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Bowman AR, Rodríguez Echarri A, Kiani F, Iyikanat F, Tsoulos TV, Cox JD, Sundararaman R, García de Abajo FJ, Tagliabue G. Quantum-mechanical effects in photoluminescence from thin crystalline gold films. Light Sci Appl 2024; 13:91. [PMID: 38637531 PMCID: PMC11026419 DOI: 10.1038/s41377-024-01408-2] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 04/20/2024]
Abstract
Luminescence constitutes a unique source of insight into hot carrier processes in metals, including those in plasmonic nanostructures used for sensing and energy applications. However, being weak in nature, metal luminescence remains poorly understood, its microscopic origin strongly debated, and its potential for unraveling nanoscale carrier dynamics largely unexploited. Here, we reveal quantum-mechanical effects in the luminescence emanating from thin monocrystalline gold flakes. Specifically, we present experimental evidence, supported by first-principles simulations, to demonstrate its photoluminescence origin (i.e., radiative emission from electron/hole recombination) when exciting in the interband regime. Our model allows us to identify changes to the measured gold luminescence due to quantum-mechanical effects as the gold film thickness is reduced. Excitingly, such effects are observable in the luminescence signal from flakes up to 40 nm in thickness, associated with the out-of-plane discreteness of the electronic band structure near the Fermi level. We qualitatively reproduce the observations with first-principles modeling, thus establishing a unified description of luminescence in gold monocrystalline flakes and enabling its widespread application as a probe of carrier dynamics and light-matter interactions in this material. Our study paves the way for future explorations of hot carriers and charge-transfer dynamics in a multitude of material systems.
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Affiliation(s)
- Alan R Bowman
- Laboratory of Nanoscience for Energy Technologies (LNET), STI, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alvaro Rodríguez Echarri
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
- MBI-Max-Born-Institut, Berlin, Germany
| | - Fatemeh Kiani
- Laboratory of Nanoscience for Energy Technologies (LNET), STI, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fadil Iyikanat
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Ted V Tsoulos
- Laboratory of Nanoscience for Energy Technologies (LNET), STI, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Joel D Cox
- POLIMA-Center for Polariton-driven Light-Matter Interactions, University of Southern Denmark, Odense M, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M, Denmark
| | - Ravishankar Sundararaman
- Department of Materials Science & Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - F Javier García de Abajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Giulia Tagliabue
- Laboratory of Nanoscience for Energy Technologies (LNET), STI, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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2
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Merckx VSFT, Gomes SIF, Wang D, Verbeek C, Jacquemyn H, Zahn FE, Gebauer G, Bidartondo MI. Mycoheterotrophy in the wood-wide web. Nat Plants 2024:10.1038/s41477-024-01677-0. [PMID: 38641664 DOI: 10.1038/s41477-024-01677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
The prevalence and potential functions of common mycorrhizal networks, or the 'wood-wide web', resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants.
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Affiliation(s)
- Vincent S F T Merckx
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, the Netherlands.
- Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.
| | - Sofia I F Gomes
- Above-belowground Interactions, Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Deyi Wang
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Cas Verbeek
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, the Netherlands
- Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans Jacquemyn
- Plant Population Biology and Conservation, Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
| | - Franziska E Zahn
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Gerhard Gebauer
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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3
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Reicher A, Reiniš J, Ciobanu M, Růžička P, Malik M, Siklos M, Kartysh V, Tomek T, Koren A, Rendeiro AF, Kubicek S. Pooled multicolour tagging for visualizing subcellular protein dynamics. Nat Cell Biol 2024:10.1038/s41556-024-01407-w. [PMID: 38641660 DOI: 10.1038/s41556-024-01407-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.
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Affiliation(s)
- Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Maria Ciobanu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pavel Růžička
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Kartysh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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4
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Conti S, Venturini V, Cañellas-Socias A, Cortina C, Abenza JF, Stephan-Otto Attolini C, Middendorp Guerra E, Xu CK, Li JH, Rossetti L, Stassi G, Roca-Cusachs P, Diz-Muñoz A, Ruprecht V, Guck J, Batlle E, Labernadie A, Trepat X. Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells. Nat Commun 2024; 15:3363. [PMID: 38637494 PMCID: PMC11026456 DOI: 10.1038/s41467-024-47227-2] [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: 03/01/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
Colorectal cancer (CRC) tumors are composed of heterogeneous and plastic cell populations, including a pool of cancer stem cells that express LGR5. Whether these distinct cell populations display different mechanical properties, and how these properties might contribute to metastasis is poorly understood. Using CRC patient derived organoids (PDOs), we find that compared to LGR5- cells, LGR5+ cancer stem cells are stiffer, adhere better to the extracellular matrix (ECM), move slower both as single cells and clusters, display higher nuclear YAP, show a higher survival rate in response to mechanical confinement, and form larger transendothelial gaps. These differences are largely explained by the downregulation of the membrane to cortex attachment proteins Ezrin/Radixin/Moesin (ERMs) in the LGR5+ cells. By analyzing single cell RNA-sequencing (scRNA-seq) expression patterns from a patient cohort, we show that this downregulation is a robust signature of colorectal tumors. Our results show that LGR5- cells display a mechanically dynamic phenotype suitable for dissemination from the primary tumor whereas LGR5+ cells display a mechanically stable and resilient phenotype suitable for extravasation and metastatic growth.
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Affiliation(s)
- Sefora Conti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Valeria Venturini
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Barcelona, Spain
| | - Juan F Abenza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Emily Middendorp Guerra
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Barcelona, Spain
| | - Catherine K Xu
- Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Jia Hui Li
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Leone Rossetti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Giorgio Stassi
- Department of Surgical Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Facultat de Medicina, University of Barcelona (UB), Barcelona, Spain
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Verena Ruprecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Department of Physics, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Max-Planck Zentrum für Physik und Medizin, Erlangen, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Anna Labernadie
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Principe Felipe (CIPF), Valencia, Spain.
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.
- Facultat de Medicina, University of Barcelona (UB), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain.
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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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Holton E, Grohn J, Ward H, Manohar SG, O'Reilly JX, Kolling N. Goal commitment is supported by vmPFC through selective attention. Nat Hum Behav 2024:10.1038/s41562-024-01844-5. [PMID: 38632389 DOI: 10.1038/s41562-024-01844-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/01/2024] [Indexed: 04/19/2024]
Abstract
When striking a balance between commitment to a goal and flexibility in the face of better options, people often demonstrate strong goal perseveration. Here, using functional MRI (n = 30) and lesion patient (n = 26) studies, we argue that the ventromedial prefrontal cortex (vmPFC) drives goal commitment linked to changes in goal-directed selective attention. Participants performed an incremental goal pursuit task involving sequential decisions between persisting with a goal versus abandoning progress for better alternative options. Individuals with stronger goal perseveration showed higher goal-directed attention in an interleaved attention task. Increasing goal-directed attention also affected abandonment decisions: while pursuing a goal, people lost their sensitivity to valuable alternative goals while remaining more sensitive to changes in the current goal. In a healthy population, individual differences in both commitment biases and goal-oriented attention were predicted by baseline goal-related activity in the vmPFC. Among lesion patients, vmPFC damage reduced goal commitment, leading to a performance benefit.
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Affiliation(s)
- Eleanor Holton
- Department of Experimental Psychology, University of Oxford, Oxford, UK.
| | - Jan Grohn
- Department of Experimental Psychology, University of Oxford, Oxford, UK
- Wellcome Centre for Integrative Neuroimaging (WIN), University of Oxford, Oxford, UK
| | - Harry Ward
- Centre for Experimental Medicine and Rheumatology, Queen Mary University London (QMUL), London, UK
| | - Sanjay G Manohar
- Department of Experimental Psychology, University of Oxford, Oxford, UK
- Wellcome Centre for Integrative Neuroimaging (WIN), University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jill X O'Reilly
- Department of Experimental Psychology, University of Oxford, Oxford, UK
- Wellcome Centre for Integrative Neuroimaging (WIN), University of Oxford, Oxford, UK
| | - Nils Kolling
- Wellcome Centre for Integrative Neuroimaging (WIN), University of Oxford, Oxford, UK
- Stem Cell and Brain Research Institute U1208, Inserm, Université Claude Bernard Lyon 1, Bron, France
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7
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Costa F, Schaft EV, Huiskamp G, Aarnoutse EJ, Van't Klooster MA, Krayenbühl N, Ramantani G, Zijlmans M, Indiveri G, Sarnthein J. Robust compression and detection of epileptiform patterns in ECoG using a real-time spiking neural network hardware framework. Nat Commun 2024; 15:3255. [PMID: 38627406 PMCID: PMC11021517 DOI: 10.1038/s41467-024-47495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Interictal Epileptiform Discharges (IED) and High Frequency Oscillations (HFO) in intraoperative electrocorticography (ECoG) may guide the surgeon by delineating the epileptogenic zone. We designed a modular spiking neural network (SNN) in a mixed-signal neuromorphic device to process the ECoG in real-time. We exploit the variability of the inhomogeneous silicon neurons to achieve efficient sparse and decorrelated temporal signal encoding. We interface the full-custom SNN device to the BCI2000 real-time framework and configure the setup to detect HFO and IED co-occurring with HFO (IED-HFO). We validate the setup on pre-recorded data and obtain HFO rates that are concordant with a previously validated offline algorithm (Spearman's ρ = 0.75, p = 1e-4), achieving the same postsurgical seizure freedom predictions for all patients. In a remote on-line analysis, intraoperative ECoG recorded in Utrecht was compressed and transferred to Zurich for SNN processing and successful IED-HFO detection in real-time. These results further demonstrate how automated remote real-time detection may enable the use of HFO in clinical practice.
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Affiliation(s)
- Filippo Costa
- Klinik für Neurochirurgie, Universitätsspital Zürich und Universität Zürich, Zürich, Switzerland.
- Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland.
| | - Eline V Schaft
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geertjan Huiskamp
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erik J Aarnoutse
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maryse A Van't Klooster
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Niklaus Krayenbühl
- Division of Pediatric Neurosurgery, University Children's Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Georgia Ramantani
- Division of Pediatric Neurosurgery, University Children's Hospital Zurich and University of Zurich, Zurich, Switzerland
- Zentrum für Neurowissenschaften (ZNZ) Neuroscience Center Zurich, Universität Zürich und ETH Zürich, Zurich, Switzerland
| | - Maeike Zijlmans
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
| | - Giacomo Indiveri
- Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland
- Zentrum für Neurowissenschaften (ZNZ) Neuroscience Center Zurich, Universität Zürich und ETH Zürich, Zurich, Switzerland
| | - Johannes Sarnthein
- Klinik für Neurochirurgie, Universitätsspital Zürich und Universität Zürich, Zürich, Switzerland.
- Zentrum für Neurowissenschaften (ZNZ) Neuroscience Center Zurich, Universität Zürich und ETH Zürich, Zurich, Switzerland.
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8
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Ginno PA, Borgers H, Ernst C, Schneider A, Behm M, Aitken SJ, Taylor MS, Odom DT. Single-mitosis dissection of acute and chronic DNA mutagenesis and repair. Nat Genet 2024:10.1038/s41588-024-01712-y. [PMID: 38627597 DOI: 10.1038/s41588-024-01712-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/08/2024] [Indexed: 04/24/2024]
Abstract
How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, during single mitoses and at single-strand resolution. To distinguish between chronic (reactive oxygen species (ROS)) and acute (ultraviolet light (UV)) mutagenesis, we microfluidically separate pairs of sister cells from the first mitosis following burst UV damage. Strikingly, UV mutations manifest as sister-specific events, revealing mirror-image mutation phasing genome-wide. In contrast, ROS mutagenesis in transcribed regions is reduced strand agnostically. Successive rounds of genome replication over persisting UV damage drives multiallelic variation at CC dinucleotides. Finally, we show that mutation phasing can be resolved to single strands across the entire genome of liver tumors from F1 mice. This strategy can be broadly used to distinguish the contributions of overlapping cancer relevant mutational processes.
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Affiliation(s)
- Paul Adrian Ginno
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Helena Borgers
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Christina Ernst
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anja Schneider
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Mikaela Behm
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Sarah J Aitken
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Duncan T Odom
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany.
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK.
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9
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Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nat Ecol Evol 2024:10.1038/s41559-024-02398-5. [PMID: 38622362 DOI: 10.1038/s41559-024-02398-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024]
Abstract
Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.
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Affiliation(s)
- Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Marquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josefa Cruz
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Xavier Franch-Marro
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | - Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Marcela Nouzova
- Institute of Parasitology, CAS, České Budějovice, Czech Republic
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia; Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Fernando G Noriega
- Biology and BSI, Florida International University, Miami, FL, USA
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | | | - Caroline B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Karl R Wotton
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Isabel Almudi
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - David Martin
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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10
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Cheng F, Pavliuk O, Hardt S, Hunt LA, Cai B, Kubart T, Hammarström L, Plumeré N, Berggren G, Tian H. Embedding biocatalysts in a redox polymer enhances the performance of dye-sensitized photocathodes in bias-free photoelectrochemical water splitting. Nat Commun 2024; 15:3202. [PMID: 38615087 PMCID: PMC11016092 DOI: 10.1038/s41467-024-47517-9] [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: 12/12/2023] [Accepted: 04/03/2024] [Indexed: 04/15/2024] Open
Abstract
Dye-sensitized photoelectrodes consisting of photosensitizers and molecular catalysts with tunable structures and adjustable energy levels are attractive for low-cost and eco-friendly solar-assisted synthesis of energy rich products. Despite these advantages, dye-sensitized NiO photocathodes suffer from severe electron-hole recombination and facile molecule detachment, limiting photocurrent and stability in photoelectrochemical water-splitting devices. In this work, we develop an efficient and robust biohybrid dye-sensitized NiO photocathode, in which the intermolecular charge transfer is enhanced by a redox polymer. Owing to efficient assisted electron transfer from the dye to the catalyst, the biohybrid NiO photocathode showed a satisfactory photocurrent of 141±17 μA·cm-2 at neutral pH at 0 V versus reversible hydrogen electrode and a stable continuous output within 5 h. This photocathode is capable of driving overall water splitting in combination with a bismuth vanadate photoanode, showing distinguished solar-to-hydrogen efficiency among all reported water-splitting devices based on dye-sensitized photocathodes. These findings demonstrate the opportunity of building green biohybrid systems for artificial synthesis of solar fuels.
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Affiliation(s)
- Fangwen Cheng
- Department of Chemistry─Ångström laboratory, Physical Chemistry, Uppsala University, Box 521, 75120, Uppsala, Sweden
| | - Olha Pavliuk
- Department of Chemistry─Ångström laboratory, Molecular Biomimetics, Uppsala University, Box 523, 75120, Uppsala, Sweden
| | - Steffen Hardt
- Institute of Energy and Climate Research, Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Leigh Anna Hunt
- Department of Chemistry─Ångström laboratory, Physical Chemistry, Uppsala University, Box 521, 75120, Uppsala, Sweden
| | - Bin Cai
- Department of Chemistry─Ångström laboratory, Physical Chemistry, Uppsala University, Box 521, 75120, Uppsala, Sweden
| | - Tomas Kubart
- Department of Electrical Engineering, Solid-State Electronics, Uppsala University, Box 65, 75103, Uppsala, Sweden
| | - Leif Hammarström
- Department of Chemistry─Ångström laboratory, Physical Chemistry, Uppsala University, Box 521, 75120, Uppsala, Sweden
| | - Nicolas Plumeré
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstrasse 53, 94315, Straubing, Germany.
| | - Gustav Berggren
- Department of Chemistry─Ångström laboratory, Molecular Biomimetics, Uppsala University, Box 523, 75120, Uppsala, Sweden.
| | - Haining Tian
- Department of Chemistry─Ångström laboratory, Physical Chemistry, Uppsala University, Box 521, 75120, Uppsala, Sweden.
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11
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Barnstedt O, Mocellin P, Remy S. A hippocampus-accumbens code guides goal-directed appetitive behavior. Nat Commun 2024; 15:3196. [PMID: 38609363 PMCID: PMC11015045 DOI: 10.1038/s41467-024-47361-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The dorsal hippocampus (dHPC) is a key brain region for the expression of spatial memories, such as navigating towards a learned reward location. The nucleus accumbens (NAc) is a prominent projection target of dHPC and implicated in value-based action selection. Yet, the contents of the dHPC→NAc information stream and their acute role in behavior remain largely unknown. Here, we found that optogenetic stimulation of the dHPC→NAc pathway while mice navigated towards a learned reward location was both necessary and sufficient for spatial memory-related appetitive behaviors. To understand the task-relevant coding properties of individual NAc-projecting hippocampal neurons (dHPC→NAc), we used in vivo dual-color two-photon imaging. In contrast to other dHPC neurons, the dHPC→NAc subpopulation contained more place cells, with enriched spatial tuning properties. This subpopulation also showed enhanced coding of non-spatial task-relevant behaviors such as deceleration and appetitive licking. A generalized linear model revealed enhanced conjunctive coding in dHPC→NAc neurons which improved the identification of the reward zone. We propose that dHPC routes specific reward-related spatial and behavioral state information to guide NAc action selection.
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Affiliation(s)
- Oliver Barnstedt
- Department of Cellular Neuroscience, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 39120, Magdeburg, Germany.
- Institute for Biology, Otto-von-Guericke University, 39120, Magdeburg, Germany.
| | - Petra Mocellin
- Department of Cellular Neuroscience, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
- International Max Planck Research, School for Brain & Behavior (IMPRS), 53175, Bonn, Germany
- Department of Molecular and Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720-3370, USA
| | - Stefan Remy
- Department of Cellular Neuroscience, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 39120, Magdeburg, Germany.
- Center for Behavioral Brain Sciences (CBBS), 39106, Magdeburg, Germany.
- German Center for Mental Health (DZGP), partner site Halle-Jena-Magdeburg, 39118, Magdeburg, Germany.
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12
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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? Nat Plants 2024:10.1038/s41477-024-01674-3. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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13
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Zorea A, Pellow D, Levin L, Pilosof S, Friedman J, Shamir R, Mizrahi I. Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. Nat Commun 2024; 15:3147. [PMID: 38605009 PMCID: PMC11009399 DOI: 10.1038/s41467-024-47272-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.
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Affiliation(s)
- Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - David Pellow
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Jonathan Friedman
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
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14
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Gagl B, Gregorová K. Investigating lexical categorization in reading based on joint diagnostic and training approaches for language learners. NPJ Sci Learn 2024; 9:29. [PMID: 38600183 PMCID: PMC11006909 DOI: 10.1038/s41539-024-00237-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Efficient reading is essential for societal participation, so reading proficiency is a central educational goal. Here, we use an individualized diagnostics and training framework to investigate processes in visual word recognition and evaluate its usefulness for detecting training responders. We (i) motivated a training procedure based on the Lexical Categorization Model (LCM) to introduce the framework. The LCM describes pre-lexical orthographic processing implemented in the left-ventral occipital cortex and is vital to reading. German language learners trained their lexical categorization abilities while we monitored reading speed change. In three studies, most language learners increased their reading skills. Next, we (ii) estimated, for each word, the LCM-based features and assessed each reader's lexical categorization capabilities. Finally, we (iii) explored machine learning procedures to find the optimal feature selection and regression model to predict the benefit of the lexical categorization training for each individual. The best-performing pipeline increased reading speed from 23% in the unselected group to 43% in the machine-selected group. This selection process strongly depended on parameters associated with the LCM. Thus, training in lexical categorization can increase reading skills, and accurate computational descriptions of brain functions that allow the motivation of a training procedure combined with machine learning can be powerful for individualized reading training procedures.
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Affiliation(s)
- Benjamin Gagl
- Self-learning Systems Laboratory, Department of Special Education and Rehabilitation, University of Cologne, Cologne, Germany.
- Department of Psychology and Sports Sciences, Goethe University, Frankfurt am Main, Germany.
| | - Klara Gregorová
- Department of Psychology and Sports Sciences, Goethe University, Frankfurt am Main, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital & German Center of Prevention Research on Mental Health, Würzburg, Germany
- Department of Psychology, Julius-Maximilians-University of Würzburg, Würzburg, Germany
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15
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Fishman L, Modak A, Nechooshtan G, Razin T, Erhard F, Regev A, Farrell JA, Rabani M. Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nat Commun 2024; 15:3104. [PMID: 38600066 PMCID: PMC11006943 DOI: 10.1038/s41467-024-47290-9] [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: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Avani Modak
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Talya Razin
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA, 02139, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, 02142, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA.
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.
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16
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Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D'Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J. Transcription-coupled repair of DNA-protein cross-links depends on CSA and CSB. Nat Cell Biol 2024:10.1038/s41556-024-01391-1. [PMID: 38600235 DOI: 10.1038/s41556-024-01391-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA-protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Aleida C Acampora
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Aldo S Bader
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elnatan Bitensky
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fatih Aygenli
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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17
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Girardi D, Finizio S, Donnelly C, Rubini G, Mayr S, Levati V, Cuccurullo S, Maspero F, Raabe J, Petti D, Albisetti E. Three-dimensional spin-wave dynamics, localization and interference in a synthetic antiferromagnet. Nat Commun 2024; 15:3057. [PMID: 38594233 PMCID: PMC11004151 DOI: 10.1038/s41467-024-47339-9] [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: 06/16/2023] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Spin waves are collective perturbations in the orientation of the magnetic moments in magnetically ordered materials. Their rich phenomenology is intrinsically three-dimensional; however, the three-dimensional imaging of spin waves has so far not been possible. Here, we image the three-dimensional dynamics of spin waves excited in a synthetic antiferromagnet, with nanoscale spatial resolution and sub-ns temporal resolution, using time-resolved magnetic laminography. In this way, we map the distribution of the spin-wave modes throughout the volume of the structure, revealing unexpected depth-dependent profiles originating from the interlayer dipolar interaction. We experimentally demonstrate the existence of complex three-dimensional interference patterns and analyze them via micromagnetic modelling. We find that these patterns are generated by the superposition of spin waves with non-uniform amplitude profiles, and that their features can be controlled by tuning the composition and structure of the magnetic system. Our results open unforeseen possibilities for the study and manipulation of complex spin-wave modes within nanostructures and magnonic devices.
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Affiliation(s)
- Davide Girardi
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Simone Finizio
- Swiss Light Source, Paul Scherrer Institut; Forschungsstrasse 111 5232 PSI, Villigen, Switzerland
| | - Claire Donnelly
- Max Planck Institute for Chemical Physics of Solids; Nöthnitzer Str. 40, 01187, Dresden, Germany
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, Hiroshima, 739-8526, Japan
| | - Guglielmo Rubini
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Sina Mayr
- Swiss Light Source, Paul Scherrer Institut; Forschungsstrasse 111 5232 PSI, Villigen, Switzerland
- Laboratory for Mesoscopic Systems, Department of Materials, ETH Zurich, 8093, Zurich, Switzerland
| | - Valerio Levati
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Simone Cuccurullo
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Federico Maspero
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Jörg Raabe
- Swiss Light Source, Paul Scherrer Institut; Forschungsstrasse 111 5232 PSI, Villigen, Switzerland
| | - Daniela Petti
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy.
| | - Edoardo Albisetti
- Dipartimento di Fisica, Politecnico di Milano; Piazza Leonardo da Vinci 32, Milano, 20133, Italy.
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18
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Packheiser J, Hartmann H, Fredriksen K, Gazzola V, Keysers C, Michon F. A systematic review and multivariate meta-analysis of the physical and mental health benefits of touch interventions. Nat Hum Behav 2024:10.1038/s41562-024-01841-8. [PMID: 38589702 DOI: 10.1038/s41562-024-01841-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/29/2024] [Indexed: 04/10/2024]
Abstract
Receiving touch is of critical importance, as many studies have shown that touch promotes mental and physical well-being. We conducted a pre-registered (PROSPERO: CRD42022304281) systematic review and multilevel meta-analysis encompassing 137 studies in the meta-analysis and 75 additional studies in the systematic review (n = 12,966 individuals, search via Google Scholar, PubMed and Web of Science until 1 October 2022) to identify critical factors moderating touch intervention efficacy. Included studies always featured a touch versus no touch control intervention with diverse health outcomes as dependent variables. Risk of bias was assessed via small study, randomization, sequencing, performance and attrition bias. Touch interventions were especially effective in regulating cortisol levels (Hedges' g = 0.78, 95% confidence interval (CI) 0.24 to 1.31) and increasing weight (0.65, 95% CI 0.37 to 0.94) in newborns as well as in reducing pain (0.69, 95% CI 0.48 to 0.89), feelings of depression (0.59, 95% CI 0.40 to 0.78) and state (0.64, 95% CI 0.44 to 0.84) or trait anxiety (0.59, 95% CI 0.40 to 0.77) for adults. Comparing touch interventions involving objects or robots resulted in similar physical (0.56, 95% CI 0.24 to 0.88 versus 0.51, 95% CI 0.38 to 0.64) but lower mental health benefits (0.34, 95% CI 0.19 to 0.49 versus 0.58, 95% CI 0.43 to 0.73). Adult clinical cohorts profited more strongly in mental health domains compared with healthy individuals (0.63, 95% CI 0.46 to 0.80 versus 0.37, 95% CI 0.20 to 0.55). We found no difference in health benefits in adults when comparing touch applied by a familiar person or a health care professional (0.51, 95% CI 0.29 to 0.73 versus 0.50, 95% CI 0.38 to 0.61), but parental touch was more beneficial in newborns (0.69, 95% CI 0.50 to 0.88 versus 0.39, 95% CI 0.18 to 0.61). Small but significant small study bias and the impossibility to blind experimental conditions need to be considered. Leveraging factors that influence touch intervention efficacy will help maximize the benefits of future interventions and focus research in this field.
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Affiliation(s)
- Julian Packheiser
- Social Neuroscience, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany.
- Social Brain Lab, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences, Amsterdam, the Netherlands.
| | - Helena Hartmann
- Social Brain Lab, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences, Amsterdam, the Netherlands
- Center for Translational and Behavioral Neuroscience, University Hospital Essen, Essen, Germany
- Clinical Neurosciences, Department for Neurology, University Hospital Essen, Essen, Germany
| | - Kelly Fredriksen
- Social Brain Lab, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences, Amsterdam, the Netherlands
| | - Valeria Gazzola
- Social Brain Lab, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences, Amsterdam, the Netherlands
| | - Christian Keysers
- Social Brain Lab, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences, Amsterdam, the Netherlands
| | - Frédéric Michon
- Social Brain Lab, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences, Amsterdam, the Netherlands
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19
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Liu Z, Liu H, Vera AM, Yang B, Tinnefeld P, Nash MA. Engineering an artificial catch bond using mechanical anisotropy. Nat Commun 2024; 15:3019. [PMID: 38589360 PMCID: PMC11001878 DOI: 10.1038/s41467-024-46858-9] [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: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, the Netherlands
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland.
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
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20
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Aldag N, Nogueira W. Psychoacoustic and electroencephalographic responses to changes in amplitude modulation depth and frequency in relation to speech recognition in cochlear implantees. Sci Rep 2024; 14:8181. [PMID: 38589483 PMCID: PMC11002021 DOI: 10.1038/s41598-024-58225-1] [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: 04/28/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Temporal envelope modulations (TEMs) are one of the most important features that cochlear implant (CI) users rely on to understand speech. Electroencephalographic assessment of TEM encoding could help clinicians to predict speech recognition more objectively, even in patients unable to provide active feedback. The acoustic change complex (ACC) and the auditory steady-state response (ASSR) evoked by low-frequency amplitude-modulated pulse trains can be used to assess TEM encoding with electrical stimulation of individual CI electrodes. In this study, we focused on amplitude modulation detection (AMD) and amplitude modulation frequency discrimination (AMFD) with stimulation of a basal versus an apical electrode. In twelve adult CI users, we (a) assessed behavioral AMFD thresholds and (b) recorded cortical auditory evoked potentials (CAEPs), AMD-ACC, AMFD-ACC, and ASSR in a combined 3-stimulus paradigm. We found that the electrophysiological responses were significantly higher for apical than for basal stimulation. Peak amplitudes of AMFD-ACC were small and (therefore) did not correlate with speech-in-noise recognition. We found significant correlations between speech-in-noise recognition and (a) behavioral AMFD thresholds and (b) AMD-ACC peak amplitudes. AMD and AMFD hold potential to develop a clinically applicable tool for assessing TEM encoding to predict speech recognition in CI users.
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Affiliation(s)
- Nina Aldag
- Department of Otolaryngology, Hannover Medical School and Cluster of Excellence 'Hearing4all', Hanover, Germany
| | - Waldo Nogueira
- Department of Otolaryngology, Hannover Medical School and Cluster of Excellence 'Hearing4all', Hanover, Germany.
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21
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Krüger L, Gaskell-Mew L, Graham S, Shirran S, Hertel R, White MF. Reversible conjugation of a CBASS nucleotide cyclase regulates bacterial immune response to phage infection. Nat Microbiol 2024:10.1038/s41564-024-01670-5. [PMID: 38589469 DOI: 10.1038/s41564-024-01670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/07/2024] [Indexed: 04/10/2024]
Abstract
Prokaryotic antiviral defence systems are frequently toxic for host cells and stringent regulation is required to ensure survival and fitness. These systems must be readily available in case of infection but tightly controlled to prevent activation of an unnecessary cellular response. Here we investigate how the bacterial cyclic oligonucleotide-based antiphage signalling system (CBASS) uses its intrinsic protein modification system to regulate the nucleotide cyclase. By integrating a type II CBASS system from Bacillus cereus into the model organism Bacillus subtilis, we show that the protein-conjugating Cap2 (CBASS associated protein 2) enzyme links the cyclase exclusively to the conserved phage shock protein A (PspA) in the absence of phage. The cyclase-PspA conjugation is reversed by the deconjugating isopeptidase Cap3 (CBASS associated protein 3). We propose a model in which the cyclase is held in an inactive state by conjugation to PspA in the absence of phage, with conjugation released upon infection, priming the cyclase for activation.
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Affiliation(s)
- Larissa Krüger
- School of Biology, University of St Andrews, St Andrews, UK.
| | | | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews, UK
| | - Sally Shirran
- School of Biology, University of St Andrews, St Andrews, UK
| | - Robert Hertel
- Genomic and Applied Microbiology, Göttingen Centre for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews, UK.
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22
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May JN, Moss JI, Mueller F, Golombek SK, Biancacci I, Rizzo L, Elshafei AS, Gremse F, Pola R, Pechar M, Etrych T, Becker S, Trautwein C, Bülow RD, Boor P, Knuechel R, von Stillfried S, Storm G, Puri S, Barry ST, Schulz V, Kiessling F, Ashford MB, Lammers T. Histopathological biomarkers for predicting the tumour accumulation of nanomedicines. Nat Biomed Eng 2024:10.1038/s41551-024-01197-4. [PMID: 38589466 DOI: 10.1038/s41551-024-01197-4] [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: 10/10/2022] [Accepted: 02/08/2024] [Indexed: 04/10/2024]
Abstract
The clinical prospects of cancer nanomedicines depend on effective patient stratification. Here we report the identification of predictive biomarkers of the accumulation of nanomedicines in tumour tissue. By using supervised machine learning on data of the accumulation of nanomedicines in tumour models in mice, we identified the densities of blood vessels and of tumour-associated macrophages as key predictive features. On the basis of these two features, we derived a biomarker score correlating with the concentration of liposomal doxorubicin in tumours and validated it in three syngeneic tumour models in immunocompetent mice and in four cell-line-derived and six patient-derived tumour xenografts in mice. The score effectively discriminated tumours according to the accumulation of nanomedicines (high versus low), with an area under the receiver operating characteristic curve of 0.91. Histopathological assessment of 30 tumour specimens from patients and of 28 corresponding primary tumour biopsies confirmed the score's effectiveness in predicting the tumour accumulation of liposomal doxorubicin. Biomarkers of the tumour accumulation of nanomedicines may aid the stratification of patients in clinical trials of cancer nanomedicines.
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Affiliation(s)
- Jan-Niklas May
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
| | - Jennifer I Moss
- Early TDE Discovery, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Florian Mueller
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
| | - Susanne K Golombek
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
| | - Ilaria Biancacci
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
| | - Larissa Rizzo
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
| | - Asmaa Said Elshafei
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
| | - Felix Gremse
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
- Gremse-IT GmbH, Aachen, Germany
| | - Robert Pola
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pechar
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Etrych
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Svea Becker
- Clinic for Gastroenterology, Metabolic Disorders, and Internal Intensive Medicine, University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Trautwein
- Clinic for Gastroenterology, Metabolic Disorders, and Internal Intensive Medicine, University Hospital RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany
| | - Roman D Bülow
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Peter Boor
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ruth Knuechel
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Saskia von Stillfried
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Gert Storm
- Department of Pharmaceutics, Utrecht University, Utrecht, the Netherlands
- Department of Biomaterials, Science and Technology, University of Twente, Enschede, the Netherlands
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sanyogitta Puri
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Simon T Barry
- Early TDE Discovery, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Volkmar Schulz
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
- Fraunhofer Institute for Digital Medicine MEVIS, Aachen, Germany
- Physics Institute III B, RWTH Aachen University, Aachen, Germany
| | - Fabian Kiessling
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany
- Fraunhofer Institute for Digital Medicine MEVIS, Aachen, Germany
| | - Marianne B Ashford
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Twan Lammers
- Institute for Experimental Molecular Imaging, University Hospital RWTH Aachen, Aachen, Germany.
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Aachen, Germany.
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23
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Tzschaschel C, Qiu JX, Gao XJ, Li HC, Guo C, Yang HY, Zhang CP, Xie YM, Liu YF, Gao A, Bérubé D, Dinh T, Ho SC, Fang Y, Huang F, Nordlander J, Ma Q, Tafti F, Moll PJW, Law KT, Xu SY. Nonlinear optical diode effect in a magnetic Weyl semimetal. Nat Commun 2024; 15:3017. [PMID: 38589414 DOI: 10.1038/s41467-024-47291-8] [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: 07/19/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Diode effects are of great interest for both fundamental physics and modern technologies. Electrical diode effects (nonreciprocal transport) have been observed in Weyl systems. Optical diode effects arising from the Weyl fermions have been theoretically considered but not probed experimentally. Here, we report the observation of a nonlinear optical diode effect (NODE) in the magnetic Weyl semimetal CeAlSi, where the magnetization introduces a pronounced directionality in the nonlinear optical second-harmonic generation (SHG). We demonstrate a six-fold change of the measured SHG intensity between opposite propagation directions over a bandwidth exceeding 250 meV. Supported by density-functional theory, we establish the linearly dispersive bands emerging from Weyl nodes as the origin of this broadband effect. We further demonstrate current-induced magnetization switching and thus electrical control of the NODE. Our results advance ongoing research to identify novel nonlinear optical/transport phenomena in magnetic topological materials and further opens new pathways for the unidirectional manipulation of light.
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Affiliation(s)
- Christian Tzschaschel
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Berlin, Germany.
| | - Jian-Xiang Qiu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Xue-Jian Gao
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hou-Chen Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Chunyu Guo
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
- Laboratory of Quantum Materials (QMAT), Institute of Materials (IMX), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Hung-Yu Yang
- Department of Physics, Boston College, Chestnut Hill, MA, USA
| | - Cheng-Ping Zhang
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ying-Ming Xie
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yu-Fei Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Anyuan Gao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Damien Bérubé
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Thao Dinh
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Sheng-Chin Ho
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yuqiang Fang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Science, Shanghai, China
- State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering Peking University, Beijing, China
| | - Fuqiang Huang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Science, Shanghai, China
- State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering Peking University, Beijing, China
| | | | - Qiong Ma
- Department of Physics, Boston College, Chestnut Hill, MA, USA
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Ontario, Canada
| | - Fazel Tafti
- Department of Physics, Boston College, Chestnut Hill, MA, USA
| | - Philip J W Moll
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
- Laboratory of Quantum Materials (QMAT), Institute of Materials (IMX), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Kam Tuen Law
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Su-Yang Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
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24
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Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P, Wilmes P. Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease. NPJ Parkinsons Dis 2024; 10:78. [PMID: 38582855 PMCID: PMC10998870 DOI: 10.1038/s41531-024-00687-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Gut microbiome differences between people with Parkinson's disease (PD) and control subjects without Parkinsonism are widely reported, but potential alterations related to PD with mild cognitive impairment (MCI) have yet to be comprehensively explored. We compared gut microbial features of PD with MCI (n = 58) to cognitively unimpaired PD (n = 60) and control subjects (n = 90) with normal cognition. Our results did not support a specific microbiome signature related to MCI in PD.
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Affiliation(s)
- Velma T E Aho
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Matthias Klee
- Institute for Research on Socio-Economic Inequality (IRSEI), Department of Social Sciences, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Swammerdam Institute of Life Sciences at University of Amsterdam, Amsterdam, the Netherlands
| | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Parkinson's Research Clinic, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Anja K Leist
- Institute for Research on Socio-Economic Inequality (IRSEI), Department of Social Sciences, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Parkinson's Research Clinic, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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25
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Galanti L, Peritore M, Gnügge R, Cannavo E, Heipke J, Palumbieri MD, Steigenberger B, Symington LS, Cejka P, Pfander B. Dbf4-dependent kinase promotes cell cycle controlled resection of DNA double-strand breaks and repair by homologous recombination. Nat Commun 2024; 15:2890. [PMID: 38570537 PMCID: PMC10991553 DOI: 10.1038/s41467-024-46951-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: 07/19/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, DSB repair pathway choice occurs at the level of DNA end resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate end resection and repair by homologous recombination (HR). However, inability of CDK phospho-mimetic mutants to bypass this cell cycle regulation, suggests that additional cell cycle regulators may be important. Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that end resection and HR require activation by DDK. Mechanistically, DDK phosphorylates at least two resection nucleases in budding yeast: the Mre11 activator Sae2, which promotes resection initiation, as well as the Dna2 nuclease, which promotes resection elongation. Notably, synthetic activation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair pathway selection.
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Affiliation(s)
- Lorenzo Galanti
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Martina Peritore
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Johannes Heipke
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Maria Dilia Palumbieri
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Boris Pfander
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany.
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany.
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26
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Matrone GM, van Doremaele ERW, Surendran A, Laswick Z, Griggs S, Ye G, McCulloch I, Santoro F, Rivnay J, van de Burgt Y. A modular organic neuromorphic spiking circuit for retina-inspired sensory coding and neurotransmitter-mediated neural pathways. Nat Commun 2024; 15:2868. [PMID: 38570478 PMCID: PMC10991258 DOI: 10.1038/s41467-024-47226-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
Signal communication mechanisms within the human body rely on the transmission and modulation of action potentials. Replicating the interdependent functions of receptors, neurons and synapses with organic artificial neurons and biohybrid synapses is an essential first step towards merging neuromorphic circuits and biological systems, crucial for computing at the biological interface. However, most organic neuromorphic systems are based on simple circuits which exhibit limited adaptability to both external and internal biological cues, and are restricted to emulate only specific the functions of an individual neuron/synapse. Here, we present a modular neuromorphic system which combines organic spiking neurons and biohybrid synapses to replicate a neural pathway. The spiking neuron mimics the sensory coding function of afferent neurons from light stimuli, while the neuromodulatory activity of interneurons is emulated by neurotransmitters-mediated biohybrid synapses. Combining these functions, we create a modular connection between multiple neurons to establish a pre-processing retinal pathway primitive.
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Affiliation(s)
- Giovanni Maria Matrone
- Microsystems, Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612AJ, Eindhoven, The Netherlands.
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Eveline R W van Doremaele
- Microsystems, Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612AJ, Eindhoven, The Netherlands
| | - Abhijith Surendran
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Zachary Laswick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Sophie Griggs
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Gang Ye
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen, 518060, PR China
| | - Iain McCulloch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Thuwal, 23955-6900, Saudi Arabia
| | - Francesca Santoro
- Tissue Electronics, Istituto Italiano di Tecnologia, Naples, 80125, Italy
- Institute of Biological Information Processing IBI-3 Bioelectronics, Forschungszentrum Juelich, 52428, Juelich, Germany
- Neuroelectronic Interfaces, Faculty of Electrical Engineering and IT, RWTH Aachen, 52074, Aachen, Germany
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Yoeri van de Burgt
- Microsystems, Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612AJ, Eindhoven, The Netherlands.
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27
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Coraggio F, Bhushan M, Roumeliotis S, Caroti F, Bevilacqua C, Prevedel R, Rapti G. Age-progressive interplay of HSP-proteostasis, ECM-cell junctions and biomechanics ensures C. elegans astroglial architecture. Nat Commun 2024; 15:2861. [PMID: 38570505 PMCID: PMC10991496 DOI: 10.1038/s41467-024-46827-2] [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: 01/08/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Tissue integrity is sensitive to temperature, tension, age, and is sustained throughout life by adaptive cell-autonomous or extrinsic mechanisms. Safeguarding the remarkably-complex architectures of neurons and glia ensures age-dependent integrity of functional circuits. Here, we report mechanisms sustaining the integrity of C. elegans CEPsh astrocyte-like glia. We combine large-scale genetics with manipulation of genes, cells, and their environment, quantitative imaging of cellular/ subcellular features, tissue material properties and extracellular matrix (ECM). We identify mutants with age-progressive, environment-dependent defects in glial architecture, consequent disruption of neuronal architecture, and abnormal aging. Functional loss of epithelial Hsp70/Hsc70-cochaperone BAG2 causes ECM disruption, altered tissue biomechanics, and hypersensitivity of glia to environmental temperature and mechanics. Glial-cell junctions ensure epithelia-ECM-CEPsh glia association. Modifying glial junctions or ECM mechanics safeguards glial integrity against disrupted BAG2-proteostasis. Overall, we present a finely-regulated interplay of proteostasis-ECM and cell junctions with conserved components that ensures age-progressive robustness of glial architecture.
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Affiliation(s)
- Francesca Coraggio
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mahak Bhushan
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Spyridon Roumeliotis
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Francesca Caroti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carlo Bevilacqua
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert Prevedel
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Georgia Rapti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy.
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany.
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28
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McArthur G, Docherty JH, Hareram MD, Simonetti M, Vitorica-Yrezabal IJ, Douglas JJ, Larrosa I. An air- and moisture-stable ruthenium precatalyst for diverse reactivity. Nat Chem 2024:10.1038/s41557-024-01481-5. [PMID: 38570728 DOI: 10.1038/s41557-024-01481-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
Versatile, efficient and robust (pre)catalysts are pivotal in accelerating the discovery and optimization of chemical reactions, shaping diverse synthetic fields such as cross-coupling, C-H functionalization and polymer chemistry. Yet, their scarcity in certain domains has hindered the advancement and adoption of new applications. Here we present a highly reactive air- and moisture-stable ruthenium precatalyst [(tBuCN)5Ru(H2O)](BF4)2, featuring a key exchangeable water ligand. This versatile precatalyst drives an array of transformations, including late-stage C(sp2)-H arylation, primary/secondary alkylation, methylation, hydrogen/deuterium exchange, C(sp3)-H oxidation, alkene isomerization and oxidative cleavage, consistently outperforming conventionally used ruthenium (pre)catalysts. The generality and applicability of this precatalyst is exemplified through the potential for rapid screening and optimization of photocatalytic reactions with a suite of in situ generated ruthenium photocatalysts containing hitherto unknown complexes, and through the rapid discovery of reactivities previously unreported for ruthenium. The diverse applicability observed is suggestive of a generic platform for reaction simplification and accelerated synthetic discovery that will enable broader applicability and accessibility to state-of-the-art ruthenium catalysis.
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Affiliation(s)
- Gillian McArthur
- Department of Chemistry, University of Manchester, Manchester, UK
| | - Jamie H Docherty
- Department of Chemistry, University of Manchester, Manchester, UK
- Department of Chemistry, Lancaster University, Lancaster, UK
| | | | - Marco Simonetti
- Department of Chemistry, University of Manchester, Manchester, UK
- bp, Low Carbon Innovation Centre, Saltend Chemicals Park, Hull, UK
| | | | - James J Douglas
- Department of Chemistry, University of Manchester, Manchester, UK
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Igor Larrosa
- Department of Chemistry, University of Manchester, Manchester, UK.
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29
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Vensaus P, Liang Y, Ansermet JP, Soler-Illia GJAA, Lingenfelder M. Enhancement of electrocatalysis through magnetic field effects on mass transport. Nat Commun 2024; 15:2867. [PMID: 38570499 PMCID: PMC10991325 DOI: 10.1038/s41467-024-46980-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
Magnetic field effects on electrocatalysis have recently gained attention due to the substantial enhancement of the oxygen evolution reaction (OER) on ferromagnetic catalysts. When detecting an enhanced catalytic activity, the effect of magnetic fields on mass transport must be assessed. In this study, we employ a specifically designed magneto-electrochemical system and non-magnetic electrodes to quantify magnetic field effects. Our findings reveal a marginal enhancement in reactions with high reactant availability, such as the OER, whereas substantial boosts exceeding 50% are observed in diffusion limited reactions, exemplified by the oxygen reduction reaction (ORR). Direct visualization and quantification of the whirling motion of ions under a magnetic field underscore the importance of Lorentz forces acting on the electrolyte ions, and demonstrate that bubbles' movement is a secondary phenomenon. Our results advance the fundamental understanding of magnetic fields in electrocatalysis and unveil new prospects for developing more efficient and sustainable energy conversion technologies.
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Affiliation(s)
- Priscila Vensaus
- Max Planck-EPFL Laboratory for Molecular Nanoscience and Technology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Physics (IPHYS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Instituto de Nanosistemas, Escuela de Bio y Nanotecnologías, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Yunchang Liang
- Max Planck-EPFL Laboratory for Molecular Nanoscience and Technology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Physics (IPHYS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean-Philippe Ansermet
- Institute of Physics (IPHYS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Galo J A A Soler-Illia
- Instituto de Nanosistemas, Escuela de Bio y Nanotecnologías, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Magalí Lingenfelder
- Max Planck-EPFL Laboratory for Molecular Nanoscience and Technology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Institute of Physics (IPHYS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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30
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Klingelhuber F, Frendo-Cumbo S, Omar-Hmeadi M, Massier L, Kakimoto P, Taylor AJ, Couchet M, Ribicic S, Wabitsch M, Messias AC, Iuso A, Müller TD, Rydén M, Mejhert N, Krahmer N. A spatiotemporal proteomic map of human adipogenesis. Nat Metab 2024:10.1038/s42255-024-01025-8. [PMID: 38565923 DOI: 10.1038/s42255-024-01025-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
White adipocytes function as major energy reservoirs in humans by storing substantial amounts of triglycerides, and their dysfunction is associated with metabolic disorders; however, the mechanisms underlying cellular specialization during adipogenesis remain unknown. Here, we generate a spatiotemporal proteomic atlas of human adipogenesis, which elucidates cellular remodelling as well as the spatial reorganization of metabolic pathways to optimize cells for lipid accumulation and highlights the coordinated regulation of protein localization and abundance during adipocyte formation. We identify compartment-specific regulation of protein levels and localization changes of metabolic enzymes to reprogramme branched-chain amino acids and one-carbon metabolism to provide building blocks and reduction equivalents. Additionally, we identify C19orf12 as a differentiation-induced adipocyte lipid droplet protein that interacts with the translocase of the outer membrane complex of lipid droplet-associated mitochondria and regulates adipocyte lipid storage by determining the capacity of mitochondria to metabolize fatty acids. Overall, our study provides a comprehensive resource for understanding human adipogenesis and for future discoveries in the field.
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Affiliation(s)
- Felix Klingelhuber
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Scott Frendo-Cumbo
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Muhmmad Omar-Hmeadi
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Pamela Kakimoto
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Austin J Taylor
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Morgane Couchet
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Sara Ribicic
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martin Wabitsch
- Center for Rare Endocrine Diseases, Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, Ulm University Medical Centre, Ulm, Germany
| | - Ana C Messias
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Centre, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Arcangela Iuso
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Walther-Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University Munich (LMU), Munich, Germany
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
- Endocrinology unit, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Niklas Mejhert
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
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31
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Hong F, Aldhous TP, Kemmitt PD, Bower JF. A directed enolization strategy enables by-product-free construction of contiguous stereocentres en route to complex amino acids. Nat Chem 2024:10.1038/s41557-024-01473-5. [PMID: 38565976 DOI: 10.1038/s41557-024-01473-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/08/2024] [Indexed: 04/04/2024]
Abstract
Homochiral α-amino acids are widely used in pharmaceutical design as key subunits in chiral catalyst synthesis or as building blocks in synthetic biology. Many synthetic methods have been developed to access rare or unnatural variants by controlling the installation of the α-stereocentre. By contrast, and despite their importance, α-amino acids possessing β-stereocentres are much harder to synthesize. Here we demonstrate an iridium-catalysed protocol that allows the direct upconversion of simple alkenes and glycine derivatives to give β-substituted α-amino acids with exceptional levels of regio- and stereocontrol. Our method exploits the native directing ability of a glycine-derived N-H unit to facilitate Ir-catalysed enolization of the adjacent carbonyl. The resulting stereodefined enolate cross-couples with a styrene or α-olefin to install two contiguous stereocentres. The process offers very high levels of regio- and stereocontrol and occurs with complete atom economy. In broader terms, our reaction design offers a unique directing-group-controlled strategy for the direct stereocontrolled α-alkylation of carbonyl compounds, and provides a powerful approach for the synthesis of challenging contiguous stereocentres.
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Affiliation(s)
- Fenglin Hong
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Timothy P Aldhous
- Department of Chemistry, University of Liverpool, Liverpool, UK
- School of Chemistry, University of Bristol, Bristol, UK
| | - Paul D Kemmitt
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - John F Bower
- Department of Chemistry, University of Liverpool, Liverpool, UK.
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32
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Silva NT, Ramírez-Buriticá J, Pritchett DL, Carey MR. Climbing fibers provide essential instructive signals for associative learning. Nat Neurosci 2024:10.1038/s41593-024-01594-7. [PMID: 38565684 DOI: 10.1038/s41593-024-01594-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 02/05/2024] [Indexed: 04/04/2024]
Abstract
Supervised learning depends on instructive signals that shape the output of neural circuits to support learned changes in behavior. Climbing fiber (CF) inputs to the cerebellar cortex represent one of the strongest candidates in the vertebrate brain for conveying neural instructive signals. However, recent studies have shown that Purkinje cell stimulation can also drive cerebellar learning and the relative importance of these two neuron types in providing instructive signals for cerebellum-dependent behaviors remains unresolved. In the present study we used cell-type-specific perturbations of various cerebellar circuit elements to systematically evaluate their contributions to delay eyeblink conditioning in mice. Our findings reveal that, although optogenetic stimulation of either CFs or Purkinje cells can drive learning under some conditions, even subtle reductions in CF signaling completely block learning to natural stimuli. We conclude that CFs and corresponding Purkinje cell complex spike events provide essential instructive signals for associative cerebellar learning.
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Affiliation(s)
- N Tatiana Silva
- Neuroscience Program, Champalimaud Center for the Unknown, Lisbon, Portugal
| | | | - Dominique L Pritchett
- Neuroscience Program, Champalimaud Center for the Unknown, Lisbon, Portugal.
- Biology Department, Howard University, Washington, DC, USA.
| | - Megan R Carey
- Neuroscience Program, Champalimaud Center for the Unknown, Lisbon, Portugal.
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33
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Peters C, Richter KK, Wilkin S, Stark S, Mir-Makhamad B, Fernandes R, Maksudov F, Mirzaakhmedov S, Rahmonov H, Schirmer S, Ashastina K, Begmatov A, Frachetti M, Kurbanov S, Shenkar M, Hermes T, Kidd F, Omelchenko A, Huber B, Boivin N, Wang S, Lurje P, von Baeyer M, Dal Martello R, Spengler RN. Archaeological and molecular evidence for ancient chickens in Central Asia. Nat Commun 2024; 15:2697. [PMID: 38565545 PMCID: PMC10987595 DOI: 10.1038/s41467-024-46093-2] [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: 11/15/2022] [Accepted: 02/14/2024] [Indexed: 04/04/2024] Open
Abstract
The origins and dispersal of the chicken across the ancient world remains one of the most enigmatic questions regarding Eurasian domesticated animals. The lack of agreement concerning timing and centers of origin is due to issues with morphological identifications, a lack of direct dating, and poor preservation of thin, brittle bird bones. Here we show that chickens were widely raised across southern Central Asia from the fourth century BC through medieval periods, likely dispersing along the ancient Silk Road. We present archaeological and molecular evidence for the raising of chickens for egg production, based on material from 12 different archaeological sites spanning a millennium and a half. These eggshells were recovered in high abundance at all of these sites, suggesting that chickens may have been an important part of the overall diet and that chickens may have lost seasonal egg-laying.
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Affiliation(s)
- Carli Peters
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Kristine K Richter
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Institute of Evolutionary Medicine, Medical Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Sören Stark
- Institute for the Study of the Ancient World, New York University, New York City, NY, 10028, USA
| | - Basira Mir-Makhamad
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Faculty of Arts, Masaryk University, Nováka 1, 602 00, Brno-střed, Czech Republic
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, ul. Krakowskie Przedmieście 26/28, Warszawa, 00-927, Poland
- Climate Change and History Research Initiative, Princeton University, Princeton, USA
| | - Farhod Maksudov
- National Center of Archaeology, Uzbekistan Academy of Sciences, Tashkent, 100000, Uzbekistan
| | - Sirojidin Mirzaakhmedov
- Samarkand Institute of Archaeology, Agency for Cultural Heritage, 1000060, Samarkand, Uzbekistan
| | - Husniddin Rahmonov
- Samarkand Institute of Archaeology, Agency for Cultural Heritage, 1000060, Samarkand, Uzbekistan
| | - Stefanie Schirmer
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Kseniia Ashastina
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Alisher Begmatov
- Berlin-Brandenburg Academy of Sciences and Humanities, 10117, Berlin, Germany
- Department of Linguistics, University of Vienna, Wien, 1090, Austria
- Department of Archaeology, Samarkand State University, Samarkand City, 140104, Uzbekistan
| | - Michael Frachetti
- Department of Anthropology, Washington University in St Louis, St Louis, MO, 63130, USA
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Sharof Kurbanov
- Institute of History, Archaeology and Ethnography named after Ahmad Donish of the Academy of Sciences of Tajikistan, Dushanbe, Tajikistan
| | - Michael Shenkar
- Department of Islamic and Middle Eastern Studies, The Hebrew University of Jerusalem, Mt Scopus, 91905, Jerusalem, Israel
- New Uzbekistan University, 54 Mustaqillik Ave, Tashkent, 100007, Uzbekistan
| | - Taylor Hermes
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- Department of Anthropology, University of Arkansas, AR, 72701, Fayetteville, USA
| | - Fiona Kidd
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Barbara Huber
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Centre de Recherche et d'Enseignement des Géosciences de l'Environnement, Aix-Marseille Université, CNRS, IRD, INRAE, 13545, Aix-en-Provence, France
- Institute of Archaeological Science, University of Tübingen, 72070, Tübingen, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Griffith Sciences, Griffith University, Nathan, QLD, 4111, Australia
- School of Social Science, The University of Queensland, Brisbane, QLD, 4071, Australia
| | - Shujing Wang
- School of Archaeology and Museology, Peking University, Beijing, 100871, China
| | - Pavel Lurje
- State Hermitage Museum, St Petersburg, 190000, Russia
| | - Madelynn von Baeyer
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Rita Dal Martello
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Robert N Spengler
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany.
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany.
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Wu K, Benchimol E, Baksi A, Clever GH. Non-statistical assembly of multicomponent [Pd 2ABCD] cages. Nat Chem 2024; 16:584-591. [PMID: 38243023 DOI: 10.1038/s41557-023-01415-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 12/07/2023] [Indexed: 01/21/2024]
Abstract
Self-assembled hosts, inspired by biological receptors and catalysts, show application potential in sustainable synthesis, energy conversion and medicine. Implementing multiple functionalities in the form of distinguishable building blocks, however, is difficult without risking narcissistic self-sorting or a statistical mess. Here we report a systematic series of integratively self-assembled heteroleptic cages in which two square-planar PdII cations are bridged by four different bis-pyridyl ligands, A, B, C and D, via synergistic effects to exclusively form a single isomer-the lantern-shaped cage [Pd2ABCD]. This self-sorting goal-forming just one out of 55 possible structures-is reached under full thermodynamic control and can be realized progressively (by combining progenitors, such as [Pd2A2C2] with [Pd2B2D2]), directly from ligands and PdII cations or by mixing all four corresponding homoleptic cages. The rational design of complex multicomponent assemblies that enables the modular incorporation of diverse chemical moieties will advance their applicability in functional nanosystems.
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Affiliation(s)
- Kai Wu
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Elie Benchimol
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Ananya Baksi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemistry, Jadavpur University, Kolkata, India
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
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35
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Wang S, Walker-Gibbons R, Watkins B, Flynn M, Krishnan M. A charge-dependent long-ranged force drives tailored assembly of matter in solution. Nat Nanotechnol 2024; 19:485-493. [PMID: 38429493 PMCID: PMC11026162 DOI: 10.1038/s41565-024-01621-5] [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] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
The interaction between charged objects in solution is generally expected to recapitulate two central principles of electromagnetics: (1) like-charged objects repel, and (2) they do so regardless of the sign of their electrical charge. Here we demonstrate experimentally that the solvent plays a hitherto unforeseen but crucial role in interparticle interactions, and importantly, that interactions in the fluid phase can break charge-reversal symmetry. We show that in aqueous solution, negatively charged particles can attract at long range while positively charged particles repel. In solvents that exhibit an inversion of the net molecular dipole at an interface, such as alcohols, we find that the converse can be true: positively charged particles may attract whereas negatives repel. The observations hold across a wide variety of surface chemistries: from inorganic silica and polymeric particles to polyelectrolyte- and polypeptide-coated surfaces in aqueous solution. A theory of interparticle interactions that invokes solvent structuring at an interface captures the observations. Our study establishes a nanoscopic interfacial mechanism by which solvent molecules may give rise to a strong and long-ranged force in solution, with immediate ramifications for a range of particulate and molecular processes across length scales such as self-assembly, gelation and crystallization, biomolecular condensation, coacervation, and phase segregation.
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Affiliation(s)
- Sida Wang
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Bethany Watkins
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Melissa Flynn
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, Oxford, UK.
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36
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Simó C, Serra-Casablancas M, Hortelao AC, Di Carlo V, Guallar-Garrido S, Plaza-García S, Rabanal RM, Ramos-Cabrer P, Yagüe B, Aguado L, Bardia L, Tosi S, Gómez-Vallejo V, Martín A, Patiño T, Julián E, Colombelli J, Llop J, Sánchez S. Urease-powered nanobots for radionuclide bladder cancer therapy. Nat Nanotechnol 2024; 19:554-564. [PMID: 38225356 PMCID: PMC11026160 DOI: 10.1038/s41565-023-01577-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024]
Abstract
Bladder cancer treatment via intravesical drug administration achieves reasonable survival rates but suffers from low therapeutic efficacy. To address the latter, self-propelled nanoparticles or nanobots have been proposed, taking advantage of their enhanced diffusion and mixing capabilities in urine when compared with conventional drugs or passive nanoparticles. However, the translational capabilities of nanobots in treating bladder cancer are underexplored. Here, we tested radiolabelled mesoporous silica-based urease-powered nanobots in an orthotopic mouse model of bladder cancer. In vivo and ex vivo results demonstrated enhanced nanobot accumulation at the tumour site, with an eightfold increase revealed by positron emission tomography in vivo. Label-free optical contrast based on polarization-dependent scattered light-sheet microscopy of cleared bladders confirmed tumour penetration by nanobots ex vivo. Treating tumour-bearing mice with intravesically administered radio-iodinated nanobots for radionuclide therapy resulted in a tumour size reduction of about 90%, positioning nanobots as efficient delivery nanosystems for bladder cancer therapy.
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Affiliation(s)
- Cristina Simó
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine in St. Louis, St Louis, MO, USA
| | - Meritxell Serra-Casablancas
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Ana C Hortelao
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Valerio Di Carlo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Sandra Guallar-Garrido
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Sandra Plaza-García
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Rosa Maria Rabanal
- Unitat de Patologia Murina i Comparada, Department of Animal Medicine and Surgery, Veterinary Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pedro Ramos-Cabrer
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Balbino Yagüe
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Laura Aguado
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- Laboratory of Neuroimaging and Biomarkers of Inflammation, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Biomedical Sciences, Faculty Of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa Gómez-Vallejo
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Abraham Martín
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Laboratory of Neuroimaging and Biomarkers of Inflammation, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Biomedical Engineering Department, Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, The Netherlands
| | - Esther Julián
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Jordi Llop
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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37
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Wang S, Kennedy N, Fujita K, Uchida SI, Eisaki H, Johnson PD, Davis JCS, O'Mahony SM. Discovery of orbital ordering in Bi 2Sr 2CaCu 2O 8+x. Nat Mater 2024; 23:492-498. [PMID: 38438620 PMCID: PMC10990940 DOI: 10.1038/s41563-024-01817-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] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024]
Abstract
The primordial ingredient of cuprate superconductivity is the CuO2 unit cell. Theories usually concentrate on the intra-atom Coulombic interactions dominating the 3d9 and 3d10 configurations of each copper ion. However, if Coulombic interactions also occur between electrons of the 2p6 orbitals of each planar oxygen atom, spontaneous orbital ordering may split their energy levels. This long-predicted intra-unit-cell symmetry breaking should generate an orbitally ordered phase, for which the charge transfer energy ε separating the 2p6 and 3d10 orbitals is distinct for the two oxygen atoms. Here we introduce sublattice-resolved ε(r) imaging to CuO2 studies and discover intra-unit-cell rotational symmetry breaking of ε(r). Spatially, this state is arranged in disordered Ising domains of orthogonally oriented orbital order bounded by dopant ions, and within whose domain walls low-energy electronic quadrupolar two-level systems occur. Overall, these data reveal a Q = 0 orbitally ordered state that splits the oxygen energy levels by ~50 meV, in underdoped CuO2.
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Affiliation(s)
- Shuqiu Wang
- Clarendon Laboratory, University of Oxford, Oxford, UK.
- Department of Physics, Cornell University, Ithaca, NY, USA.
- H. H. Wills Physics Laboratory, University of Bristol, Bristol, UK.
| | - Niall Kennedy
- Clarendon Laboratory, University of Oxford, Oxford, UK
- School of Physics, University College Cork, Cork, Ireland
| | - Kazuhiro Fujita
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | | | - Hiroshi Eisaki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Peter D Johnson
- Clarendon Laboratory, University of Oxford, Oxford, UK
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - J C Séamus Davis
- Clarendon Laboratory, University of Oxford, Oxford, UK.
- Department of Physics, Cornell University, Ithaca, NY, USA.
- School of Physics, University College Cork, Cork, Ireland.
- Max Planck Institute for Chemical Physics of Solids, Dresden, Germany.
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38
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Théry M, Blanchoin L. Reconstituting the dynamic steady states of actin networks in vitro. Nat Cell Biol 2024; 26:494-497. [PMID: 38538835 DOI: 10.1038/s41556-024-01379-x] [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: 04/18/2024]
Affiliation(s)
- Manuel Théry
- Université Paris Sciences et Lettres, CEA, ESPCI, Institut Pierre-Gilles de Gennes, CytoMorpho Lab, Paris, France.
- Université Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble, France.
| | - Laurent Blanchoin
- Université Paris Sciences et Lettres, CEA, ESPCI, Institut Pierre-Gilles de Gennes, CytoMorpho Lab, Paris, France.
- Université Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble, France.
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39
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Milioto C, Carcolé M, Giblin A, Coneys R, Attrebi O, Ahmed M, Harris SS, Lee BI, Yang M, Ellingford RA, Nirujogi RS, Biggs D, Salomonsson S, Zanovello M, de Oliveira P, Katona E, Glaria I, Mikheenko A, Geary B, Udine E, Vaizoglu D, Anoar S, Jotangiya K, Crowley G, Smeeth DM, Adams ML, Niccoli T, Rademakers R, van Blitterswijk M, Devoy A, Hong S, Partridge L, Coyne AN, Fratta P, Alessi DR, Davies B, Busche MA, Greensmith L, Fisher EMC, Isaacs AM. PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in C9orf72 ALS/FTD neurons. Nat Neurosci 2024; 27:643-655. [PMID: 38424324 PMCID: PMC11001582 DOI: 10.1038/s41593-024-01589-4] [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: 02/08/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Dipeptide repeat proteins are a major pathogenic feature of C9orf72 amyotrophic lateral sclerosis (C9ALS)/frontotemporal dementia (FTD) pathology, but their physiological impact has yet to be fully determined. Here we generated C9orf72 dipeptide repeat knock-in mouse models characterized by expression of 400 codon-optimized polyGR or polyPR repeats, and heterozygous C9orf72 reduction. (GR)400 and (PR)400 knock-in mice recapitulate key features of C9ALS/FTD, including cortical neuronal hyperexcitability, age-dependent spinal motor neuron loss and progressive motor dysfunction. Quantitative proteomics revealed an increase in extracellular matrix (ECM) proteins in (GR)400 and (PR)400 spinal cord, with the collagen COL6A1 the most increased protein. TGF-β1 was one of the top predicted regulators of this ECM signature and polyGR expression in human induced pluripotent stem cell neurons was sufficient to induce TGF-β1 followed by COL6A1. Knockdown of TGF-β1 or COL6A1 orthologues in polyGR model Drosophila exacerbated neurodegeneration, while expression of TGF-β1 or COL6A1 in induced pluripotent stem cell-derived motor neurons of patients with C9ALS/FTD protected against glutamate-induced cell death. Altogether, our findings reveal a neuroprotective and conserved ECM signature in C9ALS/FTD.
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Affiliation(s)
- Carmelo Milioto
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mireia Carcolé
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ashling Giblin
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rachel Coneys
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Olivia Attrebi
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mhoriam Ahmed
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Samuel S Harris
- UK Dementia Research Institute, University College London, London, UK
| | - Byung Il Lee
- UK Dementia Research Institute, University College London, London, UK
| | - Mengke Yang
- UK Dementia Research Institute, University College London, London, UK
| | | | - Raja S Nirujogi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sally Salomonsson
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Matteo Zanovello
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Paula de Oliveira
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Eszter Katona
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Idoia Glaria
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Research Support Service, Institute of Agrobiotechnology, CSIC-Government of Navarra, Mutilva, Spain
| | - Alla Mikheenko
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Bethany Geary
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Evan Udine
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Deniz Vaizoglu
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Sharifah Anoar
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Khrisha Jotangiya
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Gerard Crowley
- UK Dementia Research Institute, University College London, London, UK
| | - Demelza M Smeeth
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mirjam L Adams
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Teresa Niccoli
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rosa Rademakers
- VIB Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Anny Devoy
- UK Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Soyon Hong
- UK Dementia Research Institute, University College London, London, UK
| | - Linda Partridge
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ben Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - Marc Aurel Busche
- UK Dementia Research Institute, University College London, London, UK
| | - Linda Greensmith
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK.
| | - Adrian M Isaacs
- UK Dementia Research Institute, University College London, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK.
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40
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Rauber S, Mohammadian H, Schmidkonz C, Atzinger A, Soare A, Treutlein C, Kemble S, Mahony CB, Geisthoff M, Angeli MR, Raimondo MG, Xu C, Yang KT, Lu L, Labinsky H, Saad MSA, Gwellem CA, Chang J, Huang K, Kampylafka E, Knitza J, Bilyy R, Distler JHW, Hanlon MM, Fearon U, Veale DJ, Roemer FW, Bäuerle T, Maric HM, Maschauer S, Ekici AB, Buckley CD, Croft AP, Kuwert T, Prante O, Cañete JD, Schett G, Ramming A. CD200 + fibroblasts form a pro-resolving mesenchymal network in arthritis. Nat Immunol 2024; 25:682-692. [PMID: 38396288 DOI: 10.1038/s41590-024-01774-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Fibroblasts are important regulators of inflammation, but whether fibroblasts change phenotype during resolution of inflammation is not clear. Here we use positron emission tomography to detect fibroblast activation protein (FAP) as a means to visualize fibroblast activation in vivo during inflammation in humans. While tracer accumulation is high in active arthritis, it decreases after tumor necrosis factor and interleukin-17A inhibition. Biopsy-based single-cell RNA-sequencing analyses in experimental arthritis show that FAP signal reduction reflects a phenotypic switch from pro-inflammatory MMP3+/IL6+ fibroblasts (high FAP internalization) to pro-resolving CD200+DKK3+ fibroblasts (low FAP internalization). Spatial transcriptomics of human joints indicates that pro-resolving niches of CD200+DKK3+ fibroblasts cluster with type 2 innate lymphoid cells, whereas MMP3+/IL6+ fibroblasts colocalize with inflammatory immune cells. CD200+DKK3+ fibroblasts stabilized the type 2 innate lymphoid cell phenotype and induced resolution of arthritis via CD200-CD200R1 signaling. Taken together, these data suggest a dynamic molecular regulation of the mesenchymal compartment during resolution of inflammation.
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Affiliation(s)
- Simon Rauber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hashem Mohammadian
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christian Schmidkonz
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Industrial Engineering and Health, Technical University Amberg-Weiden, Institute of Medical Engineering, Weiden, Germany
| | - Armin Atzinger
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alina Soare
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christoph Treutlein
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Samuel Kemble
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Christopher B Mahony
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Manuel Geisthoff
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mario R Angeli
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Maria G Raimondo
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Cong Xu
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kai-Ting Yang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Le Lu
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hannah Labinsky
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mina S A Saad
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Charles A Gwellem
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jiyang Chang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kaiyue Huang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Eleni Kampylafka
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Johannes Knitza
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Rostyslav Bilyy
- Department of Histology, Cytology, Embryology, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
- Institute of Cellular Biology and Pathology 'Nicolae Simionescu', Bucharest, Romania
| | - Jörg H W Distler
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Clinic for Rheumatology, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Hiller Research Center, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Megan M Hanlon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Douglas J Veale
- EULAR Centre for Arthritis & Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Frank W Roemer
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Tobias Bäuerle
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hans M Maric
- Rudolf-Virchow-Center for Integrative and Translational Imaging, University of Würzburg, Würzburg, Germany
| | - Simone Maschauer
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Adam P Croft
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Torsten Kuwert
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Olaf Prante
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Georg Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
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Lepikko S, Jaques YM, Junaid M, Backholm M, Lahtinen J, Julin J, Jokinen V, Sajavaara T, Sammalkorpi M, Foster AS, Ras RHA. Droplet slipperiness despite surface heterogeneity at molecular scale. Nat Chem 2024; 16:506-513. [PMID: 37872419 PMCID: PMC10997520 DOI: 10.1038/s41557-023-01346-3] [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: 10/04/2022] [Accepted: 09/15/2023] [Indexed: 10/25/2023]
Abstract
Friction determines whether liquid droplets slide off a solid surface or stick to it. Surface heterogeneity is generally acknowledged as the major cause of increased contact angle hysteresis and contact line friction of droplets. Here we challenge this long-standing premise for chemical heterogeneity at the molecular length scale. By tuning the coverage of self-assembled monolayers (SAMs), water contact angles change gradually from about 10° to 110° yet contact angle hysteresis and contact line friction are low for the low-coverage hydrophilic SAMs as well as high-coverage hydrophobic SAMs. Their slipperiness is not expected based on the substantial chemical heterogeneity of the SAMs featuring uncoated areas of the substrate well beyond the size of a water molecule as probed by metal reactants. According to molecular dynamics simulations, the low friction of both low- and high-coverage SAMs originates from the mobility of interfacial water molecules. These findings reveal a yet unknown and counterintuitive mechanism for slipperiness, opening new avenues for enhancing the mobility of droplets.
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Affiliation(s)
- Sakari Lepikko
- Department of Applied Physics, Aalto University, Espoo, Finland
- Centre of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo, Finland
| | - Ygor Morais Jaques
- Department of Applied Physics, Aalto University, Espoo, Finland
- Centre of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo, Finland
- Department of Chemistry and Materials Science, Aalto University, Espoo, Finland
| | - Muhammad Junaid
- Department of Applied Physics, Aalto University, Espoo, Finland
- Centre of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo, Finland
| | - Matilda Backholm
- Department of Applied Physics, Aalto University, Espoo, Finland
- Centre of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo, Finland
| | - Jouko Lahtinen
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Jaakko Julin
- Department of Physics, University of Jyväskylä, Jyväskylä, Finland
| | - Ville Jokinen
- Department of Chemistry and Materials Science, Aalto University, Espoo, Finland
| | - Timo Sajavaara
- Department of Physics, University of Jyväskylä, Jyväskylä, Finland
| | - Maria Sammalkorpi
- Centre of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo, Finland
- Department of Chemistry and Materials Science, Aalto University, Espoo, Finland
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Adam S Foster
- Department of Applied Physics, Aalto University, Espoo, Finland
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Robin H A Ras
- Department of Applied Physics, Aalto University, Espoo, Finland.
- Centre of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo, Finland.
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42
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Schäper S, Brito AD, Saraiva BM, Squyres GR, Holmes MJ, Garner EC, Hensel Z, Henriques R, Pinho MG. Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus. Nat Microbiol 2024; 9:1049-1063. [PMID: 38480900 PMCID: PMC10994846 DOI: 10.1038/s41564-024-01629-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024]
Abstract
Bacterial cell division requires recruitment of peptidoglycan (PG) synthases to the division site by the tubulin homologue, FtsZ. Septal PG synthases promote septum growth. FtsZ treadmilling is proposed to drive the processive movement of septal PG synthases and septal constriction in some bacteria; however, the precise mechanisms spatio-temporally regulating PG synthase movement and activity and FtsZ treadmilling are poorly understood. Here using single-molecule imaging of division proteins in the Gram-positive pathogen Staphylococcus aureus, we showed that the septal PG synthase complex FtsW/PBP1 and its putative activator protein, DivIB, move with similar velocity around the division site. Impairing FtsZ treadmilling did not affect FtsW or DivIB velocities or septum constriction rates. Contrarily, PG synthesis inhibition decelerated or stopped directional movement of FtsW and DivIB, and septum constriction. Our findings suggest that a single population of processively moving FtsW/PBP1 associated with DivIB drives cell constriction independently of FtsZ treadmilling in S. aureus.
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Affiliation(s)
- Simon Schäper
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
| | - António D Brito
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Bruno M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Matthew J Holmes
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Zach Hensel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
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43
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Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T, Felchle H, Ebbecke T, Hayward RJ, Deutschbauer AM, Barquist L, Westermann AJ. An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity. Nat Microbiol 2024; 9:1130-1144. [PMID: 38528147 PMCID: PMC10994844 DOI: 10.1038/s41564-024-01642-9] [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: 02/17/2023] [Accepted: 02/07/2024] [Indexed: 03/27/2024]
Abstract
Plasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs). Integrating this expression atlas with published transposon mutant fitness data, we predict conditionally important sRNAs. These include MasB, which downregulates tetracycline tolerance. Using MS2 affinity purification and RNA-seq, we identify a putative MasB target and assess its role in the context of the MasB-associated phenotype. These data-publicly available through the Theta-Base web browser ( http://micromix.helmholtz-hiri.de/bacteroides/ )-constitute a valuable resource for the microbiome community.
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Affiliation(s)
- Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Elise Bornet
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shuba Varshini Alampalli
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Taís Franco de Carvalho
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Hannah Felchle
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Department of Radiation Oncology, Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Munich, Germany
| | - Titus Ebbecke
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany.
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Herzig Sheinfux H, Orsini L, Jung M, Torre I, Ceccanti M, Marconi S, Maniyara R, Barcons Ruiz D, Hötger A, Bertini R, Castilla S, Hesp NCH, Janzen E, Holleitner A, Pruneri V, Edgar JH, Shvets G, Koppens FHL. High-quality nanocavities through multimodal confinement of hyperbolic polaritons in hexagonal boron nitride. Nat Mater 2024; 23:499-505. [PMID: 38321241 DOI: 10.1038/s41563-023-01785-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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/05/2023] [Indexed: 02/08/2024]
Abstract
Compressing light into nanocavities substantially enhances light-matter interactions, which has been a major driver for nanostructured materials research. However, extreme confinement generally comes at the cost of absorption and low resonator quality factors. Here we suggest an alternative optical multimodal confinement mechanism, unlocking the potential of hyperbolic phonon polaritons in isotopically pure hexagonal boron nitride. We produce deep-subwavelength cavities and demonstrate several orders of magnitude improvement in confinement, with estimated Purcell factors exceeding 108 and quality factors in the 50-480 range, values approaching the intrinsic quality factor of hexagonal boron nitride polaritons. Intriguingly, the quality factors we obtain exceed the maximum predicted by impedance-mismatch considerations, indicating that confinement is boosted by higher-order modes. We expect that our multimodal approach to nanoscale polariton manipulation will have far-reaching implications for ultrastrong light-matter interactions, mid-infrared nonlinear optics and nanoscale sensors.
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Affiliation(s)
- Hanan Herzig Sheinfux
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
- Department of Physics, Bar-Ilan University, Ramat Gan, Israel
| | - Lorenzo Orsini
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Minwoo Jung
- Department of Physics, Cornell University, Ithaca, NY, USA
| | - Iacopo Torre
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Matteo Ceccanti
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Simone Marconi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Rinu Maniyara
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - David Barcons Ruiz
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Alexander Hötger
- Walter Schottky Institut and Physik Department, Technische Universitat Munchen, Garching, Germany
| | - Ricardo Bertini
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Sebastián Castilla
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Niels C H Hesp
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Eli Janzen
- Tim Taylor Department of Chemical Engineering, Kansas State University, Durland Hall, Manhattan, KS, USA
| | - Alexander Holleitner
- Walter Schottky Institut and Physik Department, Technische Universitat Munchen, Garching, Germany
| | - Valerio Pruneri
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - James H Edgar
- Tim Taylor Department of Chemical Engineering, Kansas State University, Durland Hall, Manhattan, KS, USA
| | - Gennady Shvets
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Frank H L Koppens
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain.
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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45
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Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC. Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Nat Microbiol 2024; 9:1089-1102. [PMID: 38538833 PMCID: PMC10994853 DOI: 10.1038/s41564-024-01644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024]
Abstract
Secretion systems are protein export machines that enable bacteria to exploit their environment through the release of protein effectors. The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota. Here we trap the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex. Cryo-EM analysis of purified substrate-bound T9SS translocons reveals an extended translocon structure in which the previously described translocon core is augmented by a periplasmic structure incorporating the proteins SprE, PorD and a homologue of the canonical periplasmic chaperone Skp. Substrate proteins bind to the extracellular loops of a carrier protein within the translocon pore. As transport intermediates accumulate on the translocon when energetic input is removed, we deduce that release of the substrate-carrier protein complex from the translocon is the energy-requiring step in T9SS transport.
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Affiliation(s)
- Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Xiaolong Liu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Kjær
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- Newcastle University Biosciences Institute, Newcastle University, Newcastle, UK
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
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46
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Ekvall M, Bergenstråhle L, Andersson A, Czarnewski P, Olegård J, Käll L, Lundeberg J. Spatial landmark detection and tissue registration with deep learning. Nat Methods 2024; 21:673-679. [PMID: 38438615 PMCID: PMC11009106 DOI: 10.1038/s41592-024-02199-5] [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: 07/10/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024]
Abstract
Spatial landmarks are crucial in describing histological features between samples or sites, tracking regions of interest in microscopy, and registering tissue samples within a common coordinate framework. Although other studies have explored unsupervised landmark detection, existing methods are not well-suited for histological image data as they often require a large number of images to converge, are unable to handle nonlinear deformations between tissue sections and are ineffective for z-stack alignment, other modalities beyond image data or multimodal data. We address these challenges by introducing effortless landmark detection, a new unsupervised landmark detection and registration method using neural-network-guided thin-plate splines. Our proposed method is evaluated on a diverse range of datasets including histology and spatially resolved transcriptomics, demonstrating superior performance in both accuracy and stability compared to existing approaches.
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Affiliation(s)
- Markus Ekvall
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden.
| | - Ludvig Bergenstråhle
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Alma Andersson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Paulo Czarnewski
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Johannes Olegård
- Department of Computer and Systems Sciences, Stockholm University, Kista, Sweden
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden.
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47
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Sych T, Schlegel J, Barriga HMG, Ojansivu M, Hanke L, Weber F, Beklem Bostancioglu R, Ezzat K, Stangl H, Plochberger B, Laurencikiene J, El Andaloussi S, Fürth D, Stevens MM, Sezgin E. High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler. Nat Biotechnol 2024; 42:587-590. [PMID: 37308687 PMCID: PMC11021190 DOI: 10.1038/s41587-023-01825-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 05/10/2023] [Indexed: 06/14/2023]
Abstract
We introduce a method, single-particle profiler, that provides single-particle information on the content and biophysical properties of thousands of particles in the size range 5-200 nm. We use our single-particle profiler to measure the messenger RNA encapsulation efficiency of lipid nanoparticles, the viral binding efficiencies of different nanobodies, and the biophysical heterogeneity of liposomes, lipoproteins, exosomes and viruses.
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Affiliation(s)
- Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Jan Schlegel
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Hanna M G Barriga
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Miina Ojansivu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Florian Weber
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
- Department Medical Engineering, University of Applied Sciences Upper Austria, Linz, Austria
| | | | - Kariem Ezzat
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Herbert Stangl
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Chemistry, Vienna, Austria
| | - Birgit Plochberger
- Department Medical Engineering, University of Applied Sciences Upper Austria, Linz, Austria
- LBG Ludwig Boltzmann Institute for Traumatology, Nanoscopy, Vienna, Austria
| | - Jurga Laurencikiene
- Lipid Laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | | | - Daniel Fürth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Molly M Stevens
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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Baker BA, Gutiérrez-Preciado A, Rodríguez Del Río Á, McCarthy CGP, López-García P, Huerta-Cepas J, Susko E, Roger AJ, Eme L, Moreira D. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nat Microbiol 2024; 9:964-975. [PMID: 38519541 DOI: 10.1038/s41564-024-01647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.
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Affiliation(s)
- Brittany A Baker
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Charley G P McCarthy
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Edward Susko
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
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49
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Ugolini M, Kerlin MA, Kuznetsova K, Oda H, Kimura H, Vastenhouw NL. Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol 2024; 26:604-612. [PMID: 38589534 PMCID: PMC11021188 DOI: 10.1038/s41556-024-01389-9] [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: 05/30/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. It remains unclear, however, if and how transcription bodies affect gene expression. Here we disrupted the formation of two prominent endogenous transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analysed the effect on gene expression using enriched SLAM-seq and live-cell imaging. We find that the disruption of transcription bodies results in the misregulation of hundreds of genes. Here we focus on genes that are upregulated. These genes have accessible chromatin and are poised to be transcribed in the presence of the two transcription bodies, but they do not go into elongation. Live-cell imaging shows that disruption of the two large transcription bodies enables these poised genes to be transcribed in ectopic transcription bodies, suggesting that the large transcription bodies sequester a pause release factor. Supporting this hypothesis, we find that CDK9-the kinase that releases paused polymerase II-is highly enriched in the two large transcription bodies. Overexpression of CDK9 in wild-type embryos results in the formation of ectopic transcription bodies and thus phenocopies the removal of the two large transcription bodies. Taken together, our results show that transcription bodies regulate transcription by sequestering machinery, thereby preventing genes elsewhere in the nucleus from being transcribed.
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Affiliation(s)
- Martino Ugolini
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Maciej A Kerlin
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Institute of Human Genetics, CNRS, Montpellier, France
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nadine L Vastenhouw
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland.
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
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50
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Montero JJ, Trozzo R, Sugden M, Öllinger R, Belka A, Zhigalova E, Waetzig P, Engleitner T, Schmidt-Supprian M, Saur D, Rad R. Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx. Nat Methods 2024; 21:584-596. [PMID: 38409225 PMCID: PMC11009108 DOI: 10.1038/s41592-024-02190-0] [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: 03/06/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
Although long noncoding RNAs (lncRNAs) dominate the transcriptome, their functions are largely unexplored. The extensive overlap of lncRNAs with coding and regulatory sequences restricts their systematic interrogation by DNA-directed perturbation. Here we developed genome-scale lncRNA transcriptome screening using Cas13d/CasRx. We show that RNA targeting overcomes limitations inherent to other screening methods, thereby considerably expanding the explorable space of the lncRNAome. By evolving the screening system toward pan-cancer applicability, it supports molecular and phenotypic data integration to contextualize screening hits or infer lncRNA function. We thereby addressed challenges posed by the enormous transcriptome size and tissue specificity through a size-reduced multiplexed gRNA library termed Albarossa, targeting 24,171 lncRNA genes. Its rational design incorporates target prioritization based on expression, evolutionary conservation and tissue specificity, thereby reconciling high discovery power and pan-cancer representation with scalable experimental throughput. Applied across entities, the screening platform identified numerous context-specific and common essential lncRNAs. Our work sets the stage for systematic exploration of lncRNA biology in health and disease.
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Affiliation(s)
- Juan J Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
| | - Riccardo Trozzo
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Maya Sugden
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Alexander Belka
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Ekaterina Zhigalova
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Paul Waetzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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