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Bestsennaia E, Maslov I, Balandin T, Alekseev A, Yudenko A, Abu Shamseye A, Zabelskii D, Baumann A, Catapano C, Karathanasis C, Gordeliy V, Heilemann M, Gensch T, Borshchevskiy V. Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy. Angew Chem Int Ed Engl 2024; 63:e202307555. [PMID: 38226794 DOI: 10.1002/anie.202307555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2 . Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
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Affiliation(s)
- Ekaterina Bestsennaia
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Maslov
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and the Biomedical Research Institute, Hasselt University, B3590, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Taras Balandin
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexey Alekseev
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Anna Yudenko
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Assalla Abu Shamseye
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
- European XFEL, 22869, Schenefeld, Germany
| | - Arnd Baumann
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Claudia Catapano
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
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Végh EI, Douka K. SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. Bioinformatics 2024; 40:btae054. [PMID: 38337062 PMCID: PMC10918634 DOI: 10.1093/bioinformatics/btae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/08/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data. RESULTS SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually. AVAILABILITY AND IMPLEMENTATION The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).
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Affiliation(s)
- Emese I Végh
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Archaeology, Environmental Changes, and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
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Raemen L, Claes L, Buelens T, Vankerckhoven L, Van Oudenhove L, Luyckx K. Personal identity, somatic symptoms, and symptom-related thoughts, feelings, and behaviors in adolescence: Examining between- and within-person associations and the role of depressive symptoms. J Youth Adolesc 2023:10.1007/s10964-023-01811-9. [PMID: 37329388 DOI: 10.1007/s10964-023-01811-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Recent literature highlights the complex relationship between personal identity and body-related pathology, yet there is a lack of integrative longitudinal research on the relationship between identity and somatic symptoms. The present study investigated the longitudinal associations between identity functioning and (psychological characteristics of) somatic symptoms, and examined the role of depressive symptoms in this relationship. A total of 599 community adolescents (Time 1: 41.3% female; Mage = 14.93, SD = 1.77, range = 12-18 years) participated in three annual assessments. Using cross-lagged panel models, a bidirectional relationship between identity and (psychological characteristics of) somatic symptoms, mediated by depressive symptoms, emerged at the between-person level; whereas only a unidirectional relationship from psychological characteristics of somatic symptoms to identity functioning, mediated by depressive symptoms, emerged at the within-person level. Identity and depressive symptoms were bidirectionally related at both levels. The present study suggests that adolescent identity development is closely related to somatic and emotional distress.
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Affiliation(s)
- Leni Raemen
- Faculty of Psychology and Educational Sciences, KU Leuven, Leuven, Belgium.
- Child & Youth Institute, KU Leuven, Leuven, Belgium.
| | - Laurence Claes
- Faculty of Psychology and Educational Sciences, KU Leuven, Leuven, Belgium
- Child & Youth Institute, KU Leuven, Leuven, Belgium
- Faculty of Medicine and Health Sciences (CAPRI), University of Antwerp, Antwerp, Belgium
| | - Tinne Buelens
- Department of Clinical Psychology, University of Amsterdam, Amsterdam, The Netherlands
| | - Lore Vankerckhoven
- Faculty of Psychology and Educational Sciences, KU Leuven, Leuven, Belgium
- Child & Youth Institute, KU Leuven, Leuven, Belgium
| | - Lukas Van Oudenhove
- Laboratory for Brain-Gut Axis Studies (LaBGAS), Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Cognitive and Affective Neuroscience Lab, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Koen Luyckx
- Faculty of Psychology and Educational Sciences, KU Leuven, Leuven, Belgium
- Child & Youth Institute, KU Leuven, Leuven, Belgium
- UNIBS, University of the Free State, Bloemfontein, South Africa
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Reverberi S, Dolfen N, Van Roy A, Albouy G, King BR. Sleep does not influence schema-facilitated motor memory consolidation. PLoS One 2023; 18:e0280591. [PMID: 36656898 PMCID: PMC9851548 DOI: 10.1371/journal.pone.0280591] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
STUDY OBJECTIVES Novel information is rapidly learned when it is compatible with previous knowledge. This "schema" effect, initially described for declarative memories, was recently extended to the motor memory domain. Importantly, this beneficial effect was only observed 24 hours-but not immediately-following motor schema acquisition. Given the established role of sleep in memory consolidation, we hypothesized that sleep following the initial learning of a schema is necessary for the subsequent rapid integration of novel motor information. METHODS Two experiments were conducted to investigate the effect of diurnal and nocturnal sleep on schema-mediated motor sequence memory consolidation. In Experiment 1, participants first learned an 8-element motor sequence through repeated practice (Session 1). They were then afforded a 90-minute nap opportunity (N = 25) or remained awake (N = 25) before learning a second motor sequence (Session 2) which was highly compatible with that learned prior to the sleep/wake interval. Experiment 2 was similar; however, Sessions 1 and 2 were separated by a 12-hour interval that included nocturnal sleep (N = 28) or only wakefulness (N = 29). RESULTS For both experiments, we found no group differences in motor sequence performance (reaction time and accuracy) following the sleep/wake interval. Furthermore, in Experiment 1, we found no correlation between sleep features (non-REM sleep duration, spindle and slow wave activity) and post-sleep behavioral performance. CONCLUSIONS The results of this research suggest that integration of novel motor information into a cognitive-motor schema does not specifically benefit from post-learning sleep.
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Affiliation(s)
- Serena Reverberi
- Department of Movement Sciences, Motor Control and Neural Plasticity Research Group, KU Leuven, Leuven, Belgium
- LBI—KU Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Nina Dolfen
- Department of Movement Sciences, Motor Control and Neural Plasticity Research Group, KU Leuven, Leuven, Belgium
- LBI—KU Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Anke Van Roy
- Department of Health and Kinesiology, College of Health, University of Utah, Salt Lake City, UT, United States of America
| | - Genevieve Albouy
- Department of Movement Sciences, Motor Control and Neural Plasticity Research Group, KU Leuven, Leuven, Belgium
- LBI—KU Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Department of Health and Kinesiology, College of Health, University of Utah, Salt Lake City, UT, United States of America
- * E-mail:
| | - Bradley R. King
- Department of Health and Kinesiology, College of Health, University of Utah, Salt Lake City, UT, United States of America
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Kwon YM, Vranken N, Hoge C, Lichak MR, Norovich AL, Francis KX, Camacho-Garcia J, Bista I, Wood J, McCarthy S, Chow W, Tan HH, Howe K, Bandara S, von Lintig J, Rüber L, Durbin R, Svardal H, Bendesky A. Genomic consequences of domestication of the Siamese fighting fish. Sci Adv 2022; 8:eabm4950. [PMID: 35263139 PMCID: PMC8906746 DOI: 10.1126/sciadv.abm4950] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/13/2022] [Indexed: 05/08/2023]
Abstract
Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but the genetic bases of their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced 98 individuals across five closely related species. We find evidence of bidirectional hybridization between domesticated ornamental betta and other wild Betta species. We discover dmrt1 as the main sex determination gene in ornamental betta and that it has lower penetrance in wild B. splendens. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body or on the shape of individual fins and that most are unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication and launch betta as a powerful new system for evolutionary genetics.
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Affiliation(s)
- Young Mi Kwon
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nathan Vranken
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Carla Hoge
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Madison R. Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Amy L. Norovich
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Kerel X. Francis
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | | | - Iliana Bista
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Shane McCarthy
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | | | - Sepalika Bandara
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Johannes von Lintig
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Lukas Rüber
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland
- Naturhistorisches Museum Bern, Bern 3005, Switzerland
| | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hannes Svardal
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Naturalis Biodiversity Center, 2333 Leiden, Netherlands
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
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