1
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Meyer C, Larghero P, Lopes BA, Marschalek R. The KMT2A/MLL consensus gene structure: a comprehensive update for research and diagnostic implications. Leukemia 2024:10.1038/s41375-024-02261-3. [PMID: 38678092 DOI: 10.1038/s41375-024-02261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/02/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Affiliation(s)
- C Meyer
- Goethe-University, Institute of Pharm. Biology/DCAL, Frankfurt/Main, Germany
| | - P Larghero
- Goethe-University, Institute of Pharm. Biology/DCAL, Frankfurt/Main, Germany
| | - B A Lopes
- Goethe-University, Institute of Pharm. Biology/DCAL, Frankfurt/Main, Germany
- GenLAb/Program of Molecular Carcinogenesis, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - R Marschalek
- Goethe-University, Institute of Pharm. Biology/DCAL, Frankfurt/Main, Germany.
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2
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Zhang ZJ, Jacob N, Bhatia S, Boos P, Chen X, DeMuth JC, Messinis AM, Jei BB, Oliveira JCA, Radović A, Neidig ML, Wencel-Delord J, Ackermann L. Iron-catalyzed stereoselective C-H alkylation for simultaneous construction of C-N axial and C-central chirality. Nat Commun 2024; 15:3503. [PMID: 38664372 PMCID: PMC11045758 DOI: 10.1038/s41467-024-47589-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
The assembly of chiral molecules with multiple stereogenic elements is challenging, and, despite of indisputable advances, largely limited to toxic, cost-intensive and precious metal catalysts. In sharp contrast, we herein disclose a versatile C-H alkylation using a non-toxic, low-cost iron catalyst for the synthesis of substituted indoles with two chiral elements. The key for achieving excellent diastereo- and enantioselectivity was substitution on a chiral N-heterocyclic carbene ligand providing steric hindrance and extra represented by noncovalent interaction for the concomitant generation of C-N axial chirality and C-stereogenic center. Experimental and computational mechanistic studies have unraveled the origin of the catalytic efficacy and stereoselectivity.
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Affiliation(s)
- Zi-Jing Zhang
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Nicolas Jacob
- Laboratoire d'Innovation Moléculaire et Applications (UMR CNRS 7042), Université de Strasbourg/Université de Haute-Alsace, ECPM, 67087, Strasbourg, France
| | - Shilpa Bhatia
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA
| | - Philipp Boos
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Xinran Chen
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Joshua C DeMuth
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA
| | - Antonis M Messinis
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Becky Bongsuiru Jei
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - João C A Oliveira
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Aleksa Radović
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA
| | - Michael L Neidig
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK.
| | - Joanna Wencel-Delord
- Laboratoire d'Innovation Moléculaire et Applications (UMR CNRS 7042), Université de Strasbourg/Université de Haute-Alsace, ECPM, 67087, Strasbourg, France.
- Institut für Organische Chemie, Universität Würzburg, 97074 Würzburg, Germany.
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, 37077, Göttingen, Germany.
- Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, 37077, Göttingen, Germany.
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3
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Bove M, Palmieri MA, Santoro M, Agosti LP, Gaetani S, Romano A, Dimonte S, Costantino G, Sikora V, Tucci P, Schiavone S, Morgese MG, Trabace L. Amygdalar neurotransmission alterations in the BTBR mice model of idiopathic autism. Transl Psychiatry 2024; 14:193. [PMID: 38632257 PMCID: PMC11024334 DOI: 10.1038/s41398-024-02905-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Autism Spectrum Disorders (ASD) are principally diagnosed by three core behavioural symptoms, such as stereotyped repertoire, communication impairments and social dysfunctions. This complex pathology has been linked to abnormalities of corticostriatal and limbic circuits. Despite experimental efforts in elucidating the molecular mechanisms behind these abnormalities, a clear etiopathogenic hypothesis is still lacking. To this aim, preclinical studies can be really helpful to longitudinally study behavioural alterations resembling human symptoms and to investigate the underlying neurobiological correlates. In this regard, the BTBR T+ Itpr3tf/J (BTBR) mice are an inbred mouse strain that exhibits a pattern of behaviours well resembling human ASD-like behavioural features. In this study, the BTBR mice model was used to investigate neurochemical and biomolecular alterations, regarding Nerve Growth Factor (NGF) and Brain-Derived Neurotrophic Factor (BDNF), together with GABAergic, glutamatergic, cholinergic, dopaminergic and noradrenergic neurotransmissions and their metabolites in four different brain areas, i.e. prefrontal cortex, hippocampus, amygdala and hypothalamus. In our results, BTBR strain reported decreased noradrenaline, acetylcholine and GABA levels in prefrontal cortex, while hippocampal measurements showed reduced NGF and BDNF expression levels, together with GABA levels. Concerning hypothalamus, no differences were retrieved. As regarding amygdala, we found reduced dopamine levels, accompanied by increased dopamine metabolites in BTBR mice, together with decreased acetylcholine, NGF and GABA levels and enhanced glutamate content. Taken together, our data showed that the BTBR ASD model, beyond its face validity, is a useful tool to untangle neurotransmission alterations that could be underpinned to the heterogeneous ASD-like behaviours, highlighting the crucial role played by amygdala.
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Affiliation(s)
- Maria Bove
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Maria Adelaide Palmieri
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Martina Santoro
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, 00185, Rome, Italy
| | - Lisa Pia Agosti
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Silvana Gaetani
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, 00185, Rome, Italy
| | - Adele Romano
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, 00185, Rome, Italy
| | - Stefania Dimonte
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Giuseppe Costantino
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Vladyslav Sikora
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
- Department of Pathology, Sumy State University, 40007, Sumy, Ukraine
| | - Paolo Tucci
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Stefania Schiavone
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Maria Grazia Morgese
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy
| | - Luigia Trabace
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 20, 71122, Foggia, Italy.
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4
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Zhang M, Pal A, Lyu X, Wu Y, Sitti M. Artificial-goosebump-driven microactuation. Nat Mater 2024; 23:560-569. [PMID: 38336868 PMCID: PMC10990938 DOI: 10.1038/s41563-024-01810-6] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Microactuators provide controllable driving forces for precise positioning, manipulation and operation at the microscale. Development of microactuators using active materials is often hampered by their fabrication complexity and limited motion at small scales. Here we report light-fuelled artificial goosebumps to actuate passive microstructures, inspired by the natural reaction of hair bristling (piloerection) on biological skin. We use light-responsive liquid crystal elastomers as the responsive artificial skin to move three-dimensionally printed passive polymer microstructures. When exposed to a programmable femtosecond laser, the liquid crystal elastomer skin generates localized artificial goosebumps, resulting in precise actuation of the surrounding microstructures. Such microactuation can tilt micro-mirrors for the controlled manipulation of light reflection and disassemble capillary-force-induced self-assembled microstructures globally and locally. We demonstrate the potential application of the proposed microactuation system for information storage. This methodology provides precise, localized and controllable manipulation of microstructures, opening new possibilities for the development of programmable micromachines.
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Affiliation(s)
- Mingchao Zhang
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Aniket Pal
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
- Institute of Applied Mechanics, University of Stuttgart, Stuttgart, Germany
| | - Xianglong Lyu
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
- Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Yingdan Wu
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
- State Key Laboratory of Robotics and System, Harbin Institute of Technology, Harbin, China
| | - Metin Sitti
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany.
- Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
- School of Medicine and College of Engineering, Koç University, Istanbul, Turkey.
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5
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Ordon J, Thouin J, Nakano RT, Ma KW, Zhang P, Huettel B, Garrido-Oter R, Schulze-Lefert P. Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota. Nat Microbiol 2024; 9:1117-1129. [PMID: 38503974 PMCID: PMC10994850 DOI: 10.1038/s41564-024-01619-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/22/2024] [Indexed: 03/21/2024]
Abstract
DNA-amplicon-based microbiota profiling can estimate species diversity and abundance but cannot resolve genetic differences within individuals of the same species. Here we report the development of modular bacterial tags (MoBacTags) encoding DNA barcodes that enable tracking of near-isogenic bacterial commensals in an array of complex microbiome communities. Chromosomally integrated DNA barcodes are then co-amplified with endogenous marker genes of the community by integrating corresponding primer binding sites into the barcode. We use this approach to assess the contributions of individual bacterial genes to Arabidopsis thaliana root microbiota establishment with synthetic communities that include MoBacTag-labelled strains of Pseudomonas capeferrum. Results show reduced root colonization for certain mutant strains with defects in gluconic-acid-mediated host immunosuppression, which would not be detected with traditional amplicon sequencing. Our work illustrates how MoBacTags can be applied to assess scaling of individual bacterial genetic determinants in the plant microbiota.
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Affiliation(s)
- Jana Ordon
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Julien Thouin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ryohei Thomas Nakano
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Ka-Wai Ma
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Innovative Genomics Institute (IGI), University of California, Berkeley, CA, USA
| | - Bruno Huettel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Earlham Institute, Norwich, UK
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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6
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Keilwerth M, Mao W, Malischewski M, Jannuzzi SAV, Breitwieser K, Heinemann FW, Scheurer A, DeBeer S, Munz D, Bill E, Meyer K. The synthesis and characterization of an iron(VII) nitrido complex. Nat Chem 2024; 16:514-520. [PMID: 38291260 PMCID: PMC10997499 DOI: 10.1038/s41557-023-01418-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
Complexes of iron in high oxidation states are captivating research subjects due to their pivotal role as active intermediates in numerous catalytic processes. Structural and spectroscopic studies of well-defined model complexes often provide evidence of these intermediates. In addition to the fundamental molecular and electronic structure insights gained by these complexes, their reactivity also affects our understanding of catalytic reaction mechanisms for small molecule and bond-activation chemistry. Here, we report the synthesis, structural and spectroscopic characterization of a stable, octahedral Fe(VI) nitrido complex and an authenticated, unique Fe(VII) species, prepared by one-electron oxidation. The super-oxidized Fe(VII) nitride rearranges to an Fe(V) imide through an intramolecular amination mechanism and ligand exchange, which is characterized spectroscopically and computationally. This enables combined reactivity and stability studies on a single molecular system of a rare high-valent complex redox pair. Quantum chemical calculations complement the spectroscopic parameters and provide evidence for a diamagnetic (S = 0) d 2 Fe(VI) and a genuine S = 1/2, d 1 Fe(VII) configuration of these super-oxidized nitrido complexes.
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Affiliation(s)
- Martin Keilwerth
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Inorganic Chemistry, Erlangen, Germany
| | - Weiqing Mao
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Inorganic Chemistry, Erlangen, Germany
| | - Moritz Malischewski
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Inorganic Chemistry, Berlin, Germany
| | - Sergio A V Jannuzzi
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Kevin Breitwieser
- Saarland University, Inorganic Chemistry, Coordination Chemistry, Saarbrücken, Germany
| | - Frank W Heinemann
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Inorganic Chemistry, Erlangen, Germany
| | - Andreas Scheurer
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Inorganic Chemistry, Erlangen, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
| | - Dominik Munz
- Saarland University, Inorganic Chemistry, Coordination Chemistry, Saarbrücken, Germany.
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Karsten Meyer
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Inorganic Chemistry, Erlangen, Germany.
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7
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Albert MC, Uranga-Murillo I, Arias M, De Miguel D, Peña N, Montinaro A, Varanda AB, Theobald SJ, Areso I, Saggau J, Koch M, Liccardi G, Peltzer N, Rybniker J, Hurtado-Guerrero R, Merino P, Monzón M, Badiola JJ, Reindl-Schwaighofer R, Sanz-Pamplona R, Cebollada-Solanas A, Megyesfalvi Z, Dome B, Secrier M, Hartmann B, Bergmann M, Pardo J, Walczak H. Identification of FasL as a crucial host factor driving COVID-19 pathology and lethality. Cell Death Differ 2024:10.1038/s41418-024-01278-6. [PMID: 38514848 DOI: 10.1038/s41418-024-01278-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
The dysregulated immune response and inflammation resulting in severe COVID-19 are still incompletely understood. Having recently determined that aberrant death-ligand-induced cell death can cause lethal inflammation, we hypothesized that this process might also cause or contribute to inflammatory disease and lung failure following SARS-CoV-2 infection. To test this hypothesis, we developed a novel mouse-adapted SARS-CoV-2 model (MA20) that recapitulates key pathological features of COVID-19. Concomitantly with occurrence of cell death and inflammation, FasL expression was significantly increased on inflammatory monocytic macrophages and NK cells in the lungs of MA20-infected mice. Importantly, therapeutic FasL inhibition markedly increased survival of both, young and old MA20-infected mice coincident with substantially reduced cell death and inflammation in their lungs. Intriguingly, FasL was also increased in the bronchoalveolar lavage fluid of critically-ill COVID-19 patients. Together, these results identify FasL as a crucial host factor driving the immuno-pathology that underlies COVID-19 severity and lethality, and imply that patients with severe COVID-19 may significantly benefit from therapeutic inhibition of FasL.
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Affiliation(s)
- Marie-Christine Albert
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
| | - Iratxe Uranga-Murillo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Maykel Arias
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Diego De Miguel
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
| | - Natacha Peña
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
| | - Antonella Montinaro
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Ana Beatriz Varanda
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, 50931, Germany
| | - Itziar Areso
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Julia Saggau
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Genome instability, inflammation and cell death laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
| | - Manuel Koch
- Institue for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, Cologne, 50931, Germany
| | - Gianmaria Liccardi
- Genome instability, inflammation and cell death laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
| | - Nieves Peltzer
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- Department of Translational Genomics, University of Cologne, Cologne, 50931, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, 50931, Germany
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), University of Zaragoza, Zaragoza, 50018, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark
- Fundación ARAID, Zaragoza, 50018, Spain
| | - Pedro Merino
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), University of Zaragoza, Zaragoza, 50018, Spain
| | - Marta Monzón
- Research Centre for Encephalopaties and Transmissible Emerging Diseases, Institute for Health Research Aragón (IIS), University of Zaragoza, Zaragoza, 50013, Spain
- Department of Human Anatomy and Histology, University of Zaragoza, Zaragoza, 50009, Spain
| | - Juan J Badiola
- Research Centre for Encephalopaties and Transmissible Emerging Diseases, Institute for Health Research Aragón (IIS), University of Zaragoza, Zaragoza, 50013, Spain
| | | | - Rebeca Sanz-Pamplona
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Fundación ARAID, Zaragoza, 50018, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Alberto Cebollada-Solanas
- Aragon Biomedical Research Center (CIBA), Instituto Aragonés de Ciencias de la Salud (IACS), Unidad de Biocomputación, Zaragoza, 50018, Spain
| | - Zsolt Megyesfalvi
- Deparment of Thoracic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, 1122, Hungary
- National Koranyi Institute of Pulmonology, Budapest, 1121, Hungary
| | - Balazs Dome
- Deparment of Thoracic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, 1122, Hungary
- National Koranyi Institute of Pulmonology, Budapest, 1121, Hungary
- Department of Translational Medicine, Lund University, Lund, SE-22100, Sweden
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Boris Hartmann
- Virology Group, Institute for Veterinary Disease Control at AGES, Moedling, 2340, Austria
| | - Michael Bergmann
- Div. of Visceral Surgery, Dept. of General Surgery, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, 1090, Austria
| | - Julián Pardo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Henning Walczak
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany.
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany.
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
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8
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Illig M, Jahnke K, Weise LP, Scheffold M, Mersdorf U, Drechsler H, Zhang Y, Diez S, Kierfeld J, Göpfrich K. Triggered contraction of self-assembled micron-scale DNA nanotube rings. Nat Commun 2024; 15:2307. [PMID: 38485920 PMCID: PMC10940629 DOI: 10.1038/s41467-024-46339-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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Contractile rings are formed from cytoskeletal filaments during cell division. Ring formation is induced by specific crosslinkers, while contraction is typically associated with motor protein activity. Here, we engineer DNA nanotubes and peptide-functionalized starPEG constructs as synthetic crosslinkers to mimic this process. The crosslinker induces bundling of ten to hundred DNA nanotubes into closed micron-scale rings in a one-pot self-assembly process yielding several thousand rings per microliter. Molecular dynamics simulations reproduce the detailed architectural properties of the DNA rings observed in electron microscopy. Theory and simulations predict DNA ring contraction - without motor proteins - providing mechanistic insights into the parameter space relevant for efficient nanotube sliding. In agreement between simulation and experiment, we obtain ring contraction to less than half of the initial ring diameter. DNA-based contractile rings hold promise for an artificial division machinery or contractile muscle-like materials.
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Affiliation(s)
- Maja Illig
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120, Heidelberg, Germany
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Kevin Jahnke
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120, Heidelberg, Germany
- Harvard University, School of Engineering and Applied Sciences (SEAS), 9 Oxford Street, 02138, Cambridge, MA, USA
| | - Lukas P Weise
- TU Dortmund University, Department of Physics, Otto-Hahn-Str. 4, 44221, Dortmund, Germany
| | - Marlene Scheffold
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ulrike Mersdorf
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Hauke Drechsler
- B CUBE - Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Tübingen University, Center for Plant Molecular Biology (ZMBP), Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Jan Kierfeld
- TU Dortmund University, Department of Physics, Otto-Hahn-Str. 4, 44221, Dortmund, Germany.
| | - Kerstin Göpfrich
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120, Heidelberg, Germany.
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120, Heidelberg, Germany.
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9
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Eckhardt CJ, Chattopadhyay S, Kennes DM, Demler EA, Sentef MA, Michael MH. Theory of resonantly enhanced photo-induced superconductivity. Nat Commun 2024; 15:2300. [PMID: 38485935 PMCID: PMC10940728 DOI: 10.1038/s41467-024-46632-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Optical driving of materials has emerged as a versatile tool to control their properties, with photo-induced superconductivity being among the most fascinating examples. In this work, we show that light or lattice vibrations coupled to an electronic interband transition naturally give rise to electron-electron attraction that may be enhanced when the underlying boson is driven into a non-thermal state. We find this phenomenon to be resonantly amplified when tuning the boson's frequency close to the energy difference between the two electronic bands. This result offers a simple microscopic mechanism for photo-induced superconductivity and provides a recipe for designing new platforms in which light-induced superconductivity can be realized. We discuss two-dimensional heterostructures as a potential test ground for light-induced superconductivity concretely proposing a setup consisting of a graphene-hBN-SrTiO3 heterostructure, for which we estimate a superconducting Tc that may be achieved upon driving the system.
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Affiliation(s)
- Christian J Eckhardt
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761, Hamburg, Germany
- Institut für Theorie der Statistischen Physik, RWTH Aachen University and JARA-Fundamentals of Future Information Technology, 52056, Aachen, Germany
| | | | - Dante M Kennes
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761, Hamburg, Germany
- Institut für Theorie der Statistischen Physik, RWTH Aachen University and JARA-Fundamentals of Future Information Technology, 52056, Aachen, Germany
| | - Eugene A Demler
- Institute for Theoretical Physics, ETH Zürich, 8093, Zürich, Switzerland
| | - Michael A Sentef
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Theoretical Physics and Bremen Center for Computational Materials Science, University of Bremen, 28359, Bremen, Germany
- H H Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, UK
| | - Marios H Michael
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761, Hamburg, Germany.
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10
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Geldsetzer P, Tisdale RL, Stehr L, Michalik F, Lemp J, Aryal KK, Damasceno A, Houehanou C, Jørgensen JMA, Lunet N, Mayige M, Saeedi Moghaddam S, Mwangi KJ, Bommer C, Marcus ME, Theilmann M, Ebert C, Atun R, Davies JI, Flood D, Manne-Goehler J, Seiglie J, Bärnighausen T, Vollmer S. The prevalence of cardiovascular disease risk factors among adults living in extreme poverty. Nat Hum Behav 2024:10.1038/s41562-024-01840-9. [PMID: 38480824 DOI: 10.1038/s41562-024-01840-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/24/2024] [Indexed: 04/10/2024]
Abstract
Evidence on cardiovascular disease (CVD) risk factor prevalence among adults living below the World Bank's international line for extreme poverty (those with income <$1.90 per day) globally is sparse. Here we pooled individual-level data from 105 nationally representative household surveys across 78 countries, representing 85% of people living in extreme poverty globally, and sorted individuals by country-specific measures of household income or wealth to identify those in extreme poverty. CVD risk factors (hypertension, diabetes, smoking, obesity and dyslipidaemia) were present among 17.5% (95% confidence interval (CI) 16.7-18.3%), 4.0% (95% CI 3.6-4.5%), 10.6% (95% CI 9.0-12.3%), 3.1% (95% CI 2.8-3.3%) and 1.4% (95% CI 0.9-1.9%) of adults in extreme poverty, respectively. Most were not treated for CVD-related conditions (for example, among those with hypertension earning <$1.90 per day, 15.2% (95% CI 13.3-17.1%) reported taking blood pressure-lowering medication). The main limitation of the study is likely measurement error of poverty level and CVD risk factors that could have led to an overestimation of CVD risk factor prevalence among adults in extreme poverty. Nonetheless, our results could inform equity discussions for resource allocation and design of effective interventions.
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Affiliation(s)
- Pascal Geldsetzer
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
| | - Rebecca L Tisdale
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Stehr
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
| | - Felix Michalik
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
| | - Julia Lemp
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
| | - Krishna K Aryal
- Department for International Development/Nepal Health Sector Programme 3/Monitoring Evaluation and Operational Research, Abt Associates, Kathmandu, Nepal
| | - Albertino Damasceno
- Department of Public and Forensic Health Sciences and Medical Education, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Corine Houehanou
- Laboratory of Epidemiology of Chronic and Neurological Diseases, Faculty of Health Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Jutta Mari Adelin Jørgensen
- Institute of Global Health, Dept of Public Health and Epidemiology, Copenhagen University, Copenhagen, Denmark
| | - Nuno Lunet
- Department of Public and Forensic Health Sciences and Medical Education, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Mary Mayige
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Sahar Saeedi Moghaddam
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Christian Bommer
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
- Centre for Modern Indian Studies, University of Goettingen, Göttingen, Germany
| | - Maja-Emilia Marcus
- Centre for Modern Indian Studies, University of Goettingen, Göttingen, Germany
- Department of Economics, University of Goettingen, Göttingen, Germany
| | - Michaela Theilmann
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
| | - Cara Ebert
- RWI-Leibniz Institute for Economic Research, Essen (Berlin Office), Berlin, Germany
| | - Rifat Atun
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Global Health and Social Medicine, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Justine Ina Davies
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Global Surgery, Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - David Flood
- Division of Hospital Medicine, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer Manne-Goehler
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Medical Practice Evaluation Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jacqueline Seiglie
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Till Bärnighausen
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
- Harvard Center for Population and Development Studies, Cambridge, MA, USA
| | - Sebastian Vollmer
- Centre for Modern Indian Studies, University of Goettingen, Göttingen, Germany
- Department of Economics, University of Goettingen, Göttingen, Germany
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11
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Luo T, Ilyas B, Hoegen AV, Lee Y, Park J, Park JG, Gedik N. Time-of-flight detection of terahertz phonon-polariton. Nat Commun 2024; 15:2276. [PMID: 38480696 PMCID: PMC10937925 DOI: 10.1038/s41467-024-46515-1] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/16/2024] [Indexed: 03/17/2024] Open
Abstract
A polariton is a fundamental quasiparticle that arises from strong light-matter interaction and as such has attracted wide scientific and practical interest. When light is strongly coupled to the crystal lattice, it gives rise to phonon-polaritons (PPs), which have been proven useful in the dynamical manipulation of quantum materials and the advancement of terahertz technologies. Yet, current detection and characterization methods of polaritons are still limited. Traditional techniques such as Raman or transient grating either rely on fine-tuning of external parameters or complex phase extraction techniques. To overcome these inherent limitations, we propose and demonstrate a technique based on a time-of-flight measurement of PPs. We resonantly launch broadband PPs with intense terahertz fields and measure the time-of-flight of each spectral component with time-resolved second harmonic generation. The time-of-flight information, combined with the PP attenuation, enables us to resolve the real and imaginary parts of the PP dispersion relation. We demonstrate this technique in the van der Waals magnets NiI2 and MnPS3 and reveal a hidden magnon-phonon interaction. We believe that this approach will unlock new opportunities for studying polaritons across diverse material systems and enhance our understanding of strong light-matter interaction.
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Affiliation(s)
- Tianchuang Luo
- Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - Batyr Ilyas
- Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - A von Hoegen
- Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - Youjin Lee
- Department of Physics and Astronomy, Seoul National University, Seoul, South Korea
| | - Jaena Park
- Department of Physics and Astronomy, Seoul National University, Seoul, South Korea
| | - Je-Geun Park
- Department of Physics and Astronomy, Seoul National University, Seoul, South Korea
| | - Nuh Gedik
- Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA.
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12
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Spooner RK, Hizli BJ, Bahners BH, Schnitzler A, Florin E. Modulation of DBS-induced cortical responses and movement by the directionality and magnitude of current administered. NPJ Parkinsons Dis 2024; 10:53. [PMID: 38459031 PMCID: PMC10923868 DOI: 10.1038/s41531-024-00663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
Subthalamic deep brain stimulation (STN-DBS) is an effective therapy for alleviating motor symptoms in people with Parkinson's disease (PwP), although some may not receive optimal clinical benefits. One potential mechanism of STN-DBS involves antidromic activation of the hyperdirect pathway (HDP), thus suppressing cortical beta synchrony to improve motor function, albeit the precise mechanisms underlying optimal DBS parameters are not well understood. To address this, 18 PwP with STN-DBS completed a 2 Hz monopolar stimulation of the left STN during MEG. MEG data were imaged in the time-frequency domain using minimum norm estimation. Peak vertex time series data were extracted to interrogate the directional specificity and magnitude of DBS current on evoked and induced cortical responses and accelerometer metrics of finger tapping using linear mixed-effects models and mediation analyses. We observed increases in evoked responses (HDP ~ 3-10 ms) and synchronization of beta oscillatory power (14-30 Hz, 10-100 ms) following DBS pulse onset in the primary sensorimotor cortex (SM1), supplementary motor area (SMA) and middle frontal gyrus (MFG) ipsilateral to the site of stimulation. DBS parameters significantly modulated neural and behavioral outcomes, with clinically effective contacts eliciting significant increases in medium-latency evoked responses, reductions in induced SM1 beta power, and better movement profiles compared to suboptimal contacts, often regardless of the magnitude of current applied. Finally, HDP-related improvements in motor function were mediated by the degree of SM1 beta suppression in a setting-dependent manner. Together, these data suggest that DBS-evoked brain-behavior dynamics are influenced by the level of beta power in key hubs of the basal ganglia-cortical loop, and this effect is exacerbated by the clinical efficacy of DBS parameters. Such data provides novel mechanistic and clinical insight, which may prove useful for characterizing DBS programming strategies to optimize motor symptom improvement in the future.
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Affiliation(s)
- Rachel K Spooner
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
| | - Baccara J Hizli
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Bahne H Bahners
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Department of Neurology, Center for Movement Disorders and Neuromodulation, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Alfons Schnitzler
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Department of Neurology, Center for Movement Disorders and Neuromodulation, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Esther Florin
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
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13
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Ni B, Vivod D, Avaro J, Qi H, Zahn D, Wang X, Cölfen H. Reversible chirality inversion of an AuAg x-cysteine coordination polymer by pH change. Nat Commun 2024; 15:2042. [PMID: 38448402 PMCID: PMC10918179 DOI: 10.1038/s41467-024-45935-3] [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: 03/18/2023] [Accepted: 02/03/2024] [Indexed: 03/08/2024] Open
Abstract
Responsive chiral systems have attracted considerable attention, given their potential for diverse applications in biology, optoelectronics, photonics, and related fields. Here we show the reversible chirality inversion of an AuAgx-cysteine (AuAgx-cys) coordination polymer (CP) by pH changes. The polymer can be obtained by mixing HAuCl4 and AgNO3 with L-cysteine (or D-cysteine) in appropriate proportions in H2O (or other surfactant solutions). Circular dichroism (CD) spectrum is used to record the strong optical activity of the AuAg0.06-L-cys enantiomer (denoted as L0.06), which can be switched to that of the corresponding D0.06 enantiomer by alkalization (final dispersion pH > 13) and can be switched back after neutralization (final dispersion pH <8). Multiple structural changes at different pH values (≈9.6, ≈13) are observed through UV-Vis and CD spectral measurements, as well as other controlled experiments. Exploration of the CP synthesis kinetics suggests that the covalent bond formation is rapid and then the conformation of the CP materials would continuously evolve. The reaction stoichiometry investigation shows that the formation of CP materials with chirality inversion behavior requires the balancing between different coordination and polymerization processes. This study provides insights into the potential of inorganic stereochemistry in developing promising functional materials.
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Affiliation(s)
- Bing Ni
- Physical Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| | - Dustin Vivod
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Chair for Theoretical Chemistry/Computer Chemistry Centre (CCC) Nägelsbachstrasse 25, 91058, Erlangen, Germany
| | - Jonathan Avaro
- Center for X-ray Analytics, Biomimetic Membranes and Textile, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Haoyuan Qi
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
| | - Dirk Zahn
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemistry and Pharmacy, Chair for Theoretical Chemistry/Computer Chemistry Centre (CCC) Nägelsbachstrasse 25, 91058, Erlangen, Germany
| | - Xun Wang
- Key Lab of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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14
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Sortino L, Gale A, Kühner L, Li C, Biechteler J, Wendisch FJ, Kianinia M, Ren H, Toth M, Maier SA, Aharonovich I, Tittl A. Optically addressable spin defects coupled to bound states in the continuum metasurfaces. Nat Commun 2024; 15:2008. [PMID: 38443418 PMCID: PMC10914779 DOI: 10.1038/s41467-024-46272-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Van der Waals (vdW) materials, including hexagonal boron nitride (hBN), are layered crystalline solids with appealing properties for investigating light-matter interactions at the nanoscale. hBN has emerged as a versatile building block for nanophotonic structures, and the recent identification of native optically addressable spin defects has opened up exciting possibilities in quantum technologies. However, these defects exhibit relatively low quantum efficiencies and a broad emission spectrum, limiting potential applications. Optical metasurfaces present a novel approach to boost light emission efficiency, offering remarkable control over light-matter coupling at the sub-wavelength regime. Here, we propose and realise a monolithic scalable integration between intrinsic spin defects in hBN metasurfaces and high quality (Q) factor resonances, exceeding 102, leveraging quasi-bound states in the continuum (qBICs). Coupling between defect ensembles and qBIC resonances delivers a 25-fold increase in photoluminescence intensity, accompanied by spectral narrowing to below 4 nm linewidth and increased narrowband spin-readout efficiency. Our findings demonstrate a new class of metasurfaces for spin-defect-based technologies and pave the way towards vdW-based nanophotonic devices with enhanced efficiency and sensitivity for quantum applications in imaging, sensing, and light emission.
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Affiliation(s)
- Luca Sortino
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Angus Gale
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Lucca Kühner
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Chi Li
- School of Physics and Astronomy, Monash University, Wellington Rd, Clayton, VIC 3800, Australia
| | - Jonas Biechteler
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Fedja J Wendisch
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Mehran Kianinia
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Haoran Ren
- School of Physics and Astronomy, Monash University, Wellington Rd, Clayton, VIC 3800, Australia
| | - Milos Toth
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- ARC Centre of Excellence for Transformative Meta-Optical Systems, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Stefan A Maier
- School of Physics and Astronomy, Monash University, Wellington Rd, Clayton, VIC 3800, Australia
- The Blackett Laboratory, Department of Physics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Igor Aharonovich
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- ARC Centre of Excellence for Transformative Meta-Optical Systems, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Andreas Tittl
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, 80539, Munich, Germany.
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15
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He G, Peis L, Cuddy EF, Zhao Z, Li D, Zhang Y, Stumberger R, Moritz B, Yang H, Gao H, Devereaux TP, Hackl R. Anharmonic strong-coupling effects at the origin of the charge density wave in CsV 3Sb 5. Nat Commun 2024; 15:1895. [PMID: 38429269 PMCID: PMC10907679 DOI: 10.1038/s41467-024-45865-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
The formation of charge density waves is a long-standing open problem, particularly in dimensions higher than one. Various observations in the vanadium antimonides discovered recently further underpin this notion. Here, we study the Kagome metal CsV3Sb5 using polarized inelastic light scattering and density functional theory calculations. We observe a significant gap anisotropy with 2 Δ max / k B T CDW ≈ 20 , far beyond the prediction of mean-field theory. The analysis of the A1g and E2g phonons, including those emerging below TCDW, indicates strong phonon-phonon coupling, presumably mediated by a strong electron-phonon interaction. Similarly, the asymmetric Fano-type lineshape of the A1g amplitude mode suggests strong electron-phonon coupling below TCDW. The large electronic gap, the enhanced anharmonic phonon-phonon coupling, and the Fano shape of the amplitude mode combined are more supportive of a strong-coupling phonon-driven charge density wave transition than of a Fermi surface instability or an exotic mechanism in CsV3Sb5.
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Affiliation(s)
- Ge He
- Walther Meissner Institut, Bayerische Akademie der Wissenschaften, Garching, 85748, Germany.
- Department of Physics, University College Cork, College Road, Cork, T12 K8AF, Ireland.
| | - Leander Peis
- Walther Meissner Institut, Bayerische Akademie der Wissenschaften, Garching, 85748, Germany
- School of Natural Sciences, Technische Universität München, Garching, 85748, Germany
- IFW Dresden, Helmholtzstrasse 20, Dresden, 01069, Germany
- Capgemini, Frankfurter Ring 81, 80807, München, Germany
| | - Emma Frances Cuddy
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Zhen Zhao
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dong Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuhang Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Romona Stumberger
- Walther Meissner Institut, Bayerische Akademie der Wissenschaften, Garching, 85748, Germany
- School of Natural Sciences, Technische Universität München, Garching, 85748, Germany
- Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany
| | - Brian Moritz
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Haitao Yang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongjun Gao
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Thomas Peter Devereaux
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA.
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.
- Geballe Laboratory for Advanced Materials, Stanford University, Stanford, CA, 94305, USA.
| | - Rudi Hackl
- Walther Meissner Institut, Bayerische Akademie der Wissenschaften, Garching, 85748, Germany.
- School of Natural Sciences, Technische Universität München, Garching, 85748, Germany.
- IFW Dresden, Helmholtzstrasse 20, Dresden, 01069, Germany.
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16
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Muller TH, Butler JL, Veselic S, Miranda B, Wallis JD, Dayan P, Behrens TEJ, Kurth-Nelson Z, Kennerley SW. Distributional reinforcement learning in prefrontal cortex. Nat Neurosci 2024; 27:403-408. [PMID: 38200183 PMCID: PMC10917656 DOI: 10.1038/s41593-023-01535-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/29/2023] [Indexed: 01/12/2024]
Abstract
The prefrontal cortex is crucial for learning and decision-making. Classic reinforcement learning (RL) theories center on learning the expectation of potential rewarding outcomes and explain a wealth of neural data in the prefrontal cortex. Distributional RL, on the other hand, learns the full distribution of rewarding outcomes and better explains dopamine responses. In the present study, we show that distributional RL also better explains macaque anterior cingulate cortex neuronal responses, suggesting that it is a common mechanism for reward-guided learning.
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Affiliation(s)
- Timothy H Muller
- Department of Experimental Psychology, University of Oxford, Oxford, UK.
- Department of Clinical and Movement Neurosciences, University College London, London, UK.
| | - James L Butler
- Department of Experimental Psychology, University of Oxford, Oxford, UK
- Department of Clinical and Movement Neurosciences, University College London, London, UK
| | - Sebastijan Veselic
- Department of Experimental Psychology, University of Oxford, Oxford, UK
- Department of Clinical and Movement Neurosciences, University College London, London, UK
- Wellcome Trust Centre for Human Neuroimaging, University College London, London, UK
| | - Bruno Miranda
- Department of Clinical and Movement Neurosciences, University College London, London, UK
- Institute of Physiology and Institute of Molecular Medicine, Lisbon School of Medicine, University of Lisbon, Lisbon, Portugal
| | - Joni D Wallis
- Department of Psychology and Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Peter Dayan
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- University of Tübingen, Tübingen, Germany
| | - Timothy E J Behrens
- Wellcome Trust Centre for Human Neuroimaging, University College London, London, UK
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, UK
| | - Zeb Kurth-Nelson
- Google DeepMind, London, UK.
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, UK.
| | - Steven W Kennerley
- Department of Experimental Psychology, University of Oxford, Oxford, UK.
- Department of Clinical and Movement Neurosciences, University College London, London, UK.
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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17
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Scacchi E, Paszkiewicz G, Thi Nguyen K, Meda S, Burian A, de Back W, Timmermans MCP. A diffusible small-RNA-based Turing system dynamically coordinates organ polarity. Nat Plants 2024; 10:412-422. [PMID: 38409292 DOI: 10.1038/s41477-024-01634-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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
The formation of a flat and thin leaf presents a developmentally challenging problem, requiring intricate regulation of adaxial-abaxial (top-bottom) polarity. The patterning principles controlling the spatial arrangement of these domains during organ growth have remained unclear. Here we show that this regulation in Arabidopsis thaliana is achieved by an organ-autonomous Turing reaction-diffusion system centred on mobile small RNAs. The data illustrate how Turing dynamics transiently instructed by prepatterned information is sufficient to self-sustain properly oriented polarity in a dynamic, growing organ, presenting intriguing parallels to left-right patterning in the vertebrate embryo. Computational modelling demonstrates that this self-organizing system continuously adapts to coordinate the robust planar polarity of a flat leaf while affording flexibility to generate the tissue patterns of evolutionarily diverse organ shapes. Our findings identify a small-RNA-based Turing network as a dynamic regulator of organ polarity that accounts for leaf shape diversity at the level of the individual organ, plant or species.
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Affiliation(s)
- Emanuele Scacchi
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany.
| | - Gael Paszkiewicz
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Khoa Thi Nguyen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Shreyas Meda
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Agata Burian
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Walter de Back
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
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18
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Titze VM, Caixeiro S, Dinh VS, König M, Rübsam M, Pathak N, Schumacher AL, Germer M, Kukat C, Niessen CM, Schubert M, Gather MC. Hyperspectral confocal imaging for high-throughput readout and analysis of bio-integrated microlasers. Nat Protoc 2024; 19:928-959. [PMID: 38238582 DOI: 10.1038/s41596-023-00924-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/03/2023] [Indexed: 03/10/2024]
Abstract
Integrating micro- and nanolasers into live cells, tissue cultures and small animals is an emerging and rapidly evolving technique that offers noninvasive interrogation and labeling with unprecedented information density. The bright and distinct spectra of such lasers make this approach particularly attractive for high-throughput applications requiring single-cell specificity, such as multiplexed cell tracking and intracellular biosensing. The implementation of these applications requires high-resolution, high-speed spectral readout and advanced analysis routines, which leads to unique technical challenges. Here, we present a modular approach consisting of two separate procedures. The first procedure instructs users on how to efficiently integrate different types of lasers into living cells, and the second procedure presents a workflow for obtaining intracellular lasing spectra with high spectral resolution and up to 125-kHz readout rate and starts from the construction of a custom hyperspectral confocal microscope. We provide guidance on running hyperspectral imaging routines for various experimental designs and recommend specific workflows for processing the resulting large data sets along with an open-source Python library of functions covering the analysis pipeline. We illustrate three applications including the rapid, large-volume mapping of absolute refractive index by using polystyrene microbead lasers, the intracellular sensing of cardiac contractility with polystyrene microbead lasers and long-term cell tracking by using semiconductor nanodisk lasers. Our sample preparation and imaging procedures require 2 days, and setting up the hyperspectral confocal microscope for microlaser characterization requires <2 weeks to complete for users with limited experience in optical and software engineering.
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Affiliation(s)
- Vera M Titze
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany.
| | - Soraya Caixeiro
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany
| | - Vinh San Dinh
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
- Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois, USA
| | - Matthias König
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany
| | - Matthias Rübsam
- Department of Cell Biology of the Skin, University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany
| | - Nachiket Pathak
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany
| | - Anna-Lena Schumacher
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Maximilian Germer
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Carien M Niessen
- Department of Cell Biology of the Skin, University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany
| | - Marcel Schubert
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany.
| | - Malte C Gather
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
- Humboldt Centre for Nano- and Biophotonics, University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany.
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19
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Bennecke W, Windischbacher A, Schmitt D, Bange JP, Hemm R, Kern CS, D'Avino G, Blase X, Steil D, Steil S, Aeschlimann M, Stadtmüller B, Reutzel M, Puschnig P, Jansen GSM, Mathias S. Disentangling the multiorbital contributions of excitons by photoemission exciton tomography. Nat Commun 2024; 15:1804. [PMID: 38413573 PMCID: PMC10899218 DOI: 10.1038/s41467-024-45973-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Excitons are realizations of a correlated many-particle wave function, specifically consisting of electrons and holes in an entangled state. Excitons occur widely in semiconductors and are dominant excitations in semiconducting organic and low-dimensional quantum materials. To efficiently harness the strong optical response and high tuneability of excitons in optoelectronics and in energy-transformation processes, access to the full wavefunction of the entangled state is critical, but has so far not been feasible. Here, we show how time-resolved photoemission momentum microscopy can be used to gain access to the entangled wavefunction and to unravel the exciton's multiorbital electron and hole contributions. For the prototypical organic semiconductor buckminsterfullerene (C60), we exemplify the capabilities of exciton tomography and achieve unprecedented access to key properties of the entangled exciton state including localization, charge-transfer character, and ultrafast exciton formation and relaxation dynamics.
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Affiliation(s)
- Wiebke Bennecke
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Andreas Windischbacher
- Institute of Physics, University of Graz, NAWI Graz, Universitätsplatz 5, 8010, Graz, Austria
| | - David Schmitt
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Jan Philipp Bange
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Ralf Hemm
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern-Landau, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany
| | - Christian S Kern
- Institute of Physics, University of Graz, NAWI Graz, Universitätsplatz 5, 8010, Graz, Austria
| | - Gabriele D'Avino
- Univ. Grenoble Alpes, CNRS, Inst NEEL, F-38042, Grenoble, France
| | - Xavier Blase
- Univ. Grenoble Alpes, CNRS, Inst NEEL, F-38042, Grenoble, France
| | - Daniel Steil
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Sabine Steil
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Martin Aeschlimann
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern-Landau, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany
| | - Benjamin Stadtmüller
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern-Landau, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany
| | - Marcel Reutzel
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Peter Puschnig
- Institute of Physics, University of Graz, NAWI Graz, Universitätsplatz 5, 8010, Graz, Austria
| | - G S Matthijs Jansen
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.
| | - Stefan Mathias
- I. Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.
- International Center for Advanced Studies of Energy Conversion (ICASEC), University of Göttingen, Göttingen, Germany.
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20
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Torres DE, Kramer HM, Tracanna V, Fiorin GL, Cook DE, Seidl MF, Thomma BPHJ. Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nat Commun 2024; 15:1701. [PMID: 38402218 PMCID: PMC10894299 DOI: 10.1038/s41467-024-45884-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: 09/14/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024] Open
Abstract
The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.
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Affiliation(s)
- David E Torres
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vittorio Tracanna
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Manhattan, KS, USA
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany.
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21
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Ma X, Han Y, Zhang YS, Geng Y, Majumdar A, Lagerwall JPF. Tunable templating of photonic microparticles via liquid crystal order-guided adsorption of amphiphilic polymers in emulsions. Nat Commun 2024; 15:1404. [PMID: 38360960 PMCID: PMC10869789 DOI: 10.1038/s41467-024-45674-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
Multiple emulsions are usually stabilized by amphiphilic molecules that combine the chemical characteristics of the different phases in contact. When one phase is a liquid crystal (LC), the choice of stabilizer also determines its configuration, but conventional wisdom assumes that the orientational order of the LC has no impact on the stabilizer. Here we show that, for the case of amphiphilic polymer stabilizers, this impact can be considerable. The mode of interaction between stabilizer and LC changes if the latter is heated close to its isotropic state, initiating a feedback loop that reverberates on the LC in form of a complete structural rearrangement. We utilize this phenomenon to dynamically tune the configuration of cholesteric LC shells from one with radial helix and spherically symmetric Bragg diffraction to a focal conic domain configuration with highly complex optics. Moreover, we template photonic microparticles from the LC shells by photopolymerizing them into solids, retaining any selected LC-derived structure. Our study places LC emulsions in a new light, calling for a reevaluation of the behavior of stabilizer molecules in contact with long-range ordered phases, while also enabling highly interesting photonic elements with application opportunities across vast fields.
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Affiliation(s)
- Xu Ma
- Experimental Soft Matter Physics group, Department of Physics & Materials Science, University of Luxembourg, 1511, Luxembourg, Luxembourg
| | - Yucen Han
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, United Kingdom
| | - Yan-Song Zhang
- Experimental Soft Matter Physics group, Department of Physics & Materials Science, University of Luxembourg, 1511, Luxembourg, Luxembourg
| | - Yong Geng
- Experimental Soft Matter Physics group, Department of Physics & Materials Science, University of Luxembourg, 1511, Luxembourg, Luxembourg
| | - Apala Majumdar
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, United Kingdom
| | - Jan P F Lagerwall
- Experimental Soft Matter Physics group, Department of Physics & Materials Science, University of Luxembourg, 1511, Luxembourg, Luxembourg.
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22
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Guria C, Zhong Q, Ozdemir SK, Patil YSS, El-Ganainy R, Harris JGE. Resolving the topology of encircling multiple exceptional points. Nat Commun 2024; 15:1369. [PMID: 38355733 PMCID: PMC10867139 DOI: 10.1038/s41467-024-45530-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Non-Hermiticity has emerged as a new paradigm for controlling coupled-mode systems in ways that cannot be achieved with conventional techniques. One aspect of this control that has received considerable attention recently is the encircling of exceptional points (EPs). To date, most work has focused on systems consisting of two modes that are tuned by two control parameters and have isolated EPs. While these systems exhibit exotic features related to EP encircling, it has been shown that richer behavior occurs in systems with more than two modes. Such systems can be tuned by more than two control parameters, and contain EPs that form a knot-like structure. Control loops that encircle this structure cause the system's eigenvalues to trace out non-commutative braids. Here we consider a hybrid scenario: a three-mode system with just two control parameters. We describe the relationship between control loops and their topology in the full and two-dimensional parameter space. We demonstrate this relationship experimentally using a three-mode mechanical system in which the control parameters are provided by optomechanical interaction with a high-finesse optical cavity.
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Affiliation(s)
- Chitres Guria
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Qi Zhong
- Department of Physics, Michigan Technological University, Houghton, MI, 49931, USA
- Department of Engineering Science and Mechanics, and Materials Research Institute, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sahin Kaya Ozdemir
- Department of Engineering Science and Mechanics, and Materials Research Institute, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yogesh S S Patil
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Ramy El-Ganainy
- Department of Physics, Michigan Technological University, Houghton, MI, 49931, USA.
- Henes Center for Quantum Phenomena, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Jack Gwynne Emmet Harris
- Department of Physics, Yale University, New Haven, CT, 06520, USA.
- Department of Applied Physics, Yale University, New Haven, CT, 06520, USA.
- Yale Quantum Institute, Yale University, New Haven, CT, 06520, USA.
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23
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Centola M, Poppleton E, Ray S, Centola M, Welty R, Valero J, Walter NG, Šulc P, Famulok M. A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. Nat Nanotechnol 2024; 19:226-236. [PMID: 37857824 PMCID: PMC10873200 DOI: 10.1038/s41565-023-01516-x] [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] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.
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Affiliation(s)
- Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
| | - Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Max-Planck-Institute for Medical Research, Heidelberg, Germany
| | - Sujay Ray
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | | | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
- Interdisciplinary Nanoscience Center - INANO-MBG, iNANO-huset, Århus, Denmark
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA.
| | - Petr Šulc
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany.
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24
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van der Weijden VA, Stötzel M, Iyer DP, Fauler B, Gralinska E, Shahraz M, Meierhofer D, Vingron M, Rulands S, Alexandrov T, Mielke T, Bulut-Karslioglu A. FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy. Nat Cell Biol 2024; 26:181-193. [PMID: 38177284 PMCID: PMC10866708 DOI: 10.1038/s41556-023-01325-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Mammalian developmental timing is adjustable in vivo by preserving pre-implantation embryos in a dormant state called diapause. Inhibition of the growth regulator mTOR (mTORi) pauses mouse development in vitro, yet how embryonic dormancy is maintained is not known. Here we show that mouse embryos in diapause are sustained by using lipids as primary energy source. In vitro, supplementation of embryos with the metabolite L-carnitine balances lipid consumption, puts the embryos in deeper dormancy and boosts embryo longevity. We identify FOXO1 as an essential regulator of the energy balance in dormant embryos and propose, through meta-analyses of dormant cell signatures, that it may be a common regulator of dormancy across adult tissues. Our results lift a constraint on in vitro embryo survival and suggest that lipid metabolism may be a critical metabolic transition relevant for longevity and stem cell function across tissues.
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Affiliation(s)
- Vera A van der Weijden
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maximilian Stötzel
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Dhanur P Iyer
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Beatrix Fauler
- Microscopy and Cryo-Electron Microscopy Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elzbieta Gralinska
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Mohammed Shahraz
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Arnold Sommerfeld Center for Theoretical Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Aydan Bulut-Karslioglu
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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25
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Gritti N, Power RM, Graves A, Huisken J. Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging. Nat Methods 2024; 21:311-321. [PMID: 38177507 PMCID: PMC10864180 DOI: 10.1038/s41592-023-02127-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: 11/10/2022] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Time-lapse fluorescence microscopy is key to unraveling biological development and function; however, living systems, by their nature, permit only limited interrogation and contain untapped information that can only be captured by more invasive methods. Deep-tissue live imaging presents a particular challenge owing to the spectral range of live-cell imaging probes/fluorescent proteins, which offer only modest optical penetration into scattering tissues. Herein, we employ convolutional neural networks to augment live-imaging data with deep-tissue images taken on fixed samples. We demonstrate that convolutional neural networks may be used to restore deep-tissue contrast in GFP-based time-lapse imaging using paired final-state datasets acquired using near-infrared dyes, an approach termed InfraRed-mediated Image Restoration (IR2). Notably, the networks are remarkably robust over a wide range of developmental times. We employ IR2 to enhance the information content of green fluorescent protein time-lapse images of zebrafish and Drosophila embryo/larval development and demonstrate its quantitative potential in increasing the fidelity of cell tracking/lineaging in developing pescoids. Thus, IR2 is poised to extend live imaging to depths otherwise inaccessible.
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Affiliation(s)
- Nicola Gritti
- Morgridge Institute for Research, Madison, WI, USA
- Mesoscopic Imaging Facility, European Molecular Biology Laboratory Barcelona, Barcelona, Spain
| | - Rory M Power
- Morgridge Institute for Research, Madison, WI, USA
- EMBL Imaging Center, European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany
| | | | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin Madison, Madison, WI, USA.
- Department of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
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26
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Bai J, Mosbach S, Taylor CJ, Karan D, Lee KF, Rihm SD, Akroyd J, Lapkin AA, Kraft M. A dynamic knowledge graph approach to distributed self-driving laboratories. Nat Commun 2024; 15:462. [PMID: 38263405 PMCID: PMC10805810 DOI: 10.1038/s41467-023-44599-9] [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: 07/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
The ability to integrate resources and share knowledge across organisations empowers scientists to expedite the scientific discovery process. This is especially crucial in addressing emerging global challenges that require global solutions. In this work, we develop an architecture for distributed self-driving laboratories within The World Avatar project, which seeks to create an all-encompassing digital twin based on a dynamic knowledge graph. We employ ontologies to capture data and material flows in design-make-test-analyse cycles, utilising autonomous agents as executable knowledge components to carry out the experimentation workflow. Data provenance is recorded to ensure its findability, accessibility, interoperability, and reusability. We demonstrate the practical application of our framework by linking two robots in Cambridge and Singapore for a collaborative closed-loop optimisation for a pharmaceutically-relevant aldol condensation reaction in real-time. The knowledge graph autonomously evolves toward the scientist's research goals, with the two robots effectively generating a Pareto front for cost-yield optimisation in three days.
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Affiliation(s)
- Jiaru Bai
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Sebastian Mosbach
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Connor J Taylor
- Astex Pharmaceuticals, 436 Cambridge Science Park Milton Road, Cambridge, CB4 0QA, UK
- Innovation Centre in Digital Molecular Technologies, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Dogancan Karan
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Kok Foong Lee
- CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, UK
| | - Simon D Rihm
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Jethro Akroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Alexei A Lapkin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
- Innovation Centre in Digital Molecular Technologies, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Markus Kraft
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore.
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore, Singapore.
- The Alan Turing Institute, London, NW1 2DB, UK.
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27
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Martens KJA, Turkowyd B, Hohlbein J, Endesfelder U. Temporal analysis of relative distances (TARDIS) is a robust, parameter-free alternative to single-particle tracking. Nat Methods 2024:10.1038/s41592-023-02149-7. [PMID: 38225387 DOI: 10.1038/s41592-023-02149-7] [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: 05/03/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024]
Abstract
In single-particle tracking, individual particles are localized and tracked over time to probe their diffusion and molecular interactions. Temporal crossing of trajectories, blinking particles, and false-positive localizations present computational challenges that have remained difficult to overcome. Here we introduce a robust, parameter-free alternative to single-particle tracking: temporal analysis of relative distances (TARDIS). In TARDIS, an all-to-all distance analysis between localizations is performed with increasing temporal shifts. These pairwise distances represent either intraparticle distances originating from the same particle, or interparticle distances originating from unrelated particles, and are fitted analytically to obtain quantitative measures on particle dynamics. We showcase that TARDIS outperforms tracking algorithms, benchmarked on simulated and experimental data of varying complexity. We further show that TARDIS performs accurately in complex conditions characterized by high particle density, strong emitter blinking or false-positive localizations, and is in fact limited by the capabilities of localization algorithms. TARDIS' robustness enables fivefold shorter measurements without loss of information.
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Affiliation(s)
- Koen J A Martens
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA.
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, the Netherlands.
| | - Bartosz Turkowyd
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, the Netherlands
- Microspectroscopy Research Facility, Wageningen University and Research, Wageningen, the Netherlands
| | - Ulrike Endesfelder
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
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28
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Caprini L, Löwen H, Geilhufe RM. Ultrafast entropy production in pump-probe experiments. Nat Commun 2024; 15:94. [PMID: 38169471 PMCID: PMC10761836 DOI: 10.1038/s41467-023-44277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
The ultrafast control of materials has opened the possibility to investigate non-equilibrium states of matter with striking properties, such as transient superconductivity and ferroelectricity, ultrafast magnetization and demagnetization, as well as Floquet engineering. The characterization of the ultrafast thermodynamic properties within the material is key for their control and design. Here, we develop the ultrafast stochastic thermodynamics for laser-excited phonons. We calculate the entropy production and heat absorbed from experimental data for single phonon modes of driven materials from time-resolved X-ray scattering experiments where the crystal is excited by a laser pulse. The spectral entropy production is calculated for SrTiO3 and KTaO3 for different temperatures and reveals a striking relation with the power spectrum of the displacement-displacement correlation function by inducing a broad peak beside the eigenmode-resonance.
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Affiliation(s)
- Lorenzo Caprini
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - R Matthias Geilhufe
- Department of Physics, Chalmers University of Technology, 412 96, Göteborg, Sweden.
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29
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Eren RO, Kaya GG, Schwarzer R, Pasparakis M. IKKε and TBK1 prevent RIPK1 dependent and independent inflammation. Nat Commun 2024; 15:130. [PMID: 38167258 PMCID: PMC10761900 DOI: 10.1038/s41467-023-44372-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: 03/07/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
TBK1 and IKKε regulate multiple cellular processes including anti-viral type-I interferon responses, metabolism and TNF receptor signaling. However, the relative contributions and potentially redundant functions of IKKε and TBK1 in cell death, inflammation and tissue homeostasis remain poorly understood. Here we show that IKKε compensates for the loss of TBK1 kinase activity to prevent RIPK1-dependent and -independent inflammation in mice. Combined inhibition of IKKε and TBK1 kinase activities caused embryonic lethality that was rescued by heterozygous expression of kinase-inactive RIPK1. Adult mice expressing kinase-inactive versions of IKKε and TBK1 developed systemic inflammation that was induced by both RIPK1-dependent and -independent mechanisms. Combined inhibition of IKKε and TBK1 kinase activities in myeloid cells induced RIPK1-dependent cell death and systemic inflammation mediated by IL-1 family cytokines. Tissue-specific studies showed that IKKε and TBK1 were required to prevent cell death and inflammation in the intestine but were dispensable for liver and skin homeostasis. Together, these findings revealed that IKKε and TBK1 exhibit tissue-specific functions that are important to prevent cell death and inflammation and maintain tissue homeostasis.
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Affiliation(s)
- Remzi Onur Eren
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Göksu Gökberk Kaya
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Robin Schwarzer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Genentech Inc, South San Francisco, USA
| | - Manolis Pasparakis
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany.
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30
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Cao S, Ivanov T, Heuer J, Ferguson CTJ, Landfester K, Caire da Silva L. Dipeptide coacervates as artificial membraneless organelles for bioorthogonal catalysis. Nat Commun 2024; 15:39. [PMID: 38169470 PMCID: PMC10761997 DOI: 10.1038/s41467-023-44278-9] [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: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Artificial organelles can manipulate cellular functions and introduce non-biological processes into cells. Coacervate droplets have emerged as a close analog of membraneless cellular organelles. Their biomimetic properties, such as molecular crowding and selective partitioning, make them promising components for designing cell-like materials. However, their use as artificial organelles has been limited by their complex molecular structure, limited control over internal microenvironment properties, and inherent colloidal instability. Here we report the design of dipeptide coacervates that exhibit enhanced stability, biocompatibility, and a hydrophobic microenvironment. The hydrophobic character facilitates the encapsulation of hydrophobic species, including transition metal-based catalysts, enhancing their efficiency in aqueous environments. Dipeptide coacervates carrying a metal-based catalyst are incorporated as active artificial organelles in cells and trigger an internal non-biological chemical reaction. The development of coacervates with a hydrophobic microenvironment opens an alternative avenue in the field of biomimetic materials with applications in catalysis and synthetic biology.
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Affiliation(s)
- Shoupeng Cao
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Tsvetomir Ivanov
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Julian Heuer
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Calum T J Ferguson
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany.
- Department of Chemistry, McGill University, Montreal, H3A 0B8, Canada.
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31
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Gao L, Behrens A, Rodschinka G, Forcelloni S, Wani S, Strasser K, Nedialkova DD. Selective gene expression maintains human tRNA anticodon pools during differentiation. Nat Cell Biol 2024; 26:100-112. [PMID: 38191669 PMCID: PMC10791582 DOI: 10.1038/s41556-023-01317-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/16/2023] [Indexed: 01/10/2024]
Abstract
Transfer RNAs are essential for translating genetic information into proteins. The human genome contains hundreds of predicted tRNA genes, many in multiple copies. How their expression is regulated to control tRNA repertoires is unknown. Here we combined quantitative tRNA profiling and chromatin immunoprecipitation with sequencing to measure tRNA expression following the differentiation of human induced pluripotent stem cells into neuronal and cardiac cells. We find that tRNA transcript levels vary substantially, whereas tRNA anticodon pools, which govern decoding rates, are more stable among cell types. Mechanistically, RNA polymerase III transcribes a wide range of tRNA genes in human induced pluripotent stem cells but on differentiation becomes constrained to a subset we define as housekeeping tRNAs. This shift is mediated by decreased mTORC1 signalling, which activates the RNA polymerase III repressor MAF1. Our data explain how tRNA anticodon pools are buffered to maintain decoding speed across cell types and reveal that mTORC1 drives selective tRNA expression during differentiation.
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Affiliation(s)
- Lexi Gao
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrew Behrens
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Geraldine Rodschinka
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sergio Forcelloni
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sascha Wani
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Katrin Strasser
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Danny D Nedialkova
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany.
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32
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Laumeier R, Brändle M, Rödel MO, Brunzel S, Brandl R, Pinkert S. The global importance and interplay of colour-based protective and thermoregulatory functions in frogs. Nat Commun 2023; 14:8117. [PMID: 38114472 PMCID: PMC10730650 DOI: 10.1038/s41467-023-43729-7] [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: 03/24/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Small-scale studies have shown that colour lightness variation can have important physiological implications in ectotherms, with darker species having greater heating rates, as well as protection against pathogens and photooxidative damage. Using data for 41% (3059) of all known frog and toad species (Anura) from across the world, we reveal ubiquitous and strong clines of decreasing colour lightness towards colder regions and regions with higher pathogen pressure and UVB radiation. The relative importance of pathogen resistance is higher in the tropics and that of thermoregulation is higher in temperate regions. The results suggest that these functions influence colour lightness evolution in anurans and filtered for more similarly coloured species under climatic extremes, while their concurrent importance resulted in high within-assemblage variation in productive regions. Our findings indicate three important functions of colour lightness in anurans - thermoregulation, pathogen and UVB protection - and broaden support for colour lightness-environment relationships in ectotherms.
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Affiliation(s)
- Ricarda Laumeier
- Department of Animal Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany.
- Department of Biodiversity and Species Conservation, Faculty of Landscape Architecture, Horticulture and Forestry, University of Applied Science Erfurt, Leipziger Straße 77, 99085, Erfurt, Germany.
| | - Martin Brändle
- Department of Animal Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany
| | - Mark-Oliver Rödel
- Department of Evolutionary Diversity Dynamics, Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Stefan Brunzel
- Department of Biodiversity and Species Conservation, Faculty of Landscape Architecture, Horticulture and Forestry, University of Applied Science Erfurt, Leipziger Straße 77, 99085, Erfurt, Germany
| | - Roland Brandl
- Department of Animal Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany
| | - Stefan Pinkert
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, 06511, New Haven, CT, USA
- Department of Conservation Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany
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33
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Bardach L, Neuendorf C, Murayama K, Fahrbach T, Knigge M, Nagengast B, Trautwein U. Does students' awareness of school-track-related stereotypes exacerbate inequalities in education? NPJ Sci Learn 2023; 8:59. [PMID: 38097600 PMCID: PMC10721808 DOI: 10.1038/s41539-023-00203-9] [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] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Early ability tracking increases inequalities in education. It has been proposed that the awareness of negative school-track-related stereotypes contributes to educational inequalities, as stereotype awareness interferes with students' abilities to thrive, particularly those in lower, stigmatized tracks. The present study tested this assumption in a sample of 3880 German secondary school students from three tracks, who were assessed four times on stereotype awareness regarding their own school track and academic outcomes (achievement, engagement, self-concept) between Grades 5 and 8. Students in the lowest track reported higher levels of stereotype awareness than higher track students or students attending a combined track. Stereotype awareness increased across time in all tracks. Contrary to our preregistered hypotheses, however, the results from multigroup models revealed that (changes in) stereotype awareness were not more strongly related to (changes in) most outcomes in the lowest track in comparison with the other two tracks.
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Affiliation(s)
- Lisa Bardach
- University of Tübingen, Hector Research Institute of Education Sciences and Psychology, Tübingen, Germany.
| | - Claudia Neuendorf
- University of Tübingen, Hector Research Institute of Education Sciences and Psychology, Tübingen, Germany
- University of Potsdam, Education Department, Potsdam, Germany
| | - Kou Murayama
- University of Tübingen, Hector Research Institute of Education Sciences and Psychology, Tübingen, Germany
| | - Thorsten Fahrbach
- University of Tübingen, Hector Research Institute of Education Sciences and Psychology, Tübingen, Germany
| | - Michel Knigge
- Humboldt University Berlin, Department of Rehabilitation Sciences, Berlin, Germany
| | - Benjamin Nagengast
- University of Tübingen, Hector Research Institute of Education Sciences and Psychology, Tübingen, Germany
- Korea University, Department of Education and the Brain & Motivation Research Institute (bMRI), Seoul, Republic of Korea
| | - Ulrich Trautwein
- University of Tübingen, Hector Research Institute of Education Sciences and Psychology, Tübingen, Germany
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34
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Belyy A, Heilen P, Hagel P, Hofnagel O, Raunser S. Structure and activation mechanism of the Makes caterpillars floppy 1 toxin. Nat Commun 2023; 14:8226. [PMID: 38086871 PMCID: PMC10716152 DOI: 10.1038/s41467-023-44069-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The bacterial Makes caterpillars floppy 1 (Mcf1) toxin promotes apoptosis in insects, leading to loss of body turgor and death. The molecular mechanism underlying Mcf1 intoxication is poorly understood. Here, we present the cryo-EM structure of Mcf1 from Photorhabdus luminescens, revealing a seahorse-like shape with a head and tail. While the three head domains contain two effectors, as well as an activator-binding domain (ABD) and an autoprotease, the tail consists of two putative translocation and three putative receptor-binding domains. Rearrangement of the tail moves the C-terminus away from the ABD and allows binding of the host cell ADP-ribosylation factor 3, inducing conformational changes that position the cleavage site closer to the protease. This distinct activation mechanism that is based on a hook-loop interaction results in three autocleavage reactions and the release of two toxic effectors. Unexpectedly, the BH3-like domain containing ABD is not an active effector. Our findings allow us to understand key steps of Mcf1 intoxication at the molecular level.
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Affiliation(s)
- Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Philipp Heilen
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Philine Hagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.
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35
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Zhang M, Lee Y, Zheng Z, Khan MTA, Lyu X, Byun J, Giessen H, Sitti M. Micro- and nanofabrication of dynamic hydrogels with multichannel information. Nat Commun 2023; 14:8208. [PMID: 38081820 PMCID: PMC10713606 DOI: 10.1038/s41467-023-43921-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/23/2023] [Indexed: 04/28/2024] Open
Abstract
Creating micro/nanostructures containing multi-channel information within responsive hydrogels presents exciting opportunities for dynamically changing functionalities. However, fabricating these structures is immensely challenging due to the soft and dynamic nature of hydrogels, often resulting in unintended structural deformations or destruction. Here, we demonstrate that dehydrated hydrogels, treated by a programmable femtosecond laser, can allow for a robust fabrication of micro/nanostructures. The dehydration enhances the rigidity of the hydrogels and temporarily locks the dynamic behaviours, significantly promoting their structural integrity during the fabrication process. By utilizing versatile dosage domains of the femtosecond laser, we create micro-grooves on the hydrogel surface through the use of a high-dosage mode, while also altering the fluorescent intensity within the rest of the non-ablated areas via a low-dosage laser. In this way, we rationally design a pixel unit containing three-channel information: structural color, polarization state, and fluorescent intensity, and encode three complex image information sets into these channels. Distinct images at the same location were simultaneously printed onto the hydrogel, which can be observed individually under different imaging modes without cross-talk. Notably, the recovered dynamic responsiveness of the hydrogel enables a multi-information-encoded surface that can sequentially display different information as the temperature changes.
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Affiliation(s)
- Mingchao Zhang
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569, Stuttgart, Germany
| | - Yohan Lee
- 4th Physics Institute and Research Center SCoPE, University of Stuttgart, 70569, Stuttgart, Germany
| | - Zhiqiang Zheng
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569, Stuttgart, Germany
| | - Muhammad Turab Ali Khan
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569, Stuttgart, Germany
| | - Xianglong Lyu
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569, Stuttgart, Germany
- Institute for Biomedical Engineering, ETH Zürich, 8092, Zürich, Switzerland
| | - Junghwan Byun
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569, Stuttgart, Germany
| | - Harald Giessen
- 4th Physics Institute and Research Center SCoPE, University of Stuttgart, 70569, Stuttgart, Germany
| | - Metin Sitti
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569, Stuttgart, Germany.
- Institute for Biomedical Engineering, ETH Zürich, 8092, Zürich, Switzerland.
- School of Medicine and College of Engineering, Koç University, 34450, Istanbul, Turkey.
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36
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Jeckel H, Nosho K, Neuhaus K, Hastewell AD, Skinner DJ, Saha D, Netter N, Paczia N, Dunkel J, Drescher K. Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations. Nat Microbiol 2023; 8:2378-2391. [PMID: 37973866 PMCID: PMC10686836 DOI: 10.1038/s41564-023-01518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
Development of microbial communities is a complex multiscale phenomenon with wide-ranging biomedical and ecological implications. How biological and physical processes determine emergent spatial structures in microbial communities remains poorly understood due to a lack of simultaneous measurements of gene expression and cellular behaviour in space and time. Here we combined live-cell microscopy with a robotic arm for spatiotemporal sampling, which enabled us to simultaneously acquire phenotypic imaging data and spatiotemporal transcriptomes during Bacillus subtilis swarm development. Quantitative characterization of the spatiotemporal gene expression patterns revealed correlations with cellular and collective properties, and phenotypic subpopulations. By integrating these data with spatiotemporal metabolome measurements, we discovered a spatiotemporal cross-feeding mechanism fuelling swarm development: during their migration, earlier generations deposit metabolites which are consumed by later generations that swarm across the same location. These results highlight the importance of spatiotemporal effects during the emergence of phenotypic subpopulations and their interactions in bacterial communities.
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Affiliation(s)
- Hannah Jeckel
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kazuki Nosho
- Biozentrum, University of Basel, Basel, Switzerland
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Alasdair D Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dominic J Skinner
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| | - Dibya Saha
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Knut Drescher
- Biozentrum, University of Basel, Basel, Switzerland.
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37
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Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. Nat Plants 2023; 9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.
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Affiliation(s)
- Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Mathias Scharmann
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, Germany
| | - Takanori Wakatake
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Louisa Channon
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | | | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station & Program in Ecology, Evolution, and Behavior, Michigan State University, Hickory Corners, MI, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Sachiko Masuda
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerd Vogg
- Botanical Garden, University of Würzburg, Würzburg, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany.
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38
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Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H. Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype. Nat Commun 2023; 14:7908. [PMID: 38036533 PMCID: PMC10689823 DOI: 10.1038/s41467-023-43657-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.
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Affiliation(s)
- Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jianing Xie
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Xiufen Cheng
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soheila Rezaei Adariani
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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39
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Frisch ML, Wu L, Atlan C, Ren Z, Han M, Tucoulou R, Liang L, Lu J, Guo A, Nong HN, Arinchtein A, Sprung M, Villanova J, Richard MI, Strasser P. Unraveling the synergistic effects of Cu-Ag tandem catalysts during electrochemical CO 2 reduction using nanofocused X-ray probes. Nat Commun 2023; 14:7833. [PMID: 38030620 PMCID: PMC10687089 DOI: 10.1038/s41467-023-43693-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
Controlling the selectivity of the electrocatalytic reduction of carbon dioxide into value-added chemicals continues to be a major challenge. Bulk and surface lattice strain in nanostructured electrocatalysts affect catalytic activity and selectivity. Here, we unravel the complex dynamics of synergistic lattice strain and stability effects of Cu-Ag tandem catalysts through a previously unexplored combination of in situ nanofocused X-ray absorption spectroscopy and Bragg coherent diffraction imaging. Three-dimensional strain maps reveal the lattice dynamics inside individual nanoparticles as a function of applied potential and product yields. Dynamic relations between strain, redox state, catalytic activity and selectivity are derived. Moderate Ag contents effectively reduce the competing evolution of H2 and, concomitantly, lead to an enhanced corrosion stability. Findings from this study evidence the power of advanced nanofocused spectroscopy techniques to provide new insights into the chemistry and structure of nanostructured catalysts.
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Affiliation(s)
- Marvin L Frisch
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
| | - Longfei Wu
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
- Alexander von Humboldt Foundation, Jean-Paul-Str. 12, 53173, Bonn, Germany
| | - Clément Atlan
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000, France
- CEA Grenoble, IRIG/MEM/NRX, Université Grenoble Alpes, Grenoble, 38054, France
| | - Zhe Ren
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany
| | - Madeleine Han
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000, France
| | - Rémi Tucoulou
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000, France
| | - Liang Liang
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
| | - Jiasheng Lu
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
| | - An Guo
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
| | - Hong Nhan Nong
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
| | - Aleks Arinchtein
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany
| | - Julie Villanova
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000, France
| | - Marie-Ingrid Richard
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000, France
- CEA Grenoble, IRIG/MEM/NRX, Université Grenoble Alpes, Grenoble, 38054, France
| | - Peter Strasser
- Department of Chemistry, Chemical Engineering Division, Technische Universitaet Berlin, Str. des 17. Juni 124, 10623, Berlin, Germany.
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40
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Zhao K, Gao Y, Wang X, Lis BM, Liu J, Jin B, Smith J, Huang C, Gao W, Wang X, Wang X, Zheng A, Huang Z, Hu J, Schömacker R, Wachs IE, Li F. Lithium carbonate-promoted mixed rare earth oxides as a generalized strategy for oxidative coupling of methane with exceptional yields. Nat Commun 2023; 14:7749. [PMID: 38012194 PMCID: PMC10682025 DOI: 10.1038/s41467-023-43682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
The oxidative coupling of methane to higher hydrocarbons offers a promising autothermal approach for direct methane conversion, but its progress has been hindered by yield limitations, high temperature requirements, and performance penalties at practical methane partial pressures (~1 atm). In this study, we report a class of Li2CO3-coated mixed rare earth oxides as highly effective redox catalysts for oxidative coupling of methane under a chemical looping scheme. This catalyst achieves a single-pass C2+ yield up to 30.6%, demonstrating stable performance at 700 °C and methane partial pressures up to 1.4 atm. In-situ characterizations and quantum chemistry calculations provide insights into the distinct roles of the mixed oxide core and Li2CO3 shell, as well as the interplay between the Pr oxidation state and active peroxide formation upon Li2CO3 coating. Furthermore, we establish a generalized correlation between Pr4+ content in the mixed lanthanide oxide and hydrocarbons yield, offering a valuable optimization strategy for this class of oxidative coupling of methane redox catalysts.
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Affiliation(s)
- Kun Zhao
- North Carolina State University, Campus Box 7905, Raleigh, NC, USA
- CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Yunfei Gao
- Institute of Clean Coal Technology, East China University of Science and Technology, Shanghai, China.
| | - Xijun Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Bar Mosevitzky Lis
- Operando Molecular Spectroscopy & Catalysis Laboratory, Department of Chemical & Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Junchen Liu
- North Carolina State University, Campus Box 7905, Raleigh, NC, USA
| | - Baitang Jin
- North Carolina State University, Campus Box 7905, Raleigh, NC, USA
| | - Jacob Smith
- North Carolina State University, Campus Box 7905, Raleigh, NC, USA
| | - Chuande Huang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wenpei Gao
- North Carolina State University, Campus Box 7905, Raleigh, NC, USA
| | - Xiaodong Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xin Wang
- Institute of Clean Coal Technology, East China University of Science and Technology, Shanghai, China
| | - Anqing Zheng
- CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Zhen Huang
- CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Jianli Hu
- Department of Chemical & Biomedical Engineering, West Virginia University, Morgantown, WV, USA
| | - Reinhard Schömacker
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, Berlin, Germany
| | - Israel E Wachs
- Operando Molecular Spectroscopy & Catalysis Laboratory, Department of Chemical & Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA.
| | - Fanxing Li
- North Carolina State University, Campus Box 7905, Raleigh, NC, USA.
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41
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Taleb F, Alfaro-Gomez M, Al-Dabbagh MD, Ornik J, Viana J, Jäckel A, Mach C, Helminiak J, Kleine-Ostman T, Kürner T, Koch M, Mittleman DM, Castro-Camus E. Propagation of THz radiation in air over a broad range of atmospheric temperature and humidity conditions. Sci Rep 2023; 13:20782. [PMID: 38012178 PMCID: PMC10682482 DOI: 10.1038/s41598-023-47586-8] [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: 09/04/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
As the need for higher data rates for communication increases, the terahertz (THz) band has drawn considerable attention. This spectral region promises a much wider bandwidth and the transmission of large amounts of data at high speeds. However, there are still challenges that need to be addressed before the THz telecommunications technology hits the consumer market. One of the recurring concerns is that THz radiation is greatly absorbed by atmospheric water-vapor. Although many studies have presented the attenuation of THz signals under different atmospheric conditions, these results analyze specific temperature or humidity values, leaving the need for a more comprehensive analysis over a wider range of climate conditions. In this work, we present the first study of the attenuation of THz radiation over a broad range of temperatures and humidity values. It is worth noticing that all of our measurements have been undertaken at atmospheric pressure unlike many previous studies where the pressure was not kept constant for various temperatures. Furthermore, we extend our analysis beyond the impact of absolute humidity on the bit error rate in THz communications. We also discuss the refractivity of the atmosphere, examining its variations across different temperatures and humidity levels. THz propagation is studied using two different measurement systems, a long-path THz time-domain spectrometer as well as a quasi-optic setup with vector network analyze. We also compare the results with the ITU-R P.676-13 propagation model. We conclude that the attenuation at the absorption peaks increases linearly with water content and has no dependence on the temperature, while the refractive index, away from absorption lines, namely at 300 GHz shows a sub-linear increase with humidity.
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Affiliation(s)
- Fatima Taleb
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Mariana Alfaro-Gomez
- Universidad Autonoma de Aguascalientes, Av. Universidad 940, Cd. Universitaria, 20100, Aguascalientes, Mexico
| | | | - Jan Ornik
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Juan Viana
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Alexander Jäckel
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Cornelius Mach
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Jan Helminiak
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | | | - Thomas Kürner
- Institut für Nachrichtentechnik, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Martin Koch
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Daniel M Mittleman
- School of Engineering, Brown University, 184 Hope Street, Providence, RI, 02912, USA
| | - Enrique Castro-Camus
- Department of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany.
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42
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McFleder RL, Makhotkina A, Groh J, Keber U, Imdahl F, Peña Mosca J, Peteranderl A, Wu J, Tabuchi S, Hoffmann J, Karl AK, Pagenstecher A, Vogel J, Beilhack A, Koprich JB, Brotchie JM, Saliba AE, Volkmann J, Ip CW. Brain-to-gut trafficking of alpha-synuclein by CD11c + cells in a mouse model of Parkinson's disease. Nat Commun 2023; 14:7529. [PMID: 37981650 PMCID: PMC10658151 DOI: 10.1038/s41467-023-43224-z] [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: 05/09/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023] Open
Abstract
Inflammation in the brain and gut is a critical component of several neurological diseases, such as Parkinson's disease (PD). One trigger of the immune system in PD is aggregation of the pre-synaptic protein, α-synuclein (αSyn). Understanding the mechanism of propagation of αSyn aggregates is essential to developing disease-modifying therapeutics. Using a brain-first mouse model of PD, we demonstrate αSyn trafficking from the brain to the ileum of male mice. Immunohistochemistry revealed that the ileal αSyn aggregations are contained within CD11c+ cells. Using single-cell RNA sequencing, we demonstrate that ileal CD11c+ cells are microglia-like and the same subtype of cells is activated in the brain and ileum of PD mice. Moreover, by utilizing mice expressing the photo-convertible protein, Dendra2, we show that CD11c+ cells traffic from the brain to the ileum. Together these data provide a mechanism of αSyn trafficking between the brain and gut.
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Affiliation(s)
- Rhonda L McFleder
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | | | - Janos Groh
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Ursula Keber
- Department of Neuropathology, Philipps University of Marburg, Marburg, Germany
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Josefina Peña Mosca
- Department of Internal Medicine II, Center for Experimental Molecular Medicine (ZEMM), Würzburg University Hospital, Würzburg, Germany
| | - Alina Peteranderl
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Jingjing Wu
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Sawako Tabuchi
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Jan Hoffmann
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Ann-Kathrin Karl
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Axel Pagenstecher
- Department of Neuropathology, Philipps University of Marburg, Marburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Andreas Beilhack
- Department of Internal Medicine II, Center for Experimental Molecular Medicine (ZEMM), Würzburg University Hospital, Würzburg, Germany
| | - James B Koprich
- Atuka Inc., Toronto, ON, Canada
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Jonathan M Brotchie
- Atuka Inc., Toronto, ON, Canada
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Jens Volkmann
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Chi Wang Ip
- Department of Neurology, University Hospital of Würzburg, Würzburg, Germany.
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43
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Li Y, Wei Y, Wang Z, Liu X, Colnaghi T, Han L, Rao Z, Zhou X, Huber L, Dsouza R, Gong Y, Neugebauer J, Marek A, Rampp M, Bauer S, Li H, Baker I, Stephenson LT, Gault B. Quantitative three-dimensional imaging of chemical short-range order via machine learning enhanced atom probe tomography. Nat Commun 2023; 14:7410. [PMID: 37973821 PMCID: PMC10654683 DOI: 10.1038/s41467-023-43314-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Chemical short-range order (CSRO) refers to atoms of specific elements self-organising within a disordered crystalline matrix to form particular atomic neighbourhoods. CSRO is typically characterized indirectly, using volume-averaged or through projection microscopy techniques that fail to capture the three-dimensional atomistic architectures. Here, we present a machine-learning enhanced approach to break the inherent resolution limits of atom probe tomography enabling three-dimensional imaging of multiple CSROs. We showcase our approach by addressing a long-standing question encountered in body-centred-cubic Fe-Al alloys that see anomalous property changes upon heat treatment. We use it to evidence non-statistical B2-CSRO instead of the generally-expected D03-CSRO. We introduce quantitative correlations among annealing temperature, CSRO, and nano-hardness and electrical resistivity. Our approach is further validated on modified D03-CSRO detected in Fe-Ga. The proposed strategy can be generally employed to investigate short/medium/long-range ordering phenomena in different materials and help design future high-performance materials.
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Affiliation(s)
- Yue Li
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany.
| | - Ye Wei
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Zhangwei Wang
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, China.
| | - Xiaochun Liu
- Institute of Metals, College of Materials Science and Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Timoteo Colnaghi
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Liuliu Han
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Ziyuan Rao
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Xuyang Zhou
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Liam Huber
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Raynol Dsouza
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Yilun Gong
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Jörg Neugebauer
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Andreas Marek
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Markus Rampp
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Stefan Bauer
- Max Planck Institute for Intelligent Systems, Max-Planck-Ring 4, 72076, Tübingen, Germany
| | - Hongxiang Li
- State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, 100083, Beijing, China
| | - Ian Baker
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Leigh T Stephenson
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Baptiste Gault
- Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237, Düsseldorf, Germany.
- Department of Materials, Imperial College, South Kensington, London, SW7 2AZ, UK.
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44
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Richmond RC, Howe LJ, Heilbron K, Jones S, Liu J, Wang X, Weedon MN, Rutter MK, Lawlor DA, Davey Smith G, Vetter C. Correlations in sleeping patterns and circadian preference between spouses. Commun Biol 2023; 6:1156. [PMID: 37957254 PMCID: PMC10643442 DOI: 10.1038/s42003-023-05521-7] [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: 02/14/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Spouses may affect each other's sleeping behaviour. In 47,420 spouse-pairs from the UK Biobank, we found a weak positive phenotypic correlation between spouses for self-reported sleep duration (r = 0.11; 95% CI = 0.10, 0.12) and a weak inverse correlation for chronotype (diurnal preference) (r = -0.11; -0.12, -0.10), which replicated in up to 127,035 23andMe spouse-pairs. Using accelerometer data on 3454 UK Biobank spouse-pairs, the correlation for derived sleep duration was similar to self-report (r = 0.12; 0.09, 0.15). Timing of diurnal activity was positively correlated (r = 0.24; 0.21, 0.27) in contrast to the inverse correlation for chronotype. In Mendelian randomization analysis, positive effects of sleep duration (mean difference=0.13; 0.04, 0.23 SD per SD) and diurnal activity (0.49; 0.03, 0.94) were observed, as were inverse effects of chronotype (-0.15; -0.26, -0.04) and snoring (-0.15; -0.27, -0.04). Findings support the notion that an individual's sleep may impact that of their partner, promoting opportunities for sleep interventions at the family-level.
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Affiliation(s)
- Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, UK.
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, UK
| | - Karl Heilbron
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samuel Jones
- Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Junxi Liu
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, UK
- Oxford Population Health, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Xin Wang
- 23andMe, Inc., 223 N Mathilda Avenue, Sunnyvale, CA, USA
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Martin K Rutter
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Diabetes, Endocrinology and Metabolism Centre, Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Deborah A Lawlor
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, UK
- National Institute of Health Research Biomedical Research Centre, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, UK
- National Institute of Health Research Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Céline Vetter
- Circadian and Sleep Epidemiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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45
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Turker S, Kuhnke P, Jiang Z, Hartwigsen G. Disrupted network interactions serve as a neural marker of dyslexia. Commun Biol 2023; 6:1114. [PMID: 37923809 PMCID: PMC10624919 DOI: 10.1038/s42003-023-05499-2] [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: 03/02/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Dyslexia, a frequent learning disorder, is characterized by severe impairments in reading and writing and hypoactivation in reading regions in the left hemisphere. Despite decades of research, it remains unclear to date if observed behavioural deficits are caused by aberrant network interactions during reading and whether differences in functional activation and connectivity are directly related to reading performance. Here we provide a comprehensive characterization of reading-related brain connectivity in adults with and without dyslexia. We find disrupted functional coupling between hypoactive reading regions, especially between the left temporo-parietal and occipito-temporal cortices, and an extensive functional disruption of the right cerebellum in adults with dyslexia. Network analyses suggest that individuals with dyslexia process written stimuli via a dorsal decoding route and show stronger reading-related interaction with the right cerebellum. Moreover, increased connectivity within networks is linked to worse reading performance in dyslexia. Collectively, our results provide strong evidence for aberrant task-related connectivity as a neural marker for dyslexia that directly impacts behavioural performance. The observed differences in activation and connectivity suggest that one effective way to alleviate reading problems in dyslexia is through modulating interactions within the reading network with neurostimulation methods.
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Affiliation(s)
- Sabrina Turker
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103, Leipzig, Germany.
- Wilhelm Wundt Institute for Psychology, Leipzig University, 04103, Leipzig, Germany.
| | - Philipp Kuhnke
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103, Leipzig, Germany
- Wilhelm Wundt Institute for Psychology, Leipzig University, 04103, Leipzig, Germany
| | - Zhizhao Jiang
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103, Leipzig, Germany
| | - Gesa Hartwigsen
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103, Leipzig, Germany
- Wilhelm Wundt Institute for Psychology, Leipzig University, 04103, Leipzig, Germany
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46
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Valcarcel-Jimenez L, Frezza C. Fumarate hydratase (FH) and cancer: a paradigm of oncometabolism. Br J Cancer 2023; 129:1546-1557. [PMID: 37689804 PMCID: PMC10645937 DOI: 10.1038/s41416-023-02412-w] [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: 06/14/2023] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
Fumarate hydratase (FH) is an enzyme of the Tricarboxylic Acid (TCA) cycle whose mutations lead to hereditary and sporadic forms of cancer. Although more than twenty years have passed since its discovery as the leading cause of the cancer syndrome Hereditary leiomyomatosis and Renal Cell Carcinoma (HLRCC), it is still unclear how the loss of FH causes cancer in a tissue-specific manner and with such aggressive behaviour. It has been shown that FH loss, via the accumulation of FH substrate fumarate, activates a series of oncogenic cascades whose contribution to transformation is still under investigation. In this review, we will summarise these recent findings in an integrated fashion and put forward the case that understanding the biology of FH and how its mutations promote transformation will be vital to establish novel paradigms of oncometabolism.
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Affiliation(s)
- Lorea Valcarcel-Jimenez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.
| | - Christian Frezza
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Genetics, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
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47
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Wang ZX, Livingstone K, Hümpel C, Daniliuc CG, Mück-Lichtenfeld C, Gilmour R. Regioselective, catalytic 1,1-difluorination of enynes. Nat Chem 2023; 15:1515-1522. [PMID: 37845310 PMCID: PMC10624631 DOI: 10.1038/s41557-023-01344-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Fluorinated small molecules are prevalent across the functional small-molecule spectrum, but the scarcity of naturally occurring sources creates an opportunity for creative endeavour in developing routes to access these important materials. Iodine(I)/iodine(III) catalysis has proven to be particularly well-suited to this task, enabling abundant alkene substrates to be readily intercepted by in situ-generated λ3-iodanes and processed to high-value (di)fluorinated products. These organocatalysis paradigms often emulate metal-based processes by engaging the π bond and, in the case of styrenes, facilitating fluorinative phenonium-ion rearrangements to generate difluoromethylene units. Here we demonstrate that enynes are competent proxies for styrenes, thereby mitigating the recurrent need for aryl substituents, and enabling highly versatile homopropargylic difluorides to be generated in an operationally simple manner. The scope of the method is disclosed, together with application in target synthesis (>30 examples, up to >90% yield).
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Affiliation(s)
- Zi-Xuan Wang
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität (WWU) Münster, Münster, Germany
| | - Keith Livingstone
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität (WWU) Münster, Münster, Germany
| | - Carla Hümpel
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität (WWU) Münster, Münster, Germany
| | - Constantin G Daniliuc
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität (WWU) Münster, Münster, Germany
| | | | - Ryan Gilmour
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität (WWU) Münster, Münster, Germany.
- Cells in Motion (CiM) Interfaculty Center, Westfälische Wilhelms-Universität (WWU) Münster, Münster, Germany.
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48
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Zeyn Y, Hausmann K, Halilovic M, Beyer M, Ibrahim HS, Brenner W, Mahboobi S, Bros M, Sippl W, Krämer OH. Histone deacetylase inhibitors modulate hormesis in leukemic cells with mutant FMS-like tyrosine kinase-3. Leukemia 2023; 37:2319-2323. [PMID: 37735559 PMCID: PMC10624624 DOI: 10.1038/s41375-023-02036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Affiliation(s)
- Yanira Zeyn
- Department of Toxicology, University Medical Center, 55131, Mainz, Germany
- Department of Dermatology, University Medical Center Mainz, Mainz, Germany
| | - Kristin Hausmann
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-, Wittenberg, Halle (Saale), Germany
| | - Melisa Halilovic
- Department of Toxicology, University Medical Center, 55131, Mainz, Germany
| | - Mandy Beyer
- Department of Toxicology, University Medical Center, 55131, Mainz, Germany
| | - Hany S Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-, Wittenberg, Halle (Saale), Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
| | - Walburgis Brenner
- Department of Obstetrics and Gynecology, University Medical Center Mainz, Mainz, Germany
| | - Siavosh Mahboobi
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040, Regensburg, Germany
| | - Matthias Bros
- Department of Dermatology, University Medical Center Mainz, Mainz, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-, Wittenberg, Halle (Saale), Germany.
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center, 55131, Mainz, Germany.
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49
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Petersen C, Hamerich IK, Adair KL, Griem-Krey H, Torres Oliva M, Hoeppner MP, Bohannan BJM, Schulenburg H. Host and microbiome jointly contribute to environmental adaptation. ISME J 2023; 17:1953-1965. [PMID: 37673969 PMCID: PMC10579302 DOI: 10.1038/s41396-023-01507-9] [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] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm lines, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.
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Affiliation(s)
- Carola Petersen
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Inga K Hamerich
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Karen L Adair
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Hanne Griem-Krey
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | | | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | | | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany.
- Max-Planck Institute for Evolutionary Biology, Ploen, Germany.
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50
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Llamas E, Koyuncu S, Lee HJ, Wehrmann M, Gutierrez-Garcia R, Dunken N, Charura N, Torres-Montilla S, Schlimgen E, Mandel AM, Theile EB, Grossbach J, Wagle P, Lackmann JW, Schermer B, Benzing T, Beyer A, Pulido P, Rodriguez-Concepcion M, Zuccaro A, Vilchez D. In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation. Nat Aging 2023; 3:1345-1357. [PMID: 37783816 PMCID: PMC10645592 DOI: 10.1038/s43587-023-00502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
In humans, aggregation of polyglutamine repeat (polyQ) proteins causes disorders such as Huntington's disease. Although plants express hundreds of polyQ-containing proteins, no pathologies arising from polyQ aggregation have been reported. To investigate this phenomenon, we expressed an aggregation-prone fragment of human huntingtin (HTT) with an expanded polyQ stretch (Q69) in Arabidopsis thaliana plants. In contrast to animal models, we find that Arabidopsis sp. suppresses Q69 aggregation through chloroplast proteostasis. Inhibition of chloroplast proteostasis diminishes the capacity of plants to prevent cytosolic Q69 aggregation. Moreover, endogenous polyQ-containing proteins also aggregate on chloroplast dysfunction. We find that Q69 interacts with the chloroplast stromal processing peptidase (SPP). Synthetic Arabidopsis SPP prevents polyQ-expanded HTT aggregation in human cells. Likewise, ectopic SPP expression in Caenorhabditis elegans reduces neuronal Q67 aggregation and subsequent neurotoxicity. Our findings suggest that synthetic plant proteins, such as SPP, hold therapeutic potential for polyQ disorders and other age-related diseases involving protein aggregation.
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Affiliation(s)
- Ernesto Llamas
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Hyun Ju Lee
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Markus Wehrmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Ricardo Gutierrez-Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Nick Dunken
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Nyasha Charura
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | | | - Elena Schlimgen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Amrei M Mandel
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Erik Boelen Theile
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Jan Grossbach
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Jan-Wilm Lackmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Pablo Pulido
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Alga Zuccaro
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
- Institute for Genetics, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
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