kcal mol(-1) (3.78 eV).
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Affiliation(s)
- Nathan J DeYonker
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA
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Abstract
DNA-based techniques are providing valuable new approaches to tracking predator-prey interactions. The gut contents of invertebrate predators can be analysed using species-specific primers to amplify prey DNA to confirm trophic links. The problem is that each predator needs to be analysed with primers for the tens of potential prey available at a field site, even though the mean number of species detected in each gut may be as few as one or two. Conducting all these PCRs (polymerase chain reactions) is a lengthy process, and effectively precludes the analysis of the hundreds of predators that might be required for a meaningful ecological study. We report a rapid, more sensitive and practical approach. Multiplex PCRs, incorporating fluorescent markers, were found to be effective at amplifying degraded DNA from predators' guts and could amplify mitochondrial DNA fragments from 10+ species simultaneously without 'drop outs'. The combined PCR products were then separated by size on polyacrylamide gels on an ABI377 sequencer. New primers to detect the remains of aphids, earthworms, weevils and molluscs in the guts of carabid predators were developed and characterized. The multiplex-sequencer approach was then applied to field-caught beetles, some of which contained DNA from as many as four different prey at once. The main prey detected in the beetles proved to be earthworms and molluscs, although aphids and weevils were also consumed. The potential of this system for use in food-web research is discussed.
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Affiliation(s)
- G L Harper
- Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff, CF10 3TL, UK
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Blumenthal MN, Ober C, Beaty TH, Bleecker ER, Langefeld CD, King RA, Lester L, Cox N, Barnes K, Togias A, Mathias R, Meyers DA, Oetting W, Rich SS. Genome scan for loci linked to mite sensitivity: the Collaborative Study on the Genetics of Asthma (CSGA). Genes Immun 2004; 5:226-31. [PMID: 15029235 DOI: 10.1038/sj.gene.6364063] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mite sensitivity has been reported to be a major risk factor for asthma. As part of the Collaborative Study on the Genetics of Asthma (CSGA), a genome scan using mite reactivity (Dermatophagoides Pteronyssinus (Der p) and Dermatophagoides farinae (Der f)) as the phenotype was conducted. In 287 CSGA families, 122 were informative for linkage. Evidence supporting linkage was observed for regions on chromosome 19 (D19S591, lod=2.43, P=0.0008; D19S1037, lod=1.57, P=0.007) and chromosome 20 (D20S473/D20S604, lod=1.41, P=0.01). All three ethnic groups appeared to contribute to the evidence for linkage on chromosome 20. African-American families gave strongest support for linkage on chromosomes 3 (D3S2409, lod=1.33, P=0.01), 12 (D12S373, lod=1.51, P=0.008) and 18 (ATA82B02, lod=1.32, P=0.01). Caucasian families showed strong evidence for linkage on chromosome 19 (D19S591, lod=3.51, P=0.00006). Hispanic families supported linkage on chromosomes 11 (D11S1984, lod=1.56, P=0.007), 13 (D13S787, lod=1.30, P=0.01) and 20 (D20S470, lod=1.71, P=0.005). These results suggest that multiple genes may be involved in controlling skin reactivity to Dermatophoigoies.
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Affiliation(s)
- M N Blumenthal
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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Affiliation(s)
- Rollin A. King
- Department of Chemistry, Bethel College, 3900 Bethel Drive, St. Paul, Minnesota 55112-6999
| | - Benjamin Murrin
- Department of Chemistry, Bethel College, 3900 Bethel Drive, St. Paul, Minnesota 55112-6999
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Abstract
Forty populations of Potamogeton pectinatus L. were sampled from around the Baltic Sea basin. Analysis of 62 ISSR 'loci' showed that the number of clones per population is very variable but shows a tendency to decrease with latitude. Analysis of molecular variance revealed that, overall, just over half the variability is stored within populations and just under half between them (phi(ST) 0.496). In pairwise comparisons, most populations are significantly differentiated. Genetic distance between populations, as measured by phi(ST), increases with geographical distance. Levels of population differentiation, however, are lower on the southeastern Swedish coast than elsewhere, a reduction correlated with the importance of this area as a staging post for the massive migrations of waterfowl from arctic Russia and western Siberia. Cumulative plots of phi(ST) against geographical distance along this coast suggest that, although it does not prevent significant population differentiation, bird traffic reduces it over distances of 150-200 km.
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Affiliation(s)
- R A King
- IACR-LARS, Long Ashton, Bristol BS41 9AF, UK
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Abstract
We have identified and isolated ectopically expressed tyrosinase transcripts in normal human melanocytes and lymphocytes and in a human melanoma (MNT-1) cell line to establish a baseline for the expression pattern of this gene in normal tissue. Tyrosinase mRNA from human lymphoblastoid cell lines was reverse transcribed and amplified using specific "nested" primers. This amplification yielded eight identifiable transcripts; five that resulted from alternative splicing patterns arising from the utilization of normal and alternative splice sequences. Identical splicing patterns were found in transcripts from human primary melanocytes in culture and a melanoma cell line, indicating that lymphoblastoid cell lines provide an accurate reflection of transcript processing in melanocytes. Similar splicing patterns have also been found with murine melanocyte tyrosinase transcripts. Our results demonstrate that alternative splicing of human tyrosinase gene transcript produces a number of predictable and identifiable transcripts, and that human lymphoblastoid cell lines provide a source of ectopically expressed transcripts that can be used to study the biology of tyrosinase gene expression in humans.
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Affiliation(s)
- J P Fryer
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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Morshed SA, Parveen S, Leckman JF, Mercadante MT, Bittencourt Kiss MH, Miguel EC, Arman A, Yazgan Y, Fujii T, Paul S, Peterson BS, Zhang H, King RA, Scahill L, Lombroso PJ. Antibodies against neural, nuclear, cytoskeletal, and streptococcal epitopes in children and adults with Tourette's syndrome, Sydenham's chorea, and autoimmune disorders. Biol Psychiatry 2001; 50:566-77. [PMID: 11690591 DOI: 10.1016/s0006-3223(01)01096-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Some cases of Tourette's syndrome (TS) are hypothesized to be caused by autoantibodies that develop in response to a preceding group A beta hemolytic streptococcal infection. METHODS To test this hypothesis, we looked for the presence ot total and IgG antibodies against neural, nuclear, cytoskeletal and streptococcal epitopes using indirect immunofluorescent assays and Western blot techniques in three patient groups: TS (n = 81), SC (n = 27), and a group of autoimmune disorders (n = 52) and in normal controls (n = 67). Subjects were ranked after titrations of autoantibodies from 0 to 227 according to their level of immunoreactivity. RESULTS TS patients had a significantly higher mean rank for total antineural and antinuclear antibodies, as well as antistreptolysin O titers. However, among children and adolescents, only the total antinuclear antibodies were increased in TS patients compared to age matched controls. Compared to SC patients, TS patients had a significantly lower mean rank for total and IgG class antineural antibodies, significantly lower IgG class anticytoskeletal antibodies, and a significantly higher rank for total antinuclear antibodies. Compared to a mixed group of autoimmune disorders, the TS patients had a significantly lower mean rank for total and IgG class antineural antibodies, total and IgG class antinuclear antibodies, IgG class anticytoskeletal antibodies, and a significantly higher rank for antistreptococcal antibodies. CONCLUSIONS TS patients had significantly higher levels of total antineural and antinuclear antibodies than did controls. Their relation to IgG class antineural and antinuclear antibodies, markers for prior streptococcal infection, and other clinical characteristics, especially chronological age, was equivocal.
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Affiliation(s)
- S A Morshed
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520-7900, USA
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King RA, Scahill L. Emotional and behavioral difficulties associated with Tourette syndrome. Adv Neurol 2001; 85:79-88. [PMID: 11530448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- R A King
- Yale Child Study Center, New Haven, Connecticut, USA
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Leckman JF, Peterson BS, King RA, Scahill L, Cohen DJ. Phenomenology of tics and natural history of tic disorders. Adv Neurol 2001; 85:1-14. [PMID: 11530419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- J F Leckman
- Child Study Center, Children's Clinical Research Center, Departments of Pediatrics, Psychiatry, Psychology, Yale University, New Haven, Connecticut, USA
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Zalsman G, Frisch A, King RA, Pauls DL, Grice DE, Gelernter J, Alsobrook J, Michaelovsky E, Apter A, Tyano S, Weizman A, Leckman JF. Case control and family-based studies of tryptophan hydroxylase gene A218C polymorphism and suicidality in adolescents. Am J Med Genet 2001; 105:451-7. [PMID: 11449398 DOI: 10.1002/ajmg.1406] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The association of suicidality with polymorphism A218C in intron 7 of tryptophan hydroxylase (TPH) gene remains controversial. The aim of this study was to use family-based methods to examine this association in adolescents in order to eliminate the difficulty of sampling a control group from the same ethnic population. Eighty-eight inpatient adolescents who recently attempted suicide were assessed by structured interview for detailed clinical history, diagnoses, suicide intent, suicide risk, impulsivity, aggression, and depression. DNA samples were collected from all subjects, from both biological parents of 40 subjects and from one parent of 9 subjects; TPH allele frequencies were calculated and tested for association to phenotype, stratified by severity, using the haplotype relative risk (HRR) and transmission disequilibrium test (TDT) methods (n = 49). The frequencies were also compared for all the Jewish subjects (n = 84) to the known frequencies of these alleles in healthy Jewish populations. There was no significant allelic association of A218C polymorphism with suicidal behavior or other phenotypic measures according to the HRR method (chi-square = 0.094; P = 0.76), the TDT (chi-square = 0.258; P = 0.61), or association analysis to known population frequencies (chi-square = 1.667, P = 0.19 for Ashkenazi, and chi-square = 0.810, P = 0.37 for non-Ashkenazi). Analysis of variance with the Scheffè test demonstrated a significant difference between CC and AA genotypes in suicide risk and depression among the patients (n = 88). The findings suggest that polymorphism A218C has no major relevance to the pathogenesis of adolescent suicidal behavior, but may have a subtle effect on some related phenotypes.
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Affiliation(s)
- G Zalsman
- Geha Psychiatric Hospital, Petach Tikva, Israel.
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King RA, Schwab-Stone M, Flisher AJ, Greenwald S, Kramer RA, Goodman SH, Lahey BB, Shaffer D, Gould MS. Psychosocial and risk behavior correlates of youth suicide attempts and suicidal ideation. J Am Acad Child Adolesc Psychiatry 2001; 40:837-46. [PMID: 11437023 DOI: 10.1097/00004583-200107000-00019] [Citation(s) in RCA: 272] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To identify the independent psychosocial and risk behavior correlates of suicidal ideation and attempts. METHOD The relationships between suicidal ideation or attempts and family environment, subject characteristics, and various risk behaviors were examined among 1,285 randomly selected children and adolescents, aged 9 through 17 years, of whom 42 (3.3%) had attempted suicide and 67 (5.2%) had expressed suicidal ideation only. The youths and their parents were enumerated and interviewed between December 1991 and July 1992 as part of the NIMH Methods for the Epidemiology of Child and Adolescent Mental Disorders (MECA) Study. RESULTS Compared with subjects with suicidal ideation only, attempters were significantly more likely to have experienced stressful life events, to have become sexually active, to have smoked more than one cigarette daily, and to have a history of ever having smoked marijuana. After adjusting for sociodemographic characteristics, a statistically significant association was found between suicidal ideation or attempt and stressful life events, poor family environment, parental psychiatric history, low parental monitoring, low instrumental and social competence, sexual activity, marijuana use, recent drunkenness, current smoking, and physical fighting. Even after further adjusting for the presence of a mood, anxiety, or disruptive disorder, a significant association persisted between suicidal ideation or attempts and poor family environment, low parental monitoring, low youth instrumental competence, sexual activity, recent drunkenness, current smoking, and physical fighting. CONCLUSION Low parental monitoring and risk behaviors (such as smoking, physical fighting, alcohol intoxication, and sexual activity) are independently associated with increased risk of suicidal ideation and attempts, even after adjusting for the presence of psychiatric disorder and sociodemographic variables.
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Affiliation(s)
- R A King
- Yale Child Study Center, New Haven, CT 06520-7900, USA
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Abstract
This paper reviews prior research studies examining neurobiological correlates and treatment response of depression in children, adolescents, and adults. Although there are some similarities in research findings observed across the life cycle, both children and adolescents have been found to differ from depressed adults on measures of basal cortisol secretion, corticotropin stimulation post-corticotropin releasing hormone (CRH) infusion, response to several serotonergic probes, immunity indices, and efficacy of tricyclic medications. These differences are proposed to be due to 1) developmental factors, 2) stage of illness factors (e.g., number of episodes, total duration of illness), or 3) heterogeneity in clinical outcome (e.g., recurrent unipolar course vs. new-onset bipolar disorder). Relevant clinical and preclinical studies that provide support for these alternate explanations of the discrepant findings are reviewed, and directions for future research are discussed. To determine whether child-, adolescent-, and adult-onset depression represent the same condition, it is recommended that researchers 1) use the same neuroimaging paradigms in child, adolescent, and adult depressed cohorts; 2) carefully characterize subjects' stage of illness; and 3) conduct longitudinal clinical and repeat neurobiological assessments of patients of different ages at various stages of illness. In addition, careful attention to familial subtypes (e.g., depressive spectrum disorders vs. familial pure depressive disorders) and environmental factors (e.g., trauma history) are suggested for future investigations.
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Affiliation(s)
- J Kaufman
- Yale University School of Medicine, Department of Psychiatry, New Haven, Connecticut 06511, USA
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48
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Young TL, Atwood LD, Ronan SM, Dewan AT, Alvear AB, Peterson J, Holleschau A, King RA. Further refinement of the MYP2 locus for autosomal dominant high myopia by linkage disequilibrium analysis. Ophthalmic Genet 2001; 22:69-75. [PMID: 11449316 DOI: 10.1076/opge.22.2.69.2233] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
INTRODUCTION High myopia (>-6.00 diopters) is a complex common disorder that predisposes individuals to retinal detachment, glaucoma, macular degeneration, and premature cataracts. A recent linkage analysis of seven families with autosomal dominant high myopia has identified one locus (MYP2) for high myopia on chromosome 18p11.31 (Young et al.: Am J Hum Genet 1998;63:109-119). Haplotype analysis revealed an initial interval of 7.6 centimorgans (cM). METHODS Transmission disequilibrium tests (TDT) with both the Statistical Analysis for Genetic Epidemiology (SAGE) 3.1 TDTEX and GENEHUNTER 2 (GH2) programs were performed using chromosome 18p marker alleles for this interval. RESULTS Using SAGE analysis, the following p values were obtained for markers in marker order in this region: D18S1146 (p = 0.227), D18S481 (p = 0.001), D18S63 (p = 0.062), D18S1138 (p = 0.0004), D18S52 (p = 1.79 x 10(-6)), and D18S62 (p = 0.141). GH2 TDT analysis revealed the following p values for the best allele for the markers: D18S1146 (p = 0.083), D18S481 (p = 0.108), D18S63 (p = 0.034), D18S1138 (p = 0.011), D18S52 (p = 0.007), and D18S62 (p = 0.479). CONCLUSION These data suggest that the gene for 18p11.31-linked high myopia is most proximal to marker D18S52, with a likely interval of 0.8 cM between markers D18S63 and D18S52. Due to the contraction of the interval size by TDT, these results provide a basis for focused positional cloning and candidate gene analysis at the MYP2 locus.
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Affiliation(s)
- T L Young
- Department of Ophthalmology, University of Minnesota Medical Center, Minneapolis, Minnesota, USA.
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Abstract
Bicyclic aziridines formed by the irradiation of pyridinium salts in basic solution have recently been recognized to have great synthetic potential. We have undertaken a joint computational and experimental investigation of the mechanism of this photoreaction. We have computationally determined the structures and relative energies of the relevant stationary points on the lowest potential energy surface (PES) of the pyridinium and methylpyridinium ions. Two important intermediates are shown to be bound minima on the ground-state PES: azoniabenzvalene and a 6-aza[3.1.0]bicyclic ion with an exo-oriented substituent (analogous to prefulvene). We advance a mechanism which involves initial formation of this exo-bicyclic ion, followed by nitrogen migration around the ring via the azoniabenzvalene intermediate. Thus, the barrier separating the two intermediates is the factor that determines the degree of scrambling observed in the photoproducts when the carbon atoms are labeled with deuterium or substituted with additional methyl groups. For N-methylpyridinium, the exo-methyl bicyclic ion was computed to be approximately 1 kcalmol(-1) lower in energy than N-methyl-azoniabenzvalene. The transition state was computed to lie several kcal mol(-1) above the exo-methyl bicyclic ion (+8.4kcalmol(-1), 6-31G* RHF; +3.7kcalmol(-1), 6-31G* B3LYP), but still well below the energy available from the 254 nm excitation of the N-methylpyridinium ion. The computed relative energies correspond splendidly with several experimental findings which include the preference for exo products, the results of deuterium labeling, and the impact of additional substituent methyl groups on the product distribution.
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Affiliation(s)
- R A King
- Laboratorium für Physikalische Chemie, ETH Zentrum, Zürich, Switzerland
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50
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Abstract
Nascent RNA encoded by putL, a cis-acting antitermination site of bacteriophage HK022, increases readthrough of terminators by directly modifying the transcript elongation complex. To characterize the interaction between the antiterminator RNA and RNA polymerase, we stalled the elongation complex downstream of putL and determined the sensitivity of the transcript to ribonuclease cleavage. Part of PutL RNA was protected from cleavage by wild-type polymerase, but not by a mutant with a defect in put-dependent antitermination. We also exposed the stalled complex to oligonucleotides complementary to putL RNA, restarted transcription, and measured antitermination. Some, but not all, complementary oligonucleotides inhibited antitermination. Finally, cleavage of the RNA between putL and the 3'-end released putL RNA from the stalled complex and prevented antitermination.
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Affiliation(s)
- R Sen
- Section on Microbial Genetics, Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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