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Rupprecht P, Duss SN, Becker D, Lewis CM, Bohacek J, Helmchen F. Centripetal integration of past events in hippocampal astrocytes regulated by locus coeruleus. Nat Neurosci 2024; 27:927-939. [PMID: 38570661 PMCID: PMC11089000 DOI: 10.1038/s41593-024-01612-8] [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: 07/26/2022] [Accepted: 02/26/2024] [Indexed: 04/05/2024]
Abstract
An essential feature of neurons is their ability to centrally integrate information from their dendrites. The activity of astrocytes, in contrast, has been described as mostly uncoordinated across cellular compartments without clear central integration. Here we report conditional integration of calcium signals in astrocytic distal processes at their soma. In the hippocampus of adult mice of both sexes, we found that global astrocytic activity, as recorded with population calcium imaging, reflected past neuronal and behavioral events on a timescale of seconds. Salient past events, indicated by pupil dilations, facilitated the propagation of calcium signals from distal processes to the soma. Centripetal propagation to the soma was reproduced by optogenetic activation of the locus coeruleus, a key regulator of arousal, and reduced by pharmacological inhibition of α1-adrenergic receptors. Together, our results suggest that astrocytes are computational units of the brain that slowly and conditionally integrate calcium signals upon behaviorally relevant events.
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Affiliation(s)
- Peter Rupprecht
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zürich, Switzerland.
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zürich, Switzerland.
| | - Sian N Duss
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zürich, Switzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zürich, Switzerland
| | - Denise Becker
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zürich, Switzerland
| | - Christopher M Lewis
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zürich, Switzerland
| | - Johannes Bohacek
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zürich, Switzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zürich, Switzerland
| | - Fritjof Helmchen
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zürich, Switzerland.
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zürich, Switzerland.
- University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zürich, Switzerland.
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2
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Oppliger J, Denner MM, Küspert J, Frison R, Wang Q, Morawietz A, Ivashko O, Dippel AC, Zimmermann MV, Biało I, Martinelli L, Fauqué B, Choi J, Garcia-Fernandez M, Zhou KJ, Christensen NB, Kurosawa T, Momono N, Oda M, Natterer FD, Fischer MH, Neupert T, Chang J. Weak signal extraction enabled by deep neural network denoising of diffraction data. NAT MACH INTELL 2024; 6:180-186. [PMID: 38404481 PMCID: PMC10883886 DOI: 10.1038/s42256-024-00790-1] [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: 08/26/2022] [Accepted: 01/08/2024] [Indexed: 02/27/2024]
Abstract
The removal or cancellation of noise has wide-spread applications in imaging and acoustics. In applications in everyday life, such as image restoration, denoising may even include generative aspects, which are unfaithful to the ground truth. For scientific use, however, denoising must reproduce the ground truth accurately. Denoising scientific data is further challenged by unknown noise profiles. In fact, such data will often include noise from multiple distinct sources, which substantially reduces the applicability of simulation-based approaches. Here we show how scientific data can be denoised by using a deep convolutional neural network such that weak signals appear with quantitative accuracy. In particular, we study X-ray diffraction and resonant X-ray scattering data recorded on crystalline materials. We demonstrate that weak signals stemming from charge ordering, insignificant in the noisy data, become visible and accurate in the denoised data. This success is enabled by supervised training of a deep neural network with pairs of measured low- and high-noise data. We additionally show that using artificial noise does not yield such quantitatively accurate results. Our approach thus illustrates a practical strategy for noise filtering that can be applied to challenging acquisition problems.
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Affiliation(s)
- Jens Oppliger
- Physik-Institut, Universität Zürich, Zurich, Switzerland
| | | | - Julia Küspert
- Physik-Institut, Universität Zürich, Zurich, Switzerland
| | - Ruggero Frison
- Physik-Institut, Universität Zürich, Zurich, Switzerland
| | - Qisi Wang
- Physik-Institut, Universität Zürich, Zurich, Switzerland
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Oleh Ivashko
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | | | | | - Izabela Biało
- Physik-Institut, Universität Zürich, Zurich, Switzerland
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Krakow, Poland
| | | | - Benoît Fauqué
- JEIP, USR 3573 CNRS, Collège de France, PSL University, Paris, France
| | | | | | | | | | - Tohru Kurosawa
- Department of Physics, Hokkaido University, Sapporo, Japan
| | - Naoki Momono
- Department of Physics, Hokkaido University, Sapporo, Japan
- Department of Applied Sciences, Muroran Institute of Technology, Muroran, Japan
| | - Migaku Oda
- Department of Physics, Hokkaido University, Sapporo, Japan
| | | | | | - Titus Neupert
- Physik-Institut, Universität Zürich, Zurich, Switzerland
| | - Johan Chang
- Physik-Institut, Universität Zürich, Zurich, Switzerland
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3
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Hasan N, Driban M, Mohammed AR, Schwarz S, Yoosuf S, Barthelmes D, Vupparaboina KK, Al-Sheikh M, Chhablani J. Effects of hydroxychloroquine therapy on choroidal volume and choroidal vascularity index. Eye (Lond) 2024; 38:620-624. [PMID: 37770532 PMCID: PMC10858202 DOI: 10.1038/s41433-023-02747-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: 01/18/2023] [Revised: 08/09/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023] Open
Abstract
PURPOSE To determine changes in choroidal volume (CV) and choroidal vascularity index (CVI) in patients on hydroxychloroquine (HCQ) therapy. METHODS Retrospective analysis of patients on HCQ therapy. CV and CVI were assessed below the central foveal region on spectral-domain optical coherence tomography using an automatic denoising and localization algorithm. CV and CVI were compared with age-matched controls. Regression analyses were performed to generate associations between CV and CVI with demographics and HCQ treatment parameters. Associations were assessed using a generalized estimating equation model adjusted for intra-subject inter-eye correlations. RESULTS A total of 137 adult patients (23 males and 114 females) were included. Mean age was 45.6 ± 13.7 years and most patients identified as Caucasian (79%). Total duration of HCQ therapy ranged from 3 months to 20 years. Daily HCQ intake varied from 150-600 mg (mean = 304 mg), while cumulative doses ranged from 18-2,800 g. At presentation, the median CV was 0.51 (IQR:0.356-0.747) mm, and median CVI was 0.559 (IQR:0.528-0.578). Increased cumulative HCQ dose was associated with decreased CV (p = 0.006). Compared to age-matched controls, CV, CVI, and luminal area were significantly lower in the study group (p = 0.0003, 0.0001, and 0.0002). CONCLUSION In this study, we present a novel analysis of key biomarkers which predate the occurrence of HCQ retinopathy. Choroidal volume and vascularity index are significantly reduced in patients on HCQ therapy, especially at higher cumulative doses. These findings suggest new tools to guide medical decision-making for patients receiving HCQ therapy for rheumatologic diseases.
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Affiliation(s)
- Nasiq Hasan
- Dr. Agarwal's Eye Hospital, Tirunelveli, Tamil Nadu, India
| | - Matthew Driban
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Swen Schwarz
- University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Shakira Yoosuf
- Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | | | - Mayss Al-Sheikh
- University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jay Chhablani
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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4
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Yew CL, Tsuchimatsu T, Shimizu-Inatsugi R, Yasuda S, Hatakeyama M, Kakui H, Ohta T, Suwabe K, Watanabe M, Takayama S, Shimizu KK. Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility. Nat Commun 2023; 14:7618. [PMID: 38030610 PMCID: PMC10687001 DOI: 10.1038/s41467-023-43275-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
The evolutionary transition to self-compatibility facilitates polyploid speciation. In Arabidopsis relatives, the self-incompatibility system is characterized by epigenetic dominance modifiers, among which small RNAs suppress the expression of a recessive SCR/SP11 haplogroup. Although the contribution of dominance to polyploid self-compatibility is speculated, little functional evidence has been reported. Here we employ transgenic techniques to the allotetraploid plant A. kamchatica. We find that when the dominant SCR-B is repaired by removing a transposable element insertion, self-incompatibility is restored. This suggests that SCR was responsible for the evolution of self-compatibility. By contrast, the reconstruction of recessive SCR-D cannot restore self-incompatibility. These data indicate that the insertion in SCR-B conferred dominant self-compatibility to A. kamchatica. Dominant self-compatibility supports the prediction that dominant mutations increasing selfing rate can pass through Haldane's sieve against recessive mutations. The dominance regulation between subgenomes inherited from progenitors contrasts with previous studies on novel epigenetic mutations at polyploidization termed genome shock.
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Grants
- JPMJCR16O3 MEXT | JST | Core Research for Evolutional Science and Technology (CREST)
- 310030_212551, 31003A_182318, 31003A_159767, 31003A_140917, 310030_212674 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- 310030_212674 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- grant numbers 16H06469, 16K21727, 22H02316, 22K21352, 22H05172 and 22H05179 MEXT | Japan Society for the Promotion of Science (JSPS)
- Postdoctoral fellowship, 22K21352, 16H06467 and 17H05833 MEXT | Japan Society for the Promotion of Science (JSPS)
- 21H02162, 22H05172 and 22H05179 MEXT | Japan Society for the Promotion of Science (JSPS)
- 21H04711 and 21H05030 MEXT | Japan Society for the Promotion of Science (JSPS)
- URPP Evolutoin in Action, Global Strategy and Partnerships Funding Scheme Universität Zürich (University of Zurich)
- URPP Evolutoini in Action Universität Zürich (University of Zurich)
- fellowship European Molecular Biology Organization (EMBO)
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Affiliation(s)
- Chow-Lih Yew
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Takashi Tsuchimatsu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
- Department of Biological Sciences, University of Tokyo, Tokyo, 113-0033, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Shinsuke Yasuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
- Functional Genomics Center Zurich, 8057, Zurich, Switzerland
| | - Hiroyuki Kakui
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
- Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, University of Tokyo, Nishitokyo, 188-0002, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Takuma Ohta
- Graduate School of Bioresources, Mie University, Tsu, 514-0102, Japan
| | - Keita Suwabe
- Graduate School of Bioresources, Mie University, Tsu, 514-0102, Japan
| | - Masao Watanabe
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Seiji Takayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
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5
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Heinze SD, Berger S, Engleitner S, Daube M, Hajnal A. Prolonging somatic cell proliferation through constitutive hox gene expression in C. elegans. Nat Commun 2023; 14:6850. [PMID: 37891160 PMCID: PMC10611754 DOI: 10.1038/s41467-023-42644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
hox genes encode a conserved family of homeodomain transcription factors that are essential to determine the identity of body segments during embryogenesis and maintain adult somatic stem cells competent to regenerate organs. In contrast to higher organisms, somatic cells in C. elegans irreversibly exit the cell cycle after completing their cell lineage and the adult soma cannot regenerate. Here, we show that hox gene expression levels in C. elegans determine the temporal competence of somatic cells to proliferate. Down-regulation of the central hox gene lin-39 in dividing vulval cells results in their premature cell cycle exit, whereas constitutive lin-39 expression causes precocious Pn.p cell and sex myoblast divisions and prolongs the proliferative phase of the vulval cells past their normal point of arrest. Furthermore, ectopic expression of hox genes in the quiescent anchor cell re-activates the cell cycle and induces proliferation until young adulthood. Thus, constitutive expression of a single hox transcription factor is sufficient to prolong somatic cell proliferation beyond the restriction imposed by the cell lineage. The down-regulation of hox gene expression in most somatic cells at the end of larval development may be one cause for the absence of cell proliferation in adult C. elegans.
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Affiliation(s)
- Svenia D Heinze
- Department of Molecular Life Sciences, University Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Molecular Life Science PhD Program, University and ETH Zürich, CH-8057, Zürich, Switzerland
| | - Simon Berger
- Department of Molecular Life Sciences, University Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Institute for Chemical- and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093, Zürich, Switzerland
| | - Stefanie Engleitner
- Department of Molecular Life Sciences, University Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Molecular Life Science PhD Program, University and ETH Zürich, CH-8057, Zürich, Switzerland
| | - Michael Daube
- Department of Molecular Life Sciences, University Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Alex Hajnal
- Department of Molecular Life Sciences, University Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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6
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Remm S, De Vecchis D, Schöppe J, Hutter CAJ, Gonda I, Hohl M, Newstead S, Schäfer LV, Seeger MA. Structural basis for triacylglyceride extraction from mycobacterial inner membrane by MFS transporter Rv1410. Nat Commun 2023; 14:6449. [PMID: 37833269 PMCID: PMC10576003 DOI: 10.1038/s41467-023-42073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Mycobacterium tuberculosis is protected from antibiotic therapy by a multi-layered hydrophobic cell envelope. Major facilitator superfamily (MFS) transporter Rv1410 and the periplasmic lipoprotein LprG are involved in transport of triacylglycerides (TAGs) that seal the mycomembrane. Here, we report a 2.7 Å structure of a mycobacterial Rv1410 homologue, which adopts an outward-facing conformation and exhibits unusual transmembrane helix 11 and 12 extensions that protrude ~20 Å into the periplasm. A small, very hydrophobic cavity suitable for lipid transport is constricted by a functionally important ion-lock likely involved in proton coupling. Combining mutational analyses and MD simulations, we propose that TAGs are extracted from the core of the inner membrane into the central cavity via lateral clefts present in the inward-facing conformation. The functional role of the periplasmic helix extensions is to channel the extracted TAG into the lipid binding pocket of LprG.
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Affiliation(s)
- Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany
| | - Jendrik Schöppe
- Institute of Biochemistry, University of Zurich, Zürich, Switzerland
- Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
- Linkster Therapeutics, Zürich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland.
- National Center for Mycobacteria, Zurich, Switzerland.
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7
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Akiyama R, Goto T, Tameshige T, Sugisaka J, Kuroki K, Sun J, Akita J, Hatakeyama M, Kudoh H, Kenta T, Tonouchi A, Shimahara Y, Sese J, Kutsuna N, Shimizu-Inatsugi R, Shimizu KK. Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. Nat Commun 2023; 14:5792. [PMID: 37737204 PMCID: PMC10517152 DOI: 10.1038/s41467-023-41260-3] [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: 11/04/2022] [Accepted: 08/29/2023] [Indexed: 09/23/2023] Open
Abstract
Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed "in natura".
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Takao Goto
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192, Japan
| | - Jiro Sugisaka
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Ken Kuroki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8517, Japan
| | - Junichi Akita
- Department of Electric and Computer Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-kogen, Ueda, 386-2204, Japan
| | - Aya Tonouchi
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yuki Shimahara
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Humanome Lab, Inc., L-HUB 3F, 1-4, Shumomiyabi-cho, Shinjuku, Tokyo, 162-0822, Japan
- AIST-Tokyo Tech RWBC-OIL, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Natsumaro Kutsuna
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan.
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8
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Woods JF, Gallego L, Maisch A, Renggli D, Cuocci C, Blacque O, Steinfeld G, Kaech A, Spingler B, Vargas Jentzsch A, Rickhaus M. Saddles as rotational locks within shape-assisted self-assembled nanosheets. Nat Commun 2023; 14:4725. [PMID: 37550281 PMCID: PMC10406840 DOI: 10.1038/s41467-023-40475-8] [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: 04/05/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023] Open
Abstract
Two-dimensional (2D) materials are a key target for many applications in the modern day. Self-assembly is one approach that can bring us closer to this goal, which usually relies upon strong, directional interactions instead of covalent bonds. Control over less directional forces is more challenging and usually does not result in as well-defined materials. Explicitly incorporating topography into the design as a guiding effect to enhance the interacting forces can help to form highly ordered structures. Herein, we show the process of shape-assisted self-assembly to be consistent across a range of derivatives that highlights the restriction of rotational motion and is verified using a diverse combination of solid state analyses. A molecular curvature governed angle distribution nurtures monomers into loose columns that then arrange to form 2D structures with long-range order observed in both crystalline and soft materials. These features strengthen the idea that shape becomes an important design principle leading towards precise molecular self-assembly and the inception of new materials.
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Affiliation(s)
- Joseph F Woods
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Lucía Gallego
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Amira Maisch
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Dominik Renggli
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Corrado Cuocci
- Institute of Crystallography, CNR, Via Amendola, 122/O, 70126, Bari, Italy
| | - Olivier Blacque
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | | | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, 8057, Zurich, Switzerland
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Andreas Vargas Jentzsch
- SAMS Research Group, University of Strasbourg, Institut Charles Sadron, CNRS, 67200, Strasbourg, France
| | - Michel Rickhaus
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
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9
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Zanoni P, Steindl K, Sticht H, Oneda B, Joset P, Ivanovski I, Horn AHC, Cabello EM, Laube J, Zweier M, Baumer A, Rauch A, Khan N. The genetic landscape and clinical implication of pediatric Moyamoya angiopathy in an international cohort. Eur J Hum Genet 2023; 31:784-792. [PMID: 37012328 PMCID: PMC10325976 DOI: 10.1038/s41431-023-01320-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 04/05/2023] Open
Abstract
Pediatric Moyamoya Angiopathy (MMA) is a progressive intracranial occlusive arteriopathy that represents a leading cause of transient ischemic attacks and strokes in childhood. Despite this, up to now no large, exclusively pediatric MMA cohort has been subjected to systematic genetic investigation. In this study, we performed molecular karyotyping, exome sequencing and automated structural assessment of missense variants on a series of 88 pediatric MMA patients and correlated genetic, angiographic and clinical (stroke burden) findings. The two largest subgroups in our cohort consisted of RNF213 and neurofibromatosis type 1 (NF1) patients. While deleterious RNF213 variants were associated with a severe MMA clinical course with early symptom onset, frequent posterior cerebral artery involvement and higher stroke rates in multiple territories, NF1 patients had a similar infarct burden compared to non-NF1 individuals and were often diagnosed incidentally during routine MRIs. Additionally, we found that MMA-associated RNF213 variants have lower predicted functional impact compared to those associated with aortic disease. We also raise the question of MMA as a feature of recurrent as well as rare chromosomal imbalances and further support the possible association of MMA with STAT3 deficiency. In conclusion, we provide a comprehensive characterization at the genetic and clinical level of a large exclusively pediatric MMA population. Due to the clinical differences found across genetic subgroups, we propose genetic testing for risk stratification as part of the routine assessment of pediatric MMA patients.
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Affiliation(s)
- Paolo Zanoni
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland.
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Elena M Cabello
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Julia Laube
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland.
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, 8000, Switzerland.
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8000, Switzerland.
- Moyamoya Center, University Children's Hospital, University of Zurich, Zurich, 8032, Switzerland.
| | - Nadia Khan
- Moyamoya Center, University Children's Hospital, University of Zurich, Zurich, 8032, Switzerland.
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10
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Zurbuchen Y, Michler J, Taeschler P, Adamo S, Cervia C, Raeber ME, Acar IE, Nilsson J, Warnatz K, Soyka MB, Moor AE, Boyman O. Human memory B cells show plasticity and adopt multiple fates upon recall response to SARS-CoV-2. Nat Immunol 2023; 24:955-965. [PMID: 37106039 PMCID: PMC10232369 DOI: 10.1038/s41590-023-01497-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
The B cell response to different pathogens uses tailored effector mechanisms and results in functionally specialized memory B (Bm) cell subsets, including CD21+ resting, CD21-CD27+ activated and CD21-CD27- Bm cells. The interrelatedness between these Bm cell subsets remains unknown. Here we showed that single severe acute respiratory syndrome coronavirus 2-specific Bm cell clones showed plasticity upon antigen rechallenge in previously exposed individuals. CD21- Bm cells were the predominant subsets during acute infection and early after severe acute respiratory syndrome coronavirus 2-specific immunization. At months 6 and 12 post-infection, CD21+ resting Bm cells were the major Bm cell subset in the circulation and were also detected in peripheral lymphoid organs, where they carried tissue residency markers. Tracking of individual B cell clones by B cell receptor sequencing revealed that previously fated Bm cell clones could redifferentiate upon antigen rechallenge into other Bm cell subsets, including CD21-CD27- Bm cells, demonstrating that single Bm cell clones can adopt functionally different trajectories.
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Affiliation(s)
- Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Jan Michler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Klaus Warnatz
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael B Soyka
- Department of Otorhinolaryngology, Head and Neck Surgery, University and University Hospital Zurich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland.
- Faculty of Medicine and Faculty of Science, University of Zurich, Zurich, Switzerland.
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11
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Lysenko V, Schürch PM, Tuzlak S, van Wijk NWV, Kovtonyuk LV, Becher B, Manz MG, Kreutmair S, Theocharides APA. Blocking the CD47-SIRPα interaction reverses the disease phenotype in a polycythemia vera mouse model. Leukemia 2023:10.1038/s41375-023-01903-2. [PMID: 37095207 DOI: 10.1038/s41375-023-01903-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
Polycythemia vera (PV) is a hematopoietic stem cell neoplasm driven by somatic mutations in JAK2, leading to increased red blood cell (RBC) production uncoupled from mechanisms that regulate physiological erythropoiesis. At steady-state, bone marrow macrophages promote erythroid maturation, whereas splenic macrophages phagocytose aged or damaged RBCs. The binding of the anti-phagocytic ("don't eat me") CD47 ligand expressed on RBCs to the SIRPα receptor on macrophages inhibits phagocytic activity protecting RBCs from phagocytosis. In this study, we explore the role of the CD47-SIRPα interaction on the PV RBC life cycle. Our results show that blocking CD47-SIRPα in a PV mouse model due to either anti-CD47 treatment or loss of the inhibitory SIRPα-signal corrects the polycythemia phenotype. Anti-CD47 treatment marginally impacted PV RBC production while not influencing erythroid maturation. However, upon anti-CD47 treatment, high-parametric single-cell cytometry identified an increase of MerTK+ splenic monocyte-derived effector cells, which differentiate from Ly6Chi monocytes during inflammatory conditions, acquire an inflammatory phagocytic state. Furthermore, in vitro, functional assays showed that splenic JAK2 mutant macrophages were more "pro-phagocytic," suggesting that PV RBCs exploit the CD47-SIRPα interaction to escape innate immune attacks by clonal JAK2 mutant macrophages.
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Affiliation(s)
- Veronika Lysenko
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Patrick M Schürch
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Selma Tuzlak
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Nicole Wildner-Verhey van Wijk
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Larisa V Kovtonyuk
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Stefanie Kreutmair
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Alexandre P A Theocharides
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland.
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12
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Wu Y, Bottes S, Fisch R, Zehnder C, Cole JD, Pilz GA, Helmchen F, Simons BD, Jessberger S. Chronic in vivo imaging defines age-dependent alterations of neurogenesis in the mouse hippocampus. Nat Aging 2023; 3:380-390. [PMID: 37117787 PMCID: PMC10154232 DOI: 10.1038/s43587-023-00370-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/20/2023] [Indexed: 04/30/2023]
Abstract
Neural stem cells (NSCs) generate new neurons throughout life in the mammalian hippocampus1. Advancing age leads to a decline in neurogenesis, which is associated with impaired cognition2,3. The cellular mechanisms causing reduced neurogenesis with advancing age remain largely unknown. We genetically labeled NSCs through conditional recombination driven by the regulatory elements of the stem-cell-expressed gene GLI family zinc finger 1 (Gli1) and used chronic intravital imaging to follow individual NSCs and their daughter cells over months within their hippocampal niche4,5. We show that aging affects multiple steps, from cell cycle entry of quiescent NSCs to determination of the number of surviving cells, ultimately causing reduced clonal output of individual NSCs. Thus, we here define the developmental stages that may be targeted to enhance neurogenesis with the aim of maintaining hippocampal plasticity with advancing age.
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Affiliation(s)
- Yicheng Wu
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Sara Bottes
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Roberto Fisch
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Cinzia Zehnder
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - John Darby Cole
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Gregor-Alexander Pilz
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
- BioMedical Center, Department of Cell Biology and Anatomy, Ludwig Maximilians University, Planegg-Martinsried, Germany
| | - Fritjof Helmchen
- Laboratory of Neural Circuit Dynamics, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Benjamin D Simons
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland.
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13
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Götz M, Barth A, Bohr SSR, Börner R, Chen J, Cordes T, Erie DA, Gebhardt C, Hadzic MCAS, Hamilton GL, Hatzakis NS, Hugel T, Kisley L, Lamb DC, de Lannoy C, Mahn C, Dunukara D, de Ridder D, Sanabria H, Schimpf J, Seidel CAM, Sigel RKO, Sletfjerding MB, Thomsen J, Vollmar L, Wanninger S, Weninger KR, Xu P, Schmid S. A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories. Nat Commun 2022; 13:5402. [PMID: 36104339 PMCID: PMC9474500 DOI: 10.1038/s41467-022-33023-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 03/20/2022] [Accepted: 08/30/2022] [Indexed: 01/04/2023] Open
Abstract
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We test them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise levels, varied model complexity, non-equilibrium dynamics, and kinetic heterogeneity. Our results highlight the current strengths and limitations in inferring kinetic information from smFRET trajectories. In addition, we formulate concrete recommendations and identify key targets for future developments, aimed to advance our understanding of biomolecular dynamics through quantitative experiment-derived models.
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Affiliation(s)
- Markus Götz
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
- PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany.
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Richard Börner
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
- Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, 09648, Mittweida, Germany
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, USA
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | | | - George L Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Don C Lamb
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Carlos de Lannoy
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Chelsea Mahn
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dushani Dunukara
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Julia Schimpf
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Magnus Berg Sletfjerding
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Leonie Vollmar
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Simon Wanninger
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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14
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Duffet L, Kosar S, Panniello M, Viberti B, Bracey E, Zych AD, Radoux-Mergault A, Zhou X, Dernic J, Ravotto L, Tsai YC, Figueiredo M, Tyagarajan SK, Weber B, Stoeber M, Gogolla N, Schmidt MH, Adamantidis AR, Fellin T, Burdakov D, Patriarchi T. A genetically encoded sensor for in vivo imaging of orexin neuropeptides. Nat Methods 2022; 19:231-241. [PMID: 35145320 PMCID: PMC8831244 DOI: 10.1038/s41592-021-01390-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 04/28/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023]
Abstract
Orexins (also called hypocretins) are hypothalamic neuropeptides that carry out essential functions in the central nervous system; however, little is known about their release and range of action in vivo owing to the limited resolution of current detection technologies. Here we developed a genetically encoded orexin sensor (OxLight1) based on the engineering of circularly permutated green fluorescent protein into the human type-2 orexin receptor. In mice OxLight1 detects optogenetically evoked release of endogenous orexins in vivo with high sensitivity. Photometry recordings of OxLight1 in mice show rapid orexin release associated with spontaneous running behavior, acute stress and sleep-to-wake transitions in different brain areas. Moreover, two-photon imaging of OxLight1 reveals orexin release in layer 2/3 of the mouse somatosensory cortex during emergence from anesthesia. Thus, OxLight1 enables sensitive and direct optical detection of orexin neuropeptides with high spatiotemporal resolution in living animals.
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Affiliation(s)
- Loïc Duffet
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Seher Kosar
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Mariangela Panniello
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Bianca Viberti
- Center for Experimental Neurology (ZEN), Department of Neurology, Inselspital University Hospital Bern, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Edward Bracey
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Anna D Zych
- Circuits for Emotion Research Group, Max Planck Institute of Neurobiology, Martinsried, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | | | - Xuehan Zhou
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Jan Dernic
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Luca Ravotto
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Yuan-Chen Tsai
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Marta Figueiredo
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Shiva K Tyagarajan
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Bruno Weber
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Miriam Stoeber
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Nadine Gogolla
- Circuits for Emotion Research Group, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Markus H Schmidt
- Center for Experimental Neurology (ZEN), Department of Neurology, Inselspital University Hospital Bern, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Antoine R Adamantidis
- Center for Experimental Neurology (ZEN), Department of Neurology, Inselspital University Hospital Bern, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Tommaso Fellin
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Denis Burdakov
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Tommaso Patriarchi
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland.
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15
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Ng KKS, Kobayashi MJ, Fawcett JA, Hatakeyama M, Paape T, Ng CH, Ang CC, Tnah LH, Lee CT, Nishiyama T, Sese J, O'Brien MJ, Copetti D, Isa MNM, Ong RC, Putra M, Siregar IZ, Indrioko S, Kosugi Y, Izuno A, Isagi Y, Lee SL, Shimizu KK. The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Commun Biol 2021; 4:1166. [PMID: 34620991 PMCID: PMC8497594 DOI: 10.1038/s42003-021-02682-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/12/2020] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.
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Affiliation(s)
- Kevin Kit Siong Ng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Masaki J Kobayashi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Jeffrey A Fawcett
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
- RIKEN iTHEMS, Wako, Saitama, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Timothy Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Choon Cheng Ang
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Tomoaki Nishiyama
- Division of Integrated Omics research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-Tokyo Tech RWBC-OIL, Meguro-ku, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Michael J O'Brien
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/Tulipán s/n., E-28933, Móstoles, Spain
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Mahardika Putra
- Faculty of Forestry, Bogor Agricultural University, Bogor, Indonesia
| | | | - Sapto Indrioko
- Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia
| | - Yoshiko Kosugi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ayako Izuno
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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16
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Fröhlich M, Bartolotta N, Fryns C, Wagner C, Momon L, Jaffrezic M, Mitra Setia T, van Noordwijk MA, van Schaik CP. Multicomponent and multisensory communicative acts in orang-utans may serve different functions. Commun Biol 2021; 4:917. [PMID: 34316012 PMCID: PMC8316500 DOI: 10.1038/s42003-021-02429-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 12/07/2020] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
From early infancy, human face-to-face communication is multimodal, comprising a plethora of interlinked communicative and sensory modalities. Although there is also growing evidence for this in nonhuman primates, previous research rarely disentangled production from perception of signals. Consequently, the functions of integrating articulators (i.e. production organs involved in multicomponent acts) and sensory channels (i.e. modalities involved in multisensory acts) remain poorly understood. Here, we studied close-range social interactions within and beyond mother-infant pairs of Bornean and Sumatran orang-utans living in wild and captive settings, to examine use of and responses to multicomponent and multisensory communication. From the perspective of production, results showed that multicomponent acts were used more than the respective unicomponent acts when the presumed goal did not match the dominant outcome for a specific communicative act, and were more common among non-mother-infant dyads and Sumatran orang-utans. From the perception perspective, we found that multisensory acts were more effective than the respective unisensory acts, and were used more in wild compared to captive populations. We argue that multisensory acts primarily facilitate effectiveness, whereas multicomponent acts become relevant when interaction outcomes are less predictable. These different functions underscore the importance of distinguishing between production and perception in studies of communication.
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Affiliation(s)
- Marlen Fröhlich
- Department of Anthropology, University of Zurich, Zurich, Switzerland.
| | | | - Caroline Fryns
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Colin Wagner
- DEPE-IPHC - Département Ecologie, Physiologie et Ethologie, University of Strasbourg, Strasbourg, France
| | - Laurene Momon
- DEPE-IPHC - Département Ecologie, Physiologie et Ethologie, University of Strasbourg, Strasbourg, France
| | - Marvin Jaffrezic
- DEPE-IPHC - Département Ecologie, Physiologie et Ethologie, University of Strasbourg, Strasbourg, France
| | | | | | - Carel P van Schaik
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zurich, Zurich, Switzerland
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17
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Läubli NF, Burri JT, Marquard J, Vogler H, Mosca G, Vertti-Quintero N, Shamsudhin N, deMello A, Grossniklaus U, Ahmed D, Nelson BJ. 3D mechanical characterization of single cells and small organisms using acoustic manipulation and force microscopy. Nat Commun 2021; 12:2583. [PMID: 33972516 PMCID: PMC8110787 DOI: 10.1038/s41467-021-22718-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 05/23/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Quantitative micromechanical characterization of single cells and multicellular tissues or organisms is of fundamental importance to the study of cellular growth, morphogenesis, and cell-cell interactions. However, due to limited manipulation capabilities at the microscale, systems used for mechanical characterizations struggle to provide complete three-dimensional coverage of individual specimens. Here, we combine an acoustically driven manipulation device with a micro-force sensor to freely rotate biological samples and quantify mechanical properties at multiple regions of interest within a specimen. The versatility of this tool is demonstrated through the analysis of single Lilium longiflorum pollen grains, in combination with numerical simulations, and individual Caenorhabditis elegans nematodes. It reveals local variations in apparent stiffness for single specimens, providing previously inaccessible information and datasets on mechanical properties that serve as the basis for biophysical modelling and allow deeper insights into the biomechanics of these living systems.
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Affiliation(s)
- Nino F Läubli
- Multi-Scale Robotics Lab, ETH Zurich, Zurich, Switzerland
| | - Jan T Burri
- Multi-Scale Robotics Lab, ETH Zurich, Zurich, Switzerland
| | | | - Hannes Vogler
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Gabriella Mosca
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Nadia Vertti-Quintero
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich, Switzerland
| | | | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Daniel Ahmed
- Multi-Scale Robotics Lab, ETH Zurich, Zurich, Switzerland.
- Acoustic Robotics Systems Lab, ETH Zurich, Rüschlikon, Switzerland.
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18
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Borrelli C, Valenta T, Handler K, Vélez K, Gurtner A, Moro G, Lafzi A, Roditi LDV, Hausmann G, Arnold IC, Moor AE, Basler K. Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells. Nat Commun 2021; 12:1368. [PMID: 33649334 PMCID: PMC7921392 DOI: 10.1038/s41467-021-21591-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/14/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The homeostasis of the gut epithelium relies upon continuous renewal and proliferation of crypt-resident intestinal epithelial stem cells (IESCs). Wnt/β-catenin signaling is required for IESC maintenance, however, it remains unclear how this pathway selectively governs the identity and proliferative decisions of IESCs. Here, we took advantage of knock-in mice harboring transgenic β-catenin alleles with mutations that specifically impair the recruitment of N- or C-terminal transcriptional co-factors. We show that C-terminally-recruited transcriptional co-factors of β-catenin act as all-or-nothing regulators of Wnt-target gene expression. Blocking their interactions with β-catenin rapidly induces loss of IESCs and intestinal homeostasis. Conversely, N-terminally recruited co-factors fine-tune β-catenin's transcriptional output to ensure proper self-renewal and proliferative behaviour of IESCs. Impairment of N-terminal interactions triggers transient hyperproliferation of IESCs, eventually resulting in exhaustion of the self-renewing stem cell pool. IESC mis-differentiation, accompanied by unfolded protein response stress and immune infiltration, results in a process resembling aberrant "villisation" of intestinal crypts. Our data suggest that IESC-specific Wnt/β-catenin output requires selective modulation of gene expression by transcriptional co-factors.
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Affiliation(s)
- Costanza Borrelli
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Tomas Valenta
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, 4, Czech Republic.
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Karelia Vélez
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Alessandra Gurtner
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Giulia Moro
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Atefeh Lafzi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - George Hausmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Isabelle C Arnold
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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19
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Abstract
The anion channel TMEM16A is activated by intracellular Ca2+ in a highly cooperative process. By combining electrophysiology and autocorrelation analysis, we investigated the mechanism of channel activation and the concurrent rearrangement of the gate in the narrow part of the pore. Features in the fluctuation characteristics of steady-state current indicate the sampling of intermediate conformations that are successively occupied during gating. The initial step is related to conformational changes induced by Ca2+ binding, which is ensued by rearrangements that open the pore. Mutations in the gate shift the equilibrium of transitions in a manner consistent with a progressive destabilization of this region during pore opening. We come up with a mechanism of channel activation where the binding of Ca2+ induces conformational changes in the protein that, in a sequential manner, propagate from the binding site and couple to the gate in the narrow pore to allow ion permeation.
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Affiliation(s)
- Andy K M Lam
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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20
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Abstract
The binding of cytoplasmic Ca2+ to the anion-selective channel TMEM16A triggers a conformational change around its binding site that is coupled to the release of a gate at the constricted neck of an hourglass-shaped pore. By combining mutagenesis, electrophysiology, and cryo-electron microscopy, we identified three hydrophobic residues at the intracellular entrance of the neck as constituents of this gate. Mutation of each of these residues increases the potency of Ca2+ and results in pronounced basal activity. The structure of an activating mutant shows a conformational change of an α-helix that contributes to Ca2+ binding as a likely cause for the basal activity. Although not in physical contact, the three residues are functionally coupled to collectively contribute to the stabilization of the gate in the closed conformation of the pore, thus explaining the low open probability of the channel in the absence of Ca2+.
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Affiliation(s)
- Andy K M Lam
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Jan Rheinberger
- Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands.
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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21
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Yde Ohki CM, Grossmann L, Alber E, Dwivedi T, Berger G, Werling AM, Walitza S, Grünblatt E. The stress-Wnt-signaling axis: a hypothesis for attention-deficit hyperactivity disorder and therapy approaches. Transl Psychiatry 2020; 10:315. [PMID: 32948744 PMCID: PMC7501308 DOI: 10.1038/s41398-020-00999-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 12/27/2022] Open
Abstract
Attention-deficit hyperactivity disorder (ADHD) is one of the most common psychiatric neurodevelopmental disorders in children and adolescents. Although ADHD has been studied for nearly a century, the cause and pathophysiology of ADHD is yet largely unknown. However, findings from previous studies have resulted in the formation of a new hypothesis: Apart from the well-known multifactorial etiology of ADHD, recent evidence suggests that the interaction between genetic and environmental factors and especially Wnt- and mTOR-signaling pathways might have an important role in the pathophysiology of ADHD. The Wnt-signaling pathway is known to orchestrate cellular proliferation, polarity, and differentiation, and the mTOR pathway is involved in several significant processes of neurodevelopment and synaptic plasticity. As a result, dysregulations of these pathways in a time-dependent manner could lead to neurodevelopmental delays, resulting in ADHD phenotype. This review presents further evidence supporting our hypothesis by combining results from studies on ADHD and Wnt- or mTOR-signaling and the influence of genetics, methylphenidate treatment, Omega-3 supplementation, and stress.
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Affiliation(s)
- Cristine Marie Yde Ohki
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
| | - Leoni Grossmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
| | - Emma Alber
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
| | - Tanushree Dwivedi
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
| | - Gregor Berger
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
| | - Anna Maria Werling
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zürich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zürich, Switzerland.
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zürich, Switzerland.
- Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland.
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22
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Schorer M, Lambert K, Rakebrandt N, Rost F, Kao KC, Yermanos A, Spörri R, Oderbolz J, Raeber ME, Keller CW, Lünemann JD, Rogler G, Boyman O, Oxenius A, Joller N. Rapid expansion of Treg cells protects from collateral colitis following a viral trigger. Nat Commun 2020; 11:1522. [PMID: 32251280 PMCID: PMC7090079 DOI: 10.1038/s41467-020-15309-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 03/29/2019] [Accepted: 02/28/2020] [Indexed: 12/12/2022] Open
Abstract
Foxp3+ regulatory T (Treg) cells are essential for maintaining peripheral tolerance and preventing autoimmunity. While genetic factors may predispose for autoimmunity, additional environmental triggers, such as viral infections, are usually required to initiate the onset of disease. Here, we show that viral infection with LCMV results in type I IFN-dependent Treg cell loss that is rapidly compensated by the conversion and expansion of Vβ5+ conventional T cells into iTreg cells. Using Vβ5-deficient mice, we show that these Vβ5+ iTreg cells are dispensable for limiting anti-viral immunity. Rather, the delayed replenishment of Treg cells in Vβ5-deficient mice compromises suppression of microbiota-dependent activation of CD8+ T cells, resulting in colitis. Importantly, recovery from clinical symptoms in IBD patients is marked by expansion of the corresponding Vβ2+ Treg population in humans. Collectively, we provide a link between a viral trigger and an impaired Treg cell compartment resulting in the initiation of immune pathology.
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Affiliation(s)
- Michelle Schorer
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Katharina Lambert
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Nikolas Rakebrandt
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Felix Rost
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Kung-Chi Kao
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alexander Yermanos
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Laboratory for Systems and Synthetic Immunology, D-BSSE, ETH Zurich, 4058, Basel, Switzerland
| | - Roman Spörri
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Josua Oderbolz
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, Häldeliweg 4, 8044, Zurich, Switzerland
| | - Christian W Keller
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Neurology with Institute of Translational Neurology, University Hospital Munster, 48149, Munster, Germany
| | - Jan D Lünemann
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Neurology with Institute of Translational Neurology, University Hospital Munster, 48149, Munster, Germany
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Häldeliweg 4, 8044, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Pestalozzistrasse 3/5, 8091, Zurich, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Nicole Joller
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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