1
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Porras MÁG, Assié A, Tietjen M, Violette M, Kleiner M, Gruber-Vodicka H, Dubilier N, Leisch N. An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host. Nat Microbiol 2024:10.1038/s41564-024-01808-5. [PMID: 39242818 DOI: 10.1038/s41564-024-01808-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 08/13/2024] [Indexed: 09/09/2024]
Abstract
A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.
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Affiliation(s)
| | - Adrien Assié
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Målin Tietjen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marlene Violette
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- European Molecular Biology Laboratory, Heidelberg, Germany.
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2
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Sharma N, Jung M, Mishra PK, Mun JY, Rhee HW. FLEX: genetically encodable enzymatic fluorescence signal amplification using engineered peroxidase. Cell Chem Biol 2024; 31:S2451-9456(24)00081-3. [PMID: 38513646 DOI: 10.1016/j.chembiol.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Fluorescent tagging of biomolecules enables their sensitive detection during separation and determining their subcellular location. In this context, peroxidase-based reactions are actively utilized for signal amplification. To harness this potential, we developed a genetically encodable enzymatic fluorescence signal amplification method using APEX (FLEX). We synthesized a fluorescent probe, Jenfluor triazole (JFT1), which effectively amplifies and restricts fluorescence signals under fixed conditions, enabling fluorescence-based detection of subcellularly localized electron-rich metabolites. Moreover, JFT1 exhibited stable fluorescence signals even under osmium-treated and polymer-embedded conditions, which supported findings from correlative light and electron microscopy (CLEM) using APEX. Using various APEX-conjugated proteins of interest (POIs) targeted to different organelles, we successfully visualized their localization through FLEX imaging while effectively preserving organelle ultrastructures. FLEX provides insights into dynamic lysosome-mitochondria interactions upon exposure to chemical stressors. Overall, FLEX holds significant promise as a sensitive and versatile system for fluorescently detecting APEX2-POIs in multiscale biological samples.
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Affiliation(s)
- Nirmali Sharma
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Minkyo Jung
- Neural Circuits Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | | | - Ji Young Mun
- Neural Circuits Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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3
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Joli N, Concia L, Mocaer K, Guterman J, Laude J, Guerin S, Sciandra T, Bruyant F, Ait-Mohamed O, Beguin M, Forget MH, Bourbousse C, Lacour T, Bailleul B, Nef C, Savoie M, Tremblay JE, Campbell DA, Lavaud J, Schwab Y, Babin M, Bowler C. Hypometabolism to survive the long polar night and subsequent successful return to light in the diatom Fragilariopsis cylindrus. THE NEW PHYTOLOGIST 2024; 241:2193-2208. [PMID: 38095198 DOI: 10.1111/nph.19387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 02/09/2024]
Abstract
Diatoms, the main eukaryotic phytoplankton of the polar marine regions, are essential for the maintenance of food chains specific to Arctic and Antarctic ecosystems, and are experiencing major disturbances under current climate change. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their endurance during the long polar night. Here, using the polar diatom Fragilariopsis cylindrus, we report an integrative analysis combining transcriptomic, microscopic and biochemical approaches to shed light on the strategies used to survive the polar night. We reveal that in prolonged darkness, diatom cells enter a state of quiescence with reduced metabolic and transcriptional activity, during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness, including the appearance of a large vacuole. Our results further show that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis, demonstrating the remarkable robustness of polar diatoms to prolonged darkness at low temperature.
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Affiliation(s)
- Nathalie Joli
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Lorenzo Concia
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Karel Mocaer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) & Collaboration for Joint PhD Degree between the European Molecular Biology Laboratory and the Heidelberg University, Faculty of Biosciences, 69117, Heidelberg, Germany
| | - Julie Guterman
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Juliette Laude
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Sebastien Guerin
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Theo Sciandra
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Flavienne Bruyant
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Ouardia Ait-Mohamed
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Marine Beguin
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Marie-Helene Forget
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Thomas Lacour
- Laboratoire PHYSiologie des micro ALGues (PDG-ODE-PHYTOX-PHYSALG), Centre Atlantique, 44 311, Nantes, France
| | - Benjamin Bailleul
- Laboratory of Chloroplast Biology and Light Sensing in Microalgae, Institut de Biologie Physico Chimique, CNRS, Sorbonne Université, Paris, 75005, France
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Mireille Savoie
- Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada
| | | | | | - Johann Lavaud
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
- UMR 6539 LEMAR-Laboratory of Environmental Marine Sciences, CNRS/Univ Brest/Ifremer/IRD, IUEM-Institut Européen de la Mer, Technopôle Brest-Iroise, rue Dumont d'Urville, 29280, Plouzané, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit and Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Marcel Babin
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
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4
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Drescher B, Sant HH, Schalek RL, Lichtman JW, Katz PS. Sample preparation methods for volume electron microscopy in mollusc Berghia stephanieae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581936. [PMID: 38464069 PMCID: PMC10925166 DOI: 10.1101/2024.02.25.581936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Creating a high-resolution brain atlas in diverse species offers crucial insights into general principles underlying brain function and development. A volume electron microscopy approach to generate such neural maps has been gaining importance due to advances in imaging, data storage capabilities, and data analysis protocols. Sample preparation remains challenging and is a crucial step to accelerate the imaging and data processing pipeline. Here, we introduce several replicable methods for processing the brains of the gastropod mollusc, Berghia stephanieae for volume electron microscopy. Although high-pressure freezing is the most reliable method, the depth of cryopreservation is a severe limitation for large tissue samples. We introduce a BROPA-based method using pyrogallol and methods to rapidly process samples that can save hours at the bench. This is the first report on sample preparation and imaging pipeline for volume electron microscopy in a gastropod mollusc, opening up the potential for connectomic analysis and comparisons with other phyla.
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5
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Nalezinková M, Loskot J, Myslivcová Fučíková A. The use of scanning electron microscopy and fixation methods to evaluate the interaction of blood with the surfaces of medical devices. Sci Rep 2024; 14:4622. [PMID: 38409219 PMCID: PMC10897226 DOI: 10.1038/s41598-024-55136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
Testing the hemocompatibility of medical devices after their interaction with blood entails the need to evaluate the activation of blood elements and the degree of their coagulation and adhesion to the device surface. One possible way to achieve this is to use scanning electron microscopy (SEM). The aim was to develop a novel SEM-based method to assess the thrombogenic potential of medical devices and their adhesiveness to blood cells. As a part of this task, also find a convenient procedure of efficient and non-destructive sample fixation for SEM while reducing the use of highly toxic substances and shortening the fixation time. A polymeric surgical mesh was exposed to blood so that blood elements adhered to its surface. Such prepared samples were then chemically fixed for a subsequent SEM measurement; a number of fixation procedures were tested to find the optimal one. The fixation results were evaluated from SEM images, and the degree of blood elements' adhesion was determined from the images using ImageJ software. The best fixation was achieved with the May-Grünwald solution, which is less toxic than chemicals traditionally used. Moreover, manipulation with highly toxic osmium tetroxide can be avoided in the proposed procedure. A convenient methodology for SEM image analysis has been developed too, enabling to quantitatively evaluate the interaction of blood with the surfaces of various medical devices. Our method replaces the subjective assessment of surface coverage with a better-defined procedure, thus offering more precise and reliable results.
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Affiliation(s)
- Martina Nalezinková
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic.
| | - Jan Loskot
- Department of Physics, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
| | - Alena Myslivcová Fučíková
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
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6
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Resseguier J, Nguyen-Chi M, Wohlmann J, Rigaudeau D, Salinas I, Oehlers SH, Wiegertjes GF, Johansen FE, Qiao SW, Koppang EO, Verrier B, Boudinot P, Griffiths G. Identification of a pharyngeal mucosal lymphoid organ in zebrafish and other teleosts: Tonsils in fish? SCIENCE ADVANCES 2023; 9:eadj0101. [PMID: 37910624 PMCID: PMC10619939 DOI: 10.1126/sciadv.adj0101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023]
Abstract
The constant exposure of the fish branchial cavity to aquatic pathogens causes local mucosal immune responses to be extremely important for their survival. Here, we used a marker for T lymphocytes/natural killer (NK) cells (ZAP70) and advanced imaging techniques to investigate the lymphoid architecture of the zebrafish branchial cavity. We identified a sub-pharyngeal lymphoid organ, which we tentatively named "Nemausean lymphoid organ" (NELO). NELO is enriched in T/NK cells, plasma/B cells, and antigen-presenting cells embedded in a network of reticulated epithelial cells. The presence of activated T cells and lymphocyte proliferation, but not V(D)J recombination or hematopoiesis, suggests that NELO is a secondary lymphoid organ. In response to infection, NELO displays structural changes including the formation of T/NK cell clusters. NELO and gill lymphoid tissues form a cohesive unit within a large mucosal lymphoid network. Collectively, we reveal an unreported mucosal lymphoid organ reminiscent of mammalian tonsils that evolved in multiple teleost fish families.
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Affiliation(s)
- Julien Resseguier
- Section for Physiology and Cell Biology, Departments of Biosciences and Immunology, University of Oslo, Oslo, Norway
| | - Mai Nguyen-Chi
- LPHI, CNRS, Université de Montpellier, Montpellier, France
| | - Jens Wohlmann
- Electron-Microscopy laboratory, Departments of Biosciences, University of Oslo, Oslo, Norway
| | | | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Stefan H. Oehlers
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore 138648, Singapore
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Finn-Eirik Johansen
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Erling O. Koppang
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Bernard Verrier
- Laboratory of Tissue Biology and Therapeutic Engineering, UMR 5305, IBCP, CNRS, University Lyon 1, Lyon, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Gareth Griffiths
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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7
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Formery L, Peluso P, Kohnle I, Malnick J, Thompson JR, Pitel M, Uhlinger KR, Rokhsar DS, Rank DR, Lowe CJ. Molecular evidence of anteroposterior patterning in adult echinoderms. Nature 2023; 623:555-561. [PMID: 37914929 DOI: 10.1038/s41586-023-06669-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/22/2023] [Indexed: 11/03/2023]
Abstract
The origin of the pentaradial body plan of echinoderms from a bilateral ancestor is one of the most enduring zoological puzzles1,2. Because echinoderms are defined by morphological novelty, even the most basic axial comparisons with their bilaterian relatives are problematic. To revisit this classical question, we used conserved anteroposterior axial molecular markers to determine whether the highly derived adult body plan of echinoderms masks underlying patterning similarities with other deuterostomes. We investigated the expression of a suite of conserved transcription factors with well-established roles in the establishment of anteroposterior polarity in deuterostomes3-5 and other bilaterians6-8 using RNA tomography and in situ hybridization in the sea star Patiria miniata. The relative spatial expression of these markers in P. miniata ambulacral ectoderm shows similarity with other deuterostomes, with the midline of each ray representing the most anterior territory and the most lateral parts exhibiting a more posterior identity. Strikingly, there is no ectodermal territory in the sea star that expresses the characteristic bilaterian trunk genetic patterning programme. This finding suggests that from the perspective of ectoderm patterning, echinoderms are mostly head-like animals and provides a developmental rationale for the re-evaluation of the events that led to the evolution of the derived adult body plan of echinoderms.
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Affiliation(s)
- L Formery
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
| | - P Peluso
- Pacific Biosciences, Menlo Park, CA, USA
| | - I Kohnle
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - J Malnick
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - J R Thompson
- School of Biological Sciences, University of Southampton, Southampton, UK
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - M Pitel
- Columbia Equine Hospital, Gresham, OR, USA
| | - K R Uhlinger
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - D S Rokhsar
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - D R Rank
- Pacific Biosciences, Menlo Park, CA, USA
| | - C J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA.
- Chan Zuckerberg BioHub, San Francisco, CA, USA.
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8
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Najle SR, Grau-Bové X, Elek A, Navarrete C, Cianferoni D, Chiva C, Cañas-Armenteros D, Mallabiabarrena A, Kamm K, Sabidó E, Gruber-Vodicka H, Schierwater B, Serrano L, Sebé-Pedrós A. Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell 2023; 186:4676-4693.e29. [PMID: 37729907 PMCID: PMC10580291 DOI: 10.1016/j.cell.2023.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
The assembly of the neuronal and other major cell type programs occurred early in animal evolution. We can reconstruct this process by studying non-bilaterians like placozoans. These small disc-shaped animals not only have nine morphologically described cell types and no neurons but also show coordinated behaviors triggered by peptide-secreting cells. We investigated possible neuronal affinities of these peptidergic cells using phylogenetics, chromatin profiling, and comparative single-cell genomics in four placozoans. We found conserved cell type expression programs across placozoans, including populations of transdifferentiating and cycling cells, suggestive of active cell type homeostasis. We also uncovered fourteen peptidergic cell types expressing neuronal-associated components like the pre-synaptic scaffold that derive from progenitor cells with neurogenesis signatures. In contrast, earlier-branching animals like sponges and ctenophores lacked this conserved expression. Our findings indicate that key neuronal developmental and effector gene modules evolved before the advent of cnidarian/bilaterian neurons in the context of paracrine cell signaling.
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Affiliation(s)
- Sebastián R Najle
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Chiva
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Didac Cañas-Armenteros
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Arrate Mallabiabarrena
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany; American Museum of Natural History, Richard Gilder Graduate School, NY, USA
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain.
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9
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Hussain NM, Amin B, O’Halloran M, Elahi A. Development and Characterization of Interstitial-Fluid-Mimicking Solutions for Pre-Clinical Assessment of Hypoxia. Diagnostics (Basel) 2023; 13:3125. [PMID: 37835868 PMCID: PMC10572912 DOI: 10.3390/diagnostics13193125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Asphyxia, a leading cause of illness and death in newborns, can be improved by early detection and management. Arterial blood gas (ABG) analysis is commonly used to diagnose and manage asphyxia, but it is invasive and carries risks. Dermal interstitial fluid (ISF) is an alternative physiological fluid that can provide valuable information about a person's health. ISF is more sensitive to severe hypoxia and metabolic disorders compared to blood, making it an attractive option for minimally invasive asphyxia detection using biosensors. However, obtaining ISF samples from humans is challenging due to ethical concerns and sampling difficulties. To address this, researchers are developing ISF-mimicking solutions as substitutes for early testing and evaluation of biosensors. This paper focuses on the development of these solutions for bench-based testing and validation of continuous asphyxia-monitoring biosensors. With an understanding of the factors influencing system quality and performance, these solutions can aid in the design of biosensors for in vivo monitoring of dermal ISF. Monitoring interstitial fluid pH levels can provide valuable insights into the severity and progression of asphyxia, aiding in accurate diagnosis and informed treatment decisions. In this study, buffer solutions were prepared to mimic the pH of ISF, and their electrical properties were analyzed. The results suggest that certain buffers can effectively mimic metabolic acidosis associated with asphyxia (pH < 7.30), while others can mimic metabolic alkalosis (pH > 7.45). Overall, this research contributes to the development of ISF-mimicking solutions and lays the groundwork for biosensor systems that monitor dermal ISF in real time.
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Affiliation(s)
- Nadia Muhammad Hussain
- Translational Medical Device Lab, University of Galway, H91 TK33 Galway, Ireland; (B.A.); (M.O.); (A.E.)
- Electrical and Electronic Engineering, University of Galway, H91 TK33 Galway, Ireland
| | - Bilal Amin
- Translational Medical Device Lab, University of Galway, H91 TK33 Galway, Ireland; (B.A.); (M.O.); (A.E.)
- Electrical and Electronic Engineering, University of Galway, H91 TK33 Galway, Ireland
- School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Martin O’Halloran
- Translational Medical Device Lab, University of Galway, H91 TK33 Galway, Ireland; (B.A.); (M.O.); (A.E.)
- Electrical and Electronic Engineering, University of Galway, H91 TK33 Galway, Ireland
- School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Adnan Elahi
- Translational Medical Device Lab, University of Galway, H91 TK33 Galway, Ireland; (B.A.); (M.O.); (A.E.)
- Electrical and Electronic Engineering, University of Galway, H91 TK33 Galway, Ireland
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10
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Mocaer K, Mizzon G, Gunkel M, Halavatyi A, Steyer A, Oorschot V, Schorb M, Le Kieffre C, Yee DP, Chevalier F, Gallet B, Decelle J, Schwab Y, Ronchi P. Targeted volume correlative light and electron microscopy of an environmental marine microorganism. J Cell Sci 2023; 136:jcs261355. [PMID: 37455654 PMCID: PMC10445747 DOI: 10.1242/jcs.261355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.
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Affiliation(s)
- Karel Mocaer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and the Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, CIID, 69120 Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, 69120 Heidelberg, Germany
| | - Manuel Gunkel
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anna Steyer
- EMBL Imaging Centre, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Viola Oorschot
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Daniel P. Yee
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Fabien Chevalier
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Johan Decelle
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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11
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Goh R, Yoshida E, Schaible E, Behrens R, Monnier CA, Killingsworth B, Kong KW, Hiew SH, Miserez A, Hoon S, Waite JH. Nanolattice-Forming Hybrid Collagens in Protective Shark Egg Cases. Biomacromolecules 2022; 23:2878-2890. [PMID: 35748755 DOI: 10.1021/acs.biomac.2c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanoscopic structural control with long-range ordering remains a profound challenge in nanomaterial fabrication. The nanoarchitectured egg cases of elasmobranchs rely on a hierarchically ordered latticework for their protective function─serving as an exemplary system for nanoscale self-assembly. Although the proteinaceous precursors are known to undergo intermediate liquid crystalline phase transitions before being structurally arrested in the final nanolattice architecture, their sequences have so far remained unknown. By leveraging RNA-seq and proteomic techniques, we identified a cohort of nanolattice-forming proteins comprising a collagenous midblock flanked by domains typically associated with innate immunity and network-forming collagens. Structurally homologous proteins were found in the genomes of other egg-case-producing cartilaginous fishes, suggesting a conserved molecular self-assembly strategy. The identity and stabilizing role of cross-links were subsequently elucidated using mass spectrometry and in situ small-angle X-ray scattering. Our findings provide a new design approach for protein-based liquid crystalline elastomers and the self-assembly of nanolattices.
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Affiliation(s)
- Rubayn Goh
- Materials Department, University of California, Santa Barbara, California 93106, United States.,Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 136834, Singapore
| | - Eric Yoshida
- Materials Department, University of California, Santa Barbara, California 93106, United States
| | - Eric Schaible
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rachel Behrens
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Christophe A Monnier
- Marine Science Institute, University of California, Santa Barbara, California 93106, United States
| | - Bradley Killingsworth
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Kiat Whye Kong
- Molecular Engineering Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore 639798, Singapore.,School of Biological Sciences, NTU, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore 639798, Singapore.,School of Biological Sciences, NTU, Singapore 637551, Singapore
| | - Shawn Hoon
- Molecular Engineering Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - J Herbert Waite
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, United States
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12
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Dalum AS, Kraus A, Khan S, Davydova E, Rigaudeau D, Bjørgen H, López-Porras A, Griffiths G, Wiegertjes GF, Koppang EO, Salinas I, Boudinot P, Rességuier J. High-Resolution, 3D Imaging of the Zebrafish Gill-Associated Lymphoid Tissue (GIALT) Reveals a Novel Lymphoid Structure, the Amphibranchial Lymphoid Tissue. Front Immunol 2021; 12:769901. [PMID: 34880866 PMCID: PMC8647647 DOI: 10.3389/fimmu.2021.769901] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022] Open
Abstract
The zebrafish is extensively used as an animal model for human and fish diseases. However, our understanding of the structural organization of its immune system remains incomplete, especially the mucosa-associated lymphoid tissues (MALTs). Teleost MALTs are commonly perceived as diffuse and scattered populations of immune cells throughout the mucosa. Yet, structured MALTs have been recently discovered in Atlantic salmon (Salmo salar L.), including the interbranchial lymphoid tissue (ILT) in the gills. The existence of the ILT was only recently identified in zebrafish and other fish species, highlighting the need for in-depth characterizations of the gill-associated lymphoid tissue (GIALT) in teleosts. Here, using 3-D high-resolution microscopy, we analyze the GIALT of adult zebrafish with an immuno-histology approach that reveals the organization of lymphoid tissues via the labeling of T/NK cells with an antibody directed to a highly conserved epitope on the kinase ZAP70. We show that the GIALT in zebrafish is distributed over at least five distinct sub-regions, an organization found in all pairs of gill arches. The GIALT is diffuse in the pharyngeal part of the gill arch, the interbranchial septum and the filaments/lamellae, and structured in two sub-regions: the ILT, and a newly discovered lymphoid structure located along each side of the gill arch, which we named the Amphibranchial Lymphoid Tissue (ALT). Based on RAG2 expression, neither the ILT nor the ALT constitute additional thymi. The ALT shares several features with the ILT such as presence of abundant lymphoid cells and myeloid cells embedded in a network of reticulated epithelial cells. Further, the ILT and the ALT are also a site for T/NK cell proliferation. Both ILT and ALT show structural changes after infection with Spring Viraemia of Carp Virus (SVCV). Together, these data suggest that ALT and ILT play an active role in immune responses. Comparative studies show that whereas the ILT seems absent in most neoteleosts ("Percomorphs"), the ALT is widely present in cyprinids, salmonids and neoteleosts, suggesting that it constitutes a conserved tissue involved in the protection of teleosts via the gills.
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Affiliation(s)
- Alf S. Dalum
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Aurora Kraus
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Shanawaz Khan
- Department of Biosciences, FYSCELL, University of Oslo, Oslo, Norway
| | - Erna Davydova
- Department of Biosciences, BMB, University of Oslo, Oslo, Norway
| | | | - Håvard Bjørgen
- Section of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | | | - Gareth Griffiths
- Department of Biosciences, FYSCELL, University of Oslo, Oslo, Norway
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Erling O. Koppang
- Section of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Pierre Boudinot
- INRAE, UVSQ, VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Julien Rességuier
- Department of Biosciences, FYSCELL, University of Oslo, Oslo, Norway
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13
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Munyenyembe K, Timmons C, Weiner AKM, Katz LA, Yan Y. DAPI staining and DNA content estimation of nuclei in uncultivable microbial eukaryotes (Arcellinida and Ciliates). Eur J Protistol 2021; 81:125840. [PMID: 34717075 PMCID: PMC8699166 DOI: 10.1016/j.ejop.2021.125840] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/09/2021] [Accepted: 08/30/2021] [Indexed: 01/03/2023]
Abstract
Though representing a major component of eukaryotic biodiversity, many microbial eukaryotes remain poorly studied, including the focus of the present work, testate amoebae of the order Arcellinida (Amoebozoa) and non-model lineages of ciliates (Alveolata). In particular, knowledge of genome structures and changes in genome content over the often-complex life cycles of these lineages remains enigmatic. However, the limited available knowledge suggests that microbial eukaryotes have the potential to challenge our textbook views on eukaryotic genomes and genome evolution. In this study, we developed protocols for DAPI (4',6-diamidino-2-phenylindole) staining of Arcellinida nuclei and adapted protocols for ciliates. In addition, image analysis software was used to estimate the DNA content in the nuclei of Arcellinida and ciliates, and the measurements of target organisms were compared to those of well-known model organisms.The results demonstrate that the methods we have developed for nuclear staining in these lineages are effective and can be applied to other microbial eukaryotic groups by adjusting certain stages in the protocols.
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Affiliation(s)
- Ketty Munyenyembe
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Caitlin Timmons
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Agnes K M Weiner
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Laura A Katz
- Smith College, Department of Biological Sciences, Northampton, MA, USA; University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, USA.
| | - Ying Yan
- Smith College, Department of Biological Sciences, Northampton, MA, USA.
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14
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Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). ISME JOURNAL 2019; 14:104-122. [PMID: 31562384 PMCID: PMC6908604 DOI: 10.1038/s41396-019-0508-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 11/30/2022]
Abstract
Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.
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15
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Gruber-Vodicka HR, Leisch N, Kleiner M, Hinzke T, Liebeke M, McFall-Ngai M, Hadfield MG, Dubilier N. Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2. Nat Microbiol 2019; 4:1465-1474. [PMID: 31182796 PMCID: PMC6784892 DOI: 10.1038/s41564-019-0475-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/26/2019] [Indexed: 02/02/2023]
Abstract
Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans1,2. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host3–6. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)7,8 and has a genomic repertoire similar to that of rickettsial parasites9,10, but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host’s internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations11–13. This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan’s nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter. Using a multi-omics approach, together with imaging analyses, the authors characterize the two intracellular bacterial symbionts of Trichoplax, one of the simplest animals.
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Affiliation(s)
| | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Tjorven Hinzke
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Margaret McFall-Ngai
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Michael G Hadfield
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA.
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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16
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Rubin-Blum M, Antony CP, Sayavedra L, Martínez-Pérez C, Birgel D, Peckmann J, Wu YC, Cardenas P, MacDonald I, Marcon Y, Sahling H, Hentschel U, Dubilier N. Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts. THE ISME JOURNAL 2019; 13:1209-1225. [PMID: 30647460 PMCID: PMC6474228 DOI: 10.1038/s41396-019-0346-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 01/26/2023]
Abstract
Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.
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Affiliation(s)
- Maxim Rubin-Blum
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
- Israel Limnology and Oceanography Research, Tel Shikmona, 3108000, Haifa, Israel.
| | - Chakkiath Paul Antony
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Lizbeth Sayavedra
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Clara Martínez-Pérez
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146, Hamburg, Germany
| | - Jörn Peckmann
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146, Hamburg, Germany
| | - Yu-Chen Wu
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Paco Cardenas
- Department of Medicinal Chemistry, Pharmacognosy, BioMedical Centre, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ian MacDonald
- Florida State University, POB 3064326, Tallahassee, FL, 32306, USA
| | - Yann Marcon
- Wegener Institute Helmholtz Centre for Polar and Marine Research, HGF-MPG Group for Deep Sea Ecology and Technology, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Heiko Sahling
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany.
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17
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Garcia Bento MA, López Greco LS, Zara FJ. Seminal fluid production and sperm packaging in dromiid crabs (Brachyura, Podotremata). ZOOLOGY 2018; 132:17-30. [PMID: 30736926 DOI: 10.1016/j.zool.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 11/24/2022]
Abstract
Reproductive anatomy, including sperm storage structures and sperm transfer, is an important feature used to analyze phylogenetic relationships among taxa. We describe the male reproductive anatomy, seminal fluid production and packaging of spermatozoa in the vas deferens of primitive crabs. In all species of Dromiidae, the testes were tubular type and the vas deferens is a tube with a simple epithelium. The spermatozoa are in a central mass immersed in type I secretion, forming a large spermatic cord. In Moreiradromia antillensis and Dromia erythropus the spermatic cord is surrounded by a more complex secretion layer composed by protein granules and polysaccharides that seem to be responsible to form the sperm plaque which was absent in Hypoconcha. The sperm plaque was found in all Dromiinae species, which may result from the mating and probably act as a barrier to subsequent copulations. These patterns of elongated coenospermic spermatophore found here are unique and different from the spermatophores of all true crabs and may be considered a plesiomorphic state to spermatophoric structure in Brachyura. Our results show a novel type of spermatozoa packaging and new insights into how sperm might be transferred in Podotremata.
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Affiliation(s)
- Maria Alice Garcia Bento
- Universidade Estadual Paulista (UNESP), FCAV, Laboratório de Morfologia de Invertebrados (IML), Departamento de Biologia Aplicada à Agropecuária e Centro de Aquicultura da Unesp (CAUNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, 14884-900, São Paulo, Brasil.
| | - Laura S López Greco
- Universidad de Buenos Aires, CONICET, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Laboratorio de Biología de la Reproducción y el Crecimiento de Crustáceos Decápodos, C1428EGA, Buenos Aires, Argentina.
| | - Fernando José Zara
- Universidade Estadual Paulista (UNESP), FCAV, Laboratório de Morfologia de Invertebrados (IML), Departamento de Biologia Aplicada à Agropecuária e Centro de Aquicultura da Unesp (CAUNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, 14884-900, São Paulo, Brasil; Universidade Estadual Paulista (UNESP), IB, Avenida 24 A, 1515, Rio Claro, 13506-900, São Paulo, Brasil.
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18
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Kun A, González-Camacho F, Hernández S, Moreno-García A, Calero O, Calero M. Characterization of Amyloid-β Plaques and Autofluorescent Lipofuscin Aggregates in Alzheimer's Disease Brain: A Confocal Microscopy Approach. Methods Mol Biol 2018; 1779:497-512. [PMID: 29886553 DOI: 10.1007/978-1-4939-7816-8_31] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The study of brain pathology by fluorescence microscopy finds in the autofluorescence of the tissue an additional difficulty for the recognition of markers of interest. In particular, in the immunofluorescence study of brains from Alzheimer's disease (AD) patients, several approaches have been attempted to eliminate or mask the presence of autofluorescent aggregates. In the present work, we propose a method to characterize by fluorescent microscopy senile plaques discriminating them from autofluorescent aggregates, such as lipofuscin granules.This work describes four protocols carried out in human brain tissue of patients with AD, covering adequate tissue preparation, immunofluorescence acquisition, and data analysis: 1. Tissues processing of frozen samples for optimal epitope conservation. 2. Analysis of the fluorescence emission spectrum of the tissue by performing a confocal microscopy λ-scan. 3. Analysis of fluorescence emission of both intact and formic acid-treated tissues in four channels corresponding to the emission in blue, green, near red, and far-red regions. 4. Analysis a specific immunostaining of amyloid beta in senile plaques, using fluorescent-labeled antibodies by using specific emission channels to avoid detection of tissue autofluorescence.
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Affiliation(s)
- Alejandra Kun
- Biochemistry Section, Proteins and Nucleic Acids Department, Instituto de Investigaciones Biológicas Clemente Estable, Science School, Universidad de la República, Montevideo, Uruguay.
| | - Fernando González-Camacho
- Confocal Microscopy Unit, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Hernández
- Confocal Microscopy Unit, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Olga Calero
- Chronic Disease Programme-CROSADIS, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Calero
- Chronic Disease Programme-CROSADIS, CIBERNED, Queen Sofia Foundation Alzheimer Center, CIEN Foundation, Instituto de Salud Carlos III, Madrid, Spain
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19
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Hollergschwandtner E, Schwaha T, Neumüller J, Kaindl U, Gruber D, Eckhard M, Stöger-Pollach M, Reipert S. Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity. PeerJ 2017; 5:e3923. [PMID: 29093995 PMCID: PMC5661469 DOI: 10.7717/peerj.3923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/23/2017] [Indexed: 11/20/2022] Open
Abstract
Background Biomineralization, e.g., in sea urchins or mollusks, includes the assembly of mesoscopic superstructures from inorganic crystalline components and biopolymers. The resulting mesocrystals inspire biophysicists and material scientists alike, because of their extraordinary physical properties. Current efforts to replicate mesocrystal synthesis in vitro require understanding the principles of their self-assembly in vivo. One question, not addressed so far, is whether intracellular crystals of proteins can assemble with biopolymers into functional mesocrystal-like structures. During our electron microscopy studies into Artemia franciscana (Crustacea: Branchiopoda), we found initial evidence of such proteinaceous mesostructures. Results EM preparations with high-pressure freezing and accelerated freeze substitution revealed an extraordinary intracellular source of mesostructured inclusions in both the cyto-and nucleoplasm of the epidermal lining of ovisacs of A. franciscana. Confocal reflection microscopy not only confirmed our finding; it also revealed reflective, light dispersing activity of these flake-like structures, their positioning and orientation with respect to the ovisac inside. Both the striation of alternating electron dense and electron-lucent components and the sharp edges of the flakes indicate self-assembly of material of yet unknown origin under supposed participation of crystallization. However, selected area electron diffraction could not verify the status of crystallization. Energy dispersive X-ray analysis measured a marked increase in nitrogen within the flake-like inclusion, and the almost complete absence of elements that are typically involved in inorganic crystallization. This rise in nitrogen could possibility be related to higher package density of proteins, achieved by mesostructure assembly. Conclusions The ovisac lining of A. franciscana is endowed with numerous mesostructured inclusions that have not been previously reported. We hypothesize that their self-assembly was from proteinaceous polycrystalline units and carbohydrates. These mesostructured flakes displayed active optical properties, as an umbrella-like, reflective cover of the ovisac, which suggests a functional role in the reproduction of A. franciscana. In turn, studies into ovisac mesostructured inclusions could help to optimizing rearing Artemia as feed for fish farming. We propose Artemia ovisacs as an in vivo model system for studying mesostructure formation.
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Affiliation(s)
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Josef Neumüller
- Center of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Ulrich Kaindl
- Center of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Daniela Gruber
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Margret Eckhard
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Michael Stöger-Pollach
- University Service Center for TEM (USTEM), Vienna University of Technology, Vienna, Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
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Leisch N, Pende N, Weber PM, Gruber-Vodicka HR, Verheul J, Vischer NOE, Abby SS, Geier B, den Blaauwen T, Bulgheresi S. Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of Robbea hypermnestra. Nat Microbiol 2016; 2:16182. [PMID: 27723729 DOI: 10.1038/nmicrobiol.2016.182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/26/2016] [Indexed: 11/10/2022]
Abstract
The reproduction mode of uncultivable microorganisms deserves investigation as it can largely diverge from conventional transverse binary fission. Here, we show that the rod-shaped gammaproteobacterium thriving on the surface of the Robbea hypermnestra nematode divides by FtsZ-based, non-synchronous invagination of its poles-that is, the host-attached and fimbriae-rich pole invaginates earlier than the distal one. We conclude that, in a naturally occurring animal symbiont, binary fission is host-oriented and does not require native FtsZ to polymerize into a ring at any septation stage.
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Affiliation(s)
- Nikolaus Leisch
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Nika Pende
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Philipp M Weber
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | | | - Jolanda Verheul
- Bacterial Cell Biology, Swammerdam Institute of Life Sciences, Faculty of Science, University of Amsterdam, Boelelaan 1108, 1081 HZ Amsterdam, Netherlands
| | - Norbert O E Vischer
- Bacterial Cell Biology, Swammerdam Institute of Life Sciences, Faculty of Science, University of Amsterdam, Boelelaan 1108, 1081 HZ Amsterdam, Netherlands
| | - Sophie S Abby
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Tanneke den Blaauwen
- Bacterial Cell Biology, Swammerdam Institute of Life Sciences, Faculty of Science, University of Amsterdam, Boelelaan 1108, 1081 HZ Amsterdam, Netherlands
| | - Silvia Bulgheresi
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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