1
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Avissar-Whiting M, Belliard F, Bertozzi SM, Brand A, Brown K, Clément-Stoneham G, Dawson S, Dey G, Ecer D, Edmunds SC, Farley A, Fischer TD, Franko M, Fraser JS, Funk K, Ganier C, Harrison M, Hatch A, Hazlett H, Hindle S, Hook DW, Hurst P, Kamoun S, Kiley R, Lacy MM, LaFlamme M, Lawrence R, Lemberger T, Leptin M, Lumb E, MacCallum CJ, Marcum CS, Marinello G, Mendonça A, Monaco S, Neves K, Pattinson D, Polka JK, Puebla I, Rittman M, Royle SJ, Saderi D, Sever R, Shearer K, Spiro JE, Stern B, Taraborelli D, Vale R, Vasquez CG, Waltman L, Watt FM, Weinberg ZY, Williams M. Recommendations for accelerating open preprint peer review to improve the culture of science. PLoS Biol 2024; 22:e3002502. [PMID: 38421949 PMCID: PMC10903809 DOI: 10.1371/journal.pbio.3002502] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.
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Affiliation(s)
- Michele Avissar-Whiting
- Office of the President, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Frédérique Belliard
- TU Delft OPEN Publishing, Delft University of Technology—TU Delft Library, Delft, the Netherlands
| | - Stefano M. Bertozzi
- Department of Public Health, UC Berkeley School of Public Health, Berkeley, California, United States of America
| | - Amy Brand
- The MIT Press, MIT, Cambridge, Massachusetts, United States of America
| | - Katherine Brown
- Development, The Company of Biologists, Cambridge, United Kingdom
| | | | | | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Daniel Ecer
- Technology, Sciety/eLife, Cambridge, United Kingdom
| | | | - Ashley Farley
- Knowledge & Research Services, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Tara D. Fischer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maryrose Franko
- Health Research Alliance, Swanton, Vermont, United States of America
| | - James S. Fraser
- Bioengineering and Therapeutic Sciences, University of California San Francisco & ASAPbio, San Francisco, California, United States of America
| | - Kathryn Funk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Clarisse Ganier
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, United Kingdom
| | | | - Anna Hatch
- Office of the President, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Haley Hazlett
- The San Francisco Declaration on Research Assessment, Rockville, Maryland, United States of America
| | | | | | - Phil Hurst
- Publishing Section, The Royal Society, London, United Kingdom
| | | | | | - Michael M. Lacy
- The American Society for Cell Biology, Rockville, Maryland, United States of America
| | - Marcel LaFlamme
- Open Research, PLOS, San Francisco, California, United States of America
| | | | | | - Maria Leptin
- President’s Office, European Research Council, Brussels, Belgium
| | | | | | | | | | | | | | - Kleber Neves
- Science Program, Instituto Serrapilheira, Rio de Janeiro, Brazil
| | | | | | | | | | - Stephen J. Royle
- Biomedical Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Richard Sever
- Cold Spring Harbor Laboratory, New York, New York, United States of America
| | - Kathleen Shearer
- COAR (Confederation of Open Access Repositories), Göttingen, Germany
| | - John E. Spiro
- Simons Foundation, New York, New York, United States of America
| | - Bodo Stern
- Office of the President, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Dario Taraborelli
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Ron Vale
- Janelia Research Campus, HHMI, Ashburn, Virginia, United States of America
| | - Claudia G. Vasquez
- Biochemistry Department, University of Washington, Seattle, United States of America
| | - Ludo Waltman
- Centre for Science and Technology Studies (CWTS), Leiden University, Leiden, the Netherlands
| | | | - Zara Y. Weinberg
- Biochemistry & Biophysics Department, University of California San Francisco, San Francisco, California, United States of America
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2
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Helsen J, Sherlock G, Dey G. Experimental evolution for cell biology. Trends Cell Biol 2023; 33:903-912. [PMID: 37188561 PMCID: PMC10592577 DOI: 10.1016/j.tcb.2023.04.006] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
Evolutionary cell biology explores the origins, principles, and core functions of cellular features and regulatory networks through the lens of evolution. This emerging field relies heavily on comparative experiments and genomic analyses that focus exclusively on extant diversity and historical events, providing limited opportunities for experimental validation. In this opinion article, we explore the potential for experimental laboratory evolution to augment the evolutionary cell biology toolbox, drawing inspiration from recent studies that combine laboratory evolution with cell biological assays. Primarily focusing on approaches for single cells, we provide a generalizable template for adapting experimental evolution protocols to provide fresh insight into long-standing questions in cell biology.
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Affiliation(s)
- Jana Helsen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
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3
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Helsen J, Reza MH, Sherlock G, Dey G. Spindle architecture constrains karyotype in budding yeast. bioRxiv 2023:2023.10.25.563899. [PMID: 37961714 PMCID: PMC10634821 DOI: 10.1101/2023.10.25.563899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The eukaryotic cell division machinery must rapidly and reproducibly duplicate and partition the cell's chromosomes in a carefully coordinated process. However, chromosome number varies dramatically between genomes, even on short evolutionary timescales. We sought to understand how the mitotic machinery senses and responds to karyotypic changes by using a set of budding yeast strains in which the native chromosomes have been successively fused. Using a combination of cell biological profiling, genetic engineering, and experimental evolution, we show that chromosome fusions are well tolerated up until a critical point. However, with fewer than five centromeres, outward forces in the metaphase spindle cannot be countered by kinetochore-microtubule attachments, triggering mitotic defects. Our findings demonstrate that spindle architecture is a constraining factor for karyotype evolution.
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Affiliation(s)
- Jana Helsen
- Cell Biology and Biophysics, European Molecular Biology Laboratory; Heidelberg, 69117, Germany
- Department of Genetics, Stanford University School of Medicine; Stanford, 94305, USA
| | - Md Hashim Reza
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research; Bengaluru, 560064, India
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine; Stanford, 94305, USA
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory; Heidelberg, 69117, Germany
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4
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Shah H, Dey G. A diffusion barrier limits nuclear leaks. Nat Cell Biol 2023; 25:1411-1412. [PMID: 37783793 DOI: 10.1038/s41556-023-01243-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Affiliation(s)
- Hiral Shah
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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5
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Chacko LA, Mikus F, Ariotti N, Dey G, Ananthanarayanan V. Microtubule-mitochondrial attachment facilitates cell division symmetry and mitochondrial partitioning in fission yeast. J Cell Sci 2023; 136:286576. [PMID: 36633091 PMCID: PMC10112971 DOI: 10.1242/jcs.260705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/13/2023] Open
Abstract
Association with microtubules inhibits the fission of mitochondria in Schizosaccharomyces pombe. Here, we show that this attachment of mitochondria to microtubules is an important cell-intrinsic factor in determining cell division symmetry. By comparing mutant cells that exhibited enhanced attachment and no attachment of mitochondria to microtubules (Dnm1Δ and Mmb1Δ, respectively), we show that microtubules in these mutants displayed aberrant dynamics compared to wild-type cells, which resulted in errors in nuclear positioning. This translated to cell division asymmetry in a significant proportion of both Dnm1Δ and Mmb1Δ cells. Asymmetric division in Dnm1Δ and Mmb1Δ cells resulted in unequal distribution of mitochondria, with the daughter cell that received more mitochondria growing faster than the other daughter cell. Taken together, we show the existence of homeostatic feedback controls between mitochondria and microtubules in fission yeast, which directly influence mitochondrial partitioning and, thereby, cell growth. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Leeba Ann Chacko
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Felix Mikus
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Nicholas Ariotti
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Gautam Dey
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Giri S, Dey G, Sahu R, Paul P, Nandi G, Dua TK. Traditional Uses, Phytochemistry and Pharmacological Activities of Woodfordia fruticosa (L) Kurz: A Comprehensive Review. Indian J Pharm Sci 2023. [DOI: 10.36468/pharmaceutical-sciences.1062] [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: 03/03/2023] Open
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7
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Hinterndorfer K, Laporte MH, Mikus F, Tafur L, Bourgoint C, Prouteau M, Dey G, Loewith R, Guichard P, Hamel V. Ultrastructure expansion microscopy reveals the cellular architecture of budding and fission yeast. J Cell Sci 2022; 135:286062. [PMID: 36524422 PMCID: PMC10112979 DOI: 10.1242/jcs.260240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
ABSTRACT
The budding and fission yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have served as invaluable model organisms to study conserved fundamental cellular processes. Although super-resolution microscopy has in recent years paved the way to a better understanding of the spatial organization of molecules in cells, its wide use in yeasts has remained limited due to the specific know-how and instrumentation required, contrasted with the relative ease of endogenous tagging and live-cell fluorescence microscopy. To facilitate super-resolution microscopy in yeasts, we have extended the ultrastructure expansion microscopy (U-ExM) method to both S. cerevisiae and S. pombe, enabling a 4-fold isotropic expansion. We demonstrate that U-ExM allows imaging of the microtubule cytoskeleton and its associated spindle pole body, notably unveiling the Sfi1p–Cdc31p spatial organization on the appendage bridge structure. In S. pombe, we validate the method by monitoring the homeostatic regulation of nuclear pore complex number through the cell cycle. Combined with NHS-ester pan-labelling, which provides a global cellular context, U-ExM reveals the subcellular organization of these two yeast models and provides a powerful new method to augment the already extensive yeast toolbox.
This article has an associated First Person interview with Kerstin Hinterndorfer and Felix Mikus, two of the joint first authors of the paper.
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Affiliation(s)
- Kerstin Hinterndorfer
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Marine H. Laporte
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Felix Mikus
- European Molecular Biology Laboratory 2 Cell Biology and Biophysics , , Heidelberg , Germany
| | - Lucas Tafur
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Clélia Bourgoint
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Manoel Prouteau
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Gautam Dey
- European Molecular Biology Laboratory 2 Cell Biology and Biophysics , , Heidelberg , Germany
| | - Robbie Loewith
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Paul Guichard
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Virginie Hamel
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
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8
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Dey G. Preprint Highlight: Growth temperature is the principal driver of chromatinization in archaea. Mol Biol Cell 2022; 33:mbcP22021007. [DOI: 10.1091/mbc.p22-02-1007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Almost all organisms express proteins that coat and organize DNA (nucleoid-associated proteins or NAPs). NAPs (such as histones in eukaryotes) play many roles, from scaffolding and protecting the DNA to regulating transcription, replication and epigenetic signaling, making it difficult to reconstruct their evolutionary histories and original functions. Here comparative genomics with protein abundance measurements across a range of archaea reveal a wide spectrum of NAP levels strongly correlated with growth temperature. Surprisingly, a family within the large taxonomic grouping of the Diaforarchaea appear to encode no NAPs at all. This work suggests that DNA-binding activities evolved primarily as a way to cope with heat stress, with implications for the evolution of chromatin in other archaea and a thermophilic origin for the first eukaryotes.
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Affiliation(s)
- Gautam Dey
- European Molecular Biology Laboratory, Heidelberg, Germany
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9
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Elting MW, Zareiesfandabadi P, Sharma A, Begley M, Dey G. How the fission yeast nucleus gets its shape: altering force balance via laser ablation during mitosis. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2750] [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: 11/25/2022] Open
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10
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Brierley L, Nanni F, Polka JK, Dey G, Pálfy M, Fraser N, Coates JA. Tracking changes between preprint posting and journal publication during a pandemic. PLoS Biol 2022; 20:e3001285. [PMID: 35104285 PMCID: PMC8806067 DOI: 10.1371/journal.pbio.3001285] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 05/12/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Amid the Coronavirus Disease 2019 (COVID-19) pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press, and policymakers for the first time. This phenomenon has sharpened long-standing questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record? We assessed preprints from bioRxiv and medRxiv that had been posted and subsequently published in a journal through April 30, 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version. We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 7.2% of non-COVID-19-related and 17.2% of COVID-19-related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not qualitatively change the conclusions of the paper.
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Affiliation(s)
- Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Gautam Dey
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Máté Pálfy
- The Company of Biologists, Histon, Cambridge, United Kingdom
| | | | - Jonathon Alexis Coates
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry Queen Mary University of London, London, United Kingdom
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11
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Abstract
The nucleus displays a wide range of sizes and shapes in different species and cell types, yet its size scaling and many of the key structural constituents that determine its shape are highly conserved. In this review, we discuss the cellular properties and processes that contribute to nuclear size and shape control, drawing examples from across eukaryotes and highlighting conserved themes and pathways. We then outline physiological roles that have been uncovered for specific nuclear morphologies and disease pathologies associated with aberrant nuclear morphology. We argue that a comparative approach, assessing and integrating observations from different systems, will be a powerful way to help us address the open questions surrounding functional roles of nuclear size and shape in cell physiology.
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Affiliation(s)
- Helena Cantwell
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Meyerhofstr.1, 69117 Heidelberg, Germany.
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12
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Fraser N, Brierley L, Dey G, Polka JK, Pálfy M, Nanni F, Coates JA. The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape. PLoS Biol 2021; 19:e3000959. [PMID: 33798194 PMCID: PMC8046348 DOI: 10.1371/journal.pbio.3000959] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [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: 10/08/2020] [Revised: 04/14/2021] [Accepted: 03/08/2021] [Indexed: 01/02/2023] Open
Abstract
The world continues to face a life-threatening viral pandemic. The virus underlying the Coronavirus Disease 2019 (COVID-19), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has caused over 98 million confirmed cases and 2.2 million deaths since January 2020. Although the most recent respiratory viral pandemic swept the globe only a decade ago, the way science operates and responds to current events has experienced a cultural shift in the interim. The scientific community has responded rapidly to the COVID-19 pandemic, releasing over 125,000 COVID-19-related scientific articles within 10 months of the first confirmed case, of which more than 30,000 were hosted by preprint servers. We focused our analysis on bioRxiv and medRxiv, 2 growing preprint servers for biomedical research, investigating the attributes of COVID-19 preprints, their access and usage rates, as well as characteristics of their propagation on online platforms. Our data provide evidence for increased scientific and public engagement with preprints related to COVID-19 (COVID-19 preprints are accessed more, cited more, and shared more on various online platforms than non-COVID-19 preprints), as well as changes in the use of preprints by journalists and policymakers. We also find evidence for changes in preprinting and publishing behaviour: COVID-19 preprints are shorter and reviewed faster. Our results highlight the unprecedented role of preprints and preprint servers in the dissemination of COVID-19 science and the impact of the pandemic on the scientific communication landscape.
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Affiliation(s)
| | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, United Kingdom
| | - Gautam Dey
- MRC Lab for Molecular Cell Biology, UCL, London, United Kingdom
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Máté Pálfy
- The Company of Biologists, Cambridge, United Kingdom
| | | | - Jonathon Alexis Coates
- Hughes Hall College, University of Cambridge, Cambridge, United Kingdom
- William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London, United Kingdom
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13
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Abstract
The defining feature of the eukaryotic cell, the nucleus, is bounded by a double envelope. This envelope and the nuclear pores within it play a critical role in separating the genome from the cytoplasm. It also presents cells with a challenge. How are cells to remodel the nuclear compartment boundary during mitosis without compromising nuclear function? In the two billion years since the emergence of the first cells with a nucleus, eukaryotes have evolved a range of strategies to do this. At one extreme, the nucleus is disassembled upon entry into mitosis and then reassembled anew in the two daughter cells. At the other, cells maintain an intact nuclear compartment boundary throughout the division process. In this review, we discuss common features of the division process that underpin remodelling mechanisms, the topological challenges involved and speculate on the selective pressures that may drive the evolution of distinct modes of division.
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Affiliation(s)
- Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Buzz Baum
- Lab of Molecular Biology, Cambridge, CB2 0QH, United Kingdom; Lab for Molecular Cell Biology, UCL, London, WC1E 6BT, United Kingdom.
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14
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Baum B, Dey G. Moving simply: Naegleria crawls and feeds using an ancient Arp2/3-dependent mechanism. J Cell Biol 2020; 219:e202009031. [PMID: 33064835 PMCID: PMC7577051 DOI: 10.1083/jcb.202009031] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Arp2/3-nucleated actin filaments drive crawling motility and phagocytosis in animal cells and slime molds. In this issue, Velle and Fritz-Laylin (2020. J. Cell Biol.https://doi.org/10.1083/jcb.202007158) now show that Naegleria gruberi, belonging to a lineage that diverged from opisthokonts around a billion years ago, uses similar mechanisms to crawl and phagocytose bacteria.
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Affiliation(s)
- Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Gautam Dey
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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15
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Dey G, Culley S, Curran S, Schmidt U, Henriques R, Kukulski W, Baum B. Closed mitosis requires local disassembly of the nuclear envelope. Nature 2020; 585:119-123. [PMID: 32848252 PMCID: PMC7610560 DOI: 10.1038/s41586-020-2648-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/21/2020] [Indexed: 01/15/2023]
Abstract
At the end of mitosis, eukaryotic cells must segregate the two copies of their replicated genome into two new nuclear compartments1. They do this either by first dismantling and later reassembling the nuclear envelope in an 'open mitosis' or by reshaping an intact nucleus and then dividing it into two in a 'closed mitosis'2,3. Mitosis has been studied in a wide variety of eukaryotes for more than a century4, but how the double membrane of the nuclear envelope is split into two at the end of a closed mitosis without compromising the impermeability of the nuclear compartment remains unknown5. Here, using the fission yeast Schizosaccharomyces pombe (a classical model for closed mitosis5), genetics, live-cell imaging and electron tomography, we show that nuclear fission is achieved via local disassembly of nuclear pores within the narrow bridge that links segregating daughter nuclei. In doing so, we identify the protein Les1, which is localized to the inner nuclear envelope and restricts the process of local nuclear envelope breakdown to the bridge midzone to prevent the leakage of material from daughter nuclei. The mechanism of local nuclear envelope breakdown in a closed mitosis therefore closely mirrors nuclear envelope breakdown in open mitosis3, revealing an unexpectedly high conservation of nuclear remodelling mechanisms across diverse eukaryotes.
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Affiliation(s)
- Gautam Dey
- MRC Laboratory for Molecular Cell Biology, London, UK.
| | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, London, UK
| | | | - Uwe Schmidt
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | | | | | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, London, UK.
- Institute for the Physics of Living Systems, University College London, London, UK.
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16
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Bottanelli F, Cadot B, Campelo F, Curran S, Davidson PM, Dey G, Raote I, Straube A, Swaffer MP. Science during lockdown - from virtual seminars to sustainable online communities. J Cell Sci 2020; 133:133/15/jcs249607. [PMID: 32801132 PMCID: PMC7438008 DOI: 10.1242/jcs.249607] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The COVID-19 pandemic has disrupted traditional modes of scientific communication. In-person conferences and seminars have been cancelled and most scientists around the world have been confined to their homes. Although challenging, this situation has presented an opportunity to adopt new ways to communicate science and build scientific relationships within a digital environment, thereby reducing the environmental impact and increasing the inclusivity of scientific events. As a group of researchers who have recently created online seminar series for our respective research communities, we have come together to share our experiences and insights. Only a few weeks into this process, and often learning ‘on the job’, we have collectively encountered different problems and solutions. Here, we share our advice on formats and tools, security concerns, spreading the word to your community and creating a diverse, inclusive and collegial space online. We hope our experience will help others launch their own online initiatives, helping to shape the future of scientific communication as we move past the current crisis. Summary: A practical guide to organising sustainable and inclusive virtual seminar series.
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Affiliation(s)
- Francesca Bottanelli
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Bruno Cadot
- Institut de Myologie, INSERM UMR974, Sorbonne Université, Paris 75013, France
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain
| | - Scott Curran
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Patricia M Davidson
- Institut de Myologie, INSERM UMR974, Sorbonne Université, Paris 75013, France
| | - Gautam Dey
- MRC Lab for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Ishier Raote
- Centre for Genonmic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Anne Straube
- Centre for Mechanochemical Cell Biology & Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
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17
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Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås AC, Robinson NP, Baum B. The proteasome controls ESCRT-III-mediated cell division in an archaeon. Science 2020; 369:eaaz2532. [PMID: 32764038 PMCID: PMC7116001 DOI: 10.1126/science.aaz2532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III-mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.
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Affiliation(s)
- Gabriel Tarrason Risa
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Fredrik Hurtig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sian Bray
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Anne E Hafner
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Lena Harker-Kirschneck
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Peter Faull
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Colin Davis
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Dimitra Papatziamou
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Catherine Fan
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Leticia Meneguello
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Mairi Kilkenny
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Diorge P Souza
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Luca Pellegrini
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Robertus A M de Bruin
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Anđela Šarić
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Nicholas P Robinson
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK.
- Institute for the Physics of Living Systems, UCL, London, UK
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18
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Pulschen AA, Mutavchiev DR, Culley S, Sebastian KN, Roubinet J, Roubinet M, Risa GT, van Wolferen M, Roubinet C, Schmidt U, Dey G, Albers SV, Henriques R, Baum B. Live Imaging of a Hyperthermophilic Archaeon Reveals Distinct Roles for Two ESCRT-III Homologs in Ensuring a Robust and Symmetric Division. Curr Biol 2020; 30:2852-2859.e4. [PMID: 32502411 PMCID: PMC7372223 DOI: 10.1016/j.cub.2020.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
Live-cell imaging has revolutionized our understanding of dynamic cellular processes in bacteria and eukaryotes. Although similar techniques have been applied to the study of halophilic archaea [1-5], our ability to explore the cell biology of thermophilic archaea has been limited by the technical challenges of imaging at high temperatures. Sulfolobus are the most intensively studied members of TACK archaea and have well-established molecular genetics [6-9]. Additionally, studies using Sulfolobus were among the first to reveal striking similarities between the cell biology of eukaryotes and archaea [10-15]. However, to date, it has not been possible to image Sulfolobus cells as they grow and divide. Here, we report the construction of the Sulfoscope, a heated chamber on an inverted fluorescent microscope that enables live-cell imaging of thermophiles. By using thermostable fluorescent probes together with this system, we were able to image Sulfolobus acidocaldarius cells live to reveal tight coupling between changes in DNA condensation, segregation, and cell division. Furthermore, by imaging deletion mutants, we observed functional differences between the two ESCRT-III proteins implicated in cytokinesis, CdvB1 and CdvB2. The deletion of cdvB1 compromised cell division, causing occasional division failures, whereas the ΔcdvB2 exhibited a profound loss of division symmetry, generating daughter cells that vary widely in size and eventually generating ghost cells. These data indicate that DNA separation and cytokinesis are coordinated in Sulfolobus, as is the case in eukaryotes, and that two contractile ESCRT-III polymers perform distinct roles to ensure that Sulfolobus cells undergo a robust and symmetrical division.
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Affiliation(s)
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Kim Nadine Sebastian
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | | | | | | | - Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Chantal Roubinet
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Uwe Schmidt
- Center for System Biology Dresden (CSBD), 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, UCL, London WC1E 6BT, UK.
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19
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Gan L, Seki A, Shen K, Iyer H, Han K, Hayer A, Wollman R, Ge X, Lin JR, Dey G, Talbot WS, Meyer T. The lysosomal GPCR-like protein GPR137B regulates Rag and mTORC1 localization and activity. Nat Cell Biol 2019; 21:614-626. [PMID: 31036939 PMCID: PMC6649673 DOI: 10.1038/s41556-019-0321-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 11/01/2017] [Accepted: 03/27/2019] [Indexed: 12/13/2022]
Abstract
Cell growth is controlled by a lysosomal signaling complex containing Rag small GTPases and mTORC1 kinase. Here we carried out a microscopy-based genome-wide human siRNA screen and discovered a lysosome-localized G-protein coupled receptor (GPCR)-like protein, GPR137B, that interacts with Rag GTPases, increases Rag localization and activity, and thereby regulates mTORC1 translocation and activity. High GPR137B expression can recruit and activate mTORC1 in the absence of amino acids. Furthermore, GPR137B also regulates the dissociation of activated Rag from lysosomes, suggesting that GPR137B controls a cycle of Rag activation and dissociation from lysosomes. GPR137B knockout cells exhibited defective autophagy and an expanded lysosome compartment, similar to Rag knockout cells. Like zebrafish RagA mutants, GPR137B mutant zebrafish had upregulated TFEB target gene expression and an expanded lysosome compartment in microglia. Thus, GPR137B is a GPCR-like lysosomal regulatory protein that controls dynamic Rag and mTORC1 localization and activity as well as lysosome morphology.
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Affiliation(s)
- Lin Gan
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Akiko Seki
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Kimberle Shen
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Harini Iyer
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Kyuho Han
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Arnold Hayer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Roy Wollman
- Department of Integrative Biology and Physiology and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Xuecai Ge
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Jerry R Lin
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Gautam Dey
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - William S Talbot
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
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20
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Gupta GD, Dey G, Mg S, Ramalingam B, Shameer K, Thottacherry JJ, Kalappurakkal JM, Howes MT, Chandran R, Das A, Menon S, Parton RG, Sowdhamini R, Thattai M, Mayor S. Correction: Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways. PLoS One 2018; 13:e0204770. [PMID: 30240414 PMCID: PMC6150516 DOI: 10.1371/journal.pone.0204770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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21
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Abstract
Much of the visible living world around us is characterized by cells that contain a nucleus enclosing the genetic material, a highly specialized network of dynamic interconnected membrane compartments, energy-producing mitochondria, and a cytoskeletal meshwork that can produce a dazzling variety of cellular shapes. These “eukaryotic” cells, which only represent a small fraction of the total cellular diversity on earth, have an internal organization that is strikingly different from that of “prokaryotes,” which lack nuclei or any internal membrane-bound compartments. Given the great structural chasm between these cell types, the question of eukaryotic origins is one of the most enduring mysteries in modern biology. Over the course of the 20th century, advances in cytology, the characterization of DNA as the universal genetic material, and pioneering work on phylogenies of ribosomal RNA all combined to establish a common origin for all life and identified a deep split in the prokaryotic world between the domains of archaea (once called Archaebacteria) and bacteria (once called Eubacteria). At the close of the 20th century, phylogenetic data had been used to support either the three-domain view of life (monophyletic Bacteria, Archaea, and Eukarya) or a competing two-domain model, which features a paraphyletic archaeal grade from which the eukaryotes emerged. These two competing views are relevant to the origin of the eukaryotes since they each suggest different characteristics of the eukaryotic progenitor. Apart from the convincing demonstration that plastids, of which chloroplasts are the most familiar, and mitochondria are derived from endosymbiotic bacteria, the field of eukaryotic origins remains full of uncertainties and controversy. Cell biological arguments have been used to support a bewildering variety of models for the origins of the nucleus and other aspects of eukaryotic cellular organization. Studies of the breadth of eukaryotic diversity help paint a convincing picture of a last eukaryotic common ancestor possessed of mitochondria, a complete cytoskeleton and trafficking machinery. In parallel, newly sequenced bacterial and archaeal genomes have revealed prokaryotic homologues for many genes originally deemed eukaryotic “inventions,” reducing the perceived gap between prokaryotic and eukaryotic complexity. The last few years in particular have generated a great deal of excitement, as newly discovered archaeal genomes, which includes a complete genome from the recently cultured Asgard archaeon Prometheoarchaeum syntrophicum, have shifted the consensus steadily toward models of eukaryotes emerging from the symbiosis of an Asgard-like archaeal host and a protomitochondrial bacterial cell. Recent advances in super-resolution microscopy, meta-genomics, and gene editing techniques mean that archaea and bacteria can be studied in greater cellular and ecological detail than ever before, raising hopes that insights from comparative cell biology will help us distinguish between competing models of eukaryogenesis in the near future.
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22
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Elliott SD, Dey G, Maimaiti Y. Classification of processes for the atomic layer deposition of metals based on mechanistic information from density functional theory calculations. J Chem Phys 2018; 146:052822. [PMID: 28178842 DOI: 10.1063/1.4975085] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.
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Affiliation(s)
- S D Elliott
- Tyndall National Institute, University College Cork, Lee Maltings, Dyke Parade, Cork T12 R5CP, Ireland
| | - G Dey
- Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
| | - Y Maimaiti
- Tyndall National Institute, University College Cork, Lee Maltings, Dyke Parade, Cork T12 R5CP, Ireland
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23
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Dey G, Thattai M, Baum B. On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype. Trends Cell Biol 2016; 26:476-485. [PMID: 27319280 PMCID: PMC4917890 DOI: 10.1016/j.tcb.2016.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 01/16/2023]
Abstract
If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although ‘Loki’ cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon. Eukaryotes are thought to be a product of symbiosis between archaea and bacteria. The recently discovered Lokiarchaeum (‘Loki’) encodes more Eukaryotic Signature Proteins (ESPs) than any other archaeon, making it the closest living relative to the putative ancestor of eukaryotes. Lokiarchaeum is the first prokaryote found to encode small GTPases, gelsolin, BAR domains, and longin domains, leading many to suggest that it might be compartmentalized and be capable of membrane trafficking. Many models for the evolution of eukaryotes invoke an archaeal ancestor that is capable of phagocytosis to explain the entry of the future mitochondrion into the host cell. Understanding the cell biology of Lokiarchaeum will be key to understanding the morphological transitions that characterized the evolution of eukaryotic cellular architecture, but Loki has not yet been cultured or seen.
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Affiliation(s)
- Gautam Dey
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Mukund Thattai
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bengaluru 560065, India
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
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24
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Miyazaki Y, Mizumoto K, Dey G, Kudo T, Perrino J, Chen LC, Meyer T, Wandless TJ. A method to rapidly create protein aggregates in living cells. Nat Commun 2016; 7:11689. [PMID: 27229621 PMCID: PMC4894968 DOI: 10.1038/ncomms11689] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 04/05/2016] [Accepted: 04/19/2016] [Indexed: 12/31/2022] Open
Abstract
The accumulation of protein aggregates is a common pathological hallmark of many neurodegenerative diseases. However, we do not fully understand how aggregates are formed or the complex network of chaperones, proteasomes and other regulatory factors involved in their clearance. Here, we report a chemically controllable fluorescent protein that enables us to rapidly produce small aggregates inside living cells on the order of seconds, as well as monitor the movement and coalescence of individual aggregates into larger structures. This method can be applied to diverse experimental systems, including live animals, and may prove valuable for understanding cellular responses and diseases associated with protein aggregates.
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Affiliation(s)
- Yusuke Miyazaki
- Department of Chemical &Systems Biology Stanford University, Stanford, California 94305, USA
| | - Kota Mizumoto
- Department of Biology Stanford University, Stanford, California 94305, USA
| | - Gautam Dey
- Department of Chemical &Systems Biology Stanford University, Stanford, California 94305, USA
| | - Takamasa Kudo
- Department of Chemical &Systems Biology Stanford University, Stanford, California 94305, USA
| | - John Perrino
- Cell Sciences Imaging Facility Stanford University, Stanford, California 94305, USA
| | - Ling-Chun Chen
- Department of Chemical &Systems Biology Stanford University, Stanford, California 94305, USA
| | - Tobias Meyer
- Department of Chemical &Systems Biology Stanford University, Stanford, California 94305, USA
| | - Thomas J Wandless
- Department of Chemical &Systems Biology Stanford University, Stanford, California 94305, USA
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25
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Panja S, Dey G, Bharti R, Kumari K, Maiti TK, Mandal M, Chattopadhyay S. Tailor-Made Temperature-Sensitive Micelle for Targeted and On-Demand Release of Anticancer Drugs. ACS Appl Mater Interfaces 2016; 8:12063-12074. [PMID: 27128684 DOI: 10.1021/acsami.6b03820] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The design of nanomedicines from the tuned architecture polymer is a leading object of immense research in recent years. Here, smart thermoresponsive micelles were prepared from novel architecture four-arm star block copolymers, namely, pentaerythritol polycaprolactone-b-poly(N-isopropylacrylamide) and pentaerythritol polycaprolactone-b-poly(N-vinylcaprolactam). The polymers were synthesized and tagged with folic acid (FA) to render them as efficient cancer cell targeting cargos. FA-conjugated block copolymers were self-assembled to a nearly spherical (ranging from 15 to 170 nm) polymeric micelle (FA-PM) with a sufficiently lower range of critical micelle concentration (0.59 × 10(-2) to 1.52 × 10(-2) mg/mL) suitable for performing as an efficient drug carrier. The blocks show lower critical solution temperature (LCST) ranging from 30 to 39 °C with high DOX-loading content (24.3%, w/w) as compared to that reported for a linear polymer in the contemporary literature. The temperature-induced reduction in size (57%) of the FA-PM enables a high rate of DOX release (78.57% after 24 h) at a temperature above LCST. The DOX release rate has also been tuned by on-demand administration of temperature. The in vitro biocompatibilities of the blank and DOX-loaded FA-PMs have been studied by the MTT assay. The cellular uptake study proves selective internalization of the FA-PM into cancerous cells (C6 glioma) compared that into normal cells (HaCaT). In vivo administration of the DOX-loaded FA-PMs into the C6 glioma rat tumor model resulted in significant accumulation in tumor sites, which drastically inhibited the tumor volume by ∼83.9% with respect to control without any significant systemic toxicity.
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Affiliation(s)
- S Panja
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - G Dey
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - R Bharti
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - K Kumari
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - T K Maiti
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - M Mandal
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - S Chattopadhyay
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
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26
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Bharti R, Dey G, Ojha PK, Rajput S, Jaganathan SK, Sen R, Mandal M. Diacerein-mediated inhibition of IL-6/IL-6R signaling induces apoptotic effects on breast cancer. Oncogene 2015; 35:3965-75. [PMID: 26616855 DOI: 10.1038/onc.2015.466] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 09/29/2015] [Accepted: 10/05/2015] [Indexed: 02/08/2023]
Abstract
Interleukin-6 (IL-6) signaling network has been implicated in oncogenic transformations making it attractive target for the discovery of novel cancer therapeutics. In this study, potent antiproliferative and apoptotic effect of diacerein were observed against breast cancer. In vitro apoptosis was induced by this drug in breast cancer cells as verified by increased sub-G1 population, LIVE/DEAD assay, cell cytotoxicity and presence of terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells, as well as downregulation of antiapoptotic proteins Bcl-2 and Bcl-xL and upregulation of apoptotic protein Bax. In addition, apoptosis induction was found to be caspase dependent. Further molecular investigations indicated that diacerein instigated apoptosis was associated with inhibition of IL-6/IL-6R autocrine signaling axis. Suppression of STAT3, MAPK and Akt pathways were also observed as a consequence of diacerein-mediated upstream inhibition of IL-6/IL-6R. Fluorescence study and western blot analysis revealed cytosolic accumulation of STAT3 in diacerein-treated cells. The docking study showed diacerein/IL-6R interaction that was further validated by competitive binding assay and isothermal titration calorimetry. Most interestingly, it was found that diacerein considerably suppressed tumor growth in MDA-MB-231 xenograft model. The in vivo antitumor effect was correlated with decreased proliferation (Ki-67), increased apoptosis (TUNEL) and inhibition of IL-6/IL-6R-mediated STAT3, MAPK and Akt pathway in tumor remnants. Taken together, diacerein offered a novel blueprint for cancer therapy by hampering IL-6/IL-6R/STAT3/MAPK/Akt network.
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Affiliation(s)
- R Bharti
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - G Dey
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - P K Ojha
- Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Rajput
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - S K Jaganathan
- IJN-UTM Cardiovascular Engineering Centre, Faculty of Biosciences and Medical Engineering, Universiti Teknologi, Malaysia
| | - R Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - M Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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27
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Dey G, Meyer T. Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome. Cell Syst 2015; 1:106-15. [PMID: 27135799 DOI: 10.1016/j.cels.2015.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/03/2015] [Accepted: 08/10/2015] [Indexed: 12/22/2022]
Abstract
Information about functional connections between genes can be derived from patterns of coupled loss of their homologs across multiple species. This comparative approach, termed phylogenetic profiling, has been successfully used to infer genetic interactions in bacteria and eukaryotes. Rapid progress in sequencing eukaryotic species has enabled the recent phylogenetic profiling of the human genome, resulting in systematic functional predictions for uncharacterized human genes. Importantly, groups of co-evolving genes reveal widespread modularity in the underlying genetic network, facilitating experimental analyses in human cells as well as comparative studies of conserved functional modules across species. This strategy is particularly successful in identifying novel metabolic proteins and components of multi-protein complexes. The targeted sequencing of additional key eukaryotes and the incorporation of improved methods to generate and compare phylogenetic profiles will further boost the predictive power and utility of this evolutionary approach to the functional analysis of gene interaction networks.
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Affiliation(s)
- Gautam Dey
- Chemical and Systems Biology, Stanford University, Stanford CA 94305, USA.
| | - Tobias Meyer
- Chemical and Systems Biology, Stanford University, Stanford CA 94305, USA.
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Dey G, Jaimovich A, Collins SR, Seki A, Meyer T. Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling. Cell Rep 2015; 10:993-1006. [PMID: 25683721 DOI: 10.1016/j.celrep.2015.01.025] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/17/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023] Open
Abstract
Functional links between genes can be predicted using phylogenetic profiling, by correlating the appearance and loss of homologs in subsets of species. However, effective genome-wide phylogenetic profiling has been hindered by the large fraction of human genes related to each other through historical duplication events. Here, we overcame this challenge by automatically profiling over 30,000 groups of homologous human genes (orthogroups) representing the entire protein-coding genome across 177 eukaryotic species (hOP profiles). By generating a full pairwise orthogroup phylogenetic co-occurrence matrix, we derive unbiased genome-wide predictions of functional modules (hOP modules). Our approach predicts functions for hundreds of poorly characterized genes. The results suggest evolutionary constraints that lead components of protein complexes and metabolic pathways to co-evolve while genes in signaling and transcriptional networks do not. As a proof of principle, we validated two subsets of candidates experimentally for their predicted link to the actin-nucleating WASH complex and cilia/basal body function.
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Affiliation(s)
- Gautam Dey
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ariel Jaimovich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Sean R Collins
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Akiko Seki
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
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Gupta GD, Dey G, MG S, Ramalingam B, Shameer K, Thottacherry JJ, Kalappurakkal JM, Howes MT, Chandran R, Das A, Menon S, Parton RG, Sowdhamini R, Thattai M, Mayor S. Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways. PLoS One 2014; 9:e100554. [PMID: 24971745 PMCID: PMC4074053 DOI: 10.1371/journal.pone.0100554] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 09/07/2013] [Accepted: 05/28/2014] [Indexed: 12/11/2022] Open
Abstract
Single-cell-resolved measurements reveal heterogeneous distributions of clathrin-dependent (CD) and -independent (CLIC/GEEC: CG) endocytic activity in Drosophila cell populations. dsRNA-mediated knockdown of core versus peripheral endocytic machinery induces strong changes in the mean, or subtle changes in the shapes of these distributions, respectively. By quantifying these subtle shape changes for 27 single-cell features which report on endocytic activity and cell morphology, we organize 1072 Drosophila genes into a tree-like hierarchy. We find that tree nodes contain gene sets enriched in functional classes and protein complexes, providing a portrait of core and peripheral control of CD and CG endocytosis. For 470 genes we obtain additional features from separate assays and classify them into early- or late-acting genes of the endocytic pathways. Detailed analyses of specific genes at intermediate levels of the tree suggest that Vacuolar ATPase and lysosomal genes involved in vacuolar biogenesis play an evolutionarily conserved role in CG endocytosis.
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Affiliation(s)
- Gagan D. Gupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Gautam Dey
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Swetha MG
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Balaji Ramalingam
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Khader Shameer
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Joseph Jose Thottacherry
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Joseph Mathew Kalappurakkal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Mark T. Howes
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Ruma Chandran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Anupam Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Sindhu Menon
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Robert G. Parton
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - R. Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Mukund Thattai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Satyajit Mayor
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
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30
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Dey G, Gupta GD, Ramalingam B, Sathe M, Mayor S, Thattai M. Exploiting cell-to-cell variability to detect cellular perturbations. PLoS One 2014; 9:e90540. [PMID: 24594940 PMCID: PMC3942435 DOI: 10.1371/journal.pone.0090540] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/11/2014] [Indexed: 12/20/2022] Open
Abstract
Any single-cell-resolved measurement generates a population distribution of phenotypes, characterized by a mean, a variance, and a shape. Here we show that changes in the shape of a phenotypic distribution can signal perturbations to cellular processes, providing a way to screen for underlying molecular machinery. We analyzed images of a Drosophila S2R+ cell line perturbed by RNA interference, and tracked 27 single-cell features which report on endocytic activity, and cell and nuclear morphology. In replicate measurements feature distributions had erratic means and variances, but reproducible shapes; RNAi down-regulation reliably induced shape deviations in at least one feature for 1072 out of 7131 genes surveyed, as revealed by a Kolmogorov-Smirnov-like statistic. We were able to use these shape deviations to identify a spectrum of genes that influenced cell morphology, nuclear morphology, and multiple pathways of endocytosis. By preserving single-cell data, our method was even able to detect effects invisible to a population-averaged analysis. These results demonstrate that cell-to-cell variability contains accessible and useful biological information, which can be exploited in existing cell-based assays.
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Affiliation(s)
- Gautam Dey
- Stanford University, Palo Alto, California, United States of America
| | | | - Balaji Ramalingam
- Centre for Cellular and Molecular Platforms (C-CAMP), Bangalore, India
| | - Mugdha Sathe
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Satyajit Mayor
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
| | - Mukund Thattai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India
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31
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Han K, Jaimovich A, Dey G, Ruggero D, Meyuhas O, Sonenberg N, Meyer T. Parallel measurement of dynamic changes in translation rates in single cells. Nat Methods 2013; 11:86-93. [PMID: 24213167 DOI: 10.1038/nmeth.2729] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/18/2013] [Indexed: 01/22/2023]
Abstract
Protein concentrations are often regulated by dynamic changes in translation rates. Nevertheless, it has been challenging to directly monitor changes in translation in living cells. We have developed a reporter system to measure real-time changes of translation rates in human or mouse individual cells by conjugating translation regulatory motifs to sequences encoding a nuclear targeted fluorescent protein and a controllable destabilization domain. Application of the method showed that individual cells undergo marked fluctuations in the translation rate of mRNAs whose 5' terminal oligopyrimidine (5' TOP) motif regulates the synthesis of ribosomal proteins. Furthermore, we show that small reductions in amino acid levels signal through different mTOR-dependent pathways to control TOP mRNA translation, whereas larger reductions in amino acid levels control translation through eIF2A. Our study demonstrates that dynamic measurements of single-cell activities of translation regulatory motifs can be used to identify and investigate fundamental principles of translation.
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Affiliation(s)
- Kyuho Han
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Ariel Jaimovich
- 1] Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA. [2] Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Gautam Dey
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Oded Meyuhas
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research, Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nahum Sonenberg
- 1] Department of Biochemistry, McGill University Montreal, Quebec, Canada. [2] Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
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Rajput S, Dey KK, Ipsita P, Sen K, Dey G, Bharti R, Parida S, Parekh A, Mandal M. 201 Combinatorial Effect of ZD6474 and Thymoquinone Inhibits Src Mediated ERK-1/2/STAT3 Signalling and Renders Antimetastasis in Breast Cancer. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)71999-8] [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: 10/27/2022]
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Carvalho M, Schwudke D, Sampaio JL, Palm W, Riezman I, Dey G, Gupta GD, Mayor S, Riezman H, Shevchenko A, Kurzchalia TV, Eaton S. Survival strategies of a sterol auxotroph. Development 2010; 137:3675-85. [PMID: 20940226 DOI: 10.1242/dev.044560] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The high sterol concentration in eukaryotic cell membranes is thought to influence membrane properties such as permeability, fluidity and microdomain formation. Drosophila cannot synthesize sterols, but do require them for development. Does this simply reflect a requirement for sterols in steroid hormone biosynthesis, or is bulk membrane sterol also essential in Drosophila? If the latter is true, how do they survive fluctuations in sterol availability and maintain membrane homeostasis? Here, we show that Drosophila require both bulk membrane sterol and steroid hormones in order to complete adult development. When sterol availability is restricted, Drosophila larvae modulate their growth to maintain membrane sterol levels within tight limits. When dietary sterol drops below a minimal threshold, larvae arrest growth and development in a reversible manner. Strikingly, membrane sterol levels in arrested larvae are dramatically reduced (dropping sixfold on average) in most tissues except the nervous system. Thus, sterols are dispensable for maintaining the basic membrane biophysical properties required for cell viability; these functions can be performed by non-sterol lipids when sterols are unavailable. However, bulk membrane sterol is likely to have essential functions in specific tissues during development. In tissues in which sterol levels drop, the overall level of sphingolipids increases and the proportion of different sphingolipid variants is altered. These changes allow survival, but not growth, when membrane sterol levels are low. This relationship between sterols and sphingolipids could be an ancient and conserved principle of membrane homeostasis.
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Affiliation(s)
- Maria Carvalho
- Max-Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse-108, 01307 Dresden, Germany
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Gupta GD, M. G. S, Kumari S, Lakshminarayan R, Dey G, Mayor S. Analysis of endocytic pathways in Drosophila cells reveals a conserved role for GBF1 in internalization via GEECs. PLoS One 2009; 4:e6768. [PMID: 19707569 PMCID: PMC2728541 DOI: 10.1371/journal.pone.0006768] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 07/28/2009] [Indexed: 11/18/2022] Open
Abstract
In mammalian cells, endocytosis of the fluid phase and glycosylphosphatidylinositol-anchored proteins (GPI-APs) forms GEECs (GPI-AP enriched early endosomal compartments) via an Arf1- and Cdc42-mediated, dynamin independent mechanism. Here we use four different fluorescently labeled probes and several markers in combination with quantitative kinetic assays, RNA interference and high resolution imaging to delineate major endocytic routes in Drosophila cultured cells. We find that the hallmarks of the pinocytic GEEC pathway are conserved in Drosophila and identify garz, the fly ortholog of the GTP exchange factor GBF1, as a novel component of this pathway. Live confocal and TIRF imaging reveals that a fraction of GBF1 GFP dynamically associates with ABD RFP (a sensor for activated Arf1 present on nascent pinosomes). Correspondingly, a GTP exchange mutant of GBF1 has altered ABD RFP localization in the evanescent field and is impaired in fluid phase uptake. Furthermore, GBF1 activation is required for the GEEC pathway even in the presence of Brefeldin A, implying that, like Arf1, it has a role in endocytosis that is separable from its role in secretion.
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Affiliation(s)
- Gagan D. Gupta
- National Centre for Biological Sciences, Bangalore, India
- * E-mail: (GDG); (SM)
| | - Swetha M. G.
- National Centre for Biological Sciences, Bangalore, India
| | - Sudha Kumari
- National Centre for Biological Sciences, Bangalore, India
| | | | - Gautam Dey
- National Centre for Biological Sciences, Bangalore, India
| | - Satyajit Mayor
- National Centre for Biological Sciences, Bangalore, India
- * E-mail: (GDG); (SM)
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36
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Sircar D, Dey G, Mitra A. A Validated HPLC Method for Simultaneous Determination of 2-Hydroxy-4-methoxybenzaldehyde and 2-Hydroxy-4-methoxybenzoic Acid in Root Organs of Hemidesmus indicus. Chromatographia 2007. [DOI: 10.1365/s10337-006-0146-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Dey G, Palit S, Banerjee R, Maiti BR. Purification and characterization of maltooligosaccharide-forming amylase from Bacillus circulans GRS 313. J Ind Microbiol Biotechnol 2002; 28:193-200. [PMID: 11986918 DOI: 10.1038/sj/jim/7000220] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2000] [Accepted: 10/22/2001] [Indexed: 11/08/2022]
Abstract
A maltooligosaccharide-forming amylase that hydrolyzes starch into maltotriose and maltopentaose was found in the culture filtrate of a strain of Bacillus circulans GRS 313 isolated from local soil. The enzyme was purified by organic solvent fractionation, Sephadex G-100 gel filtration and CM-Sephadex column chromatography. Optimum pH and temperature of amylase were evaluated using response surface methodology (RSM) and were found to be 48 degrees C and 4.9, respectively. The enzyme was stable up to 60 degrees C and its pH stability was in the range of 5.0-8.0. The Km and Vmax of the amylase with starch were 11.66 mg/ml and 68.97 U, respectively, and the energy of activation, Ea, was 7.52 kcal/mol. Dextrin inhibited the enzyme competitively, with a Ki of 6.1 mg/ml, and glucose caused noncompetitive inhibition with a Ki of 9.5 mg/ml. The enzyme was inhibited by Hg2+, Mn2+, Fe3+ and Cu2+ and enhanced by Co2+ and Mg2+. EDTA reversed the inhibitory effect of the metals. Paper chromatographic and high-performance liquid chromatography analysis of the products of the amylolytic reaction showed the presence of maltotriose, maltotetraose, maltopentaose, maltose and glucose in the starch hydrolysate.
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Affiliation(s)
- G Dey
- Microbial Biotechnology and Downstream Processing Laboratory, Agricultural and Food Engineering Department, IIT-Kharagpur 721302, India
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Dasgupta A, Ghosh RN, Sarkar R, Laha RN, Ghosh TK, Dey G, Mukherjee C, Das S. Argyrophilic nucleolar organizer regions (AgNOR) in tumours of pharynx and larynx. Indian J Otolaryngol Head Neck Surg 1996. [DOI: 10.1007/bf03048667] [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: 11/30/2022] Open
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Advis JP, Kuljis RO, Dey G. Distribution of luteinizing hormone-releasing hormone (LHRH) content and total LHRH-degrading activity (LHRH-DA) in the hypothalamus of the ewe. Endocrinology 1985; 116:2410-8. [PMID: 3888610 DOI: 10.1210/endo-116-6-2410] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hypothalamic enzymatic activities capable of degrading LHRH may play a physiological role in the neuroendocrine control of LHRH. There is increasing evidence, however, that these enzymes are not peptide specific. The present study in the ewe analyzed the possibility that the specificity of LHRH-degrading activity (LHRH-DA) could be conferred by the relative location of LHRH-DA with respect to that of the LHRH peptide itself. LHRH content was correlated with LHRH-DA in discrete hypothalamic samples containing LHRH-positive cell bodies and axons and in immediately adjacent areas apparently devoid of LHRH immunoreactivity. LHRH content was assessed by RIA, and LHRH-DA was determined by HPLC of the LHRH decapeptide and its degradation fragments. The sampling of discrete hypothalamic areas was designed after immunocytochemical localization of LHRH. LHRH-containing cell bodies were observed in the medial preoptic area, projecting LHRH-positive fibers to the infundibular region. At all hypothalamic levels, there was a tight correlation (r greater than 0.95; P less than 0.01) among the regional distribution of LHRH-DA, LHRH content, and the presence of LHRH-like immunoreactivity. LHRH-DA, in addition, was present in areas of low (e.g. lateral hypothalamus) or undetectable (e.g. cerebral cortex) LHRH content that were devoid of LHRH-like immunoreactivity. The appearance of LHRH degradation fragments suggests that the initial cleavage of LHRH by LHRH-DA occurs at the Tyr5-Gly6 bond at all hypothalamic levels studied. These findings indicate that part of the total hypothalamic LHRH-DA may be located within the LHRH hypophysiotropic pathway. This suggests an anatomical locus for a possible physiological interaction between LHRH and LHRH-DA.
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