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Voronov D, Paganos P, Magri MS, Cuomo C, Maeso I, Gómez-Skarmeta JL, Arnone MI. Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single-cell level. Development 2024; 151:dev202278. [PMID: 39058236 DOI: 10.1242/dev.202278] [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: 08/24/2023] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
Drafting gene regulatory networks (GRNs) requires embryological knowledge pertaining to the cell type families, information on the regulatory genes, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis. We use multi-omics involving next-generation sequencing to obtain the necessary information for drafting the Strongylocentrotus purpuratus (Sp) posterior gut GRN. Here, we present an update to the GRN using: (1) a single-cell RNA-sequencing-derived cell atlas highlighting the 2 day-post-fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at the single-cell level; (2) a set of putative cis-regulatory modules and transcription factor-binding sites obtained from chromatin accessibility ATAC-seq data; and (3) interactions directionality obtained from differential bulk RNA sequencing following knockdown of the transcription factor Sp-Pdx1, a key regulator of gut patterning in sea urchins. Combining these datasets, we draft the GRN for the hindgut Sp-Pdx1-positive cells in the 2 dpf gastrula embryo. Overall, our data suggest the complex connectivity of the posterior gut GRN and increase the resolution of gene regulatory cascades operating within it.
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Affiliation(s)
- Danila Voronov
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Periklis Paganos
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Marta S Magri
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Claudia Cuomo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Jose Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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2
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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Miranda-Negrón Y, García-Arrarás JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601561. [PMID: 39005414 PMCID: PMC11244903 DOI: 10.1101/2024.07.01.601561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In holothurians, the regenerative process following evisceration involves the development of a "rudiment" or "anlage" at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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3
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Cocurullo M, Paganos P, Benvenuto G, Arnone MI. Characterization of thyrotropin-releasing hormone producing neurons in sea urchin, from larva to juvenile. Front Neurosci 2024; 18:1378520. [PMID: 38660219 PMCID: PMC11039832 DOI: 10.3389/fnins.2024.1378520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Most sea urchin species are indirect developers, going through a larval stage called pluteus. The pluteus possesses its own nervous system, consisting mainly of the apical organ neurons (controlling metamorphosis and settlement) and ciliary band neurons (controlling swimming behavior and food collection). Additional neurons are located in various areas of the gut. In recent years, the molecular complexity of this apparently "simple" nervous system has become apparent, with at least 12 neuronal populations identified through scRNA-sequencing in the species Strongylocentrotus purpuratus. Among these, there is a cluster of neurosecretory cells that produce a thyrotropin-releasing hormone-type neuropeptide (TRHergic) and that are also photosensory (expressing a Go-Opsin). However, much less is known about the organization of the nervous system in other sea urchin species. The aim of this work was to thoroughly characterize the localization of the TRHergic cells from early pluteus to juvenile stages in the Mediterranean sea urchin species Paracentrotus lividus combining immunostaining and whole mount in situ hybridization. We also compared the localization of TRHergic cells in early plutei of two other sea urchin species, Arbacia lixula and Heliocidaris tuberculata. This work provides new information on the anatomy and development of the nervous system in sea urchins. Moreover, by comparing the molecular signature of the TRHergic cells in P. lividus and S. purpuratus, we have obtained new insights how TRH-type neuropeptide signaling evolved in relatively closely related species.
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Affiliation(s)
| | | | | | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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4
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Benvenuto G, Leone S, Astoricchio E, Bormke S, Jasek S, D'Aniello E, Kittelmann M, McDonald K, Hartenstein V, Baena V, Escrivà H, Bertrand S, Schierwater B, Burkhardt P, Ruiz-Trillo I, Jékely G, Ullrich-Lüter J, Lüter C, D'Aniello S, Arnone MI, Ferraro F. Evolution of the ribbon-like organization of the Golgi apparatus in animal cells. Cell Rep 2024; 43:113791. [PMID: 38428420 DOI: 10.1016/j.celrep.2024.113791] [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: 05/11/2023] [Revised: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024] Open
Abstract
The "ribbon," a structural arrangement in which Golgi stacks connect to each other, is considered to be restricted to vertebrate cells. Although ribbon disruption is linked to various human pathologies, its functional role in cellular processes remains unclear. In this study, we investigate the evolutionary origin of the Golgi ribbon. We observe a ribbon-like architecture in the cells of several metazoan taxa suggesting its early emergence in animal evolution predating the appearance of vertebrates. Supported by AlphaFold2 modeling, we propose that the evolution of Golgi reassembly and stacking protein (GRASP) binding by golgin tethers may have driven the joining of Golgi stacks resulting in the ribbon-like configuration. Additionally, we find that Golgi ribbon assembly is a shared developmental feature of deuterostomes, implying a role in embryogenesis. Overall, our study points to the functional significance of the Golgi ribbon beyond vertebrates and underscores the need for further investigations to unravel its elusive biological roles.
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Affiliation(s)
- Giovanna Benvenuto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Serena Leone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Emanuele Astoricchio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | | | - Sanja Jasek
- Living Systems Institute, University of Exeter, Exeter, UK; Heidelberg University, Centre for Organismal Studies (COS), Heidelberg, Germany
| | - Enrico D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Maike Kittelmann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Kent McDonald
- Electron Microscope Lab, University of California Berkeley, Berkeley, CA, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Valentina Baena
- Department of Cell Biology, UConn Health, Farmington, CT, USA
| | - Héctor Escrivà
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Bernd Schierwater
- Institute of Ecology and Evolution, Hannover University of Veterinary Medicine Foundation, Hannover, Germany
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK; Heidelberg University, Centre for Organismal Studies (COS), Heidelberg, Germany
| | | | | | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Francesco Ferraro
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy.
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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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6
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Lee Y, Tjeerdema E, Kling S, Chang N, Hamdoun A. Solute carrier (SLC) expression reveals skeletogenic cell diversity. Dev Biol 2023; 503:68-82. [PMID: 37611888 DOI: 10.1016/j.ydbio.2023.08.004] [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: 06/22/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
Within the developing embryo is a microcosm of cell type diversity. Single cell RNA-sequencing (scRNA-seq) is used to reveal cell types, typically by grouping cells according to their gene regulatory states. However, both across and within these regulatory states are additional layers of cellular diversity represented by the differential expression of genes that govern cell function. Here, we analyzed scRNA-seq data representing the late gastrula stage of Strongylocentrotus purpuratus (purple sea urchin) to understand the patterning of transporters belonging to the ABC and SLC families. These transporters handle diverse substrates from amino acids to signaling molecules, nutrients and xenobiotics. Using transporter-based clustering, we identified unique transporter patterns that are both shared across cell lineages, as well as those that were unique to known cell types. We further explored three patterns of transporter expression in mesodermal cells including secondary mesenchyme cells (pigment cells and blastocoelar cells) and skeletogenic cells (primary mesenchyme cells). The results revealed the enrichment of SMTs potentially involved in nutrient absorption (SLC5A9, SLC7A11, SLC35F3, and SLC52A3) and skeletogenesis (SLC9A3, SLC13A2/3/5, and SLC39A13) in pigment cells and blastocoelar cells respectively. The results indicated that the strategy of clustering by cellular activity can be useful for discovering cellular populations that would otherwise remain obscured.
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Affiliation(s)
- Yoon Lee
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Evan Tjeerdema
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Svenja Kling
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Nathan Chang
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Amro Hamdoun
- Center for Marine Biology and Biomedicine Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA.
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7
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Cocurullo M, Paganos P, Annunziata R, Voronov D, Arnone MI. Single-Cell Transcriptomic Analysis Reveals the Molecular Profile of Go-Opsin Photoreceptor Cells in Sea Urchin Larvae. Cells 2023; 12:2134. [PMID: 37681865 PMCID: PMC10486798 DOI: 10.3390/cells12172134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
The ability to perceive and respond to light stimuli is fundamental not only for spatial vision but also to many other light-mediated interactions with the environment. In animals, light perception is performed by specific cells known as photoreceptors and, at molecular level, by a group of GPCRs known as opsins. Sea urchin larvae possess a group of photoreceptor cells (PRCs) deploying a Go-Opsin (Opsin3.2) which have been shown to share transcription factors and morphology with PRCs of the ciliary type, raising new questions related to how this sea urchin larva PRC is specified and whether it shares a common ancestor with ciliary PRCs or it if evolved independently through convergent evolution. To answer these questions, we combined immunohistochemistry and fluorescent in situ hybridization to investigate how the Opsin3.2 PRCs develop in the sea urchin Strongylocentrotus purpuratus larva. Subsequently, we applied single-cell transcriptomics to investigate the molecular signature of the Sp-Opsin3.2-expressing cells and show that they deploy an ancient regulatory program responsible for photoreceptors specification. Finally, we also discuss the possible functions of the Opsin3.2-positive cells based on their molecular fingerprint, and we suggest that they are involved in a variety of signaling pathways, including those entailing the thyrotropin-releasing hormone.
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Affiliation(s)
| | | | | | | | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (M.C.); (P.P.); (R.A.); (D.V.)
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8
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Piovani L, Leite DJ, Yañez Guerra LA, Simpson F, Musser JM, Salvador-Martínez I, Marlétaz F, Jékely G, Telford MJ. Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories. SCIENCE ADVANCES 2023; 9:eadg6034. [PMID: 37531419 PMCID: PMC10396302 DOI: 10.1126/sciadv.adg6034] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/30/2023] [Indexed: 08/04/2023]
Abstract
Pelagic larval stages are widespread across animals, yet it is unclear whether larvae were present in the last common ancestor of animals or whether they evolved multiple times due to common selective pressures. Many marine larvae are at least superficially similar; they are small, swim through the beating of bands of cilia, and sense the environment with an apical organ. To understand these similarities, we have generated single-cell atlases for marine larvae from two animal phyla and have compared their cell types. We found clear similarities among ciliary band cells and between neurons of the apical organ in the two larvae pointing to possible homology of these structures, suggesting a single origin of larvae within Spiralia. We also find several clade-specific innovations in each larva, including distinct myocytes and shell gland cells in the oyster larva. Oyster shell gland cells express many recently evolved genes that have made previous gene age estimates for the origin of trochophore larvae too young.
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Affiliation(s)
- Laura Piovani
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Daniel J. Leite
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Fraser Simpson
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Jacob M. Musser
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Irepan Salvador-Martínez
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ferdinand Marlétaz
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - Maximilian J. Telford
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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9
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Hildebrand J, Chang WW, Hu MY, Stumpp M. Characterization of digestive proteases in the gut of a basal deuterostome. J Exp Biol 2023; 226:jeb245789. [PMID: 37470128 DOI: 10.1242/jeb.245789] [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: 03/06/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Digestive systems are complex organs that allow organisms to absorb energy from their environment to fuel vital processes such as growth, development and the maintenance of homeostasis. A comprehensive understanding of digestive physiology is therefore essential to fully understand the energetics of an organism. The digestion of proteins is of particular importance because most heterotrophic organisms are not able to synthesize all essential amino acids. While Echinoderms are basal deuterostomes that share a large genetic similarity with vertebrates, their digestion physiology remains largely unexplored. Using a genetic approach, this work demonstrated that several protease genes including an enteropeptidase, aminopeptidase, carboxypeptidase and trypsin involved in mammalian digestive networks are also found in sea urchin larvae. Through characterization including perturbation experiments with different food treatments and pharmacological inhibition of proteases using specific inhibitors, as well as transcriptomic analysis, we conclude that the trypsin-2 gene codes for a crucial enzyme for protein digestion in Strongylocentrotus purpuratus. Measurements of in vivo digestion rates in the transparent sea urchin larva were not altered by pharmacological inhibition of trypsin (using soybean trypsin inhibitor) or serine proteases (aprotinin), suggesting that proteases are not critically involved in the initial step of microalgal breakdown. This work provides new insights into the digestive physiology of a basal deuterostome and allows comparisons from the molecular to the functional level in the digestive systems of vertebrates and mammals. This knowledge will contribute to a better understanding for conserved digestive mechanisms that evolved in close interaction with their biotic and abiotic environment.
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Affiliation(s)
- Jasper Hildebrand
- Zoological Institute, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - William W Chang
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Marian Y Hu
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Meike Stumpp
- Zoological Institute, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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