1
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Bonetti L, Fernández-Rubio G, Carlomagno F, Dietz M, Pantazis D, Vuust P, Kringelbach ML. Spatiotemporal brain hierarchies of auditory memory recognition and predictive coding. Nat Commun 2024; 15:4313. [PMID: 38773109 DOI: 10.1038/s41467-024-48302-4] [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] [Received: 06/06/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024] Open
Abstract
Our brain is constantly extracting, predicting, and recognising key spatiotemporal features of the physical world in order to survive. While neural processing of visuospatial patterns has been extensively studied, the hierarchical brain mechanisms underlying conscious recognition of auditory sequences and the associated prediction errors remain elusive. Using magnetoencephalography (MEG), we describe the brain functioning of 83 participants during recognition of previously memorised musical sequences and systematic variations. The results show feedforward connections originating from auditory cortices, and extending to the hippocampus, anterior cingulate gyrus, and medial cingulate gyrus. Simultaneously, we observe backward connections operating in the opposite direction. Throughout the sequences, the hippocampus and cingulate gyrus maintain the same hierarchical level, except for the final tone, where the cingulate gyrus assumes the top position within the hierarchy. The evoked responses of memorised sequences and variations engage the same hierarchical brain network but systematically differ in terms of temporal dynamics, strength, and polarity. Furthermore, induced-response analysis shows that alpha and beta power is stronger for the variations, while gamma power is enhanced for the memorised sequences. This study expands on the predictive coding theory by providing quantitative evidence of hierarchical brain mechanisms during conscious memory and predictive processing of auditory sequences.
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Affiliation(s)
- L Bonetti
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University & The Royal Academy of Music, Aarhus/Aalborg, Denmark.
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, Oxford, United Kingdom.
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom.
- Department of Psychology, University of Bologna, Bologna, Italy.
| | - G Fernández-Rubio
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University & The Royal Academy of Music, Aarhus/Aalborg, Denmark
| | - F Carlomagno
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University & The Royal Academy of Music, Aarhus/Aalborg, Denmark
- Department of Education, Psychology, Communication, University of Bari Aldo Moro, Bari, Italy
| | - M Dietz
- Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - D Pantazis
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - P Vuust
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University & The Royal Academy of Music, Aarhus/Aalborg, Denmark
| | - M L Kringelbach
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University & The Royal Academy of Music, Aarhus/Aalborg, Denmark
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, Oxford, United Kingdom
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
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2
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Kurmasheva N, Said A, Wong B, Kinderman P, Han X, Rahimic AHF, Kress A, Carter-Timofte ME, Holm E, van der Horst D, Kollmann CF, Liu Z, Wang C, Hoang HD, Kovalenko E, Chrysopoulou M, Twayana KS, Ottosen RN, Svenningsen EB, Begnini F, Kiib AE, Kromm FEH, Weiss HJ, Di Carlo D, Muscolini M, Higgins M, van der Heijden M, Bardoul A, Tong T, Ozsvar A, Hou WH, Schack VR, Holm CK, Zheng Y, Ruzek M, Kalucka J, de la Vega L, Elgaher WAM, Korshoej AR, Lin R, Hiscott J, Poulsen TB, O'Neill LA, Roy DG, Rinschen MM, van Montfoort N, Diallo JS, Farin HF, Alain T, Olagnier D. Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways. Nat Commun 2024; 15:4096. [PMID: 38750019 PMCID: PMC11096414 DOI: 10.1038/s41467-024-48422-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
The presence of heterogeneity in responses to oncolytic virotherapy poses a barrier to clinical effectiveness, as resistance to this treatment can occur through the inhibition of viral spread within the tumor, potentially leading to treatment failures. Here we show that 4-octyl itaconate (4-OI), a chemical derivative of the Krebs cycle-derived metabolite itaconate, enhances oncolytic virotherapy with VSVΔ51 in various models including human and murine resistant cancer cell lines, three-dimensional (3D) patient-derived colon tumoroids and organotypic brain tumor slices. Furthermore, 4-OI in combination with VSVΔ51 improves therapeutic outcomes in a resistant murine colon tumor model. Mechanistically, we find that 4-OI suppresses antiviral immunity in cancer cells through the modification of cysteine residues in MAVS and IKKβ independently of the NRF2/KEAP1 axis. We propose that the combination of a metabolite-derived drug with an oncolytic virus agent can greatly improve anticancer therapeutic outcomes by direct interference with the type I IFN and NF-κB-mediated antiviral responses.
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Affiliation(s)
- Naziia Kurmasheva
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Aida Said
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Boaz Wong
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Ottawa Hospital Research Insitute, Ottawa, ON, K1H 8L6, Canada
| | - Priscilla Kinderman
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Xiaoying Han
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Anna H F Rahimic
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Alena Kress
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University, 60438, Frankfurt am Main, Germany
| | | | - Emilia Holm
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | | | | | - Zhenlong Liu
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Chen Wang
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Huy-Dung Hoang
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Elina Kovalenko
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | | | | | - Rasmus N Ottosen
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | | | - Fabio Begnini
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Anders E Kiib
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | | | - Hauke J Weiss
- School of Biochemistry and Immunology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Ireland
| | - Daniele Di Carlo
- Pasteur Laboratories, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00161, Italy
| | - Michela Muscolini
- Pasteur Laboratories, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00161, Italy
| | - Maureen Higgins
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Mirte van der Heijden
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angelina Bardoul
- Cancer Axis, CHUM Research Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada
- Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Tong Tong
- Department of Neurosurgery, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
- DCCC Brain Tumor Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Attila Ozsvar
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
| | - Wen-Hsien Hou
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Vivien R Schack
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Christian K Holm
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Yunan Zheng
- Small Molecule Therapeutics & Platform Technologies, AbbVie Inc., 1 North Waukegon Road, North Chicago, IL, 60064, USA
| | - Melanie Ruzek
- AbbVie, Bioresearch Center, 100 Research Drive, Worcester, MA, 01608, USA
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Laureano de la Vega
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Walid A M Elgaher
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, E8.1, 66123, Saarbrücken, Germany
| | - Anders R Korshoej
- Department of Neurosurgery, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
- DCCC Brain Tumor Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rongtuan Lin
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - John Hiscott
- Pasteur Laboratories, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00161, Italy
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Luke A O'Neill
- School of Biochemistry and Immunology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Ireland
| | - Dominic G Roy
- Cancer Axis, CHUM Research Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada
- Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Markus M Rinschen
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
- III. Department of Medicine and Hamburg Center for Kidney Health, Hamburg, Germany
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Nadine van Montfoort
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jean-Simon Diallo
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Ottawa Hospital Research Insitute, Ottawa, ON, K1H 8L6, Canada
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Frankfurt/Mainz partner site and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Tommy Alain
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - David Olagnier
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark.
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3
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Dunstan MA, Manvell AS, Yutronkie NJ, Aribot F, Bendix J, Rogalev A, Pedersen KS. Tunable valence tautomerism in lanthanide-organic alloys. Nat Chem 2024; 16:735-740. [PMID: 38374454 DOI: 10.1038/s41557-023-01422-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/12/2023] [Indexed: 02/21/2024]
Abstract
The inimitable electronic structures of the lanthanide (Ln) ions are key to advanced materials and technologies involving these elements. The trivalent ions are ubiquitous and are used much more widely than the divalent and tetravalent analogues, which possess vastly different optical and magnetic properties. Hence, alteration of the valence electron count by external stimuli can lead to dramatic changes in materials properties. Compounds exhibiting a temperature-induced complete Ln(III) ⇄ Ln(II) switch, referred to as a valence tautomeric (VT) transition, are rare. Here we present an abrupt and hysteretic VT transition in a lanthanide-based coordination polymer, SmI2(pyrazine)3, driven by the interconversion of Sm(II)-pyrazine(0) and Sm(III)-pyrazine(·-) redox pairs. Alloying SmI2(pyrazine)3 with Yb(II) yields isomorphous Sm1-xYbxI2(pyrazine)3 solid solutions with VT transition critical temperatures ranging widely from 200 K to ∼50 K at ambient pressure. These findings demonstrate a simple strategy to realize thermally switchable magnetic materials with chemically tunable transition temperatures.
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Affiliation(s)
- Maja A Dunstan
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Anna S Manvell
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Frédéric Aribot
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jesper Bendix
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Andrei Rogalev
- European Synchrotron Radiation Facility, Grenoble, France
| | - Kasper S Pedersen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.
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4
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Estrada Saldaña JC, Vekris A, Pavešič L, Žitko R, Grove-Rasmussen K, Nygård J. Correlation between two distant quasiparticles in separate superconducting islands mediated by a single spin. Nat Commun 2024; 15:3465. [PMID: 38658553 PMCID: PMC11043349 DOI: 10.1038/s41467-024-47694-7] [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: 04/20/2023] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
Controlled coupling between distant particles is a key requirement for the implementation of quantum information technologies. A promising platform are hybrid systems of semiconducting quantum dots coupled to superconducting islands, where the tunability of the dots is combined with the macroscopic coherence of the islands to produce states with non-local correlations, e.g. in Cooper pair splitters. Electrons in hybrid quantum dots are typically not amenable to long-distance spin alignment as they tend to be screened into a localized singlet state by bound superconducting quasiparticles. However, two quasiparticles coming from different superconductors can overscreen the quantum dot into a doublet state, leading to ferromagnetic correlations between the superconducting islands. We present experimental evidence of a stabilized overscreened state, implying correlated quasiparticles over a micrometer distance. We propose alternating chains of quantum dots and superconducting islands as a novel platform for controllable large-scale spin coupling.
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Affiliation(s)
| | - Alexandros Vekris
- Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, 2100, Copenhagen, Denmark
- Sino-Danish College (SDC), University of Chinese Academy of Sciences, Beijing, China
| | - Luka Pavešič
- Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia
| | - Rok Žitko
- Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia.
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.
| | - Kasper Grove-Rasmussen
- Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jesper Nygård
- Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, 2100, Copenhagen, Denmark.
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5
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Mikkelsen JH, Stødkilde K, Jensen MP, Hansen AG, Wu Q, Lorentzen J, Graversen JH, Andersen GR, Fenton RA, Etzerodt A, Thiel S, Andersen CBF. Trypanosoma brucei Invariant Surface Glycoprotein 75 Is an Immunoglobulin Fc Receptor Inhibiting Complement Activation and Antibody-Mediated Cellular Phagocytosis. J Immunol 2024; 212:1334-1344. [PMID: 38391367 DOI: 10.4049/jimmunol.2300862] [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] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Various subspecies of the unicellular parasite Trypanosoma brucei cause sleeping sickness, a neglected tropical disease affecting millions of individuals and domestic animals. Immune evasion mechanisms play a pivotal role in parasite survival within the host and enable the parasite to establish a chronic infection. In particular, the rapid switching of variant surface glycoproteins covering a large proportion of the parasite's surface enables the parasite to avoid clearance by the adaptive immune system of the host. In this article, we present the crystal structure and discover an immune-evasive function of the extracellular region of the T. brucei invariant surface gp75 (ISG75). Structural analysis determined that the ISG75 ectodomain is organized as a globular head domain and a long slender coiled-coil domain. Subsequent ligand screening and binding analysis determined that the head domain of ISG75 confers interaction with the Fc region of all subclasses of human IgG. Importantly, the ISG75-IgG interaction strongly inhibits both activation of the classical complement pathway and Ab-dependent cellular phagocytosis by competing with C1q and host cell FcγR CD32. Our data reveal a novel immune evasion mechanism of T. brucei, with ISG75 able to inactivate the activities of Abs recognizing the parasite surface proteins.
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Affiliation(s)
| | | | | | | | - Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Josefine Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jonas Heilskov Graversen
- Department of Cancer and Inflammation, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Gregers Rom Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anders Etzerodt
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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6
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Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
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Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Frain KM, Dedic E, Nel L, Bohush A, Olesen E, Thaysen K, Wüstner D, Stokes DL, Pedersen BP. Conformational changes in the Niemann-Pick type C1 protein NCR1 drive sterol translocation. Proc Natl Acad Sci U S A 2024; 121:e2315575121. [PMID: 38568972 PMCID: PMC11009665 DOI: 10.1073/pnas.2315575121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/22/2024] [Indexed: 04/05/2024] Open
Abstract
The membrane protein Niemann-Pick type C1 (NPC1, named NCR1 in yeast) is central to sterol homeostasis in eukaryotes. Saccharomyces cerevisiae NCR1 is localized to the vacuolar membrane, where it is suggested to carry sterols across the protective glycocalyx and deposit them into the vacuolar membrane. However, documentation of a vacuolar glycocalyx in fungi is lacking, and the mechanism for sterol translocation has remained unclear. Here, we provide evidence supporting the presence of a glycocalyx in isolated S. cerevisiae vacuoles and report four cryo-EM structures of NCR1 in two distinct conformations, named tense and relaxed. These two conformations illustrate the movement of sterols through a tunnel formed by the luminal domains, thus bypassing the barrier presented by the glycocalyx. Based on these structures and on comparison with other members of the Resistance-Nodulation-Division (RND) superfamily, we propose a transport model that links changes in the luminal domains with a cycle of protonation and deprotonation within the transmembrane region of the protein. Our model suggests that NPC proteins work by a generalized RND mechanism where the proton motive force drives conformational changes in the transmembrane domains that are allosterically coupled to luminal/extracellular domains to promote sterol transport.
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Affiliation(s)
- Kelly M. Frain
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Lynette Nel
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Anastasiia Bohush
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus Institute of Advanced Studies, Aarhus University, AarhusC 8000, Denmark
| | - Esben Olesen
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, OdenseM 5230, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, OdenseM 5230, Denmark
| | - David L. Stokes
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016
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8
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Brodersen KE, Mosshammer M, Bittner MJ, Hallstrøm S, Santner J, Riemann L, Kühl M. Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs. Microbiol Spectr 2024; 12:e0333523. [PMID: 38426746 PMCID: PMC10986515 DOI: 10.1128/spectrum.03335-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Seagrasses can enhance nutrient mobilization in their rhizosphere via complex interactions with sediment redox conditions and microbial populations. Yet, limited knowledge exists on how seagrass-derived rhizosphere dynamics affect nitrogen cycling. Using optode and gel-sampler-based chemical imaging, we show that radial O2 loss (ROL) from rhizomes and roots leads to the formation of redox gradients around below-ground tissues of seagrass (Zostera marina), which are co-localized with regions of high ammonium concentrations in the rhizosphere. Combining such chemical imaging with fine-scale sampling for microbial community and gene expression analyses indicated that multiple biogeochemical pathways and microbial players can lead to high ammonium concentration within the oxidized regions of the seagrass rhizosphere. Symbiotic N2-fixing bacteria (Bradyrhizobium) were particularly abundant and expressed the diazotroph functional marker gene nifH in Z. marina rhizosphere areas with high ammonium concentrations. Such an association between Z. marina and Bradyrhizobium can facilitate ammonium mobilization, the preferred nitrogen source for seagrasses, enhancing seagrass productivity within nitrogen-limited environments. ROL also caused strong gradients of sulfide at anoxic/oxic interfaces in rhizosphere areas, where we found enhanced nifH transcription by sulfate-reducing bacteria. Furthermore, we found a high abundance of methylotrophic and sulfide-oxidizing bacteria in rhizosphere areas, where O2 was released from seagrass rhizomes and roots. These bacteria could play a beneficial role for the plants in terms of their methane and sulfide oxidation, as well as their formation of growth factors and phytohormones. ROL from below-ground tissues of seagrass, thus, seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations. IMPORTANCE Seagrasses are important marine habitats providing several ecosystem services in coastal waters worldwide, such as enhancing marine biodiversity and mitigating climate change through efficient carbon sequestration. Notably, the fitness of seagrasses is affected by plant-microbe interactions. However, these microscale interactions are challenging to study and large knowledge gaps prevail. Our study shows that redox microgradients in the rhizosphere of seagrass select for a unique microbial community that can enhance the ammonium availability for seagrass. We provide first experimental evidence that Rhizobia, including the symbiotic N2-fixing bacteria Bradyrhizobium, can contribute to the bacterial ammonium production in the seagrass rhizosphere. The release of O2 from rhizomes and roots also caused gradients of sulfide in rhizosphere areas with enhanced nifH transcription by sulfate-reducing bacteria. O2 release from seagrass root systems thus seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.
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Affiliation(s)
| | - Maria Mosshammer
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Meriel J. Bittner
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jakob Santner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln an der Donau, Austria
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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9
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Trepel J, le Roux E, Abraham AJ, Buitenwerf R, Kamp J, Kristensen JA, Tietje M, Lundgren EJ, Svenning JC. Meta-analysis shows that wild large herbivores shape ecosystem properties and promote spatial heterogeneity. Nat Ecol Evol 2024; 8:705-716. [PMID: 38337048 DOI: 10.1038/s41559-024-02327-6] [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] [Received: 06/07/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
Megafauna (animals ≥45 kg) have probably shaped the Earth's terrestrial ecosystems for millions of years with pronounced impacts on biogeochemistry, vegetation, ecological communities and evolutionary processes. However, a quantitative global synthesis on the generality of megafauna effects on ecosystems is lacking. Here we conducted a meta-analysis of 297 studies and 5,990 individual observations across six continents to determine how wild herbivorous megafauna influence ecosystem structure, ecological processes and spatial heterogeneity, and whether these impacts depend on body size and environmental factors. Despite large variability in megafauna effects, we show that megafauna significantly alter soil nutrient availability, promote open vegetation structure and reduce the abundance of smaller animals. Other responses (14 out of 26), including, for example, soil carbon, were not significantly affected. Further, megafauna significantly increase ecosystem heterogeneity by affecting spatial heterogeneity in vegetation structure and the abundance and diversity of smaller animals. Given that spatial heterogeneity is considered an important driver of biodiversity across taxonomic groups and scales, these results support the hypothesis that megafauna may promote biodiversity at large scales. Megafauna declined precipitously in diversity and abundance since the late Pleistocene, and our results indicate that their restoration would substantially influence Earth's terrestrial ecosystems.
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Affiliation(s)
- Jonas Trepel
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark.
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark.
- Department of Conservation Biology, University of Göttingen, Göttingen, Germany.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark.
| | - Elizabeth le Roux
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Andrew J Abraham
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Robert Buitenwerf
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Johannes Kamp
- Department of Conservation Biology, University of Göttingen, Göttingen, Germany
| | - Jeppe A Kristensen
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Melanie Tietje
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Erick J Lundgren
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark.
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark.
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia.
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus C, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark
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10
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Kudrin P, Singh A, Meierhofer D, Kuśnierczyk A, Ørom UAV. N4-acetylcytidine (ac4C) promotes mRNA localization to stress granules. EMBO Rep 2024; 25:1814-1834. [PMID: 38413733 PMCID: PMC11014937 DOI: 10.1038/s44319-024-00098-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Stress granules are an integral part of the stress response that are formed from non-translating mRNAs aggregated with proteins. While much is known about stress granules, the factors that drive their mRNA localization are incompletely described. Modification of mRNA can alter the properties of the nucleobases and affect processes such as translation, splicing and localization of individual transcripts. Here, we show that the RNA modification N4-acetylcytidine (ac4C) on mRNA associates with transcripts enriched in stress granules and that stress granule localized transcripts with ac4C are specifically translationally regulated. We also show that ac4C on mRNA can mediate localization of the protein NOP58 to stress granules. Our results suggest that acetylation of mRNA regulates localization of both stress-sensitive transcripts and RNA-binding proteins to stress granules and adds to our understanding of the molecular mechanisms responsible for stress granule formation.
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Affiliation(s)
- Pavel Kudrin
- Institute of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411, Tartu, Estonia
| | - Ankita Singh
- Institute of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Anna Kuśnierczyk
- Proteomics and Modomics Experimental Core (PROMEC), Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology and the Central Norway Regional Health Authority, 7030, Trondheim, Norway
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11
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Nagy GN, Zhao XF, Karlsson R, Wang K, Duman R, Harlos K, El Omari K, Wagner A, Clausen H, Miller RL, Giger RJ, Jones EY. Structure and function of Semaphorin-5A glycosaminoglycan interactions. Nat Commun 2024; 15:2723. [PMID: 38548715 PMCID: PMC10978931 DOI: 10.1038/s41467-024-46725-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
Integration of extracellular signals by neurons is pivotal for brain development, plasticity, and repair. Axon guidance relies on receptor-ligand interactions crosstalking with extracellular matrix components. Semaphorin-5A (Sema5A) is a bifunctional guidance cue exerting attractive and inhibitory effects on neuronal growth through the interaction with heparan sulfate (HS) and chondroitin sulfate (CS) glycosaminoglycans (GAGs), respectively. Sema5A harbors seven thrombospondin type-1 repeats (TSR1-7) important for GAG binding, however the underlying molecular basis and functions in vivo remain enigmatic. Here we dissect the structural basis for Sema5A:GAG specificity and demonstrate the functional significance of this interaction in vivo. Using x-ray crystallography, we reveal a dimeric fold variation for TSR4 that accommodates GAG interactions. TSR4 co-crystal structures identify binding residues validated by site-directed mutagenesis. In vitro and cell-based assays uncover specific GAG epitopes necessary for TSR association. We demonstrate that HS-GAG binding is preferred over CS-GAG and mediates Sema5A oligomerization. In vivo, Sema5A:GAG interactions are necessary for Sema5A function and regulate Plexin-A2 dependent dentate progenitor cell migration. Our study rationalizes Sema5A associated developmental and neurological disorders and provides mechanistic insights into how multifaceted guidance functions of a single transmembrane cue are regulated by proteoglycans.
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Affiliation(s)
- Gergely N Nagy
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| | - Xiao-Feng Zhao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen-N, Denmark
| | - Karen Wang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen-N, Denmark
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen-N, Denmark.
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Neurology, Ann Arbor, MI, USA.
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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12
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Bidart GN, Teze D, Jansen CU, Pasutto E, Putkaradze N, Sesay AM, Fredslund F, Lo Leggio L, Ögmundarson O, Sukumara S, Qvortrup K, Welner DH. Chemoenzymatic indican for light-driven denim dyeing. Nat Commun 2024; 15:1489. [PMID: 38413572 PMCID: PMC10899603 DOI: 10.1038/s41467-024-45749-3] [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] [Received: 08/01/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Blue denim, a billion-dollar industry, is currently dyed with indigo in an unsustainable process requiring harsh reducing and alkaline chemicals. Forming indigo directly in the yarn through indican (indoxyl-β-glucoside) is a promising alternative route with mild conditions. Indican eliminates the requirement for reducing agent while still ending as indigo, the only known molecule yielding the unique hue of blue denim. However, a bulk source of indican is missing. Here, we employ enzyme and process engineering guided by techno-economic analyses to develop an economically viable drop-in indican synthesis technology. Rational engineering of PtUGT1, a glycosyltransferase from the indigo plant, alleviated the severe substrate inactivation observed with the wildtype enzyme at the titers needed for bulk production. We further describe a mild, light-driven dyeing process. Finally, we conduct techno-economic, social sustainability, and comparative life-cycle assessments. These indicate that the presented technologies have the potential to significantly reduce environmental impacts from blue denim dyeing with only a modest cost increase.
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Affiliation(s)
- Gonzalo Nahuel Bidart
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - David Teze
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Charlotte Uldahl Jansen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, DK-2800, Kgs. Lyngby, Denmark
| | - Eleonora Pasutto
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Natalia Putkaradze
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Anna-Mamusu Sesay
- Lab for Sustainability and Design, Designskolen Kolding, Ågade 10, DK-6000, Kolding, Denmark
| | - Folmer Fredslund
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
| | - Olafur Ögmundarson
- Faculty of Food Science and Nutrition, University of Iceland, Aragata 14, 102, Reykjavík, Iceland
| | - Sumesh Sukumara
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, DK-2800, Kgs. Lyngby, Denmark.
| | - Ditte Hededam Welner
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark.
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13
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Bender SWB, Dreisler MW, Zhang M, Kæstel-Hansen J, Hatzakis NS. SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis. Nat Commun 2024; 15:1763. [PMID: 38409214 PMCID: PMC10897458 DOI: 10.1038/s41467-024-46106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
The morphology of protein assemblies impacts their behaviour and contributes to beneficial and aberrant cellular responses. While single-molecule localization microscopy provides the required spatial resolution to investigate these assemblies, the lack of universal robust analytical tools to extract and quantify underlying structures limits this powerful technique. Here we present SEMORE, a semi-automatic machine learning framework for universal, system- and input-dependent, analysis of super-resolution data. SEMORE implements a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descriptors. We demonstrate SEMORE on simulations and diverse raw super-resolution data: time-resolved insulin aggregates, and published data of dSTORM imaging of nuclear pore complexes, fibroblast growth receptor 1, sptPALM of Syntaxin 1a and dynamic live-cell PALM of ryanodine receptors. SEMORE extracts and quantifies all protein assemblies, their temporal morphology evolution and provides quantitative insights, e.g. classification of heterogeneous insulin aggregation pathways and NPC geometry in minutes. SEMORE is a general analysis platform for super-resolution data, and being a time-aware framework can also support the rise of 4D super-resolution data.
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Affiliation(s)
- Steen W B Bender
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Marcus W Dreisler
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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14
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Brealey JC, Kodama M, Rasmussen JA, Hansen SB, Santos-Bay L, Lecaudey LA, Hansen M, Fjære E, Myrmel LS, Madsen L, Bernhard A, Sveier H, Kristiansen K, Gilbert MTP, Martin MD, Limborg MT. Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems 2024; 9:e0104323. [PMID: 38294254 PMCID: PMC10886447 DOI: 10.1128/msystems.01043-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.
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Affiliation(s)
- Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Laurène A Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Aquaculture Department, SINTEF Ocean, Trondheim, Norway
| | - Martin Hansen
- Department of Environmental Science, Environmental Metabolomics Lab, Aarhus University, Roskilde, Denmark
| | - Even Fjære
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Norway, Bergen, Norway
| | | | | | - Karsten Kristiansen
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
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15
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Ludwigsen CB, Andersen OB, Marzeion B, Malles JH, Müller Schmied H, Döll P, Watson C, King MA. Global and regional ocean mass budget closure since 2003. Nat Commun 2024; 15:1416. [PMID: 38360958 PMCID: PMC10869725 DOI: 10.1038/s41467-024-45726-w] [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: 06/30/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
In recent sea level studies, discrepancies have arisen in ocean mass observations obtained from the Gravity Recovery and Climate Experiment and its successor, GRACE Follow-On, with GRACE estimates consistently appearing lower than density-corrected ocean volume observations since 2015. These disparities have raised concerns about potential systematic biases in sea-level observations, with significant implications for our understanding of this essential climate variable. Here, we reconstruct the global and regional ocean mass change through models of ice and water mass changes on land and find that it closely aligns with both GRACE and density-corrected ocean volume observations after implementing recent adjustments to the wet troposphere correction and halosteric sea level. While natural variability in terrestrial water storage is important on interannual timescales, we find that the net increase in ocean mass over 20 years can be almost entirely attributed to ice wastage and human management of water resources.
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Affiliation(s)
- Carsten Bjerre Ludwigsen
- Technical University of Denmark, DTU Space, Lyngby, Denmark.
- The Australian Centre for Excellence in Antarctic Science, University of Tasmania, Hobart, TAS, 7001, Australia.
| | | | - Ben Marzeion
- Institute of Geography and MARUM-Center for Marine Environmental Research, University of Bremen, Bremen, Germany
| | - Jan-Hendrik Malles
- Institute of Geography and MARUM-Center for Marine Environmental Research, University of Bremen, Bremen, Germany
| | - Hannes Müller Schmied
- Institute of Physical Geography, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Leibniz Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Petra Döll
- Institute of Physical Geography, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Leibniz Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Christopher Watson
- The Australian Centre for Excellence in Antarctic Science, University of Tasmania, Hobart, TAS, 7001, Australia
- School of Geography, Planning, and Spatial Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Matt A King
- The Australian Centre for Excellence in Antarctic Science, University of Tasmania, Hobart, TAS, 7001, Australia
- School of Geography, Planning, and Spatial Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
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16
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Liu X, McPherson JN, Andersen CE, Jørgensen MSB, Larsen RW, Yutronkie NJ, Wilhelm F, Rogalev A, Giménez-Marqués M, Mínguez Espallargas G, Göb CR, Pedersen KS. A zero-valent palladium cluster-organic framework. Nat Commun 2024; 15:1177. [PMID: 38331922 PMCID: PMC10853280 DOI: 10.1038/s41467-024-45363-3] [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: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Acquiring spatial control of nanoscopic metal clusters is central to their function as efficient multi-electron catalysts. However, dispersing metal clusters on surfaces or in porous hosts is accompanied by an intrinsic heterogeneity that hampers detailed understanding of the chemical structure and its relation to reactivities. Tethering pre-assembled molecular metal clusters into polymeric, crystalline 2D or 3D networks constitutes an unproven approach to realizing ordered arrays of chemically well-defined metal clusters. Herein, we report the facile synthesis of a {Pd3} cluster-based organometallic framework from a molecular triangulo-Pd3(CNXyl)6 (Xyl = xylyl; Pd3) cluster under chemically mild conditions. The formally zero-valent Pd3 cluster readily engages in a complete ligand exchange when exposed to a similar, ditopic isocyanide ligand, resulting in polymerization into a 2D coordination network (Pd3-MOF). The structure of Pd3-MOF could be unambiguously determined by continuous rotation 3D electron diffraction (3D-ED) experiments to a resolution of ~1.0 Å (>99% completeness), showcasing the applicability of 3D-ED to nanocrystalline, organometallic polymers. Pd3-MOF displays Pd03 cluster nodes, which possess significant thermal and aerobic stability, and activity towards hydrogenation catalysis. Importantly, the realization of Pd3-MOF paves the way for the exploitation of metal clusters as building blocks for rigidly interlocked metal nanoparticles at the molecular limit.
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Affiliation(s)
- Xiyue Liu
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - James N McPherson
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark.
| | - Carl Emil Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - Mike S B Jørgensen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - René Wugt Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark
| | - Nathan J Yutronkie
- European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble Cedex 9, France
| | - Fabrice Wilhelm
- European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble Cedex 9, France
| | - Andrei Rogalev
- European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble Cedex 9, France
| | - Mónica Giménez-Marqués
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, Paterna, 46980, Valencia, Spain
| | | | - Christian R Göb
- Rigaku Europe SE, Hugenottenallee 167, 63263, Neu-Isenburg, Germany
| | - Kasper S Pedersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs, Lyngby, Denmark.
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17
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Kristensen R, Andersen JB, Rybtke M, Jansen CU, Fritz BG, Kiilerich RO, Uhd J, Bjarnsholt T, Qvortrup K, Tolker-Nielsen T, Givskov M, Jakobsen TH. Inhibition of Pseudomonas aeruginosa quorum sensing by chemical induction of the MexEF-oprN efflux pump. Antimicrob Agents Chemother 2024; 68:e0138723. [PMID: 38189278 PMCID: PMC10848761 DOI: 10.1128/aac.01387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/17/2023] [Indexed: 01/09/2024] Open
Abstract
The cell-to-cell communication system quorum sensing (QS), used by various pathogenic bacteria to synchronize gene expression and increase host invasion potentials, is studied as a potential target for persistent infection control. To search for novel molecules targeting the QS system in the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, a chemical library consisting of 3,280 small compounds from LifeArc was screened. A series of 10 conjugated phenones that have not previously been reported to target bacteria were identified as inhibitors of QS in P. aeruginosa. Two lead compounds (ethylthio enynone and propylthio enynone) were re-synthesized for verification of activity and further elucidation of the mode of action. The isomeric pure Z-ethylthio enynone was used for RNA sequencing, revealing a strong inhibitor of QS-regulated genes, and the QS-regulated virulence factors rhamnolipid and pyocyanin were significantly decreased by treatment with the compounds. A transposon mutagenesis screen performed in a newly constructed lasB-gfp monitor strain identified the target of Z-ethylthio enynone in P. aeruginosa to be the MexEF-OprN efflux pump, which was further established using defined mex knockout mutants. Our data indicate that the QS inhibitory capabilities of Z-ethylthio enynone were caused by the drainage of intracellular signal molecules as a response to chemical-induced stimulation of the MexEF-oprN efflux pump, thereby inhibiting the autogenerated positive feedback and its enhanced signal-molecule synthesis.
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Affiliation(s)
- Rasmus Kristensen
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bo Andersen
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | | | - Blaine Gabriel Fritz
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Overgaard Kiilerich
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Uhd
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Tim Tolker-Nielsen
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Michael Givskov
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Department of Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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18
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McRae EKS, Wan CJK, Kristoffersen EL, Hansen K, Gianni E, Gallego I, Curran JF, Attwater J, Holliger P, Andersen ES. Cryo-EM structure and functional landscape of an RNA polymerase ribozyme. Proc Natl Acad Sci U S A 2024; 121:e2313332121. [PMID: 38207080 PMCID: PMC10801858 DOI: 10.1073/pnas.2313332121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) - including a variant that uses trinucleotide triphosphates (triplets) as substrates - have been created by in vitro evolution and are the closest functional analogues of the replicase, but the structural basis for their function is poorly understood. Here we use single-particle cryogenic electron microscopy (cryo-EM) and high-throughput mutation analysis to obtain the structure of a triplet polymerase ribozyme (TPR) apoenzyme and map its functional landscape. The cryo-EM structure at 5-Å resolution reveals the TPR as an RNA heterodimer comprising a catalytic subunit and a noncatalytic, auxiliary subunit, resembling the shape of a left hand with thumb and fingers at a 70° angle. The two subunits are connected by two distinct kissing-loop (KL) interactions that are essential for polymerase function. Our combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme, whereby heterodimer formation and KL interactions preorganize the TPR for optimal primer-template duplex binding, triplet substrate discrimination, and templated RNA synthesis. These results provide a better understanding of TPR structure and function and should aid the engineering of more efficient PRs.
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Affiliation(s)
- Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Christopher J. K. Wan
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Emil L. Kristoffersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Kalinka Hansen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
| | - Edoardo Gianni
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Isaac Gallego
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Joseph F. Curran
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - James Attwater
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Philipp Holliger
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
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19
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Christensen CF, Laurichesse Q, Loudhaief R, Colombani J, Andersen DS. Drosophila activins adapt gut size to food intake and promote regenerative growth. Nat Commun 2024; 15:273. [PMID: 38177201 PMCID: PMC10767106 DOI: 10.1038/s41467-023-44553-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
Rapidly renewable tissues adapt different strategies to cope with environmental insults. While tissue repair is associated with increased intestinal stem cell (ISC) proliferation and accelerated tissue turnover rates, reduced calorie intake triggers a homeostasis-breaking process causing adaptive resizing of the gut. Here we show that activins are key drivers of both adaptive and regenerative growth. Activin-β (Actβ) is produced by stem and progenitor cells in response to intestinal infections and stimulates ISC proliferation and turnover rates to promote tissue repair. Dawdle (Daw), a divergent Drosophila activin, signals through its receptor, Baboon, in progenitor cells to promote their maturation into enterocytes (ECs). Daw is dynamically regulated during starvation-refeeding cycles, where it couples nutrient intake with progenitor maturation and adaptive resizing of the gut. Our results highlight an activin-dependent mechanism coupling nutrient intake with progenitor-to-EC maturation to promote adaptive resizing of the gut and further establish activins as key regulators of adult tissue plasticity.
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Affiliation(s)
- Christian F Christensen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Build. 3, 3rd floor, 2100 Copenhagen O, Copenhagen, Denmark
| | - Quentin Laurichesse
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Build. 3, 3rd floor, 2100 Copenhagen O, Copenhagen, Denmark
| | - Rihab Loudhaief
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Build. 3, 3rd floor, 2100 Copenhagen O, Copenhagen, Denmark
| | - Julien Colombani
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Build. 3, 3rd floor, 2100 Copenhagen O, Copenhagen, Denmark.
| | - Ditte S Andersen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Build. 3, 3rd floor, 2100 Copenhagen O, Copenhagen, Denmark.
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20
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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21
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Petersen MS, Pérez-Alós L, í Kongsstovu SK, Eliasen EH, Hansen CB, Larsen S, Hansen JL, Bayarri-Olmos R, Fjallsbak JP, Weihe P, Garred P. Diverging humoral and cellular immune responses due to Omicron-a national study from the Faroe Islands. Microbiol Spectr 2023; 11:e0086523. [PMID: 37909772 PMCID: PMC10714973 DOI: 10.1128/spectrum.00865-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/30/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The immunity following infection and vaccination with the SARS-CoV-2 Omicron variant is poorly understood. We investigated immunity assessed with antibody and T-cell responses under different scenarios in vaccinated and unvaccinated individuals with and without Omicron infection. We found that the humoral response was higher among vaccinated-naïve than unvaccinated convalescent. Unvaccinated with and without infection had comparable low humoral responses, whereas vaccinated with a second or third dose, independent of infection status, had increasingly higher levels. Only a minor fraction of unvaccinated individuals had detectable humoral responses following Omicron infection, while almost all had positive T-cell responses. In conclusion, primary Omicron infection mounts a low humoral immune response, enhanced by prior vaccination. Omicron infection induced a robust T-cell response in both unvaccinated and vaccinated, demonstrating that immune evasion of primary Omicron infection affects humoral immunity more than T-cell immunity.
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Affiliation(s)
- Maria Skaalum Petersen
- Department of Research, The National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Laura Pérez-Alós
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Eina Hansen Eliasen
- Department of Research, The National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sólrun Larsen
- Chief Medical Officer Office, Tórshavn, Faroe Islands
| | | | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Recombinant Protein and Antibody Unit, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Pál Weihe
- Department of Research, The National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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22
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Adam I, Riebel K, Stål P, Wood N, Previs MJ, Elemans CPH. Daily vocal exercise is necessary for peak performance singing in a songbird. Nat Commun 2023; 14:7787. [PMID: 38086817 PMCID: PMC10716414 DOI: 10.1038/s41467-023-43592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Vocal signals, including human speech and birdsong, are produced by complicated, precisely coordinated body movements, whose execution is fitness-determining in resource competition and mate choice. While the acquisition and maintenance of motor skills generally requires practice to develop and maintain both motor circuitry and muscle performance, it is unknown whether vocal muscles, like limb muscles, exhibit exercise-induced plasticity. Here, we show that juvenile and adult zebra finches (Taeniopygia castanotis) require daily vocal exercise to first gain and subsequently maintain peak vocal muscle performance. Experimentally preventing male birds from singing alters both vocal muscle physiology and vocal performance within days. Furthermore, we find females prefer song of vocally exercised males in choice experiments. Vocal output thus contains information on recent exercise status, and acts as an honest indicator of past exercise investment in songbirds, and possibly in all vocalising vertebrates.
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Affiliation(s)
- Iris Adam
- Department of Biology, University of Southern Denmark, Odense, Denmark.
| | - Katharina Riebel
- Institute of Biology, Animal Sciences & Health, Leiden University, Leiden, The Netherlands
| | - Per Stål
- Department of Integrative Medical Biology, Umea University, Umeå, Sweden
| | - Neil Wood
- Department of Molecular Physiology and Biophysics, Larner College of Medicine, University of Vermont, Burlington, NJ, USA
| | - Michael J Previs
- Department of Molecular Physiology and Biophysics, Larner College of Medicine, University of Vermont, Burlington, NJ, USA
| | - Coen P H Elemans
- Department of Biology, University of Southern Denmark, Odense, Denmark.
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23
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Due Tankmar M, Reichel M, Arribas-Hernández L, Brodersen P. A YTHDF-PABP interaction is required for m 6 A-mediated organogenesis in plants. EMBO Rep 2023; 24:e57741. [PMID: 38009565 DOI: 10.15252/embr.202357741] [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: 07/01/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
N6-methyladenosine (m6 A) in mRNA is key to eukaryotic gene regulation. Many m6 A functions involve RNA-binding proteins that recognize m6 A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3, and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4, and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.
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Affiliation(s)
| | - Marlene Reichel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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24
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Rognant S, Baldwin SN, Pritchard HAT, Greenstein A, Calloe K, Aalkjaer C, Jepps TA. Acute, pro-contractile effects of prorenin on rat mesenteric arteries. FASEB J 2023; 37:e23282. [PMID: 37994700 DOI: 10.1096/fj.202301480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
Prorenin and the prorenin receptor ((P)RR) are important, yet controversial, members of the renin-angiotensin-aldosterone system. The ((P)RR) is expressed throughout the body, including the vasculature, however, the direct effect of prorenin on arterial contractility is yet to be determined. Within rat mesenteric arteries, immunostaining and proximity ligation assays were used to determine the interacting partners of (P)RR in freshly isolated vascular smooth muscle cells (VSMCs). Wire myography examined the functional effect of prorenin. Simultaneous changes in [Ca2+ ]i and force were recorded in arteries loaded with Fura-2AM. Spontaneously transient outward currents were recorded via perforated whole-cell patch-clamp configuration in freshly isolated VSMCs. We found that the (P)RR is located within a distance of less than 40 nm from the V-ATPase, caveolin-1, ryanodine receptors, and large conductance Ca2+ -activated K+ channels (BKCa ) in VSMCs. [Ca2+ ]i imaging and isometric tension recordings indicate that 1 nM prorenin enhanced α1-adrenoreceptor-mediated contraction, associated with an increased number of Ca2+ waves, independent of voltage-gated Ca2+ channels activation. Incubation of VSMCs with 1 nM prorenin decreased the amplitude and frequency of spontaneously transient outward currents and attenuated BKCa -mediated relaxation. Inhibition of the V-ATPase with 100 nM bafilomycin prevented prorenin-mediated inhibition of BKCa -derived relaxation. Renin (1 nM) had no effect on BKCa -mediated relaxation. In conclusion, prorenin enhances arterial contractility by inhibition of BKCa and increasing intracellular Ca2+ release. It is likely that this effect is mediated through a local shift in pH upon activation of the (P)RR and stimulation of the V-ATPase.
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Affiliation(s)
- Salomé Rognant
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Samuel N Baldwin
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Harry A T Pritchard
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester University Teaching Hospitals NHS Foundation Trust, University of Manchester, Manchester, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Adam Greenstein
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester University Teaching Hospitals NHS Foundation Trust, University of Manchester, Manchester, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Kirstine Calloe
- Section for Pathobiological Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Thomas A Jepps
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
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25
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Kofoed RH, Simpson EM, Hynynen K, Aubert I. Sonoselective delivery using ultrasound and microbubbles combined with intravenous rAAV9 CLDN5-GFP does not increase endothelial gene expression. Gene Ther 2023; 30:807-811. [PMID: 36781945 DOI: 10.1038/s41434-023-00389-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 10/28/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Transcranial ultrasound combined with intravenous microbubbles can be used to increase blood-brain barrier permeability or, at lower pressures, to mediate sonoselective gene delivery to endothelial cells. Previously, sonoselective gene delivery with plasmid-coated microbubbles as gene carriers resulted in transient transgene expression in the brain endothelium. We investigated the potential of recombinant adeno-associated virus 9 (rAAV9), a serotype known for its efficient transduction and long-term transgene expression, for sonoselective gene delivery to endothelial cells of the brain. We found that rAAV9 led to gene delivery to brain endothelial cells following intravenous administration at a dosage of 1 × 1011 GC/g. However, the sonoselective gene delivery approach with intravenous rAAV9, using the same parameters as previously used for plasmid delivery, did not increase transgene expression in brain endothelial cells targeted. These results suggest that intravenous rAAV9 are using mechanisms of entry into the cerebrovasculature that are not significantly influenced by sonoselective treatments known to facilitate endothelial cell entry of plasmids coated onto microbubbles.
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Affiliation(s)
- Rikke Hahn Kofoed
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Kullervo Hynynen
- Physical Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Isabelle Aubert
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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26
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Qin X, Hansen HA, Honkala K, Melander MM. Cation-induced changes in the inner- and outer-sphere mechanisms of electrocatalytic CO 2 reduction. Nat Commun 2023; 14:7607. [PMID: 37993426 PMCID: PMC10665450 DOI: 10.1038/s41467-023-43300-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 05/28/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
The underlying mechanism of cation effects on CO2RR remains debated. Herein, we study cation effects by simulating both outer-sphere electron transfer (OS-ET) and inner-sphere electron transfer (IS-ET) pathways during CO2RR via constrained density functional theory molecular dynamics (cDFT-MD) and slow-growth DFT-MD (SG-DFT-MD), respectively. Our results show without any cations, only OS-ET is feasible with a barrier of 1.21 eV. In the presence of K+ (Li+), OS-ET shows a very high barrier of 2.93 eV (4.15 eV) thus being prohibited. However, cations promote CO2 activation through IS-ET with the barrier of only 0.61 eV (K+) and 0.91 eV (Li+), generating the key intermediate (adsorbed CO[Formula: see text]). Without cations, CO2-to-CO[Formula: see text](ads) conversion cannot proceed. Our findings reveal cation effects arise from short-range Coulomb interactions with reaction intermediates. These results disclose that cations modulate the inner- and outer-sphere pathways of CO2RR, offering substantial insights on the cation specificity in the initial CO2RR steps.
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Affiliation(s)
- Xueping Qin
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs. Lyngby, 2800, Denmark.
| | - Heine A Hansen
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs. Lyngby, 2800, Denmark
| | - Karoliina Honkala
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Marko M Melander
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.
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27
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Dimitrov D, Xu X, Su X, Shrestha N, Liu Y, Kennedy JD, Lyu L, Nogués-Bravo D, Rosindell J, Yang Y, Fjeldså J, Liu J, Schmid B, Fang J, Rahbek C, Wang Z. Diversification of flowering plants in space and time. Nat Commun 2023; 14:7609. [PMID: 37993449 PMCID: PMC10665465 DOI: 10.1038/s41467-023-43396-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
The rapid diversification and high species richness of flowering plants is regarded as 'Darwin's second abominable mystery'. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous-Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.
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Affiliation(s)
- Dimitar Dimitrov
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020, Bergen, Norway
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Xiaoting Xu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- Land Consolidation and Rehabilitation Center, Ministry of Natural Resources, Beijing, 100035, China
| | - Nawal Shrestha
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Yunpeng Liu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jonathan D Kennedy
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Lisha Lyu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, Shenzhen, China
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Yong Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, 159 Longpan Rd., Nanjing, 210037, China
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Bernhard Schmid
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jingyun Fang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
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28
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Yang Z, Qiao Y, Konakalla NC, Strøbech E, Harris P, Peschel G, Agler-Rosenbaum M, Weber T, Andreasson E, Ding L. Streptomyces alleviate abiotic stress in plant by producing pteridic acids. Nat Commun 2023; 14:7398. [PMID: 37968347 PMCID: PMC10652019 DOI: 10.1038/s41467-023-43177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
Soil microbiota can confer fitness advantages to plants and increase crop resilience to drought and other abiotic stressors. However, there is little evidence on the mechanisms correlating a microbial trait with plant abiotic stress tolerance. Here, we report that Streptomyces effectively alleviate drought and salinity stress by producing spiroketal polyketide pteridic acid H (1) and its isomer F (2), both of which promote root growth in Arabidopsis at a concentration of 1.3 nM under abiotic stress. Transcriptomics profiles show increased expression of multiple stress responsive genes in Arabidopsis seedlings after pteridic acids treatment. We confirm in vivo a bifunctional biosynthetic gene cluster for pteridic acids and antimicrobial elaiophylin production. We propose it is mainly disseminated by vertical transmission and is geographically distributed in various environments. This discovery reveals a perspective for understanding plant-Streptomyces interactions and provides a promising approach for utilising beneficial Streptomyces and their secondary metabolites in agriculture to mitigate the detrimental effects of climate change.
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Affiliation(s)
- Zhijie Yang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs, Lyngby, Denmark
| | - Yijun Qiao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs, Lyngby, Denmark
| | - Naga Charan Konakalla
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, SE-230 53, Alnarp, Sweden
| | - Emil Strøbech
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs, Lyngby, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Søltofts Plads, Building 206, 2800 Kgs, Lyngby, Denmark
| | - Gundela Peschel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Miriam Agler-Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, SE-230 53, Alnarp, Sweden
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs, Lyngby, Denmark.
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29
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Beaumont RN, Flatley C, Vaudel M, Wu X, Chen J, Moen GH, Skotte L, Helgeland Ø, Solé-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PÉ, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask D, Bustamante M, Hansen T, Pearson ER, Reynolds RM, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S, Freathy RM, Feenstra B, Njølstad PR. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. Nat Genet 2023; 55:1807-1819. [PMID: 37798380 PMCID: PMC10632150 DOI: 10.1038/s41588-023-01520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n = 65,405), maternal (n = 61,228) and paternal (n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
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Affiliation(s)
- Robin N Beaumont
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Xiaoping Wu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Solé-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | | | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sara Elizabeth Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Carol A Wang
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Sundararajan Srinivasan
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | | | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
| | - Catherine Allard
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marika Groleau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Teemu Kuulasmaa
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Daniel J Leirer
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Frédérique White
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Haoxiang Cheng
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Cathrine Ebbing
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Line Engelbrechtsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Herlev Hospital, Herlev, Denmark
| | - Christian Erikstrup
- Department Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marisa Estarlich
- Faculty of Nursing and Chiropody, Universitat de València, C/Menendez Pelayo, Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Stephen Franks
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine-Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Eero Kajantie
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Camilla S Morgen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Ellen A Nohr
- Institute of Clinical research, University of Southern Denmark, Odense, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | - Beverley M Shields
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Camilla Stoltenberg
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | | | - Marja Vaarasmaki
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Department of Obstetrics and Gynaecology, Oulu University Hospital, Oulu, Finland
| | - Bjarni J Vilhjalmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Dorte Gybel-Brask
- Psychotherapeutic Outpatient Clinic, Mental Health Services, Capital Region, Copenhagen, Denmark
| | - Mariona Bustamante
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewan R Pearson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Rebecca M Reynolds
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah A Lawlor
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - David M Evans
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Rachel M Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
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30
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Fahlquist-Hagert C, Wittenborn TR, Terczyńska-Dyla E, Kastberg KS, Yang E, Rallistan AN, Markett QR, Winther G, Fonager S, Voss LF, Pedersen MK, van Campen N, Ferapontov A, Jensen L, Huang J, Nieland JD, van der Poel CE, Palmfeldt J, Carroll MC, Utz PJ, Luo Y, Lin L, Degn SE. Antigen presentation by B cells enables epitope spreading across an MHC barrier. Nat Commun 2023; 14:6941. [PMID: 37907556 PMCID: PMC10618542 DOI: 10.1038/s41467-023-42541-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
Circumstantial evidence suggests that B cells may instruct T cells to break tolerance. Here, to test this hypothesis, we used a murine model in which a single B cell clone precipitates an autoreactive response resembling systemic lupus erythematosus (SLE). The initiating clone did not need to enter germinal centers to precipitate epitope spreading. Rather, it localized to extrafollicular splenic bridging channels early in the response. Autoantibody produced by the initiating clone was not sufficient to drive the autoreactive response. Subsequent epitope spreading depended on antigen presentation and was compartmentalized by major histocompatibility complex (MHC). B cells carrying two MHC haplotypes could bridge the MHC barrier between B cells that did not share MHC. Thus, B cells directly relay autoreactivity between two separate compartments of MHC-restricted T cells, leading to inclusion of distinct B cell populations in germinal centers. Our findings demonstrate that B cells initiate and propagate the autoimmune response.
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Affiliation(s)
- Cecilia Fahlquist-Hagert
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Thomas R Wittenborn
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Ewa Terczyńska-Dyla
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | | | - Emily Yang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
| | - Alysa Nicole Rallistan
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
| | - Quinton Raymond Markett
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
| | - Gudrun Winther
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Sofie Fonager
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Lasse F Voss
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Mathias K Pedersen
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Nina van Campen
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Department of Biomedical Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexey Ferapontov
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- CellPAT Center for Cellular Signal Patterns, iNANO, Aarhus University, Aarhus C, Denmark
| | - Lisbeth Jensen
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Jinrong Huang
- DREAM Laboratory for Applied Genome Technologies, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Shenzhen, China
| | - John D Nieland
- Department of Health Science and Technology, Faculty of Medicine, Aalborg University, Gistrup, Denmark
| | - Cees E van der Poel
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Dragonfly Therapeutics, Waltham, MA, USA
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Yonglun Luo
- DREAM Laboratory for Applied Genome Technologies, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Shenzhen, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus N, Denmark
| | - Lin Lin
- DREAM Laboratory for Applied Genome Technologies, Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus N, Denmark
| | - Søren E Degn
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus C, Denmark.
- CellPAT Center for Cellular Signal Patterns, iNANO, Aarhus University, Aarhus C, Denmark.
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31
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Nielsen BF, Sneppen K, Simonsen L. The counterintuitive implications of superspreading diseases. Nat Commun 2023; 14:6954. [PMID: 37907452 PMCID: PMC10618522 DOI: 10.1038/s41467-023-42612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023] Open
Abstract
The superspreading that characterized SARS and now COVID-19 can be rapidly quantified; however, its implications for outbreak control were never well understood. Recent studies point to its profound impact on outbreak dynamics and prospects for effective control of a future Disease X. These insights necessitate research into the mechanisms, impact and different modes of superspreading more widely.
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Affiliation(s)
- Bjarke Frost Nielsen
- PandemiX Center of Excellence, Roskilde University, Roskilde, Denmark.
- High Meadows Environmental Institute, Princeton University, Princeton, NJ, USA.
| | - Kim Sneppen
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lone Simonsen
- PandemiX Center of Excellence, Roskilde University, Roskilde, Denmark
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32
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Salomon K, Abramyan AM, Plenge P, Wang L, Bundgaard C, Bang-Andersen B, Loland CJ, Shi L. Dynamic extracellular vestibule of human SERT: Unveiling druggable potential with high-affinity allosteric inhibitors. Proc Natl Acad Sci U S A 2023; 120:e2304089120. [PMID: 37792512 PMCID: PMC10576121 DOI: 10.1073/pnas.2304089120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/15/2023] [Indexed: 10/06/2023] Open
Abstract
The serotonin transporter (SERT) tightly regulates synaptic serotonin levels and has been the primary target of antidepressants. Binding of inhibitors to the allosteric site of human SERT (hSERT) impedes the dissociation of antidepressants bound at the central site and may enhance the efficacy of such antidepressants to potentially reduce their dosage and side effects. Here, we report the identification of a series of high-affinity allosteric inhibitors of hSERT in a unique scaffold, with the lead compound, Lu AF88273 (3-(1-(2-(1H-indol-3-yl)ethyl)piperidin-4-yl)-6-chloro-1H-indole), having 2.1 nM allosteric potency in inhibiting imipramine dissociation. In addition, we find that Lu AF88273 also inhibits serotonin transport in a noncompetitive manner. The binding pose of Lu AF88273 in the allosteric site of hSERT is determined with extensive molecular dynamics simulations and rigorous absolute binding free energy perturbation (FEP) calculations, which show that a part of the compound occupies a dynamically formed small cavity. The predicted binding location and pose are validated by site-directed mutagenesis and can explain much of the structure-activity relationship of these inhibitors using the relative binding FEP calculations. Together, our findings provide a promising lead compound and the structural basis for the development of allosteric drugs targeting hSERT. Further, they demonstrate that the divergent allosteric sites of neurotransmitter transporters can be selectively targeted.
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Affiliation(s)
- Kristine Salomon
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200Copenhagen N, Denmark
| | - Ara M. Abramyan
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, NIH, Baltimore, MD21224
- Schrödinger, Inc., San Diego, CA92121
| | - Per Plenge
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200Copenhagen N, Denmark
| | | | - Christoffer Bundgaard
- Medicinal Chemistry and Translational DMPK, H. Lundbeck A/S, DK-2500Copenhagen-Valby, Denmark
| | - Benny Bang-Andersen
- Medicinal Chemistry and Translational DMPK, H. Lundbeck A/S, DK-2500Copenhagen-Valby, Denmark
| | - Claus J. Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200Copenhagen N, Denmark
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, NIH, Baltimore, MD21224
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33
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Ju W, Bagger A, Saharie NR, Möhle S, Wang J, Jaouen F, Rossmeisl J, Strasser P. Electrochemical carbonyl reduction on single-site M-N-C catalysts. Commun Chem 2023; 6:212. [PMID: 37777576 PMCID: PMC10542751 DOI: 10.1038/s42004-023-01008-y] [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: 05/10/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023] Open
Abstract
Electrochemical conversion of organic compounds holds promise for advancing sustainable synthesis and catalysis. This study explored electrochemical carbonyl hydrogenation on single-site M-N-C (Metal Nitrogen-doped Carbon) catalysts using formaldehyde, acetaldehyde, and acetone as model reactants. We strive to correlate and understand the selectivity dependence on the nature of the metal centers. Density Functional Theory calculations revealed similar binding energetics for carbonyl groups through oxygen-down or carbon-down adsorption due to oxygen and carbon scaling. Fe-N-C exhibited specific oxyphilicity and could selectively reduce aldehydes to hydrocarbons. By contrast, the carbophilic Co-N-C selectively converted acetaldehyde and acetone to ethanol and 2-propanol, respectively. We claim that the oxyphilicity of the active sites and consequent adsorption geometry (oxygen-down vs. carbon-down) are crucial in controlling product selectivity. These findings offer mechanistic insights into electrochemical carbonyl hydrogenation and can guide the development of efficient and sustainable electrocatalytic valorization of biomass-derived compounds.
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Affiliation(s)
- Wen Ju
- Chemical Engineering Division, Department of Chemistry, Technical University Berlin, Berlin, Germany
| | - Alexander Bagger
- Department of Physics, Technical University of Denmark, Lyngby, Denmark
| | | | - Sebastian Möhle
- Chemical Engineering Division, Department of Chemistry, Technical University Berlin, Berlin, Germany
| | - Jingyi Wang
- Chemical Engineering Division, Department of Chemistry, Technical University Berlin, Berlin, Germany
| | - Frederic Jaouen
- Institute Charles Gerhardt Montpellier, Univ. Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jan Rossmeisl
- Department of Chemistry, University Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Peter Strasser
- Chemical Engineering Division, Department of Chemistry, Technical University Berlin, Berlin, Germany.
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34
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Jarlhelt I, Pérez-Alós L, Bayarri-Olmos R, Hansen CB, Petersen MS, Weihe P, Armenteros JJA, Madsen JR, Nielsen JPS, Hilsted LM, Iversen KK, Bundgaard H, Nielsen SD, Garred P. Distinguishing SARS-CoV-2 infection and vaccine responses up to 18 months post-infection using nucleocapsid protein and receptor-binding domain antibodies. Microbiol Spectr 2023; 11:e0179623. [PMID: 37738355 PMCID: PMC10580960 DOI: 10.1128/spectrum.01796-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023] Open
Abstract
The prediction of the durability of immunity against COVID-19 is relevant, and longitudinal studies are essential for unraveling the details regarding protective SARS-CoV-2 antibody responses. It has become challenging to discriminate between COVID-19 vaccine- and infection-induced immune responses since all approved vaccines in Europe and the USA are based on the viral spike (S) protein, which is also the most commonly used antigen in immunoassays measuring immunoglobulins (Igs) against SARS-CoV-2. We have developed a nucleocapsid (N) protein-based sandwich ELISA for detecting pan anti-SARS-CoV-2 Ig with a sensitivity and specificity of 97%. Generalized mixed models were used to determine the degree of long-term humoral immunity against the N protein and the receptor-binding domain (RBD) of the S protein in a cohort of infected individuals to distinguish between COVID-19 vaccine- and infection-induced immunity. N-specific waning could be observed in individuals who did not experience reinfection, while individuals who experienced reinfection had a new significant increase in N-specific Ig levels. In individuals that seroconverted without a reinfection, 70.1% remained anti-N seropositive after 550 days. The anti-RBD Ig dynamics were unaffected by reinfection but exhibited a clear increase in RBD-specific Ig when vaccination was initiated. In conclusion, a clear difference in the dynamics of the antibody response against N protein and RBD was observed over time. Anti-N protein-specific Igs can be detected up to 18 months after SARS-CoV-2 infection allowing long-term discrimination of infectious and vaccine antibody responses.IMPORTANCELongitudinal studies are essential to unravel details regarding the protective antibody responses after COVID-19 infection and vaccination. It has become challenging to distinguish long-term immune responses to SARS-CoV-2 infection and vaccination since most approved vaccines are based on the viral spike (S) protein, which is also mostly used in immunoassays measuring immunoglobulins (Igs) against SARS-CoV-2. We have developed a novel nucleocapsid (N) protein-based sandwich ELISA for detecting pan-anti-SARS-CoV-2 Ig, exhibiting high sensitivity and specificity. Generalized mixed models were used to determine long-term humoral immunity in a cohort of infected individuals from the Faroe Islands, distinguishing between COVID-19 vaccine- and infection-induced immunity. A clear difference in the dynamics of the antibody response against N protein and S protein was observed over time, and the anti-N protein-specific Igs could be detected up to 18 months after SARS-CoV-2 infection. This enables long-term discrimination between natural infection and vaccine-dependent antibody responses.
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Affiliation(s)
- Ida Jarlhelt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
| | - Laura Pérez-Alós
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
| | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
- Recombinant Protein and Antibody Unit, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
| | - Maria Skaalum Petersen
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands, Denmark
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands, Denmark
| | - Pál Weihe
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands, Denmark
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands, Denmark
| | | | - Johannes Roth Madsen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
- Department of Emergency Medicine, Herlev-Gentofte Hospital, Copenhagen, Denmark
| | - Jacob Pohl Stangerup Nielsen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
- Department of Emergency Medicine, Herlev-Gentofte Hospital, Copenhagen, Denmark
| | | | - Kasper Karmark Iversen
- Department of Emergency Medicine, Herlev-Gentofte Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Heart Center, Department of Cardiology, Rigshospitalet, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Rigshospitalet, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
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Affiliation(s)
- Jeanine S. Geelhoed
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
| | - Casper A. Thorup
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Filip J. R. Meysman
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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36
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Pérez-Alós L, Hansen CB, Almagro Armenteros JJ, Madsen JR, Heftdal LD, Hasselbalch RB, Pries-Heje MM, Bayarri-Olmos R, Jarlhelt I, Hamm SR, Møller DL, Sørensen E, Ostrowski SR, Frikke-Schmidt R, Hilsted LM, Bundgaard H, Nielsen SD, Iversen KK, Garred P. Previous immunity shapes immune responses to SARS-CoV-2 booster vaccination and Omicron breakthrough infection risk. Nat Commun 2023; 14:5624. [PMID: 37699890 PMCID: PMC10497567 DOI: 10.1038/s41467-023-41342-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
The heterogeneity of the SARS-CoV-2 immune responses has become considerably more complex over time and diverse immune imprinting is observed in vaccinated individuals. Despite vaccination, following the emergence of the Omicron variant, some individuals appear more susceptible to primary infections and reinfections than others, underscoring the need to elucidate how immune responses are influenced by previous infections and vaccination. IgG, IgA, neutralizing antibodies and T-cell immune responses in 1,325 individuals (955 of which were infection-naive) were investigated before and after three doses of the BNT162b2 vaccine, examining their relation to breakthrough infections and immune imprinting in the context of Omicron. Our study shows that both humoral and cellular responses following vaccination were generally higher after SARS-CoV-2 infection compared to infection-naive. Notably, viral exposure before vaccination was crucial to achieving a robust IgA response. Individuals with lower IgG, IgA, and neutralizing antibody responses postvaccination had a significantly higher risk of reinfection and future Omicron infections. This was not observed for T-cell responses. A primary infection before Omicron and subsequent reinfection with Omicron dampened the humoral and cellular responses compared to a primary Omicron infection, consistent with immune imprinting. These results underscore the significant impact of hybrid immunity for immune responses in general, particularly for IgA responses even after revaccination, and the importance of robust humoral responses in preventing future infections.
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Affiliation(s)
- Laura Pérez-Alós
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Johannes Roth Madsen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Line Dam Heftdal
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Haematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rasmus Bo Hasselbalch
- Department of Cardiology, Copenhagen University Hospital Herlev and Gentofte, Copenhagen, Denmark
- Department of Emergency Medicine, Copenhagen University Hospital Herlev and Gentofte, Copenhagen, Denmark
| | - Mia Marie Pries-Heje
- The Heart Center, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Recombinant Protein and Antibody Unit, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ida Jarlhelt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sebastian Rask Hamm
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Dina Leth Møller
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Section 2034, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Section 2034, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Linda Maria Hilsted
- Department of Clinical Biochemistry, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henning Bundgaard
- The Heart Center, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Karmark Iversen
- Department of Cardiology, Copenhagen University Hospital Herlev and Gentofte, Copenhagen, Denmark
- Department of Emergency Medicine, Copenhagen University Hospital Herlev and Gentofte, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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37
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Koher A, Jørgensen F, Petersen MB, Lehmann S. Epidemic modelling of monitoring public behavior using surveys during pandemic-induced lockdowns. Commun Med (Lond) 2023; 3:80. [PMID: 37291090 DOI: 10.1038/s43856-023-00310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Implementing a lockdown for disease mitigation is a balancing act: Non-pharmaceutical interventions can reduce disease transmission significantly, but interventions also have considerable societal costs. Therefore, decision-makers need near real-time information to calibrate the level of restrictions. METHODS We fielded daily surveys in Denmark during the second wave of the COVID-19 pandemic to monitor public response to the announced lockdown. A key question asked respondents to state their number of close contacts within the past 24 hours. Here, we establish a link between survey data, mobility data, and hospitalizations via epidemic modelling of a short time-interval around Denmark's December 2020 lockdown. Using Bayesian analysis, we then evaluate the usefulness of survey responses as a tool to monitor the effects of lockdown and then compare the predictive performance to that of mobility data. RESULTS We find that, unlike mobility, self-reported contacts decreased significantly in all regions before the nation-wide implementation of non-pharmaceutical interventions and improved predicting future hospitalizations compared to mobility data. A detailed analysis of contact types indicates that contact with friends and strangers outperforms contact with colleagues and family members (outside the household) on the same prediction task. CONCLUSIONS Representative surveys thus qualify as a reliable, non-privacy invasive monitoring tool to track the implementation of non-pharmaceutical interventions and study potential transmission paths.
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Affiliation(s)
- Andreas Koher
- DTU Compute, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Sune Lehmann
- DTU Compute, Technical University of Denmark, Lyngby, Denmark.
- Center for Social Data Science, University of Copenhagen, Copenhagen, Denmark.
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38
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Germain RR, Feng S, Chen G, Graves GR, Tobias JA, Rahbek C, Lei F, Fjeldså J, Hosner PA, Gilbert MTP, Zhang G, Nogués-Bravo D. Species-specific traits mediate avian demographic responses under past climate change. Nat Ecol Evol 2023:10.1038/s41559-023-02055-3. [PMID: 37106156 DOI: 10.1038/s41559-023-02055-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.
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Affiliation(s)
- Ryan R Germain
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Shaohong Feng
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China
| | - Guangji Chen
- BGI Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Life Sciences, Imperial College London, Ascot, UK
- Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jon Fjeldså
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Papaleo E, Tiberti M, Arnaudi M, Pecorari C, Faienza F, Cantwell L, Degn K, Pacello F, Battistoni A, Lambrughi M, Filomeni G. TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins. Cell Death Dis 2023; 14:284. [PMID: 37085483 PMCID: PMC10121659 DOI: 10.1038/s41419-023-05780-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1. Interestingly, the SNO site (C501) of TRAP1 is in the proximity of another cysteine (C527). This feature suggests that the S-nitrosylated C501 could engage in a disulfide bridge with C527 in TRAP1, resembling the well-known ability of S-nitrosylated cysteines to resolve in disulfide bridge with vicinal cysteines. We used enhanced sampling simulations and in-vitro biochemical assays to address the structural mechanisms induced by TRAP1 S-nitrosylation. We showed that the SNO site induces conformational changes in the proximal cysteine and favors conformations suitable for disulfide bridge formation. We explored 4172 known S-nitrosylated proteins using high-throughput structural analyses. Furthermore, we used a coarse-grained model for 44 protein targets to account for protein flexibility. This resulted in the identification of up to 1248 proximal cysteines, which could sense the redox state of the SNO site, opening new perspectives on the biological effects of redox switches. In addition, we devised two bioinformatic workflows ( https://github.com/ELELAB/SNO_investigation_pipelines ) to identify proximal or vicinal cysteines for a SNO site with accompanying structural annotations. Finally, we analyzed mutations in tumor suppressors or oncogenes in connection with the conformational switch induced by S-nitrosylation. We classified the variants as neutral, stabilizing, or destabilizing for the propensity to be S-nitrosylated and undergo the population-shift mechanism. The methods applied here provide a comprehensive toolkit for future high-throughput studies of new protein candidates, variant classification, and a rich data source for the research community in the NO field.
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Affiliation(s)
- Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Chiara Pecorari
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Lisa Cantwell
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
- Center for Healthy Aging, Copenhagen University, 2200, Copenhagen, Denmark
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40
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Acciai C, Schneider JW, Nielsen MW. Estimating social bias in data sharing behaviours: an open science experiment. Sci Data 2023; 10:233. [PMID: 37085512 PMCID: PMC10120507 DOI: 10.1038/s41597-023-02129-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 04/23/2023] Open
Abstract
Open data sharing is critical for scientific progress. Yet, many authors refrain from sharing scientific data, even when they have promised to do so. Through a preregistered, randomized audit experiment (N = 1,634), we tested possible ethnic, gender and status-related bias in scientists' data-sharing willingness. 814 (54%) authors of papers where data were indicated to be 'available upon request' responded to our data requests, and 226 (14%) either shared or indicated willingness to share all or some data. While our preregistered hypotheses regarding bias in data-sharing willingness were not confirmed, we observed systematically lower response rates for data requests made by putatively Chinese treatments compared to putatively Anglo-Saxon treatments. Further analysis indicated a theoretically plausible heterogeneity in the causal effect of ethnicity on data-sharing. In interaction analyses, we found indications of lower responsiveness and data-sharing willingness towards male but not female data requestors with Chinese names. These disparities, which likely arise from stereotypic beliefs about male Chinese requestors' trustworthiness and deservingness, impede scientific progress by preventing the free circulation of knowledge.
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Affiliation(s)
- Claudia Acciai
- Department of Sociology, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.
| | - Jesper W Schneider
- Danish Centre for Studies in Research and Research Policy, Department of Political Science, Aarhus University, Bartholins Allé 7, 8000, Aarhus C, Denmark
| | - Mathias W Nielsen
- Department of Sociology, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.
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41
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Jin Y, Ivanov M, Dittrich AN, Nelson AD, Marquardt S. LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis. EMBO J 2023:e110921. [PMID: 37051749 DOI: 10.15252/embj.2022110921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/14/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 04/14/2023] Open
Abstract
How the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering-associated intergenic lncRNA (FLAIL) in Arabidopsis through early flowering flail mutants. Expression of FLAIL RNA from a different chromosomal location in combination with strand-specific RNA knockdown characterized FLAIL as a trans-acting RNA molecule. FLAIL directly binds to differentially expressed target genes that control flowering via RNA-DNA interactions through conserved sequence motifs. FLAIL interacts with protein and RNA components of the spliceosome to affect target mRNA expression through co-transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence of FLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model where FLAIL-mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development.
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Affiliation(s)
- Yu Jin
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
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42
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Sánchez-Baena J, Politi C, Maucher F, Ferlaino F, Pohl T. Heating a dipolar quantum fluid into a solid. Nat Commun 2023; 14:1868. [PMID: 37015907 PMCID: PMC10073146 DOI: 10.1038/s41467-023-37207-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Raising the temperature of a material enhances the thermal motion of particles. Such an increase in thermal energy commonly leads to the melting of a solid into a fluid and eventually vaporises the liquid into a gaseous phase of matter. Here, we study the finite-temperature physics of dipolar quantum fluids and find surprising deviations from this general phenomenology. In particular, we describe how heating a dipolar superfluid from near-zero temperatures can induce a phase transition to a supersolid state with a broken translational symmetry. We discuss the observation of this effect in experiments on ultracold dysprosium atoms, which opens the door for exploring the unusual thermodynamics of dipolar quantum fluids.
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Affiliation(s)
- J Sánchez-Baena
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark.
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord B4-B5, 08034, Barcelona, Spain.
| | - C Politi
- Institut für Quantenoptik und Quanteninformation, Österreichische Akademie der Wissenschaften, Innsbruck, Austria
- Institut für Experimentalphysik, Universität Innsbruck, Innsbruck, Austria
| | - F Maucher
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark
- Departament de Física, Universitat de les Illes Balears & IAC-3, Campus UIB, E-07122, Palma de Mallorca, Spain
| | - F Ferlaino
- Institut für Quantenoptik und Quanteninformation, Österreichische Akademie der Wissenschaften, Innsbruck, Austria
- Institut für Experimentalphysik, Universität Innsbruck, Innsbruck, Austria
| | - T Pohl
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark.
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Naseem MT, Beaven R, Koyama T, Naz S, Su SY, Leader DP, A Klaerke D, Calloe K, Denholm B, Halberg KV. NHA1 is a cation/proton antiporter essential for the water-conserving functions of the rectal complex in Tribolium castaneum. Proc Natl Acad Sci U S A 2023; 120:e2217084120. [PMID: 36943876 PMCID: PMC10068851 DOI: 10.1073/pnas.2217084120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Indexed: 03/23/2023] Open
Abstract
More than half of all extant metazoan species on earth are insects. The evolutionary success of insects is linked with their ability to osmoregulate, suggesting that they have evolved unique physiological mechanisms to maintain water balance. In beetles (Coleoptera)-the largest group of insects-a specialized rectal ("cryptonephridial") complex has evolved that recovers water from the rectum destined for excretion and recycles it back to the body. However, the molecular mechanisms underpinning the remarkable water-conserving functions of this system are unknown. Here, we introduce a transcriptomic resource, BeetleAtlas.org, for the exceptionally desiccation-tolerant red flour beetle Tribolium castaneum, and demonstrate its utility by identifying a cation/H+ antiporter (NHA1) that is enriched and functionally significant in the Tribolium rectal complex. NHA1 localizes exclusively to a specialized cell type, the leptophragmata, in the distal region of the Malpighian tubules associated with the rectal complex. Computational modeling and electrophysiological characterization in Xenopus oocytes show that NHA1 acts as an electroneutral K+/H+ antiporter. Furthermore, genetic silencing of Nha1 dramatically increases excretory water loss and reduces organismal survival during desiccation stress, implying that NHA1 activity is essential for maintaining systemic water balance. Finally, we show that Tiptop, a conserved transcription factor, regulates NHA1 expression in leptophragmata and controls leptophragmata maturation, illuminating the developmental mechanism that establishes the functions of this cell. Together, our work provides insights into the molecular architecture underpinning the function of one of the most powerful water-conserving mechanisms in nature, the beetle rectal complex.
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Affiliation(s)
- Muhammad T Naseem
- Department of Biology, Section for Cell and Neurobiology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Robin Beaven
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Takashi Koyama
- Department of Biology, Section for Cell and Neurobiology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Sehrish Naz
- Department of Biology, Section for Cell and Neurobiology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Sheng-Yuan Su
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - David P Leader
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Dan A Klaerke
- Department of Veterinary and Animal Sciences, Section for Pathobiological Sciences, University of Copenhagen DK-1870, Frederiksberg, Denmark
| | - Kirstine Calloe
- Department of Veterinary and Animal Sciences, Section for Pathobiological Sciences, University of Copenhagen DK-1870, Frederiksberg, Denmark
| | - Barry Denholm
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Kenneth V Halberg
- Department of Biology, Section for Cell and Neurobiology, University of Copenhagen, Copenhagen DK-2100, Denmark
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44
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Søgaard AB, Pedersen AB, Løvschall KB, Monge P, Jakobsen JH, Džabbarova L, Nielsen LF, Stevanovic S, Walther R, Zelikin AN. Transmembrane signaling by a synthetic receptor in artificial cells. Nat Commun 2023; 14:1646. [PMID: 36964156 PMCID: PMC10039019 DOI: 10.1038/s41467-023-37393-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 03/13/2023] [Indexed: 03/26/2023] Open
Abstract
Signal transduction across biological membranes is among the most important evolutionary achievements. Herein, for the design of artificial cells, we engineer fully synthetic receptors with the capacity of transmembrane signaling, using tools of chemistry. Our receptors exhibit similarity with their natural counterparts in having an exofacial ligand for signal capture, being membrane anchored, and featuring a releasable messenger molecule that performs enzyme activation as a downstream signaling event. The main difference from natural receptors is the mechanism of signal transduction, which is achieved using a self-immolative linker. The receptor scaffold is modular and can readily be re-designed to respond to diverse activation signals including biological or chemical stimuli. We demonstrate an artificial signaling cascade that achieves transmembrane enzyme activation, a hallmark of natural signaling receptors. Results of this work are relevant for engineering responsive artificial cells and interfacing them and/or biological counterparts in co-cultures.
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Affiliation(s)
- Ane Bretschneider Søgaard
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- iNano Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
| | | | | | - Pere Monge
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | | | | | | | | | - Raoul Walther
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Alexander N Zelikin
- Department of Chemistry, Aarhus University, Aarhus C, Denmark.
- iNano Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark.
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45
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Bjerg JJ, Lustermans JJM, Marshall IPG, Mueller AJ, Brokjær S, Thorup CA, Tataru P, Schmid M, Wagner M, Nielsen LP, Schramm A. Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria. Nat Commun 2023; 14:1614. [PMID: 36959175 PMCID: PMC10036481 DOI: 10.1038/s41467-023-37272-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.
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Affiliation(s)
- Jesper J Bjerg
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark.
- Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium.
| | - Jamie J M Lustermans
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Ian P G Marshall
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Anna J Mueller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology (DOME), University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Signe Brokjær
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Casper A Thorup
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Paula Tataru
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus C, Denmark
| | - Markus Schmid
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology (DOME), University of Vienna, Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology (DOME), University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Lars Peter Nielsen
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark.
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Madsen JR, Holm BE, Pérez-Alós L, Bayarri-Olmos R, Rosbjerg A, Fogh K, Pries-Heje MM, Møller DL, Hansen CB, Heftdal LD, Hasselbalch RB, Hamm SR, Frikke-Schmidt R, Hilsted L, Nielsen SD, Iversen KK, Bundgaard H, Garred P. Short-Lived Antibody-Mediated Saliva Immunity against SARS-CoV-2 after Vaccination. Microbiol Spectr 2023; 11:e0494722. [PMID: 36877077 PMCID: PMC10101069 DOI: 10.1128/spectrum.04947-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/01/2022] [Accepted: 02/09/2023] [Indexed: 03/07/2023] Open
Abstract
Knowledge about the effect of vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on immunity reflected in the saliva is sparse. We examined the antibody response in saliva compared to that in serum 2 and 6 months after the first vaccination with the BNT162b2 vaccine. Four hundred fifty-nine health care professionals were included in a prospective observational study measuring antibody levels in saliva and corresponding serum samples at 2 and 6 months after BNT162b2 vaccination. Vaccinated, previously SARS-CoV-2-infected individuals (hybrid immunity) had higher IgG levels in saliva at 2 months than vaccinated, infection-naive individuals (P < 0.001). After 6 months, saliva IgG levels declined in both groups (P < 0.001), with no difference between groups (P = 0.37). Furthermore, serum IgG levels declined from 2 to 6 months in both groups (P < 0.001). IgG antibodies in saliva and serum correlated in individuals with hybrid immunity at 2 and 6 months (ρ = 0.58, P = 0.001, and ρ = 0.53, P = 0.052, respectively). In vaccinated, infection-naive individuals, a correlation was observed at 2 months (ρ = 0.42, P < 0.001) but not after 6 months (ρ = 0.14, P = 0.055). IgA and IgM antibodies were hardly detectable in saliva at any time point, regardless of previous infection. In serum, IgA was detected at 2 months in previously infected individuals. BNT162b2 vaccination induced a detectable IgG anti-SARS-CoV-2 RBD response in saliva at both 2 and 6 months after vaccination, being more prominent in previously infected than infection-naive individuals. However, a significant decrease in salivary IgG was observed after 6 months, suggesting a rapid decline in antibody-mediated saliva immunity against SARS-CoV-2, after both infection and systemic vaccination. IMPORTANCE Knowledge about the persistence of salivary immunity after SARS-CoV-2 vaccination is limited, and information on this topic could prove important for vaccine strategy and development. We hypothesized that salivary immunity would wane rapidly after vaccination. We measured anti-SARS-CoV-2 IgG, IgA, and IgM concentrations in saliva and serum in both previously infected and infection-naive individuals, 2 and 6 months after first vaccination with BNT162b2, in 459 hospital employees from Copenhagen University Hospital. We observed that IgG was the primary salivary antibody 2 months after vaccination in both previously infected and infection-naive individuals, but dropped significantly after 6 months. Neither IgA nor IgM was detectable in saliva at either time point. Findings indicate that salivary immunity against SARS-CoV-2 rapidly declines following vaccination in both previously infected and infection-naive individuals. We believe this study shines a light on the workings of salivary immunity after SARS-CoV-2 infection, which could prove relevant for vaccine development.
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Affiliation(s)
- Johannes Roth Madsen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bettina Eide Holm
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Laura Pérez-Alós
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anne Rosbjerg
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kamille Fogh
- Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Emergency Medicine, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mia Marie Pries-Heje
- The Heart Center, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dina Leth Møller
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Line Dam Heftdal
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Bo Hasselbalch
- Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Emergency Medicine, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Rask Hamm
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Linda Hilsted
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Viro-immunology Research Unit, Department of Infectious Diseases, Section 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Karmark Iversen
- Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Emergency Medicine, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- The Heart Center, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Betthäuser BA, Bach-Mortensen AM, Engzell P. A systematic review and meta-analysis of the evidence on learning during the COVID-19 pandemic. Nat Hum Behav 2023; 7:375-385. [PMID: 36717609 DOI: 10.1038/s41562-022-01506-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/30/2022] [Indexed: 01/31/2023]
Abstract
To what extent has the learning progress of school-aged children slowed down during the COVID-19 pandemic? A growing number of studies address this question, but findings vary depending on context. Here we conduct a pre-registered systematic review, quality appraisal and meta-analysis of 42 studies across 15 countries to assess the magnitude of learning deficits during the pandemic. We find a substantial overall learning deficit (Cohen's d = -0.14, 95% confidence interval -0.17 to -0.10), which arose early in the pandemic and persists over time. Learning deficits are particularly large among children from low socio-economic backgrounds. They are also larger in maths than in reading and in middle-income countries relative to high-income countries. There is a lack of evidence on learning progress during the pandemic in low-income countries. Future research should address this evidence gap and avoid the common risks of bias that we identify.
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Affiliation(s)
- Bastian A Betthäuser
- Centre for Research on Social Inequalities (CRIS), Sciences Po, Paris, France.
- Department of Social Policy and Intervention, University of Oxford, Oxford, UK.
- Nuffield College, University of Oxford, Oxford, UK.
| | | | - Per Engzell
- Nuffield College, University of Oxford, Oxford, UK
- Social Research Institute, University College London, London, UK
- Swedish Institute for Social Research, Stockholm University, Stockholm, Sweden
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Eisenhofer R, Odriozola I, Alberdi A. Impact of microbial genome completeness on metagenomic functional inference. ISME Commun 2023; 3:12. [PMID: 36797336 PMCID: PMC9935889 DOI: 10.1038/s43705-023-00221-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this overlooked bias in metagenomic functional inference.
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Affiliation(s)
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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49
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Affiliation(s)
- Kristian Steensen Nielsen
- Department of Psychology, University of Cambridge, Cambridge, UK.
- Department of Management, Society and Communication, Copenhagen Business School, Copenhagen, Denmark.
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Fogh K, Larsen TG, Hansen CB, Hasselbalch RB, Eriksen ARR, Bundgaard H, Frikke-Schmidt R, Hilsted LM, Østergaard L, Johansen IS, Hageman I, Garred P, Iversen K. Self-Reported Long COVID and Its Association with the Presence of SARS-CoV-2 Antibodies in a Danish Cohort up to 12 Months after Infection. Microbiol Spectr 2022; 10:e0253722. [PMID: 36350150 PMCID: PMC9769646 DOI: 10.1128/spectrum.02537-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/02/2022] [Indexed: 11/11/2022] Open
Abstract
The majority of long coronavirus disease (COVID) symptoms are not specific to COVID-19 and could be explained by other conditions. The present study aimed to explore whether Danish individuals with a perception that they suffer from long COVID have antibodies against the nucleocapsid antigen, as a proxy for detecting previous infection. The study was conducted in February and March 2021, right after the second surge of the COVID-19 pandemic in Denmark. All members of the social media group on Facebook "Covidramte med senfølger" ("long COVID sufferers'') above the age of 17 years and living in Denmark were invited to participate in a short electronic questionnaire about long COVID risk factors and symptoms. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein was detected in blood samples as a proxy for natural SARS-CoV-2 infection. The final study population comprised 341 participants (90.6% females) who completed blood sampling and answered the questionnaire. A total of 232 (68%) were seropositive (median age, 49.5 years; interquartile range [IQR], 41 to 55 years; 90.1% females). There was no significant difference between sexes and serostatus. Seronegative and seropositive individuals had a similar burden of symptoms that could be attributed to long COVID. Time since perceived COVID-19 was significantly longer in the group of seronegative individuals than the seropositive ones (P < 0.001). This study suggests that long-COVID sufferers are mostly women and showed that a third of the participants did not have detectable anti-N-protein antibodies. It emphasizes the importance of early confirmation of COVID-19, as this study indicates an overlap between long-COVID symptoms and symptoms that are possibly of another origin. IMPORTANCE This cohort study included questionnaire data as well as anti-nucleocapsid antibody analysis, allowing us to determine whether participants were seropositive due to vaccination or natural infection. The study emphasizes the importance of early confirmation of COVID-19, as antibodies recede with time, and it indicates an overlap between long COVID symptoms and symptoms possibly of another origin.
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Affiliation(s)
- Kamille Fogh
- Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Emergency Medicine, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Tine Graakjær Larsen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Cecilie B. Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Rasmus B. Hasselbalch
- Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Emergency Medicine, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Alexandra R. R. Eriksen
- Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Emergency Medicine, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Linda M. Hilsted
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Isik S. Johansen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Kasper Iversen
- Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Emergency Medicine, Copenhagen University Hospital, Herlev and Gentofte, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital, Faculty of Health and Medical Sciences, Copenhagen, Denmark
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