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Raspe S, Kümmerlen K, Harzsch S. Immunolocalization of SIFamide-like neuropeptides in the adult and developing central nervous system of the amphipod Parhyale hawaiensis (Malacostraca, Peracarida, Amphipoda). ARTHROPOD STRUCTURE & DEVELOPMENT 2023; 77:101309. [PMID: 37879171 DOI: 10.1016/j.asd.2023.101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
Immunohistochemical analyses on the distribution of neuropeptides in the pancrustacean brain in the past have focussed mostly on representatives of the decapod ("ten-legged") pancrustaceans whereas other taxa are understudied in this respect. The current report examines the post-embryogenic and adult brain and ventral nerve cord of the amphipod pancrustacean Parhyale hawaiensis (Dana. 1853; Peracarida, Amphipoda, Hyalide), a subtropical species with a body size of 1.5 cm and a direct post-embryonic development using immunohistochemistry to label the neuropeptide SIFamide and synaptic proteins (synapsins). We found strong SIFamide-like labelling in proto-, deuto- and tritocerebrum, especially in the lamina, the lateral protocerebrum, lateral assessory lobe, the central body, olfactory lobe, medial antenna 1 neuropil and antenna 2 neuropil. Out of a total of 28 ± 5 (N = 12) SIFamide-positive neurons in the central brain of adult P. hawaiensis, we found three individually identifiable somata which were consistently present within the brain of adult and subadult animals. Additionally, the subesophageal and two adjacent thoracic ganglia were analysed in only adult animals and also showed a strong SIFamide-like immunoreactivity. We compare our findings to other pancrustaceans including hexapods and discuss them in an evolutionary context.
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Affiliation(s)
- Sophie Raspe
- University of Greifswald, Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, Soldmannstrasse 23, D-17498 Greifswald, Germany
| | - Katja Kümmerlen
- University of Greifswald, Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, Soldmannstrasse 23, D-17498 Greifswald, Germany
| | - Steffen Harzsch
- University of Greifswald, Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, Soldmannstrasse 23, D-17498 Greifswald, Germany.
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2
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Cislo DJ, Yang F, Qin H, Pavlopoulos A, Bowick MJ, Streichan SJ. Active cell divisions generate fourfold orientationally ordered phase in living tissue. NATURE PHYSICS 2023; 19:1201-1210. [PMID: 37786880 PMCID: PMC10545346 DOI: 10.1038/s41567-023-02025-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2023] [Indexed: 10/04/2023]
Abstract
Morphogenesis, the process through which genes generate form, establishes tissue-scale order as a template for constructing the complex shapes of the body plan. The extensive growth required to build these ordered substrates is fuelled by cell proliferation, which, naively, should destroy order. Understanding how active morphogenetic mechanisms couple cellular and mechanical processes to generate order-rather than annihilate it-remains an outstanding question in animal development. We show that cell divisions are the primary drivers of tissue flow, leading to a fourfold orientationally ordered phase. Waves of anisotropic cell proliferation propagate across the embryo with precise patterning. Defects introduced into the nascent lattice by cell divisions are moved out of the tissue bulk towards the boundary by subsequent divisions. Specific cell proliferation rates and orientations enable cell divisions to organize rather than fluidize the tissue. We observe this using live imaging and tissue cartography to analyse the dynamics of fourfold tissue ordering in the trunk segmental ectoderm of the crustacean Parhyale hawaiensis beginning 72 h after egg lay. The result is a robust, active mechanism for generating global orientational order in a non-equilibrium system that sets the stage for the subsequent development of shape and form.
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Affiliation(s)
- Dillon J. Cislo
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
| | - Fengshuo Yang
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Haodong Qin
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Anastasios Pavlopoulos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Mark J. Bowick
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, CA, USA
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Tserevelakis GJ, Velentza S, Liaskas I, Archontidis T, Pavlopoulos A, Zacharakis G. Imaging Parhyale hawaiensis embryogenesis with frequency domain photoacoustic microscopy: A novel tool in developmental biology. JOURNAL OF BIOPHOTONICS 2022; 15:e202200202. [PMID: 36059080 DOI: 10.1002/jbio.202200202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
We present the application of a low-cost frequency domain photoacoustic (FDPA) microscope for the label-free imaging of live developing embryos of the crustacean model organism Parhyale hawaiensis. By modulating the intensity of a continuous wave laser source at 9.5 MHz, we achieve the excitation of monochromatic PA waves, which are detected to provide amplitude and phase recordings. The data are subsequently processed to generate accurate maximum amplitude projection and surface reconstructions, delineating the morphological features of the embryos with high resolution and contrast. The findings of this study pave the way for the broader adoption of inexpensive PA diagnostic techniques in developmental biology, shedding light on various fundamental processes in established and emerging model organisms.
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Affiliation(s)
- George J Tserevelakis
- Foundation for Research and Technology Hellas, Institute of Electronic Structure and Laser, Crete, Greece
| | - Sofia Velentza
- Foundation for Research and Technology Hellas, Institute of Electronic Structure and Laser, Crete, Greece
| | - Ioannis Liaskas
- Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Crete, Greece
| | - Themis Archontidis
- Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Crete, Greece
| | - Anastasios Pavlopoulos
- Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Crete, Greece
| | - Giannis Zacharakis
- Foundation for Research and Technology Hellas, Institute of Electronic Structure and Laser, Crete, Greece
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Sun DA, Bredeson JV, Bruce HS, Patel NH. Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis. Development 2022; 149:275484. [PMID: 35608283 DOI: 10.1242/dev.200793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
Abstract
Emerging research organisms enable the study of biology that cannot be addressed using classical 'model' organisms. New data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-seq to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis and limb development. In addition, we use short- and long-read RNA-seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.
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Affiliation(s)
- Dennis A Sun
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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Rallis J, Pavlopoulos A. Cellular basis of limb morphogenesis. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100887. [PMID: 35150918 DOI: 10.1016/j.cois.2022.100887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
How the size and shape of developing tissues is encoded in the genome has been a longstanding riddle for biologists. Constituent cells integrate several genetic and mechanical signals to decide whether to divide, die, change shape or position. We review here how morphogenetic cell behaviors contribute to leg formation from imaginal disc epithelia in the insect Drosophila melanogaster, as well as to direct embryonic limb outgrowths in the non-insect pancrustacean Parhyale hawaiensis. Considering the deep conservation of developmental programs for limb patterning among arthropods and other bilaterians, moving forward, it will be exciting to see how these genetic similarities reflect at the cellular and tissue mechanics level.
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Affiliation(s)
- John Rallis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece; Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Anastasios Pavlopoulos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece.
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Espinosa-Medina I, Garcia-Marques J, Cepko C, Lee T. High-throughput dense reconstruction of cell lineages. Open Biol 2019; 9:190229. [PMID: 31822210 PMCID: PMC6936253 DOI: 10.1098/rsob.190229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
The first meeting exclusively dedicated to the 'High-throughput dense reconstruction of cell lineages' took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.
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Affiliation(s)
- Isabel Espinosa-Medina
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Jorge Garcia-Marques
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Connie Cepko
- Department of Genetics and Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
| | - Tzumin Lee
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
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Wittfoth C, Harzsch S, Wolff C, Sombke A. The "amphi"-brains of amphipods: new insights from the neuroanatomy of Parhyale hawaiensis (Dana, 1853). Front Zool 2019; 16:30. [PMID: 31372174 PMCID: PMC6660712 DOI: 10.1186/s12983-019-0330-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Over the last years, the amphipod crustacean Parhyale hawaiensis has developed into an attractive marine animal model for evolutionary developmental studies that offers several advantages over existing experimental organisms. It is easy to rear in laboratory conditions with embryos available year-round and amenable to numerous kinds of embryological and functional genetic manipulations. However, beyond these developmental and genetic analyses, research on the architecture of its nervous system is fragmentary. In order to provide a first neuroanatomical atlas of the brain, we investigated P. hawaiensis using immunohistochemical labelings combined with laser-scanning microscopy, X-ray microcomputed tomography, histological sectioning and 3D reconstructions. RESULTS As in most amphipod crustaceans, the brain is dorsally bent out of the body axis with downward oriented lateral hemispheres of the protocerebrum. It comprises almost all prominent neuropils that are part of the suggested ground pattern of malacostracan crustaceans (except the lobula plate and projection neuron tract neuropil). Beyond a general uniformity of these neuropils, the brain of P. hawaiensis is characterized by an elaborated central complex and a modified lamina (first order visual neuropil), which displays a chambered appearance. In the light of a recent analysis on photoreceptor projections in P. hawaiensis, the observed architecture of the lamina corresponds to specialized photoreceptor terminals. Furthermore, in contrast to previous descriptions of amphipod brains, we suggest the presence of a poorly differentiated hemiellipsoid body and an inner chiasm and critically discuss these aspects. CONCLUSIONS Despite a general uniformity of amphipod brains, there is also a certain degree of variability in architecture and size of different neuropils, reflecting various ecologies and life styles of different species. In contrast to other amphipods, the brain of P. hawaiensis does not display any striking modifications or bias towards processing one particular sensory modality. Thus, we conclude that this brain represents a common type of an amphipod brain. Considering various established protocols for analyzing and manipulating P. hawaiensis, this organism is a suitable model to gain deeper understanding of brain anatomy e.g. by using connectome approaches, and this study can serve as first solid basis for following studies.
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Affiliation(s)
- Christin Wittfoth
- Department of Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Soldmannstr. 23, 17487 Greifswald, Germany
| | - Steffen Harzsch
- Department of Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Soldmannstr. 23, 17487 Greifswald, Germany
| | - Carsten Wolff
- Department of Biology, Comparative Zoology, Humboldt University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Andy Sombke
- Department of Integrative Zoology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
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Romero-Carvajal A, Turnbull MW, Baeza JA. Embryonic Development in the Peppermint Shrimp, Lysmata boggessi (Caridea: Lysmatidae). THE BIOLOGICAL BULLETIN 2018; 234:165-179. [PMID: 29949441 DOI: 10.1086/698468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There are a limited number of model species for decapod experimental embryology. To improve our understanding of developmental pattern evolution in the Decapoda, here we describe the early embryonic development of the caridean shrimp Lysmata boggessi, from immediately after fertilization to the hatching of the zoea larva, using fluorescence microscopy and whole-mount nuclear staining with 4',6-diamidino-2-phenylindole. Lysmata boggessi follows the standard caridean pattern of early development, with early holoblastic cleavage that will later become superficial, to form a blastoderm. We found no evidence of stereotypical cleavage and the formation of blastomere interlocking bands, which suggests there is diversity in developmental patterns within the Caridea. Gastrulation starts 37 hours after fertilization, and the embryonized nauplius is formed 2 days later. Enlarged headlobes, early retinal differentiation, and delayed pereopod development are characteristics of the post-naupliar stages in this species. To facilitate comparative studies with other crustacean species, we propose a staging method based on our findings. Lysmata boggessi is a protandric simultaneous hermaphrodite that is relatively easy to breed in captivity and amenable to laboratory experimentation in studies of embryonic development.
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Davolos D, Vonk R, Latella L, De Matthaeis E. The name of a model species: the case of Orchestia cavimana (Crustacea: Amhipoda: Talitridae). THE EUROPEAN ZOOLOGICAL JOURNAL 2018. [DOI: 10.1080/24750263.2018.1473513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- D. Davolos
- Research, Certification, Verification Area, Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements, INAIL, Rome, Italy
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - R. Vonk
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - L. Latella
- Museo Civico di Storia Naturale of Verona, Verona, Italy
| | - E. De Matthaeis
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
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Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A. Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. eLife 2018; 7:34410. [PMID: 29595475 PMCID: PMC5929908 DOI: 10.7554/elife.34410] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic. During early life, animals develop from a single fertilized egg cell to hundreds, millions or even trillions of cells. These cells specialize to do different tasks; forming different tissues and organs like muscle, skin, lungs and liver. For more than a century, scientists have strived to understand the details of how animal cells become different and specialize, and have created many new techniques and technologies to help them achieve this goal. Limbs – such as arms, legs and wings – form from small lumps of cells called limb buds. Scientists use the shrimp-like crustacean, Parhyale hawaiensis, to study development, including limb growth. This species is useful because it is easy to grow, manipulate and observe its developing young in the laboratory. Understanding how its limbs develop offers important new insights into how limbs develop in other animals too. Wolff, Tinevez, Pietzsch et al. have now combined advanced microscopy with custom computer software, called Massive Multi-view Tracker (MaMuT) to investigate this. As limbs develop in Parhyale, the MaMuT software tracks how cells behave, and how they are organized. This analysis revealed that for cells to produce a limb bud, they need to split at an early stage into separate groups. These groups are organized along two body axes, one that goes from head to tail, and one that runs from back to belly. The limb grows perpendicular to these main body axes, along a new ‘proximal-distal’ axis that goes from nearest to furthest from the body. Wolff et al. found that the cells that contribute to the extremities of the limb divide faster than the ones that stay closer to the body. Finally, the results show that when cells in a limb divide, they mostly divide along the proximal-distal axis, producing one cell that is further from the body than the other. These cell activities may help limbs to get longer as they grow. Notably, the groups of cells seen by Wolff et al. were expressing genes that had previously been identified in developing limbs. This helps to validate the new results and to identify which active genes control the behaviors of the analyzed cells. These findings reveal new ways to study animal development. This approach could have many research uses and may help to link the mechanisms of cell biology to their effects. It could also contribute to new understanding of developmental and genetic conditions that affect human health.
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Affiliation(s)
- Carsten Wolff
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Tobias Pietzsch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Benjamin Harich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Léo Guignard
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Lai AG, Aboobaker AA. EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes. Dev Biol 2018; 433:118-131. [PMID: 29198565 DOI: 10.1016/j.ydbio.2017.10.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023]
Abstract
How do animals regenerate specialised tissues or their entire body after a traumatic injury, how has this ability evolved and what are the genetic and cellular components underpinning this remarkable feat? While some progress has been made in understanding mechanisms, relatively little is known about the evolution of regenerative ability. Which elements of regeneration are due to lineage specific evolutionary novelties or have deeply conserved roots within the Metazoa remains an open question. The renaissance in regeneration research, fuelled by the development of modern functional and comparative genomics, now enable us to gain a detailed understanding of both the mechanisms and evolutionary forces underpinning regeneration in diverse animal phyla. Here we review existing and emerging model systems, with the focus on invertebrates, for studying regeneration. We summarize findings across these taxa that tell us something about the evolution of adult stem cell types that fuel regeneration and the growing evidence that many highly regenerative animals harbor adult stem cells with a gene expression profile that overlaps with germline stem cells. We propose a framework in which regenerative ability broadly evolves through changes in the extent to which stem cells generated through embryogenesis are maintained into the adult life history.
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Affiliation(s)
- Alvina G Lai
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - A Aziz Aboobaker
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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12
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Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Sémon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. eLife 2016; 5:20062. [PMID: 27849518 PMCID: PMC5111886 DOI: 10.7554/elife.20062] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI:http://dx.doi.org/10.7554/eLife.20062.001 The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory. Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available. Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases. Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production. DOI:http://dx.doi.org/10.7554/eLife.20062.002
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Affiliation(s)
- Damian Kao
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alvina G Lai
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Silvana Rosic
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | - Nikolaos Konstantinides
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Erin Jarvis
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | | | | | - Marie Sémon
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Marco Grillo
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Heather Bruce
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Suyash Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andy Le
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andrew Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Michael B Eisen
- Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Cassandra Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - William E Browne
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States
| | - Carsten Wolff
- Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany
| | - Michalis Averof
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Nipam H Patel
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Peter Sarkies
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Aziz Aboobaker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Abstract
A small transparent crustacean called Parhyale hawaiensis has become a powerful model system for the study of limb and appendage regeneration.
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Affiliation(s)
- Enrique Amaya
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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