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Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol Cell 2024; 84:2698-2716.e9. [PMID: 39059370 DOI: 10.1016/j.molcel.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
Abstract
The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marie-Christin Spindler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Glen M Hocky
- Department of Chemistry and Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, USA.
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA.
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2
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Torello Pianale L, Caputo F, Olsson L. Four ways of implementing robustness quantification in strain characterisation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:195. [PMID: 38115067 PMCID: PMC10729505 DOI: 10.1186/s13068-023-02445-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND In industrial bioprocesses, microorganisms are generally selected based on performance, whereas robustness, i.e., the ability of a system to maintain a stable performance, has been overlooked due to the challenges in its quantification and implementation into routine experimental procedures. This work presents four ways of implementing robustness quantification during strain characterisation. One Saccharomyces cerevisiae laboratory strain (CEN.PK113-7D) and two industrial strains (Ethanol Red and PE2) grown in seven different lignocellulosic hydrolysates were assessed for growth-related functions (specific growth rate, product yields, etc.) and eight intracellular parameters (using fluorescent biosensors). RESULTS Using flasks and high-throughput experimental setups, robustness was quantified in relation to: (i) stability of growth functions in response to the seven hydrolysates; (ii) stability of growth functions across different strains to establish the impact of perturbations on yeast metabolism; (iii) stability of intracellular parameters over time; (iv) stability of intracellular parameters within a cell population to indirectly quantify population heterogeneity. Ethanol Red was the best-performing strain under all tested conditions, achieving the highest growth function robustness. PE2 displayed the highest population heterogeneity. Moreover, the intracellular environment varied in response to non-woody or woody lignocellulosic hydrolysates, manifesting increased oxidative stress and unfolded protein response, respectively. CONCLUSIONS Robustness quantification is a powerful tool for strain characterisation as it offers novel information on physiological and biochemical parameters. Owing to the flexibility of the robustness quantification method, its implementation was successfully validated at single-cell as well as high-throughput levels, showcasing its versatility and potential for several applications.
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Affiliation(s)
- Luca Torello Pianale
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Fabio Caputo
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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Torello Pianale L, Olsson L. ScEnSor Kit for Saccharomyces cerevisiae Engineering and Biosensor-Driven Investigation of the Intracellular Environment. ACS Synth Biol 2023; 12:2493-2497. [PMID: 37552581 PMCID: PMC10443032 DOI: 10.1021/acssynbio.3c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 08/10/2023]
Abstract
In this study, the three-step build-transform-assess toolbox for real-time monitoring of the yeast intracellular environment has been expanded and upgraded to the two-module ScEnSor (S. cerevisiae Engineering + Biosensor) Kit. The Biosensor Module includes eight fluorescent reporters for the intracellular environment; three of them (unfolded protein response, pyruvate metabolism, and ethanol consumption) were newly implemented to complement the original five. The Genome-Integration Module comprises a set of backbone plasmids for the assembly of 1-6 transcriptional units (each consisting of promoter, coding sequence, and terminator) for efficient marker-free single-locus genome integration (in HO and/or X2 loci). Altogether, the ScEnSor Kit enables rapid and easy construction of strains with new transcriptional units as well as high-throughput investigation of the yeast intracellular environment.
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Affiliation(s)
- Luca Torello Pianale
- Industrial
Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial
Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, 412 96, Gothenburg, Sweden
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Xie Y, Liu T, Gresham D, Holt LJ. mRNA condensation fluidizes the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542963. [PMID: 37398029 PMCID: PMC10312499 DOI: 10.1101/2023.05.30.542963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The intracellular environment is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cell physiology. When exposed to stress, mRNAs released after translational arrest condense with RNA binding proteins, resulting in the formation of membraneless RNA protein (RNP) condensates known as processing bodies (P-bodies) and stress granules (SGs). However, the impact of the assembly of these condensates on the biophysical properties of the crowded cytoplasmic environment remains unclear. Here, we find that upon exposure to stress, polysome collapse and condensation of mRNAs increases mesoscale particle diffusivity in the cytoplasm. Increased mesoscale diffusivity is required for the efficient formation of Q-bodies, membraneless organelles that coordinate degradation of misfolded peptides that accumulate during stress. Additionally, we demonstrate that polysome collapse and stress granule formation has a similar effect in mammalian cells, fluidizing the cytoplasm at the mesoscale. We find that synthetic, light-induced RNA condensation is sufficient to fluidize the cytoplasm, demonstrating a causal effect of RNA condensation. Together, our work reveals a new functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to effectively respond to stressful conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
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Piljukov VJ, Sillamaa S, Sedman T, Garber N, Rätsep M, Freiberg A, Sedman J. Mitochondrial Irc3 helicase of the thermotolerant yeast Ogataea polymorpha displays dual DNA- and RNA-stimulated ATPase activity. Mitochondrion 2023; 69:130-139. [PMID: 36764503 DOI: 10.1016/j.mito.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Irc3 is one of the six mitochondrial helicases described in Saccharomyces cerevisiae. Physiological functions of Irc3 are not completely understood as both DNA metabolic processes and mRNA translation have been suggested to be direct targets of the helicase. In vitro analysis of Irc3 has been hampered by the modest thermostability of the S. cerevisiae protein. Here, we purified a homologous helicase (Irc3op) of the thermotolerant yeast Ogataea polymorpha that retains structural integrity and catalytic activity at temperatures above 40 °C. Irc3op can complement the respiratory deficiency phenotype of a S. cerevisiae irc3Δ mutant, indicating conservation of biochemical functions. The ATPase activity of Irc3op is best stimulated by branched and double- stranded DNA cofactors. Single-stranded DNA binds Irc3op tightly but is a weak activator of the ATPase activity. We could also detect a lower level stimulation with RNA, especially with molecules possessing a compact three-dimensional structure. These results support the idea that that Irc3 might have dual specificity and remodel both DNA and RNA molecules in vivo. Furthermore, our analysis of kinetic parameters predicts that Irc3 could have a regulatory function via sensing changes of the mitochondrial ATP pool or respond to the accumulation of single-stranded DNA.
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Affiliation(s)
- Vlad-Julian Piljukov
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Sirelin Sillamaa
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Tiina Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Natalja Garber
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Margus Rätsep
- Laboratory of Biophysics, Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Arvi Freiberg
- Laboratory of Biophysics, Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Juhan Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia.
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Žunar B, Ito T, Mosrin C, Sugahara Y, Bénédetti H, Guégan R, Vallée B. Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae. Biomater Res 2022; 26:85. [PMID: 36539854 PMCID: PMC9769040 DOI: 10.1186/s40824-022-00337-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive. METHODS We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging. RESULTS When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients. CONCLUSIONS F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability.
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Affiliation(s)
- Bojan Žunar
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France ,grid.4808.40000 0001 0657 4636Department of Chemistry and Biochemistry, Laboratory for Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Taiga Ito
- grid.5290.e0000 0004 1936 9975Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Christine Mosrin
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
| | - Yoshiyuki Sugahara
- grid.5290.e0000 0004 1936 9975Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Hélène Bénédetti
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
| | - Régis Guégan
- grid.5290.e0000 0004 1936 9975Global Center for Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan ,grid.112485.b0000 0001 0217 6921Institut des Sciences de la Terre d’Orléans (ISTO), UMR 7327, CNRS-Université d’Orléans, 1A Rue de la Férollerie, 45071 Orléans, Cedex 2 France
| | - Béatrice Vallée
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
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Takaine M, Imamura H, Yoshida S. High and stable ATP levels prevent aberrant intracellular protein aggregation in yeast. eLife 2022; 11:67659. [PMID: 35438635 PMCID: PMC9018071 DOI: 10.7554/elife.67659] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/18/2022] [Indexed: 12/24/2022] Open
Abstract
Adenosine triphosphate (ATP) at millimolar levels has recently been implicated in the solubilization of cellular proteins. However, the significance of this high ATP level under physiological conditions and the mechanisms that maintain ATP remain unclear. We herein demonstrated that AMP-activated protein kinase (AMPK) and adenylate kinase (ADK) cooperated to maintain cellular ATP levels regardless of glucose levels. Single-cell imaging of ATP-reduced yeast mutants revealed that ATP levels in these mutants underwent stochastic and transient depletion, which promoted the cytotoxic aggregation of endogenous proteins and pathogenic proteins, such as huntingtin and α-synuclein. Moreover, pharmacological elevations in ATP levels in an ATP-reduced mutant prevented the accumulation of α-synuclein aggregates and its cytotoxicity. The present study demonstrates that cellular ATP homeostasis ensures proteostasis and revealed that suppressing the high volatility of cellular ATP levels prevented cytotoxic protein aggregation, implying that AMPK and ADK are important factors that prevent proteinopathies, such as neurodegenerative diseases. Cells use a chemical called adenosine triphosphate (ATP) as a controllable source of energy. Like a battery, each ATP molecule contains a specific amount of energy that can be released when needed. Cells just need enough ATP to survive, but most cells store a lot more than they need. It is unclear why cells keep so much ATP, or whether this excess ATP has any other purpose. To answer these questions, Takaine et al. identified mutants of the yeast Saccharomyces cerevisiae that had low levels of ATP, and studied how these cells differ from normal yeast The results showed that, in S. cerevisiae cells with lower and variable levels of ATP, proteins stick together, forming clumps. Proteins are molecules that perform diverse roles, keeping cells alive. When they clump together, they stop working and can cause cells to die. Further experiments showed that reducing the levels of ATP just for a short time increased the rate at which proteins stick together. Taken together, Takaine et al.’s results suggest that ATP plays a role in stopping proteins from sticking together, explaining why cells may store excess ATP, since it could aid survival. Protein clumps, also called aggregates, are a key feature of various illnesses, including neurodegenerative diseases such as Alzheimer’s. Takaine et al. provide a possible cause for why proteins aggregate in these diseases, which may be worth further study.
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Affiliation(s)
- Masak Takaine
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi, Japan
| | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Satoshi Yoshida
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi, Japan.,School of International Liberal Studies, Waseda University, Tokyo, Japan.,Japan Science and Technology Agency, PREST, Tokyo, Japan
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8
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Assessment of Cytotoxicity of α-Synuclein in Budding Yeast Using a Spot Growth Assay and Fluorescent Microscopy. Methods Mol Biol 2021. [PMID: 34043202 DOI: 10.1007/978-1-0716-1495-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The budding yeast Saccharomyces cerevisiae is a model organism amenable both to genetic analysis and cell biology. Due to these advantages, yeast has provided platforms to examine the properties of pathogenic proteins involved in human diseases. The methods used to examine the cytotoxicity and intracellular localization of α-Synuclein, a human neuronal protein implicated in Parkinson's disease, using yeast have been described herein. These methods are readily accessible to researchers or graduate students unfamiliar with experiments using yeast and applicable to larger scale analyses, such as high-throughput genetic and chemical screenings.
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Köhler S, Schmidt H, Fülle P, Hirrlinger J, Winkler U. A Dual Nanosensor Approach to Determine the Cytosolic Concentration of ATP in Astrocytes. Front Cell Neurosci 2020; 14:565921. [PMID: 33192312 PMCID: PMC7530325 DOI: 10.3389/fncel.2020.565921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/26/2020] [Indexed: 11/17/2022] Open
Abstract
Adenosine triphosphate (ATP) is the central energy carrier of all cells and knowledge on the dynamics of the concentration of ATP ([ATP]) provides important insights into the energetic state of a cell. Several genetically encoded fluorescent nanosensors for ATP were developed, which allow following the cytosolic [ATP] at high spatial and temporal resolution using fluorescence microscopy. However, to calibrate the fluorescent signal to [ATP] has remained challenging. To estimate basal cytosolic [ATP] ([ATP]0) in astrocytes, we here took advantage of two ATP nanosensors of the ATeam-family (ATeam1.03; ATeam1.03YEMK) with different affinities for ATP. Altering [ATP] by external stimuli resulted in characteristic pairs of signal changes of both nanosensors, which depend on [ATP]0. Using this dual nanosensor strategy and epifluorescence microscopy, [ATP]0 was estimated to be around 1.5 mM in primary cultures of cortical astrocytes from mice. Furthermore, in astrocytes in acutely isolated cortical slices from mice expressing both nanosensors after stereotactic injection of AAV-vectors, 2-photon microscopy revealed [ATP]0 of 0.7 mM to 1.3 mM. Finally, the change in [ATP] induced in the cytosol of cultured cortical astrocytes by application of azide, glutamate, and an increased extracellular concentration of K+ were calculated as −0.50 mM, −0.16 mM, and 0.07 mM, respectively. In summary, the dual nanosensor approach adds another option for determining the concentration of [ATP] to the increasing toolbox of fluorescent nanosensors for metabolites. This approach can also be applied to other metabolites when two sensors with different binding properties are available.
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Affiliation(s)
- Susanne Köhler
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany
| | - Hartmut Schmidt
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany
| | - Paula Fülle
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany.,Wilhelm-Ostwald-Schule, Gymnasium der Stadt Leipzig, Leipzig, Germany
| | - Johannes Hirrlinger
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany.,Department of Neurogenetics, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Ulrike Winkler
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany
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