1
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Sato Y, Shibata N, Hashimoto C, Agata K. Migratory regulation by MTA homologous genes is essential for the uniform distribution of planarian adult pluripotent stem cells. Dev Growth Differ 2022; 64:150-162. [PMID: 35124813 DOI: 10.1111/dgd.12773] [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: 08/25/2021] [Revised: 12/09/2021] [Accepted: 12/19/2021] [Indexed: 12/31/2022]
Abstract
The migration of adult stem cells in vivo is an important issue, but the complex tissue structures involved, and limited accessibility of the cells hinder a detailed investigation. To overcome these problems, the freshwater planarian Dugesia japonica was used because it has a simple body plan and abundant adult pluripotent stem cells (neoblasts) distributed uniformly throughout its body. To investigate the migratory mechanisms of neoblasts, two planarian homologous genes of metastatic tumor antigen (MTA-A and MTA-B), a protein involved in cancer metastasis that functions through histone deacetylation, were identified, and their function was analyzed using RNA interference (RNAi). MTA-A or MTA-B knockdown disrupted homeostatic tissue turnover and regeneration in planarians. Whereas neoblasts in MTA-A (RNAi) and MTA-B (RNAi) animals were maintained, neoblast differentiation was inhibited. Furthermore, the normal uniform neoblast distribution pattern changed to a branch-like pattern in MTA-A (RNAi) and MTA-B (RNAi) animals. To examine the neoblast migratory ability, a partial X-ray irradiation assay was performed in D. japonica. Using this assay system, the MTA-A knockdown neoblasts migrated collectively in a branch-like pattern, and the MTA-B knockdown neoblasts were not able to migrate. These results indicated that MTA-A was required for the exit of neoblasts from the branch-like region, and that MTA-B was required for neoblast migration. Thus, the migration mediated by MTA-A and MTA-B enabled uniform neoblast distribution and was required for neoblast differentiation to achieve tissue homeostasis and regeneration.
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Affiliation(s)
- Yuki Sato
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Department of Life Science, Faculty of Science, Gakushuin University, Tokyo, Japan
| | - Norito Shibata
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Department of Integrated Science and Technology, National Institute of Technology, Tsuyama College, Tsuyama, Japan
| | - Chikara Hashimoto
- JT Biohistory Research Hall, Takatsuki, Japan.,Department of Biology, Graduate School of Science, Osaka University, Osaka, Japan
| | - Kiyokazu Agata
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Department of Life Science, Faculty of Science, Gakushuin University, Tokyo, Japan
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2
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Transcription Factors Active in the Anterior Blastema of Schmidtea mediterranea. Biomolecules 2021; 11:biom11121782. [PMID: 34944426 PMCID: PMC8698962 DOI: 10.3390/biom11121782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/28/2022] Open
Abstract
Regeneration, the restoration of body parts after injury, is quite widespread in the animal kingdom. Species from virtually all Phyla possess regenerative abilities. Human beings, however, are poor regenerators. Yet, the progress of knowledge and technology in the fields of bioengineering, stem cells, and regenerative biology have fostered major advancements in regenerative medical treatments, which aim to regenerate tissues and organs and restore function. Human induced pluripotent stem cells can differentiate into any cell type of the body; however, the structural and cellular complexity of the human tissues, together with the inability of our adult body to control pluripotency, require a better mechanistic understanding. Planarians, with their capacity to regenerate lost body parts thanks to the presence of adult pluripotent stem cells could help providing such an understanding. In this paper, we used a top-down approach to shortlist blastema transcription factors (TFs) active during anterior regeneration. We found 44 TFs—31 of which are novel in planarian—that are expressed in the regenerating blastema. We analyzed the function of half of them and found that they play a role in the regeneration of anterior structures, like the anterior organizer, the positional instruction muscle cells, the brain, the photoreceptor, the intestine. Our findings revealed a glimpse of the complexity of the transcriptional network governing anterior regeneration in planarians, confirming that this animal model is the perfect playground to study in vivo how pluripotency copes with adulthood.
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3
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Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A. Alternative Animal Models of Aging Research. Front Mol Biosci 2021; 8:660959. [PMID: 34079817 PMCID: PMC8166319 DOI: 10.3389/fmolb.2021.660959] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.
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Affiliation(s)
- Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ekaterina Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stan Braude
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Alessandro Cellerino
- Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Central Animal Laboratory, University Hospital Essen, Essen, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Andreas Hoeflich
- Division Signal Transduction, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Eva Terzibasi Tozzini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxim Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
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4
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Williams KB, Bischof J, Lee FJ, Miller KA, LaPalme JV, Wolfe BE, Levin M. Regulation of axial and head patterning during planarian regeneration by a commensal bacterium. Mech Dev 2020; 163:103614. [DOI: 10.1016/j.mod.2020.103614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
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5
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Miyamoto M, Hattori M, Hosoda K, Sawamoto M, Motoishi M, Hayashi T, Inoue T, Umesono Y. The pharyngeal nervous system orchestrates feeding behavior in planarians. SCIENCE ADVANCES 2020; 6:eaaz0882. [PMID: 32285000 PMCID: PMC7141820 DOI: 10.1126/sciadv.aaz0882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/14/2020] [Indexed: 05/06/2023]
Abstract
Planarians exhibit traits of cephalization but are unique among bilaterians in that they ingest food by means of goal-directed movements of a trunk-positioned pharynx, following protrusion of the pharynx out of the body, raising the question of how planarians control such a complex set of body movements for achieving robust feeding. Here, we use the freshwater planarian Dugesia japonica to show that an isolated pharynx amputated from the planarian body self-directedly executes its entire sequence of feeding functions: food sensing, approach, decisions about ingestion, and intake. Gene-specific silencing experiments by RNA interference demonstrated that the pharyngeal nervous system (PhNS) is required not only for feeding functions of the pharynx itself but also for food-localization movements of individual animals, presumably via communication with the brain. These findings reveal an unexpected central role of the PhNS in the linkage between unique morphological phenotypes and feeding behavior in planarians.
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Affiliation(s)
- Mai Miyamoto
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Miki Hattori
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kazutaka Hosoda
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Mika Sawamoto
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Minako Motoishi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
- Corresponding author. (Y.U.); (T.I.)
| | - Yoshihiko Umesono
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Corresponding author. (Y.U.); (T.I.)
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6
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Ivankovic M, Haneckova R, Thommen A, Grohme MA, Vila-Farré M, Werner S, Rink JC. Model systems for regeneration: planarians. Development 2019; 146:146/17/dev167684. [PMID: 31511248 DOI: 10.1242/dev.167684] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Planarians are a group of flatworms. Some planarian species have remarkable regenerative abilities, which involve abundant pluripotent adult stem cells. This makes these worms a powerful model system for understanding the molecular and evolutionary underpinnings of regeneration. By providing a succinct overview of planarian taxonomy, anatomy, available tools and the molecular orchestration of regeneration, this Primer aims to showcase both the unique assets and the questions that can be addressed with this model system.
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Affiliation(s)
- Mario Ivankovic
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Radmila Haneckova
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Albert Thommen
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Markus A Grohme
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Miquel Vila-Farré
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Steffen Werner
- FOM Institute AMOLF, Department of Systems Biology, Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Jochen C Rink
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany .,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
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7
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Zhang S, Ireland D, Sipes NS, Behl M, Collins EMS. Screening for neurotoxic potential of 15 flame retardants using freshwater planarians. Neurotoxicol Teratol 2019; 73:54-66. [PMID: 30943442 PMCID: PMC9524722 DOI: 10.1016/j.ntt.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 10/27/2022]
Abstract
Asexual freshwater planarians are an attractive invertebrate model for high-throughput neurotoxicity screening, because they possess multiple quantifiable behaviors to assess distinct neuronal functions. Planarians uniquely allow direct comparisons between developing and adult animals to distinguish developmentally selective effects from general neurotoxicity. In this study, we used our automated planarian screening platform to compare the neurotoxicity of 15 flame retardants (FRs), consisting of representative phased-out brominated (BFRs) and replacement organophosphorus FRs (OPFRs). OPFRs have emerged as a proposed safer alternative to BFRs; however, limited information is available on their health effects. We found 11 of the 15 FRs (3/6 BFRs, 7/8 OPFRs, and Firemaster 550) caused adverse effects in both adult and developing planarians with similar nominal lowest-effect-levels for BFRs and OPFRs. This suggests that replacement OPFRs are comparably neurotoxic to the phased-out compounds. BFRs were primarily systemically toxic, whereas OPFRs, except Tris(2-chloroethyl) phosphate, shared a behavioral phenotype in response to noxious heat at sublethal concentrations, indicating specific neurotoxic effects. We found this behavioral phenotype was correlated with cholinesterase inhibition, thus linking behavioral outcomes to molecular targets. By directly comparing effects on adult and developing planarians, we further found that one BFR (3,3',5,5'-Tetrabromobisphenol A) caused a developmental selective defect. Together, these results demonstrate that our planarian screening platform yields high content data from various behavioral and morphological endpoints, allowing us to distinguish selective neurotoxic effects and effects specific to the developing nervous system. Ten of these 11 bioactive FRs were previously found to be bioactive in other models, including cell culture and alternative animal models (nematodes and zebrafish). This level of concordance across different platforms emphasizes the urgent need for further evaluation of OPFRs in mammalian systems.
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Affiliation(s)
- Siqi Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Danielle Ireland
- Division of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA; Department of Biology, Swarthmore College Swarthmore, PA 19081, USA
| | - Nisha S Sipes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Mamta Behl
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Eva-Maria S Collins
- Division of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA; Department of Physics, University of California San Diego, La Jolla, CA 92093, USA; Department of Biology, Swarthmore College Swarthmore, PA 19081, USA.
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8
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Cao PL, Kumagai N, Inoue T, Agata K, Makino T. JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration. Genome Biol Evol 2019; 11:552-564. [PMID: 30698705 PMCID: PMC6390904 DOI: 10.1093/gbe/evz021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
The capacity for regeneration varies greatly among metazoans, yet little is known about the evolutionary processes leading to such different regeneration abilities. In particular, highly regenerative species such as planarians and cnidarians can regenerate the whole body from an amputated fragment; however, a common molecular basis, if any, among these species remains unclear. Here, we show that genes encoding Jumonji C (JmjC) domain-containing proteins are associated with high regeneration ability. We classified 132 fully sequenced metazoans into two groups with high or low regeneration abilities and identified 118 genes conserved in the high regenerative group that were lost in species in the low regeneration group during evolution. Ninety-six percent of them were JmjC domain-encoding genes. We denoted the candidate genes as high regenerative species-specific JmjC domain-encoding genes (HRJDs). We observed losses of HRJDs in Helobdella robusta, which lost its high regeneration ability during evolution based on phylogenetic analysis. By RNA sequencing analyses, we observed that HRJD orthologs were differentially expressed during regeneration in two Cnidarians, as well as Platyhelminthes and Urochordata, which are highly regenerative species. Furthermore, >50% of the head and tail parts of amputated planarians (Dugesia japonica) died during regeneration after RNA interference of HRJD orthologs. These results indicate that HRJD are strongly associated with a high regeneration ability in metazoans. HRJD paralogs regulate gene expression by histone demethylation; thus, HRJD may be related to epigenetic regulation controlling stem cell renewal and stem cell differentiation during regeneration. We propose that HRJD play a central role in epigenetic regulation during regeneration.
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Affiliation(s)
- Ping-Lin Cao
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Nobuyoshi Kumagai
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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9
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Kashima M, Agata K, Shibata N. Searching for non-transposable targets of planarian nuclear PIWI in pluripotent stem cells and differentiated cells. Dev Growth Differ 2018; 60:260-277. [DOI: 10.1111/dgd.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Makoto Kashima
- Department of Biophysics; Graduate School of Science; Kyoto University; Kyoto Japan
| | - Kiyokazu Agata
- Department of Biophysics; Graduate School of Science; Kyoto University; Kyoto Japan
| | - Norito Shibata
- Department of Biophysics; Graduate School of Science; Kyoto University; Kyoto Japan
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10
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Yuan J, Wang Z, Zou D, Peng Q, Peng R, Zou F. Expression profiling of planarians shed light on a dual role of programmed cell death during the regeneration. J Cell Biochem 2018; 119:5875-5884. [PMID: 29575081 DOI: 10.1002/jcb.26779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/02/2018] [Indexed: 01/20/2023]
Abstract
Most animals hold the ability to regenerate damaged cells, tissues, and even any lost part of their bodies. To date, there is little known about the precise regulatory mechanism of regeneration and many fundamental questions remain unanswered. To further understand the precise regulatory mechanism of regeneration, we used planarian Dugesia japonica as a model and sequenced the transcriptomes of their regenerated tissues at different regeneration stages. Through de novo assembly and expression profiling, we found that Heat shock protein and MAPK pathway were involved into early response of regeneration in D. japonica. In addition, immune response, cell proliferation, and migration were activated during regeneration. Of notes, our results revealed a specific functional role of programmed cell death (PCD) in regeneration of D. japonica. PCD may not only remove the damaged and superfluous tissues for further patterning with regenerated tissues, but also provide signals to trigger neoblasts proliferation and differentiation directly. Together, our results revealed Heat shock protein and MAPK pathway mediated early response of regeneration and found a dual role of PCD in regeneration D. japonica. Meanwhile, we constructed regulatory networks of apoptosis, autophagy, and related signaling pathways and proposed a schematic model, which provided a global landscape of regeneration.
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Affiliation(s)
- Junsong Yuan
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhihong Wang
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Di Zou
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Quekun Peng
- Department of Biomedical Science, Chengdu Medical College, Chengdu, Sichuan, China
| | - Rui Peng
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Fangdong Zou
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
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11
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An Y, Kawaguchi A, Zhao C, Toyoda A, Sharifi-Zarchi A, Mousavi SA, Bagherzadeh R, Inoue T, Ogino H, Fujiyama A, Chitsaz H, Baharvand H, Agata K. Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians. ZOOLOGICAL LETTERS 2018; 4:24. [PMID: 30181897 PMCID: PMC6114478 DOI: 10.1186/s40851-018-0102-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/03/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Planarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain. Dugesia japonica is a typical planarian species that is widely distributed in the East Asia. Extensive cellular and molecular experimental methods have been developed to identify the functions of thousands of genes in this species, making this planarian a good experimental model for regeneration biology and neurobiology. However, no genome-level information is available for D. japonica, and few gene regulatory networks have been identified thus far. RESULTS To obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using Xenopus laevis indicated that one of the CNEs in the Djndk gene may be a regulatory element, suggesting that the regulation of the ndk gene and the brain formation mechanism may be conserved between vertebrates and invertebrates. CONCLUSION This draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp.
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Affiliation(s)
- Yang An
- Department of Biophysics, Kyoto University, Kyoto, Japan
- Present address: Immolife-biotech Co., Ltd., Nanjing, China
| | - Akane Kawaguchi
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
- Present address: Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Chen Zhao
- School of Pharmacy, Fudan University, Shanghai, China
- Present address: Immolife-biotech Co., Ltd., Nanjing, China
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ali Sharifi-Zarchi
- Department of Computer Science, Colorado State University, Fort Collins, USA
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Seyed Ahmad Mousavi
- Department of Computer Science, Colorado State University, Fort Collins, USA
| | - Reza Bagherzadeh
- Department of Biophysics, Kyoto University, Kyoto, Japan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
- Present address: Department of Life Science, Gakushuin University, Tokyo, Japan
| | - Takeshi Inoue
- Department of Biophysics, Kyoto University, Kyoto, Japan
- Present address: Department of Life Science, Gakushuin University, Tokyo, Japan
| | - Hajime Ogino
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
- Present address: Amphibian Research Center, Hiroshima University, Higashi-hiroshima, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Hamidreza Chitsaz
- Department of Computer Science, Colorado State University, Fort Collins, USA
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Kiyokazu Agata
- Department of Biophysics, Kyoto University, Kyoto, Japan
- Present address: Department of Life Science, Gakushuin University, Tokyo, Japan
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12
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Almazan EMP, Lesko SL, Markey MP, Rouhana L. Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers. Dev Biol 2017; 433:433-447. [PMID: 28774726 PMCID: PMC5750089 DOI: 10.1016/j.ydbio.2017.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/05/2017] [Accepted: 07/27/2017] [Indexed: 12/20/2022]
Abstract
Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities. In order to circumvent these limitations and increase the genetic information available for comparative studies, we sequenced the transcriptome of Girardia dorotocephala, a planarian species pandemic and commercially available in North America. A total of 254,802,670 paired sequence reads were obtained from RNA extracted from intact individuals, regenerating fragments, as well as freshly excised auricles of a clonal line of G. dorotocephala (MA-C2), and used for de novo assembly of its transcriptome. The resulting transcriptome draft was validated through functional analysis of genetic markers of stem cells and their progeny in G. dorotocephala. Akin to orthologs in other planarian species, G. dorotocephala Piwi1 (GdPiwi1) was found to be a robust marker of the planarian stem cell population and GdPiwi2 an essential component for stem cell-driven regeneration. Identification of G. dorotocephala homologs of the early stem cell descendent marker PROG-1 revealed a family of lysine-rich proteins expressed during epithelial cell differentiation. Sequences from the MA-C2 transcriptome were found to be 98-99% identical to nucleotide sequences from G. dorotocephala populations with different chromosomal number, demonstrating strong conservation regardless of karyotype evolution. Altogether, this work establishes G. dorotocephala as a viable and accessible option for analysis of gene function in North America.
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Affiliation(s)
- Eugene Matthew P Almazan
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, United States
| | - Sydney L Lesko
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, United States
| | - Michael P Markey
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, United States
| | - Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, United States.
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13
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Lai AG, Pouchkina-Stantcheva N, Di Donfrancesco A, Kildisiute G, Sahu S, Aboobaker AA. The protein subunit of telomerase displays patterns of dynamic evolution and conservation across different metazoan taxa. BMC Evol Biol 2017; 17:107. [PMID: 28441946 PMCID: PMC5405514 DOI: 10.1186/s12862-017-0949-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Most animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Given the importance of TERT and telomere biology in core metazoan life history traits, like ageing and the control of somatic cell proliferation, we hypothesised that TERT would have patterns of sequence and regulatory evolution reflecting the diverse life histories across the Animal Kingdom. RESULTS We performed a complete investigation of the evolutionary history of TERT across animals. We show that although TERT is almost ubiquitous across Metazoa, it has undergone substantial sequence evolution within canonical motifs. Beyond the known canonical motifs, we also identify and compare regions that are highly variable between lineages, but show conservation within phyla. Recent data have highlighted the importance of alternative splice forms of TERT in non-canonical functions and although animals may share some conserved introns, we find that the selection of exons for alternative splicing appears to be highly variable, and regulation by alternative splicing appears to be a very dynamic feature of TERT evolution. We show that even within a closely related group of triclad flatworms, where alternative splicing of TERT was previously correlated with reproductive strategy, we observe highly diverse splicing patterns. CONCLUSIONS Our work establishes that the evolutionary history and structural evolution of TERT involves previously unappreciated levels of change and the emergence of lineage specific motifs. The sequence conservation we describe within phyla suggests that these new motifs likely serve essential biological functions of TERT, which along with changes in splicing, underpin diverse functions of TERT important for animal life histories.
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Affiliation(s)
- Alvina G Lai
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
| | | | | | - Gerda Kildisiute
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Sounak Sahu
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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14
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Ross KG, Currie KW, Pearson BJ, Zayas RM. Nervous system development and regeneration in freshwater planarians. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [DOI: 10.1002/wdev.266] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/10/2017] [Accepted: 01/20/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Kelly G. Ross
- Department of Biology San Diego State University San Diego CA USA
| | - Ko W. Currie
- Program in Developmental and Stem Cell Biology The Hospital for Sick Children Toronto Canada
- Department of Molecular Genetics University of Toronto Toronto Canada
- Ontario Institute for Cancer Research Toronto Canada
| | - Bret J. Pearson
- Program in Developmental and Stem Cell Biology The Hospital for Sick Children Toronto Canada
- Department of Molecular Genetics University of Toronto Toronto Canada
- Ontario Institute for Cancer Research Toronto Canada
| | - Ricardo M. Zayas
- Department of Biology San Diego State University San Diego CA USA
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15
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Shimoyama S, Inoue T, Kashima M, Agata K. Multiple Neuropeptide-Coding Genes Involved in Planarian Pharynx Extension. Zoolog Sci 2016; 33:311-9. [PMID: 27268986 DOI: 10.2108/zs150170] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Planarian feeding behavior involves three steps: moving toward food, extending the pharynx from their planarian's ventral side after arriving at the food, and ingesting the food through the pharynx. Although pharynx extension is a remarkable behavior, it remains unknown what neuronal cell types are involved in its regulation. To identify neurons involved in regulating pharynx extension, we quantitatively analyzed pharynx extension and sought to identify these neurons by RNA interference (RNAi) and in situ hybridization. This assay, when performed using planarians with amputation of various body parts, clearly showed that the head portion is indispensable for inducing pharynx extension. We thus tested the effects of knockdown of brain neurons such as serotonergic, GABAergic, and dopaminergic neurons by RNAi, but did not observe any effects on pharynx extension behavior. However, animals with RNAi of the Prohormone Convertase 2 (PC2, a neuropeptide processing enzyme) gene did not perform the pharynx extension behavior, suggesting the possible involvement of neuropeptide(s in the regulation of pharynx extension. We screened 24 neuropeptide-coding genes, analyzed their functions by RNAi using the pharynx extension assay system, and identified at least five neuropeptide genes involved in pharynx extension. These was expressed in different cells or neurons, and some of them were expressed in the brain, suggesting complex regulation of planarian feeding behavior by the nervous system.
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Affiliation(s)
- Seira Shimoyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takeshi Inoue
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Makoto Kashima
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
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16
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Teramoto M, Kudome-Takamatsu T, Nishimura O, An Y, Kashima M, Shibata N, Agata K. Molecular markers for X-ray-insensitive differentiated cells in the Inner and outer regions of the mesenchymal space in planarian Dugesia japonica. Dev Growth Differ 2016; 58:609-19. [PMID: 27530596 DOI: 10.1111/dgd.12309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 05/24/2016] [Accepted: 06/05/2016] [Indexed: 12/01/2022]
Abstract
Planarian's strong regenerative ability is dependent on stem cells (called neoblasts) that are X-ray-sensitive and proliferative stem cells. In addition to neoblasts, another type of X-ray-sensitive cells was newly identified by recent research. Thus, planarian's X-ray-sensitive cells can be divided into at least two populations, Type 1 and Type 2, the latter corresponding to planarian's classically defined "neoblasts". Here, we show that Type 1 cells were distributed in the outer region (OR) immediately underneath the muscle layer at all axial levels from head to tail, while the Type 2 cells were distributed in a more internal region (IR) of the mesenchymal space at the axial levels from neck to tail. To elucidate the biological significance of these two regions, we searched for genes expressed in differentiated cells that were locate close to these X-ray-sensitive cell populations in the mesenchymal space, and identified six genes mainly expressed in the OR or IR, named OR1, OR2, OR3, IR1, IR2 and IR3. The predicted amino acid sequences of these genes suggested that differentiated cells expressing OR1, OR3, IR1, or IR2 provide Type 1 and Type 2 cells with specific extracellular matrix (ECM) environments.
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Affiliation(s)
- Machiko Teramoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Osamu Nishimura
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kyoto, Japan.,Center for Life Science Technologies, RIKEN, Kobe, Hyogo, Japan
| | - Yang An
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Immolife-biotech Co. Ltd., Nanking, China
| | - Makoto Kashima
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Norito Shibata
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,Department of Integrated Science and Technology, National Institute of Technology, Tsuyama College 624-1, Tsuyama-City, Okayama, Japan
| | - Kiyokazu Agata
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan. .,Center for Developmental Biology, RIKEN, Kobe, Hyogo, Japan. .,Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kyoto, Japan.
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17
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Li MH. Development of in vivo biotransformation enzyme assays for ecotoxicity screening: In vivo measurement of phases I and II enzyme activities in freshwater planarians. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 130:19-28. [PMID: 27062342 DOI: 10.1016/j.ecoenv.2016.03.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 06/05/2023]
Abstract
The development of a high-throughput tool is required for screening of environmental pollutants and assessing their impacts on aquatic animals. Freshwater planarians can be used in rapid and sensitive toxicity bioassays. Planarians are known for their remarkable regeneration ability but much less known for their metabolic and xenobiotic biotransformation abilities. In this study, the activities of different phase I and II enzymes were determined in vivo by directly measuring fluorescent enzyme substrate disappearance or fluorescent enzyme metabolite production in planarian culture media. For phase I enzyme activity, O-deethylation activities with alkoxyresorufin could not be detected in planarian culture media. By contrast, O-deethylation activities with alkoxycoumarin were detected in planarian culture media. Increases in 7-ethoxycoumarin O-deethylase (ECOD) activities was only observed in planarians exposed to 1μM, but not 10μM, β-naphthoflavone for 24h. ECOD activity was inhibited in planarians exposed to 10 and 100μM rifampicin or carbamazepine for 24h. For phase II enzyme activity, DT-diaphorase, arylsulfatases, uridine 5'-diphospho (UDP)-glucuronosyltransferase or catechol-O-methyltransferase activity was determined in culture media containing planarians. The results of this study indicate that freshwater planarians are a promising model organism to monitor exposure to environmental pollutants or assess their impacts through the in vivo measurement of phase I and II enzyme activities.
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Affiliation(s)
- Mei-Hui Li
- Environmental Toxicology Laboratory, Department of Geography, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
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18
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Goupil LS, Ivry SL, Hsieh I, Suzuki BM, Craik CS, O’Donoghue AJ, McKerrow JH. Cysteine and Aspartyl Proteases Contribute to Protein Digestion in the Gut of Freshwater Planaria. PLoS Negl Trop Dis 2016; 10:e0004893. [PMID: 27501047 PMCID: PMC4976874 DOI: 10.1371/journal.pntd.0004893] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/11/2016] [Indexed: 01/06/2023] Open
Abstract
Proteases perform numerous vital functions in flatworms, many of which are likely to be conserved throughout the phylum Platyhelminthes. Within this phylum are several parasitic worms that are often poorly characterized due to their complex life-cycles and lack of responsiveness to genetic manipulation. The flatworm Schmidtea mediterranea, or planaria, is an ideal model organism to study the complex role of protein digestion due to its simple life cycle and amenability to techniques like RNA interference (RNAi). In this study, we were interested in deconvoluting the digestive protease system that exists in the planarian gut. To do this, we developed an alcohol-induced regurgitation technique to enrich for the gut enzymes in S. mediterranea. Using a panel of fluorescent substrates, we show that this treatment produces a sharp increase in proteolytic activity. These enzymes have broad yet diverse substrate specificity profiles. Proteomic analysis of the gut contents revealed the presence of cysteine and metallo-proteases. However, treatment with class-specific inhibitors showed that aspartyl and cysteine proteases are responsible for the majority of protein digestion. Specific RNAi knockdown of the cathepsin B-like cysteine protease (SmedCB) reduced protein degradation in vivo. Immunohistochemistry and whole-mount in situ hybridization (WISH) confirmed that the full-length and active forms of SmedCB are found in secretory cells surrounding the planaria intestinal lumen. Finally, we show that the knockdown of SmedCB reduces the speed of tissue regeneration. Defining the roles of proteases in planaria can provide insight to functions of conserved proteases in parasitic flatworms, potentially uncovering drug targets in parasites.
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Affiliation(s)
- Louise S. Goupil
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Sam L. Ivry
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Ivy Hsieh
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - Brian M. Suzuki
- Skaggs School of Pharmacy and Pharmaceutical Chemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Chemistry, University of California, San Diego, La Jolla, California, United States of America
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Chemistry, University of California, San Diego, La Jolla, California, United States of America
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19
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Shibata N, Kashima M, Ishiko T, Nishimura O, Rouhana L, Misaki K, Yonemura S, Saito K, Siomi H, Siomi M, Agata K. Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian. Dev Cell 2016; 37:226-37. [DOI: 10.1016/j.devcel.2016.04.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/18/2016] [Accepted: 04/11/2016] [Indexed: 11/29/2022]
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20
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Hosoda K, Morimoto M, Motoishi M, Nishimura O, Agata K, Umesono Y. Simple blood-feeding method for live imaging of gut tube remodeling in regenerating planarians. Dev Growth Differ 2016; 58:260-9. [PMID: 26948408 DOI: 10.1111/dgd.12270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/19/2016] [Accepted: 01/24/2016] [Indexed: 11/27/2022]
Abstract
Live cell imaging is a powerful technique to study cellular dynamics in vivo during animal development and regeneration. However, few live imaging methods have been reported for studying planarian regeneration. Here, we developed a simple method for steady visualization of gut tube remodeling during regeneration of a living freshwater planarian, Dugesia japonica. When planarians were fed blood several times, gut branches were well-visualized in living intact animals under normal bright-field illumination. Interestingly, tail fragments derived from these colored planarians enabled successive observation of the processes of the formation of a single anterior gut branch in the prepharyngeal region from the preexisting two posterior gut branches in the same living animals during head regeneration. Furthermore, we combined this method and RNA interference (RNAi) and thereby showed that a D. japonica raf-related gene (DjrafA) and mek-related gene (DjmekA) we identified both play a major role in the activation of extracellular signal-regulated kinase (ERK) signaling during planarian regeneration, as indicated by their RNAi-induced defects on gut tube remodeling in a time-saving initial screening using blood-feeding without immunohistochemical detection of the gut. Thus, this blood-feeding method is useful for live imaging of gut tube remodeling, and provides an advance for the field of regeneration study in planarians.
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Affiliation(s)
- Kazutaka Hosoda
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Mizuki Morimoto
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Minako Motoishi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Osamu Nishimura
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kiyokazu Agata
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiko Umesono
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
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21
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Kashima M, Kumagai N, Agata K, Shibata N. Heterogeneity of chromatoid bodies in adult pluripotent stem cells of planarianDugesia japonica. Dev Growth Differ 2016; 58:225-37. [DOI: 10.1111/dgd.12268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/18/2015] [Accepted: 12/31/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Makoto Kashima
- Department of Biophysics; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo-ku Kyoto 606-8502 Japan
| | - Nobuyoshi Kumagai
- Department of Biophysics; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo-ku Kyoto 606-8502 Japan
| | - Kiyokazu Agata
- Department of Biophysics; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo-ku Kyoto 606-8502 Japan
| | - Norito Shibata
- Department of Biophysics; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo-ku Kyoto 606-8502 Japan
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22
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Tasaki J, Uchiyama-Tasaki C, Rouhana L. Analysis of Stem Cell Motility In Vivo Based on Immunodetection of Planarian Neoblasts and Tracing of BrdU-Labeled Cells After Partial Irradiation. Methods Mol Biol 2016; 1365:323-338. [PMID: 26498794 DOI: 10.1007/978-1-4939-3124-8_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Planarian flatworms have become an important system for the study of stem cell behavior and regulation in vivo. These organisms are able to regenerate any part of their body upon damage or amputation. A crucial cellular event in the process of planarian regeneration is the migration of pluripotent stem cells (known as neoblasts) to the site of injury. Here we describe two approaches for analyzing migration of planarian stem cells to an area where these have been ablated by localized X-ray irradiation. The first approach involves immunolabeling of mitotic neoblasts, while the second is based on tracing stem cells and their progeny after BrdU incorporation. The use of planarians in studies of cell motility is suitable for the identification of factors that influence stem cell migration in vivo and is amenable to RNA interference or pharmacological screening.
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Affiliation(s)
- Junichi Tasaki
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA
| | - Chihiro Uchiyama-Tasaki
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA
| | - Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
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23
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Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K. Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica. PLoS One 2015; 10:e0143525. [PMID: 26588467 PMCID: PMC4654569 DOI: 10.1371/journal.pone.0143525] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/05/2015] [Indexed: 11/21/2022] Open
Abstract
We established a laboratory clonal strain of freshwater planarian (Dugesia japonica) that was derived from a single individual and that continued to undergo autotomous asexual reproduction for more than 20 years, and we performed large-scale genome sequencing and transcriptome analysis on it. Despite the fact that a completely clonal strain of the planarian was used, an unusually large number of mutations were detected. To enable quantitative genetic analysis of such a unique organism, we developed a new model called the Reference Gene Model, and used it to conduct large-scale transcriptome analysis. The results revealed large numbers of mutations not only outside but also inside gene-coding regions. Non-synonymous SNPs were detected in 74% of the genes for which valid ORFs were predicted. Interestingly, the high-mutation genes, such as metabolism- and defense-related genes, were correlated with genes that were previously identified as diverse genes among different planarian species. Although a large number of amino acid substitutions were apparently accumulated during asexual reproduction over this long period of time, the planarian maintained normal body-shape, behaviors, and physiological functions. The results of the present study reveal a unique aspect of asexual reproduction.
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Affiliation(s)
- Osamu Nishimura
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Kazutaka Hosoda
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Eri Kawaguchi
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Shigenobu Yazawa
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Cellular and Structural Physiology Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Tetsutaro Hayashi
- Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Nakamachi, Chuo-ku, Kobe, Hyogo, Japan
- Advanced Center for Computing and Communication, RIKEN, 2–1 Hirosawa, Wako, Saitama, Japan
| | - Takeshi Inoue
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Yoshihiko Umesono
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Kiyokazu Agata
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- * E-mail:
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24
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Geng X, Wang G, Qin Y, Zang X, Li P, Geng Z, Xue D, Dong Z, Ma K, Chen G, Xu C. iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians. PLoS One 2015; 10:e0132045. [PMID: 26131905 PMCID: PMC4488856 DOI: 10.1371/journal.pone.0132045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 06/09/2015] [Indexed: 02/07/2023] Open
Abstract
The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
| | - Gaiping Wang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Yanli Qin
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Pengfei Li
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Zhi Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Deming Xue
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Zimei Dong
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Kexue Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Guangwen Chen
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
- * E-mail: (CSX); (GWC)
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
- * E-mail: (CSX); (GWC)
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Hwang B, An Y, Agata K, Umesono Y. Two distinct roles of the yorkie/yap gene during homeostasis in the planarian Dugesia japonica. Dev Growth Differ 2015; 57:209-17. [PMID: 25708270 PMCID: PMC4415594 DOI: 10.1111/dgd.12195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/18/2014] [Accepted: 12/21/2014] [Indexed: 12/21/2022]
Abstract
Adult planarians possess somatic pluripotent stem cells called neoblasts that give rise to all missing cell types during regeneration and homeostasis. Recent studies revealed that the Yorkie (Yki)/Yes-associated protein (YAP) transcriptional coactivator family plays an important role in the regulation of tissue growth during development and regeneration, and therefore we investigated the role of a planarian yki-related gene (termed Djyki) during regeneration and homeostasis of the freshwater planarian Dugesia japonica. We found that knockdown of the function of Djyki by RNA interference (RNAi) downregulated neoblast proliferation and caused regeneration defects after amputation. In addition, Djyki RNAi caused edema during homeostasis. These seemingly distinct defects induced by Djyki RNAi were rescued by simultaneous RNAi of a planarian mats-related gene (termed Djmats), suggesting an important role of Djmats in the negative regulation of Djyki, in accordance with the conservation of the functional relationship of these two genes during the course of evolution. Interestingly, Djyki RNAi did not prevent normal protonephridial structure, suggesting that Djyki RNAi induced the edema phenotype without affecting the excretory system. Further analyses revealed that increased expression of the D. japonica gene DjaquaporinA (DjaqpA), which belongs to a large gene family that encodes a water channel protein for the regulation of transcellular water flow, promoted the induction of edema, but not defects in neoblast dynamics, in Djyki(RNAi) animals. Thus, we conclude that Djyki plays two distinct roles in the regulation of active proliferation of stem cells and in osmotic water transport across the body surface in D. japonica.
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Affiliation(s)
- Byulnim Hwang
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto
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Wheeler NJ, Agbedanu PN, Kimber MJ, Ribeiro P, Day TA, Zamanian M. Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery. Parasit Vectors 2015; 8:34. [PMID: 25600302 PMCID: PMC4304616 DOI: 10.1186/s13071-014-0622-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neglected diseases caused by helminth infections impose a massive hindrance to progress in the developing world. While basic research on parasitic flatworms (platyhelminths) continues to expand, researchers have yet to broadly adopt a free-living model to complement the study of these important parasites. METHODS We report the high-coverage sequencing (RNA-Seq) and assembly of the transcriptome of the planarian Girardia tigrina across a set of dynamic conditions. The assembly was annotated and extensive orthology analysis was used to seed a pipeline for the rational prioritization and validation of putative anthelmintic targets. A small number of targets conserved between parasitic and free-living flatworms were comparatively interrogated. RESULTS 240 million paired-end reads were assembled de novo to produce a strictly filtered predicted proteome consisting of over 22,000 proteins. Gene Ontology annotations were extended to 16,467 proteins. 2,693 sequences were identified in orthology groups spanning flukes, tapeworms and planaria, with 441 highlighted as belonging to druggable protein families. Chemical inhibitors were used on three targets in pharmacological screens using both planaria and schistosomula, revealing distinct motility phenotypes that were shown to correlate with planarian RNAi phenotypes. CONCLUSIONS This work provides the first comprehensive and annotated sequence resource for the model planarian G. tigrina, alongside a prioritized list of candidate drug targets conserved among parasitic and free-living flatworms. As proof of principle, we show that a simple RNAi and pharmacology pipeline in the more convenient planarian model system can inform parasite biology and serve as an efficient screening tool for the identification of lucrative anthelmintic targets.
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Affiliation(s)
- Nicolas J Wheeler
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50010, USA.
| | - Prince N Agbedanu
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50010, USA.
| | - Michael J Kimber
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50010, USA.
| | - Paula Ribeiro
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
| | - Tim A Day
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50010, USA.
| | - Mostafa Zamanian
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50010, USA. .,Institute of Parasitology, McGill University, Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
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On-chip immobilization of planarians for in vivo imaging. Sci Rep 2014; 4:6388. [PMID: 25227263 PMCID: PMC4165980 DOI: 10.1038/srep06388] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/14/2014] [Indexed: 11/08/2022] Open
Abstract
Planarians are an important model organism for regeneration and stem cell research. A complete understanding of stem cell and regeneration dynamics in these animals requires time-lapse imaging in vivo, which has been difficult to achieve due to a lack of tissue-specific markers and the strong negative phototaxis of planarians. We have developed the Planarian Immobilization Chip (PIC) for rapid, stable immobilization of planarians for in vivo imaging without injury or biochemical alteration. The chip is easy and inexpensive to fabricate, and worms can be mounted for and removed after imaging within minutes. We show that the PIC enables significantly higher-stability immobilization than can be achieved with standard techniques, allowing for imaging of planarians at sub-cellular resolution in vivo using brightfield and fluorescence microscopy. We validate the performance of the PIC by performing time-lapse imaging of planarian wound closure and sequential imaging over days of head regeneration. We further show that the device can be used to immobilize Hydra, another photophobic regenerative model organism. The simple fabrication, low cost, ease of use, and enhanced specimen stability of the PIC should enable its broad application to in vivo studies of stem cell and regeneration dynamics in planarians and Hydra.
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Rouhana L, Weiss JA, Forsthoefel DJ, Lee H, King RS, Inoue T, Shibata N, Agata K, Newmark PA. RNA interference by feeding in vitro-synthesized double-stranded RNA to planarians: methodology and dynamics. Dev Dyn 2013; 242:718-30. [PMID: 23441014 DOI: 10.1002/dvdy.23950] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The ability to assess gene function is essential for understanding biological processes. Currently, RNA interference (RNAi) is the only technique available to assess gene function in planarians, in which it has been induced by means of injection of double-stranded RNA (dsRNA), soaking, or ingestion of bacteria expressing dsRNA. RESULTS We describe a simple and robust RNAi protocol, involving in vitro synthesis of dsRNA that is fed to the planarians. Advantages of this protocol include the ability to produce dsRNA from any vector without subcloning, resolution of ambiguities in quantity and quality of input dsRNA, as well as time and ease of application. We have evaluated the logistics of inducing RNAi in planarians using this methodology in careful detail, from the ingestion and processing of dsRNA in the intestine, to timing and efficacy of knockdown in neoblasts, germline, and soma. We also present systematic comparisons of effects of amount, frequency, and mode of dsRNA delivery. CONCLUSIONS This method gives robust and reproducible results and is amenable to high-throughput studies. Overall, this RNAi methodology provides a significant advance by combining the strengths of current protocols available for dsRNA delivery in planarians and has the potential to benefit RNAi methods in other systems.
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Affiliation(s)
- Labib Rouhana
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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Chan JD, Zarowiecki M, Marchant JS. Ca²⁺ channels and praziquantel: a view from the free world. Parasitol Int 2012; 62:619-28. [PMID: 23246536 DOI: 10.1016/j.parint.2012.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/06/2012] [Indexed: 01/22/2023]
Abstract
Targeting the cellular Ca(2+) channels and pumps that underpin parasite Ca(2+) homeostasis may realize novel antihelmintic agents. Indeed, the antischistosomal drug praziquantel (PZQ) is a key clinical agent that has been proposed to work in this manner. Heterologous expression data has implicated an action of PZQ on voltage-operated Ca(2+) channels, although the relevant in vivo target of this drug has remained undefined over three decades of clinical use. The purpose of this review is to bring new perspective to this issue by discussing the potential utility of free-living planarian flatworms for providing new insight into the mechanism of PZQ action. First, we discuss in vivo functional genetic data from the planarian system that broadly supports the molecular data collected in heterologous systems and the 'Ca(2+) hypothesis' of PZQ action. On the basis of these similarities we highlight our current knowledge of platyhelminth voltage operated Ca(2+) channels, their unique molecular pharmacology and the downstream functional PZQ interactome engaged by dysregulation of Ca(2+) influx that has potential to yield novel antischistosomal targets. Overall the broad dataset underscores a common theme of PZQ-evoked disruptions of Ca(2+) homeostasis in trematodes, cestodes and turbellarians, and showcases the utility of the planarian model for deriving insight into drug action and targets in parasitic flatworms.
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Affiliation(s)
- John D Chan
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, USA; The Stem Cell Institute, University of Minnesota Medical School, MN 55455, USA
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