1
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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RDC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
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Gregor R, Johnston J, Coe LSY, Evans N, Forsythe D, Jones R, Muratore D, de Oliveira BFR, Szabo R, Wan Y, Williams J, Chappell CR, Matsuda SB, Ortiz Alvarez de la Campa M, Weissman JL. Building a queer- and trans-inclusive microbiology conference. mSystems 2023; 8:e0043323. [PMID: 37800938 PMCID: PMC10783533 DOI: 10.1128/msystems.00433-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
Microbiology conferences can be powerful places to build collaborations and exchange ideas, but for queer and transgender (trans) scientists, they can also become sources of alienation and isolation. Many conference organizers would like to create welcoming and inclusive events but feel ill-equipped to make this vision a reality, and a historical lack of representation of queer and trans folks in microbiology means we rarely occupy these key leadership roles ourselves. Looking more broadly, queer and trans scientists are systematically marginalized across scientific fields, leading to disparities in career outcomes, professional networks, and opportunities, as well as the loss of unique scientific perspectives at all levels. For queer and trans folks with multiple, intersecting, marginalized identities, these barriers often become even more severe. Here, we draw from our experiences as early-career microbiologists to provide concrete, practical advice to help conference organizers across research communities design inclusive, safe, and welcoming conferences, where queer and trans scientists can flourish.
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Affiliation(s)
- Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Juliet Johnston
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, Georgia, USA
| | - Lisa Shu Yang Coe
- Division of Science, Biology Program, New York University Abu Dhabi, Abu Dhabi, UAE
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Natalya Evans
- Marine Science Institute, University of California, Santa Barbara, California, USA
| | - Desiree Forsythe
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Robert Jones
- U.S. Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, USA
| | | | | | - Rachel Szabo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jelani Williams
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | | | - Shayle B. Matsuda
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, Illinois, USA
| | | | - Queer and Trans in Microbiology Consortium
FagreAnna C.FreseSteven A.HamiltonMariaLabbateMaurizioMollnerMcKMoroenyaneItumelengPacciani-MoriLeonardoPiedadeGonçalo J.PontrelliSammyYangMica Y.WeissAnna C. B.ZablockiOlivierVyasHeema Kumari Nilesh
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, Georgia, USA
- Division of Science, Biology Program, New York University Abu Dhabi, Abu Dhabi, UAE
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Marine Science Institute, University of California, Santa Barbara, California, USA
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
- U.S. Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, Illinois, USA
- Department of Molecular Microbiology & Immunology, Brown University, Providence, Rhode Island, USA
| | - J. L. Weissman
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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3
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Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SLL, Barbera GL, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O’Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Res Sq 2023:rs.3.rs-3189768. [PMID: 37577622 PMCID: PMC10418563 DOI: 10.21203/rs.3.rs-3189768/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paulo Wender P. Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Andres M. Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States
| | - Emily C. Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nicole E. Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mirte C. M. Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, 178 Montecasino Boulevard, Fourways, Johannesburg, Gauteng, 2191, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Private Bag X5050, Thohoyandou, Limpopo, 950, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paula C. Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Rua Carvalho de Mendonça, 144, Santos, SP, 11070-100, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 319 Life Sciences Building, University Park, PA, 16802, United States
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 320 Life Sciences Building, University Park, PA, 16802, United States
| | - Matthew F. Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Daniel Alvarado-Villalobos
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) & Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, 20715, United States
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Department of Biology, University of Fribourg, Chemin du Musée, 10, Fribourg, FR, 1700, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Josep Massana-Codina
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Berenike C. Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Daniel Petras
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Auf der Morgenstelle 24, Tuebingen, 72076, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, United States
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Cheongpa-ro 47 gil 100, Seoul, 04310, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- King’s College London, Strand, London, WC2R 2LS, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 110 Scripps Way, Jupiter, FL, 33458, United States
| | - Mariana Silva dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet B202, Lyngby, 2800, Denmark
| | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Technikerstr. 25, Innsbruck, 6020, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14,, Vienna, 1090, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02142, United States
| | - Ellis Charles O’Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Xueli Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, Singapore, 636921, Singapore
| | - Jerry J. Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Infectious Diseases Institute, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | | | - Hector H. F. Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, 1777 Carvalho Leal Avenue, Manaus, AM, 69065-001, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jason A. Clement
- Baruch S. Blumberg Institute, 3805 Old Easton Rd., Doylestown, PA, 18902, United States
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, United States
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Weniger Hall, room 341, Corvallis, OR, 97331, United States
| | - Sidnee E. Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, 1255 E 13th Ave, Basement, Eugene, OR, 97402, United States
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, CA, 92521, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
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4
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Shan X, Goyal A, Gregor R, Cordero OX. Annotation-free discovery of functional groups in microbial communities. Nat Ecol Evol 2023; 7:716-724. [PMID: 36997739 DOI: 10.1038/s41559-023-02021-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/16/2023] [Indexed: 04/01/2023]
Abstract
Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa whose abundance is more stable and better-associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent of error-prone functional gene annotations remains a major open problem. Here we tackle this structure-function problem by developing a novel unsupervised approach that coarse-grains taxa into functional groups, solely on the basis of the patterns of statistical variation in species abundances and functional read-outs. We demonstrate the power of this approach on three distinct datasets. On data of replicate microcosms with heterotrophic soil bacteria, our unsupervised algorithm recovered experimentally validated functional groups that divide metabolic labour and remain stable despite large variation in species composition. When leveraged against the ocean microbiome data, our approach discovered a functional group that combines aerobic and anaerobic ammonia oxidizers whose summed abundance tracks closely with nitrate concentrations in the water column. Finally, we show that our framework can enable the detection of species groups that are probably responsible for the production or consumption of metabolites abundant in animal gut microbiomes, serving as a hypothesis-generating tool for mechanistic studies. Overall, this work advances our understanding of structure-function relationships in complex microbiomes and provides a powerful approach to discover functional groups in an objective and systematic manner.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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5
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Gregor R, Probst M, Eyal S, Aksenov A, Sasson G, Horovitz I, Dorrestein PC, Meijler MM, Mizrahi I. Mammalian gut metabolomes mirror microbiome composition and host phylogeny. ISME J 2022; 16:1262-1274. [PMID: 34903850 PMCID: PMC9038745 DOI: 10.1038/s41396-021-01152-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 10/18/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022]
Abstract
In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.
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Affiliation(s)
- Rachel Gregor
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Maraike Probst
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Stav Eyal
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Alexander Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Goor Sasson
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Igal Horovitz
- The Zoological Center Tel Aviv-Ramat Gan, Ramat Gan, Israel
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Michael M Meijler
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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6
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Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods 2021; 19:134-136. [PMID: 34862502 DOI: 10.1038/s41592-021-01339-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
| | - Vanessa V Phelan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Deepa Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin P Bowen
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deirdre Belle-Oudry
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dale A Cummings
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.,Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Jessica M Deutsch
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eoin Fahy
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mirtha Navarro-Hoyos
- BIoactivity for Sustainable Development Group (BIODESS), Department of Chemistry, University of Costa Rica, San Jose, Costa Rica
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katherine Louie
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Michael M Meijler
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rachel L Neve
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Trent R Northen
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Pullman
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Aaron W Puri
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.,Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Robin Schmid
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Monica Thukral
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Felipe Vasquez-Castro
- Centro Nacional de Innovaciones Biotecnologicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. .,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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7
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Delago A, Gregor R, Dubinsky L, Dandela R, Hendler A, Krief P, Rayo J, Aharoni A, Meijler MM. A Bacterial Quorum Sensing Molecule Elicits a General Stress Response in Saccharomyces cerevisiae. Front Microbiol 2021; 12:632658. [PMID: 34603220 PMCID: PMC8481950 DOI: 10.3389/fmicb.2021.632658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria assess their population density through a chemical communication mechanism termed quorum sensing, in order to coordinate group behavior. Most research on quorum sensing has focused primarily on its role as an intraspecies chemical signaling mechanism that enables the regulation of certain phenotypes through targeted gene expression. However, in recent years several seminal studies have revealed important phenomena in which quorum sensing molecules appear to serve additional roles as interspecies signals that may regulate microbial ecology. In this study, we asked whether the budding yeast Saccharomyces cerevisiae can sense chemical signals from prokaryotes. When exposed to a variety of quorum sensing molecules from different bacterial species and from Candida albicans we found that N-(3-oxododecanoyl)-L-homoserine lactone (C12) from the opportunistic human pathogen Pseudomonas aeruginosa induces a remarkable stress response in yeast. Microarray experiments confirmed and aided in interpreting these findings, showing a unique and specific expression pattern that differed significantly from the response to previously described stress factors. We further characterized this response and report preliminary findings on the molecular basis for the recognition of C12 by the yeast.
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Affiliation(s)
- Antonia Delago
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rachel Gregor
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Luba Dubinsky
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rambabu Dandela
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Adi Hendler
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Pnina Krief
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Josep Rayo
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Amir Aharoni
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Michael M Meijler
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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8
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Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol 2021; 39:169-173. [PMID: 33169034 PMCID: PMC7971188 DOI: 10.1038/s41587-020-0700-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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] [Received: 01/13/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022]
Abstract
We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.
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Affiliation(s)
- Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Ivan Laponogov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Zheng Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Sophie L F Doran
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Ilaria Belluomo
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Dennis Veselkov
- Intelligify Limited, London, UK
- Department of Computing, Imperial College, South Kensington Campus, London, UK
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Louis Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Katherine N Maloney
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Aleksandr Smirnov
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kenneth L Jones
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Justin J J van der Hooft
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Mabel Gonzalez
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Chris Callewaert
- Center for Microbial Ecology and Technology, Ghent, Belgium
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea Albarracín Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea M Smania
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erika Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael M Meijler
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stav Eyal
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Brooke Anderson
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Raphaël Lugan
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Pauline Le Boulch
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Yann Guitton
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Stephanie Prevost
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Audrey Poirier
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Gaud Dervilly
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Bruno Le Bizec
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Noga Sikron Persi
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Chao Song
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Kelem Gashu
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Roxana Coras
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Monica Guma
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Reza Mirnezami
- Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, UK
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation
| | - Larisa N Kulikova
- Рeoples' Friendship University of Russia (RUDN University), Moscow, Russian Federation
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
| | - Kirill Veselkov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK.
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9
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Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol 2021. [PMID: 33169034 DOI: 10.1038/s41587-41020-40700-41583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.
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Affiliation(s)
- Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Ivan Laponogov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Zheng Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Sophie L F Doran
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Ilaria Belluomo
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Dennis Veselkov
- Intelligify Limited, London, UK
- Department of Computing, Imperial College, South Kensington Campus, London, UK
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Louis Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Katherine N Maloney
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Aleksandr Smirnov
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kenneth L Jones
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Justin J J van der Hooft
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Mabel Gonzalez
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Chris Callewaert
- Center for Microbial Ecology and Technology, Ghent, Belgium
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea Albarracín Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea M Smania
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erika Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael M Meijler
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stav Eyal
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Brooke Anderson
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Raphaël Lugan
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Pauline Le Boulch
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Yann Guitton
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Stephanie Prevost
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Audrey Poirier
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Gaud Dervilly
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Bruno Le Bizec
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Noga Sikron Persi
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Chao Song
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Kelem Gashu
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Roxana Coras
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Monica Guma
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Reza Mirnezami
- Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, UK
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation
| | - Larisa N Kulikova
- Рeoples' Friendship University of Russia (RUDN University), Moscow, Russian Federation
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
| | - Kirill Veselkov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK.
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10
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Abstract
The common language of bacteria and higher life forms is a lexicon of small molecules that the research community is only beginning to decipher. While many new signaling molecules have been discovered in recent years, the identification of their targets is mostly lagging. This review will focus on the latest chemical-probe based research aimed at understanding how bacteria interact chemically with mammals and plants. In general, chemical biology strategies remain under-utilized in this complex field of research, with a few key exceptions, and we hope that this review encourages others to implement these techniques in their research. Specifically, we highlight the chemical biology techniques used in recent studies, especially activity-based protein profiling, that have been applied to unravel the chemical mechanisms of interkingdom interactions.
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Affiliation(s)
- R Gregor
- Department of Chemistry and National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, 84105, Israel.
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11
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Garg N, Luzzatto-Knaan T, Melnik AV, Caraballo-Rodríguez AM, Floros DJ, Petras D, Gregor R, Dorrestein PC, Phelan VV. Natural products as mediators of disease. Nat Prod Rep 2017; 34:194-219. [PMID: 27874907 PMCID: PMC5299058 DOI: 10.1039/c6np00063k] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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: 12/13/2022]
Abstract
Covering: up to 2016Humans are walking microbial ecosystems, each harboring a complex microbiome with the genetic potential to produce a vast array of natural products. Recent sequencing data suggest that our microbial inhabitants are critical for maintaining overall health. Shifts in microbial communities have been correlated to a number of diseases including infections, inflammation, cancer, and neurological disorders. Some of these clinically and diagnostically relevant phenotypes are a result of the presence of small molecules, yet we know remarkably little about their contributions to the health of individuals. Here, we review microbe-derived natural products as mediators of human disease.
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Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | | | - Dimitrios J. Floros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Vanessa V. Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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12
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Dandela R, Mashiach R, Adepu R, Gregor R, Athamna M, Zecharia E, Ernst O, Zor T, Meijler MM. Synthesis and evaluation of a tag-free photoactive phospho-ceramide analogue-1 (PCERA-1) probe to study immunomodulation in macrophages. Chem Commun (Camb) 2017; 53:3842-3845. [DOI: 10.1039/c6cc09849e] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospho-ceramide analogue-1 (PCERA-1), a synthetic analogue of ceramide-1-phosphate (C1P), has been previously shown to act as a potent modulator of macrophage activity and inflammation.
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Affiliation(s)
- Rambabu Dandela
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Roi Mashiach
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Raju Adepu
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Rachel Gregor
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Muhammad Athamna
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Efrat Zecharia
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Orna Ernst
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Tsaffrir Zor
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Michael M. Meijler
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
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13
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Amara N, Gregor R, Rayo J, Dandela R, Daniel E, Liubin N, Willems HME, Ben-Zvi A, Krom BP, Meijler MM. Cover Picture: Fine-Tuning Covalent Inhibition of Bacterial Quorum Sensing (ChemBioChem 9/2016). Chembiochem 2016. [DOI: 10.1002/cbic.201600232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Neri Amara
- Department of Chemistry and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Be'er Sheva Israel
| | - Rachel Gregor
- Department of Chemistry and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Be'er Sheva Israel
| | - Josep Rayo
- Department of Chemistry and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Be'er Sheva Israel
| | - Rambabu Dandela
- Department of Chemistry and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Be'er Sheva Israel
| | - Erik Daniel
- Department of Chemistry and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Be'er Sheva Israel
| | - Nina Liubin
- Department of Life Sciences and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Beersheva Israel
| | - H. Marjo E. Willems
- Department of Preventive Dentistry; Academic Centre for Dentistry Amsterdam; Free University Amsterdam and the University of Amsterdam; Amsterdam The Netherlands
| | - Anat Ben-Zvi
- Department of Life Sciences and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Beersheva Israel
| | - Bastiaan P. Krom
- Department of Preventive Dentistry; Academic Centre for Dentistry Amsterdam; Free University Amsterdam and the University of Amsterdam; Amsterdam The Netherlands
| | - Michael M. Meijler
- Department of Chemistry and; The National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Be'er Sheva Israel
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14
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Amara N, Gregor R, Rayo J, Dandela R, Daniel E, Liubin N, Willems HME, Ben-Zvi A, Krom BP, Meijler MM. Fine-Tuning Covalent Inhibition of Bacterial Quorum Sensing. Chembiochem 2016; 17:825-35. [PMID: 26840534 DOI: 10.1002/cbic.201500676] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 12/15/2015] [Indexed: 01/04/2023]
Abstract
Emerging antibiotic resistance among human pathogens has galvanized efforts to find alternative routes to combat bacterial virulence. One new approach entails interfering with the ability of bacteria to coordinate population-wide gene expression, or quorum sensing (QS), thus inhibiting the production of virulence factors and biofilm formation. We have recently developed such a strategy by targeting LasR, the master regulator of QS in the opportunistic human pathogen Pseudomonas aeruginosa, through the rational design of covalent inhibitors closely based on the core structure of the native ligand. We now report several groups of new inhibitors, one of which, fluoro-substituted ITC-12, displayed complete covalent modification of LasR, as well as effective QS inhibition in vitro and promising in vivo results. In addition to their potential clinical relevance, this series of synthetic QS modulators can be used as a tool to further unravel the complicated QS regulation in P. aeruginosa.
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Affiliation(s)
- Neri Amara
- Department of Chemistry and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rachel Gregor
- Department of Chemistry and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Josep Rayo
- Department of Chemistry and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rambabu Dandela
- Department of Chemistry and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Erik Daniel
- Department of Chemistry and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Nina Liubin
- Department of Life Sciences and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beersheva, Israel
| | - H Marjo E Willems
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Free University Amsterdam and the University of Amsterdam, Amsterdam, The Netherlands
| | - Anat Ben-Zvi
- Department of Life Sciences and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Free University Amsterdam and the University of Amsterdam, Amsterdam, The Netherlands
| | - Michael M Meijler
- Department of Chemistry and, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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15
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Thiel A, Sokhoyan V, Gutz E, van Pee H, Anisovich AV, Bacelar JCS, Bantes B, Bartholomy O, Bayadilov D, Beck R, Beloglazov Y, Castelijns R, Crede V, Dutz H, Elsner D, Ewald R, Frommberger F, Fuchs M, Funke C, Gregor R, Gridnev A, Hillert W, Hoffmeister P, Horn I, Jaegle I, Junkersfeld J, Kalinowsky H, Kammer S, Kleber V, Klein F, Klein F, Klempt E, Kotulla M, Krusche B, Lang M, Löhner H, Lopatin I, Lugert S, Mertens T, Messchendorp JG, Metag V, Metsch B, Nanova M, Nikonov V, Novinski D, Novotny R, Ostrick M, Pant L, Pfeiffer M, Piontek D, Roy A, Sarantsev AV, Schmidt C, Schmieden H, Shende S, Süle A, Sumachev VV, Szczepanek T, Thoma U, Trnka D, Varma R, Walther D, Wendel C, Wilson A. Three-body nature of N(*) and Δ(*) resonances from sequential decay chains. Phys Rev Lett 2015; 114:091803. [PMID: 25793801 DOI: 10.1103/physrevlett.114.091803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 06/04/2023]
Abstract
The Nπ^{0}π^{0} decays of positive-parity N^{*} and Δ^{*} resonances at about 2 GeV are studied at ELSA by photoproduction of two neutral pions off protons. The data reveal clear evidence for several intermediate resonances: Δ(1232), N(1520)3/2^{-}, and N(1680)5/2^{+}, with spin parities J^{P}=3/2^{+}, 3/2^{-}, and 5/2^{+}. The partial wave analysis (within the Bonn-Gatchina approach) identifies N(1440)1/2^{+} and the N(ππ)_{S wave} (abbreviated as Nσ here) as further isobars and assigns the final states to the formation of nucleon and Δ resonances and to nonresonant contributions. We observe the known Δ(1232)π decays of Δ(1910)1/2^{+}, Δ(1920)3/2^{+}, Δ(1905)5/2^{+}, Δ(1950)7/2^{+}, and of the corresponding spin-parity series in the nucleon sector, N(1880)1/2^{+}, N(1900)3/2^{+}, N(2000)5/2^{+}, and N(1990)7/2^{+}. For the nucleon resonances, these decay modes are reported here for the first time. Further new decay modes proceed via N(1440)1/2^{+}π, N(1520)3/2^{-}π, N(1680)5/2^{+}π, and Nσ. The latter decay modes are observed in the decay of N^{*} resonances and at most weakly in Δ^{*} decays. It is argued that these decay modes provide evidence for a 3-quark nature of N^{*} resonances rather than a quark-diquark structure.
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Affiliation(s)
- A Thiel
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - V Sokhoyan
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - E Gutz
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - H van Pee
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - A V Anisovich
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - J C S Bacelar
- Kernfysisch Versneller Instituut, University of Groningen, 9747 AA Groningen, The Netherlands
| | - B Bantes
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - O Bartholomy
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - D Bayadilov
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - R Beck
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - Yu Beloglazov
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - R Castelijns
- Kernfysisch Versneller Instituut, University of Groningen, 9747 AA Groningen, The Netherlands
| | - V Crede
- Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
| | - H Dutz
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - D Elsner
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - R Ewald
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - F Frommberger
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - M Fuchs
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - Ch Funke
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - R Gregor
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - A Gridnev
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - W Hillert
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - Ph Hoffmeister
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - I Horn
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - I Jaegle
- Physikalisches Institut, Universität Basel, 4056 Basel, Switzerland
| | - J Junkersfeld
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - H Kalinowsky
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - S Kammer
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - V Kleber
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - Frank Klein
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - Friedrich Klein
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - E Klempt
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - M Kotulla
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
- Physikalisches Institut, Universität Basel, 4056 Basel, Switzerland
| | - B Krusche
- Physikalisches Institut, Universität Basel, 4056 Basel, Switzerland
| | - M Lang
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - H Löhner
- Kernfysisch Versneller Instituut, University of Groningen, 9747 AA Groningen, The Netherlands
| | - I Lopatin
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - S Lugert
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - T Mertens
- Physikalisches Institut, Universität Basel, 4056 Basel, Switzerland
| | - J G Messchendorp
- Kernfysisch Versneller Instituut, University of Groningen, 9747 AA Groningen, The Netherlands
| | - V Metag
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - B Metsch
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - M Nanova
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - V Nikonov
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - D Novinski
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - R Novotny
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - M Ostrick
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - L Pant
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - M Pfeiffer
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - D Piontek
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - A Roy
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - A V Sarantsev
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - Ch Schmidt
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - H Schmieden
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - S Shende
- Kernfysisch Versneller Instituut, University of Groningen, 9747 AA Groningen, The Netherlands
| | - A Süle
- Physikalisches Institut, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - V V Sumachev
- Petersburg Nuclear Physics Institute, Gatchina, Leningrad district 188300, Russia
| | - T Szczepanek
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - U Thoma
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - D Trnka
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - R Varma
- II. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - D Walther
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - Ch Wendel
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
| | - A Wilson
- Helmholtz-Institut für Strahlen- und Kernphysik, Friedrich-Wilhelms Universität, 53115 Bonn, Germany
- Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
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16
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Tarbert CM, Watts DP, Glazier DI, Aguar P, Ahrens J, Annand JRM, Arends HJ, Beck R, Bekrenev V, Boillat B, Braghieri A, Branford D, Briscoe WJ, Brudvik J, Cherepnya S, Codling R, Downie EJ, Foehl K, Grabmayr P, Gregor R, Heid E, Hornidge D, Jahn O, Kashevarov VL, Knezevic A, Kondratiev R, Korolija M, Kotulla M, Krambrich D, Krusche B, Lang M, Lisin V, Livingston K, Lugert S, MacGregor IJD, Manley DM, Martinez M, McGeorge JC, Mekterovic D, Metag V, Nefkens BMK, Nikolaev A, Novotny R, Owens RO, Pedroni P, Polonski A, Prakhov SN, Price JW, Rosner G, Rost M, Rostomyan T, Schadmand S, Schumann S, Sober D, Starostin A, Supek I, Thomas A, Unverzagt M, Walcher T, Zana L, Zehr F. Neutron skin of (208)pb from coherent pion photoproduction. Phys Rev Lett 2014; 112:242502. [PMID: 24996085 DOI: 10.1103/physrevlett.112.242502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Indexed: 06/03/2023]
Abstract
Information on the size and shape of the neutron skin on (208)Pb is extracted from coherent pion photoproduction cross sections measured using the Crystal Ball detector together with the Glasgow tagger at the MAMI electron beam facility. On exploitation of an interpolated fit of a theoretical model to the measured cross sections, the half-height radius and diffuseness of the neutron distribution are found to be c(n)=6.70±0.03(stat.) fm and a(n)=0.55±0.01(stat.)(-0.03)(+0.02)(sys.) fm, respectively, corresponding to a neutron skin thickness Δr(np)=0.15±0.03(stat.)(-0.03)(+0.01)(sys.) fm. The results give the first successful extraction of a neutron skin thickness with an electromagnetic probe and indicate that the skin of (208)Pb has a halo character. The measurement provides valuable new constraints on both the structure of nuclei and the equation of state for neutron-rich matter.
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Affiliation(s)
- C M Tarbert
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - D P Watts
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - D I Glazier
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - P Aguar
- Institut für Kernphysik, University of Mainz, Germany
| | - J Ahrens
- Institut für Kernphysik, University of Mainz, Germany
| | - J R M Annand
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - H J Arends
- Institut für Kernphysik, University of Mainz, Germany
| | - R Beck
- Institut für Kernphysik, University of Mainz, Germany and Helmholtz-Institut für Strahlen- und Kernphysik, University Bonn, Germany
| | - V Bekrenev
- Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - B Boillat
- Institut für Physik, University of Basel, Basel, Switzerland
| | | | - D Branford
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - W J Briscoe
- Center for Nuclear Studies, The George Washington University, Washington, D.C. 20052, USA
| | - J Brudvik
- University of California at Los Angeles, Los Angeles, California 90095, USA
| | | | - R Codling
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E J Downie
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - K Foehl
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - P Grabmayr
- Physikalisches Institut Universität Tübingen, Tübingen, Germany
| | - R Gregor
- II. Physikalisches Institut, University of Giessen, Germany
| | - E Heid
- Institut für Kernphysik, University of Mainz, Germany
| | - D Hornidge
- Mount Allison University, Sackville, New Brunswick E4L 1E6, Canada
| | - O Jahn
- Institut für Kernphysik, University of Mainz, Germany
| | | | - A Knezevic
- Rudjer Boskovic Institute, Zagreb, Croatia
| | | | - M Korolija
- Rudjer Boskovic Institute, Zagreb, Croatia
| | - M Kotulla
- Institut für Physik, University of Basel, Basel, Switzerland
| | - D Krambrich
- Institut für Kernphysik, University of Mainz, Germany and Helmholtz-Institut für Strahlen- und Kernphysik, University Bonn, Germany
| | - B Krusche
- Institut für Physik, University of Basel, Basel, Switzerland
| | - M Lang
- Institut für Kernphysik, University of Mainz, Germany and Helmholtz-Institut für Strahlen- und Kernphysik, University Bonn, Germany
| | - V Lisin
- Institute for Nuclear Research, Moscow, Russia
| | - K Livingston
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - S Lugert
- II. Physikalisches Institut, University of Giessen, Germany
| | - I J D MacGregor
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - D M Manley
- Kent State University, Kent, Ohio 44240, USA
| | - M Martinez
- Institut für Kernphysik, University of Mainz, Germany
| | - J C McGeorge
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - V Metag
- II. Physikalisches Institut, University of Giessen, Germany
| | - B M K Nefkens
- University of California at Los Angeles, Los Angeles, California 90095, USA
| | - A Nikolaev
- Institut für Kernphysik, University of Mainz, Germany and Helmholtz-Institut für Strahlen- und Kernphysik, University Bonn, Germany
| | - R Novotny
- II. Physikalisches Institut, University of Giessen, Germany
| | - R O Owens
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - A Polonski
- Institute for Nuclear Research, Moscow, Russia
| | - S N Prakhov
- University of California at Los Angeles, Los Angeles, California 90095, USA
| | - J W Price
- University of California at Los Angeles, Los Angeles, California 90095, USA
| | - G Rosner
- SUPA, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - M Rost
- Institut für Kernphysik, University of Mainz, Germany
| | | | - S Schadmand
- II. Physikalisches Institut, University of Giessen, Germany
| | - S Schumann
- Institut für Kernphysik, University of Mainz, Germany and Helmholtz-Institut für Strahlen- und Kernphysik, University Bonn, Germany
| | - D Sober
- The Catholic University of America, Washington, D.C. 20064, USA
| | - A Starostin
- University of California at Los Angeles, Los Angeles, California 90095, USA
| | - I Supek
- Rudjer Boskovic Institute, Zagreb, Croatia
| | - A Thomas
- Institut für Kernphysik, University of Mainz, Germany
| | - M Unverzagt
- Institut für Kernphysik, University of Mainz, Germany and Helmholtz-Institut für Strahlen- und Kernphysik, University Bonn, Germany
| | - Th Walcher
- Institut für Kernphysik, University of Mainz, Germany
| | - L Zana
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - F Zehr
- Institut für Physik, University of Basel, Basel, Switzerland
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17
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Sikora MH, Watts DP, Glazier DI, Aguar-Bartolomé P, Akasoy LK, Annand JRM, Arends HJ, Bantawa K, Beck R, Bekrenev VS, Berghäuser H, Braghieri A, Branford D, Briscoe WJ, Brudvik J, Cherepnya S, Codling RFB, Demissie BT, Downie EJ, Drexler P, Fil'kov LV, Freehart B, Gregor R, Hamilton D, Heid E, Hornidge D, Howdle DA, Jaegle I, Jahn O, Jude TC, Kashevarov VL, Keshelashvili I, Kondratiev R, Korolija M, Kotulla M, Koulbardis AA, Kruglov SP, Krusche B, Lisin V, Livingston K, MacGregor IJD, Maghrbi Y, Manley DM, Marinides Z, Martinez M, McGeorge JC, McKinnon B, McNicoll EF, Mekterovic D, Metag V, Micanovic S, Middleton DG, Mushkarenkov A, Nefkens BMK, Nikolaev A, Novotny R, Ostrick M, Otte PB, Oussena B, Pedroni P, Pheron F, Polonski A, Prakhov S, Robinson J, Rosner G, Rostomyan T, Schumann S, Sober DI, Starostin A, Strakovsky II, Suarez IM, Supek I, Thiel M, Thomas A, Unverzagt M, Werthmüller D, Workman RL, Zamboni I, Zehr F. Measurement of the 1H(γ, p)π0 reaction using a novel nucleon spin polarimeter. Phys Rev Lett 2014; 112:022501. [PMID: 24484003 DOI: 10.1103/physrevlett.112.022501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Indexed: 06/03/2023]
Abstract
We report the first large-acceptance measurement of polarization transfer from a polarized photon beam to a recoiling nucleon. The measurement pioneers a novel polarimetry technique, which can be applied to many other nuclear and hadron physics experiments. The commissioning reaction of 1H(γ, p)π0 in the range 0.4<Eγ<1.4 GeV validates the technique and provides essential new data to constrain the excitation spectrum of the nucleon.
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Affiliation(s)
- M H Sikora
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - D P Watts
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - D I Glazier
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - P Aguar-Bartolomé
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - L K Akasoy
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - J R M Annand
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - H J Arends
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - K Bantawa
- Kent State University, Kent, Ohio 44242, USA
| | - R Beck
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, D-53115 Bonn, Germany
| | - V S Bekrenev
- Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
| | - H Berghäuser
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | | | - D Branford
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - W J Briscoe
- The George Washington University, Washington, D.C. 20052, USA
| | - J Brudvik
- University of California Los Angeles, Los Angeles, California 90095-1547, USA
| | - S Cherepnya
- Lebedev Physical Institute, 119991 Moscow, Russia
| | - R F B Codling
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - B T Demissie
- The George Washington University, Washington, D.C. 20052, USA
| | - E J Downie
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany and SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom and The George Washington University, Washington, D.C. 20052, USA
| | - P Drexler
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | - L V Fil'kov
- Lebedev Physical Institute, 119991 Moscow, Russia
| | - B Freehart
- The George Washington University, Washington, D.C. 20052, USA
| | - R Gregor
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | - D Hamilton
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E Heid
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany and The George Washington University, Washington, D.C. 20052, USA
| | - D Hornidge
- Mount Allison University, Sackville, New Brunswick E4L3B5, Canada
| | - D A Howdle
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - I Jaegle
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
| | - O Jahn
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - T C Jude
- SUPA, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | | | - I Keshelashvili
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
| | - R Kondratiev
- Institute for Nuclear Research, 125047 Moscow, Russia
| | - M Korolija
- Rudjer Boskovic Institute, HR-10000 Zagreb, Croatia
| | - M Kotulla
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | - A A Koulbardis
- Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
| | - S P Kruglov
- Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
| | - B Krusche
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
| | - V Lisin
- Institute for Nuclear Research, 125047 Moscow, Russia
| | - K Livingston
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - I J D MacGregor
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Y Maghrbi
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
| | - D M Manley
- Kent State University, Kent, Ohio 44242, USA
| | - Z Marinides
- The George Washington University, Washington, D.C. 20052, USA
| | - M Martinez
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - J C McGeorge
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - B McKinnon
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E F McNicoll
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - D Mekterovic
- Rudjer Boskovic Institute, HR-10000 Zagreb, Croatia
| | - V Metag
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | - S Micanovic
- Rudjer Boskovic Institute, HR-10000 Zagreb, Croatia
| | - D G Middleton
- Mount Allison University, Sackville, New Brunswick E4L3B5, Canada
| | | | - B M K Nefkens
- University of California Los Angeles, Los Angeles, California 90095-1547, USA
| | - A Nikolaev
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, D-53115 Bonn, Germany
| | - R Novotny
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | - M Ostrick
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - P B Otte
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - B Oussena
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany and The George Washington University, Washington, D.C. 20052, USA
| | - P Pedroni
- INFN Sezione di Pavia, I-27100 Pavia, Italy
| | - F Pheron
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
| | - A Polonski
- Institute for Nuclear Research, 125047 Moscow, Russia
| | - S Prakhov
- University of California Los Angeles, Los Angeles, California 90095-1547, USA
| | - J Robinson
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - G Rosner
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - S Schumann
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - D I Sober
- The Catholic University of America, Washington D.C. 20064, USA
| | - A Starostin
- University of California Los Angeles, Los Angeles, California 90095-1547, USA
| | - I I Strakovsky
- The George Washington University, Washington, D.C. 20052, USA
| | - I M Suarez
- University of California Los Angeles, Los Angeles, California 90095-1547, USA
| | - I Supek
- Rudjer Boskovic Institute, HR-10000 Zagreb, Croatia
| | - M Thiel
- II Physikalisches Institut, University of Giessen, D-35392 Giessen, Germany
| | - A Thomas
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - M Unverzagt
- Institut für Kernphysik, University of Mainz, D-55099 Mainz, Germany
| | - D Werthmüller
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
| | - R L Workman
- The George Washington University, Washington, D.C. 20052, USA
| | - I Zamboni
- Rudjer Boskovic Institute, HR-10000 Zagreb, Croatia
| | - F Zehr
- Department Physik, University of Basel, CH-4056 Basel, Switzerland
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18
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Krambrich D, Zehr F, Fix A, Roca L, Aguar P, Ahrens J, Annand JRM, Arends HJ, Beck R, Bekrenev V, Boillat B, Braghieri A, Branford D, Briscoe WJ, Brudvik J, Cherepnya S, Codling R, Downie EJ, Dexler P, Glazier DI, Grabmayr P, Gregor R, Heid E, Hornidge D, Jahn O, Kashevarov VL, Knezevic A, Kondratiev R, Korolija M, Kotulla M, Krusche B, Kulbardis A, Lang M, Lisin V, Livingston K, Lugert S, MacGregor IJD, Manley DM, Martinez M, McGeorge JC, Mekterovic D, Metag V, Nefkens BMK, Nikolaev A, Pedroni P, Pheron F, Polonski A, Prakhov SN, Price JW, Rosner G, Rost M, Rostomyan T, Schumann S, Sober D, Starostin A, Supek I, Tarbert CM, Thomas A, Unverzagt M, Walcher T, Watts DP. Beam-helicity asymmetries in double-pion photoproduction off the proton. Phys Rev Lett 2009; 103:052002. [PMID: 19792489 DOI: 10.1103/physrevlett.103.052002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 06/18/2009] [Indexed: 05/28/2023]
Abstract
Beam-helicity asymmetries have been measured at the MAMI accelerator in Mainz in the three isospin channels gamma[over -->]p-->pi(+)pi(0)n, gamma[over -->]p-->pi(0)pi(0)p, and gamma[over -->]p-->pi(+)pi(-)p. The circularly polarized photons, produced from bremsstrahlung of longitudinally polarized electrons, were tagged with the Glasgow magnetic spectrometer. Charged pions and the decay photons of pi(0) mesons were detected in a 4pi electromagnetic calorimeter which combined the Crystal Ball detector with the TAPS detector. The precisely measured asymmetries are very sensitive to details of the production processes and are thus key observables in the modeling of the reaction dynamics.
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Affiliation(s)
- D Krambrich
- Institut für Kernphysik, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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19
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Jaegle I, Mertens T, Anisovich AV, Bacelar JCS, Bantes B, Bartholomy O, Bayadilov D, Beck R, Beloglazov YA, Castelijns R, Crede V, Dutz H, Ehmanns A, Elsner D, Essig K, Ewald R, Fabry I, Fuchs M, Funke C, Gothe R, Gregor R, Gridnev AB, Gutz E, Höffgen S, Hoffmeister P, Horn I, Junkersfeld J, Kalinowsky H, Kammer S, Kleber V, Klein F, Klein F, Klempt E, Konrad M, Kotulla M, Krusche B, Lang M, Langheinrich J, Löhner H, Lopatin IV, Lotz J, Lugert S, Menze D, Messchendorp JG, Metag V, Morales C, Nanova M, Nikonov VA, Novinski D, Novotny R, Ostrick M, Pant LM, van Pee H, Pfeiffer M, Radkov A, Roy A, Sarantsev AV, Schadmand S, Schmidt C, Schmieden H, Schoch B, Shende SV, Sokhoyan V, Süle A, Sumachev VV, Szczepanek T, Thoma U, Trnka D, Varma R, Walther D, Weinheimer C, Wendel C. Quasifree photoproduction of eta mesons off the neutron. Phys Rev Lett 2008; 100:252002. [PMID: 18643655 DOI: 10.1103/physrevlett.100.252002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Indexed: 05/26/2023]
Abstract
Quasifree photoproduction of eta mesons off nucleons bound in the deuteron has been measured with the CBELSA/TAPS detector for incident photon energies up to 2.5 GeV at the Bonn ELSA accelerator. The eta mesons have been detected in coincidence with recoil protons and recoil neutrons, which allows a detailed comparison of the quasifree n(gamma,eta)n and p(gamma,eta)p reactions. The excitation function for eta production off the neutron shows a pronounced bumplike structure at W=1.68 GeV (E{gamma} approximately 1 GeV), which is absent for the proton.
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Affiliation(s)
- I Jaegle
- Department Physik, Universität Basel, Switzerland
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Kotulla M, Trnka D, Mühlich P, Anton G, Bacelar JCS, Bartholomy O, Bayadilov D, Beloglazov YA, Bogendörfer R, Castelijns R, Crede V, Dutz H, Ehmanns A, Elsner D, Ewald R, Fabry I, Fuchs M, Essig K, Funke C, Gothe R, Gregor R, Gridnev AB, Gutz E, Höffgen S, Hoffmeister P, Horn I, Hössl J, Jaegle I, Junkersfeld J, Kalinowsky H, Klein F, Klein F, Klempt E, Konrad M, Kopf B, Krusche B, Langheinrich J, Löhner H, Lopatin IV, Lotz J, Lugert S, Menze D, Messchendorp JG, Mertens T, Metag V, Mosel U, Nanova M, Novotny R, Ostrick M, Pant LM, van Pee H, Pfeiffer M, Roy A, Radkov A, Schadmand S, Schmidt C, Schmieden H, Schoch B, Shende S, Suft G, Sumachev VV, Szczepanek T, Süle A, Thoma U, Varma R, Walther D, Weinheimer C, Wendel C. Modification of the omega-meson lifetime in nuclear matter. Phys Rev Lett 2008; 100:192302. [PMID: 18518443 DOI: 10.1103/physrevlett.100.192302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Indexed: 05/26/2023]
Abstract
Information on hadron properties in the nuclear medium has been derived from the photoproduction of omega mesons on the nuclei C, Ca, Nb, and Pb using the Crystal Barrel/TAPS detector at the ELSA tagged photon facility in Bonn. The dependence of the omega-meson cross section on the nuclear mass number has been compared with three different types of models: a Glauber analysis, a Boltzmann-Uehling-Uhlenbeck analysis of the Giessen theory group, and a calculation by the Valencia theory group. In all three cases, the inelastic omega width is found to be 130-150 MeV/c(2) at normal nuclear matter density for an average 3-momentum of 1.1 GeV/c. In the rest frame of the omega meson, this inelastic omega width corresponds to a reduction of the omega lifetime by a factor approximately 30. For the first time, the momentum dependent omegaN cross section has been extracted from the experiment and is in the range of 70 mb.
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Affiliation(s)
- M Kotulla
- II Physikalisches Institut, Universität Giessen, Giessen, Germany
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Tarbert CM, Watts DP, Aguar P, Ahrens J, Annand JRM, Arends HJ, Beck R, Bekrenev V, Boillat B, Braghieri A, Branford D, Briscoe WJ, Brudvik J, Cherepnya S, Codling R, Downie EJ, Föhl K, Glazier DI, Grabmayr P, Gregor R, Heid E, Hornidge D, Jahn O, Kashevarov VL, Knezevic A, Kondratiev R, Korolija M, Kotulla M, Krambrich D, Krusche B, Lang M, Lisin V, Livingston K, Lugert S, Macgregor IJD, Manley DM, Martinez M, McGeorge JC, Mekterovic D, Metag V, Nefkens BMK, Nikolaev A, Novotny R, Owens RO, Pedroni P, Polonski A, Prakhov SN, Price JW, Rosner G, Rost M, Rostomyan T, Schadmand S, Schumann S, Sober D, Starostin A, Supek I, Thomas A, Unverzagt M, Walcher T, Zehr F. Incoherent neutral pion photoproduction on 12C. Phys Rev Lett 2008; 100:132301. [PMID: 18517938 DOI: 10.1103/physrevlett.100.132301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Indexed: 05/26/2023]
Abstract
We present the first detailed measurement of incoherent photoproduction of neutral pions to a discrete state of a residual nucleus. The 12C(gamma,pi(0))(12)C*(4.4 MeV) reaction has been studied with the Glasgow photon tagger at MAMI employing a new technique which uses the large solid angle Crystal Ball detector both as a pi(0) spectrometer and to detect decay photons from the excited residual nucleus. The technique has potential applications to a broad range of future nuclear measurements with the Crystal Ball and similar detector systems elsewhere. Such data are sensitive to the propagation of the Delta in the nuclear medium and will give the first information on matter transition form factors from measurements with an electromagnetic probe. The incoherent cross sections are compared to two theoretical predictions including a Delta-hole model.
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Affiliation(s)
- C M Tarbert
- School of Physics, University of Edinburgh, Edinburgh, United Kingdom
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Trnka D, Anton G, Bacelar JCS, Bartholomy O, Bayadilov D, Beloglazov YA, Bogendörfer R, Castelijns R, Crede V, Dutz H, Ehmanns A, Elsner D, Ewald R, Fabry I, Fuchs M, Essig K, Funke C, Gothe R, Gregor R, Gridnev AB, Gutz E, Höffgen S, Hoffmeister P, Horn I, Hössl J, Jaegle I, Junkersfeld J, Kalinowsky H, Klein F, Klein F, Klempt E, Konrad M, Kopf B, Kotulla M, Krusche B, Langheinrich J, Löhner H, Lopatin IV, Lotz J, Lugert S, Menze D, Messchendorp JG, Mertens T, Metag V, Morales C, Nanova M, Novotny R, Ostrick M, Pant LM, van Pee H, Pfeiffer M, Roy A, Radkov A, Schadmand S, Schmidt C, Schmieden H, Schoch B, Shende S, Suft G, Sumachev VV, Szczepanek T, Süle A, Thoma U, Varma R, Walther D, Weinheimer C, Wendel C. Observation of in-medium modifications of the omega meson. Phys Rev Lett 2005; 94:192303. [PMID: 16090166 DOI: 10.1103/physrevlett.94.192303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Indexed: 05/03/2023]
Abstract
The photoproduction of omega mesons on nuclei has been investigated using the Crystal Barrel/TAPS experiment at the ELSA tagged photon facility in Bonn. The aim is to study possible in-medium modifications of the omega meson via the reaction gamma + A --> omega + X --> pi(0)gamma + X('). Results obtained for Nb are compared to a reference measurement on a LH2 target. While for recoiling, long-lived mesons (pi(0), eta, and eta;(')), which decay outside of the nucleus, a difference in the line shape for the two data samples is not observed, we find a significant enhancement towards lower masses for omega mesons produced on the Nb target. For momenta less than 500 MeV/c an in-medium omega meson mass of M(medium) = [722(+4)(-4)(stat)+35-5(syst)] MeV/c(2) has been deduced at an estimated average nuclear density of 0.6rho(0).
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Affiliation(s)
- D Trnka
- II. Physikalisches Institut, Universität Giessen, Germany
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Gregor R. [Psychiatric rehabilitation in the aspect of a large psychiatric institution]. Psychiatr Pol 1991; 25:86-90. [PMID: 1821996] [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: 12/28/2022]
Affiliation(s)
- R Gregor
- Oddziału Psychiatrycznego Szpitala z poliklinika, Trinec Czecho-Słowacja
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Gregor R. [An unusual attempted suicide by lead poisoning]. Cas Lek Cesk 1991; 130:210-2. [PMID: 2013074] [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: 12/29/2022]
Affiliation(s)
- R Gregor
- Psychiatrické oddĕlení nemocnice s poliklinikou, Trinec
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Gregor R. [Psychiatric rehabilitation from the viewpoint of a large psychiatric facility]. Cesk Psychiatr 1990; 86:183-9. [PMID: 2225189] [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] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The paper makes the reader familiar with the results of activities of the central rehabilitation department in the Psychiatric Sanatorium in Kromĕríz. It postulates views regarding the technique of work with patients and pays special attention to the rehabilitation of patients with schizophrenic psychosis. In these patients the results of rehabilitation care at different rating levels were evaluated. In the field of ergotherapy the schizophrenic patients were evaluated by the therapists and instructors of occupational therapy on entry of and departure from the workshop or class, using the Engelsman--Hájek scale. Based on the results the hypothesis was confirmed of a lower working performance of patients with schizophrenic psychosis, as compared with other diagnostic groups. In the field of remedial exercise and special forms of psychiatric rehabilitation, such as educational and recreational activities, patients with schizophrenic psychosis were evaluated by a doctor and psychologist of the rehabilitation department of the psychiatric sanatorium for after--treatment of psychoses. The patients were evaluated by Wing's scale for chronic schizophrenia and by means of the Scale for Evaluation of Working Performance and Behaviour. According to the results of both scales no significant differences were found between the experimental groups where different forms of rehabilitation were accentuated, as compared with the control group engaged only in occupational therapy. Both scales revealed in both experimental groups highly significant improvement as regards resocialization within a very short period during which the patients were subjected to intense rehabilitation. Based on these results the author recommends further rehabilitation provisions.
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Affiliation(s)
- R Gregor
- Psychiatrické oddĕlení NsP, Trinec
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