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Ćorić A, Stockinger AW, Schaffer P, Rokvić D, Tessmar-Raible K, Raible F. A Fast And Versatile Method for Simultaneous HCR, Immunohistochemistry And Edu Labeling (SHInE). Integr Comp Biol 2023; 63:372-381. [PMID: 36866518 PMCID: PMC10445416 DOI: 10.1093/icb/icad007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Access to newer, fast, and cheap sequencing techniques, particularly on the single-cell level, have made transcriptomic data of tissues or single cells accessible to many researchers. As a consequence, there is an increased need for in situ visualization of gene expression or encoded proteins to validate, localize, or help interpret such sequencing data, as well as put them in context with cellular proliferation. A particular challenge for labeling and imaging transcripts are complex tissues that are often opaque and/or pigmented, preventing easy visual inspection. Here, we introduce a versatile protocol that combines in situ hybridization chain reaction, immunohistochemistry, and proliferative cell labeling using 5-ethynyl-2'-deoxyuridine, and demonstrate its compatibility with tissue clearing. As a proof-of-concept, we show that our protocol allows for the parallel analysis of cell proliferation, gene expression, and protein localization in bristleworm heads and trunks.
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Affiliation(s)
- Aida Ćorić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Alexander W Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Petra Schaffer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Dunja Rokvić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Carl-von-Ossietzky University, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
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2
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Álvarez‐Campos P, Planques A, Bideau L, Vervoort M, Gazave E. On the hormonal control of posterior regeneration in the annelid
Platynereis dumerilii. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B: MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 340:298-315. [PMID: 37160758 DOI: 10.1002/jez.b.23182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022]
Abstract
Regeneration is the process by which many animals are able to restore lost or injured body parts. After amputation of the posterior part of its body, the annelid Platynereis dumerilii is able to regenerate the pygidium, the posteriormost part of its body that bears the anus, and a subterminal growth zone containing stem cells that allows the subsequent addition of new segments. The ability to regenerate their posterior part (posterior regeneration) is promoted, in juvenile worms, by a hormone produced by the brain and is lost when this hormonal activity becomes low at the time the worms undergo their sexual maturation. By characterizing posterior regeneration at the morphological and molecular levels in worms that have been decapitated, we show that the presence of the head is essential for multiple aspects of posterior regeneration, as well as for the subsequent production of new segments. We also show that methylfarnesoate, the molecule proposed to be the brain hormone, can partially rescue the posterior regeneration defects observed in decapitated worms. Our results are therefore consistent with a key role of brain hormonal activity in the control of regeneration and growth in P. dumerilii, and support the hypothesis of the involvement of methylfarnesoate in this control.
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Affiliation(s)
| | | | - Loïc Bideau
- Université Paris Cité, CNRS Institut Jacques Monod Paris France
| | - Michel Vervoort
- Université Paris Cité, CNRS Institut Jacques Monod Paris France
| | - Eve Gazave
- Université Paris Cité, CNRS Institut Jacques Monod Paris France
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Poehn B, Krishnan S, Zurl M, Coric A, Rokvic D, Häfker NS, Jaenicke E, Arboleda E, Orel L, Raible F, Wolf E, Tessmar-Raible K. A Cryptochrome adopts distinct moon- and sunlight states and functions as sun- versus moonlight interpreter in monthly oscillator entrainment. Nat Commun 2022; 13:5220. [PMID: 36064778 PMCID: PMC9445029 DOI: 10.1038/s41467-022-32562-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
The moon's monthly cycle synchronizes reproduction in countless marine organisms. The mass-spawning bristle worm Platynereis dumerilii uses an endogenous monthly oscillator set by full moon to phase reproduction to specific days. But how do organisms recognize specific moon phases? We uncover that the light receptor L-Cryptochrome (L-Cry) discriminates between different moonlight durations, as well as between sun- and moonlight. A biochemical characterization of purified L-Cry protein, exposed to naturalistic sun- or moonlight, reveals the formation of distinct sun- and moonlight states characterized by different photoreduction- and recovery kinetics of L-Cry's co-factor Flavin Adenine Dinucleotide. In Platynereis, L-Cry's sun- versus moonlight states correlate with distinct subcellular localizations, indicating different signaling. In contrast, r-Opsin1, the most abundant ocular opsin, is not required for monthly oscillator entrainment. Our work reveals a photo-ecological concept for natural light interpretation involving a "valence interpreter" that provides entraining photoreceptor(s) with light source and moon phase information.
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Affiliation(s)
- Birgit Poehn
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Shruthi Krishnan
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Martin Zurl
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Aida Coric
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Dunja Rokvic
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - N Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Elmar Jaenicke
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Enrique Arboleda
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007, Lyon, France
| | - Lukas Orel
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria.
- Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria.
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
- Carl-von-Ossietzky University, Carl-von-Ossietzky-Straße 9-11, 26111, Oldenburg, Germany.
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Whole-body integration of gene expression and single-cell morphology. Cell 2021; 184:4819-4837.e22. [PMID: 34380046 PMCID: PMC8445025 DOI: 10.1016/j.cell.2021.07.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/05/2021] [Accepted: 07/14/2021] [Indexed: 01/10/2023]
Abstract
Animal bodies are composed of cell types with unique expression programs that implement their distinct locations, shapes, structures, and functions. Based on these properties, cell types assemble into specific tissues and organs. To systematically explore the link between cell-type-specific gene expression and morphology, we registered an expression atlas to a whole-body electron microscopy volume of the nereid Platynereis dumerilii. Automated segmentation of cells and nuclei identifies major cell classes and establishes a link between gene activation, chromatin topography, and nuclear size. Clustering of segmented cells according to gene expression reveals spatially coherent tissues. In the brain, genetically defined groups of neurons match ganglionic nuclei with coherent projections. Besides interneurons, we uncover sensory-neurosecretory cells in the nereid mushroom bodies, which thus qualify as sensory organs. They furthermore resemble the vertebrate telencephalon by molecular anatomy. We provide an integrated browser as a Fiji plugin for remote exploration of all available multimodal datasets. A cellular atlas integrates gene expression and ultrastructure for an entire annelid Morphometry of all segmented cells, nuclei, and chromatin categorizes cell classes Molecular anatomy and projectome of head ganglionic nuclei and mushroom bodies An open-source browser for multimodal big image data exploration and analysis
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Revilla-i-Domingo R, Rajan VBV, Waldherr M, Prohaczka G, Musset H, Orel L, Gerrard E, Smolka M, Stockinger A, Farlik M, Lucas RJ, Raible F, Tessmar-Raible K. Characterization of cephalic and non-cephalic sensory cell types provides insight into joint photo- and mechanoreceptor evolution. eLife 2021; 10:e66144. [PMID: 34350831 PMCID: PMC8367381 DOI: 10.7554/elife.66144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 08/04/2021] [Indexed: 12/11/2022] Open
Abstract
Rhabdomeric opsins (r-opsins) are light sensors in cephalic eye photoreceptors, but also function in additional sensory organs. This has prompted questions on the evolutionary relationship of these cell types, and if ancient r-opsins were non-photosensory. A molecular profiling approach in the marine bristleworm Platynereis dumerilii revealed shared and distinct features of cephalic and non-cephalic r-opsin1-expressing cells. Non-cephalic cells possess a full set of phototransduction components, but also a mechanosensory signature. Prompted by the latter, we investigated Platynereis putative mechanotransducer and found that nompc and pkd2.1 co-expressed with r-opsin1 in TRE cells by HCR RNA-FISH. To further assess the role of r-Opsin1 in these cells, we studied its signaling properties and unraveled that r-Opsin1 is a Gαq-coupled blue light receptor. Profiling of cells from r-opsin1 mutants versus wild-types, and a comparison under different light conditions reveals that in the non-cephalic cells light - mediated by r-Opsin1 - adjusts the expression level of a calcium transporter relevant for auditory mechanosensation in vertebrates. We establish a deep-learning-based quantitative behavioral analysis for animal trunk movements and identify a light- and r-Opsin-1-dependent fine-tuning of the worm's undulatory movements in headless trunks, which are known to require mechanosensory feedback. Our results provide new data on peripheral cell types of likely light sensory/mechanosensory nature. These results point towards a concept in which such a multisensory cell type evolved to allow for fine-tuning of mechanosensation by light. This implies that light-independent mechanosensory roles of r-opsins may have evolved secondarily.
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Affiliation(s)
- Roger Revilla-i-Domingo
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Vinoth Babu Veedin Rajan
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Monika Waldherr
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Günther Prohaczka
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Hugo Musset
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Lukas Orel
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Elliot Gerrard
- Division of Neuroscience & Experimental Psychology, University of ManchesterManchesterUnited Kingdom
| | - Moritz Smolka
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of ViennaViennaAustria
| | - Alexander Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of Dermatology, Medical University of ViennaViennaAustria
| | - Robert J Lucas
- Division of Neuroscience & Experimental Psychology, University of ManchesterManchesterUnited Kingdom
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
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Planques A, Kerner P, Ferry L, Grunau C, Gazave E, Vervoort M. DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii. BMC Biol 2021; 19:148. [PMID: 34340707 PMCID: PMC8330077 DOI: 10.1186/s12915-021-01074-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Methylation of cytosines in DNA (5mC methylation) is a major epigenetic modification that modulates gene expression and constitutes the basis for mechanisms regulating multiple aspects of embryonic development and cell reprogramming in vertebrates. In mammals, 5mC methylation of promoter regions is linked to transcriptional repression. Transcription regulation by 5mC methylation notably involves the nucleosome remodeling and deacetylase complex (NuRD complex) which bridges DNA methylation and histone modifications. However, less is known about regulatory mechanisms involving 5mC methylation and their function in non-vertebrate animals. In this paper, we study 5mC methylation in the marine annelid worm Platynereis dumerilii, an emerging evolutionary and developmental biology model capable of regenerating the posterior part of its body post-amputation. RESULTS Using in silico and experimental approaches, we show that P. dumerilii displays a high level of DNA methylation comparable to that of mammalian somatic cells. 5mC methylation in P. dumerilii is dynamic along the life cycle of the animal and markedly decreases at the transition between larval to post-larval stages. We identify a full repertoire of mainly single-copy genes encoding the machinery associated with 5mC methylation or members of the NuRD complex in P. dumerilii and show that this repertoire is close to the one inferred for the last common ancestor of bilaterians. These genes are dynamically expressed during P. dumerilii development and regeneration. Treatment with the DNA hypomethylating agent Decitabine impairs P. dumerilii larval development and regeneration and has long-term effects on post-regenerative growth. CONCLUSIONS Our data reveal high levels of 5mC methylation in the annelid P. dumerilii, highlighting that this feature is not specific to vertebrates in the bilaterian clade. Analysis of DNA methylation levels and machinery gene expression during development and regeneration, as well as the use of a chemical inhibitor of DNA methylation, suggest an involvement of 5mC methylation in P. dumerilii development and regeneration. We also present data indicating that P. dumerilii constitutes a promising model to study biological roles and mechanisms of DNA methylation in non-vertebrate bilaterians and to provide new knowledge about evolution of the functions of this key epigenetic modification in bilaterian animals.
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Affiliation(s)
- Anabelle Planques
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Laure Ferry
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75006, Paris, France
| | - Christoph Grunau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, F-66860, Perpignan, France
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
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Retinal Pigment Epithelium and Neural Retinal Progenitors Interact via Semaphorin 6D to Facilitate Optic Cup Morphogenesis. eNeuro 2021; 8:ENEURO.0053-21.2021. [PMID: 33811086 PMCID: PMC8116109 DOI: 10.1523/eneuro.0053-21.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/21/2022] Open
Abstract
Cell movement propels embryonic tissues to acquire shapes required for mature function. The movements are driven both by acto-myosin signaling and by cells interacting with the extracellular matrix (ECM). Unknown is whether cell-cell interactions within a tissue are also required, and the molecular mechanisms by which such communication might occur. Here, we use the developing visual system of zebrafish as a model to understand the role cell-cell communication plays in tissue morphogenesis in the embryonic nervous system. We identify that cell-cell-mediated contact between two distinct cell populations, progenitors of the neural retina and retinal pigment epithelium (RPE), facilitates epithelial flow to produce the mature cupped retina. We identify for the first time the need in eye morphogenesis for distinct populations of progenitors to interact, and suggest a novel role for a member of a key developmental signaling family, the transmembrane Semaphorin6d, as mediating communication between distinct cell types to control tissue morphogenesis.
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Fontinha BM, Zekoll T, Al-Rawi M, Gallach M, Reithofer F, Barker AJ, Hofbauer M, Fischer RM, von Haeseler A, Baier H, Tessmar-Raible K. TMT-Opsins differentially modulate medaka brain function in a context-dependent manner. PLoS Biol 2021; 19:e3001012. [PMID: 33411725 PMCID: PMC7837489 DOI: 10.1371/journal.pbio.3001012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/26/2021] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
Vertebrate behavior is strongly influenced by light. Light receptors, encoded by functional opsin proteins, are present inside the vertebrate brain and peripheral tissues. This expression feature is present from fishes to human and appears to be particularly prominent in diurnal vertebrates. Despite their conserved widespread occurrence, the nonvisual functions of opsins are still largely enigmatic. This is even more apparent when considering the high number of opsins. Teleosts possess around 40 opsin genes, present from young developmental stages to adulthood. Many of these opsins have been shown to function as light receptors. This raises the question of whether this large number might mainly reflect functional redundancy or rather maximally enables teleosts to optimally use the complex light information present under water. We focus on tmt-opsin1b and tmt-opsin2, c-opsins with ancestral-type sequence features, conserved across several vertebrate phyla, expressed with partly similar expression in non-rod, non-cone, non-retinal-ganglion-cell brain tissues and with a similar spectral sensitivity. The characterization of the single mutants revealed age- and light-dependent behavioral changes, as well as an impact on the levels of the preprohormone sst1b and the voltage-gated sodium channel subunit scn12aa. The amount of daytime rest is affected independently of the eyes, pineal organ, and circadian clock in tmt-opsin1b mutants. We further focused on daytime behavior and the molecular changes in tmt-opsin1b/2 double mutants, and found that-despite their similar expression and spectral features-these opsins interact in part nonadditively. Specifically, double mutants complement molecular and behavioral phenotypes observed in single mutants in a partly age-dependent fashion. Our work provides a starting point to disentangle the highly complex interactions of vertebrate nonvisual opsins, suggesting that tmt-opsin-expressing cells together with other visual and nonvisual opsins provide detailed light information to the organism for behavioral fine-tuning. This work also provides a stepping stone to unravel how vertebrate species with conserved opsins, but living in different ecological niches, respond to similar light cues and how human-generated artificial light might impact on behavioral processes in natural environments.
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Affiliation(s)
- Bruno M. Fontinha
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Theresa Zekoll
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Mariam Al-Rawi
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Miguel Gallach
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Florian Reithofer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | | | - Maximilian Hofbauer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
- loopbio, Vienna, Austria
| | - Ruth M. Fischer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Herwig Baier
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
- FENS-Kavli Network of Excellence, Brussels, Belgium
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9
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Pende M, Vadiwala K, Schmidbaur H, Stockinger AW, Murawala P, Saghafi S, Dekens MPS, Becker K, Revilla-i-Domingo R, Papadopoulos SC, Zurl M, Pasierbek P, Simakov O, Tanaka EM, Raible F, Dodt HU. A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. SCIENCE ADVANCES 2020; 6:eaba0365. [PMID: 32523996 PMCID: PMC7259959 DOI: 10.1126/sciadv.aba0365] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.
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Affiliation(s)
- Marko Pende
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hannah Schmidbaur
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander W. Stockinger
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Marcus P. S. Dekens
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Sofia-Christina Papadopoulos
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Martin Zurl
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Elly M. Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Florian Raible
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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10
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Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 2020; 8:e8806. [PMID: 32219032 PMCID: PMC7085896 DOI: 10.7717/peerj.8806] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual targets. Taken together, this information will guide the methods development process for investigators that seek to perform FISH in organisms that lack documented or optimized protocols.
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Affiliation(s)
- Alexander P Young
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| | - Daniel J Jackson
- Department of Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
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11
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Lauter G, Söll I, Hauptmann G. Sensitive Multiplexed Fluorescent In Situ Hybridization Using Enhanced Tyramide Signal Amplification and Its Combination with Immunofluorescent Protein Visualization in Zebrafish. Methods Mol Biol 2020; 2047:397-409. [PMID: 31552667 DOI: 10.1007/978-1-4939-9732-9_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fluorescent in situ hybridization (FISH) provides sensitive detection and visualization of RNA transcripts in tissues and cells with high resolution. We present here a multiplex RNA FISH method using enhanced tyramide signal amplification (TSA) for colocalization analysis of three different transcripts in intact zebrafish brains. To achieve enhancement of fluorescent signals, essential steps of the FISH procedure are optimized including embryo permeability, hybridization efficacy, and fluorogenic TSA-reaction conditions. Critical to this protocol, the enzymatic peroxidase (PO) reactivity is significantly improved by the application of viscosity-increasing polymers, PO accelerators, and highly effective bench-made tyramide substrates. These advancements lead to an optimized TSA-FISH protocol with dramatically increased signal intensity and signal-to-background ratio allowing for visualization of three mRNA transcript patterns simultaneously. The TSA-FISH procedure can be combined with immunofluorescence (IF) to compare mRNA transcript and protein expression patterns.
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Affiliation(s)
- Gilbert Lauter
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
| | - Iris Söll
- Department of Molecular Biosciences, The Wenner-Gren Institute, MBW, Stockholm University, Stockholm, Sweden
| | - Giselbert Hauptmann
- Department of Molecular Biosciences, The Wenner-Gren Institute, MBW, Stockholm University, Stockholm, Sweden.
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12
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Vopalensky P, Tosches MA, Achim K, Handberg-Thorsager M, Arendt D. From spiral cleavage to bilateral symmetry: the developmental cell lineage of the annelid brain. BMC Biol 2019; 17:81. [PMID: 31640768 PMCID: PMC6805352 DOI: 10.1186/s12915-019-0705-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/01/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND During early development, patterns of cell division-embryonic cleavage-accompany the gradual restriction of blastomeres to specific cell fates. In Spiralia, which include annelids, mollusks, and flatworms, "spiral cleavage" produces a highly stereotypic, spiral-like arrangement of blastomeres and swimming trochophore-type larvae with rotational (spiral) symmetry. However, starting at larval stages, spiralian larvae acquire elements of bilateral symmetry, before they metamorphose into fully bilateral juveniles. How this spiral-to-bilateral transition occurs is not known and is especially puzzling for the early differentiating brain and head sensory organs, which emerge directly from the spiral cleavage pattern. Here we present the developmental cell lineage of the Platynereis larval episphere. RESULTS Live-imaging recordings from the zygote to the mid-trochophore stage (~ 30 hpf) of the larval episphere of the marine annelid Platynereis dumerilii reveal highly stereotypical development and an invariant cell lineage of early differentiating cell types. The larval brain and head sensory organs develop from 11 pairs of bilateral founders, each giving rise to identical clones on the right and left body sides. Relating the origin of each bilateral founder pair back to the spiral cleavage pattern, we uncover highly divergent origins: while some founder pairs originate from corresponding cells in the spiralian lineage on each body side, others originate from non-corresponding cells, and yet others derive from a single cell within one quadrant. Integrating lineage and gene expression data for several embryonic and larval stages, we find that the conserved head patterning genes otx and six3 are expressed in bilateral founders representing divergent lineage histories and giving rise to early differentiating cholinergic neurons and head sensory organs, respectively. CONCLUSIONS We present the complete developmental cell lineage of the Platynereis larval episphere, and thus the first comprehensive account of the spiral-to-bilateral transition in a developing spiralian. The bilateral symmetry of the head emerges from pairs of bilateral founders, similar to the trunk; however, the head founders are more numerous and show striking left-right asymmetries in lineage behavior that we relate to differential gene expression.
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Affiliation(s)
- Pavel Vopalensky
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Maria Antonietta Tosches
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Kaia Achim
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Mette Handberg-Thorsager
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden, 01307, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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13
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Klann M, Seaver EC. Functional role of pax6 during eye and nervous system development in the annelid Capitella teleta. Dev Biol 2019; 456:86-103. [PMID: 31445008 DOI: 10.1016/j.ydbio.2019.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022]
Abstract
The transcription factor Pax6 is an important regulator of early animal development. Loss of function mutations of pax6 in a range of animals result in a reduction or complete loss of the eye, a reduction of a subset of neurons, and defects in axon growth. There are no studies focusing on the role of pax6 during development of any lophotrochozoan representative, however, expression of pax6 in the developing eye and nervous system in a number of species suggest that pax6 plays a highly conserved role in eye and nervous system formation. We investigated the functional role of pax6 during development of the marine annelid Capitella teleta. Expression of pax6 transcripts in C. teleta larvae is similar to patterns found in other animals, with distinct subdomains in the brain and ventral nerve cord as well as in the larval and juvenile eye. To perturb pax6 function, two different splice-blocking morpholinos and a translation-blocking morpholino were used. Larvae resulting from microinjections with either splice-blocking morpholino show a reduction of the pax6 transcript. Development of both the larval eyes and the central nervous system architecture are highly disrupted following microinjection of each of the three morpholinos. The less severe phenotype observed when only the homeodomain is disrupted suggests that presence of the paired domain is sufficient for partial function of the Pax6 protein. Preliminary downstream target analysis confirms disruption in expression of some components of the retinal gene regulatory network, as well as disruption of genes involved in nervous system development. Results from this study, taken together with studies from other species, reveal an evolutionarily conserved role for pax6 in eye and neural specification and development.
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Affiliation(s)
- Marleen Klann
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, Fl, 32080, USA
| | - Elaine C Seaver
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, Fl, 32080, USA.
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14
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Bernardo-Garcia FJ, Syed M, Jékely G, Sprecher SG. Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans. EvoDevo 2019; 10:4. [PMID: 30873275 PMCID: PMC6399963 DOI: 10.1186/s13227-019-0117-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/15/2019] [Indexed: 12/14/2022] Open
Abstract
Across metazoans, visual systems employ different types of photoreceptor neurons (PRs) to detect light. These include rhabdomeric PRs, which exist in distantly related phyla and possess an evolutionarily conserved phototransduction cascade. While the development of rhabdomeric PRs has been thoroughly studied in the fruit fly Drosophila melanogaster, we still know very little about how they form in other species. To investigate this question, we tested whether the transcription factor Glass, which is crucial for instructing rhabdomeric PR formation in Drosophila, may play a similar role in other metazoans. Glass homologues exist throughout the animal kingdom, indicating that this protein evolved prior to the metazoan radiation. Interestingly, our work indicates that glass is not expressed in rhabdomeric photoreceptors in the planarian Schmidtea mediterranea nor in the annelid Platynereis dumerilii. Combined with a comparative analysis of the Glass DNA-binding domain, our data suggest that the fate of rhabdomeric PRs is controlled by Glass-dependent and Glass-independent mechanisms in different animal clades.
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Affiliation(s)
- F Javier Bernardo-Garcia
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.,2Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Maryam Syed
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gáspár Jékely
- 3Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Simon G Sprecher
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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15
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Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. eLife 2019; 8:e41556. [PMID: 30767890 PMCID: PMC6377233 DOI: 10.7554/elife.41556] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Many marine animals, ranging from corals to fishes, synchronise reproduction to lunar cycles. In the annelid Platynereis dumerilii, this timing is orchestrated by an endogenous monthly (circalunar) clock entrained by moonlight. Whereas daily (circadian) clocks cause extensive transcriptomic and proteomic changes, the quality and quantity of regulations by circalunar clocks have remained largely elusive. By establishing a combined transcriptomic and proteomic profiling approach, we provide first systematic insight into the molecular changes in Platynereis heads between circalunar phases, and across sexual differentiation and maturation. Whereas maturation elicits large transcriptomic and proteomic changes, the circalunar clock exhibits only minor transcriptomic, but strong proteomic regulation. Our study provides a versatile extraction technique and comprehensive resources. It corroborates that circadian and circalunar clock effects are likely distinct and identifies key molecular brain signatures for reproduction, sex and circalunar clock phase. Examples include prepro-whitnin/proctolin and ependymin-related proteins as circalunar clock targets.
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Affiliation(s)
- Sven Schenk
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Stephanie C Bannister
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Fritz J Sedlazeck
- Center of Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Dorothea Anrather
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F Perutz Laboratories, Vienna, Austria
| | - Bui Quang Minh
- Center of Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Andrea Bileck
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F Perutz Laboratories, Vienna, Austria
| | - Arndt von Haeseler
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
- Center of Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Florian Raible
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
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16
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Kostyuchenko RP, Kozin VV, Filippova NA, Sorokina EV. FoxA expression pattern in two polychaete species, Alitta virens and Platynereis dumerilii: Examination of the conserved key regulator of the gut development from cleavage through larval life, postlarval growth, and regeneration. Dev Dyn 2019; 248:728-743. [PMID: 30566266 DOI: 10.1002/dvdy.7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/23/2018] [Accepted: 11/29/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND foxA orthologs are involved in various processes from embryo patterning to regulation of metabolism. Since foxA conserved role in the development of the gut of errant annelids has never been thoroughly studied, we used a candidate gene approach to unravel the molecular profile of the alimentary canal in two closely related nereid worms with a trochophore-type lecithotrophic larva. RESULTS The character of foxA expression in the two polychaetes was similar but not identical. The genes were successively activated first in blastoporal cells, then in the stomodeum, the midgut, and hindgut primordia, and in the cells of central and peripheral nervous system. Before the start of active feeding of nectochaetes, we observed a short phase of foxA expression in the entire digestive tract. After amputation of posterior segments, foxA expression was established de novo in the new terminal part of the intestine, and then in the developing hindgut and the anus. CONCLUSIONS We discovered an early marker of endoderm formation previously unknown in errant annelids. Its expression dynamics provided valuable insights into the gut development. Comparative analysis of foxA activity suggests its primary role in gastrulation morphogenesis independently of its type and in midgut and foregut specification. Developmental Dynamics 248:728-743, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Roman P Kostyuchenko
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Vitaly V Kozin
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Nadezhda A Filippova
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Ekaterina V Sorokina
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
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17
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Planques A, Malem J, Parapar J, Vervoort M, Gazave E. Morphological, cellular and molecular characterization of posterior regeneration in the marine annelid Platynereis dumerilii. Dev Biol 2018; 445:189-210. [PMID: 30445055 DOI: 10.1016/j.ydbio.2018.11.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/29/2018] [Accepted: 11/08/2018] [Indexed: 01/08/2023]
Abstract
Regeneration, the ability to restore body parts after an injury or an amputation, is a widespread but highly variable and complex phenomenon in animals. While having fascinated scientists for centuries, fundamental questions about the cellular basis of animal regeneration as well as its evolutionary history remain largely unanswered. Here, we present a study of regeneration of the marine annelid Platynereis dumerilii, an emerging comparative developmental biology model, which, like many other annelids, displays important regenerative abilities. When P. dumerilii worms are amputated, they are able to regenerate the posteriormost differentiated part of their body and a stem cell-rich growth zone that allows the production of new segments replacing the amputated ones. We show that posterior regeneration is a rapid process that follows a well reproducible path and timeline, going through specific stages that we thoroughly defined. Wound healing is achieved one day after amputation and a regeneration blastema forms one day later. At this time point, some tissue specification already occurs, and a functional posterior growth zone is re-established as early as three days after amputation. Regeneration timing is only influenced, in a minor manner, by worm size. Comparable regenerative abilities are found for amputations performed at different positions along the antero-posterior axis of the worm, except when amputation planes are very close to the pharynx. Regenerative abilities persist upon repeated amputations without important alterations of the process. We also show that intense cell proliferation occurs during regeneration and that cell divisions are required for regeneration to proceed normally. Finally, 5-ethynyl-2'-deoxyuridine (EdU) pulse and chase experiments suggest that blastemal cells mostly derive from the segment immediately abutting the amputation plane. The detailed characterization of P. dumerilii posterior body regeneration presented in this article provides the foundation for future mechanistic and comparative studies of regeneration in this species.
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Affiliation(s)
- Anabelle Planques
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Julien Malem
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Julio Parapar
- Departamento de Bioloxía, Universidade da Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain
| | - Michel Vervoort
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
| | - Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
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18
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Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii. Proc Natl Acad Sci U S A 2018; 114:5878-5885. [PMID: 28584082 DOI: 10.1073/pnas.1610602114] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The comparative study of cell types is a powerful approach toward deciphering animal evolution. To avoid selection biases, however, comparisons ideally involve all cell types present in a multicellular organism. Here, we use image registration and a newly developed "Profiling by Signal Probability Mapping" algorithm to generate a cellular resolution 3D expression atlas for an entire animal. We investigate three-segmented young worms of the marine annelid Platynereis dumerilii, with a rich diversity of differentiated cells present in relatively low number. Starting from whole-mount expression images for close to 100 neural specification and differentiation genes, our atlas identifies and molecularly characterizes 605 bilateral pairs of neurons at specific locations in the ventral nerve cord. Among these pairs, we identify sets of neurons expressing similar combinations of transcription factors, located at spatially coherent anterior-posterior, dorsal-ventral, and medial-lateral coordinates that we interpret as cell types. Comparison with motor and interneuron types in the vertebrate neural tube indicates conserved combinations, for example, of cell types cospecified by Gata1/2/3 and Tal transcription factors. These include V2b interneurons and the central spinal fluid-contacting Kolmer-Agduhr cells in the vertebrates, and several neuron types in the intermediate ventral ganglionic mass in the annelid. We propose that Kolmer-Agduhr cell-like mechanosensory neurons formed part of the mucociliary sole in protostome-deuterostome ancestors and diversified independently into several neuron types in annelid and vertebrate descendants.
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19
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Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body. Mol Biol Evol 2018; 35:1047-1062. [PMID: 29373712 PMCID: PMC5913682 DOI: 10.1093/molbev/msx336] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Animal bodies comprise diverse arrays of cells. To characterize cellular identities across an entire body, we have compared the transcriptomes of single cells randomly picked from dissociated whole larvae of the marine annelid Platynereis dumerilii. We identify five transcriptionally distinct groups of differentiated cells, each expressing a unique set of transcription factors and effector genes that implement cellular phenotypes. Spatial mapping of cells into a cellular expression atlas, and wholemount in situ hybridization of group-specific genes reveals spatially coherent transcriptional domains in the larval body, comprising, for example, apical sensory-neurosecretory cells versus neural/epidermal surface cells. These domains represent new, basic subdivisions of the annelid body based entirely on differential gene expression, and are composed of multiple, transcriptionally similar cell types. They do not represent clonal domains, as revealed by developmental lineage analysis. We propose that the transcriptional domains that subdivide the annelid larval body represent families of related cell types that have arisen by evolutionary diversification. Their possible evolutionary conservation makes them a promising tool for evo-devo research.
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Affiliation(s)
- Kaia Achim
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nils Eling
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Paola Yanina Bertucci
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jacob Musser
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pavel Vopalensky
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thibaut Brunet
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul Collier
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John C Marioni
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
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20
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Ayers T, Tsukamoto H, Gühmann M, Veedin Rajan VB, Tessmar-Raible K. A G o-type opsin mediates the shadow reflex in the annelid Platynereis dumerilii. BMC Biol 2018; 16:41. [PMID: 29669554 PMCID: PMC5904973 DOI: 10.1186/s12915-018-0505-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/12/2018] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The presence of photoreceptive molecules outside the eye is widespread among animals, yet their functions in the periphery are less well understood. Marine organisms, such as annelid worms, exhibit a 'shadow reflex', a defensive withdrawal behaviour triggered by a decrease in illumination. Herein, we examine the cellular and molecular underpinnings of this response, identifying a role for a photoreceptor molecule of the Go-opsin class in the shadow response of the marine bristle worm Platynereis dumerilii. RESULTS We found Pdu-Go-opsin1 expression in single specialised cells located in adult Platynereis head and trunk appendages, known as cirri. Using gene knock-out technology and ablation approaches, we show that the presence of Go-opsin1 and the cirri is necessary for the shadow reflex. Consistently, quantification of the shadow reflex reveals a chromatic dependence upon light of approximately 500 nm in wavelength, matching the photoexcitation characteristics of the Platynereis Go-opsin1. However, the loss of Go-opsin1 does not abolish the shadow reflex completely, suggesting the existence of a compensatory mechanism, possibly acting through a ciliary-type opsin, Pdu-c-opsin2, with a Lambdamax of approximately 490 nm. CONCLUSIONS We show that a Go-opsin is necessary for the shadow reflex in a marine annelid, describing a functional example for a peripherally expressed photoreceptor, and suggesting that, in different species, distinct opsins contribute to varying degrees to the shadow reflex.
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Affiliation(s)
- Thomas Ayers
- Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
| | - Hisao Tsukamoto
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, Okazaki, 444-8585, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, 240-0193, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, 332-0012, Japan
| | - Martin Gühmann
- Max Planck Institute for Developmental Biology, Paul-Ehrlich Straße 20, 72076, Tübingen, Germany
| | - Vinoth Babu Veedin Rajan
- Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, 1030, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria.
- Research Platform 'Rhythms of Life', University of Vienna, 1030, Vienna, Austria.
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21
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Gazave E, Lemaître QIB, Balavoine G. The Notch pathway in the annelid Platynereis: insights into chaetogenesis and neurogenesis processes. Open Biol 2017; 7:rsob.160242. [PMID: 28148821 PMCID: PMC5356439 DOI: 10.1098/rsob.160242] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
Notch is a key signalling pathway playing multiple and varied functions during development. Notch regulates the selection of cells with a neurogenic fate and maintains a pool of yet uncommitted precursors through lateral inhibition, both in insects and in vertebrates. Here, we explore the functions of Notch in the annelid Platynereis dumerilii (Lophotrochozoa). Conserved components of the pathway are identified and a scenario for their evolution in metazoans is proposed. Unexpectedly, neither Notch nor its ligands are expressed in the neurogenic epithelia of the larva at the time when massive neurogenesis begins. Using chemical inhibitors and neural markers, we demonstrate that Notch plays no major role in the general neurogenesis of larvae. Instead, we find Notch components expressed in nascent chaetal sacs, the organs that produce the annelid bristles. Impairing Notch signalling induces defects in chaetal sac formation, abnormalities in chaetae producing cells and a change of identity of chaeta growth accessory cells. This is the first bilaterian species in which the early neurogenesis processes appear to occur without a major involvement of the Notch pathway. Instead, Notch is co-opted to pattern annelid-specific organs, likely through a lateral inhibition process. These features reinforce the view that Notch signalling has been recruited multiple times in evolution due to its remarkable ‘toolkit’ nature.
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Affiliation(s)
- Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Quentin I B Lemaître
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Guillaume Balavoine
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
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22
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Kerbl A, Martín-Durán JM, Worsaae K, Hejnol A. Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae). EvoDevo 2016; 7:20. [PMID: 27583125 PMCID: PMC5006589 DOI: 10.1186/s13227-016-0058-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Annelida is a morphologically diverse animal group that exhibits a remarkable variety in nervous system architecture (e.g., number and location of longitudinal cords, architecture of the brain). Despite this heterogeneity of neural arrangements, the molecular profiles related to central nervous system patterning seem to be conserved even between distantly related annelids. In particular, comparative molecular studies on brain and anterior neural region patterning genes have focused so far mainly on indirect-developing macrofaunal taxa. Therefore, analyses on microscopic, direct-developing annelids are important to attain a general picture of the evolutionary events underlying the vast diversity of annelid neuroanatomy. RESULTS We have analyzed the expression domains of 11 evolutionarily conserved genes involved in brain and anterior neural patterning in adult females of the direct-developing meiofaunal annelid Dinophilus gyrociliatus. The small, compact brain shows expression of dimmed, foxg, goosecoid, homeobrain, nk2.1, orthodenticle, orthopedia, pax6, six3/6 and synaptotagmin-1. Although most of the studied markers localize to specific brain areas, the genes six3/6 and synaptotagmin-1 are expressed in nearly all perikarya of the brain. All genes except for goosecoid, pax6 and nk2.2 overlap in the anterior brain region, while the respective expression domains are more separated in the posterior brain. CONCLUSIONS Our findings reveal that the expression patterns of the genes foxg, orthodenticle, orthopedia and six3/6 correlate with those described in Platynereis dumerilii larvae, and homeobrain, nk2.1, orthodenticle and synaptotagmin-1 resemble the pattern of late larvae of Capitella teleta. Although data on other annelids are limited, molecular similarities between adult Dinophilus and larval Platynereis and Capitella suggest an overall conservation of molecular mechanisms patterning the anterior neural regions, independent from developmental and ecological strategies, or of the size and configuration of the nervous system.
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Affiliation(s)
- Alexandra Kerbl
- Marine Biology Section, Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 4, 2100 Copenhagen, Denmark
| | - José M Martín-Durán
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate, 55, 5006 Bergen, Norway
| | - Katrine Worsaae
- Marine Biology Section, Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 4, 2100 Copenhagen, Denmark
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate, 55, 5006 Bergen, Norway
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23
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Kozin VV, Filimonova DA, Kupriashova EE, Kostyuchenko RP. Mesoderm patterning and morphogenesis in the polychaete Alitta virens (Spiralia, Annelida): Expression of mesodermal markers Twist, Mox, Evx and functional role for MAP kinase signaling. Mech Dev 2016; 140:1-11. [PMID: 27000638 DOI: 10.1016/j.mod.2016.03.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 12/11/2022]
Abstract
Mesoderm represents the evolutionary youngest germ layer and forms numerous novel tissues in bilaterian animals. Despite the established conservation of the gene regulatory networks that drive mesoderm differentiation (e.g. myogenesis), mechanisms of mesoderm specification are highly variable in distant model species. Thus, broader phylogenetic sampling is required to reveal common features of mesoderm formation across bilaterians. Here we focus on a representative of Spiralia, the marine annelid Alitta virens, whose mesoderm development is still poorly investigated on the molecular level. We characterize three novel early mesodermal markers for A. virens - Twist, Mox, and Evx - which are differentially expressed within the mesodermal lineages. The Twist mRNA is ubiquitously distributed in the fertilized egg and exhibits specific expression in endomesodermal- and ectomesodermal-founder cells at gastrulation. Twist is expressed around the blastopore and later in a segmental metameric pattern. We consider this expression to be ancestral, and in support of the enterocoelic hypothesis of mesoderm evolution. We also revealed an early pattern of the MAPK activation in A. virens that is different from the previously reported pattern in spiralians. Inhibition of the MAPK pathway by U0126 disrupts the metameric Twist and Mox expression, indicating an early requirement of the MAPK cascade for proper morphogenesis of endomesodermal tissues.
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Affiliation(s)
- Vitaly V Kozin
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia.
| | - Daria A Filimonova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| | - Ekaterina E Kupriashova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| | - Roman P Kostyuchenko
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia.
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24
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Neurotrophin, p75, and Trk Signaling Module in the Developing Nervous System of the Marine Annelid Platynereis dumerilii. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2456062. [PMID: 27069919 PMCID: PMC4812194 DOI: 10.1155/2016/2456062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 01/19/2023]
Abstract
In vertebrates, neurotrophic signaling plays an important role in neuronal development, neural circuit formation, and neuronal plasticity, but its evolutionary origin remains obscure. We found and validated nucleotide sequences encoding putative neurotrophic ligands (neurotrophin, NT) and receptors (Trk and p75) in two annelids, Platynereis dumerilii (Errantia) and Capitella teleta (Sedentaria, for which some sequences were found recently by Wilson, 2009). Predicted protein sequences and structures of Platynereis neurotrophic molecules reveal a high degree of conservation with the vertebrate counterparts; some amino acids signatures present in the annelid Trk sequences are absent in the basal chordate amphioxus, reflecting secondary loss in the cephalochordate lineage. In addition, expression analysis of NT, Trk, and p75 during Platynereis development by whole-mount mRNA in situ hybridization supports a role of these molecules in nervous system and circuit development. These annelid data corroborate the hypothesis that the neurotrophic signaling and its involvement in shaping neural networks predate the protostome-deuterostome split and were present in bilaterian ancestors.
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25
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26
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Gühmann M, Jia H, Randel N, Verasztó C, Bezares-Calderón LA, Michiels NK, Yokoyama S, Jékely G. Spectral Tuning of Phototaxis by a Go-Opsin in the Rhabdomeric Eyes of Platynereis. Curr Biol 2015; 25:2265-71. [PMID: 26255845 DOI: 10.1016/j.cub.2015.07.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 05/26/2015] [Accepted: 07/07/2015] [Indexed: 11/30/2022]
Abstract
Phototaxis is characteristic of the pelagic larval stage of most bottom-dwelling marine invertebrates. Larval phototaxis is mediated by simple eyes that can express various types of light-sensitive G-protein-coupled receptors known as opsins. Since opsins diversified early during metazoan evolution in the marine environment, understanding underwater light detection could elucidate this diversification. Opsins have been classified into three major families, the r-opsins, the c-opsins, and the Go/RGR opsins, a family uniting Go-opsins, retinochromes, RGR opsins, and neuropsins. The Go-opsins form an ancient and poorly characterized group retained only in marine invertebrate genomes. Here, we characterize a Go-opsin from the marine annelid Platynereis dumerilii. We found Go-opsin1 coexpressed with two r-opsins in depolarizing rhabdomeric photoreceptor cells in the pigmented eyes of Platynereis larvae. We purified recombinant Go-opsin1 and found that it absorbs in the blue-cyan range of the light spectrum. To characterize the function of Go-opsin1, we generated a Go-opsin1 knockout Platynereis line by zinc-finger-nuclease-mediated genome engineering. Go-opsin1 knockout larvae were phototactic but showed reduced efficiency of phototaxis to wavelengths matching the in vitro Go-opsin1 spectrum. Our results highlight spectral tuning of phototaxis as a potential mechanism contributing to opsin diversity.
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Affiliation(s)
- Martin Gühmann
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | - Huiyong Jia
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Nadine Randel
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | - Csaba Verasztó
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | | | - Nico K Michiels
- Department of Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Shozo Yokoyama
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Gáspár Jékely
- Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany.
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27
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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat Biotechnol 2015; 33:503-9. [PMID: 25867922 DOI: 10.1038/nbt.3209] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 03/13/2015] [Indexed: 01/12/2023]
Abstract
Understanding cell type identity in a multicellular organism requires the integration of gene expression profiles from individual cells with their spatial location in a particular tissue. Current technologies allow whole-transcriptome sequencing of spatially identified cells but lack the throughput needed to characterize complex tissues. Here we present a high-throughput method to identify the spatial origin of cells assayed by single-cell RNA-sequencing within a tissue of interest. Our approach is based on comparing complete, specificity-weighted mRNA profiles of a cell with positional gene expression profiles derived from a gene expression atlas. We show that this method allocates cells to precise locations in the brain of the marine annelid Platynereis dumerilii with a success rate of 81%. Our method is applicable to any system that has a reference gene expression database of sufficiently high resolution.
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28
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Kozin VV, Kostyuchenko RP. Vasa, PL10, and Piwi gene expression during caudal regeneration of the polychaete annelid Alitta virens. Dev Genes Evol 2015; 225:129-38. [PMID: 25772273 DOI: 10.1007/s00427-015-0496-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/03/2015] [Indexed: 01/23/2023]
Abstract
Polychaetes are famous for their outstanding ability to regenerate lost body parts. Moreover, these worms possess a number of ancestral features in anatomy, development, and genetics, making them particularly suitable for comparative studies. Thus, fundamental as well as new undisclosed so far features of regenerative processes may be revealed, using polychaetes as a model. In the present work, we aimed to analyze the molecular basis of caudal regeneration in the nereid polychaete Alitta virens (formerly Nereis virens). We focused on homologues genes of RNA helicases Vasa and PL10 and ncRNA-binding proteins Piwi. These markers are suggested to play a significant role in maintenance of undifferentiated state of primordial germ cells and multipotent stem cells across invertebrates. In normal conditions, A. virens homologues of Vasa, PL10, and Piwi were differentially expressed in the subterminal growth zone and germline cells. Caudal amputation induced expression of studied genes de novo, which further accompanies all steps of regeneration. An early appearance of the transcripts in wound epithelium and internal blastemal cells suggests involvement of these genes in the well-known cell dedifferentiation events that assure polychaete regeneration. Provided interpretation of the gene expression dynamics implies the primary restoration of the pygidium and growth zone, which promotes following segment formation. Obtained results are valuable as a molecular fingerprint of the alterations occurring in regulatory state of locally regenerating tissues.
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Affiliation(s)
- Vitaly V Kozin
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034, St. Petersburg, Russia
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29
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Lauri A, Brunet T, Handberg-Thorsager M, Fischer AHL, Simakov O, Steinmetz PRH, Tomer R, Keller PJ, Arendt D. Development of the annelid axochord: insights into notochord evolution. Science 2014; 345:1365-8. [PMID: 25214631 DOI: 10.1126/science.1253396] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The origin of chordates has been debated for more than a century, with one key issue being the emergence of the notochord. In vertebrates, the notochord develops by convergence and extension of the chordamesoderm, a population of midline cells of unique molecular identity. We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix. Ancestral state reconstruction suggests that contractile mesodermal midline cells existed in bilaterian ancestors. We propose that these cells, via vacuolization and stiffening, gave rise to the chordate notochord.
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Affiliation(s)
- Antonella Lauri
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg
| | - Thibaut Brunet
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg
| | - Mette Handberg-Thorsager
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg. Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Antje H L Fischer
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg
| | - Oleg Simakov
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg
| | - Patrick R H Steinmetz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg
| | - Raju Tomer
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg. Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Philipp J Keller
- Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg. Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany.
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30
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Gazave E, Guillou A, Balavoine G. History of a prolific family: the Hes/Hey-related genes of the annelid Platynereis. EvoDevo 2014; 5:29. [PMID: 25250171 PMCID: PMC4172395 DOI: 10.1186/2041-9139-5-29] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The Hes superfamily or Hes/Hey-related genes encompass a variety of metazoan-specific bHLH genes, with somewhat fuzzy phylogenetic relationships. Hes superfamily members are involved in a variety of major developmental mechanisms in metazoans, notably in neurogenesis and segmentation processes, in which they often act as direct effector genes of the Notch signaling pathway. RESULTS We have investigated the molecular and functional evolution of the Hes superfamily in metazoans using the lophotrochozoan Platynereis dumerilii as model. Our phylogenetic analyses of more than 200 Metazoan Hes/Hey-related genes revealed the presence of five families, three of them (Hes, Hey and Helt) being pan-metazoan. Those families were likely composed of a unique representative in the last common metazoan ancestor. The evolution of the Hes family was shaped by many independent lineage specific tandem duplication events. The expression patterns of 13 of the 15 Hes/Hey-related genes in Platynereis indicate a broad functional diversification. Nevertheless, a majority of these genes are involved in two crucial developmental processes in annelids: neurogenesis and segmentation, resembling functions highlighted in other animal models. CONCLUSIONS Combining phylogenetic and expression data, our study suggests an unusual evolutionary history for the Hes superfamily. An ancestral multifunctional annelid Hes gene may have undergone multiples rounds of duplication-degeneration-complementation processes in the lineage leading to Platynereis, each gene copies ensuring their maintenance in the genome by subfunctionalisation. Similar but independent waves of duplications are at the origin of the multiplicity of Hes genes in other metazoan lineages.
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Affiliation(s)
- Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, CNRS/Université Paris Diderot-Paris 7, 15 rue H. Brion, Paris cedex 13 75205, France
| | - Aurélien Guillou
- Institut Jacques Monod, CNRS, UMR 7592, CNRS/Université Paris Diderot-Paris 7, 15 rue H. Brion, Paris cedex 13 75205, France
| | - Guillaume Balavoine
- Institut Jacques Monod, CNRS, UMR 7592, CNRS/Université Paris Diderot-Paris 7, 15 rue H. Brion, Paris cedex 13 75205, France
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31
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Zantke J, Bannister S, Rajan VBV, Raible F, Tessmar-Raible K. Genetic and genomic tools for the marine annelid Platynereis dumerilii. Genetics 2014; 197:19-31. [PMID: 24807110 PMCID: PMC4012478 DOI: 10.1534/genetics.112.148254] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 02/17/2014] [Indexed: 01/27/2023] Open
Abstract
The bristle worm Platynereis dumerilii displays many interesting biological characteristics. These include its reproductive timing, which is synchronized to the moon phase, its regenerative capacity that is hormonally controlled, and a slow rate of evolution, which permits analyses of ancestral genes and cell types. As a marine annelid, Platynereis is also representative of the marine ecosystem, as well as one of the three large animal subphyla, the Lophotrochozoa. Here, we provide an overview of the molecular resources, functional techniques, and behavioral assays that have recently been established for the bristle worm. This combination of tools now places Platynereis in an excellent position to advance research at the frontiers of neurobiology, chronobiology, evo-devo, and marine biology.
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Affiliation(s)
- Juliane Zantke
- Max F. Perutz Laboratories
- Research Platform Marine Rhythms of Life, University of Vienna 1030 Vienna, Austria
| | - Stephanie Bannister
- Max F. Perutz Laboratories
- Research Platform Marine Rhythms of Life, University of Vienna 1030 Vienna, Austria
| | - Vinoth Babu Veedin Rajan
- Max F. Perutz Laboratories
- Research Platform Marine Rhythms of Life, University of Vienna 1030 Vienna, Austria
| | - Florian Raible
- Max F. Perutz Laboratories
- Research Platform Marine Rhythms of Life, University of Vienna 1030 Vienna, Austria
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories
- Research Platform Marine Rhythms of Life, University of Vienna 1030 Vienna, Austria
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32
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Backfisch B, Kozin VV, Kirchmaier S, Tessmar-Raible K, Raible F. Tools for gene-regulatory analyses in the marine annelid Platynereis dumerilii. PLoS One 2014; 9:e93076. [PMID: 24714200 PMCID: PMC3979674 DOI: 10.1371/journal.pone.0093076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/03/2014] [Indexed: 01/22/2023] Open
Abstract
The advent of high-throughput sequencing technology facilitates the exploration of a variety of reference species outside the few established molecular genetic model systems. Bioinformatic and gene expression analyses provide new ways for comparative analyses between species, for instance, in the field of evolution and development. Despite these advances, a critical bottleneck for the exploration of new model species remains the establishment of functional tools, such as the ability to experimentally express genes in specific cells of an organism. We recently established a first transgenic strain of the annelid Platynereis, using a Tc1/mariner-type Mos1 transposon vector. Here, we compare Mos1 with Tol2, a member of the hAT family of transposons. In Platynereis, Tol2-based constructs showed a higher frequency of nuclear genome insertion and sustained gene expression in the G0 generation. However, in contrast to Mos1-mediated transgenes, Tol2-mediated insertions failed to retain fluorescence in the G1 generation, suggesting a germ line-based silencing mechanism. Furthermore, we present three novel expression constructs that were generated by a simple fusion-PCR approach and allow either ubiquitous or cell-specific expression of a reporter gene. Our study indicates the versatility of Tol2 for transient transgenesis, and provides a template for transgenesis work in other emerging reference species.
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Affiliation(s)
- Benjamin Backfisch
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Vitaly V. Kozin
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Stephan Kirchmaier
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Florian Raible
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
- * E-mail:
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33
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TALENs mediate efficient and heritable mutation of endogenous genes in the marine annelid Platynereis dumerilii. Genetics 2014; 197:77-89. [PMID: 24653002 PMCID: PMC4012502 DOI: 10.1534/genetics.113.161091] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Platynereis dumerilii is a marine polychaete and an established model system for studies of evolution and development. Platynereis is also a re-emerging model for studying the molecular basis of circalunar reproductive timing: a biological phenomenon observed in many marine species. While gene expression studies have provided new insight into patterns of gene regulation, a lack of reverse genetic tools has so far limited the depth of functional analyses in this species. To address this need, we established customized transcriptional activator-like effector nucleases (TALENs) as a tool to engineer targeted modifications in Platynereis genes. By adapting a workflow of TALEN construction protocols and mutation screening approaches for use in Platynereis, we engineered frameshift mutations in three endogenous Platynereis genes. We confirmed that such mutations are heritable, demonstrating that TALENs can be used to generate homozygous knockout lines in P. dumerilii. This is the first use of TALENs for generating genetic knockout mutations in an annelid model. These tools not only open the door for detailed in vivo functional analyses, but also can facilitate further technical development, such as targeted genome editing.
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34
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Lidke AK, Bannister S, Löwer AM, Apel DM, Podleschny M, Kollmann M, Ackermann CF, García-Alonso J, Raible F, Rebscher N. 17β-Estradiol induces supernumerary primordial germ cells in embryos of the polychaete Platynereis dumerilii. Gen Comp Endocrinol 2014; 196:52-61. [PMID: 24287341 DOI: 10.1016/j.ygcen.2013.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/01/2013] [Accepted: 11/14/2013] [Indexed: 01/14/2023]
Abstract
In the polychaete Platynereis dumerilii exactly four primordial germ cells (PGCs) arise in early development and are subject to a transient mitotic arrest until the animals enter gametogenesis. In order to unravel the mechanisms controlling the number of PGCs in Platynereis, we tested whether the steroid 17β-estradiol (E2) is able to induce PGC proliferation, as it had been described in other species. Our data provide strong support for such a mechanism, showing that E2 significantly increases the occurrence of larvae with supernumerary PGCs in Platynereis in a dose dependent manner. E2 responsiveness is restricted to early developmental stages, when the PGCs are specified. During these stages, embryos exhibit high expression levels of the estradiol receptor (ER). The ER transcript localizes to the yolk-free cytoplasm of unfertilized eggs and segregates into the micromeres during cleavage stages. Nuclear ER protein is found asymmetrically distributed between daughter cells. Neither transcript nor protein is detectable in PGCs at larval stages. Addition of the specific estradiol receptor inhibitor ICI-182,780 (ICI) abolishes the proliferative effect of E2, suggesting that it is mediated by ER signaling. Our study reports for the first time an ER mediated proliferative effect of E2 on PGCs in an invertebrate organism.
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Affiliation(s)
- Anika K Lidke
- Morphology and Evolution of Invertebrates, Philipps-Universität Marburg, Germany
| | - Stephanie Bannister
- Max F. Perutz Laboratories and Research Platform "Marine Rhythms of Life", University of Vienna, Vienna, Austria
| | - Andreas M Löwer
- Morphology and Evolution of Invertebrates, Philipps-Universität Marburg, Germany
| | - David M Apel
- Morphology and Evolution of Invertebrates, Philipps-Universität Marburg, Germany
| | | | | | | | - Javier García-Alonso
- Biodiversity Group, Centro Universitario Regional Este, Universidad de la República, Maldonado, Uruguay
| | - Florian Raible
- Max F. Perutz Laboratories and Research Platform "Marine Rhythms of Life", University of Vienna, Vienna, Austria
| | - Nicole Rebscher
- Morphology and Evolution of Invertebrates, Philipps-Universität Marburg, Germany.
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Lauter G, Söll I, Hauptmann G. Sensitive whole-mount fluorescent in situ hybridization in zebrafish using enhanced tyramide signal amplification. Methods Mol Biol 2014; 1082:175-185. [PMID: 24048934 DOI: 10.1007/978-1-62703-655-9_12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Whole-mount in situ hybridization is the preferred method for detecting transcript distributions in whole embryos, tissues, and organs. We present here a sensitive fluorescent in situ hybridization method for colocalization analysis of different transcripts in whole embryonic zebrafish brains. The method is based on simultaneous hybridization of differently hapten-labeled RNA probes followed by sequential rounds of horseradish peroxidase (POD)-based transcript detection. Sequential detection involves enhancement of fluorescent signals by tyramide signal amplification (TSA) and effective inactivation of the antibody-POD conjugate prior to the following detection round. We provide a detailed description of embryo preparation, hybridization, antibody detection, POD-TSA reaction, and mounting of embryos for imaging. To achieve high signal intensities, we optimized key steps of the method. This includes improvement of embryo permeability by hydrogen peroxide treatment and efficacy of hybridization and TSA-POD reaction by addition of the viscosity-increasing polymer dextran sulfate. The TSA-POD reaction conditions are further optimized by application of substituted phenol compounds as POD accelerators and use of highly efficient bench-made tyramide substrates. The obtained high signal intensities and cellular resolution of our method allows for co-expression analysis and generation of three-dimensional models. Our protocol is tailored to optimally work in zebrafish embryos, but can surely be modified for application in other species as well.
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Affiliation(s)
- Gilbert Lauter
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, Sweden
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Posterior elongation in the annelid Platynereis dumerilii involves stem cells molecularly related to primordial germ cells. Dev Biol 2013; 382:246-67. [DOI: 10.1016/j.ydbio.2013.07.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 06/28/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022]
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Circadian and circalunar clock interactions in a marine annelid. Cell Rep 2013; 5:99-113. [PMID: 24075994 PMCID: PMC3913041 DOI: 10.1016/j.celrep.2013.08.031] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 07/03/2013] [Accepted: 08/28/2013] [Indexed: 12/11/2022] Open
Abstract
Life is controlled by multiple rhythms. Although the interaction of the daily (circadian) clock with environmental stimuli, such as light, is well documented, its relationship to endogenous clocks with other periods is little understood. We establish that the marine worm Platynereis dumerilii possesses endogenous circadian and circalunar (monthly) clocks and characterize their interactions. The RNAs of likely core circadian oscillator genes localize to a distinct nucleus of the worm’s forebrain. The worm’s forebrain also harbors a circalunar clock entrained by nocturnal light. This monthly clock regulates maturation and persists even when circadian clock oscillations are disrupted by the inhibition of casein kinase 1δ/ε. Both circadian and circalunar clocks converge on the regulation of transcript levels. Furthermore, the circalunar clock changes the period and power of circadian behavior, although the period length of the daily transcriptional oscillations remains unaltered. We conclude that a second endogenous noncircadian clock can influence circadian clock function. Marine worms coexpress circadian clock gene orthologs in the forebrain and eye The circalunar clock is functional in the absence of circadian clock oscillations The circalunar clock changes the period length of circadian-clock-controlled behavior The circalunar clock does not change the period of circadian molecular oscillations
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Döring C, Gosda J, Tessmar-Raible K, Hausen H, Arendt D, Purschke G. Evolution of clitellate phaosomes from rhabdomeric photoreceptor cells of polychaetes - a study in the leech Helobdella robusta (Annelida, Sedentaria, Clitellata). Front Zool 2013; 10:52. [PMID: 24007384 PMCID: PMC3846555 DOI: 10.1186/1742-9994-10-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 08/20/2013] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION In Annelida two types of photoreceptor cells (PRCs) are regarded as generally present, rhabdomeric and ciliary PRCs. In certain taxa, however, an additional type of PRC may occur, the so called phaosomal PRC. Whereas the former two types of PRCs are always organized as an epithelium with their sensory processes projecting into an extracellular cavity formed by the PRCs and (pigmented) supportive cells, phaosomes are seemingly intracellular vacuoles housing the sensory processes. Phaosomal PRCs are the only type of PRC found in one major annelid group, Clitellata. Several hypotheses have been put forward explaining the evolutionary origin of the clitellate phaosomes. To elucidate the evolution of clitellate PRC and eyes the leech Helobdella robusta, for which a sequenced genome is available, was chosen. RESULTS TEM observations showed that extraocular and ocular PRCs are structurally identical. Bioinformatic analyses revealed predictions for four opsin genes, three of which could be amplified. All belong to the rhabdomeric opsin family and phylogenetic analyses showed them in a derived position within annelid opsins. Gene expression studies showed two of them expressed in the eye and in the extraocular PRCs. Polychaete eye-typic key enzymes for ommochromme and pterin shading pigments synthesis are not expressed in leech eyes. CONCLUSIONS By comparative gene-expression studies we herein provide strong evidence that the phaosomal PRCs typical of Clitellata are derived from the rhabdomeric PRCs characteristic for polychaete adult eyes. Thus, they represent a highly derived type of PRC that evolved in the stem lineage of Clitellata rather than another, primitive type of PRC in Metazoa. Evolution of these PRCs in Clitellata is related to a loss of the primary eyes and most of their photoreceptive elements except for the rhabdomeric PRCs. Most likely this happened while changing to an endobenthic mode of life. This hypothesis of PRC evolution is in accordance with a recently published phylogeny of Annelida based on phylogenomic data. The data provide a nice example how morphologically highly divergent light sensitive structures emerged from a standard type of photoreceptor cell.
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Affiliation(s)
- Carmen Döring
- Universität Osnabrück, Zoologie, Osnabrück 49069, Germany
| | - Jasmin Gosda
- Universität Osnabrück, Zoologie, Osnabrück 49069, Germany
- Present address: Kopernikusstrasse 5, 48477 Hörstel, Germany
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, Universität Wien, Campus Vienna Biocenter, Austria Research Plattform “Marine Rhythms of Life”, Dr. Bohr–Gasse 9/4, 1030 Wien, Austria
| | - Harald Hausen
- Sars International Centre for Marine Molecular Biology, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Detlev Arendt
- Developmental Biology Programme, European Molecular Biology Laboratory, Meyerhofstraße 1, D-69012 Heidelberg, Germany
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Fischer AHL, Tulin S, Fredman D, Smith J. Employing BAC-reporter constructs in the sea anemone Nematostella vectensis. Integr Comp Biol 2013; 53:832-46. [PMID: 23956207 DOI: 10.1093/icb/ict091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Changes in the expression and function of genes drive evolutionary change. Comparing how genes are regulated in different species is therefore becoming an important part of evo-devo studies. A key tool for investigating the regulation of genes is represented by bacterial artificial chromosomes (BAC)-reporter constructs. BACs are large insert libraries, often >100 kb, which thus capture the genomic sequences surrounding a gene of interest, including all, or nearly all, of the elements underpinning regulation. Recombinant BACs, containing a reporter gene in place of the endogenous coding sequence of genes, can be utilized to drive the expression of reporter genes under the regulatory control of the gene of interest while still embedded within its genomic context. Systematic deletions within the BAC-reporter construct can be used to identify the minimal reporter in an unbiased way, avoiding the risk of overlooking regulatory elements that may be many kilobases away from the transcription start-site. Nematostella vectensis (Edwardsiidae, Anthozoa, Cnidaria) has become an important model in regenerative biology, ecology, and especially in studies of evo-devo and gene-regulatory networks due to its interesting phylogenetic position and amenability to molecular techniques. The increasing interest in this rising model system also led to a demand for methods that can be used to study the regulation of genes in Nematostella. Here, we present our progress in employing BAC-reporter constructs to visualize gene-expression in Nematostella. Using a new Nematostella-specific recombination cassette, we made nine different BAC-reporter constructs. Although five BAC recombinants gave variable effects, three constructs, namely Nv-bra:eGFP::L10 BAC, Nv-dpp:eGFP::L10 BAC, and Nv-grm:eGFP::L10 BAC delivered promising results. We show that these three constructs express the reporter gene eGFP in 10.4-17.2% of all analyzed larvae, out of which 26.2-41.9% express GFP in a mosaic fashion within the expected domain. In addition to the expression within the known domains, we also observed cases of misexpression of eGFP and examples that could represent actual expression outside the described domain. Furthermore, we deep-sequenced and assembled five different BACs containing Nv-chordin, Nv-foxa, Nv-dpp, Nv-wnta, and Nv-wnt1, to improve assembly around these genes. The use of BAC-reporter constructs will foster cis-regulatory analyses in Nematostella and thus help to improve our understanding of the regulatory network in this cnidarian system. Ultimately, this will advance the comparison of gene-regulation across species and lead to a much better understanding of evolutionary changes and novelties.
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Affiliation(s)
- Antje H L Fischer
- *Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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Randel N, Bezares-Calderón LA, Gühmann M, Shahidi R, Jékely G. Expression dynamics and protein localization of rhabdomeric opsins in Platynereis larvae. Integr Comp Biol 2013; 53:7-16. [PMID: 23667045 PMCID: PMC3687135 DOI: 10.1093/icb/ict046] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The larval stages of polychaete annelids are often responsive to light and can possess one to six eyes. The early trochophore larvae of the errant annelid Platynereis dumerilii have a single pair of ventral eyespots, whereas older nectochaete larvae have an additional two pairs of dorsal eyes that will develop into the adult eyes. Early Platynereis trochophores show robust positive phototaxis starting on the first day of development. Even though the mechanism of phototaxis in Platynereis early trochophore larvae is well understood, no photopigment (opsin) expression has yet been described in this stage. In late trochophore larvae, a rhabdomeric-type opsin, r-opsin1, expressed in both the eyespots and the adult eyes has already been reported. Here, we identify another Platynereis rhabdomeric opsin, r-opsin3, that is expressed in a single photoreceptor in the eyespots in early trochophores, suggesting that it mediates early larval phototaxis. We also show that r-opsin1 and r-opsin3 are expressed in adjacent photoreceptor cells in the eyespots in later stages, indicating that a second eyespot-photoreceptor differentiates in late trochophore larvae. Using serial transmission electron microscopy (TEM), we identified and reconstructed both photoreceptors and a pigment cell in the late larval eyespot. We also characterized opsin expression in the adult eyes and found that the two opsins co-express there in several photoreceptor cells. Using antibodies recognizing r-opsin1 and r-opsin3 proteins, we demonstrate that both opsins localize to the rhabdomere in all six eyes. In addition, we found that r-opsin1 mRNA is localized to, and translated in, the projections of the adult eyes. The specific changes we describe in opsin transcription and translation and in the cellular complement suggest that the six larval eyes undergo spectral and functional maturation during the early planktonic phase of the Platynereis life cycle.
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Affiliation(s)
- Nadine Randel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tuebingen, Germany
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Wolenski FS, Layden MJ, Martindale MQ, Gilmore TD, Finnerty JR. Characterizing the spatiotemporal expression of RNAs and proteins in the starlet sea anemone, Nematostella vectensis. Nat Protoc 2013; 8:900-15. [PMID: 23579779 DOI: 10.1038/nprot.2013.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In an effort to reconstruct the early evolution of animal genes and proteins, there is an increasing focus on basal animal lineages such as sponges, cnidarians, ctenophores and placozoans. Among the basal animals, the starlet sea anemone Nematostella vectensis (phylum Cnidaria) has emerged as a leading laboratory model organism partly because it is well suited to experimental techniques for monitoring and manipulating gene expression. Here we describe protocols adapted for use in Nematostella to characterize the expression of RNAs by in situ hybridization using either chromogenic or fluorescence immunohistochemistry (∼1 week), as well as to characterize protein expression by whole-mount immunofluorescence (∼3 d). We also provide a protocol for labeling cnidocytes (∼3 h), the phylum-specific sensory-effector cell type that performs a variety of functions in cnidarians, including the delivery of their venomous sting.
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Backfisch B, Veedin Rajan VB, Fischer RM, Lohs C, Arboleda E, Tessmar-Raible K, Raible F. Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution. Proc Natl Acad Sci U S A 2013; 110:193-8. [PMID: 23284166 PMCID: PMC3538230 DOI: 10.1073/pnas.1209657109] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Research in eye evolution has mostly focused on eyes residing in the head. In contrast, noncephalic light sensors are far less understood and rather regarded as evolutionary innovations. We established stable transgenesis in the annelid Platynereis, a reference species for evolutionary and developmental comparisons. EGFP controlled by cis-regulatory elements of r-opsin, a characteristic marker for rhabdomeric photoreceptors, faithfully recapitulates known r-opsin expression in the adult eyes, and marks a pair of pigment-associated frontolateral eyelets in the brain. Unexpectedly, transgenic animals revealed an additional series of photoreceptors in the ventral nerve cord as well as photoreceptors that are located in each pair of the segmental dorsal appendages (notopodia) and project into the ventral nerve cord. Consistent with a photosensory function of these noncephalic cells, decapitated animals display a clear photoavoidance response. Molecular analysis of the receptors suggests that they differentiate independent of pax6, a gene involved in early eye development of many metazoans, and that the ventral cells may share origins with the Hesse organs in the amphioxus neural tube. Finally, expression analysis of opn4×-2 and opn4m-2, two zebrafish orthologs of Platynereis r-opsin, reveals that these genes share expression in the neuromasts, known mechanoreceptors of the lateral line peripheral nervous system. Together, this establishes that noncephalic photoreceptors are more widespread than assumed, and may even reflect more ancient aspects of sensory systems. Our study marks significant advance for the understanding of photoreceptor cell (PRC) evolution and development and for Platynereis as a functional lophotrochozoan model system.
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Affiliation(s)
| | | | - Ruth M. Fischer
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology, and Genetics, University of Vienna, A-1030 Vienna, Austria
| | | | | | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology, and Genetics, University of Vienna, A-1030 Vienna, Austria
| | - Florian Raible
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology, and Genetics, University of Vienna, A-1030 Vienna, Austria
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Abstract
Annelids (the segmented worms) have a long history in studies of animal developmental biology, particularly with regards to their cleavage patterns during early development and their neurobiology. With the relatively recent reorganisation of the phylogeny of the animal kingdom, and the distinction of the super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus for studying this phylum has arisen. As one of the major phyla within Lophotrochozoa, Annelida are playing an important role in deducing the developmental biology of the last common ancestor of the protostomes and deuterostomes, an animal from which >98% of all described animal species evolved.
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Affiliation(s)
- David E. K. Ferrier
- The Scottish Oceans Institute, the Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK
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Lauter G, Söll I, Hauptmann G. Two-color fluorescent in situ hybridization in the embryonic zebrafish brain using differential detection systems. BMC DEVELOPMENTAL BIOLOGY 2011; 11:43. [PMID: 21726453 PMCID: PMC3141750 DOI: 10.1186/1471-213x-11-43] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/04/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Whole-mount in situ hybridization (WISH) is extensively used to characterize gene expression patterns in developing and adult brain and other tissues. To obtain an idea whether a novel gene might be involved in specification of a distinct brain subdivision, nucleus or neuronal lineage, it is often useful to correlate its expression with that of a known regional or neuronal marker gene. Two-color fluorescent in situ hybridization (FISH) can be used to compare different transcript distributions at cellular resolution. Conventional two-color FISH protocols require two separate rounds of horseradish peroxidase (POD)-based transcript detection, which involves tyramide signal amplification (TSA) and inactivation of the first applied antibody-enzyme conjugate before the second detection round. RESULTS We show here that the alkaline phosphatase (AP) substrates Fast Red and Fast Blue can be used for chromogenic as well as fluorescent visualization of transcripts. To achieve high signal intensities we optimized embryo permeabilization properties by hydrogen peroxide treatment and hybridization conditions by application of the viscosity-increasing polymer dextran sulfate. The obtained signal enhancement allowed us to develop a sensitive two-color FISH protocol by combining AP and POD reporter systems. We show that the combination of AP-Fast Blue and POD-TSA-carboxyfluorescein (FAM) detection provides a powerful tool for simultaneous fluorescent visualization of two different transcripts in the zebrafish brain. The application of different detection systems allowed for a one-step antibody detection procedure for visualization of transcripts, which significantly reduced working steps and hands-on time shortening the protocol by one day. Inactivation of the first applied reporter enzyme became unnecessary, so that false-positive detection of co-localization by insufficient inactivation, a problem of conventional two-color FISH, could be eliminated. CONCLUSION Since POD activity is rather quickly quenched by substrate excess, less abundant transcripts can often not be efficiently visualized even when applying TSA. The use of AP-Fast Blue fluorescent detection may provide a helpful alternative for fluorescent transcript visualization, as the AP reaction can proceed for extended times with a high signal-to-noise ratio. Our protocol thus provides a novel alternative for comparison of two different gene expression patterns in the embryonic zebrafish brain at a cellular level. The principles of our method were developed for use in zebrafish but may be easily included in whole-mount FISH protocols of other model organisms.
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Affiliation(s)
- Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
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Coe genes are expressed in differentiating neurons in the central nervous system of protostomes. PLoS One 2011; 6:e21213. [PMID: 21695052 PMCID: PMC3117877 DOI: 10.1371/journal.pone.0021213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/23/2011] [Indexed: 11/19/2022] Open
Abstract
Genes of the coe (collier/olfactory/early B-cell factor) family encode Helix-Loop-Helix transcription factors that are widely conserved in metazoans and involved in many developmental processes, neurogenesis in particular. Whereas their functions during vertebrate neural tube formation have been well documented, very little is known about their expression and role during central nervous system (CNS) development in protostomes. Here we characterized the CNS expression of coe genes in the insect Drosophila melanogaster and the polychaete annelid Platynereis dumerilii, which belong to different subgroups of protostomes and show strikingly different modes of development. In the Drosophila ventral nerve cord, we found that the Collier-expressing cells form a subpopulation of interneurons with diverse molecular identities and neurotransmitter phenotypes. We also demonstrate that collier is required for the proper differentiation of some interneurons belonging to the Eve-Lateral cluster. In Platynereis dumerilii, we cloned a single coe gene, Pdu-coe, and found that it is exclusively expressed in post mitotic neural cells. Using an original technique of in silico 3D registration, we show that Pdu-coe is co-expressed with many different neuronal markers and therefore that, like in Drosophila, its expression defines a heterogeneous population of neurons with diverse molecular identities. Our detailed characterization and comparison of coe gene expression in the CNS of two distantly-related protostomes suggest conserved roles of coe genes in neuronal differentiation in this clade. As similar roles have also been observed in vertebrates, this function was probably already established in the last common ancestor of all bilaterians.
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Steinmetz PRH, Kostyuchenko RP, Fischer A, Arendt D. The segmental pattern of otx, gbx, and Hox genes in the annelid Platynereis dumerilii. Evol Dev 2011; 13:72-9. [PMID: 21210944 DOI: 10.1111/j.1525-142x.2010.00457.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SUMMARY Annelids and arthropods, despite their distinct classification as Lophotrochozoa and Ecdysozoa, present a morphologically similar, segmented body plan. To elucidate the evolution of segmentation and, ultimately, to align segments across remote phyla, we undertook a refined expression analysis to precisely register the expression of conserved regionalization genes with morphological boundaries and segmental units in the marine annelid Platynereis dumerilii. We find that Pdu-otx defines a brain region anterior to the first discernable segmental entity that is delineated by a stripe of engrailed-expressing cells. The first segment is a "cryptic" segment that lacks chaetae and parapodia. This and the subsequent three chaetigerous larval segments harbor the anterior expression boundary of gbx, hox1, hox4, and lox5 genes, respectively. This molecular segmental topography matches the segmental pattern of otx, gbx, and Hox gene expression in arthropods. Our data thus support the view that an ancestral ground pattern of segmental identities existed in the trunk of the last common protostome ancestor that was lost or modified in protostomes lacking overt segmentation.
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Affiliation(s)
- Patrick R H Steinmetz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
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Lauter G, Söll I, Hauptmann G. Multicolor fluorescent in situ hybridization to define abutting and overlapping gene expression in the embryonic zebrafish brain. Neural Dev 2011; 6:10. [PMID: 21466670 PMCID: PMC3088888 DOI: 10.1186/1749-8104-6-10] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 04/05/2011] [Indexed: 11/23/2022] Open
Abstract
Background In recent years, mapping of overlapping and abutting regulatory gene expression domains by chromogenic two-color in situ hybridization has helped define molecular subdivisions of the developing vertebrate brain and shed light on its basic organization. Despite the benefits of this technique, visualization of overlapping transcript distributions by differently colored precipitates remains difficult because of masking of lighter signals by darker color precipitates and lack of three-dimensional visualization properties. Fluorescent detection of transcript distributions may be able to solve these issues. However, despite the use of signal amplification systems for increasing sensitivity, fluorescent detection in whole-mounts suffers from rapid quenching of peroxidase (POD) activity compared to alkaline phosphatase chromogenic reactions. Thus, less strongly expressed genes cannot be efficiently detected. Results We developed an optimized procedure for fluorescent detection of transcript distribution in whole-mount zebrafish embryos using tyramide signal amplification (TSA). Conditions for hybridization and POD-TSA reaction were optimized by the application of the viscosity-increasing polymer dextran sulfate and the use of the substituted phenol compounds 4-iodophenol and vanillin as enhancers of POD activity. In combination with highly effective bench-made tyramide substrates, these improvements resulted in dramatically increased signal-to-noise ratios. The strongly enhanced signal intensities permitted fluorescent visualization of less abundant transcripts of tissue-specific regulatory genes. When performing multicolor fluorescent in situ hybridization (FISH) experiments, the highly sensitive POD reaction conditions required effective POD inactivation after each detection cycle by glycine-hydrochloric acid treatment. This optimized FISH procedure permitted the simultaneous fluorescent visualization of up to three unique transcripts in different colors in whole-mount zebrafish embryos. Conclusions Development of a multicolor FISH procedure allowed the comparison of transcript gene expression domains in the embryonic zebrafish brain to a cellular level. Likewise, this method should be applicable for mRNA colocalization studies in any other tissues or organs. The key optimization steps of this method for use in zebrafish can easily be implemented in whole-mount FISH protocols of other organisms. Moreover, our improved reaction conditions may be beneficial in any application that relies on a TSA/POD-mediated detection system, such as immunocytochemical or immunohistochemical methods.
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Affiliation(s)
- Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
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Tessmar-Raible K, Raible F, Arboleda E. Another place, another timer: Marine species and the rhythms of life. Bioessays 2011; 33:165-72. [PMID: 21254149 PMCID: PMC3182551 DOI: 10.1002/bies.201000096] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The marine ecosystem is governed by a multitude of environmental cycles, all of which are linked to the periodical recurrence of the sun or the moon. In accordance with these cycles, marine species exhibit a variety of biological rhythms, ranging from circadian and circatidal rhythms to circalunar and seasonal rhythms. However, our current molecular understanding of biological rhythms and clocks is largely restricted to solar-controlled circadian and seasonal rhythms in land model species. Here, we discuss the first molecular data emerging for circalunar and circatidal rhythms and present selected species suitable for further molecular analyses. We argue that a re-focus on marine species will be crucial to understand the principles, interactions and evolution of rhythms that govern a broad range of eukaryotes, including ourselves.
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Abstract
Examination of spatial and temporal gene expression pattern is a key step towards understanding gene function. Therefore, in situ hybridization of mRNA is one of the most powerful and widely used -techniques in biology. Recent advances allow the reliable and simultaneous detection of mRNA transcripts, or combinations of mRNA and protein, in zebrafish embryos.Here we describe a standard protocol for visualizing the precise expression pattern of a single transcript or multiple gene products. The procedure employs fixation and permeabilization of embryos, followed by hybridization with tagged antisense riboprobes. Excess probes are then washed and hybrids are detected by enzyme-mediated immunohistochemistry utilizing either chromogenic or fluorescent substrates.
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Affiliation(s)
- Yossy Machluf
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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Fischer AHL, Henrich T, Arendt D. The normal development of Platynereis dumerilii (Nereididae, Annelida). Front Zool 2010; 7:31. [PMID: 21192805 PMCID: PMC3027123 DOI: 10.1186/1742-9994-7-31] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 12/30/2010] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The polychaete annelid Platynereis dumerilii is an emerging model organism for the study of molecular developmental processes, evolution, neurobiology and marine biology. Annelids belong to the Lophotrochozoa, the so far understudied third major branch of bilaterian animals besides deuterostomes and ecdysozoans. P. dumerilii has proven highly relevant to explore ancient bilaterian conditions via comparison to the deuterostomes, because it has accumulated less evolutionary change than conventional ecdysozoan models. Previous staging was mainly referring to hours post fertilization but did not allow matching stages between studies performed at (even slightly) different temperatures. To overcome this, and to provide a first comprehensive description of P. dumerilii normal development, a temperature-independent staging system is needed. RESULTS Platynereis dumerilii normal development is subdivided into 16 stages, starting with the zygote and ending with the death of the mature worms after delivering their gametes. The stages described can be easily identified by conventional light microscopy or even by dissecting scope. Developmental landmarks such as the beginning of phototaxis, the visibility of the stomodeal opening and of the chaetae, the first occurrence of the ciliary bands, the formation of the parapodia, the extension of antennae and cirri, the onset of feeding and other characteristics are used to define different developmental stages. The morphology of all larval stages as well as of juveniles and adults is documented by light microscopy. We also provide an overview of important steps in the development of the nervous system and of the musculature, using fluorescent labeling techniques and confocal laser-scanning microscopy. Timing of each developmental stage refers to hours post fertilization at 18 ± 0.1°C. For comparison, we determined the pace of development of larvae raised at 14°C, 16°C, 20°C, 25°C, 28°C and 30°C. A staging ontology representing the comprehensive list of developmental stages of P. dumerilii is available online. CONCLUSIONS Our atlas of Platynereis dumerilii normal development represents an important resource for the growing Platynereis community and can also be applied to other nereidid annelids.
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Affiliation(s)
- Antje HL Fischer
- Developmental Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Thorsten Henrich
- Developmental Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
- International College, Osaka University, A217 School of Science Main Building 1-1, Machikaneyama-machi, Toyonaka, Osaka, 560-0043, Japan
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
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