1
|
Kang BJ, Rohwer EJ, Rohrbach D, Zyaee E, Akbarimoosavi M, Ollmann Z, Sorohhov G, Borgoo A, Cascella M, Cannizzo A, Decurtins S, Stanley RJ, Liu SX, Feurer T. Time-resolved THz Stark spectroscopy of molecules in solution. Nat Commun 2024; 15:4212. [PMID: 38760343 PMCID: PMC11101612 DOI: 10.1038/s41467-024-48164-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: 12/13/2022] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
For decades, it was considered all but impossible to perform Stark spectroscopy on molecules in a liquid solution, because their concomitant orientation to the applied electric field results in overwhelming background signals. A way out was to immobilize the solute molecules by freezing the solvent. While mitigating solute orientation, freezing removes the possibility to study molecules in liquid environments at ambient conditions. Here we demonstrate time-resolved THz Stark spectroscopy, utilizing intense single-cycle terahertz pulses as electric field source. At THz frequencies, solute molecules have no time to orient their dipole moments. Hence, dynamic Stark spectroscopy on the time scales of molecular vibrations or rotations in both non-polar and polar solvents at arbitrary temperatures is now possible. We verify THz Stark spectroscopy for two judiciously selected molecular systems and compare the results to conventional Stark spectroscopy and first principle calculations.
Collapse
Affiliation(s)
- Bong Joo Kang
- Institute of Applied Physics, University of Bern, Bern, Switzerland
- Division of Advanced Materials, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Egmont J Rohwer
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - David Rohrbach
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Elnaz Zyaee
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | | | - Zoltan Ollmann
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Gleb Sorohhov
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Alex Borgoo
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Andrea Cannizzo
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Silvio Decurtins
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Robert J Stanley
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Shi-Xia Liu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Thomas Feurer
- Institute of Applied Physics, University of Bern, Bern, Switzerland.
| |
Collapse
|
2
|
Kono S, Pan J, Chegnizadeh M, Wang X, Youssefi A, Scigliuzzo M, Kippenberg TJ. Mechanically induced correlated errors on superconducting qubits with relaxation times exceeding 0.4 ms. Nat Commun 2024; 15:3950. [PMID: 38729959 PMCID: PMC11087564 DOI: 10.1038/s41467-024-48230-3] [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: 07/06/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Superconducting qubits are among the most advanced candidates for achieving fault-tolerant quantum computing. Despite recent significant advancements in the qubit lifetimes, the origin of the loss mechanism for state-of-the-art qubits is still subject to investigation. Furthermore, the successful implementation of quantum error correction requires negligible correlated errors between qubits. Here, we realize long-lived superconducting transmon qubits that exhibit fluctuating lifetimes, averaging 0.2 ms and exceeding 0.4 ms - corresponding to quality factors above 5 million and 10 million, respectively. We then investigate their dominant error mechanism. By introducing novel time-resolved error measurements that are synchronized with the operation of the pulse tube cooler in a dilution refrigerator, we find that mechanical vibrations from the pulse tube induce nonequilibrium dynamics in highly coherent qubits, leading to their correlated bit-flip errors. Our findings not only deepen our understanding of the qubit error mechanisms but also provide valuable insights into potential error-mitigation strategies for achieving fault tolerance by decoupling superconducting qubits from their mechanical environments.
Collapse
Affiliation(s)
- Shingo Kono
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland.
| | - Jiahe Pan
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland
| | - Mahdi Chegnizadeh
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland
| | - Xuxin Wang
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland
| | - Amir Youssefi
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland
| | - Marco Scigliuzzo
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland
| | - Tobias J Kippenberg
- Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Center for Quantum Science and Engineering, EPFL, Lausanne, Switzerland.
| |
Collapse
|
3
|
Thiel H, Jehle L, Chapman RJ, Frick S, Conradi H, Kleinert M, Suchomel H, Kamp M, Höfling S, Schneider C, Keil N, Weihs G. Time-bin entanglement at telecom wavelengths from a hybrid photonic integrated circuit. Sci Rep 2024; 14:9990. [PMID: 38693329 PMCID: PMC11063055 DOI: 10.1038/s41598-024-60758-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/26/2024] [Indexed: 05/03/2024] Open
Abstract
Mass-deployable implementations for quantum communication require compact, reliable, and low-cost hardware solutions for photon generation, control and analysis. We present a fiber-pigtailed hybrid photonic circuit comprising nonlinear waveguides for photon-pair generation and a polymer interposer reaching 68 dB of pump suppression and photon separation based on a polarizing beam splitter with > 25 dB polarization extinction ratio. The optical stability of the hybrid assembly enhances the quality of the entanglement, and the efficient background suppression and photon routing further reduce accidental coincidences. We thus achieve a96 - 8 + 3 % concurrence and a96 - 5 + 2 % fidelity to a Bell state. The generated telecom-wavelength, time-bin entangled photon pairs are ideally suited for distributing Bell pairs over fiber networks with low dispersion.
Collapse
Affiliation(s)
- Hannah Thiel
- Institut für Experimentalphysik, Universität Innsbruck, 6020, Innsbruck, Austria.
| | - Lennart Jehle
- Faculty of Physics and Vienna Doctoral School in Physics and Vienna Center for Quantum Science and Technology, University of Vienna, 1090, Vienna, Austria
- Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, 10587, Berlin, Germany
| | - Robert J Chapman
- Institut für Experimentalphysik, Universität Innsbruck, 6020, Innsbruck, Austria
- Department of Physics, Optical Nanomaterial Group, Institute for Quantum Electronics, ETH Zurich, 8093, Zurich, Switzerland
| | - Stefan Frick
- Institut für Experimentalphysik, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Hauke Conradi
- Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, 10587, Berlin, Germany
| | - Moritz Kleinert
- Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, 10587, Berlin, Germany
| | - Holger Suchomel
- Technische Physik, Universität Würzburg, 97074, Würzburg, Germany
| | - Martin Kamp
- Technische Physik, Universität Würzburg, 97074, Würzburg, Germany
| | - Sven Höfling
- Technische Physik, Universität Würzburg, 97074, Würzburg, Germany
| | - Christian Schneider
- Technische Physik, Universität Würzburg, 97074, Würzburg, Germany
- Institute of Physics, University of Oldenburg, 26129, Oldenburg, Germany
| | - Norbert Keil
- Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, 10587, Berlin, Germany
| | - Gregor Weihs
- Institut für Experimentalphysik, Universität Innsbruck, 6020, Innsbruck, Austria
| |
Collapse
|
4
|
Belicova L, Van Hul N, Andersson ER. Understanding liver repair through space and time. Nat Genet 2024; 56:740-742. [PMID: 38730127 DOI: 10.1038/s41588-024-01741-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Affiliation(s)
- Lenka Belicova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Van Hul
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
5
|
Chan AYL, Gao L, Hsieh MHC, Kjerpeseth LJ, Avelar R, Banaschewski T, Chan AHY, Coghill D, Cohen JM, Gissler M, Harrison J, Ip P, Karlstad Ø, Lau WCY, Leinonen MK, Leung WC, Liao TC, Reutfors J, Shao SC, Simonoff E, Tan KCB, Taxis K, Tomlin A, Cesta CE, Lai ECC, Zoega H, Man KKC, Wong ICK. Maternal diabetes and risk of attention-deficit/hyperactivity disorder in offspring in a multinational cohort of 3.6 million mother-child pairs. Nat Med 2024; 30:1416-1423. [PMID: 38589601 DOI: 10.1038/s41591-024-02917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Previous studies report an association between maternal diabetes mellitus (MDM) and attention-deficit/hyperactivity disorder (ADHD), often overlooking unmeasured confounders such as shared genetics and environmental factors. We therefore conducted a multinational cohort study with linked mother-child pairs data in Hong Kong, New Zealand, Taiwan, Finland, Iceland, Norway and Sweden to evaluate associations between different MDM (any MDM, gestational diabetes mellitus (GDM) and pregestational diabetes mellitus (PGDM)) and ADHD using Cox proportional hazards regression. We included over 3.6 million mother-child pairs between 2001 and 2014 with follow-up until 2020. Children who were born to mothers with any type of diabetes during pregnancy had a higher risk of ADHD than unexposed children (pooled hazard ratio (HR) = 1.16, 95% confidence interval (CI) = 1.08-1.24). Higher risks of ADHD were also observed for both GDM (pooled HR = 1.10, 95% CI = 1.04-1.17) and PGDM (pooled HR = 1.39, 95% CI = 1.25-1.55). However, siblings with discordant exposure to GDM in pregnancy had similar risks of ADHD (pooled HR = 1.05, 95% CI = 0.94-1.17), suggesting potential confounding by unmeasured, shared familial factors. Our findings indicate that there is a small-to-moderate association between MDM and ADHD, whereas the association between GDM and ADHD is unlikely to be causal. This finding contrast with previous studies, which reported substantially higher risk estimates, and underscores the need to reevaluate the precise roles of hyperglycemia and genetic factors in the relationship between MDM and ADHD.
Collapse
Affiliation(s)
- Adrienne Y L Chan
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Pak Shek Kok, Hong Kong
- Research Department of Practice and Policy, UCL School of Pharmacy, London, UK
- Groningen Research Institute of Pharmacy, Unit of PharmacoTherapy, Epidemiology and Economics, University of Groningen, Groningen, The Netherlands
| | - Le Gao
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Miyuki Hsing-Chun Hsieh
- School of Pharmacy, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Lars J Kjerpeseth
- Department of Chronic Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Raquel Avelar
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Amy Hai Yan Chan
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - David Coghill
- Departments of Paediatrics and Psychiatry, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Jacqueline M Cohen
- Department of Chronic Diseases, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Mika Gissler
- Centre for Pharmacoepidemiology, Department of Medicine, Karolinska Institutet, Solna, Sweden
- Academic Primary Health Care Centre, Region Stockholm, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Research Centre for Child Psychiatry, University of Turku, Turku, Finland
| | - Jeff Harrison
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Øystein Karlstad
- Department of Chronic Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Wallis C Y Lau
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Pak Shek Kok, Hong Kong
- Research Department of Practice and Policy, UCL School of Pharmacy, London, UK
| | - Maarit K Leinonen
- Knowledge Brokers, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Wing Cheong Leung
- Department of Obstetrics and Gynaecology, Kwong Wah Hospital, Yau Ma Tei, Hong Kong
| | - Tzu-Chi Liao
- School of Pharmacy, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Johan Reutfors
- Centre for Pharmacoepidemiology, Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Shih-Chieh Shao
- School of Pharmacy, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pharmacy, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Emily Simonoff
- Department of Child and Adolescent Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Kathryn Choon Beng Tan
- Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Katja Taxis
- Groningen Research Institute of Pharmacy, Unit of PharmacoTherapy, Epidemiology and Economics, University of Groningen, Groningen, The Netherlands
| | - Andrew Tomlin
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Carolyn E Cesta
- Centre for Pharmacoepidemiology, Department of Medicine, Karolinska Institutet, Solna, Sweden.
| | - Edward Chia-Cheng Lai
- School of Pharmacy, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Helga Zoega
- Centre of Public Health Sciences, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
- School of Population Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
| | - Kenneth K C Man
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong.
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Pak Shek Kok, Hong Kong.
- Research Department of Practice and Policy, UCL School of Pharmacy, London, UK.
- Centre for Medicines Optimisation Research and Education, University College London Hospitals NHS Foundation Trust, London, UK.
| | - Ian C K Wong
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong.
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Pak Shek Kok, Hong Kong.
- School of Pharmacy, Medical Sciences Division, Macau University of Science and Technology, Taipa, Macau.
- Advance Data Analytics for Medical Science Limited, Hong Kong, Hong Kong.
- School of Pharmacy, Aston University, Birmingham, UK.
| |
Collapse
|
6
|
Santin YG, Sogues A, Bourigault Y, Remaut HK, Laloux G. Lifecycle of a predatory bacterium vampirizing its prey through the cell envelope and S-layer. Nat Commun 2024; 15:3590. [PMID: 38678033 PMCID: PMC11055950 DOI: 10.1038/s41467-024-48042-5] [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: 11/09/2023] [Accepted: 04/16/2024] [Indexed: 04/29/2024] Open
Abstract
Predatory bacteria feed upon other bacteria in various environments. Bdellovibrio exovorus is an obligate epibiotic predator that attaches on the prey cell surface, where it grows and proliferates. Although the mechanisms allowing feeding through the prey cell envelope are unknown, it has been proposed that the prey's proteinaceous S-layer may act as a defensive structure against predation. Here, we use time-lapse and cryo-electron microscopy to image the lifecycle of B. exovorus feeding on Caulobacter crescentus. We show that B. exovorus proliferates by non-binary division, primarily generating three daughter cells. Moreover, the predator feeds on C. crescentus regardless of the presence of an S-layer, challenging its assumed protective role against predators. Finally, we show that apparently secure junctions are established between prey and predator outer membranes.
Collapse
Affiliation(s)
- Yoann G Santin
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium
| | - Adrià Sogues
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Yvann Bourigault
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium
| | - Han K Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium.
| |
Collapse
|
7
|
Hori M, Steinauer A, Tetter S, Hälg J, Manz EM, Hilvert D. Stimulus-responsive assembly of nonviral nucleocapsids. Nat Commun 2024; 15:3576. [PMID: 38678040 PMCID: PMC11055949 DOI: 10.1038/s41467-024-47808-1] [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: 02/17/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.
Collapse
Affiliation(s)
- Mao Hori
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LIBN, Lausanne, Switzerland
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Jamiro Hälg
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Eva-Maria Manz
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
8
|
Folkestad SD, Paul AC, Paul Née Matveeva R, Coriani S, Odelius M, Iannuzzi M, Koch H. Understanding X-ray absorption in liquid water using triple excitations in multilevel coupled cluster theory. Nat Commun 2024; 15:3551. [PMID: 38670938 PMCID: PMC11053016 DOI: 10.1038/s41467-024-47690-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
X-ray absorption (XA) spectroscopy is an essential experimental tool to investigate the local structure of liquid water. Interpretation of the experiment poses a significant challenge and requires a quantitative theoretical description. High-quality theoretical XA spectra require reliable molecular dynamics simulations and accurate electronic structure calculations. Here, we present the first successful application of coupled cluster theory to model the XA spectrum of liquid water. We overcome the computational limitations on system size by employing a multilevel coupled cluster framework for large molecular systems. Excellent agreement with the experimental spectrum is achieved by including triple excitations in the wave function and using molecular structures from state-of-the-art path-integral molecular dynamics. We demonstrate that an accurate description of the electronic structure within the first solvation shell is sufficient to successfully model the XA spectrum of liquid water within the multilevel framework. Furthermore, we present a rigorous charge transfer analysis of the XA spectrum, which is reliable due to the accuracy and robustness of the electronic structure methodology. This analysis aligns with previous studies regarding the character of the prominent features of the XA spectrum of liquid water.
Collapse
Affiliation(s)
- Sarai Dery Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Alexander C Paul
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Regina Paul Née Matveeva
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, DTU, 2800, Kongens Lyngby, Denmark
| | - Michael Odelius
- Department of Physics, Stockholm University, 10691, Stockholm, Sweden
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.
| |
Collapse
|
9
|
Arthofer P, Panhölzl F, Delafont V, Hay A, Reipert S, Cyran N, Wienkoop S, Willemsen A, Sifaoui I, Arberas-Jiménez I, Schulz F, Lorenzo-Morales J, Horn M. A giant virus infecting the amoeboflagellate Naegleria. Nat Commun 2024; 15:3307. [PMID: 38658525 PMCID: PMC11043551 DOI: 10.1038/s41467-024-47308-2] [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: 08/02/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.
Collapse
Affiliation(s)
- Patrick Arthofer
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Florian Panhölzl
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Vincent Delafont
- Ecologie et Biologie des Interactions Laboratory (EBI), Microorganisms, hosts & environments team, Université de Poitiers, UMR CNRS, Poitiers, France
| | - Alban Hay
- Ecologie et Biologie des Interactions Laboratory (EBI), Microorganisms, hosts & environments team, Université de Poitiers, UMR CNRS, Poitiers, France
| | - Siegfried Reipert
- University of Vienna, Research Support Facilities UBB, Vienna, Austria
| | - Norbert Cyran
- University of Vienna, Research Support Facilities UBB, Vienna, Austria
| | - Stefanie Wienkoop
- University of Vienna, Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology, Vienna, Austria
| | - Anouk Willemsen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Ines Sifaoui
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Iñigo Arberas-Jiménez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
| |
Collapse
|
10
|
Mitra A, Loseva E, Peterman EJG. IFT cargo and motors associate sequentially with IFT trains to enter cilia of C. elegans. Nat Commun 2024; 15:3456. [PMID: 38658528 PMCID: PMC11043347 DOI: 10.1038/s41467-024-47807-2] [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: 07/22/2023] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Intraflagellar transport (IFT) orchestrates entry of proteins into primary cilia. At the ciliary base, assembled IFT trains, driven by kinesin-2 motors, can transport cargo proteins into the cilium, across the crowded transition zone. How trains assemble at the base and how proteins associate with them is far from understood. Here, we use single-molecule imaging in the cilia of C. elegans chemosensory neurons to directly visualize the entry of kinesin-2 motors, kinesin-II and OSM-3, as well as anterograde cargo proteins, IFT dynein and tubulin. Single-particle tracking shows that IFT components associate with trains sequentially, both in time and space. Super-resolution maps of IFT components in wild-type and mutant worms reveal ciliary ultrastructure and show that kinesin-II is essential for axonemal organization. Finally, imaging cilia lacking kinesin-II and/or transition zone function uncovers the interplay of kinesin-II and OSM-3 in driving efficient transport of IFT trains across the transition zone.
Collapse
Affiliation(s)
- Aniruddha Mitra
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Elizaveta Loseva
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
11
|
Damhofer H, Tatar T, Southgate B, Scarneo S, Agger K, Shlyueva D, Uhrbom L, Morrison GM, Hughes PF, Haystead T, Pollard SM, Helin K. TAK1 inhibition leads to RIPK1-dependent apoptosis in immune-activated cancers. Cell Death Dis 2024; 15:273. [PMID: 38632238 PMCID: PMC11024179 DOI: 10.1038/s41419-024-06654-1] [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: 11/18/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
Poor survival and lack of treatment response in glioblastoma (GBM) is attributed to the persistence of glioma stem cells (GSCs). To identify novel therapeutic approaches, we performed CRISPR/Cas9 knockout screens and discovered TGFβ activated kinase (TAK1) as a selective survival factor in a significant fraction of GSCs. Loss of TAK1 kinase activity results in RIPK1-dependent apoptosis via Caspase-8/FADD complex activation, dependent on autocrine TNFα ligand production and constitutive TNFR signaling. We identify a transcriptional signature associated with immune activation and the mesenchymal GBM subtype to be a characteristic of cancer cells sensitive to TAK1 perturbation and employ this signature to accurately predict sensitivity to the TAK1 kinase inhibitor HS-276. In addition, exposure to pro-inflammatory cytokines IFNγ and TNFα can sensitize resistant GSCs to TAK1 inhibition. Our findings reveal dependency on TAK1 kinase activity as a novel vulnerability in immune-activated cancers, including mesenchymal GBMs that can be exploited therapeutically.
Collapse
Affiliation(s)
- Helene Damhofer
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Tülin Tatar
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Scott Scarneo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Karl Agger
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Daria Shlyueva
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gillian M Morrison
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Timothy Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Steven M Pollard
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Kristian Helin
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
12
|
Eldridge DJ, Ding J, Dorrough J, Delgado-Baquerizo M, Sala O, Gross N, Le Bagousse-Pinguet Y, Mallen-Cooper M, Saiz H, Asensio S, Ochoa V, Gozalo B, Guirado E, García-Gómez M, Valencia E, Martínez-Valderrama J, Plaza C, Abedi M, Ahmadian N, Ahumada RJ, Alcántara JM, Amghar F, Azevedo L, Ben Salem F, Berdugo M, Blaum N, Boldgiv B, Bowker M, Bran D, Bu C, Canessa R, Castillo-Monroy AP, Castro I, Castro-Quezada P, Cesarz S, Chibani R, Conceição AA, Darrouzet-Nardi A, Davila YC, Deák B, Díaz-Martínez P, Donoso DA, Dougill AD, Durán J, Eisenhauer N, Ejtehadi H, Espinosa CI, Fajardo A, Farzam M, Foronda A, Franzese J, Fraser LH, Gaitán J, Geissler K, Gonzalez SL, Gusman-Montalvan E, Hernández RM, Hölzel N, Hughes FM, Jadan O, Jentsch A, Ju M, Kaseke KF, Köbel M, Lehmann A, Liancourt P, Linstädter A, Louw MA, Ma Q, Mabaso M, Maggs-Kölling G, Makhalanyane TP, Issa OM, Marais E, McClaran M, Mendoza B, Mokoka V, Mora JP, Moreno G, Munson S, Nunes A, Oliva G, Oñatibia GR, Osborne B, Peter G, Pierre M, Pueyo Y, Emiliano Quiroga R, Reed S, Rey A, Rey P, Gómez VMR, Rolo V, Rillig MC, le Roux PC, Ruppert JC, Salah A, Sebei PJ, Sharkhuu A, Stavi I, Stephens C, Teixido AL, Thomas AD, Tielbörger K, Robles ST, Travers S, Valkó O, van den Brink L, Velbert F, von Heßberg A, Wamiti W, Wang D, Wang L, Wardle GM, Yahdjian L, Zaady E, Zhang Y, Zhou X, Maestre FT. Hotspots of biogeochemical activity linked to aridity and plant traits across global drylands. Nat Plants 2024:10.1038/s41477-024-01670-7. [PMID: 38609675 DOI: 10.1038/s41477-024-01670-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Perennial plants create productive and biodiverse hotspots, known as fertile islands, beneath their canopies. These hotspots largely determine the structure and functioning of drylands worldwide. Despite their ubiquity, the factors controlling fertile islands under conditions of contrasting grazing by livestock, the most prevalent land use in drylands, remain virtually unknown. Here we evaluated the relative importance of grazing pressure and herbivore type, climate and plant functional traits on 24 soil physical and chemical attributes that represent proxies of key ecosystem services related to decomposition, soil fertility, and soil and water conservation. To do this, we conducted a standardized global survey of 288 plots at 88 sites in 25 countries worldwide. We show that aridity and plant traits are the major factors associated with the magnitude of plant effects on fertile islands in grazed drylands worldwide. Grazing pressure had little influence on the capacity of plants to support fertile islands. Taller and wider shrubs and grasses supported stronger island effects. Stable and functional soils tended to be linked to species-rich sites with taller plants. Together, our findings dispel the notion that grazing pressure or herbivore type are linked to the formation or intensification of fertile islands in drylands. Rather, our study suggests that changes in aridity, and processes that alter island identity and therefore plant traits, will have marked effects on how perennial plants support and maintain the functioning of drylands in a more arid and grazed world.
Collapse
Affiliation(s)
- David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jingyi Ding
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Josh Dorrough
- Department of Planning and Environment, Merimbula, New South Wales, Australia
- Fenner School of Environment & Society, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
| | - Osvaldo Sala
- Schools of Life Sciences, School of Sustainability, and Global Drylands Center, Arizona State University, Tempe, AZ, USA
| | - Nicolas Gross
- Université Clermont Auvergne, INRAE, VetAgro Sup, Unité Mixte de Recherche Ecosystème Prairial, Clermont-Ferrand, France
| | | | - Max Mallen-Cooper
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Hugo Saiz
- Departamento de Ciencias Agrarias y Medio Natural, Escuela Politécnica Superior, Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), Universidad de Zaragoza, Huesca, Spain
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Victoria Ochoa
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Beatriz Gozalo
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Emilio Guirado
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Miguel García-Gómez
- Departamento de Ingeniería y Morfología del Terreno, Escuela Técnica Superior de Ingenieros de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Enrique Valencia
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jaime Martínez-Valderrama
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
- Estación Experimental de Zonas Áridas (EEZA), CSIC, Campus UAL, Almería, Spain
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mehdi Abedi
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Iran
| | - Negar Ahmadian
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Iran
| | - Rodrigo J Ahumada
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Catamarca, Valle Viejo, Argentina
| | - Julio M Alcántara
- Instituto Interuniversitario de Investigación del Sistema Tierra de Andalucía, Universidad de Jaén, Jaén, Spain
| | - Fateh Amghar
- Laboratoire Biodiversité, Biotechnologie, Environnement et Développement Durable (Biodev), Université M'hamed Bougara de Boumerdès, Boumerdès, Algeria
| | - Luísa Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Farah Ben Salem
- Laboratory of Eremology and Combating Desertification (LR16IRA01), IRA, Institut des Régions Arides Medenine, Medenine, Tunisia
| | - Miguel Berdugo
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Niels Blaum
- Plant Ecology and Nature Conservation, University of Potsdam, Potsdam, Germany
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary Synthesis, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Matthew Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Donaldo Bran
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Bariloche, Bariloche, Argentina
| | - Chongfeng Bu
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Rafaella Canessa
- Plant Ecology Group, Department of Evolution and Ecology, University of Tübingen, Tübingen, Germany
- Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Andrea P Castillo-Monroy
- Grupo de Investigación en Ecología Evolutiva en los Trópicos-EETROP- Universidad de las Américas, Quito, Ecuador
| | - Ignacio Castro
- Instituto de Estudios Científicos y Tecnológicos (IDECYT), Universidad Simón Rodríguez, Caracas, Venezuela
| | - Patricio Castro-Quezada
- Grupo de Ecología Forestal y Agroecosistemas, Facultad de Ciencias Agropecuarias, Carrera de Agronomía, Universidad de Cuenca, Cuenca, Ecuador
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Roukaya Chibani
- Laboratory of Eremology and Combating Desertification (LR16IRA01), IRA, Institut des Régions Arides Medenine, Medenine, Tunisia
| | - Abel Augusto Conceição
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Yvonne C Davila
- Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Balázs Deák
- HUN-REN 'Lendület' Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Paloma Díaz-Martínez
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - David A Donoso
- Grupo de Investigación en Ecología Evolutiva en los Trópicos-EETROP- Universidad de las Américas, Quito, Ecuador
| | | | - Jorge Durán
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Hamid Ejtehadi
- Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Carlos Ivan Espinosa
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Alex Fajardo
- Instituto de Investigación Interdisciplinaria (I3), Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Mohammad Farzam
- Department of Range and Watershed Management, Faculty of Natural Resources and Environment, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ana Foronda
- Veterinary Faculty, University of Zaragoza, Zaragoza, Spain
| | - Jorgelina Franzese
- Investigaciones de Ecología en Ambientes Antropizados, Laboratorio Ecotono, INIBIOMA (Universidad Nacional del Comahue, CONICET), Bariloche, Argentina
| | - Lauchlan H Fraser
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Juan Gaitán
- Universidad Nacional de Luján-CONICET, Luján, Argentina
| | - Katja Geissler
- Plant Ecology and Nature Conservation, University of Potsdam, Potsdam, Germany
| | - Sofía Laura Gonzalez
- Instituto de Investigaciones en Biodiversidad y Medioambiente (CONICET), Universidad Nacional del Comahue, Neuquén, Argentina
| | | | - Rosa Mary Hernández
- Instituto de Estudios Científicos y Tecnológicos (IDECYT), Universidad Simón Rodríguez, Caracas, Venezuela
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Frederic Mendes Hughes
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Oswaldo Jadan
- Grupo de Ecología Forestal y Agroecosistemas, Facultad de Ciencias Agropecuarias, Carrera de Agronomía, Universidad de Cuenca, Cuenca, Ecuador
| | - Anke Jentsch
- Disturbance Ecology and Vegetation Dynamics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Mengchen Ju
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Kudzai F Kaseke
- Earth Research Institute, University of California, Santa Barbara, CA, USA
| | - Melanie Köbel
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Anika Lehmann
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Pierre Liancourt
- Plant Ecology Group, Department of Evolution and Ecology, University of Tübingen, Tübingen, Germany
- State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Anja Linstädter
- Biodiversity Research/Systematic Botany, University of Potsdam, Potsdam, Germany
| | - Michelle A Louw
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Quanhui Ma
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Mancha Mabaso
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | | | - Thulani P Makhalanyane
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Oumarou Malam Issa
- Institute of Ecology and Environmental Sciences of Paris, SU/IRD/CNRS/INRAE/UPEC, Bondy, France
| | - Eugene Marais
- Gobabeb - Namib Research Institute, Walvis Bay, Namibia
| | - Mitchel McClaran
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Betty Mendoza
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Vincent Mokoka
- Risk and Vulnerability Science Centre, University of Limpopo, Mankweng, South Africa
| | - Juan P Mora
- Instituto de Investigación Interdisciplinaria (I3), Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Gerardo Moreno
- INDEHESA, Forestry School, Universidad de Extremadura, Plasencia, Spain
| | - Seth Munson
- US Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - Alice Nunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Gabriel Oliva
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Bariloche, Bariloche, Argentina
| | - Gastón R Oñatibia
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Brooke Osborne
- Department of Environment and Society, Utah State University, Moab, UT, USA
| | - Guadalupe Peter
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Estudios Ambientales desde la NorPatagonia (CEANPa), CONICET, Viedma, Argentina
| | - Margerie Pierre
- Normandie Universite, Unirouen, Inrae, Ecodiv, Rouen, France
| | - Yolanda Pueyo
- Instituto Pirenaico de Ecología (IPE, CSIC), Zaragoza, Spain
| | - R Emiliano Quiroga
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Catamarca, Valle Viejo, Argentina
| | - Sasha Reed
- US Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pedro Rey
- Instituto Interuniversitario de Investigación del Sistema Tierra de Andalucía, Universidad de Jaén, Jaén, Spain
| | | | - Víctor Rolo
- INDEHESA, Forestry School, Universidad de Extremadura, Plasencia, Spain
| | | | - Peter C le Roux
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Jan Christian Ruppert
- Plant Ecology Group, Department of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | | | - Phokgedi Julius Sebei
- Mara Research Station, Limpopo Department of Agriculture and Rural Development, Makhado, South Africa
| | - Anarmaa Sharkhuu
- Laboratory of Ecological and Evolutionary Synthesis, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Ilan Stavi
- The Dead Sea and Arava Science Center, Yotvata, Israel
- Eilat Campus, Ben-Gurion University of the Negev, Eilat, Israel
| | - Colton Stephens
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Alberto L Teixido
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Andrew David Thomas
- Department of Geography and Earth Science, Aberystwyth University, Aberystwyth, UK
| | - Katja Tielbörger
- Plant Ecology Group, Department of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Silvia Torres Robles
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Estudios Ambientales desde la NorPatagonia (CEANPa), CONICET, Viedma, Argentina
| | - Samantha Travers
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Orsolya Valkó
- HUN-REN 'Lendület' Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Liesbeth van den Brink
- Plant Ecology Group, Department of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Frederike Velbert
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Andreas von Heßberg
- Disturbance Ecology and Vegetation Dynamics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Wanyoike Wamiti
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | - Deli Wang
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Lixin Wang
- Department of Earth and Environmental Sciences, Indiana University Indianapolis (IUI), Indianapolis, IN, USA
| | - Glenda M Wardle
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Laura Yahdjian
- Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Buenos Aires, Argentina
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Tel Aviv, Israel
- Kaye College of Education, Be'er Sheva, Israel
| | - Yuanming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Fernando T Maestre
- Environmental Sciences and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| |
Collapse
|
13
|
Athanasoulias S, Guasselli F, Doulamis N, Doulamis A, Ipiotis N, Katsari A, Stankovic L, Stankovic V. The Plegma dataset: Domestic appliance-level and aggregate electricity demand with metadata from Greece. Sci Data 2024; 11:376. [PMID: 38609400 PMCID: PMC11014970 DOI: 10.1038/s41597-024-03208-0] [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: 12/04/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The growing availability of smart meter data has facilitated the development of energy-saving services like demand response, personalized energy feedback, and non-intrusive-load-monitoring applications, all of which heavily rely on advanced machine learning algorithms trained on energy consumption datasets. To ensure the accuracy and reliability of these services, real-world smart meter data collection is crucial. The Plegma dataset described in this paper addresses this need bfy providing whole- house aggregate loads and appliance-level consumption measurements at 10-second intervals from 13 different households over a period of one year. It also includes environmental data such as humidity and temperature, building characteristics, demographic information, and user practice routines to enable quantitative as well as qualitative analysis. Plegma is the first high-frequency electricity measurements dataset in Greece, capturing the consumption behavior of people in the Mediterranean area who use devices not commonly included in other datasets, such as AC and electric-water boilers. The dataset comprises 218 million readings from 88 installed meters and sensors. The collected data are available in CSV format.
Collapse
Affiliation(s)
- Sotirios Athanasoulias
- National Technical University of Athens, School of Rural, Surveying and Geoinformatics Engineering, Athens, 157 80, Greece.
- Plegma Labs, Marousi, 151 24, Greece.
| | - Fernanda Guasselli
- Aalborg University, Department of the Built Environment, Copenhagen, 2450, Denmark
| | - Nikolaos Doulamis
- National Technical University of Athens, School of Rural, Surveying and Geoinformatics Engineering, Athens, 157 80, Greece
| | - Anastasios Doulamis
- National Technical University of Athens, School of Rural, Surveying and Geoinformatics Engineering, Athens, 157 80, Greece
| | | | | | - Lina Stankovic
- University of Strathclyde, Department of Electronic and Electrical Engineering, Glasgow, G1 1XQ, UK
| | - Vladimir Stankovic
- University of Strathclyde, Department of Electronic and Electrical Engineering, Glasgow, G1 1XQ, UK
| |
Collapse
|
14
|
Podoliak E, Lamm GHU, Marin E, Schellbach AV, Fedotov DA, Stetsenko A, Asido M, Maliar N, Bourenkov G, Balandin T, Baeken C, Astashkin R, Schneider TR, Bateman A, Wachtveitl J, Schapiro I, Busskamp V, Guskov A, Gordeliy V, Alekseev A, Kovalev K. A subgroup of light-driven sodium pumps with an additional Schiff base counterion. Nat Commun 2024; 15:3119. [PMID: 38600129 PMCID: PMC11006869 DOI: 10.1038/s41467-024-47469-0] [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: 10/12/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
Collapse
Affiliation(s)
- E Podoliak
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - G H U Lamm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - E Marin
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - A V Schellbach
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - D A Fedotov
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - A Stetsenko
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - M Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - N Maliar
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - G Bourenkov
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - T Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - C Baeken
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - R Astashkin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - T R Schneider
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - A Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - J Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - I Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - V Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - A Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - V Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - A Alekseev
- University Medical Center Göttingen, Institute for Auditory Neuroscience and InnerEarLab, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - K Kovalev
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany.
| |
Collapse
|
15
|
Mazo C, Baeta M, Petreanu L. Auditory cortex conveys non-topographic sound localization signals to visual cortex. Nat Commun 2024; 15:3116. [PMID: 38600132 PMCID: PMC11006897 DOI: 10.1038/s41467-024-47546-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
Spatiotemporally congruent sensory stimuli are fused into a unified percept. The auditory cortex (AC) sends projections to the primary visual cortex (V1), which could provide signals for binding spatially corresponding audio-visual stimuli. However, whether AC inputs in V1 encode sound location remains unknown. Using two-photon axonal calcium imaging and a speaker array, we measured the auditory spatial information transmitted from AC to layer 1 of V1. AC conveys information about the location of ipsilateral and contralateral sound sources to V1. Sound location could be accurately decoded by sampling AC axons in V1, providing a substrate for making location-specific audiovisual associations. However, AC inputs were not retinotopically arranged in V1, and audio-visual modulations of V1 neurons did not depend on the spatial congruency of the sound and light stimuli. The non-topographic sound localization signals provided by AC might allow the association of specific audiovisual spatial patterns in V1 neurons.
Collapse
Affiliation(s)
- Camille Mazo
- Champalimaud Neuroscience Programme, Champalimaud Foundation, Lisbon, Portugal.
| | - Margarida Baeta
- Champalimaud Neuroscience Programme, Champalimaud Foundation, Lisbon, Portugal
| | - Leopoldo Petreanu
- Champalimaud Neuroscience Programme, Champalimaud Foundation, Lisbon, Portugal.
| |
Collapse
|
16
|
Belluati A, Jimaja S, Chadwick RJ, Glynn C, Chami M, Happel D, Guo C, Kolmar H, Bruns N. Artificial cell synthesis using biocatalytic polymerization-induced self-assembly. Nat Chem 2024; 16:564-574. [PMID: 38049652 PMCID: PMC10997521 DOI: 10.1038/s41557-023-01391-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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023]
Abstract
Artificial cells are biomimetic microstructures that mimic functions of natural cells, can be applied as building blocks for molecular systems engineering, and host synthetic biology pathways. Here we report enzymatically synthesized polymer-based artificial cells with the ability to express proteins. Artificial cells were synthesized using biocatalytic atom transfer radical polymerization-induced self-assembly, in which myoglobin synthesizes amphiphilic block co-polymers that self-assemble into structures such as micelles, worm-like micelles, polymersomes and giant unilamellar vesicles (GUVs). The GUVs encapsulate cargo during the polymerization, including enzymes, nanoparticles, microparticles, plasmids and cell lysate. The resulting artificial cells act as microreactors for enzymatic reactions and for osteoblast-inspired biomineralization. Moreover, they can express proteins such as a fluorescent protein and actin when fed with amino acids. Actin polymerizes in the vesicles and alters the artificial cells' internal structure by creating internal compartments. Thus, biocatalytic atom transfer radical polymerization-induced self-assembly-derived GUVs can mimic bacteria as they are composed of a microscopic reaction compartment that contains genetic information for protein expression upon induction.
Collapse
Affiliation(s)
- Andrea Belluati
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow, UK.
- Department of Chemistry and Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
| | - Sètuhn Jimaja
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Robert J Chadwick
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow, UK
| | - Christopher Glynn
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow, UK
| | | | - Dominic Happel
- Department of Chemistry and Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Chao Guo
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow, UK
| | - Harald Kolmar
- Department of Chemistry and Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Nico Bruns
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow, UK.
- Department of Chemistry and Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
| |
Collapse
|
17
|
Barthélemy NR, Salvadó G, Schindler SE, He Y, Janelidze S, Collij LE, Saef B, Henson RL, Chen CD, Gordon BA, Li Y, La Joie R, Benzinger TLS, Morris JC, Mattsson-Carlgren N, Palmqvist S, Ossenkoppele R, Rabinovici GD, Stomrud E, Bateman RJ, Hansson O. Highly accurate blood test for Alzheimer's disease is similar or superior to clinical cerebrospinal fluid tests. Nat Med 2024; 30:1085-1095. [PMID: 38382645 PMCID: PMC11031399 DOI: 10.1038/s41591-024-02869-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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/12/2024] [Indexed: 02/23/2024]
Abstract
With the emergence of Alzheimer's disease (AD) disease-modifying therapies, identifying patients who could benefit from these treatments becomes critical. In this study, we evaluated whether a precise blood test could perform as well as established cerebrospinal fluid (CSF) tests in detecting amyloid-β (Aβ) plaques and tau tangles. Plasma %p-tau217 (ratio of phosporylated-tau217 to non-phosphorylated tau) was analyzed by mass spectrometry in the Swedish BioFINDER-2 cohort (n = 1,422) and the US Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) cohort (n = 337). Matched CSF samples were analyzed with clinically used and FDA-approved automated immunoassays for Aβ42/40 and p-tau181/Aβ42. The primary and secondary outcomes were detection of brain Aβ or tau pathology, respectively, using positron emission tomography (PET) imaging as the reference standard. Main analyses were focused on individuals with cognitive impairment (mild cognitive impairment and mild dementia), which is the target population for available disease-modifying treatments. Plasma %p-tau217 was clinically equivalent to FDA-approved CSF tests in classifying Aβ PET status, with an area under the curve (AUC) for both between 0.95 and 0.97. Plasma %p-tau217 was generally superior to CSF tests in classification of tau-PET with AUCs of 0.95-0.98. In cognitively impaired subcohorts (BioFINDER-2: n = 720; Knight ADRC: n = 50), plasma %p-tau217 had an accuracy, a positive predictive value and a negative predictive value of 89-90% for Aβ PET and 87-88% for tau PET status, which was clinically equivalent to CSF tests, further improving to 95% using a two-cutoffs approach. Blood plasma %p-tau217 demonstrated performance that was clinically equivalent or superior to clinically used FDA-approved CSF tests in the detection of AD pathology. Use of high-performance blood tests in clinical practice can improve access to accurate AD diagnosis and AD-specific treatments.
Collapse
Affiliation(s)
- Nicolas R Barthélemy
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Tracy Family Stable Isotope Labeling Quantitation (SILQ) Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Gemma Salvadó
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC), Washington University School of Medicine, St. Louis, MO, USA
| | - Yingxin He
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Tracy Family Stable Isotope Labeling Quantitation (SILQ) Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Shorena Janelidze
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
| | - Lyduine E Collij
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Benjamin Saef
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Henson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Charles D Chen
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian A Gordon
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yan Li
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, USA
| | - Renaud La Joie
- Department of Neurology, Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Tammie L S Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC), Washington University School of Medicine, St. Louis, MO, USA
| | - Niklas Mattsson-Carlgren
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Sebastian Palmqvist
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Rik Ossenkoppele
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Gil D Rabinovici
- Department of Neurology, Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Erik Stomrud
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA.
- Tracy Family Stable Isotope Labeling Quantitation (SILQ) Center, Washington University School of Medicine, St. Louis, MO, USA.
- Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC), Washington University School of Medicine, St. Louis, MO, USA.
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden.
- Memory Clinic, Skåne University Hospital, Malmö, Sweden.
| |
Collapse
|
18
|
Alonso-Roman R, Mosig AS, Figge MT, Papenfort K, Eggeling C, Schacher FH, Hube B, Gresnigt MS. Organ-on-chip models for infectious disease research. Nat Microbiol 2024; 9:891-904. [PMID: 38528150 DOI: 10.1038/s41564-024-01645-6] [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: 03/29/2023] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Research on microbial pathogens has traditionally relied on animal and cell culture models to mimic infection processes in the host. Over recent years, developments in microfluidics and bioengineering have led to organ-on-chip (OoC) technologies. These microfluidic systems create conditions that are more physiologically relevant and can be considered humanized in vitro models. Here we review various OoC models and how they have been applied for infectious disease research. We outline the properties that make them valuable tools in microbiology, such as dynamic microenvironments, vascularization, near-physiological tissue constitutions and partial integration of functional immune cells, as well as their limitations. Finally, we discuss the prospects for OoCs and their potential role in future infectious disease research.
Collapse
Affiliation(s)
- Raquel Alonso-Roman
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (Leibniz-HKI), Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Alexander S Mosig
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Institute of Biochemistry II, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Friedrich-Schiller University, Jena, Germany
| | - Marc Thilo Figge
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Applied Systems Biology Group, Leibniz-HKI, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Kai Papenfort
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Christian Eggeling
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology, Leibniz Center for Photonics in Infection Research e.V., Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena Center for Soft Matter, Jena, Germany
| | - Felix H Schacher
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Jena Center for Soft Matter, Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (Leibniz-HKI), Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
| | - Mark S Gresnigt
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz-HKI, Jena, Germany
| |
Collapse
|
19
|
Seidel Malkinson T, Bayle DJ, Kaufmann BC, Liu J, Bourgeois A, Lehongre K, Fernandez-Vidal S, Navarro V, Lambrecq V, Adam C, Margulies DS, Sitt JD, Bartolomeo P. Intracortical recordings reveal vision-to-action cortical gradients driving human exogenous attention. Nat Commun 2024; 15:2586. [PMID: 38531880 DOI: 10.1038/s41467-024-46013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/09/2024] [Indexed: 03/28/2024] Open
Abstract
Exogenous attention, the process that makes external salient stimuli pop-out of a visual scene, is essential for survival. How attention-capturing events modulate human brain processing remains unclear. Here we show how the psychological construct of exogenous attention gradually emerges over large-scale gradients in the human cortex, by analyzing activity from 1,403 intracortical contacts implanted in 28 individuals, while they performed an exogenous attention task. The timing, location and task-relevance of attentional events defined a spatiotemporal gradient of three neural clusters, which mapped onto cortical gradients and presented a hierarchy of timescales. Visual attributes modulated neural activity at one end of the gradient, while at the other end it reflected the upcoming response timing, with attentional effects occurring at the intersection of visual and response signals. These findings challenge multi-step models of attention, and suggest that frontoparietal networks, which process sequential stimuli as separate events sharing the same location, drive exogenous attention phenomena such as inhibition of return.
Collapse
Affiliation(s)
- Tal Seidel Malkinson
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France.
- Université de Lorraine, CNRS, IMoPA, F-54000, Nancy, France.
| | - Dimitri J Bayle
- Licae Lab, Université Paris Ouest-La Défense, 92000, Nanterre, France
| | - Brigitte C Kaufmann
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
| | - Jianghao Liu
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
- Dassault Systèmes, Vélizy-Villacoublay, France
| | - Alexia Bourgeois
- Laboratory of Cognitive Neurorehabilitation, Faculty of Medicine, University of Geneva, 1206, Geneva, Switzerland
| | - Katia Lehongre
- CENIR - Centre de Neuro-Imagerie de Recherche, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
| | - Sara Fernandez-Vidal
- CENIR - Centre de Neuro-Imagerie de Recherche, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
| | - Vincent Navarro
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
- AP-HP, Epilepsy and EEG Units, Pitié-Salpêtrière Hospital, 75013, Paris, France
- Reference center of rare epilepsies, EpiCare, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Virginie Lambrecq
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
- AP-HP, Epilepsy and EEG Units, Pitié-Salpêtrière Hospital, 75013, Paris, France
- Reference center of rare epilepsies, EpiCare, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Claude Adam
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
- AP-HP, Epilepsy and EEG Units, Pitié-Salpêtrière Hospital, 75013, Paris, France
- Reference center of rare epilepsies, EpiCare, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Daniel S Margulies
- Laboratoire INCC, équipe Perception, Action, Cognition, Université de Paris, 75005, Paris, France
| | - Jacobo D Sitt
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
| | - Paolo Bartolomeo
- Sorbonne Université, Inserm UMRS 1127, CNRS UMR 7225, Paris Brain Institute, ICM, Hôpital de la Pitié-Salpêtrière, 75013, Paris, France
| |
Collapse
|
20
|
Agarwal VG, Haussener S. Quantifying mass transport limitations in a microfluidic CO 2 electrolyzer with a gas diffusion cathode. Commun Chem 2024; 7:47. [PMID: 38443453 PMCID: PMC10914812 DOI: 10.1038/s42004-024-01122-5] [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: 04/30/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
A gas diffusion electrode (GDE) based CO2 electrolyzer shows enhanced CO2 transport to the catalyst surface, significantly increasing current density compared to traditional planar immersed electrodes. A two-dimensional model for the cathode side of a microfluidic CO2 to CO electrolysis device with a GDE is developed. The model, validated against experimental data, examines key operational parameters and electrode materials. It predicts an initial rise in CO partial current density (PCD), peaking at 75 mA cm-2 at -1.3 V vs RHE for a fully flooded catalyst layer, then declining due to continuous decrease in CO2 availability near the catalyst surface. Factors like electrolyte flow rate and CO2 gas mass flow rate influence PCD, with a trade-off between high CO PCD and CO2 conversion efficiency observed with increased CO2 gas flow. We observe that a significant portion of the catalyst layer remains underutilized, and suggest improvements like varying electrode porosity and anisotropic layers to enhance mass transport and CO PCD. This research offers insights into optimizing CO2 electrolysis device performance.
Collapse
Affiliation(s)
- Venu Gopal Agarwal
- Laboratory of Renewable Energy Science and Engineering, EPFL, Station 9, Lausanne, 1015, Switzerland
| | - Sophia Haussener
- Laboratory of Renewable Energy Science and Engineering, EPFL, Station 9, Lausanne, 1015, Switzerland.
| |
Collapse
|
21
|
Thøgersen J, Madzharova F, Weidner T, Jensen F. Aqueous pyruvate partly dissociates under deep ultraviolet irradiation but is resilient to near ultraviolet excitation. Nat Commun 2024; 15:1978. [PMID: 38438353 PMCID: PMC10912111 DOI: 10.1038/s41467-024-46309-5] [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: 11/08/2023] [Accepted: 02/14/2024] [Indexed: 03/06/2024] Open
Abstract
The deep ultraviolet photochemistry of aqueous pyruvate is believed to have been essential to the origin of life, and near ultraviolet excitation of pyruvate in aqueous aerosols is assumed to contribute significantly to the photochemistry of the Earth's atmosphere. However, the primary photochemistry of aqueous pyruvate is unknown. Here we study the susceptibility of aqueous pyruvate to photodissociation by deep ultraviolet and near ultraviolet irradiation with femtosecond spectroscopy supported by density functional theory calculations. The primary photo-dynamics of the aqueous pyruvate show that upon deep-UV excitation at 200 nm, about one in five excited pyruvate anions have dissociated by decarboxylation 100 ps after the excitation, while the rest of the pyruvate anions return to the ground state. Upon near-UV photoexcitation at a wavelength of 340 nm, the dissociation yield of aqueous pyruvate 200 ps after the excitation is insignificant and no products are observed. The experimental results are explained by our calculations, which show that aqueous pyruvate anions excited at 200 nm have sufficient excess energy for decarboxylation, whereas excitation at 340 nm provides the aqueous pyruvate anions with insufficient energy to overcome the decarboxylation barrier.
Collapse
Affiliation(s)
- Jan Thøgersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000, Aarhus C, Denmark
| | - Fani Madzharova
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000, Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000, Aarhus C, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000, Aarhus C, Denmark.
| |
Collapse
|
22
|
Titze VM, Caixeiro S, Dinh VS, König M, Rübsam M, Pathak N, Schumacher AL, Germer M, Kukat C, Niessen CM, Schubert M, Gather MC. Hyperspectral confocal imaging for high-throughput readout and analysis of bio-integrated microlasers. Nat Protoc 2024; 19:928-959. [PMID: 38238582 DOI: 10.1038/s41596-023-00924-6] [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: 05/01/2023] [Accepted: 10/03/2023] [Indexed: 03/10/2024]
Abstract
Integrating micro- and nanolasers into live cells, tissue cultures and small animals is an emerging and rapidly evolving technique that offers noninvasive interrogation and labeling with unprecedented information density. The bright and distinct spectra of such lasers make this approach particularly attractive for high-throughput applications requiring single-cell specificity, such as multiplexed cell tracking and intracellular biosensing. The implementation of these applications requires high-resolution, high-speed spectral readout and advanced analysis routines, which leads to unique technical challenges. Here, we present a modular approach consisting of two separate procedures. The first procedure instructs users on how to efficiently integrate different types of lasers into living cells, and the second procedure presents a workflow for obtaining intracellular lasing spectra with high spectral resolution and up to 125-kHz readout rate and starts from the construction of a custom hyperspectral confocal microscope. We provide guidance on running hyperspectral imaging routines for various experimental designs and recommend specific workflows for processing the resulting large data sets along with an open-source Python library of functions covering the analysis pipeline. We illustrate three applications including the rapid, large-volume mapping of absolute refractive index by using polystyrene microbead lasers, the intracellular sensing of cardiac contractility with polystyrene microbead lasers and long-term cell tracking by using semiconductor nanodisk lasers. Our sample preparation and imaging procedures require 2 days, and setting up the hyperspectral confocal microscope for microlaser characterization requires <2 weeks to complete for users with limited experience in optical and software engineering.
Collapse
Affiliation(s)
- Vera M Titze
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany.
| | - Soraya Caixeiro
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany
| | - Vinh San Dinh
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
- Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois, USA
| | - Matthias König
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany
| | - Matthias Rübsam
- Department of Cell Biology of the Skin, University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany
| | - Nachiket Pathak
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany
| | - Anna-Lena Schumacher
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Maximilian Germer
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Carien M Niessen
- Department of Cell Biology of the Skin, University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany
| | - Marcel Schubert
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany.
| | - Malte C Gather
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany.
| |
Collapse
|
23
|
Chen K, de Schrijver E, Sivaraj S, Sera F, Scovronick N, Jiang L, Roye D, Lavigne E, Kyselý J, Urban A, Schneider A, Huber V, Madureira J, Mistry MN, Cvijanovic I, Gasparrini A, Vicedo-Cabrera AM. Impact of population aging on future temperature-related mortality at different global warming levels. Nat Commun 2024; 15:1796. [PMID: 38413648 PMCID: PMC10899213 DOI: 10.1038/s41467-024-45901-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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Older adults are generally amongst the most vulnerable to heat and cold. While temperature-related health impacts are projected to increase with global warming, the influence of population aging on these trends remains unclear. Here we show that at 1.5 °C, 2 °C, and 3 °C of global warming, heat-related mortality in 800 locations across 50 countries/areas will increase by 0.5%, 1.0%, and 2.5%, respectively; among which 1 in 5 to 1 in 4 heat-related deaths can be attributed to population aging. Despite a projected decrease in cold-related mortality due to progressive warming alone, population aging will mostly counteract this trend, leading to a net increase in cold-related mortality by 0.1%-0.4% at 1.5-3 °C global warming. Our findings indicate that population aging constitutes a crucial driver for future heat- and cold-related deaths, with increasing mortality burden for both heat and cold due to the aging population.
Collapse
Affiliation(s)
- Kai Chen
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA.
- Yale Center on Climate Change and Health, Yale School of Public Health, New Haven, CT, USA.
| | - Evan de Schrijver
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | - Sidharth Sivaraj
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | - Francesco Sera
- Department of Statistics, Computer Science and Applications "G. Parenti", University of Florence, Florence, Italy
| | - Noah Scovronick
- Gangarosa Department of Environmental Health. Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Leiwen Jiang
- Asian Demographic Research Institute, Shanghai University, Shanghai, China
- Population Council, New York, NY, USA
| | - Dominic Roye
- Climate Research Foundation (FIC), Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Eric Lavigne
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
| | - Jan Kyselý
- Institute of Atmospheric Physics, Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Aleš Urban
- Institute of Atmospheric Physics, Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Alexandra Schneider
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Veronika Huber
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Epidemiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Joana Madureira
- Department of Enviromental Health, Instituto Nacional de Saúde Dr Ricardo Jorge, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - Malcolm N Mistry
- Environment & Health Modelling (EHM) Lab, Department of Public Health, Environments and Society, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Economics, Ca' Foscari University of Venice, Venice, Italy
| | - Ivana Cvijanovic
- ISGlobal - Barcelona Institute for Global Health, Barcelona, Spain
| | - Antonio Gasparrini
- Environment & Health Modelling (EHM) Lab, Department of Public Health, Environments and Society, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Ana M Vicedo-Cabrera
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| |
Collapse
|
24
|
Stríkis NM, Buarque PFSM, Cruz FW, Bernal JP, Vuille M, Tejedor E, Santos MS, Shimizu MH, Ampuero A, Du W, Sampaio G, Sales HDR, Campos JL, Kayano MT, Apaèstegui J, Fu RR, Cheng H, Edwards RL, Mayta VC, Francischini DDS, Arruda MAZ, Novello VF. Modern anthropogenic drought in Central Brazil unprecedented during last 700 years. Nat Commun 2024; 15:1728. [PMID: 38409095 DOI: 10.1038/s41467-024-45469-8] [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: 01/03/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
A better understanding of the relative roles of internal climate variability and external contributions, from both natural (solar, volcanic) and anthropogenic greenhouse gas forcing, is important to better project future hydrologic changes. Changes in the evaporative demand play a central role in this context, particularly in tropical areas characterized by high precipitation seasonality, such as the tropical savannah and semi-desertic biomes. Here we present a set of geochemical proxies in speleothems from a well-ventilated cave located in central-eastern Brazil which shows that the evaporative demand is no longer being met by precipitation, leading to a hydrological deficit. A marked change in the hydrologic balance in central-eastern Brazil, caused by a severe warming trend, can be identified, starting in the 1970s. Our findings show that the current aridity has no analog over the last 720 years. A detection and attribution study indicates that this trend is mostly driven by anthropogenic forcing and cannot be explained by natural factors alone. These results reinforce the premise of a severe long-term drought in the subtropics of eastern South America that will likely be further exacerbated in the future given its apparent connection to increased greenhouse gas emissions.
Collapse
Affiliation(s)
- Nicolas Misailidis Stríkis
- Instituto de Geociências, Universidade de São Paulo (USP), São Paulo, São Paulo-SP, Brazil.
- Departamento de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro-RJ, Brazil.
| | - Plácido Fabrício Silva Melo Buarque
- Instituto de Geociências, Universidade de São Paulo (USP), São Paulo, São Paulo-SP, Brazil
- Departamento de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro-RJ, Brazil
- Universidade Estadual de Goias (UEG), Iporá, Goiás-GO, Brazil
- Instituto Federal Goiano, Ceres, Goiás-GO, Brazil
| | - Francisco William Cruz
- Instituto de Geociências, Universidade de São Paulo (USP), São Paulo, São Paulo-SP, Brazil
| | - Juan Pablo Bernal
- Centro de Geociencias, Universidad Nacional Autónoma de México, Querétaro, México
| | - Mathias Vuille
- Department of Atmospheric and Environmental Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Ernesto Tejedor
- Department of Geology, National Museum of Natural Sciences-Spanish National Research Council (MNCN-CSIC), Madrid, Spain
| | - Matheus Simões Santos
- Departamento de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro-RJ, Brazil
| | - Marília Harumi Shimizu
- General Coordination of Earth Sciences, National Institute for Space Research (INPE), São José dos Campos, São Paulo, Brazil
| | - Angela Ampuero
- Instituto de Geociências, Universidade de São Paulo (USP), São Paulo, São Paulo-SP, Brazil
| | - Wenjing Du
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, China
| | - Gilvan Sampaio
- General Coordination of Earth Sciences, National Institute for Space Research (INPE), São José dos Campos, São Paulo, Brazil
| | - Hamilton Dos Reis Sales
- Instituto Federal de Educação, Ciência e Tecnologia do Norte de Minas Gerais, Januária, Brazil
| | - José Leandro Campos
- Instituto de Geociências, Universidade de São Paulo (USP), São Paulo, São Paulo-SP, Brazil
| | - Mary Toshie Kayano
- General Coordination of Earth Sciences, National Institute for Space Research (INPE), São José dos Campos, São Paulo, Brazil
| | - James Apaèstegui
- Instituto Geofísico del Perú, Lima, Peru
- Universidad Nacional Agraria La Molina, Programa de Maestria en Recursos Hídricos, Lima, Peru
| | - Roger R Fu
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - Hai Cheng
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, China
| | - R Lawrence Edwards
- Department of Earth Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Victor Chavez Mayta
- Department of Climate and Space Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | | | | |
Collapse
|
25
|
Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, De Baere E. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. Nat Commun 2024; 15:1600. [PMID: 38383453 PMCID: PMC10881467 DOI: 10.1038/s41467-024-45381-1] [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: 10/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
Collapse
Affiliation(s)
- Victor Lopez Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| |
Collapse
|
26
|
Meng P, Dalal H, Chen Y, Brueffer C, Gladchuk S, Alcaide M, Ehinger A, Saal LH. Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab. NPJ Breast Cancer 2024; 10:14. [PMID: 38374091 PMCID: PMC10876644 DOI: 10.1038/s41523-024-00621-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet digital PCR (ddPCR) has complementary advantages for HER2/ERBB2 diagnostics. In this study, we developed a single-reaction multiplex ddPCR assay for determination of ERBB2 CN in reference to two control regions, CEP17 and a copy-number-stable region of chr. 2p13.1, validated CN estimations to clinical in situ hybridization (ISH) HER2 status, and investigated the association of ERBB2 CN with clinical outcomes. 909 primary BC tissues were evaluated and the area under the curve for concordance to HER2 status was 0.93 and 0.96 for ERBB2 CN using either CEP17 or 2p13.1 as reference, respectively. The accuracy of ddPCR ERBB2 CN was 93.7% and 94.1% in the training and validation groups, respectively. Positive and negative predictive value for the classic HER2 amplification and non-amplification groups was 97.2% and 94.8%, respectively. An identified biological "ultrahigh" ERBB2 ddPCR CN group had significantly worse survival within patients treated with adjuvant trastuzumab for both recurrence-free survival (hazard ratio, HR: 3.3; 95% CI 1.1-9.6; p = 0.031, multivariable Cox regression) and overall survival (HR: 3.6; 95% CI 1.1-12.6; p = 0.041). For validation using RNA-seq data as a surrogate, in a population-based SCAN-B cohort (NCT02306096) of 682 consecutive patients receiving adjuvant trastuzumab, the ultrahigh-ERBB2 mRNA group had significantly worse survival. Multiplex ddPCR is useful for ERBB2 CN estimation and ultrahigh ERBB2 may be a predictive factor for decreased long-term survival after trastuzumab treatment.
Collapse
Affiliation(s)
- Pei Meng
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Hina Dalal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Yilun Chen
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Miguel Alcaide
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden.
| |
Collapse
|
27
|
Najjar Amiri A, Vit AD, Gorgulu K, Magden ES. Deep photonic network platform enabling arbitrary and broadband optical functionality. Nat Commun 2024; 15:1432. [PMID: 38365856 PMCID: PMC10873373 DOI: 10.1038/s41467-024-45846-3] [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: 05/26/2023] [Accepted: 02/03/2024] [Indexed: 02/18/2024] Open
Abstract
Expanding applications in optical communications, computing, and sensing continue to drive the need for high-performance integrated photonic components. Designing these on-chip systems with arbitrary functionality requires beyond what is possible with physical intuition, for which machine learning-based methods have recently become popular. However, computational demands for physically accurate device simulations present critical challenges, significantly limiting scalability and design flexibility of these methods. Here, we present a highly-scalable, physics-informed design platform for on-chip optical systems with arbitrary functionality, based on deep photonic networks of custom-designed Mach-Zehnder interferometers. Leveraging this platform, we demonstrate ultra-broadband power splitters and a spectral duplexer, each designed within two minutes. The devices exhibit state-of-the-art experimental performance with insertion losses below 0.66 dB, and 1-dB bandwidths exceeding 120 nm. This platform provides a tractable path towards systematic, large-scale photonic system design, enabling custom power, phase, and dispersion profiles for high-throughput communications, quantum information processing, and medical/biological sensing applications.
Collapse
Affiliation(s)
- Ali Najjar Amiri
- Department of Electrical and Electronics Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey
| | - Aycan Deniz Vit
- Department of Electrical and Electronics Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey
| | - Kazim Gorgulu
- Department of Electrical and Electronics Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey
| | - Emir Salih Magden
- Department of Electrical and Electronics Engineering, Koç University, Sariyer, Istanbul, 34450, Turkey.
| |
Collapse
|
28
|
Erazo D, Grant L, Ghisbain G, Marini G, Colón-González FJ, Wint W, Rizzoli A, Van Bortel W, Vogels CBF, Grubaugh ND, Mengel M, Frieler K, Thiery W, Dellicour S. Contribution of climate change to the spatial expansion of West Nile virus in Europe. Nat Commun 2024; 15:1196. [PMID: 38331945 PMCID: PMC10853512 DOI: 10.1038/s41467-024-45290-3] [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: 06/27/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
West Nile virus (WNV) is an emerging mosquito-borne pathogen in Europe where it represents a new public health threat. While climate change has been cited as a potential driver of its spatial expansion on the continent, a formal evaluation of this causal relationship is lacking. Here, we investigate the extent to which WNV spatial expansion in Europe can be attributed to climate change while accounting for other direct human influences such as land-use and human population changes. To this end, we trained ecological niche models to predict the risk of local WNV circulation leading to human cases to then unravel the isolated effect of climate change by comparing factual simulations to a counterfactual based on the same environmental changes but a counterfactual climate where long-term trends have been removed. Our findings demonstrate a notable increase in the area ecologically suitable for WNV circulation during the period 1901-2019, whereas this area remains largely unchanged in a no-climate-change counterfactual. We show that the drastic increase in the human population at risk of exposure is partly due to historical changes in population density, but that climate change has also been a critical driver behind the heightened risk of WNV circulation in Europe.
Collapse
Affiliation(s)
- Diana Erazo
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
| | - Luke Grant
- Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium
| | - Guillaume Ghisbain
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Giovanni Marini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | | | - William Wint
- Environmental Research Group Oxford Ltd, Department of Biology, Mansfield Road, Oxford, OX1 3SZ, UK
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Wim Van Bortel
- Unit Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Outbreak Research team, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Matthias Mengel
- Department Transformation Pathways, Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Katja Frieler
- Department Transformation Pathways, Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Wim Thiery
- Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
| |
Collapse
|
29
|
Lemane T, Lezzoche N, Lecubin J, Pelletier E, Lescot M, Chikhi R, Peterlongo P. Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA. Nat Comput Sci 2024; 4:104-109. [PMID: 38413777 DOI: 10.1038/s43588-024-00596-6] [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] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.
Collapse
Affiliation(s)
- Téo Lemane
- Univ. Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, France.
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France.
| | - Nolan Lezzoche
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
| | | | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France
| | - Magali Lescot
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France
| | - Rayan Chikhi
- Institut Pasteur, Université Paris Cité, G5 Sequence Bioinformatics, Paris, France
| | | |
Collapse
|
30
|
Goicoechea Serrano E, Blázquez-Bondia C, Jaramillo A. T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection. Sci Rep 2024; 14:2377. [PMID: 38287027 PMCID: PMC10824729 DOI: 10.1038/s41598-024-52049-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
Leveraging riboswitches, non-coding mRNA fragments pivotal to gene regulation, poses a challenge in effectively selecting and enriching these functional genetic sensors, which can toggle between ON and OFF states in response to their cognate inducers. Here, we show our engineered phage T7, enabling the evolution of a theophylline riboswitch. We have replaced T7's DNA polymerase with a transcription factor controlled by a theophylline riboswitch and have created two types of host environments to propagate the engineered phage. Both types host an error-prone T7 DNA polymerase regulated by a T7 promoter along with another critical gene-either cmk or pifA, depending on the host type. The cmk gene is necessary for T7 replication and is used in the first host type for selection in the riboswitch's ON state. Conversely, the second host type incorporates the pifA gene, leading to abortive T7 infections and used for selection in the riboswitch's OFF state. This dual-selection system, termed T7AE, was then applied to a library of 65,536 engineered T7 phages, each carrying randomized riboswitch variants. Through successive passage in both host types with and without theophylline, we observed an enrichment of phages encoding functional riboswitches that conferred a fitness advantage to the phage in both hosts. The T7AE technique thereby opens new pathways for the evolution and advancement of gene switches, including non-coding RNA-based switches, setting the stage for significant strides in synthetic biology.
Collapse
Affiliation(s)
- Eduardo Goicoechea Serrano
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- London BioFoundry, Imperial College Translation & Innovation Hub, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Carlos Blázquez-Bondia
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- De novo Synthetic Biology Lab, i2sysbio, CSIC-University of Valencia, Parc Científic Universitat de València, Calle Catedrático Agustín Escardino, 9, 46980, Paterna, Spain.
| |
Collapse
|
31
|
Lucchetti M, Werr G, Johansson S, Barbe L, Grandmougin L, Wilmes P, Tenje M. Integration of multiple flexible electrodes for real-time detection of barrier formation with spatial resolution in a gut-on-chip system. Microsyst Nanoeng 2024; 10:18. [PMID: 38268774 PMCID: PMC10805851 DOI: 10.1038/s41378-023-00640-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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/19/2023] [Accepted: 11/05/2023] [Indexed: 01/26/2024]
Abstract
In healthy individuals, the intestinal epithelium forms a tight barrier to prevent gut bacteria from reaching blood circulation. To study the effect of probiotics, dietary compounds and drugs on gut barrier formation and disruption, human gut epithelial and bacterial cells can be cocultured in an in vitro model called the human microbial crosstalk (HuMiX) gut-on-a-chip system. Here, we present the design, fabrication and integration of thin-film electrodes into the HuMiX platform to measure transepithelial electrical resistance (TEER) as a direct readout on barrier tightness in real-time. As various aspects of the HuMiX platform have already been set in their design, such as multiple compressible layers, uneven surfaces and nontransparent materials, a novel fabrication method was developed whereby thin-film metal electrodes were first deposited on flexible substrates and sequentially integrated with the HuMiX system via a transfer-tape approach. Moreover, to measure localized TEER along the cell culture chamber, we integrated multiple electrodes that were connected to an impedance analyzer via a multiplexer. We further developed a dynamic normalization method because the active measurement area depends on the measured TEER levels. The fabrication process and system setup can be applicable to other barrier-on-chip systems. As a proof-of-concept, we measured the barrier formation of a cancerous Caco-2 cell line in real-time, which was mapped at four spatially separated positions along the HuMiX culture area.
Collapse
Affiliation(s)
- Mara Lucchetti
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, L-4362 Luxembourg
| | - Gabriel Werr
- Division of Biomedical Engineering, Department of Materials Science and Engineering, Science for Life Laboratory, Uppsala University, 751 21 Uppsala, Sweden
| | - Sofia Johansson
- Division of Biomedical Engineering, Department of Materials Science and Engineering, Science for Life Laboratory, Uppsala University, 751 21 Uppsala, Sweden
| | - Laurent Barbe
- Division of Biomedical Engineering, Department of Materials Science and Engineering, Science for Life Laboratory, Uppsala University, 751 21 Uppsala, Sweden
| | - Léa Grandmougin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, L-4362 Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, L-4362 Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, L-4362 Luxembourg
| | - Maria Tenje
- Division of Biomedical Engineering, Department of Materials Science and Engineering, Science for Life Laboratory, Uppsala University, 751 21 Uppsala, Sweden
| |
Collapse
|
32
|
Mehdi E, Gundín M, Millet C, Somaschi N, Lemaître A, Sagnes I, Le Gratiet L, Fioretto DA, Belabas N, Krebs O, Senellart P, Lanco L. Giant optical polarisation rotations induced by a single quantum dot spin. Nat Commun 2024; 15:598. [PMID: 38238312 PMCID: PMC10796934 DOI: 10.1038/s41467-023-44651-8] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/27/2023] [Indexed: 01/22/2024] Open
Abstract
In the framework of optical quantum computing and communications, a major objective consists in building receiving nodes implementing conditional operations on incoming photons, using a single stationary qubit. In particular, the quest for scalable nodes motivated the development of cavity-enhanced spin-photon interfaces with solid-state emitters. An important challenge remains, however, to produce a stable, controllable, spin-dependent photon state, in a deterministic way. Here we use an electrically-contacted pillar-based cavity, embedding a single InGaAs quantum dot, to demonstrate giant polarisation rotations induced on reflected photons by a single electron spin. A complete tomography approach is introduced to extrapolate the output polarisation Stokes vector, conditioned by a specific spin state, in presence of spin and charge fluctuations. We experimentally approach polarisation states conditionally rotated by [Formula: see text], π, and [Formula: see text] in the Poincaré sphere with extrapolated fidelities of (97 ± 1) %, (84 ± 7) %, and (90 ± 8) %, respectively. We find that an enhanced light-matter coupling, together with limited cavity birefringence and reduced spectral fluctuations, allow targeting most conditional rotations in the Poincaré sphere, with a control both in longitude and latitude. Such polarisation control may prove crucial to adapt spin-photon interfaces to various configurations and protocols for quantum information.
Collapse
Affiliation(s)
- E Mehdi
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
- Université Paris Cité, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - M Gundín
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - C Millet
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - N Somaschi
- Quandela, 7 rue Leonard de Vinci, 91300, Massy, France
| | - A Lemaître
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - I Sagnes
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - L Le Gratiet
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - D A Fioretto
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
- Quandela, 7 rue Leonard de Vinci, 91300, Massy, France
| | - N Belabas
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - O Krebs
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - P Senellart
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - L Lanco
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France.
- Université Paris Cité, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France.
- Institut Universitaire de France (IUF), 75005, Paris, France.
| |
Collapse
|
33
|
Knödlseder N, Fábrega MJ, Santos-Moreno J, Manils J, Toloza L, Marín Vilar M, Fernández C, Broadbent K, Maruotti J, Lemenager H, Carolis C, Zouboulis CC, Soler C, Lood R, Brüggemann H, Güell M. Delivery of a sebum modulator by an engineered skin microbe in mice. Nat Biotechnol 2024:10.1038/s41587-023-02072-4. [PMID: 38195987 DOI: 10.1038/s41587-023-02072-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/17/2023] [Indexed: 01/11/2024]
Abstract
Microorganisms can be equipped with synthetic genetic programs for the production of targeted therapeutic molecules. Cutibacterium acnes is the most abundant commensal of the human skin, making it an attractive chassis to create skin-delivered therapeutics. Here, we report the engineering of this bacterium to produce and secrete the therapeutic molecule neutrophil gelatinase-associated lipocalin, in vivo, for the modulation of cutaneous sebum production.
Collapse
Affiliation(s)
- Nastassia Knödlseder
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - María-José Fábrega
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier Santos-Moreno
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Manils
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Toloza
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria Marín Vilar
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Fernández
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Katrina Broadbent
- Protein Technologies Facility, Center of Genomic Regulation, Barcelona, Spain
| | | | | | - Carlo Carolis
- Protein Technologies Facility, Center of Genomic Regulation, Barcelona, Spain
| | - Christos C Zouboulis
- Hochschulklinik für Dermatologie, Venerologie und Allergologie, Immunologisches Zentrum; Städtisches Klinikum Dessau; and Medizinische Hochschule Brandenburg Theodor Fontane und Fakultät für Gesundheitswissenschaften Brandenburg, Dessau-Roßlau, Germany
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Rolf Lood
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | | | - Marc Güell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
| |
Collapse
|
34
|
Ramos-Brossier M, Romeo-Guitart D, Lanté F, Boitez V, Mailliet F, Saha S, Rivagorda M, Siopi E, Nemazanyy I, Leroy C, Moriceau S, Beck-Cormier S, Codogno P, Buisson A, Beck L, Friedlander G, Oury F. Slc20a1 and Slc20a2 regulate neuronal plasticity and cognition independently of their phosphate transport ability. Cell Death Dis 2024; 15:20. [PMID: 38195526 PMCID: PMC10776841 DOI: 10.1038/s41419-023-06292-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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
In recent years, primary familial brain calcification (PFBC), a rare neurological disease characterized by a wide spectrum of cognitive disorders, has been associated to mutations in the sodium (Na)-Phosphate (Pi) co-transporter SLC20A2. However, the functional roles of the Na-Pi co-transporters in the brain remain still largely elusive. Here we show that Slc20a1 (PiT-1) and Slc20a2 (PiT-2) are the most abundant Na-Pi co-transporters expressed in the brain and are involved in the control of hippocampal-dependent learning and memory. We reveal that Slc20a1 and Slc20a2 are differentially distributed in the hippocampus and associated with independent gene clusters, suggesting that they influence cognition by different mechanisms. Accordingly, using a combination of molecular, electrophysiological and behavioral analyses, we show that while PiT-2 favors hippocampal neuronal branching and survival, PiT-1 promotes synaptic plasticity. The latter relies on a likely Otoferlin-dependent regulation of synaptic vesicle trafficking, which impacts the GABAergic system. These results provide the first demonstration that Na-Pi co-transporters play key albeit distinct roles in the hippocampus pertaining to the control of neuronal plasticity and cognition. These findings could provide the foundation for the development of novel effective therapies for PFBC and cognitive disorders.
Collapse
Affiliation(s)
- Mariana Ramos-Brossier
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France.
| | - David Romeo-Guitart
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France
| | - Fabien Lanté
- Univ. Grenoble Alpes, Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Valérie Boitez
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France
| | - François Mailliet
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France
| | - Soham Saha
- Institut Pasteur, Perception & Memory Unit, F-75015, Paris, France
- MedInsights, 6 rue de l'église, F-02810, Veuilly la Poterie, France
| | - Manon Rivagorda
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France
| | - Eleni Siopi
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France
| | - Ivan Nemazanyy
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR, 3633, Paris, France
| | - Christine Leroy
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 6, F-75015, Paris, France
| | - Stéphanie Moriceau
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France
- Platform for Neurobehavioural and metabolism, Structure Fédérative de Recherche Necker, INSERM, US24/CNRS UAR, 3633, Paris, France
- Institute of Genetic Diseases, Imagine, 75015, Paris, France
| | - Sarah Beck-Cormier
- Nantes Université, CNRS, Inserm, l'Institut du Thorax, F-44000, Nantes, France
| | - Patrice Codogno
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 6, F-75015, Paris, France
| | - Alain Buisson
- Univ. Grenoble Alpes, Inserm, U1216, Grenoble Institut Neurosciences, 38000, Grenoble, France
| | - Laurent Beck
- Nantes Université, CNRS, Inserm, l'Institut du Thorax, F-44000, Nantes, France.
| | - Gérard Friedlander
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 6, F-75015, Paris, France.
| | - Franck Oury
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Team 8, F-75015, Paris, France.
| |
Collapse
|
35
|
Botsch JJ, Junker R, Sorgenfrei M, Ogger PP, Stier L, von Gronau S, Murray PJ, Seeger MA, Schulman BA, Bräuning B. Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE. Nat Commun 2024; 15:410. [PMID: 38195637 PMCID: PMC10776854 DOI: 10.1038/s41467-023-44670-5] [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: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity.
Collapse
Affiliation(s)
- J Josephine Botsch
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Roswitha Junker
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Patricia P Ogger
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Peter J Murray
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| |
Collapse
|
36
|
Lenton TM, Abrams JF, Bartsch A, Bathiany S, Boulton CA, Buxton JE, Conversi A, Cunliffe AM, Hebden S, Lavergne T, Poulter B, Shepherd A, Smith T, Swingedouw D, Winkelmann R, Boers N. Remotely sensing potential climate change tipping points across scales. Nat Commun 2024; 15:343. [PMID: 38184618 PMCID: PMC10771461 DOI: 10.1038/s41467-023-44609-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: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
Potential climate tipping points pose a growing risk for societies, and policy is calling for improved anticipation of them. Satellite remote sensing can play a unique role in identifying and anticipating tipping phenomena across scales. Where satellite records are too short for temporal early warning of tipping points, complementary spatial indicators can leverage the exceptional spatial-temporal coverage of remotely sensed data to detect changing resilience of vulnerable systems. Combining Earth observation with Earth system models can improve process-based understanding of tipping points, their interactions, and potential tipping cascades. Such fine-resolution sensing can support climate tipping point risk management across scales.
Collapse
Affiliation(s)
| | - Jesse F Abrams
- Global Systems Institute, University of Exeter, Exeter, UK
| | - Annett Bartsch
- b.geos GmbH, Industriestrasse 1A, 2100, Korneuburg, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Sebastian Bathiany
- Earth System Modelling, School of Engineering & Design, Technical University of Munich, Munich, Germany
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | | | | | - Alessandra Conversi
- National Research Council of Italy, ISMAR-Lerici, Forte Santa Teresa, Loc. Pozzuolo, 19032, Lerici (SP), Italy
| | | | - Sophie Hebden
- Future Earth Secretariat, Stockholm, Sweden
- European Space Agency, ECSAT, Harwell, Oxfordshire, UK
| | | | | | - Andrew Shepherd
- Department of Geography and Environmental Sciences, Northumbria University, Newcastle, UK
| | - Taylor Smith
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Didier Swingedouw
- University of Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, 33600, Pessac, France
| | | | - Niklas Boers
- Global Systems Institute, University of Exeter, Exeter, UK
- Earth System Modelling, School of Engineering & Design, Technical University of Munich, Munich, Germany
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| |
Collapse
|
37
|
Klukowski P, Damberger FF, Allain FHT, Iwai H, Kadavath H, Ramelot TA, Montelione GT, Riek R, Güntert P. The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis. Sci Data 2024; 11:30. [PMID: 38177162 PMCID: PMC10767026 DOI: 10.1038/s41597-023-02879-5] [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: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
Multidimensional NMR spectra are the basis for studying proteins by NMR spectroscopy and crucial for the development and evaluation of methods for biomolecular NMR data analysis. Nevertheless, in contrast to derived data such as chemical shift assignments in the BMRB and protein structures in the PDB databases, this primary data is in general not publicly archived. To change this unsatisfactory situation, we present a standardized set of solution NMR data comprising 1329 2-4-dimensional NMR spectra and associated reference (chemical shift assignments, structures) and derived (peak lists, restraints for structure calculation, etc.) annotations. With the 100-protein NMR spectra dataset that was originally compiled for the development of the ARTINA deep learning-based spectra analysis method, 100 protein structures can be reproduced from their original experimental data. The 100-protein NMR spectra dataset is expected to help the development of computational methods for NMR spectroscopy, in particular machine learning approaches, and enable consistent and objective comparisons of these methods.
Collapse
Affiliation(s)
- Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Fred F Damberger
- Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Hideo Iwai
- Institute of Biotechnology, University of Helsinki, 00100, Helsinki, Finland
| | | | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
- Institute of Biophysical Chemistry, Goethe University, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, 192-0397, Tokyo, Japan.
| |
Collapse
|
38
|
Ben-Yami M, Skiba V, Bathiany S, Boers N. Uncertainties in critical slowing down indicators of observation-based fingerprints of the Atlantic Overturning Circulation. Nat Commun 2023; 14:8344. [PMID: 38102135 PMCID: PMC10724135 DOI: 10.1038/s41467-023-44046-9] [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: 03/14/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Observations are increasingly used to detect critical slowing down (CSD) to measure stability changes in key Earth system components. However, most datasets have non-stationary missing-data distributions, biases and uncertainties. Here we show that, together with the pre-processing steps used to deal with them, these can bias the CSD analysis. We present an uncertainty quantification method to address such issues. We show how to propagate uncertainties provided with the datasets to the CSD analysis and develop conservative, surrogate-based significance tests on the CSD indicators. We apply our method to three observational sea-surface temperature and salinity datasets and to fingerprints of the Atlantic Meridional Overturning Circulation derived from them. We find that the properties of these datasets and especially the specific gap filling procedures can in some cases indeed cause false indication of CSD. However, CSD indicators in the North Atlantic are still present and significant when accounting for dataset uncertainties and non-stationary observational coverage.
Collapse
Affiliation(s)
- Maya Ben-Yami
- Earth System Modelling, School of Engineering and Design, Technical University of Munich, Munich, Germany.
- Potsdam Institute for Climate Impact Research, Potsdam, Germany.
| | - Vanessa Skiba
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | - Sebastian Bathiany
- Earth System Modelling, School of Engineering and Design, Technical University of Munich, Munich, Germany
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | - Niklas Boers
- Earth System Modelling, School of Engineering and Design, Technical University of Munich, Munich, Germany
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
- Department of Mathematics and Global Systems Institute, University of Exeter, Exeter, UK
| |
Collapse
|
39
|
Ji K, Zhong Q, Ge L, Beaudoin G, Sagnes I, Raineri F, El-Ganainy R, Yacomotti AM. Tracking exceptional points above the lasing threshold. Nat Commun 2023; 14:8304. [PMID: 38097572 PMCID: PMC10721897 DOI: 10.1038/s41467-023-43874-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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Recent studies on exceptional points (EPs) in non-Hermitian optical systems have revealed unique traits, including unidirectional invisibility, chiral mode switching and laser self-termination. In systems featuring gain/loss components, EPs are commonly accessed below the lasing threshold, i.e., in the linear regime. In this work, we experimentally demonstrate that EP singularities in coupled semiconductor nanolasers can be accessed above the lasing threshold, where they become branch points of a nonlinear dynamical system. Contrary to the common belief that unavoidable cavity detuning impedes the formation of EPs, here we demonstrate that such detuning is necessary for compensating the carrier-induced frequency shift, hence restoring the EP. Furthermore, we find that the pump imbalance at lasing EPs varies with the total pump power, enabling their continuous tracking. This work uncovers the unstable nature of EPs above laser threshold in coupled semiconductor lasers, offering promising opportunities for the realization of self-pulsing nanolaser devices and frequency combs.
Collapse
Affiliation(s)
- Kaiwen Ji
- Centre de Nanosciences et de Nanotechnologies, CNRS, Université Paris-Saclay, 10 Boulevard Thomas Gobert, 91120, Palaiseau, France
| | - Qi Zhong
- Department of Physics, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Li Ge
- Department of Physics and Astronomy, College of Staten Island, CUNY, Staten Island, New York, 10314, USA
- Graduate Center, CUNY, New York, New York, 10016, USA
| | - Gregoire Beaudoin
- Centre de Nanosciences et de Nanotechnologies, CNRS, Université Paris-Saclay, 10 Boulevard Thomas Gobert, 91120, Palaiseau, France
| | - Isabelle Sagnes
- Centre de Nanosciences et de Nanotechnologies, CNRS, Université Paris-Saclay, 10 Boulevard Thomas Gobert, 91120, Palaiseau, France
| | - Fabrice Raineri
- Centre de Nanosciences et de Nanotechnologies, CNRS, Université Paris-Saclay, 10 Boulevard Thomas Gobert, 91120, Palaiseau, France
| | - Ramy El-Ganainy
- Department of Physics, Michigan Technological University, Houghton, Michigan, 49931, USA.
- Henes Center for Quantum Phenomena, Michigan Technological University, Houghton, Michigan, 49931, USA.
| | - Alejandro M Yacomotti
- Centre de Nanosciences et de Nanotechnologies, CNRS, Université Paris-Saclay, 10 Boulevard Thomas Gobert, 91120, Palaiseau, France.
- LP2N, Institut d'Optique Graduate School, CNRS, Université de Bordeaux, 33400, Talence, France.
| |
Collapse
|
40
|
Fung HKH, Hayashi Y, Salo VT, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat Methods 2023; 20:1900-1908. [PMID: 37932397 PMCID: PMC10703698 DOI: 10.1038/s41592-023-02053-0] [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: 12/10/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Cryo-electron tomography (cryo-ET) allows for label-free high-resolution imaging of macromolecular assemblies in their native cellular context. However, the localization of macromolecules of interest in tomographic volumes can be challenging. Here we present a ligand-inducible labeling strategy for intracellular proteins based on fluorescent, 25-nm-sized, genetically encoded multimeric particles (GEMs). The particles exhibit recognizable structural signatures, enabling their automated detection in cryo-ET data by convolutional neural networks. The coupling of GEMs to green fluorescent protein-tagged macromolecules of interest is triggered by addition of a small-molecule ligand, allowing for time-controlled labeling to minimize disturbance to native protein function. We demonstrate the applicability of GEMs for subcellular-level localization of endogenous and overexpressed proteins across different organelles in human cells using cryo-correlative fluorescence and cryo-ET imaging. We describe means for quantifying labeling specificity and efficiency, and for systematic optimization for rare and abundant protein targets, with emphasis on assessing the potential effects of labeling on protein function.
Collapse
Affiliation(s)
- Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yuki Hayashi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anastasiia Babenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brunner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
41
|
Raja A, Kuiper JJW. Evolutionary immuno-genetics of endoplasmic reticulum aminopeptidase II (ERAP2). Genes Immun 2023; 24:295-302. [PMID: 37925533 PMCID: PMC10721543 DOI: 10.1038/s41435-023-00225-8] [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: 07/31/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023]
Abstract
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a proteolytic enzyme involved in adaptive immunity. The ERAP2 gene is highly polymorphic and encodes haplotypes that confer resistance against lethal infectious diseases, but also increase the risk for autoimmune disorders. Identifying how ERAP2 influences susceptibility to these traits requires an understanding of the selective pressures that shaped and maintained allelic variation throughout human evolution. Our review discusses the genetic regulation of haplotypes and diversity in naturally occurring ERAP2 allotypes in the global population. We outline how these ERAP2 haplotypes evolved during human history and highlight the presence of Neanderthal DNA sequences in ERAP2 of modern humans. Recent evidence suggests that human adaptation during the last ~10,000 years and historic pandemics left a significant mark on the ERAP2 gene that determines susceptibility to infectious and inflammatory diseases today.
Collapse
Affiliation(s)
- Aroosha Raja
- Department of Ophthalmology, Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands.
| |
Collapse
|
42
|
Rathore M, Shweikh Y, Kelly SR, Crabb DP. Measures of multiple deprivation and visual field loss in glaucoma clinics in England: lessons from big data. Eye (Lond) 2023; 37:3615-3620. [PMID: 37165010 PMCID: PMC10686257 DOI: 10.1038/s41433-023-02567-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND/OBJECTIVES To examine the association between multiple deprivation with late diagnosis and rapid worsening of glaucoma in patients in English hospital eye services (HES). METHODS 602,439 visual fields (VFs) were extracted from five regionally different glaucoma clinics in England. Mean Deviation (MD) worse than -12 dB was used as a surrogate definition for advanced VF loss at diagnosis in patients with ≥2 reliable VF records. MD loss worse than -1 dB per year was used to define rapid VF progression in patients with ≥6 VFs. Patient data were stratified into deciles of the Index of Multiple Deprivation (IMD) from residential postcodes. RESULTS There was an association between IMD and advanced VF loss at diagnosis in 44,956 patients with 18% (293/1608) and 11% (771/6929) in the most and least deprived IMD decile, respectively. Age-corrected odds ratio (OR) for having advanced VF loss at entry into HES was 1.42 (95% confidence interval [CI] 1.21-1.67) and 0.75 (95% CI: 0.66-0.85) in the most and least deprived IMD decile respectively (reference = fifth decile). In 15,094 patients with follow up data (median [interquartile range] of 6.9 [4.5, 10.0] years), the proportion having rapid VF progression did not differ across the IMD spectrum. CONCLUSION Large-scale VF data from clinics indicates that glaucoma severity at presentation to English HES is associated with levels of multiple deprivation. We found no evidence to suggest likelihood of having rapid VF progression during follow-up is associated with IMD; this hints at equity of glaucoma care and outcomes once patients are in English HES.
Collapse
Affiliation(s)
- Mehal Rathore
- Department of Optometry and Visual Sciences, School of Health & Psychological Sciences, City, University of London, London, UK
| | - Yusrah Shweikh
- Sussex Eye Hospital, University Hospitals Sussex NHS Foundation Trust, West Sussex, UK
| | - Stephen R Kelly
- Department of Optometry and Visual Sciences, School of Health & Psychological Sciences, City, University of London, London, UK
| | - David P Crabb
- Department of Optometry and Visual Sciences, School of Health & Psychological Sciences, City, University of London, London, UK.
| |
Collapse
|
43
|
Liu NQ, Paassen I, Custers L, Zeller P, Teunissen H, Ayyildiz D, He J, Buhl JL, Hoving EW, van Oudenaarden A, de Wit E, Drost J. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. Nat Commun 2023; 14:7762. [PMID: 38040699 PMCID: PMC10692191 DOI: 10.1038/s41467-023-43498-3] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
Collapse
Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Zeller
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jiayou He
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Juliane Laura Buhl
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| |
Collapse
|
44
|
Dougherty PE, Nielsen TK, Riber L, Lading HH, Forero-Junco LM, Kot W, Raaijmakers JM, Hansen LH. Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria. ISME J 2023; 17:2415-2425. [PMID: 37919394 PMCID: PMC10689766 DOI: 10.1038/s41396-023-01547-1] [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] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 108 virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.
Collapse
Affiliation(s)
- Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Helen Helgå Lading
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
| |
Collapse
|
45
|
Dondi A, Lischetti U, Jacob F, Singer F, Borgsmüller N, Coelho R, Heinzelmann-Schwarz V, Beisel C, Beerenwinkel N. Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer. Nat Commun 2023; 14:7780. [PMID: 38012143 PMCID: PMC10682465 DOI: 10.1038/s41467-023-43387-9] [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: 01/23/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients presenting with omental metastasis and increase the PacBio sequencing depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, of which over 52,000 were not previously reported. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation of protein-coding gene expression on average. We also detect cell type-specific isoform and poly-adenylation site usage in tumor and mesothelial cells, and find that mesothelial cells transition into cancer-associated fibroblasts in the metastasis, partly through the TGF-β/miR-29/Collagen axis. Furthermore, we identify gene fusions, including an experimentally validated IGF2BP2::TESPA1 fusion, which is misclassified as high TESPA1 expression in matched short-read data, and call mutations confirmed by targeted NGS cancer gene panel results. With these findings, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.
Collapse
Affiliation(s)
- Arthur Dondi
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Ulrike Lischetti
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland.
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland.
| | - Francis Jacob
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Franziska Singer
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
- ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland
| | - Nico Borgsmüller
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Ricardo Coelho
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Viola Heinzelmann-Schwarz
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland
- University Hospital Basel, Gynecological Cancer Center, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Christian Beisel
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland.
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland.
| |
Collapse
|
46
|
Carrera-Rivera A, Reguera-Bakhache D, Larrinaga F, Lasa G, Garitano I. Structured dataset of human-machine interactions enabling adaptive user interfaces. Sci Data 2023; 10:831. [PMID: 38007459 PMCID: PMC10676433 DOI: 10.1038/s41597-023-02741-8] [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: 04/24/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023] Open
Abstract
This article introduces a dataset of human-machine interactions collected in a controlled and structured manner. The aim of this dataset is to provide insights into user behavior and support the development of adaptive Human-Machine Interfaces (HMIs). The dataset was generated using a custom-built application that leverages formally defined User Interfaces (UIs). The resulting interactions underwent processing and analysis to create a suitable dataset for professionals and data analysts interested in user interface adaptations. The data processing stage involved cleaning the data, ensuring its consistency and completeness. A data profiling analysis was conducted for checking the consistency of elements in the interaction sequences. Furthermore, for the benefit of researchers, the code used for data collection, data profiling, and usage notes on creating adaptive user interfaces are made available. These resources offer valuable support to those interested in exploring and utilizing the dataset for their research and development efforts in the field of human-machine interfaces.
Collapse
Affiliation(s)
- Angela Carrera-Rivera
- Faculty of Engineering, Electronics, and Computing. Mondragon Unibertsitatea, Arrasate-Mondragon, 20500, Spain.
| | - Daniel Reguera-Bakhache
- Faculty of Engineering, Electronics, and Computing. Mondragon Unibertsitatea, Arrasate-Mondragon, 20500, Spain
| | - Felix Larrinaga
- Faculty of Engineering, Electronics, and Computing. Mondragon Unibertsitatea, Arrasate-Mondragon, 20500, Spain
| | - Ganix Lasa
- Design Innovation Center (DBZ), Mondragon Unibertsitatea, Arrasate-Mondragon, 20500, Spain
| | - Iñaki Garitano
- Faculty of Engineering, Electronics, and Computing. Mondragon Unibertsitatea, Arrasate-Mondragon, 20500, Spain
| |
Collapse
|
47
|
Barroso-Gomila O, Merino-Cacho L, Muratore V, Perez C, Taibi V, Maspero E, Azkargorta M, Iloro I, Trulsson F, Vertegaal ACO, Mayor U, Elortza F, Polo S, Barrio R, Sutherland JD. BioE3 identifies specific substrates of ubiquitin E3 ligases. Nat Commun 2023; 14:7656. [PMID: 37996419 PMCID: PMC10667490 DOI: 10.1038/s41467-023-43326-8] [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: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Hundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.
Collapse
Affiliation(s)
- Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Coralia Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Vincenzo Taibi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Fredrik Trulsson
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Ugo Mayor
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940, Leioa, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di oncologia ed emato-oncologia, Università degli Studi di Milano, Milan, Italy
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| |
Collapse
|
48
|
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.
Collapse
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.
| |
Collapse
|
49
|
Dieudonné T, Kümmerer F, Laursen MJ, Stock C, Flygaard RK, Khalid S, Lenoir G, Lyons JA, Lindorff-Larsen K, Nissen P. Activation and substrate specificity of the human P4-ATPase ATP8B1. Nat Commun 2023; 14:7492. [PMID: 37980352 PMCID: PMC10657443 DOI: 10.1038/s41467-023-42828-9] [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: 04/12/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023] Open
Abstract
Asymmetric distribution of phospholipids in eukaryotic membranes is essential for cell integrity, signaling pathways, and vesicular trafficking. P4-ATPases, also known as flippases, participate in creating and maintaining this asymmetry through active transport of phospholipids from the exoplasmic to the cytosolic leaflet. Here, we present a total of nine cryo-electron microscopy structures of the human flippase ATP8B1-CDC50A complex at 2.4 to 3.1 Å overall resolution, along with functional and computational studies, addressing the autophosphorylation steps from ATP, substrate recognition and occlusion, as well as a phosphoinositide binding site. We find that the P4-ATPase transport site is occupied by water upon phosphorylation from ATP. Additionally, we identify two different autoinhibited states, a closed and an outward-open conformation. Furthermore, we identify and characterize the PI(3,4,5)P3 binding site of ATP8B1 in an electropositive pocket between transmembrane segments 5, 7, 8, and 10. Our study also highlights the structural basis of a broad lipid specificity of ATP8B1 and adds phosphatidylinositol as a transport substrate for ATP8B1. We report a critical role of the sn-2 ester bond of glycerophospholipids in substrate recognition by ATP8B1 through conserved S403. These findings provide fundamental insights into ATP8B1 catalytic cycle and regulation, and substrate recognition in P4-ATPases.
Collapse
Affiliation(s)
- Thibaud Dieudonné
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Felix Kümmerer
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michelle Juknaviciute Laursen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Charlott Stock
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rasmus Kock Flygaard
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Guillaume Lenoir
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Joseph A Lyons
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO) Aarhus University, Aarhus, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
50
|
Sadiq FA, De Reu K, Steenackers H, Van de Walle A, Burmølle M, Heyndrickx M. Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates. ISME Commun 2023; 3:118. [PMID: 37968339 PMCID: PMC10651889 DOI: 10.1038/s43705-023-00328-3] [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] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.
Collapse
Affiliation(s)
- Faizan Ahmed Sadiq
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium.
| | - Koen De Reu
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Hans Steenackers
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Ann Van de Walle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium.
- Ghent University, Department of Pathobiology, Pharmacology and Zoological Medicine, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| |
Collapse
|