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Fujita T, Aoki N, Mori C, Homma KJ, Yamaguchi S. SoxC and MmpReg promote blastema formation in whole-body regeneration of fragmenting potworms Enchytraeus japonensis. Nat Commun 2024; 15:6659. [PMID: 39174502 PMCID: PMC11341731 DOI: 10.1038/s41467-024-50865-1] [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: 10/03/2022] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Regeneration in many animals involves the formation of a blastema, which differentiates and organizes into the appropriate missing body parts. Although the mechanisms underlying blastema formation are often fundamental to regeneration biology, information on the cellular and molecular basis of blastema formation remains limited. Here, we focus on a fragmenting potworm (Enchytraeus japonensis), which can regenerate its whole body from small fragments. We find soxC and mmpReg as upregulated genes in the blastema. RNAi of soxC and mmpReg reduce the number of blastema cells, indicating that soxC and mmpReg promote blastema formation. Expression analyses show that soxC-expressing cells appear to gradually accumulate in blastema and constitute a large part of the blastema. Additionally, similar expression dynamics of SoxC orthologue genes in frog (Xenopus laevis) are found in the regeneration blastema of tadpole tail. Our findings provide insights into the cellular and molecular mechanisms underlying blastema formation across species.
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Affiliation(s)
- Toshiyuki Fujita
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Naoya Aoki
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Chihiro Mori
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Koichi J Homma
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Shinji Yamaguchi
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan.
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2
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Maynard A, Soretić M, Treutlein B. Single-cell genomic profiling to study regeneration. Curr Opin Genet Dev 2024; 87:102231. [PMID: 39053027 DOI: 10.1016/j.gde.2024.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/27/2024]
Abstract
Regenerative capacities and strategies vary dramatically across animals, as well as between cell types, organs, and with age. In recent years, high-throughput single-cell transcriptomics and other single-cell profiling technologies have been applied to many animal models to gain an understanding of the cellular and molecular mechanisms underlying regeneration. Here, we review recent single-cell studies of regeneration in diverse contexts and summarize key concepts that have emerged. The immense regenerative capacity of some invertebrates, exemplified by planarians, is driven mainly by the differentiation of abundant adult pluripotent stem cells, whereas in many other cases, regeneration involves the reactivation of embryonic or developmental gene-regulatory networks in differentiated cell types. However, regeneration also differs from development in many ways, including the use of regeneration-specific cell types and gene regulatory networks.
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Affiliation(s)
- Ashley Maynard
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Mateja Soretić
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Barbara Treutlein
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland.
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3
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Hulett RE, Rivera-López C, Gehrke AR, Gompers A, Srivastava M. A wound-induced differentiation trajectory for neurons. Proc Natl Acad Sci U S A 2024; 121:e2322864121. [PMID: 38976727 PMCID: PMC11260127 DOI: 10.1073/pnas.2322864121] [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: 12/28/2023] [Accepted: 05/03/2024] [Indexed: 07/10/2024] Open
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully functional new organs, including new brains, de novo. The regeneration of a new brain requires the formation of diverse neural cell types and their assembly into an organized structure with correctly wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neural subpopulations, however, how these transcriptional programs are initiated in response to injury remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia, to study wound-induced transcriptional regulatory events that lead to the production of neurons and subsequently a functional brain. Footprinting analysis using chromatin accessibility data on a chromosome-scale genome assembly revealed that binding sites for the Nuclear Factor Y (NFY) transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal function. Single-cell transcriptome analysis combined with functional studies identified soxC+ stem cells as a putative progenitor population for multiple neural subtypes. Further, we found that wound-induced soxC expression is likely under direct transcriptional control by NFY, uncovering a mechanism for the initiation of a neural differentiation pathway by early wound-induced binding of a transcriptional regulator.
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Affiliation(s)
- Ryan E. Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA02138
| | - Andrew R. Gehrke
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
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4
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Martinez P, Bailly X, Sprecher SG, Hartenstein V. The Acoel nervous system: morphology and development. Neural Dev 2024; 19:9. [PMID: 38907301 PMCID: PMC11191258 DOI: 10.1186/s13064-024-00187-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
Acoel flatworms have played a relevant role in classical (and current) discussions on the evolutionary origin of bilaterian animals. This is mostly derived from the apparent simplicity of their body architectures. This tenet has been challenged over the last couple of decades, mostly because detailed studies of their morphology and the introduction of multiple genomic technologies have unveiled a complexity of cell types, tissular arrangements and patterning mechanisms that were hidden below this 'superficial' simplicity. One tissue that has received a particular attention has been the nervous system (NS). The combination of ultrastructural and single cell methodologies has revealed unique cellular diversity and developmental trajectories for most of their neurons and associated sensory systems. Moreover, the great diversity in NS architectures shown by different acoels offers us with a unique group of animals where to study key aspects of neurogenesis and diversification od neural systems over evolutionary time.In this review we revisit some recent developments in the characterization of the acoel nervous system structure and the regulatory mechanisms that contribute to their embryological development. We end up by suggesting some promising avenues to better understand how this tissue is organized in its finest cellular details and how to achieve a deeper knowledge of the functional roles that genes and gene networks play in its construction.
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Affiliation(s)
- Pedro Martinez
- Departament de Genètica, Microbiologia I Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
- ICREA (Institut Català de Recerca I Estudis Avancats), Barcelona, Spain.
| | - Xavier Bailly
- Station Biologique de Roscoff, Multicellular Marine Models (M3) Team, FR2424, CNRS / Sorbonne Université - Place Georges Teissier, Roscoff, 29680, France
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, 10, Ch. Du Musée, Fribourg, 1700, Switzerland
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
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5
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Church SH, Mah JL, Dunn CW. Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells. PLoS Biol 2024; 22:e3002633. [PMID: 38787797 PMCID: PMC11125556 DOI: 10.1371/journal.pbio.3002633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024] Open
Abstract
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons evoke evolutionary histories, as depicted by phylogenetic trees, that define relationships between species, genes, and cells. This Essay considers each of these in turn, laying out challenges and solutions derived from a phylogenetic comparative approach and relating these solutions to previously proposed methods for the pairwise alignment of cellular dimensional maps. This Essay contends that species trees, gene trees, cell phylogenies, and cell lineages can all be reconciled as descriptions of the same concept-the tree of cellular life. By integrating phylogenetic approaches into scRNA-seq analyses, challenges for building informed comparisons across species can be overcome, and hypotheses about gene and cell evolution can be robustly tested.
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Affiliation(s)
- Samuel H. Church
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jasmine L. Mah
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Casey W. Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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6
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Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Del Olmo I, Peron S, Salamanca-Díaz DA, Mason V, Metzger B, Bely AE, Kenny NJ, Özpolat BD, Solana J. Annelid adult cell type diversity and their pluripotent cellular origins. Nat Commun 2024; 15:3194. [PMID: 38609365 PMCID: PMC11014941 DOI: 10.1038/s41467-024-47401-6] [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: 07/28/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Many annelids can regenerate missing body parts or reproduce asexually, generating all cell types in adult stages. However, the putative adult stem cell populations involved in these processes, and the diversity of cell types generated by them, are still unknown. To address this, we recover 75,218 single cell transcriptomes of the highly regenerative and asexually-reproducing annelid Pristina leidyi. Our results uncover a rich cell type diversity including annelid specific types as well as novel types. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. We find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors, in piwi+ cells. Finally, lineage reconstruction analyses reveal computational differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids by single cell transcriptomics and suggest that a piwi+ cell population with a pluripotent stem cell signature is associated with adult cell type differentiation.
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Affiliation(s)
- Patricia Álvarez-Campos
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Helena García-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Elena Emili
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alberto Pérez-Posada
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Irene Del Olmo
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sophie Peron
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - David A Salamanca-Díaz
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Vincent Mason
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Bria Metzger
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand
| | - B Duygu Özpolat
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA.
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA.
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Living Systems Institute, University of Exeter, Exeter, UK.
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Robertson HE, Sebé-Pedrós A, Saudemont B, Loe-Mie Y, Zakrzewski AC, Grau-Bové X, Mailhe MP, Schiffer P, Telford MJ, Marlow H. Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity. Nat Commun 2024; 15:2469. [PMID: 38503762 PMCID: PMC10951248 DOI: 10.1038/s41467-024-45956-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Phylogenetic analyses over the last two decades have united a few small, and previously orphan clades, the nematodermatids, acoels and xenoturbelids, into the phylum Xenacoelomorpha. Some phylogenetic analyses support a sister relationship between Xenacoelomorpha and Ambulacraria (Xenambulacraria), while others suggest that Xenacoelomorpha may be sister to the rest of the Bilateria (Nephrozoa). An understanding of the cell type complements of Xenacoelomorphs is essential to assessing these alternatives as well as to our broader understanding of bilaterian cell type evolution. Employing whole organism single-cell RNA-seq in the marine xenacoelomorph worm Xenoturbella bocki, we show that Xenambulacrarian nerve nets share regulatory features and a peptidergic identity with those found in cnidarians and protostomes and more broadly share muscle and gland cell similarities with other metazoans. Taken together, these data are consistent with broad homologies of animal gland, muscle, and neurons as well as more specific affinities between Xenoturbella and acoel gut and epidermal tissues, consistent with the monophyly of Xenacoelomorpha.
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Affiliation(s)
- Helen E Robertson
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - 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
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Anne-C Zakrzewski
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marie-Pierre Mailhe
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Philipp Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Institute of Zoology, Section Developmental Biology, University of Cologne, Köln, Wormlab, Germany
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA.
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.
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Bump P, Lubeck L. Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis. Integr Comp Biol 2023; 63:999-1009. [PMID: 37188638 PMCID: PMC10714908 DOI: 10.1093/icb/icad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023] Open
Abstract
Over the past decade, single-cell RNA-sequencing (scRNA-seq) has made it possible to study the cellular diversity of a broad range of organisms. Technological advances in single-cell isolation and sequencing have expanded rapidly, allowing the transcriptomic profile of individual cells to be captured. As a result, there has been an explosion of cell type atlases created for many different marine invertebrate species from across the tree of life. Our focus in this review is to synthesize current literature on marine invertebrate scRNA-seq. Specifically, we provide perspectives on key insights from scRNA-seq studies, including descriptive studies of cell type composition, how cells respond in dynamic processes such as development and regeneration, and the evolution of new cell types. Despite these tremendous advances, there also lie several challenges ahead. We discuss the important considerations that are essential when making comparisons between experiments, or between datasets from different species. Finally, we address the future of single-cell analyses in marine invertebrates, including combining scRNA-seq data with other 'omics methods to get a fuller understanding of cellular complexities. The full diversity of cell types across marine invertebrates remains unknown and understanding this diversity and evolution will provide rich areas for future study.
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Affiliation(s)
- Paul Bump
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lauren Lubeck
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [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: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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