1
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Kesten C, Leitner V, Dora S, Sims JW, Dindas J, Zipfel C, De Moraes CM, Sanchez-Rodriguez C. Soil-borne fungi alter the apoplastic purinergic signaling in plants by deregulating the homeostasis of extracellular ATP and its metabolite adenosine. eLife 2023; 12:e92913. [PMID: 37994905 PMCID: PMC10746138 DOI: 10.7554/elife.92913] [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: 09/19/2023] [Accepted: 11/23/2023] [Indexed: 11/24/2023] Open
Abstract
Purinergic signaling activated by extracellular nucleotides and their derivative nucleosides trigger sophisticated signaling networks. The outcome of these pathways determine the capacity of the organism to survive under challenging conditions. Both extracellular ATP (eATP) and Adenosine (eAdo) act as primary messengers in mammals, essential for immunosuppressive responses. Despite the clear role of eATP as a plant damage-associated molecular pattern, the function of its nucleoside, eAdo, and of the eAdo/eATP balance in plant stress response remain to be fully elucidated. This is particularly relevant in the context of plant-microbe interaction, where the intruder manipulates the extracellular matrix. Here, we identify Ado as a main molecule secreted by the vascular fungus Fusarium oxysporum. We show that eAdo modulates the plant's susceptibility to fungal colonization by altering the eATP-mediated apoplastic pH homeostasis, an essential physiological player during the infection of this pathogen. Our work indicates that plant pathogens actively imbalance the apoplastic eAdo/eATP levels as a virulence mechanism.
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Affiliation(s)
- Christopher Kesten
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
- Department for Plant and Environmental Sciences, University of CopenhagenCopenhagenDenmark
| | - Valentin Leitner
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
| | - Susanne Dora
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
| | - James W Sims
- Department of Environmental Systems Science, ETH ZürichZurichSwitzerland
| | - Julian Dindas
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | | | - Clara Sanchez-Rodriguez
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC)Pozuelo de AlarcónSpain
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2
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Markicevic M, Sturman O, Bohacek J, Rudin M, Zerbi V, Fulcher BD, Wenderoth N. Neuromodulation of striatal D1 cells shapes BOLD fluctuations in anatomically connected thalamic and cortical regions. eLife 2023; 12:e78620. [PMID: 37824184 PMCID: PMC10569790 DOI: 10.7554/elife.78620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
Understanding how the brain's macroscale dynamics are shaped by underlying microscale mechanisms is a key problem in neuroscience. In animal models, we can now investigate this relationship in unprecedented detail by directly manipulating cellular-level properties while measuring the whole-brain response using resting-state fMRI. Here, we focused on understanding how blood-oxygen-level-dependent (BOLD) dynamics, measured within a structurally well-defined striato-thalamo-cortical circuit in mice, are shaped by chemogenetically exciting or inhibiting D1 medium spiny neurons (MSNs) of the right dorsomedial caudate putamen (CPdm). We characterize changes in both the BOLD dynamics of individual cortical and subcortical brain areas, and patterns of inter-regional coupling (functional connectivity) between pairs of areas. Using a classification approach based on a large and diverse set of time-series properties, we found that CPdm neuromodulation alters BOLD dynamics within thalamic subregions that project back to dorsomedial striatum. In the cortex, changes in local dynamics were strongest in unimodal regions (which process information from a single sensory modality) and weakened along a hierarchical gradient towards transmodal regions. In contrast, a decrease in functional connectivity was observed only for cortico-striatal connections after D1 excitation. Our results show that targeted cellular-level manipulations affect local BOLD dynamics at the macroscale, such as by making BOLD dynamics more predictable over time by increasing its self-correlation structure. This contributes to ongoing attempts to understand the influence of structure-function relationships in shaping inter-regional communication at subcortical and cortical levels.
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Affiliation(s)
- Marija Markicevic
- Neural Control of Movement Lab, HEST, ETH ZürichZurichSwitzerland
- Neuroscience Center Zurich, University and ETH ZurichZurichSwitzerland
- Department of Radiology and Biomedical Imaging, School of Medicine, Yale UniversityNew HavenUnited States
| | - Oliver Sturman
- Neuroscience Center Zurich, University and ETH ZurichZurichSwitzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, HEST, ETH ZurichZurichSwitzerland
| | - Johannes Bohacek
- Neuroscience Center Zurich, University and ETH ZurichZurichSwitzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, HEST, ETH ZurichZurichSwitzerland
| | - Markus Rudin
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
- Institute for Biomedical Engineering, University and ETH ZurichZurichSwitzerland
| | - Valerio Zerbi
- Neuro-X Institute, School of Engineering (STI), EPFLLausanneSwitzerland
- CIBM Centre for Biomedical ImagingLausanneSwitzerland
| | - Ben D Fulcher
- School of Physics, The University of SydneyCamperdownAustralia
| | - Nicole Wenderoth
- Neural Control of Movement Lab, HEST, ETH ZürichZurichSwitzerland
- Neuroscience Center Zurich, University and ETH ZurichZurichSwitzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE)SingaporeSingapore
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3
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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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4
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Haesen S, Lembrechts JJ, De Frenne P, Lenoir J, Aalto J, Ashcroft MB, Kopecký M, Luoto M, Maclean I, Nijs I, Niittynen P, van den Hoogen J, Arriga N, Brůna J, Buchmann N, Čiliak M, Collalti A, De Lombaerde E, Descombes P, Gharun M, Goded I, Govaert S, Greiser C, Grelle A, Gruening C, Hederová L, Hylander K, Kreyling J, Kruijt B, Macek M, Máliš F, Man M, Manca G, Matula R, Meeussen C, Merinero S, Minerbi S, Montagnani L, Muffler L, Ogaya R, Penuelas J, Plichta R, Portillo-Estrada M, Schmeddes J, Shekhar A, Spicher F, Ujházyová M, Vangansbeke P, Weigel R, Wild J, Zellweger F, Van Meerbeek K. ForestClim-Bioclimatic variables for microclimate temperatures of European forests. Glob Chang Biol 2023; 29:2886-2892. [PMID: 37128754 DOI: 10.1111/gcb.16678] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 05/03/2023]
Abstract
Microclimate research gained renewed interest over the last decade and its importance for many ecological processes is increasingly being recognized. Consequently, the call for high-resolution microclimatic temperature grids across broad spatial extents is becoming more pressing to improve ecological models. Here, we provide a new set of open-access bioclimatic variables for microclimate temperatures of European forests at 25 × 25 m2 resolution.
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Affiliation(s)
- Stef Haesen
- Department of Earth and Environmental Sciences, KU Leuven, 3001, Leuven, Celestijnenlaan 200E, Belgium
- KU Leuven Plant Institute, KU Leuven, Leuven, Belgium
| | - Jonas J Lembrechts
- Research Group PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Pieter De Frenne
- Forest and Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090, Melle-Gontrode, Belgium
| | - Jonathan Lenoir
- UMR CNRS 7058 'Ecologie et Dynamique des Systèmes Anthropisés' (EDYSAN), Université de Picardie Jules Verne, Amiens, France
| | - Juha Aalto
- Finnish Meteorological Institute, P.O. Box 503, FI-00101, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2a, FIN-00014, Helsinki, Finland
| | - Michael B Ashcroft
- Centre for Sustainable Ecosystem Solutions, School of Biological Sciences, University of Wollongong, Wollongong, Australia
| | - Martin Kopecký
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6 - Suchdol, CZ-165 21, Czech Republic
| | - Miska Luoto
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2a, FIN-00014, Helsinki, Finland
| | - Ilya Maclean
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, TR10 9FE, UK
| | - Ivan Nijs
- Research Group PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Pekka Niittynen
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2a, FIN-00014, Helsinki, Finland
| | - Johan van den Hoogen
- Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Nicola Arriga
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Josef Brůna
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
| | - Nina Buchmann
- Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Marek Čiliak
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, T.G. Masaryka 24, 960 01, Zvolen, Slovakia
| | - Alessio Collalti
- Institute for Agriculture and Forestry Systems in the Mediterranean, National Research Council of Italy (CNR-ISAFOM), Perugia, Italy
| | - Emiel De Lombaerde
- Forest and Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090, Melle-Gontrode, Belgium
| | - Patrice Descombes
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Musée et Jardins Botaniques Cantonaux, 1007, Lausanne, Switzerland
| | - Mana Gharun
- Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Ignacio Goded
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Sanne Govaert
- Forest and Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090, Melle-Gontrode, Belgium
| | - Caroline Greiser
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, 106 91, Stockholm, Sweden
| | - Achim Grelle
- Department of Forestry and Wood Technology, Linnaeus University, Växjö, 351 95, Sweden
| | | | - Lucia Hederová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
| | - Kristoffer Hylander
- Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, 106 91, Stockholm, Sweden
| | - Jürgen Kreyling
- Experimental Plant Ecology, Institute of Botany and Landscape Ecology, University of Greifswald, D-17487, Greifswald, Germany
| | - Bart Kruijt
- Wageningen University and Research, Wageningen, The Netherlands
| | - Martin Macek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
| | - František Máliš
- Faculty of Forestry, Technical University in Zvolen, T.G. Masaryka 24, 960 01, Zvolen, Slovakia
| | - Matěj Man
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
| | - Giovanni Manca
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Radim Matula
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6 - Suchdol, CZ-165 21, Czech Republic
| | - Camille Meeussen
- Forest and Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090, Melle-Gontrode, Belgium
| | - Sonia Merinero
- Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, 106 91, Stockholm, Sweden
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, C/Tulipán s/n, Móstoles, 28933, Spain
| | - Stefano Minerbi
- Forest Services, Autonomous Province of Bolzano, 39100, Bolzano, Italy
| | - Leonardo Montagnani
- Forest Services, Autonomous Province of Bolzano, 39100, Bolzano, Italy
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Lena Muffler
- Plant Ecology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany
| | - Romà Ogaya
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, 08193, Catalonia, Spain
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, 08193, Catalonia, Spain
| | - Roman Plichta
- Department of Forest Botany, Dendrology and Geobiocoenology, Mendel University in Brno, Brno, Czech Republic
| | | | - Jonas Schmeddes
- Experimental Plant Ecology, Institute of Botany and Landscape Ecology, University of Greifswald, D-17487, Greifswald, Germany
| | - Ankit Shekhar
- Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Fabien Spicher
- UMR CNRS 7058 'Ecologie et Dynamique des Systèmes Anthropisés' (EDYSAN), Université de Picardie Jules Verne, Amiens, France
| | - Mariana Ujházyová
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, T.G. Masaryka 24, 960 01, Zvolen, Slovakia
| | - Pieter Vangansbeke
- Forest and Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090, Melle-Gontrode, Belgium
| | - Robert Weigel
- Plant Ecology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany
| | - Jan Wild
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
| | - Florian Zellweger
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Koenraad Van Meerbeek
- Department of Earth and Environmental Sciences, KU Leuven, 3001, Leuven, Celestijnenlaan 200E, Belgium
- KU Leuven Plant Institute, KU Leuven, Leuven, Belgium
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5
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Arzate-Mejía RG, Mansuy IM. Epigenetic Inheritance: Impact for Biology and Society-recent progress, current questions and future challenges. Environ Epigenet 2022; 8:dvac021. [PMID: 36589550 PMCID: PMC9790978 DOI: 10.1093/eep/dvac021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/19/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Epigenetic inheritance has emerged as a new research discipline that aims to study the mechanisms underlying the transmission of acquired traits across generations. Such transmission is well established in plants and invertebrates but remains not well characterized and understood in mammals. Important questions are how life experiences and environmental factors induce phenotypic changes that are passed to the offspring of exposed individuals, sometimes across several successive generations, what is the contribution of germ cells and what are the consequences for health and disease. These questions were recently discussed at the symposium Epigenetic Inheritance: Impact for Biology and Society organized every 2 years in Zürich, Switzerland. This review provides a summary of the research presented during the symposium and discusses current important questions, perspectives and challenges for the field in the future.
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Affiliation(s)
- Rodrigo G Arzate-Mejía
- Laboratory of Neuroepigenetics, Brain Research Institute, Faculty of Medicine, University of Zurich and Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
| | - Isabelle M Mansuy
- *Correspondence address. Laboratory of Neuroepigenetics, Brain Research Institute, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland. Tel: +41 44 6353360; Fax: +41 44 6353303; E-mail:
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6
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Flütsch S, Horrer D, Santelia D. Starch biosynthesis in guard cells has features of both autotrophic and heterotrophic tissues. Plant Physiol 2022; 189:541-556. [PMID: 35238373 PMCID: PMC9157084 DOI: 10.1093/plphys/kiac087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 06/01/2023]
Abstract
The pathway of starch synthesis in guard cells (GCs), despite the crucial role starch plays in stomatal movements, is not well understood. Here, we characterized starch dynamics in GCs of Arabidopsis (Arabidopsis thaliana) mutants lacking enzymes of the phosphoglucose isomerase-phosphoglucose mutase-ADP-glucose pyrophosphorylase starch synthesis pathway in leaf mesophyll chloroplasts or sugar transporters at the plastid membrane, such as glucose-6-phosphate/phosphate translocators, which are active in heterotrophic tissues. We demonstrate that GCs have metabolic features of both photoautotrophic and heterotrophic cells. GCs make starch using different carbon precursors depending on the time of day, which can originate both from GC photosynthesis and/or sugars imported from the leaf mesophyll. Furthermore, we unravel the major enzymes involved in GC starch synthesis and demonstrate that they act in a temporal manner according to the fluctuations of stomatal aperture, which is unique for GCs. Our work substantially enhances our knowledge on GC starch metabolism and uncovers targets for manipulating GC starch dynamics to improve stomatal behavior, directly affecting plant productivity.
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Affiliation(s)
- Sabrina Flütsch
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Daniel Horrer
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Diana Santelia
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
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7
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Scheidmann MC, Castro-Giner F, Strittmatter K, Krol I, Paasinen-Sohns A, Scherrer R, Donato C, Gkountela S, Szczerba BM, Diamantopoulou Z, Muenst S, Vlajnic T, Kunz L, Vetter M, Rochlitz C, Taylor V, Giachino C, Schroeder T, Platt RJ, Aceto N. An In Vivo CRISPR Screen Identifies Stepwise Genetic Dependencies of Metastatic Progression. Cancer Res 2022; 82:681-694. [PMID: 34916221 PMCID: PMC7612409 DOI: 10.1158/0008-5472.can-21-3908] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 11/14/2021] [Revised: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022]
Abstract
Blood-borne metastasis of breast cancer involves a series of tightly regulated sequential steps, including the growth of a primary tumor lesion, intravasation of circulating tumor cells (CTC), and adaptation in various distant metastatic sites. The genes orchestrating each of these steps are poorly understood in physiologically relevant contexts, owing to the rarity of experimental models that faithfully recapitulate the biology, growth kinetics, and tropism of human breast cancer. Here, we conducted an in vivo loss-of-function CRISPR screen in newly derived CTC xenografts, unique in their ability to spontaneously mirror the human disease, and identified specific genetic dependencies for each step of the metastatic process. Validation experiments revealed sensitivities to inhibitors that are already available, such as PLK1 inhibitors, to prevent CTC intravasation. Together, these findings present a new tool to reclassify driver genes involved in the spread of human cancer, providing insights into the biology of metastasis and paving the way to test targeted treatment approaches. SIGNIFICANCE A loss-of-function CRISPR screen in human CTC-derived xenografts identifies genes critical for individual steps of the metastatic cascade, suggesting novel drivers and treatment opportunities for metastatic breast cancers.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/blood
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- CRISPR-Cas Systems
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Neoplasm Metastasis
- Neoplastic Cells, Circulating/metabolism
- Neoplastic Cells, Circulating/pathology
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA-Seq/methods
- Survival Analysis
- Xenograft Model Antitumor Assays/methods
- Polo-Like Kinase 1
- Mice
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Affiliation(s)
- Manuel C. Scheidmann
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karin Strittmatter
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ilona Krol
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Aino Paasinen-Sohns
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Ramona Scherrer
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Cinzia Donato
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Sofia Gkountela
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Barbara M. Szczerba
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Zoi Diamantopoulou
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Simone Muenst
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Tatjana Vlajnic
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Leo Kunz
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marcus Vetter
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Christoph Rochlitz
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, Embryology and Stem Cell Biology Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Claudio Giachino
- Department of Biomedicine, Embryology and Stem Cell Biology Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Randall J. Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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8
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Abstract
Recent studies have suggested close functional links between overt visual attention and decision making. This suggests that the corresponding mechanisms may interface in brain regions known to be crucial for guiding visual attention - such as the frontal eye field (FEF). Here, we combined brain stimulation, eye tracking, and computational approaches to explore this possibility. We show that inhibitory transcranial magnetic stimulation (TMS) over the right FEF has a causal impact on decision making, reducing the effect of gaze dwell time on choice while also increasing reaction times. We computationally characterize this putative mechanism by using the attentional drift diffusion model (aDDM), which reveals that FEF inhibition reduces the relative discounting of the non-fixated option in the comparison process. Our findings establish an important causal role of the right FEF in choice, elucidate the underlying mechanism, and provide support for one of the key causal hypotheses associated with the aDDM.
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Affiliation(s)
- Ian Krajbich
- Departments of Psychology, Economics, The Ohio State UniversityColumbusUnited States
| | - Andres Mitsumasu
- Zurich Center for Neuroeconomics, Department of Economics, University of ZurichZurichSwitzerland
| | - Rafael Polania
- Zurich Center for Neuroeconomics, Department of Economics, University of ZurichZurichSwitzerland
- Decision Neuroscience Lab, Depterment of Heatlh Sciences and Technology, ETH ZurichZurichSwitzerland
| | - Christian C Ruff
- Zurich Center for Neuroeconomics, Department of Economics, University of ZurichZurichSwitzerland
| | - Ernst Fehr
- Zurich Center for Neuroeconomics, Department of Economics, University of ZurichZurichSwitzerland
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9
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Buccino AP, Hurwitz CL, Garcia S, Magland J, Siegle JH, Hurwitz R, Hennig MH. SpikeInterface, a unified framework for spike sorting. eLife 2020; 9:e61834. [PMID: 33170122 PMCID: PMC7704107 DOI: 10.7554/elife.61834] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Much development has been directed toward improving the performance and automation of spike sorting. This continuous development, while essential, has contributed to an over-saturation of new, incompatible tools that hinders rigorous benchmarking and complicates reproducible analysis. To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single codebase and to facilitate straightforward comparison and adoption of different approaches. With a few lines of code, researchers can reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs; and more. In this paper, we provide an overview of SpikeInterface and, with applications to real and simulated datasets, demonstrate how it can be utilized to reduce the burden of manual curation and to more comprehensively benchmark automated spike sorters.
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Affiliation(s)
- Alessio P Buccino
- Department of Biosystems Science and Engineering, ETH ZurichZürichSwitzerland
- Centre for Integrative Neuroplasticity (CINPLA), University of OsloOsloNorway
| | - Cole L Hurwitz
- School of Informatics, University of EdinburghEdinburghUnited Kingdom
| | - Samuel Garcia
- Centre de Recherche en Neuroscience de Lyon, CNRSLyonFrance
| | | | | | | | - Matthias H Hennig
- School of Informatics, University of EdinburghEdinburghUnited Kingdom
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10
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Abstract
Circulating tumor cells are tumor-derived pioneers responsible for the metastatic spread of cancer. Here, we outline recent discoveries, challenges, and future trends for circulating tumor cell investigations, arguing that the time is coming for translation of this work into clinical practice.
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Affiliation(s)
- Zoi Diamantopoulou
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
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11
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Abstract
The non-destructive collection of ultrathin sections on silicon wafers for post-embedding staining and volumetric correlative light and electron microscopy traditionally requires exquisite manual skills and is tedious and unreliable. In MagC introduced here, sample blocks are augmented with a magnetic resin enabling the remote actuation and collection of hundreds of sections on wafer. MagC allowed the correlative visualization of neuroanatomical tracers within their ultrastructural volumetric electron microscopy context.
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Affiliation(s)
- Thomas Templier
- Institute of NeuroinformaticsUniversity of Zurich and ETH ZurichZurichSwitzerland
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12
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Tsai CJ, Marino J, Adaixo R, Pamula F, Muehle J, Maeda S, Flock T, Taylor NMI, Mohammed I, Matile H, Dawson RJP, Deupi X, Stahlberg H, Schertler G. Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit. eLife 2019; 8:e46041. [PMID: 31251171 PMCID: PMC6629373 DOI: 10.7554/elife.46041] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently heterotrimeric G proteins. The recent surge in structural data has expanded our understanding of GPCR-mediated signal transduction. However, many aspects, including the existence of transient interactions, remain elusive. We present the cryo-EM structure of the light-sensitive GPCR rhodopsin in complex with heterotrimeric Gi. Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. By comparing available complexes, we found a small set of common anchoring points that are G protein-subtype specific. Taken together, our structure and analysis provide new structural basis for the molecular events of the GPCR signaling pathway.
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Affiliation(s)
- Ching-Ju Tsai
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
| | - Jacopo Marino
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
| | - Ricardo Adaixo
- Center for Cellular Imaging and NanAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | - Filip Pamula
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
| | - Jonas Muehle
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
| | - Shoji Maeda
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
| | - Tilman Flock
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
- Department of BiologyETH ZurichZürichSwitzerland
| | - Nicholas MI Taylor
- Center for Cellular Imaging and NanAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | - Inayatulla Mohammed
- Center for Cellular Imaging and NanAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | - Hugues Matile
- Pharma Research and Early Development, Therapeutic modalities, Roche Innovation Center BaselHoffmann-La Roche LtdBaselSwitzerland
| | - Roger JP Dawson
- Pharma Research and Early Development, Therapeutic modalities, Roche Innovation Center BaselHoffmann-La Roche LtdBaselSwitzerland
| | - Xavier Deupi
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
- Condensed Matter Theory GroupPaul Scherrer InstituteVilligenSwitzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry / Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
- Department of BiologyETH ZurichZürichSwitzerland
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13
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Radics B. Estimation of antihydrogen properties in experiments with small signal deficit. Proc Math Phys Eng Sci 2019; 475:20180663. [PMID: 31007549 PMCID: PMC6451969 DOI: 10.1098/rspa.2018.0663] [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: 09/27/2018] [Accepted: 01/29/2019] [Indexed: 10/07/2023] Open
Abstract
For a class of precision CPT-invariance test measurements using antihydrogen, a deficit in the data indicates the presence of the signal. The construction of classical confidence intervals for the properties of the antiatoms from measurements may pose a challenge due to the limited statistics experimentally available. We use the Feldman-Cousins (Feldman and Cousins, Phys. Rev. D, 57, 3873. (doi:10.1103/PhysRevD.57.3873)) method to estimate model parameters for such a low count rate measurement. First, we construct confidence intervals for the Poisson process with a known background and an unknown signal deficit. Then the generalized Monte Carlo version of the method is applied to the use case of the hyperfine transition frequency measurement of the ground-state antihydrogen atom, where the expected double-dip resonance line shape and the mean background is assumed to be known. We find that confidence intervals of the antihydrogen properties could be obtained already from low statistics data. We also discuss how the method may be extended to allow estimation of additional model parameters.
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Affiliation(s)
- B. Radics
- ETH Zürich, Institute for Particle Physics and Astrophysics, Zürich 8093, Switzerland
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14
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Abstract
In this paper, we demonstrate computationally the existence of magnetoelectric multipoles, arising from the second-order term in the multipole expansion of a magnetization density in a magnetic field, in non-centrosymmetric magnetic metals. While magnetoelectric multipoles have long been discussed in the context of the magnetoelectric effect in non-centrosymmetric magnetic insulators, they have not previously been identified in metallic systems, in which the mobile carriers screen any electrical polarization. Using first-principles density functional calculations, we explore three specific systems: first, a conventional centrosymmetric magnetic metal, Fe, in which we break inversion symmetry by introducing a surface, which both generates magnetoelectric monopoles and allows a perpendicular magnetoelectric response. Next, the hypothetical cation-ordered perovskite, SrCaRu2O6, in which we study the interplay between the magnitude of the polar symmetry breaking and that of the magnetic dipoles and multipoles, finding that both scale proportionally to the structural distortion. Finally, we identify a hidden antiferromultipolar order in the non-centrosymmetric, antiferromagnetic metal Ca3Ru2O7, and show that, while its competing magnetic phases have similar magnetic dipolar structures, their magnetoelectric multipolar structures are distinctly different, reflecting the strong differences in transport properties.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.
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Affiliation(s)
- Florian Thöle
- Materials Theory, ETH Zürich,Wolfgang-Pauli-Strasse 27, Zürich 8093, Switzerland
| | - Nicola A Spaldin
- Materials Theory, ETH Zürich,Wolfgang-Pauli-Strasse 27, Zürich 8093, Switzerland
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15
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Böni LJ, Zurflüh R, Widmer M, Fischer P, Windhab EJ, Rühs PA, Kuster S. Hagfish slime exudate stabilization and its effect on slime formation and functionality. Biol Open 2017; 6:1115-1122. [PMID: 28619721 PMCID: PMC5550916 DOI: 10.1242/bio.025528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/02/2017] [Indexed: 01/16/2023] Open
Abstract
Hagfish produce vast amounts of slime when under attack. The slime is the most dilute hydrogel known to date, and is a highly interesting material for biomaterial research. It forms from a glandular secrete, called exudate, which deploys upon contact with seawater. To study slime formation ex vivo and to characterize its material properties, stabilization of the sensitive slime exudate is crucial. In this study, we compared the two main stabilization methods, dispersion in high osmolarity citrate/PIPES (CP) buffer and immersion in oil, and tested the influence of time, temperature and pH on the stability of the exudate and functionality of the slime. Using water retention measurements to assess slime functionality, we found that CP buffer and oil preserved the exudate within the first 5 hours without loss of functionality. For longer storage times, slime functionality decreased for both stabilization methods, for which the breakdown mechanisms differed. Stabilization in oil likely favored temperature-sensitive osmotic-driven swelling and rupture of the mucin vesicles, causing the exudate to gel and clump. Extended storage in CP buffer resulted in an inhibited unraveling of skeins. We suggest that a water soluble protein glue, which mediates skein unraveling in functional skeins, denatures and gradually becomes insoluble during storage in CP buffer. The breakdown was accentuated when the pH of the CP buffer was raised from pH 6.7 to pH 8.5, probably caused by increased denaturation of the protein glue or by inferior vesicle stabilization. However, when fresh exudate was mixed into seawater or phosphate buffer at pH 6-9, slime functionality was not affected, showing pH insensitivity of the slime formation around a neutral pH. These insights on hagfish exudate stabilization mechanisms will support hagfish slime research at a fundamental level, and contribute to resolve the complex mechanisms of skein unraveling and slime formation.
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Affiliation(s)
- L J Böni
- Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - R Zurflüh
- Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - M Widmer
- Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - P Fischer
- Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - E J Windhab
- Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - P A Rühs
- Department of Materials, ETH Zürich, 8093 Zürich, Switzerland
| | - S Kuster
- Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
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16
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Ding Y, Qiu F, Casadevall I Solvas X, Chiu FWY, Nelson BJ, deMello A. Microfluidic-Based Droplet and Cell Manipulations Using Artificial Bacterial Flagella. Micromachines (Basel) 2016; 7:E25. [PMID: 30407399 PMCID: PMC6190376 DOI: 10.3390/mi7020025] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 01/09/2023]
Abstract
Herein, we assess the functionality of magnetic helical microswimmers as basic tools for the manipulation of soft materials, including microdroplets and single cells. Their ability to perform a range of unit operations is evaluated and the operational challenges associated with their use are established. In addition, we also report on interactions observed between the head of such helical swimmers and the boundaries of droplets and cells and discuss the possibilities of assembling an artificial swimming microorganism or a motorized cell.
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Famin Qiu
- Institute for Robotics and Intelligent Systems, ETH Zürich, Tannenstrasse 3, 8092 Zürich, Switzerland.
| | - Xavier Casadevall I Solvas
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Flora Wing Yin Chiu
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Bradley J Nelson
- Institute for Robotics and Intelligent Systems, ETH Zürich, Tannenstrasse 3, 8092 Zürich, Switzerland.
| | - Andrew deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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