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Schmutz S, Commere PH, Montcuquet N, Cumano A, Ait-Mansour C, Novault S, Hasan M. Beyond 40 fluorescent probes for deep phenotyping of blood mononuclear cells, using spectral technology. Front Immunol 2024; 15:1285215. [PMID: 38629063 PMCID: PMC11018965 DOI: 10.3389/fimmu.2024.1285215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
The analytical capability of flow cytometry is crucial for differentiating the growing number of cell subsets found in human blood. This is important for accurate immunophenotyping of patients with few cells and a large number of parameters to monitor. Here, we present a 43-parameter panel to analyze peripheral blood mononuclear cells from healthy individuals using 41 fluorescence-labelled monoclonal antibodies, an autofluorescent channel, and a viability dye. We demonstrate minimal population distortions that lead to optimized population identification and reproducible results. We have applied an advanced approach in panel design, in selection of sample acquisition parameters and in data analysis. Appropriate autofluorescence identification and integration in the unmixing matrix, allowed for resolution of unspecific signals and increased dimensionality. Addition of one laser without assigned fluorochrome resulted in decreased fluorescence spill over and improved discrimination of cell subsets. It also increased the staining index when autofluorescence was integrated in the matrix. We conclude that spectral flow cytometry is a highly valuable tool for high-end immunophenotyping, and that fine-tuning of major experimental steps is key for taking advantage of its full capacity.
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Affiliation(s)
- Sandrine Schmutz
- Cytometry and Biomarkers UTechS/Cytometry Platform, Institut Pasteur, Université Paris Cité, Paris, France
| | - Pierre-Henri Commere
- Cytometry and Biomarkers UTechS/Cytometry Platform, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Ana Cumano
- Lymphocyte and Immunity Unit, Institut National de la Santé et de la Recherche Médicale (INSERM) U1223, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Sophie Novault
- Cytometry and Biomarkers UTechS/Cytometry Platform, Institut Pasteur, Université Paris Cité, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
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2
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Orta-Resendiz A, Petitdemange C, Schmutz S, Jacquelin B, Novault S, Huot N, Müller-Trutwin M. Deep phenotyping characterization of human unconventional CD8 +NKG2A/C + T cells among T and NK cells by spectral flow cytometry. STAR Protoc 2023; 4:102734. [PMID: 38032799 PMCID: PMC10711235 DOI: 10.1016/j.xpro.2023.102734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
Here, we present a protocol for setting three spectral flow cytometry panels for the characterization of human unconventional CD8+NKG2A/C+ T cells as well as other T and natural killer cell subsets. We describe steps for standardizing, preparing, and staining the cells, the experimental setup, and the final data analysis. This protocol should be advantageous in various settings including immunophenotyping of limited samples, immune function evaluation/monitoring, as well as research in oncology, autoimmune, and infectious diseases.
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Affiliation(s)
- Aurelio Orta-Resendiz
- Institut Pasteur, Université Paris Cité, HIV, Inflammation and Persistence Unit, 75015 Paris, France.
| | - Caroline Petitdemange
- Institut Pasteur, Université Paris Cité, HIV, Inflammation and Persistence Unit, 75015 Paris, France
| | - Sandrine Schmutz
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France.
| | - Béatrice Jacquelin
- Institut Pasteur, Université Paris Cité, HIV, Inflammation and Persistence Unit, 75015 Paris, France
| | - Sophie Novault
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Nicolas Huot
- Institut Pasteur, Université Paris Cité, HIV, Inflammation and Persistence Unit, 75015 Paris, France
| | - Michaela Müller-Trutwin
- Institut Pasteur, Université Paris Cité, HIV, Inflammation and Persistence Unit, 75015 Paris, France.
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3
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Cuche C, Mastrogiovanni M, Juzans M, Laude H, Ungeheuer MN, Krentzel D, Gariboldi MI, Scott-Algara D, Madec M, Goyard S, Floch C, Chauveau-Le Friec G, Lafaye P, Renaudat C, Le Bidan M, Micallef C, Schmutz S, Mella S, Novault S, Hasan M, Duffy D, Di Bartolo V, Alcover A. T cell migration and effector function differences in familial adenomatous polyposis patients with APC gene mutations. Front Immunol 2023; 14:1163466. [PMID: 37533857 PMCID: PMC10393261 DOI: 10.3389/fimmu.2023.1163466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/11/2023] [Indexed: 08/04/2023] Open
Abstract
Familial adenomatous polyposis (FAP) is an inherited disease characterized by the development of large number of colorectal adenomas with high risk of evolving into colorectal tumors. Mutations of the Adenomatous polyposis coli (APC) gene is often at the origin of this disease, as well as of a high percentage of spontaneous colorectal tumors. APC is therefore considered a tumor suppressor gene. While the role of APC in intestinal epithelium homeostasis is well characterized, its importance in immune responses remains ill defined. Our recent work indicates that the APC protein is involved in various phases of both CD4 and CD8 T cells responses. This prompted us to investigate an array of immune cell features in FAP subjects carrying APC mutations. A group of 12 FAP subjects and age and sex-matched healthy controls were studied. We characterized the immune cell repertoire in peripheral blood and the capacity of immune cells to respond ex vivo to different stimuli either in whole blood or in purified T cells. A variety of experimental approaches were used, including, pultiparamater flow cytometry, NanosString gene expression profiling, Multiplex and regular ELISA, confocal microscopy and computer-based image analyis methods. We found that the percentage of several T and natural killer (NK) cell populations, the expression of several genes induced upon innate or adaptive immune stimulation and the production of several cytokines and chemokines was different. Moreover, the capacity of T cells to migrate in response to chemokine was consistently altered. Finally, immunological synapses between FAP cytotoxic T cells and tumor target cells were more poorly structured. Our findings of this pilot study suggest that mild but multiple immune cell dysfunctions, together with intestinal epithelial dysplasia in FAP subjects, may facilitate the long-term polyposis and colorectal tumor development. Although at an initial discovery phase due to the limited sample size of this rare disease cohort, our findings open new perspectives to consider immune cell abnormalities into polyposis pathology.
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Affiliation(s)
- Céline Cuche
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
| | - Marta Mastrogiovanni
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Marie Juzans
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Hélène Laude
- Institut Pasteur, Université Paris Cité, ICAReB-Clin, Paris, France
| | | | - Daniel Krentzel
- Institut Pasteur, Université Paris Cité, CNRS-UMR3691, Unité Imagerie et Modélisation, Paris, France
| | - Maria Isabella Gariboldi
- Institut Pasteur, Université Paris Cité, CNRS-UMR3691, Unité Imagerie et Modélisation, Paris, France
| | - Daniel Scott-Algara
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
| | - Marianne Madec
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
| | - Sophie Goyard
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme d’Innovation et de Développement de Tests Diagnostiques, Paris, France
| | - Camille Floch
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme d’Innovation et de Développement de Tests Diagnostiques, Paris, France
| | - Gaëlle Chauveau-Le Friec
- Institut Pasteur, Université Paris Cité, CNRS-UMR3528, Plateforme d’Ingénierie des Anticorps, Paris, France
| | - Pierre Lafaye
- Institut Pasteur, Université Paris Cité, CNRS-UMR3528, Plateforme d’Ingénierie des Anticorps, Paris, France
| | | | | | | | - Sandrine Schmutz
- Institut Pasteur, Université Paris Cité, Unité de Technologie et Service Cytométrie et Biomarqueurs, Paris, France
| | - Sébastien Mella
- Institut Pasteur, Université Paris Cité, Unité de Technologie et Service Cytométrie et Biomarqueurs, Paris, France
- Institut Pasteur, Université Paris Cité, Hub Bioinformatique et Biostatistique, Paris, France
| | - Sophie Novault
- Institut Pasteur, Université Paris Cité, Unité de Technologie et Service Cytométrie et Biomarqueurs, Paris, France
| | - Milena Hasan
- Institut Pasteur, Université Paris Cité, Unité de Technologie et Service Cytométrie et Biomarqueurs, Paris, France
| | - Darragh Duffy
- Institut Pasteur, Université Paris Cité, Unité Immunologie Translationnelle, Paris, France
| | - Vincenzo Di Bartolo
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
| | - Andrés Alcover
- Institut Pasteur, Université Paris Cité, INSERM-U1224, Unité Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer-Équipe Labellisée Ligue 2018, Paris, France
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4
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Jean P, Wong Jun Tai F, Singh-Estivalet A, Lelli A, Scandola C, Megharba S, Schmutz S, Roux S, Mechaussier S, Sudres M, Mouly E, Heritier AV, Bonnet C, Mallet A, Novault S, Libri V, Petit C, Michalski N. Single-cell transcriptomic profiling of the mouse cochlea: An atlas for targeted therapies. Proc Natl Acad Sci U S A 2023; 120:e2221744120. [PMID: 37339214 DOI: 10.1073/pnas.2221744120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Functional molecular characterization of the cochlea has mainly been driven by the deciphering of the genetic architecture of sensorineural deafness. As a result, the search for curative treatments, which are sorely lacking in the hearing field, has become a potentially achievable objective, particularly via cochlear gene and cell therapies. To this end, a complete inventory of cochlear cell types, with an in-depth characterization of their gene expression profiles right up to their final differentiation, is indispensable. We therefore generated a single-cell transcriptomic atlas of the mouse cochlea based on an analysis of more than 120,000 cells on postnatal day 8 (P8), during the prehearing period, P12, corresponding to hearing onset, and P20, when cochlear maturation is almost complete. By combining whole-cell and nuclear transcript analyses with extensive in situ RNA hybridization assays, we characterized the transcriptomic signatures covering nearly all cochlear cell types and developed cell type-specific markers. Three cell types were discovered; two of them contribute to the modiolus which houses the primary auditory neurons and blood vessels, and the third one consists in cells lining the scala vestibuli. The results also shed light on the molecular basis of the tonotopic gradient of the biophysical characteristics of the basilar membrane that critically underlies cochlear passive sound frequency analysis. Finally, overlooked expression of deafness genes in several cochlear cell types was also unveiled. This atlas paves the way for the deciphering of the gene regulatory networks controlling cochlear cell differentiation and maturation, essential for the development of effective targeted treatments.
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Affiliation(s)
- Philippe Jean
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Plasticity of Central Auditory Circuits, F-75012 Paris, France
| | - Fabienne Wong Jun Tai
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Amrit Singh-Estivalet
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Andrea Lelli
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Cyril Scandola
- Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging, F-75015 Paris, France
| | - Sébastien Megharba
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, F-75015 Paris, France
| | - Sandrine Schmutz
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, F-75015 Paris, France
| | - Solène Roux
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Sabrina Mechaussier
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Plasticity of Central Auditory Circuits, F-75012 Paris, France
| | - Muriel Sudres
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Enguerran Mouly
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Anne-Valérie Heritier
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Crystel Bonnet
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
| | - Adeline Mallet
- Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging, F-75015 Paris, France
| | - Sophie Novault
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, F-75015 Paris, France
| | - Valentina Libri
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, F-75015 Paris, France
| | - Christine Petit
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Auditory Therapies Innovation Laboratory, F-75012 Paris, France
- Collège de France, F-75005 Paris, France
| | - Nicolas Michalski
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, Plasticity of Central Auditory Circuits, F-75012 Paris, France
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5
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Mameri D, Hayes DS, Führer S, Fauchery E, Schmutz S, Monserat A, Hasler T, Graf DRM, Santos JM, Ferreira MT, Auer S. Cold thermopeaking-induced drift of nase Chondrostoma nasus larvae. Aquat Sci 2023; 85:56. [PMID: 36987436 PMCID: PMC10038962 DOI: 10.1007/s00027-023-00955-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
UNLABELLED Research on how intermittent water releases from hydropower plants affect the early life stages of fish has advanced in the last years, focusing not only on the direct impacts of rapid flow changes (hydropeaking), but also on the short-term fluctuations in water temperature (thermopeaking). Flow and thermal fluctuations caused by hydropeaking may affect fish movement patterns and migration at critical stages of a species' life cycle, e.g., by inducing passive downstream drift. Using two experimental outdoor channels, we investigated how nase (Chondrostoma nasus, Cypriniformes) larvae respond to a rapid drop in water temperature during hydropeaking (simulating a cold thermopeaking event), reaching on average 5.5 °C under peak flow (maximum discharge) conditions, in comparison with a hydropeaking treatment with a constant water temperature regime. Responses of fish larvae were analyzed during acclimation, up-ramping (increase in discharge), peak flow and down-ramping (decrease in discharge) phases. Fish drift increased during peak flow in the cold thermopeaking treatment compared to hydropeaking. Higher drift rates were also negatively associated with pronounced water temperature drops during peak flow conditions. In addition, the starting temperature of the experiment influenced drift during up-ramping. Overall, the results suggest that cold thermopeaking may increase drift in the early life stages of cypriniform fish compared with hydropeaking with stable water temperature. Hence, monitoring and active water temperature adjustments following hydropower releases should be adopted as strategies to mitigate power plant-related impacts on aquatic organisms. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00027-023-00955-x.
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Affiliation(s)
- D. Mameri
- Forest Research Centre (CEF) and Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - D. S. Hayes
- University of Natural Resources and Life Sciences, Vienna, Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor-Mendel-Straße 33, 1180 Wien, Austria
| | - S. Führer
- University of Natural Resources and Life Sciences, Vienna, Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor-Mendel-Straße 33, 1180 Wien, Austria
| | - E. Fauchery
- Graduate School of Engineering, University of Tours, 64 Avenue Jean Portalis, 37200 Tours, France
| | - S. Schmutz
- University of Natural Resources and Life Sciences, Vienna, Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor-Mendel-Straße 33, 1180 Wien, Austria
| | - A. Monserat
- École Nationale Supérieure de l’Energie, l’Eau et l’Environnement, 21 Avenue Des Martyrs, 38031 Grenoble, France
| | - T. Hasler
- University of Natural Resources and Life Sciences, Vienna, Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor-Mendel-Straße 33, 1180 Wien, Austria
| | - D. R. M. Graf
- University of Natural Resources and Life Sciences, Vienna, Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor-Mendel-Straße 33, 1180 Wien, Austria
| | - J. M. Santos
- Forest Research Centre (CEF) and Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - M. T. Ferreira
- Forest Research Centre (CEF) and Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - S. Auer
- University of Natural Resources and Life Sciences, Vienna, Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor-Mendel-Straße 33, 1180 Wien, Austria
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6
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Bastide S, Chomsky E, Saudemont B, Loe-Mie Y, Schmutz S, Novault S, Marlow H, Tanay A, Spitz F. TATTOO-seq delineates spatial and cell type-specific regulatory programs in the developing limb. Sci Adv 2022; 8:eadd0695. [PMID: 36516250 PMCID: PMC9750149 DOI: 10.1126/sciadv.add0695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The coordinated differentiation of progenitor cells into specialized cell types and their spatial organization into distinct domains is central to embryogenesis. Here, we developed and applied an unbiased spatially resolved single-cell transcriptomics method to identify the genetic programs underlying the emergence of specialized cell types during mouse limb development and their spatial integration. We identify multiple transcription factors whose expression patterns are predominantly associated with cell type specification or spatial position, suggesting two parallel yet highly interconnected regulatory systems. We demonstrate that the embryonic limb undergoes a complex multiscale reorganization upon perturbation of one of its spatial organizing centers, including the loss of specific cell populations, alterations of preexisting cell states' molecular identities, and changes in their relative spatial distribution. Our study shows how multidimensional single-cell, spatially resolved molecular atlases can allow the deconvolution of spatial identity and cell fate and reveal the interconnected genetic networks that regulate organogenesis and its reorganization upon genetic alterations.
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Affiliation(s)
- Sébastien Bastide
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- École Doctorale “Complexité du Vivant”, Sorbonne Université, 75005 Paris, France
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Sandrine Schmutz
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Sophie Novault
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Heather Marlow
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
| | - François Spitz
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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Peixoto MM, Soares‐da‐Silva F, Schmutz S, Mailhe M, Novault S, Cumano A, Ait‐Mansour C. Identification of fetal liver stroma in spectral cytometry using the parameter autofluorescence. Cytometry A 2022; 101:960-969. [PMID: 35491762 PMCID: PMC9790487 DOI: 10.1002/cyto.a.24567] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/07/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023]
Abstract
The fetal liver (FL) is the main hematopoietic organ during embryonic development. The FL is also the unique anatomical site where hematopoietic stem cells expand before colonizing the bone marrow, where they ensure life-long blood cell production and become mostly resting. The identification of the different cell types that comprise the hematopoietic stroma in the FL is essential to understand the signals required for the expansion and differentiation of the hematopoietic stem cells. We used a panel of monoclonal antibodies to identify FL stromal cells in a 5-laser equipped spectral flow cytometry (FCM) analyzer. The "Autofluorescence Finder" of SONY ID7000 software identified two distinct autofluorescence emission spectra. Using autofluorescence as a fluorescence parameter we could assign the two autofluorescent signals to three distinct cell types and identified surface markers that characterize these populations. We found that one autofluorescent population corresponds to hepatoblast-like cells and cholangiocytes whereas the other expresses mesenchymal transcripts and was identified as stellate cells. Importantly, after birth, autofluorescence becomes the unique identifying property of hepatoblast-like cells because mature cholangiocytes are no longer autofluorescent. These results show that autofluorescence used as a parameter in spectral FCM is a useful tool to identify new cell subsets that are difficult to analyze in conventional FCM.
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Affiliation(s)
- Márcia Mesquita Peixoto
- Immunology DepartmentUnit Lymphocytes and Immunity, Institut PasteurParisFrance,INSERM U1223ParisFrance,Université de Paris, Sorbonne Paris CitéParisFrance,Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal,Instituto Nacional de Engenharia BiomédicaUniversidade do PortoPortoPortugal,Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
| | - Francisca Soares‐da‐Silva
- Immunology DepartmentUnit Lymphocytes and Immunity, Institut PasteurParisFrance,INSERM U1223ParisFrance,Université de Paris, Sorbonne Paris CitéParisFrance
| | | | - Marie‐Pierre Mailhe
- Immunology DepartmentUnit Lymphocytes and Immunity, Institut PasteurParisFrance,INSERM U1223ParisFrance,Université de Paris, Sorbonne Paris CitéParisFrance
| | - Sophie Novault
- Flow cytometry core facility, CRT2, Institut PasteurParisFrance
| | - Ana Cumano
- Immunology DepartmentUnit Lymphocytes and Immunity, Institut PasteurParisFrance,INSERM U1223ParisFrance,Université de Paris, Sorbonne Paris CitéParisFrance
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8
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Thuillard S, Adams M, Jelmini G, Schmutz S, Sonderegger A, Sauer J. When humans and computers induce social stress through negative feedback: Effects on performance and subjective state. Computers in Human Behavior 2022. [DOI: 10.1016/j.chb.2022.107270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Dominguez-Belloso A, Schmutz S, Novault S, Travier L, Deczkowska A. Isolation and Characterization of the Immune Cells from Micro-dissected Mouse Choroid Plexuses. JoVE 2022. [DOI: 10.3791/63487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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10
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Plessier F, Schmutz S, Novault S, Marlow H. Single-Cell Transcriptomic Analysis in the Regenerating Cnidarian Nematostella vectensis. Methods Mol Biol 2022; 2450:565-581. [PMID: 35359329 PMCID: PMC9761532 DOI: 10.1007/978-1-0716-2172-1_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cnidarians have historically served as excellent laboratory models for regenerative development given their capacity to regrow large portions of the adult organism. This capacity is notably absent or poorly developed in the powerful genetic laboratory models Drosophila, C. elegans, and mouse. Increasingly, development of genetic and genomic resources and the application of next-generation sequencing-based techniques in cnidarian systems has further expanded the potential of cnidarian regenerative models. Here, we present a workflow for the characterization of the regenerative response in the sea anemone Nematostella vectensis utilizing fluorescence-activated cell sorting and a plate-based single-cell RNA-sequencing pipeline. This approach can characterize the transcriptional response during regeneration in distinct populations of cells, thus providing a quantitative view of a whole organism process at cellular resolution.
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Affiliation(s)
- Flora Plessier
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, IL, USA
- École Doctorale "Complexité du Vivant" ED515, Sorbonne Université, Paris, France
- Département de Biologie, École Normale Supérieure de Lyon, Lyon, France
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Sandrine Schmutz
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Sophie Novault
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Heather Marlow
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA.
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Sebé-Pedrós A, Saudemont B, Chomsky E, Plessier F, Mailhé MP, Renno J, Loe-Mie Y, Lifshitz A, Mukamel Z, Schmutz S, Novault S, Steinmetz PRH, Spitz F, Tanay A, Marlow H. Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. Cell 2018; 173:1520-1534.e20. [PMID: 29856957 DOI: 10.1016/j.cell.2018.05.019] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/22/2018] [Accepted: 05/09/2018] [Indexed: 01/19/2023]
Abstract
The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.
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Affiliation(s)
- Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Flora Plessier
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France; Département de Biologie, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Marie-Pierre Mailhé
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Justine Renno
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zohar Mukamel
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sandrine Schmutz
- Cytometry & Biomarkers UtechS, Cytometry Platform, Institut Pasteur, 75015 Paris, France
| | - Sophie Novault
- Cytometry & Biomarkers UtechS, Cytometry Platform, Institut Pasteur, 75015 Paris, France
| | - Patrick R H Steinmetz
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen 5006, Norway
| | - François Spitz
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Heather Marlow
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France.
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12
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Zogaris S, Tachos V, Economou AN, Chatzinikolaou Y, Koutsikos N, Schmutz S. A model-based fish bioassessment index for Eastern Mediterranean rivers: Application in a biogeographically diverse area. Sci Total Environ 2018; 622-623:676-689. [PMID: 29223894 DOI: 10.1016/j.scitotenv.2017.11.293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/25/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
In ecosystems with high fish species endemicity, such as Mediterranean-type rivers, biogeographical differences among ecoregions present serious obstacles to developing broadly-applicable river bioassessment indices. This impediment has contributed to a serious time-lag in developing EU policy-relevant fish-based indices in the Eastern Mediterranean countries. Here we present the first model-based fish index for the Eastern Mediterranean (the Hellenic Fish Index, HeFI) in an effort to overcome biogeographic differences among the area's biotically heterogeneous rivers. The index is based on modelled reference conditions and employs site-specific electrofished fish samples from an extensive dataset from Greece that covers six freshwater ecoregions, including five transboundary river basins flowing through six countries. Environmental and anthropogenic pressure data were procured from 403 sampled river sites and ecologically-relevant traits were defined for 103 collected fish species. For the development of the index, we first diagnosed least degraded sites forming a calibrated reference site dataset and secondly quantified differences of fish metrics between the reference and impaired sites. Four trait-based fish metrics showed the best ability to discriminate between impaired and reference sites. The index performed well in discriminating anthropogenic pressure classes, giving a significant negative linear response to a gradient of anthropogenic degradation. HeFI successfully assessed both small and large rivers in different freshwater ecoregions. This geographically broad-scale index development shows that key trait-based reference conditions can be produced by a predictive model in remarkably heterogeneous rivers where range-restricted fishes dominate. This index promotes a screening-level bioassessment application that may be further developed and refined with relevant monitoring.
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Affiliation(s)
- S Zogaris
- Hellenic Centre of Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, Greece.
| | - V Tachos
- Hellenic Centre of Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, Greece; Hellenic Ministry of Rural Development and Food, General Directorate of Animal Production, Athens, Greece
| | - A N Economou
- Hellenic Centre of Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, Greece
| | - Y Chatzinikolaou
- Hellenic Centre of Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, Greece
| | - N Koutsikos
- Hellenic Centre of Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, Greece
| | - S Schmutz
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
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13
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Abstract
Flow cytometry has been used for the past 40 years to define and analyze the phenotype of lymphoid and other hematopoietic cells. Initially restricted to the analysis of a few fluorochromes, currently there are dozens of different fluorescent dyes, and up to 14-18 different dyes can be combined at a time. However, several limitations still impair the analytical capabilities. Because of the multiplicity of fluorescent probes, data analysis has become increasingly complex due to the need of large, multi-parametric compensation matrices. Moreover, mutant mouse models carrying fluorescent proteins to detect and trace specific cell types in different tissues have become available, so the analysis (by flow cytometry) of auto-fluorescent cell suspensions obtained from solid organs is required. Spectral flow cytometry, which distinguishes the shapes of emission spectra along a wide range of continuous wavelengths, addresses some of these problems. The data is analyzed with an algorithm that replaces compensation matrices and treats auto-fluorescence as an independent parameter. Thus, spectral flow cytometry should be capable of discriminating fluorochromes with similar emission peaks and can provide a multi-parametric analysis without compensation requirements. This protocol describes the spectral flow cytometry analysis, allowing for a 21-parameter (19 fluorescent probes) characterization and the management of an auto-fluorescent signal, providing high resolution in minor population detection. The results presented here show that spectral flow cytometry presents advantages in the analysis of cell populations from tissues difficult to characterize in conventional flow cytometry, such as the heart and the intestine. Spectral flow cytometry thus demonstrates the multi-parametric analytical capacity of high-performing conventional flow cytometry without the requirement for compensation and enables auto-fluorescence management.
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Affiliation(s)
- Sandrine Schmutz
- Flow Cytometry Core Facility, Center for Translational Research-Technical Core, Institut Pasteur
| | - Mariana Valente
- Unit for Lymphopoiesis, Immunology Department, INSERM U1223, University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Institut Pasteur; Stem-Cell Microenvironments in Repair/Regeneration Team, Instituto de Investigação e Inovação em Saúde (i3s), INEB - Instituto de Engenharia Biomédica; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Stem Cells and Regenerative Medicine Team, UMRS 1166, ICAN - Institute of Cardiometabolism And Nutrition, UPMC - Université Pierre et Marie Curie - Paris 6, INSERM
| | - Ana Cumano
- Unit for Lymphopoiesis, Immunology Department, INSERM U1223, University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Institut Pasteur;
| | - Sophie Novault
- Flow Cytometry Core Facility, Center for Translational Research-Technical Core, Institut Pasteur;
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14
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Schmutz S, Valente M, Cumano A, Novault S. Spectral Cytometry Has Unique Properties Allowing Multicolor Analysis of Cell Suspensions Isolated from Solid Tissues. PLoS One 2016; 11:e0159961. [PMID: 27500930 PMCID: PMC4976887 DOI: 10.1371/journal.pone.0159961] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/19/2016] [Indexed: 12/17/2022] Open
Abstract
Flow cytometry, initially developed to analyze surface protein expression in hematopoietic cells, has increased in analytical complexity and is now widely used to identify cells from different tissues and organisms. As a consequence, data analysis became increasingly difficult due the need of large multi-parametric compensation matrices and to the eventual auto-fluorescence frequently found in cell suspensions obtained from solid organs. In contrast with conventional flow cytometry that detects the emission peak of fluorochromes, spectral flow cytometry distinguishes the shapes of emission spectra along a large range of continuous wave lengths. The data is analyzed with an algorithm that replaces compensation matrices and treats auto-fluorescence as an independent parameter. Thus, spectral flow cytometry should be capable to discriminate fluorochromes with similar emission peaks and provide multi-parametric analysis without compensation requirements. Here we show that spectral flow cytometry achieves a 21-parametric (19 fluorescent probes) characterization and deals with auto-fluorescent cells, providing high resolution of specifically fluorescence-labeled populations. Our results showed that spectral flow cytometry has advantages in the analysis of cell populations of tissues difficult to characterize in conventional flow cytometry, such as heart and intestine. Spectral flow cytometry thus combines the multi-parametric analytical capacity of the highest performing conventional flow cytometry without the requirement for compensation and enabling auto-fluorescence management.
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Affiliation(s)
| | - Mariana Valente
- Institut Pasteur, Immunology Department, Lymphopoiesis Unit, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
- Inserm U1223, Paris, France
- Instituto de Investigação e Inovação em Saúde (i3s) & INEB–Instituto de Engenharia Biomédica, Stem-Cell Microenvironments in Repair/Regeneration Team, Microenvironment for Newtherapies Group, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ana Cumano
- Institut Pasteur, Immunology Department, Lymphopoiesis Unit, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
- Inserm U1223, Paris, France
- * E-mail:
| | - Sophie Novault
- Institut Pasteur, Flow Cytometry Core Facility, Paris, France
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15
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Chea S, Schmutz S, Berthault C, Perchet T, Petit M, Burlen-Defranoux O, Goldrath A, Rodewald HR, Cumano A, Golub R. Single-Cell Gene Expression Analyses Reveal Heterogeneous Responsiveness of Fetal Innate Lymphoid Progenitors to Notch Signaling. Cell Rep 2016; 14:1500-1516. [PMID: 26832410 DOI: 10.1016/j.celrep.2016.01.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/01/2015] [Accepted: 01/02/2016] [Indexed: 11/27/2022] Open
Abstract
T and innate lymphoid cells (ILCs) share some aspects of their developmental programs. However, although Notch signaling is strictly required for T cell development, it is dispensable for fetal ILC development. Constitutive activation of Notch signaling, at the common lymphoid progenitor stage, drives T cell development and abrogates ILC development by preventing Id2 expression. By combining single-cell transcriptomics and clonal culture strategies, we characterize two heterogeneous α4β7-expressing lymphoid progenitor compartments. αLP1 (Flt3(+)) still retains T cell potential and comprises the global ILC progenitor, while αLP2 (Flt3(-)) consists of ILC precursors that are primed toward the different ILC lineages. Only a subset of αLP2 precursors is sensitive to Notch signaling required for their proliferation. Our study identifies, in a refined manner, the diversity of transitional stages of ILC development, their transcriptional signatures, and their differential dependence on Notch signaling.
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16
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Moussa H, Chenani H, Bouzaouache H, Carlier H, Sarkis A, Schmutz S, Lautridou C. Partial resection of the scapula and peri-scapular muscles after peri-scapular desmoid fibromatosis. About one case; interest of a rehabilitation program. Ann Phys Rehabil Med 2013. [DOI: 10.1016/j.rehab.2013.07.649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Moussa H, Chenani H, Bouzaouache H, Carlier H, Sarkis A, Schmutz S, Lautridou C. Résection partielle de la scapula et des muscles péri-scapulaires suite à une fibromatose desmoïde péri-scapulaire. À propos d’un cas ; intérêt d’un programme de rééducation. Ann Phys Rehabil Med 2013. [DOI: 10.1016/j.rehab.2013.07.648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Possot C, Schmutz S, Chea S, Boucontet L, Louise A, Cumano A, Golub R. Notch signaling is necessary for adult, but not fetal, development of RORγt(+) innate lymphoid cells. Nat Immunol 2011; 12:949-58. [PMID: 21909092 DOI: 10.1038/ni.2105] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 08/15/2011] [Indexed: 02/06/2023]
Abstract
The transcription factor RORγt is required for the development of several innate lymphoid populations, such as lymphoid tissue-inducer cells (LTi cells) and cells that secrete interleukin 17 (IL-17) or IL-22. The progenitor cells as well as the developmental stages that lead to the emergence of RORγt(+) innate lymphoid cells (ILCs) remain undefined. Here we identify the chemokine receptor CXCR6 as an additional marker of the development of ILCs and show that common lymphoid progenitors lost B cell and T cell potential as they successively acquired expression of the integrin α(4)β(7) and CXCR6. Whereas fetal RORγt(+) cells matured in the fetal liver environment, adult bone marrow-derived RORγt(+) ILCs matured outside the bone marrow, in a Notch2-dependent manner. Therefore, fetal and adult environments influence the differentiation of RORγt(+) cells differently.
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Schmutz S, Schinegger R, Muhar S, Preis S, Jungwirth M. Ökologischer Zustand der Fließgewässer Österreichs – Perspektiven bei unterschiedlichen Nutzungsszenarien der Wasserkraft. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s00506-010-0221-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Schmutz S, Bosco N, Chappaz S, Boyman O, Acha-Orbea H, Ceredig R, Rolink AG, Finke D. Cutting edge: IL-7 regulates the peripheral pool of adult ROR gamma+ lymphoid tissue inducer cells. J Immunol 2009; 183:2217-21. [PMID: 19635901 DOI: 10.4049/jimmunol.0802911] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
During fetal life, CD4(+)CD3(-) lymphoid tissue inducer (LTi) cells are required for lymph node and Peyer's patch development in mice. In adult animals, CD4(+)CD3(-) cells are found in low numbers in lymphoid organs. Whether adult CD4(+)CD3(-) cells are LTi cells and are generated and maintained through cytokine signals has not been directly addressed. In this study we show that adult CD4(+)CD3(-) cells adoptively transferred into neonatal CXCR5(-/-) mice induced the formation of intestinal lymphoid tissues, demonstrating for the first time their bona fide LTi function. Increasing IL-7 availability in wild-type mice either by IL-7 transgene expression or treatment with IL-7/anti-IL-7 complexes increased adult LTi cell numbers through de novo generation from bone marrow cells and increased the survival and proliferation of LTi cells. Our observations demonstrate that adult CD4(+)lineage(-) cells are LTi cells and that the availability of IL-7 determines the size of the adult LTi cell pool.
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Affiliation(s)
- Sandrine Schmutz
- Division of Developmental Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
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21
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Finke D, Schmutz S. Interleukin 7-induced lymphoid neogenesis in arthritis: recapitulation of a fetal developmental programme? Swiss Med Wkly 2009; 138:500-5. [PMID: 18792823 DOI: 2008/35/smw-12273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Chronic inflammatory diseases such as rheumatoid arthritis (RA) are associated with the de novo formation of organised lymphoid tissue in a subpopulation of patients. The aberrant expression of cytokines and chemokines by stromal cells plays an important role in recruitment and survival of effector cells of the immune system and the development of ectopic tertiary lymphoid organs (TLOs). TLOs may promote the persistence of inflammation and the recognition of self antigens. Recent studies in man and mice now indicate that interleukin 7 (IL-7) is implicated in the formation of TLOs and progression of chronic inflammation.
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Affiliation(s)
- Daniela Finke
- Developmental Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland.
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22
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Finke D, Schmutz S. Interleukin 7-induced lymphoid neogenesis in arthritis: recapitulation of a fetal developmental programme? Swiss Med Wkly 2008; 138:500-5. [PMID: 18792823 DOI: 10.4414/smw.2008.12273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chronic inflammatory diseases such as rheumatoid arthritis (RA) are associated with the de novo formation of organised lymphoid tissue in a subpopulation of patients. The aberrant expression of cytokines and chemokines by stromal cells plays an important role in recruitment and survival of effector cells of the immune system and the development of ectopic tertiary lymphoid organs (TLOs). TLOs may promote the persistence of inflammation and the recognition of self antigens. Recent studies in man and mice now indicate that interleukin 7 (IL-7) is implicated in the formation of TLOs and progression of chronic inflammation.
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Affiliation(s)
- Daniela Finke
- Developmental Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland.
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23
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Lingaas F, Aarskaug T, Gerlach JA, Juneja RK, Fredholm M, Sampson J, Suter N, Holmes NG, Binns MM, Ryder EJ, Van Haeringen WA, Venta PJ, Brouillette JA, Yuzbasiyan-Gurkan V, Wilton AN, Bredbacka P, Koskinen M, Dunner S, Parra D, Schmutz S, Schelling C, Schläpfer J, Dolf G. A canine linkage map: 39 linkage groups. J Anim Breed Genet 2008. [DOI: 10.1111/j.1439-0388.2001.00270.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Matulla C, Schmutz S, Melcher A, Gerersdorfer T, Haas P. Assessing the impact of a downscaled climate change simulation on the fish fauna in an Inner-Alpine River. Int J Biometeorol 2007; 52:127-37. [PMID: 17587065 DOI: 10.1007/s00484-007-0107-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 04/03/2007] [Accepted: 04/27/2007] [Indexed: 05/15/2023]
Abstract
This study assesses the impact of a changing climate on fish fauna by comparing the past mean state of fish assemblage to a possible future mean state. It is based on (1) local scale observations along an Inner-Alpine river called Mur, (2) an IPCC emission scenario (IS92a), implemented by atmosphere-ocean global circulation model (AOGCM) ECHAM4/OPYC3, and (3) a model-chain that links climate research to hydrobiology. The Mur River is still in a near-natural condition and water temperature in summer is the most important aquatic ecological constraint for fish distribution. The methodological strategy is (1) to use downscaled air temperature and precipitation scenarios for the first half of the twenty-first century, (2) to establish a model that simulates water temperature by means of air temperature and flow rate in order to generate water temperature scenarios, and (3) to evaluate the impact on fish communities using an ecological model that is driven by water temperature. This methodology links the response of fish fauna to an IPCC emission scenario and is to our knowledge an unprecedented approach. The downscaled IS92a scenarios show increased mean air temperatures during the whole year and increased precipitation totals during summer, but reduced totals for the rest of the annual cycle. These changes result in scenarios of increased water temperatures, an altered annual cycle of flow rate, and, in turn, a 70 m displacement in elevation of fish communities towards the river's head. This would enhance stress on species that rely on low water temperatures and coerce cyprinid species into advancing against retreating salmonids. Hyporhithral river sectors would turn into epipotamal sectors. Grayling (Thymallus thymallus) and Danube salmon (Hucho hucho), presently characteristic for the Mur River, would be superceded by other species. Native brown trout (Salmo trutta), already now under pressure of competition, may be at risk of losing its habitat in favour of invaders like the exotic rainbow trout (Oncorhynchus mykiss), which are better adapted to higher water temperatures. Projected changes in fish communities suggest an adverse influence on salmonid sport fishing and a loss in its high economic value.
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Affiliation(s)
- C Matulla
- Climate Research Division, Science and Technology Branch, Environment Canada, 4905 Dufferin Street, Toronto, ON, M3H 5T4, Canada.
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25
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Meier D, Bornmann C, Chappaz S, Schmutz S, Otten LA, Ceredig R, Acha-Orbea H, Finke D. Ectopic lymphoid-organ development occurs through interleukin 7-mediated enhanced survival of lymphoid-tissue-inducer cells. Immunity 2007; 26:643-54. [PMID: 17521585 DOI: 10.1016/j.immuni.2007.04.009] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Revised: 02/06/2007] [Accepted: 04/02/2007] [Indexed: 01/05/2023]
Abstract
Development of Peyer's patches and lymph nodes requires the interaction between CD4+ CD3- IL-7Ralpha+ lymphoid-tissue inducer (LTi) and VCAM-1+ organizer cells. Here we showed that by promoting their survival, enhanced expression of interleukin-7 (IL-7) in transgenic mice resulted in accumulation of LTi cells. With increased IL-7 availability, de novo formation of VCAM-1+ Peyer's patch anlagen occurred along the entire fetal gut resulting in a 5-fold increase in Peyer's patch numbers. IL-7 overexpression also led to formation of multiple organized ectopic lymph nodes and cecal patches. After immunization, ectopic lymph nodes developed normal T cell-dependent B cell responses and germinal centers. Mice overexpressing IL-7 but lacking either RORgamma, a factor required for LTi cell generation, or lymphotoxin alpha1beta2 had neither Peyer's patches nor ectopic lymph nodes. Therefore, by controlling LTi cell numbers, IL-7 can regulate the formation of both normal and ectopic lymphoid organs.
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Affiliation(s)
- Dominik Meier
- Division of Developmental Immunology, Center for Biomedicine, Department of Clinical and Biological Sciences (DKBW), University of Basel, CH-4058 Basel, Switzerland
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Jungwirth M, Haidvogl G, Hohensinner S, Muhar S, Schmutz S, Waidbacher H. Leitbild-specific measures for the rehabilitation of the heavily modified Austrian Danube River. ACTA ACUST UNITED AC 2003. [DOI: 10.1127/lr/15/2003/17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Cribiu EP, Di Berardino D, Di Meo GP, Eggen A, Gallagher DS, Gustavsson I, Hayes H, Iannuzzi L, Popescu CP, Rubes J, Schmutz S, Stranzinger G, Vaiman A, Womack J. International System for Chromosome Nomenclature of Domestic Bovids (ISCNDB 2000). Cytogenet Cell Genet 2001; 92:283-99. [PMID: 11435702 DOI: 10.1159/000056917] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sonstegard TS, Bennett GL, Kalm E, Kappes SM, Lewin HA, Olsaker I, Schmutz S, Thomsen H, Vage DI, Van Tassell CP, Xu N. Consensus and comprehensive linkage maps of bovine chromosome 25. Anim Genet 2001; 32:114-5. [PMID: 11421953 DOI: 10.1046/j.1365-2052.2001.0700f.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Sonstegard TS, Bendixen C, Bennett GL, Kalm E, Kappes SM, Lewin HA, Lien S, Nielsen VH, Olsaker I, Schmutz S, Thomsen H, Van Tassell CP, Xu N. Consensus and comprehensive linkage maps of bovine chromosome 17. Anim Genet 2001; 32:112-3. [PMID: 11421952 DOI: 10.1046/j.1365-2052.2001.0700e.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Lingaas F, Aarskaug T, Gerlach JA, Juneja RK, Fredholm M, Sampson J, Suter N, Holmes NG, Binns MM, Ryder EJ, Van Haeringen WA, Venta PJ, Brouillette JA, Yuzbasiyan-Gurkan V, Wilton AN, Bredbacka P, Koskinen M, Dunner S, Parra D, Schmutz S, Schelling C, Schlapfer J, Dolf G. A canine linkage map: 39 linkage groups. J Anim Breed Genet 2001. [DOI: 10.1046/j.1439-0388.2001.00270.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Abstract
Genetic polymorphism at Mhc class II DRB loci was investigated in samples of musk-ox from Canada and Greenland; moose from Sweden, Norway, Canada, and Alaska; roe deer from Norway and Sweden; reindeer from Svalbard and Norway; fallow deer from Norway and Sweden; and red deer from Norway. The results were compared with published data on cattle, bison, goat, sheep, and red deer. Cattle-specific primers amplified a single DRB locus in all species except fallow deer and red deer, in which two loci were found. Single strand conformation polymorphism analysis and DNA sequence analysis were employed to detect genetic polymorphism. Complete monomorphism was found in musk-ox and fallow deer. Limited polymorphism was found in the moose, roe deer, and reindeer from Svalbard, whereas intermediate to extensive DRB diversity was present in reindeer from Norway and in bison, sheep, goat, cattle, and red deer. The restricted Mhc diversity in moose, roe deer, and fallow deer is notable in relation to the dramatic population expansion of moose and roe deer in Sweden during this century and since fallow deer is used for meat and game production with good results and without any marked disease problems. The results question the view that species or populations with restricted Mhc diversity have poor resistance to infectious diseases. A phylogenetic tree analysis revealed a clustering of DRB sequences within species rather than within allelic lineages across species. The results suggest trans-species persistence of polymorphic sequence motifs rather than of allelic lineages.
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Affiliation(s)
- S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Popescu CP, Long S, Riggs P, Womack J, Schmutz S, Fries R, Gallagher DS. Standardization of cattle karyotype nomenclature: report of the committee for the standardization of the cattle karyotype. Cytogenet Cell Genet 1996; 74:259-61. [PMID: 8976379 DOI: 10.1159/000134429] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The purpose of this paper is to publish a table which correlates the previous nomenclature with marker genes mapped on cattle chromosomes. This table also presents the human correspondences and the chromosome measurements expressed as relative lengths.
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Affiliation(s)
- C P Popescu
- INRA-CRJ, CYtogenetic Laboratory, Jouy-en-Josas Cedex, France.
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Abstract
beta-mannosidosis is a recently recognized lysosomal storage disease in newborn Salers calves. Fourteen calves with beta-mannosidase deficiency were examined. Twelve calves were from routine laboratory submissions, and two calves were the result of a breeding trial. Salers calves with beta-mannosidase deficiency were of normal gestational weight, 36 +/- 6 kg, but were affected at birth. The head was moderately domed, and there was mild superior brachygnathism. The calves were recumbent and had a head tremor. There was bilateral renal enlargement, severe hypomyelination in the brain and variable thyroid gland enlargement. Severe cytoplasmic vacuolation was present within neurons, tubule epithelial cells, follicular cells and macrophages of the nervous, renal, thyroid and lymphoid tissues, respectively. Pedigree analysis and breeding trial results were consistent with an autosomal recessive disease. An initial biochemical survey of 1,494 Salers cattle indicated a carrier frequency of 23%.
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Affiliation(s)
- L Bryan
- Alberta Department of Agriculture, Animal Health Division, Airdrie, Canada
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Abstract
A fatal inherited glycoprotein storage disorder is described in Salers cattle which affects both sexes. Affected calves are unable to stand at birth, have a marked intention tremor, markedly enlarged kidneys, decreased white matter in all areas of the brain, and cytoplasmic vacuolation in multiple cell types of multiple tissues with nervous, renal, lymphoid and thyroid tissues most severely affected. Affected calves were grossly deficient in lymphocyte and brain beta-mannosidase activity and had markedly reduced but not deficient activity in liver and kidney. A test mating of obligate carriers produced three genotypes: affected, carrier, non-carrier in essentially the expected ratio of 1:2:1, consistent with autosomal recessive inheritance.
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Affiliation(s)
- L Bryan
- Regional Veterinary Laboratory, Alberta Agriculture, Airdrie, Canada
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Abstract
A relatively simple method of obtaining high resolution chromosomes from amniotic fluid cells is described. The elongated chromosomes are achieved by adding ethidium bromide (5 micrograms/ml) to the culture 4 1/2 hours before harvesting and the high resolution banding can be produced by usual banding procedures.
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