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Bennett MJ, Dobson I, Benoit DM, Francesconi MG. Utilisation of CO 2 as "Structure Modifier" of Inorganic Solids. Chemistry 2021; 28:e202103608. [PMID: 34877730 DOI: 10.1002/chem.202103608] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 11/08/2022]
Abstract
Utilisation of CO2 as a chemical reagent is challenging, due to the molecule's inherent chemical stability. However, CO2 reacts promptly at high temperature (∼1000 °C) with alkaline-earth oxides to form carbonates and such reactions are used towards capture and re-utilisation. In this work, this concept is extended and CO2 is utilised as a reagent to modify the crystal structure of mixed-metal inorganic solids. Modification of the crystal structure is a "tool" used by materials scientists to tailor the physical property of solids. CO2 gas was reacted with several isostructural mixed-metal oxides Sr2 CuO3 , Sr1.8 Ba0.2 CuO3 and Ba2 PdO3 . These oxides are carefully selected to show anion vacancies in their crystal structure, to act as host sites for CO2 molecules, leading to the formation of carbonate anions, (CO3 )2- . The corresponding oxide carbonates were formed successfully and the favourable formation of SrCO3 as secondary phase was minimised via an innovative, yet simple synthetic procedure involving alternating of CO2 and air. We also derived a simple model to predict the kinetics of the reactions for the cuprates, using first-principles density functional theory and assimilating the reaction to a gas-surface process.
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Affiliation(s)
- M J Bennett
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - I Dobson
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - D M Benoit
- Department of Physics and Mathematics, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - M G Francesconi
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
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2
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020; 583:459-468. [PMID: 32353859 PMCID: PMC7431030 DOI: 10.1038/s41586-020-2286-9] [Citation(s) in RCA: 2844] [Impact Index Per Article: 711.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020. [PMID: 32353859 DOI: 10.1038/s41586‐020‐2286‐9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,J. David Gladstone Institutes, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv 2020:2020.03.22.002386. [PMID: 32511329 PMCID: PMC7239059 DOI: 10.1101/2020.03.22.002386] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Kala B Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Rakesh Ramachandran
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco
| | | | - Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,Biophysics Graduate Program, University of California, San Francisco
| | - Markus Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Devin Cavero
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joe Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Theo Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Björn Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Kris M White
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Biochemistry & Biophysics and Quantitative Biosciences Institute UCSF 600 16th St San Francisco, CA 94143
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98103
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Adolfo García-Sastre
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Psychiatry, San Francisco, CA, 94158, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Christophe d'Enfert
- Direction Scientifique, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Matt Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Stephen Floor
- Department of Cell and Tissue Biology, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - John Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kevan Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
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5
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Abstract
In this study, ultrasonic measurements of the fetal head area and abdominal area were obtained in 1200 patients with singleton pregnancies. The results from the 434 who have delivered, indicate that a large proportion of growth-retarded infants cannot be identified by a single late ultrasonic measurement of either area, at 32–34 weeks gestation, as has been previously suggested.
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6
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Bennett MJ, Brodie C, Idris NM, El-Kheir A, Asopa S, Robbins P. Patient factors that influence cerebral desaturation during transcatheter aortic valve implantation. Br J Anaesth 2016; 117:404-5. [PMID: 27543546 DOI: 10.1093/bja/aew241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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7
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Bennett MJ, Weatherall M, Webb G, Dudnikov SF, Lloyd CT. The impact of haemodilution and bypass pump flow on cerebral oxygen desaturation during cardiopulmonary bypass--A comparison of two systems of cardiopulmonary bypass. Perfusion 2014; 30:389-94. [PMID: 25143413 DOI: 10.1177/0267659114548256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To determine the influence of haemodilution, bypass flow rates and calculated oxygen delivery during cardiopulmonary bypass (CPB) with either a conventional CPB (C-CPB) circuit or a miniaturised (Mini-CPB) circuit on cerebral oxygen desaturation. The effect of minimal haemodilution with a Mini-CPB was investigated. PARTICIPANTS Eighty patients scheduled for elective cardiac surgery. INTERVENTION Oxygenated haemoglobin (O2Hb) and tissue oxygenation index (TOI) were measured with near-infrared spectroscopy (NIRS). RESULTS The average indexed bypass pump flow was significantly lower with Mini-CPB. When combined with haemoglobin concentration, the average oxygen delivery was the same between groups. Patients in the C-CPB group had a greater duration and severity of cerebral desaturation to a level <20% below baseline values, but none reached the depth and duration of the cerebral desaturation associated with poor outcome. Cerebral oxygen desaturation with C-CPB was significantly associated with low flows during bypass, whereas desaturation with Mini-CPB was associated with low perioperative haemoglobin concentration.
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Affiliation(s)
- M J Bennett
- Department of Cardiothoracic Anaesthesia, South West Cardiothoracic Centre, Plymouth, UK
| | - M Weatherall
- Department of Clinical Perfusion, South West Cardiothoracic Centre, Plymouth, UK
| | - G Webb
- Department of Clinical Perfusion, South West Cardiothoracic Centre, Plymouth, UK
| | - S F Dudnikov
- Department of Cardiothoracic Anaesthesia, South West Cardiothoracic Centre, Plymouth, UK
| | - C T Lloyd
- Department of Cardiac Surgery, South West Cardiothoracic Centre, Plymouth, UK
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8
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Risinger AL, Li J, Bennett MJ, Rohena CC, Peng J, Schriemer DC, Mooberry SL. Taccalonolide binding to tubulin imparts microtubule stability and potent in vivo activity. Cancer Res 2013; 73:6780-92. [PMID: 24048820 DOI: 10.1158/0008-5472.can-13-1346] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The taccalonolides are highly acetylated steroids that stabilize cellular microtubules and overcome multiple mechanisms of taxane resistance. Recently, two potent taccalonolides, AF and AJ, were identified that bind to tubulin directly and enhance microtubule polymerization. Extensive studies were conducted to characterize these new taccalonolides. AF and AJ caused aberrant mitotic spindles and bundling of interphase microtubules that differed from the effects of either paclitaxel or laulimalide. AJ also distinctly affected microtubule polymerization in that it enhanced the rate and extent of polymerization in the absence of any noticeable effect on microtubule nucleation. In addition, the resulting microtubules were found to be profoundly cold stable. These data, along with studies showing synergistic antiproliferative effects between AJ and either paclitaxel or laulimalide, suggest a distinct binding site. Direct binding studies demonstrated that AJ could not be displaced from microtubules by paclitaxel, laulimalide, or denaturing conditions, suggesting irreversible binding of AJ to microtubules. Mass spectrometry confirmed a covalent interaction of AJ with a peptide of β-tubulin containing the cyclostreptin-binding sites. Importantly, AJ imparts strong inter-protofilament stability in a manner different from other microtubule stabilizers that covalently bind to tubulin, consistent with the distinct effects of the taccalonolides as compared with other stabilizers. AF was found to be a potent and effective antitumor agent that caused tumor regression in the MDA-MB-231 breast cancer xenograft model. The antitumor efficacy of some taccalonolides, which stabilize microtubules in a manner different from other microtubule stabilizers, provides the impetus to explore the therapeutic potential of this site.
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Affiliation(s)
- A L Risinger
- Authors' Affiliations: Departments of Pharmacology, Medicine, and Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas; and Department of Biochemistry & Molecular Biology, University of Calgary, Alberta, Canada
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9
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Fozard JA, King JR, Bennett MJ. Modelling auxin efflux carrier phosphorylation and localization. J Theor Biol 2012; 319:34-49. [PMID: 23160141 DOI: 10.1016/j.jtbi.2012.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 10/15/2012] [Accepted: 11/05/2012] [Indexed: 01/17/2023]
Abstract
Regulation of the activity and localization of PIN-FORMED (PIN) membrane proteins, which facilitate efflux of the plant hormone auxin from cells, is important for plants to respond to environmental stimuli and to develop new organs. The protein kinase PINOID (PID) is involved in regulating PIN phosphorylation, and this is thought to affect PIN localization by biasing recycling towards shootwards (apical) (rather than rootwards (basal)) membrane domains. PID has been observed to undergo transient internalization following auxin treatment, and it has been suggested that this may be a result of calcium-dependent sequestration of PID by the calcium-binding protein TOUCH3 (TCH3). We present a mathematical formulation of these processes and examine the resulting steady-state and time-dependent behaviours in response to transient increases in cytosolic calcium. We further combine this model with one for the recycling of PINs in polarized cells and also examine its behaviour. The results provide insight into the behaviour observed experimentally and provide the basis for subsequent studies of the tissue-level implications of these subcellular processes for phenomena such as gravitropism.
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Affiliation(s)
- J A Fozard
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom.
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10
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Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics 2011; 12:298. [PMID: 21777475 PMCID: PMC3213248 DOI: 10.1186/1471-2105-12-298] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 07/22/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data. Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to generate integrated HIV-human interaction networks. RESULTS We have developed a web-based platform, termed GPS-Prot http://www.gpsprot.org, that allows for facile integration of different HIV interaction data types as well as inclusion of interactions between human proteins derived from publicly-available databases, including MINT, BioGRID and HPRD. The software has the ability to group proteins into functional modules or protein complexes, generating more intuitive network representations and also allows for the uploading of user-generated data. CONCLUSIONS GPS-Prot is a software tool that allows users to easily create comprehensive and integrated HIV-host networks. A major advantage of this platform compared to other visualization tools is its web-based format, which requires no software installation or data downloads. GPS-Prot allows novice users to quickly generate networks that combine both genetic and protein-protein interactions between HIV and its human host into a single representation. Ultimately, the platform is extendable to other host-pathogen systems.
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Affiliation(s)
- Marie E Fahey
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
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11
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Abstract
Mitochondrial fatty acid oxidation represents an important pathway for energy generation during periods of increased energy demand such as fasting, febrile illness and muscular exertion. In liver, the primary end products of the pathway are ketone bodies, which are released into the circulation and provide energy to tissues that are not able to oxidize fatty acids such as brain. Other tissues, such as cardiac and skeletal muscle are capable of direct utilization of the fatty acids as sources of energy. This article provides an overview of the pathogenesis of fatty acid oxidation disorders. It describes the different tissue involvement with the disease processes and correlates disease phenotype with the nature of the genetic defect for the known disorders of the pathway.
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Affiliation(s)
- M J Bennett
- Department of Pathology & Laboratory Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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12
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Middleton AM, King JR, Bennett MJ, Owen MR. Mathematical modelling of the Aux/IAA negative feedback loop. Bull Math Biol 2010; 72:1383-407. [PMID: 20135237 DOI: 10.1007/s11538-009-9497-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Accepted: 10/22/2009] [Indexed: 01/13/2023]
Abstract
The hormone auxin is implicated in regulating a diverse range of developmental processes in plants. Auxin acts in part by inducing the Aux/IAA genes. The associated pathway comprises multiple negative feedback loops (whereby Aux/IAA proteins can repress Aux/IAA genes) that are disrupted by auxin mediating the turnover of Aux/IAA protein. In this paper, we develop a mathematical model of a single Aux/IAA negative feedback loop in a population of identical cells. The model has a single steady-state. We explore parameter space to uncover a number of dynamical regimes. In particular, we identify the ratio between the Aux/IAA protein and mRNA turnover rates as a key parameter in the model. When this ratio is sufficiently small, the system can evolve to a stable limit cycle, corresponding to an oscillation in Aux/IAA expression levels. Otherwise, the steady-state is either a stable-node or a stable-spiral. These observations may shed light on recent experimental results.
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Affiliation(s)
- A M Middleton
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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13
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Li P, Huey-Tubman KE, Gao T, Li X, West AP, Bennett MJ, Bjorkman PJ. Erratum: The structure of a polyQ–anti-polyQ complex reveals binding according to a linear lattice model. Nat Struct Mol Biol 2007. [DOI: 10.1038/nsmb0607-568a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Li P, Huey-Tubman KE, Gao T, Li X, West AP, Bennett MJ, Bjorkman PJ. The structure of a polyQ-anti-polyQ complex reveals binding according to a linear lattice model. Nat Struct Mol Biol 2007; 14:381-7. [PMID: 17450152 DOI: 10.1038/nsmb1234] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 03/14/2007] [Indexed: 11/09/2022]
Abstract
Huntington and related neurological diseases result from expansion of a polyglutamine (polyQ) tract. The linear lattice model for the structure and binding properties of polyQ proposes that both expanded and normal polyQ tracts in the preaggregation state are random-coil structures but that an expanded polyQ repeat contains a larger number of epitopes recognized by antibodies or other proteins. The crystal structure of polyQ bound to MW1, an antibody against polyQ, reveals that polyQ adopts an extended, coil-like structure. Consistent with the linear lattice model, multimeric MW1 Fvs bind more tightly to longer than to shorter polyQ tracts and, compared with monomeric Fv, bind expanded polyQ repeats with higher apparent affinities. These results suggest a mechanism for the toxicity of expanded polyQ and a strategy to link anti-polyQ compounds to create high-avidity therapeutics.
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Affiliation(s)
- Pingwei Li
- Division of Biology 114-96, California Institute of Technology, Pasadena, California 91125, USA.
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15
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Hunt EJ, Pritchard J, Bennett MJ, Zhu X, Barrett DA, Allen T, Bale J, Newbury HJ. TheArabidopsis thaliana/Myzus persicaemodel system demonstrates that a single gene can influence the interaction between a plant and a sap-feeding insect. Mol Ecol 2006; 15:4203-13. [PMID: 17054513 DOI: 10.1111/j.1365-294x.2006.03090.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed an Arabidopsis thaliana/Myzus persicae model system to allow the dissection of plant/insect interactions at a molecular genetic level. This allows the examination of the role of single plant genes in the interaction between the plant and an aphid. Our initial studies have exploited an Arabidopsis genotype in which the function of the amino acid transporter ANT1 has been abolished. This mutation results in a change in the proportions of several amino acids within the phloem sieve elements (SEs) resulting in an increase in the proportion of essential amino acids. This has been measured using aphid stylectomy to collect SE samples, followed by a novel micellar electrokinetic chromatography method for amino acid analysis. The SE content represents the aphid's diet, and use of electrical penetration graph technology and honeydew clocks have demonstrated that this altered diet results in a change in the feeding rate of the aphid. Balance sheets can be produced to show the amount (nmoles/24 h) of each of 18 amino acids taken up and excreted by aphids feeding on wild type and ant1 mutant plants. The data show that aphids feeding on the ant1 mutant take up larger amounts of amino acids. However, we could not detect any effect on the reproductive rate of the aphids. The results show that, under experimental conditions, this model system can be used to identify plant genes that control the behaviour and fecundity of an insect pest.
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Affiliation(s)
- E J Hunt
- CABI Bioscience Switzerland Centre, 1 Rue des Grillons, Delémont, CH-2800, Switzerland
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16
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Abstract
Protein aggregation is a feature of both normal cellular assemblies and pathological protein depositions. Although the limited order of aggregates has often impeded their structural characterization, 3D domain swapping has been implicated in the formation of several protein aggregates. Here, we review known structures displaying 3D domain swapping in the context of amyloid and related fibrils, prion proteins, and macroscopic aggregates, and we discuss the possible involvement of domain swapping in protein deposition diseases.
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Affiliation(s)
- Melanie J Bennett
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
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17
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Dharmasiri S, Swarup R, Mockaitis K, Dharmasiri N, Singh SK, Kowalchyk M, Marchant A, Mills S, Sandberg G, Bennett MJ, Estelle M. AXR4 Is Required for Localization of the Auxin Influx Facilitator AUX1. Science 2006; 312:1218-20. [PMID: 16690816 DOI: 10.1126/science.1122847] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The AUX1 and PIN auxin influx and efflux facilitators are key regulators of root growth and development. For root gravitropism to occur, AUX1 and PIN2 must transport auxin via the lateral root cap to elongating epidermal cells. Genetic studies suggest that AXR4 functions in the same pathway as AUX1. Here we show that AXR4 is a previously unidentified accessory protein of the endoplasmic reticulum (ER) that regulates localization of AUX1 but not of PIN proteins. Loss of AXR4 resulted in abnormal accumulation of AUX1 in the ER of epidermal cells, indicating that the axr4 agravitropic phenotype is caused by defective AUX1 trafficking in the root epidermis.
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Affiliation(s)
- S Dharmasiri
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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18
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Abstract
Prostate-specific membrane antigen (PSMA) is highly expressed in prostate cancer cells and nonprostatic solid tumor neovasculature and is a target for anticancer imaging and therapeutic agents. PSMA acts as a glutamate carboxypeptidase (GCPII) on small molecule substrates, including folate, the anticancer drug methotrexate, and the neuropeptide N-acetyl-l-aspartyl-l-glutamate. Here we present the 3.5-A crystal structure of the PSMA ectodomain, which reveals a homodimer with structural similarity to transferrin receptor, a receptor for iron-loaded transferrin that lacks protease activity. Unlike transferrin receptor, the protease domain of PSMA contains a binuclear zinc site, catalytic residues, and a proposed substrate-binding arginine patch. Elucidation of the PSMA structure combined with docking studies and a proposed catalytic mechanism provides insight into the recognition of inhibitors and the natural substrate N-acetyl-l-aspartyl-l-glutamate. The PSMA structure will facilitate development of chemotherapeutics, cancer-imaging agents, and agents for treatment of neurological disorders.
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Affiliation(s)
- Mindy I Davis
- Division of Biology 114-96 and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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19
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20
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Niedzinski EJ, Chen YJ, Olson DC, Parker EA, Park H, Udove JA, Scollay R, McMahon BM, Bennett MJ. Enhanced systemic transgene expression after nonviral salivary gland transfection using a novel endonuclease inhibitor/DNA formulation. Gene Ther 2004; 10:2133-8. [PMID: 14625568 DOI: 10.1038/sj.gt.3302125] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene transfer to the major salivary glands is an attractive method for the systemic delivery of therapeutic proteins. To date, nonviral gene transfer to these glands has resulted in inadequate systemic protein concentrations. We believe that identification of the barriers responsible for this inefficient transfection will enable the development of enhanced nonviral gene transfer in salivary glands and other tissues. One potential barrier is the degradation of plasmid DNA by endonucleases. To test this hypothesis, we coadministered two endonuclease inhibitors ((zinc and aurintricarboxylic acid (ATA)) with plasmid DNA, containing the secreted alkaline phosphatase gene (SEAP), to the submandibular glands of rats. The effect of zinc and ATA on SEAP expression, tissue accumulation of plasmid DNA, and plasmid DNA stability was then characterized. We observed that mixtures containing zinc/DNA, ATA/DNA, and zinc/ATA/DNA significantly enhanced both systemic transgene expression and the amount of plasmid DNA associated with treated tissues. The relative endonuclease inhibitory activity of zinc, ATA, and zinc/ATA correlated with the observed effects on transfection efficacy. The use of zinc/ATA enhanced the efficacy of salivary gland transfection by at least 1000-fold versus DNA alone. Importantly, this improved performance resulted in robust systemic secretion of an exogenous protein (SEAP), thus demonstrating the potential this nonviral gene transfer technology has as a method to treat systemic protein deficiencies.
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Abstract
OBJECTIVE To study the effect of child birth on pelvic organ mobility in a prospective observational study. METHODS A total of 200 women were recruited early in their first ongoing pregnancy and examined by translabial ultrasound in the first/early second trimester, the late third trimester, and 2-5 months postpartum. Peripartal changes in the mobility of urethra, bladder, cervix, and rectal ampulla were correlated with labor and delivery data. RESULTS A total of 169 women returned postpartum (84.5%). Highly significant increases in organ mobility on Valsalva were found after vaginal delivery (P <.001), with forceps causing the most marked changes. Length of second stage, especially active second stage, correlated with an increase in pelvic organ descent (P =.03 to P <.001). The influence of gestational age, length of first stage, and birth weight did not reach significance. CONCLUSION Vaginal birth, in particular operative delivery, negatively affects pelvic organ support. This appears to be true for all three vaginal compartments. All forms of cesarean delivery were associated with relatively less pelvic organ descent. These findings may partly explain the protective effect of elective cesarean delivery for future symptoms of pelvic floor disorders.
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Affiliation(s)
- H P Dietz
- School of Women's and Childrens' Health, University of New South Wales, Randwick, New South Wales, Australia.
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22
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Perdekamp MG, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, Van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Flow measurements via two-particle azimuthal correlations in Au + Au collisions at sqrt [s(NN)]=130 GeV. Phys Rev Lett 2002; 89:212301. [PMID: 12443403 DOI: 10.1103/physrevlett.89.212301] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2002] [Indexed: 05/24/2023]
Abstract
Two-particle azimuthal correlation functions are presented for charged hadrons produced in Au+Au collisions at the Relativistic Heavy Ion Collider (sqrt [s(NN)]=130 GeV). The measurements permit determination of elliptic flow without event-by-event estimation of the reaction plane. The extracted elliptic flow values (v2) show significant sensitivity to both the collision centrality and the transverse momenta of emitted hadrons, suggesting rapid thermalization and relatively strong velocity fields. When scaled by the eccentricity of the collision zone epsilon, the scaled elliptic flow shows little or no dependence on centrality for charged hadrons with relatively low p(T). A breakdown of this epsilon scaling is observed for charged hadrons with pT >1.0 GeV/c.
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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Bennett MJ, Huey-Tubman KE, Herr AB, West AP, Ross SA, Bjorkman PJ. A linear lattice model for polyglutamine in CAG-expansion diseases. Proc Natl Acad Sci U S A 2002; 99:11634-9. [PMID: 12193654 PMCID: PMC129321 DOI: 10.1073/pnas.182393899] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Huntington's disease and several other neurological diseases are caused by expanded polyglutamine [poly(Gln)] tracts in different proteins. Mechanisms for expanded (>36 Gln residues) poly(Gln) toxicity include the formation of aggregates that recruit and sequester essential cellular proteins [Preisinger, E., Jordan, B. M., Kazantsev, A. & Housman, D. (1999) Phil. Trans. R. Soc. London B 354, 1029-1034; Chen, S., Berthelier, V., Yang, W. & Wetzel, R. (2001) J. Mol. Biol. 311, 173-182] and functional alterations, such as improper interactions with other proteins [Cummings, C. J. & Zoghbi, H. Y. (2000) Hum. Mol. Genet. 9, 909-916]. Expansion above the "pathologic threshold" ( approximately 36 Gln) has been proposed to induce a conformational transition in poly(Gln) tracts, which has been suggested as a target for therapeutic intervention. Here we show that structural analyses of soluble huntingtin exon 1 fusion proteins with 16 to 46 glutamine residues reveal extended structures with random coil characteristics and no evidence for a global conformational change above 36 glutamines. An antibody (MW1) Fab fragment, which recognizes full-length huntingtin in mouse brain sections, binds specifically to exon 1 constructs containing normal and expanded poly(Gln) tracts, with affinity and stoichiometry that increase with poly(Gln) length. These data support a "linear lattice" model for poly(Gln), in which expanded poly(Gln) tracts have an increased number of ligand-binding sites as compared with normal poly(Gln). The linear lattice model provides a rationale for pathogenicity of expanded poly(Gln) tracts and a structural framework for drug design.
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Affiliation(s)
- Melanie J Bennett
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, el-Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Mukhopadhyay D, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Pal D, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, Van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S, Zhou S. Measurement of Lambda and Lambda(macro) particles in Au+Au collisions at the square root of S(NN) = 130 GeV. Phys Rev Lett 2002; 89:092302. [PMID: 12190391 DOI: 10.1103/physrevlett.89.092302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2002] [Indexed: 05/23/2023]
Abstract
We present results on the measurement of Lambda and Lambda(macro) production in Au+Au collisions at square root of (S (NN) = 130 GeV with the PHENIX detector at the Relativistic Heavy Ion Collider. The transverse momentum spectra were measured for minimum bias and for the 5% most central events. The Lambda;/Lambda ratios are constant as a function of p(T) and the number of participants. The measured net Lambda density is significantly larger than predicted by models based on hadronic strings (e.g., HIJING) but in approximate agreement with models which include the gluon-junction mechanism.
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235
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25
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Net charge fluctuations in Au + Au interactions at sqrt[s(NN)]=130 GeV. Phys Rev Lett 2002; 89:082301. [PMID: 12190459 DOI: 10.1103/physrevlett.89.082301] [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: 03/21/2002] [Indexed: 05/23/2023]
Abstract
Data from Au + Au interactions at sqrt[s(NN)]=130 GeV, obtained with the PHENIX detector at the Relativistic Heavy-Ion Collider, are used to investigate local net charge fluctuations among particles produced near midrapidity. According to recent suggestions, such fluctuations may carry information from the quark-gluon plasma. This analysis shows that the fluctuations are dominated by a stochastic distribution of particles, but are also sensitive to other effects, like global charge conservation and resonance decays.
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Centrality dependence of pi(+/-), K(+/-), p, and (-)p production from sqrt[s(NN)] = 130 GeV Au + Au collisions at RHIC. Phys Rev Lett 2002; 88:242301. [PMID: 12059292 DOI: 10.1103/physrevlett.88.242301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Indexed: 05/23/2023]
Abstract
Identified pi(+/-), K(+/-), p, and (-)p transverse momentum spectra at midrapidity in sqrt[s(NN)] = 130 GeV Au+Au collisions were measured by the PHENIX experiment at RHIC as a function of collision centrality. Average transverse momenta increase with the number of participating nucleons in a similar way for all particle species. Within errors, all midrapidity particle yields per participant are found to be increasing with the number of participating nucleons. There is an indication that K(+/-), p, and (-)p yields per participant increase faster than the pi(+/-) yields. In central collisions at high transverse momenta (p(T) > or =2 GeV/c), (-)p and p yields are comparable to the pi(+/-) yields.
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Affiliation(s)
- K Adcox
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, Enokizono A, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, Van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Transverse-mass dependence of two-pion correlations in Au+Au collisions at square root[s(NN)] = 130 GeV. Phys Rev Lett 2002; 88:192302. [PMID: 12005626 DOI: 10.1103/physrevlett.88.192302] [Citation(s) in RCA: 4] [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: 01/16/2002] [Indexed: 05/23/2023]
Abstract
Two-pion correlations in square root[s(NN)] = 130 GeV Au+Au collisions at RHIC have been measured over a broad range of pair transverse momentum k(T) by the PHENIX experiment at RHIC. The k(T) dependent transverse radii are similar to results from heavy-ion collisions at square root[s(NN)] = 4.1, 4.9, and 17.3 GeV, whereas the longitudinal radius increases monotonically with beam energy. The ratio of the outwards to sidewards transverse radii (R(out)/R(side)) is consistent with unity and independent of k(T).
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Hachiya T, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, Van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Measurement of single electrons and implications for charm production in Au+Au collisions at square root[s(NN)] = 130 GeV. Phys Rev Lett 2002; 88:192303. [PMID: 12005627 DOI: 10.1103/physrevlett.88.192303] [Citation(s) in RCA: 7] [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: 02/05/2002] [Indexed: 05/23/2023]
Abstract
Transverse momentum spectra of electrons from Au+Au collisions at square root[s(NN)] = 130 GeV have been measured at midrapidity by the PHENIX experiment at the Relativistic Heavy Ion Collider. The spectra show an excess above the background from photon conversions and light hadron decays. The electron signal is consistent with that expected from semileptonic decays of charm. The yield of the electron signal dN(e)/dy for p(T) > 0.8 GeV/c is 0.025+/-0.004(stat)+/-0.010(syst) in central collisions, and the corresponding charm cross section is 380+/-60(stat)+/-200(syst) microb per binary nucleon-nucleon collision.
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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Rakheja D, Bennett MJ, Foster BM, Domiati-Saad R, Rogers BB. Evidence for fatty acid oxidation in human placenta, and the relationship of fatty acid oxidation enzyme activities with gestational age. Placenta 2002; 23:447-50. [PMID: 12061861 DOI: 10.1053/plac.2002.0808] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fetal disorders of mitochondrial fatty acid oxidation have recently been associated with obstetric complications including pre-eclampsia, Hemolysis, Elevated Liver enzymes, Low Platelets (HELLP) syndrome, placental floor infarct, and Acute Fatty Liver of Pregnancy (AFLP). These diseases occur in about a third of the mothers who are heterozygous for a defect in long chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) enzyme and who bear a fetus homozygous for the defect. The mechanism of this association is not clearly understood. In this study, we provide evidence that the placenta may be the site of production of toxic intermediates of fatty acid metabolism, which accumulate to cause liver damage in the mother. We show that two critical enzymes of long chain fatty acid metabolism, long chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) and short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), are active in the normal human placenta. There is an inverse correlation between the enzyme activity of both the enzymes and maternal gestational age during the second and third trimesters. We believe that the demonstration of fatty acid oxidation enzyme activity by the placenta is the first step towards assessing a possible role for fetal/placental fatty acid oxidation defects in the pathogenesis of a subset of pregnancy complications.
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Affiliation(s)
- D Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Bennett MJ. Nurse's "lifeline" parallels ups and downs of HIV epidemic. HIV Clin 2002; 13:8-9. [PMID: 11810825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- M J Bennett
- HIV Division of LSU Health Sciences Center, USA
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov V, Koehler D, Kohama T, Kotchetkov D, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek APT, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Suppression of hadrons with large transverse momentum in central Au+Au collisions at root square[s(NN)] = 130 GeV. Phys Rev Lett 2002; 88:022301. [PMID: 11801005 DOI: 10.1103/physrevlett.88.022301] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2001] [Indexed: 05/23/2023]
Abstract
Transverse momentum spectra for charged hadrons and for neutral pions in the range 1 GeV/c<p(T)<5 GeV/c have been measured by the PHENIX experiment at RHIC in Au+Au collisions at root square[s(NN)] = 130 GeV. At high p(T) the spectra from peripheral nuclear collisions are consistent with scaling the spectra from p+p collisions by the average number of binary nucleon-nucleon collisions. The spectra from central collisions are significantly suppressed when compared to the binary-scaled p+p expectation, and also when compared to similarly binary-scaled peripheral collisions, indicating a novel nuclear-medium effect in central nuclear collisions at RHIC energies.
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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West AP, Giannetti AM, Herr AB, Bennett MJ, Nangiana JS, Pierce JR, Weiner LP, Snow PM, Bjorkman PJ. Mutational analysis of the transferrin receptor reveals overlapping HFE and transferrin binding sites. J Mol Biol 2001; 313:385-97. [PMID: 11800564 DOI: 10.1006/jmbi.2001.5048] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [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: 01/12/2023]
Abstract
The transferrin receptor (TfR) binds two proteins critical for iron metabolism: transferrin (Tf) and HFE, the protein mutated in hereditary hemochromatosis. Previous results demonstrated that Tf and HFE compete for binding to TfR, suggesting that Tf and HFE bind to the same or an overlapping site on TfR. TfR is a homodimer that binds one Tf per polypeptide chain (2:2, TfR/Tf stoichiometry), whereas both 2:1 and 2:2 TfR/HFE stoichiometries have been observed. In order to more fully characterize the interaction between HFE and TfR, we determined the binding stoichiometry using equilibrium gel-filtration and analytical ultracentrifugation. Both techniques indicate that a 2:2 TfR/HFE complex can form at submicromolar concentrations in solution, consistent with the hypothesis that HFE competes for Tf binding to TfR by blocking the Tf binding site rather than by exerting an allosteric effect. To determine whether the Tf and HFE binding sites on TfR overlap, residues at the HFE binding site on TfR were identified from the 2.8 A resolution HFE-TfR co-crystal structure, then mutated and tested for their effects on HFE and Tf binding. The binding affinities of soluble TfR mutants for HFE and Tf were determined using a surface plasmon resonance assay. Substitutions of five TfR residues at the HFE binding site (L619A, R629A, Y643A, G647A and F650Q) resulted in significant reductions in Tf binding affinity. The findings that both HFE and Tf form 2:2 complexes with TfR and that mutations at the HFE binding site affect Tf binding support a model in which HFE and Tf compete for overlapping binding sites on TfR.
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Affiliation(s)
- A P West
- Division of Biology 156-29 , California Institute of Technology, Pasadena, CA 91125, USA
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Hauton D, Bennett MJ, Evans RD. Utilisation of triacylglycerol and non-esterified fatty acid by the working rat heart: myocardial lipid substrate preference. Biochim Biophys Acta 2001; 1533:99-109. [PMID: 11566447 DOI: 10.1016/s1388-1981(01)00146-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Utilisation and subsequent metabolic fate (oxidation; tissue lipid deposition) of non-esterified fatty acid (NEFA), very-low-density lipoprotein-triacylglycerol (VLDL-TAG), and chylomicron-triacylglycerol (CM-TAG) alone or in combination by isolated working rat heart were examined. Cardiac mechanical function was maintained regardless of lipid substrate used. NEFA and CM-TAG were assimilated to a greater extent than VLDL-TAG; CM-TAG utilisation (76+/-10 nmol fatty acid/min per g wet wt.; n=8), but not VLDL-TAG utilisation (16+/-2 nmol fatty acid/min per g wet wt.; n=8), was suppressed in the presence of NEFA, but TAG (CM or VLDL) did not alter NEFA utilisation (57+/-9 nmol fatty acid/min per g wet wt.; n=8). Most (about 75%) of the lipid utilised was oxidised. In the presence of NEFA, CM-TAG deposition as tissue lipid was preserved, despite decreased CM-TAG oxidation; metabolic fate of VLDL-TAG was unaffected by NEFA. TAG (CM or VLDL) in the perfusate tended to decrease lipoprotein lipase (LPL) activity; this may be a reflection of increased LPL turnover in the presence of lipoproteins.
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Affiliation(s)
- D Hauton
- Nuffield Department of Anaesthetics, University of Oxford, Radcliffe Infirmary, Woodstock Road, OX2 6HE, Oxford, UK
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Bennett MJ. Book Review: Teitz Fundamentals of Clinical Chemistry. Ann Clin Biochem 2001. [DOI: 10.1177/000456320103800521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- M J Bennett
- University of Texas Southwestern Medical Center Dallas TX, USA
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Van Veldhoven PP, Meyhi E, Squires RH, Fransen M, Fournier B, Brys V, Bennett MJ, Mannaerts GP. Fibroblast studies documenting a case of peroxisomal 2-methylacyl-CoA racemase deficiency: possible link between racemase deficiency and malabsorption and vitamin K deficiency. Eur J Clin Invest 2001; 31:714-22. [PMID: 11473573 DOI: 10.1046/j.1365-2362.2001.00877.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND 2-Methylacyl-CoA racemase interconverts the 2-methyl group of pristanoyl-CoA or the 25-methyl group of hydroxylated cholestanoyl-CoAs, allowing further peroxisomal desaturation of these compounds in man by the branched chain acyl-CoA oxidase, which recognise only the S-isomers. Hence, oxidation studies in fibroblasts, currently based on the use of racemic substrates such as [1-14C] pristanic acid, do not allow us to distinguish between a deficient racemase or an impaired oxidase. DESIGN To evaluate the racemase activity directly, the 2R-isomer of[1-14C] pristanic acid, as well as the 2R-isomer of 2-methyl-[1-14C] hexadecanoic, a synthetic pristanic acid substitute, were prepared and their degradation by cultured human skin fibroblasts was compared to that of the racemic substrates. RESULTS In fibroblasts in a young girl, presenting with elevated urinary levels of trihydroxycholestanoic acid metabolites but normal plasma levels of very long chain fatty acids, a partial deficient degradation of racemic [1-14C] pristanic acid was observed. Incorporation of 2R-[1-14C] pristanic acid in glycerolipids of the patient's fibroblasts proceeded normally, but breakdown was impaired. Similar findings were seen with the 2R-isomer of 2-methyl-[1-14C] hexadecanoic. These data, combined with the fact that the branched chain acyl-CoA oxidase, catalyzing the first oxidation step of pristanic acid and bile acid intermediates in man, appeared normal, suggested a peroxisomal beta-oxidation defect in the patient at the level of 2-methylacyl-CoA racemase. CONCLUSION Carboxy-labelled 2R-methyl branched chain fatty acids might be useful tools to document cases of racemase deficiencies. Because a brother of the patient died with a diagnosis of vitamin K deficiency, an impaired racemase might be responsible for other cases of unexplicable malabsorption.
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Affiliation(s)
- P P Van Veldhoven
- Katholieke Universiteit Leuven, Afdeling Farmacologie, Leuven, Belgium.
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser JM, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov D, Kochetkov V, Koehler D, Kohama T, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek AP, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Measurement of the midrapidity transverse energy distribution from square root of [(s)NN] = 130 GeV Au + Au collisions at RHIC. Phys Rev Lett 2001; 87:052301. [PMID: 11497762 DOI: 10.1103/physrevlett.87.052301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2001] [Indexed: 05/23/2023]
Abstract
The first measurement of energy produced transverse to the beam direction at the Relativistic Heavy-Ion Collider at Brookhaven National Laboratory is presented. The midrapidity transverse energy density per participating nucleon rises steadily with the number of participants, closely paralleling the rise in charged-particle density, such that <E(T)>/<N(ch)> remains relatively constant as a function of centrality. The energy density calculated via Bjorken's prescription for the 2% most central Au+Au collisions at square root[s(NN)] = 130 GeV is at least epsilon(Bj) = 4.6 GeV/fm(3), which is a factor of 1.6 larger than found at sqrt[s(NN)] = 17.2 GeV ( Pb+Pb at CERN).
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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Bennett MJ, Rinaldo P. The metabolic autopsy comes of age. Clin Chem 2001; 47:1145-6. [PMID: 11427443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Jones PM, Moffitt M, Joseph D, Harthcock PA, Boriack RL, Ibdah JA, Strauss AW, Bennett MJ. Accumulation of free 3-hydroxy fatty acids in the culture media of fibroblasts from patients deficient in long-chain l-3-hydroxyacyl-CoA dehydrogenase: a useful diagnostic aid. Clin Chem 2001; 47:1190-4. [PMID: 11427448] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
BACKGROUND The diagnosis of long-chain L-3-hydroxy-acyl-coenzyme A dehydrogenase (LCHAD) deficiency frequently requires the study of cultured fibroblasts. We developed such a test that does not require disruption and loss of the cells. METHODS We measured free 3-hydroxy fatty acids (3-OHFAs) in media of skin fibroblasts cultures from 11 patients with a genetic deficiency of LCHAD and the associated disorder of mitochondrial trifunctional protein (MTFP). Fibroblasts were cultured for 24 h with 100 micromol/L nonisotopic palmitate added. 3-OHFAs were measured by selected-ion monitoring, stable-isotope dilution gas chromatography-mass spectrometry with [(13)C]-labeled internal standards. RESULTS 3-OH-hexadecanoic and 3-OH-tetradecanoic FAs were increased 14- and 11-fold, respectively, in all patients with LCHAD or MTFP deficiency when compared with control fibroblast cell lines after overnight incubation with palmitate. 3-OH-dodecanoic FA demonstrated a modest, fivefold increase in LCHAD-deficient cells. The concentrations of all 3-OHFAs were similar whether or not the medium samples were hydrolyzed to release conjugated species such as acylcarnitines, suggesting that 3-OHFAs accumulate in the media as free FAs. CONCLUSIONS Measurement of 3-OHFA excretion from LCHAD- or MTFP-deficient cell lines can be used as a diagnostic tool. Free FAs are the predominant form of these abnormal metabolic intermediates in culture media.
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Affiliation(s)
- P M Jones
- University of Texas Southwestern Medical Center, Department of Pathology, Dallas, TX 75235, USA.
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Brown NF, Mullur RS, Subramanian I, Esser V, Bennett MJ, Saudubray JM, Feigenbaum AS, Kobari JA, Macleod PM, McGarry JD, Cohen JC. Molecular characterization of L-CPT I deficiency in six patients: insights into function of the native enzyme. J Lipid Res 2001; 42:1134-42. [PMID: 11441142] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Carnitine palmitoyltransferase I (CPT I) catalyzes the formation of acylcarnitine, the first step in the oxidation of long-chain fatty acids in mitochondria. The enzyme exists as liver (L-CPT I) and muscle (M-CPT I) isoforms that are encoded by separate genes. Genetic deficiency of L-CPT I, which has been reported in 16 patients from 13 families, is characterized by episodes of hypoketotic hypoglycemia beginning in early childhood and is usually associated with fasting or illness. To date, only two mutations associated with L-CPT I deficiency have been reported. In the present study we have identified and characterized the mutations underlying L-CPT I deficiency in six patients: five with classic symptoms of L-CPT I deficiency and one with symptoms that have not previously been associated with this disorder (muscle cramps and pain). Transfection of the mutant L-CPT I cDNAs in COS cells resulted in L-CPT I mRNA levels that were comparable to those expressed from the wild-type construct. Western blotting revealed lower levels of each of the mutant proteins, indicating that the low enzyme activity associated with these mutations was due, at least in part, to protein instability. The patient with atypical symptoms had approximately 20% of normal L-CPT I activity and was homozygous for a mutation (c.1436C-->T) that substituted leucine for proline at codon 479. Assays performed with his cultured skin fibroblasts indicated that this mutation confers partial resistance to the inhibitory effects of malonyl-CoA. The demonstration of L-CPT I deficiency in this patient suggests that the spectrum of clinical sequelae associated with loss or alteration of L-CPT I function may be broader than was previously recognized.
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Affiliation(s)
- N F Brown
- Departments of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA
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Bennett MJ, Harthcock PA, Boriack RL, Cohen JC. Impaired mitochondrial fatty acid oxidative flux in fibroblasts from a patient with malonyl-CoA decarboxylase deficiency. Mol Genet Metab 2001; 73:276-9. [PMID: 11461195 DOI: 10.1006/mgme.2001.3196] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Malonyl-CoA decarboxylase deficiency is a rare inborn error of metabolism. It has been suggested but never demonstrated that many of the clinical features arise due to inhibition of mitochondrial fatty acid oxidation by accumulated malonyl-CoA. We studied the oxidation of fatty acids in cultured skin fibroblasts from a recently described patient with malonyl-CoA decarboxylase deficiency. There was a marked reduction in the oxidation of palmitic and myristic acids both under baseline conditions and when the cells were cultured in the presence of high concentrations of acetate, a malonyl-CoA precursor. These results suggest that there is inhibition of fatty acid oxidation in malonyl-CoA decarboxylase deficiency and that this inhibition may be related to some of the clinical phenotypes.
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Affiliation(s)
- M J Bennett
- Department of Pathology, University of Texas Southwestern Medical Center at Dallas, USA.
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Ibdah JA, Paul H, Zhao Y, Binford S, Salleng K, Cline M, Matern D, Bennett MJ, Rinaldo P, Strauss AW. Lack of mitochondrial trifunctional protein in mice causes neonatal hypoglycemia and sudden death. J Clin Invest 2001; 107:1403-9. [PMID: 11390422 PMCID: PMC209324 DOI: 10.1172/jci12590] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [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: 12/20/2022] Open
Abstract
Mitochondrial trifunctional protein (MTP) is a hetero-octamer of four alpha and four beta subunits that catalyzes the final three steps of mitochondrial long chain fatty acid beta-oxidation. Human MTP deficiency causes Reye-like syndrome, cardiomyopathy, or sudden unexpected death. We used gene targeting to generate an MTP alpha subunit null allele and to produce mice that lack MTP alpha and beta subunits. The Mtpa(-/-) fetuses accumulate long chain fatty acid metabolites and have low birth weight compared with the Mtpa(+/-) and Mtpa(+/+) littermates. Mtpa(-/-) mice suffer neonatal hypoglycemia and sudden death 6-36 hours after birth. Analysis of the histopathological changes in the Mtpa(-/-) pups revealed rapid development of hepatic steatosis after birth and, later, significant necrosis and acute degeneration of the cardiac and diaphragmatic myocytes. This mouse model documents that intact mitochondrial long chain fatty acid oxidation is essential for fetal development and for survival after birth. Deficiency of MTP causes fetal growth retardation, neonatal hypoglycemia, and sudden death.
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Affiliation(s)
- J A Ibdah
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA.
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Abstract
In this article, we describe a relatively simple surgical option that we believe is indicated for use in cases of cervical incompetence. We discuss the advantages of this procedure to the surgeon and patient, and give details of 59 patients who have undergone this procedure one or more times over a 13-year period. A short review of the history of treatment of cervical incompetence and of recent trends for its management is also presented.
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Affiliation(s)
- M J Bennett
- University of New South Wales, Sydney, New South Wales, Australia
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Adcox K, Adler SS, Ajitanand NN, Akiba Y, Alexander J, Aphecetche L, Arai Y, Aronson SH, Averbeck R, Awes TC, Barish KN, Barnes PD, Barrette J, Bassalleck B, Bathe S, Baublis V, Bazilevsky A, Belikov S, Bellaiche FG, Belyaev ST, Bennett MJ, Berdnikov Y, Botelho S, Brooks ML, Brown DS, Bruner N, Bucher D, Buesching H, Bumazhnov V, Bunce G, Burward-Hoy J, Butsyk S, Carey TA, Chand P, Chang J, Chang WC, Chavez LL, Chernichenko S, Chi CY, Chiba J, Chiu M, Choudhury RK, Christ T, Chujo T, Chung MS, Chung P, Cianciolo V, Cole BA, D'Enterria DG, David G, Delagrange H, Denisov A, Deshpande A, Desmond EJ, Dietzsch O, Dinesh BV, Drees A, Durum A, Dutta D, Ebisu K, Efremenko YV, El Chenawi K, En'yo H, Esumi S, Ewell L, Ferdousi T, Fields DE, Fokin SL, Fraenkel Z, Franz A, Frawley AD, Fung SY, Garpman S, Ghosh TK, Glenn A, Godoi AL, Goto Y, Greene SV, Grosse Perdekamp M, Gupta SK, Guryn W, Gustafsson HA, Haggerty JS, Hamagaki H, Hansen AG, Hara H, Hartouni EP, Hayano R, Hayashi N, He X, Hemmick TK, Heuser J, Hibino M, Hill JC, Ho DS, Homma K, Hong B, Hoover A, Ichihara T, Imai K, Ippolitov MS, Ishihara M, Jacak BV, Jang WY, Jia J, Johnson BM, Johnson SC, Joo KS, Kametani S, Kang JH, Kann M, Kapoor SS, Kelly S, Khachaturov B, Khanzadeev A, Kikuchi J, Kim DJ, Kim HJ, Kim SY, Kim YG, Kinnison WW, Kistenev E, Kiyomichi A, Klein-Boesing C, Klinksiek S, Kochenda L, Kochetkov D, Kochetkov V, Koehler D, Kohama T, Kozlov A, Kroon PJ, Kurita K, Kweon MJ, Kwon Y, Kyle GS, Lacey R, Lajoie JG, Lauret J, Lebedev A, Lee DM, Leitch MJ, Li XH, Li Z, Lim DJ, Liu MX, Liu X, Liu Z, Maguire CF, Mahon J, Makdisi YI, Manko VI, Mao Y, Mark SK, Markacs S, Martinez G, Marx MD, Masaike A, Matathias F, Matsumoto T, McGaughey PL, Melnikov E, Merschmeyer M, Messer F, Messer M, Miake Y, Miller TE, Milov A, Mioduszewski S, Mischke RE, Mishra GC, Mitchell JT, Mohanty AK, Morrison DP, Moss JM, Mühlbacher F, Muniruzzaman M, Murata J, Nagamiya S, Nagasaka Y, Nagle JL, Nakada Y, Nandi BK, Newby J, Nikkinen L, Nilsson P, Nishimura S, Nyanin AS, Nystrand J, O'Brien E, Ogilvie CA, Ohnishi H, Ojha ID, Ono M, Onuchin V, Oskarsson A, Osterman L, Otterlund I, Oyama K, Paffrath L, Palounek AP, Pantuev VS, Papavassiliou V, Pate SF, Peitzmann T, Petridis AN, Pinkenburg C, Pisani RP, Pitukhin P, Plasil F, Pollack M, Pope K, Purschke ML, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Rosati M, Rose AA, Ryu SS, Saito N, Sakaguchi A, Sakaguchi T, Sako H, Sakuma T, Samsonov V, Sangster TC, Santo R, Sato HD, Sato S, Sawada S, Schlei BR, Schutz Y, Semenov V, Seto R, Shea TK, Shein I, Shibata TA, Shigaki K, Shiina T, Shin YH, Sibiriak IG, Silvermyr D, Sim KS, Simon-Gillo J, Singh CP, Singh V, Sivertz M, Soldatov A, Soltz RA, Sorensen S, Stankus PW, Starinsky N, Steinberg P, Stenlund E, Ster A, Stoll SP, Sugioka M, Sugitate T, Sullivan JP, Sumi Y, Sun Z, Suzuki M, Takagui EM, Taketani A, Tamai M, Tanaka KH, Tanaka Y, Taniguchi E, Tannenbaum MJ, Thomas J, Thomas JH, Thomas TL, Tian W, Tojo J, Torii H, Towell RS, Tserruya I, Tsuruoka H, Tsvetkov AA, Tuli SK, Tydesjö H, Tyurin N, Ushiroda T, van Hecke HW, Velissaris C, Velkovska J, Velkovsky M, Vinogradov AA, Volkov MA, Vorobyov A, Vznuzdaev E, Wang H, Watanabe Y, White SN, Witzig C, Wohn FK, Woody CL, Xie W, Yagi K, Yokkaichi S, Young GR, Yushmanov IE, Zajc WA, Zhang Z, Zhou S. Centrality dependence of charged particle multiplicity in Au-Au collisions at square root of (s)NN = 130 GeV. Phys Rev Lett 2001; 86:3500-3505. [PMID: 11328008 DOI: 10.1103/physrevlett.86.3500] [Citation(s) in RCA: 5] [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: 12/21/2000] [Indexed: 05/23/2023]
Abstract
We present results for the charged-particle multiplicity distribution at midrapidity in Au-Au collisions at square root of [s(NN)] = 130 GeV measured with the PHENIX detector at RHIC. For the 5% most central collisions we find dN(ch)/d eta(vertical line eta = 0) = 622+/-1(stat)+/-41(syst). The results, analyzed as a function of centrality, show a steady rise of the particle density per participating nucleon with centrality.
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Affiliation(s)
- K Adcox
- Vanderbilt University, Nashville, Tennessee 37235, USA
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Swarup R, Marchant A, Bennett MJ. Auxin transport: providing a sense of direction during plant development. Biochem Soc Trans 2001; 28:481-5. [PMID: 10961944] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Auxins are key regulators of plant development. Plants employ a specialized delivery system termed polar auxin transport to convey indole-3-acetic acid from source to target tissues. Auxin transport is mediated by the combined activities of specialized influx and efflux carriers. Mutational approaches in the model plant, Arabidopsis thaliana, have led to the molecular genetic characterization of putative auxin influx and efflux carrier components, AUX1 and AtPIN1. Both genes belong to distinct gene families that are being functionally characterized by using a reverse genetic approach in Arabidopsis. AtPIN proteins are asymmetrically localized within plant plasma membranes, providing a molecular mechanism for the characteristic polarity of auxin transport. We outline the epitope tagging strategy being used in our laboratory to immunolocalize AUX1 and discuss the implications of its subcellular localization for auxin redistribution within root apical tissues. Lastly, we describe a novel carrier-based mechanism that plant cells might use to determine their relative position(s) within an auxin gradient, drawing parallels with the mechanism of glucose perception in yeast.
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Affiliation(s)
- R Swarup
- School of Biological Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
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Bennett MJ. WIDETIME: an HIV Odyssey and hopes and fears: Rusti's story. J Assoc Nurses AIDS Care 2001; 12:105-6. [PMID: 11296725 DOI: 10.1016/s1055-3290(06)60138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Matern D, Schehata BM, Shekhawa P, Strauss AW, Bennett MJ, Rinaldo P. Placental floor infarction complicating the pregnancy of a fetus with long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiency. Mol Genet Metab 2001; 72:265-8. [PMID: 11243734 DOI: 10.1006/mgme.2000.3135] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
By postmortem biochemical and molecular genetic analyses, an 8-month-old infant was diagnosed with long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency, an inborn error of mitochondrial fatty acid beta-oxidation. He was born following a pregnancy complicated by a maternal floor infarction of the placenta, a disorder of unknown etiology. We speculate that the child's autosomal recessive fatty acid beta-oxidation disorder and the pregnancy complication are causally related.
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Affiliation(s)
- D Matern
- Department of Laboratory Medicine and Pathology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA.
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Abstract
OBJECTIVES To evaluate the feasibility of molecular prenatal diagnosis in families with mitochondrial trifunctional protein (TFP) mutations and prospectively study the effects of fetal genotype on pregnancy outcome. TFP catalyzes the last 3 steps in mitochondrial long-chain fatty acid oxidation. STUDY DESIGN We performed molecular prenatal diagnosis in 9 pregnancies, 8 in 6 families with isolated long-chain 3-hydroxyacyl-coenzyme A dehydrogenase (LCHAD) deficiency and one in a family with complete TFP deficiency. Analyses were performed on chorionic villous samples in 7 pregnancies and on amniocytes in 2. RESULTS Molecular prenatal diagnosis successfully identified the fetal genotype in all 9 pregnancies. Two fetuses were affected, and both pregnancies were terminated by family decision. Two other fetuses had normal genotype and 5 others were heterozygotes. These 7 pregnancies were uncomplicated, and all the offspring are alive and apparently healthy. Genotypes of the aborted fetuses and neonates were confirmed by molecular analysis and enzymatic assays. CONCLUSIONS Molecular prenatal diagnosis is possible and valid in guiding management of pregnancies in families with known TFP defects. Women heterozygous for TFP alpha-subunit mutations who carry fetuses with wild-type or heterozygous genotypes have uncomplicated pregnancies.
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Affiliation(s)
- J A Ibdah
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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Parry G, Delbarre A, Marchant A, Swarup R, Napier R, Perrot-Rechenmann C, Bennett MJ. Novel auxin transport inhibitors phenocopy the auxin influx carrier mutation aux1. Plant J 2001; 25:399-406. [PMID: 11260496 DOI: 10.1046/j.1365-313x.2001.00970.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The hormone auxin is transported in plants through the combined actions of diffusion and specific auxin influx and efflux carriers. In contrast to auxin efflux, for which there are well documented inhibitors, understanding the developmental roles of carrier-mediated auxin influx has been hampered by the absence of specific competitive inhibitors. However, several molecules that inhibit auxin influx in cultured cells have been described recently. The physiological effects of two of these novel influx carrier inhibitors, 1-naphthoxyacetic acid (1-NOA) and 3-chloro-4-hydroxyphenylacetic acid (CHPAA), have been investigated in intact seedlings and tissue segments using classical and new auxin transport bioassays. Both molecules do disrupt root gravitropism, which is a developmental process requiring rapid auxin redistribution. Furthermore, the auxin-insensitive and agravitropic root-growth characteristics of aux1 plants were phenocopied by 1-NOA and CHPAA. Similarly, the agravitropic phenotype of inhibitor-treated seedlings was rescued by the auxin 1-naphthaleneacetic acid, but not by 2,4-dichlorophenoxyacetic acid, again resembling the relative abilities of these two auxins to rescue the phenotype of aux1. Further investigations have shown that none of these compounds block polar auxin transport, and that CHPAA exhibits some auxin-like activity at high concentrations. Whilst results indicate that 1-NOA and CHPAA represent useful tools for physiological studies addressing the role of auxin influx in planta, 1-NOA is likely to prove the more useful of the two compounds.
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Affiliation(s)
- G Parry
- Division of Plant Sciences, School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
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Abstract
Juvenile neuronal ceroid lipofuscinosis (JNCL) is a severe autosomal recessive neurodegenerative disorder resulting from mutations in the CLN3 gene. The gene product is a 438-amino acid hydrophobic peptide of unknown function containing five transmembrane domains. In order to study the tissue distribution of the peptide, polyclonal antibodies were raised in rabbits to three epitopes and were affinity purified before use. All three antibodies were used together for immunocytochemical staining of human pancreas. This staining showed localization in pancreatic islet cells. Double labelling of the tissue indicated that cells staining for the CLN3 protein were also positive for somatostatin.
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Affiliation(s)
- R L Boriack
- Department of Pathology, Children's Medical Center of Dallas, 1935 Motor Street, Dallas, Texas 75235, USA
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West AP, Bennett MJ, Sellers VM, Andrews NC, Enns CA, Bjorkman PJ. Comparison of the interactions of transferrin receptor and transferrin receptor 2 with transferrin and the hereditary hemochromatosis protein HFE. J Biol Chem 2000; 275:38135-8. [PMID: 11027676 DOI: 10.1074/jbc.c000664200] [Citation(s) in RCA: 184] [Impact Index Per Article: 7.7] [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] [Indexed: 12/20/2022] Open
Abstract
The transferrin receptor (TfR) interacts with two proteins important for iron metabolism, transferrin (Tf) and HFE, the protein mutated in hereditary hemochromatosis. A second receptor for Tf, TfR2, was recently identified and found to be functional for iron uptake in transfected cells (Kawabata, H., Germain, R. S., Vuong, P. T., Nakamaki, T., Said, J. W., and Koeffler, H. P. (2000) J. Biol. Chem. 275, 16618-16625). TfR2 has a pattern of expression and regulation that is distinct from TfR, and mutations in TfR2 have been recognized as the cause of a non-HFE linked form of hemochromatosis (Camaschella, C., Roetto, A., Cali, A., De Gobbi, M., Garozzo, G., Carella, M., Majorano, N., Totaro, A., and Gasparini, P. (2000) Nat. Genet. 25, 14-15). To investigate the relationship between TfR, TfR2, Tf, and HFE, we performed a series of binding experiments using soluble forms of these proteins. We find no detectable binding between TfR2 and HFE by co-immunoprecipitation or using a surface plasmon resonance-based assay. The affinity of TfR2 for iron-loaded Tf was determined to be 27 nm, 25-fold lower than the affinity of TfR for Tf. These results imply that HFE regulates Tf-mediated iron uptake only from the classical TfR and that TfR2 does not compete for HFE binding in cells expressing both forms of TfR.
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Affiliation(s)
- A P West
- Division of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
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