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Thompson AW, Wojtas H, Davoll M, Braasch I. Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments. G3 (BETHESDA, MD.) 2022; 12:6533448. [PMID: 35188191 PMCID: PMC8982402 DOI: 10.1093/g3journal/jkac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The Rio Pearlfish, Nematolebias whitei, is a bi-annual killifish species inhabiting seasonal pools in the Rio de Janeiro region of Brazil that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. Rio Pearlfish represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far, a sequenced genome has been unavailable. Here, we present a high quality, 1.2 Gb chromosome-level genome assembly, genome annotations, and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally cued hatching. We show conservation of 3D genome structure across teleost fish evolution, developmental stages, tissues, and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic, and multiomic explorations of “Eco-Evo-Devo” phenotypes of resilience and adaptation to extreme environments.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
| | - Harrison Wojtas
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Myles Davoll
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
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2
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Nagasawa T, Kawaguchi M, Nishi K, Yasumasu S. Molecular evolution of hatching enzymes and their paralogous genes in vertebrates. BMC Ecol Evol 2022; 22:9. [PMID: 35109790 PMCID: PMC8812170 DOI: 10.1186/s12862-022-01966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hatching is identified as one of the most important events in the reproduction of oviparous vertebrates. The genes for hatching enzymes, which are vital in the hatching process, are conserved among vertebrates. However, especially in teleost, it is difficult to trace their molecular evolution in detail due to the presence of other C6astacins, which are the subfamily to which the genes for hatching enzymes belong and are highly diverged. In particular, the hatching enzyme genes are diversified with frequent genome translocations due to retrocopy. RESULTS In this study, we took advantage of the rapid expansion of whole-genome data in recent years to examine the molecular evolutionary process of these genes in vertebrates. The phylogenetic analysis and the genomic synteny analysis revealed C6astacin genes other than the hatching enzyme genes, which was previously considered to be retained only in teleosts, was also retained in the genomes of basal ray-finned fishes, coelacanths, and cartilaginous fishes. These results suggest that the common ancestor of these genes can be traced back to at least the common ancestor of the Gnathostomata. Moreover, we also found that many of the C6astacin genes underwent multiple gene duplications during vertebrate evolution, and the results of gene expression analysis in frogs implied that genes derived from hatching enzyme genes underwent neo-functionalization. CONCLUSIONS In this study, we describe in detail the molecular evolution of the C6astacin gene in vertebrates, which has not been summarized previously. The results revealed the presence of the previously unknown C6astacin gene in the basal-lineage of jawed vertebrates and large-scale gene duplication of hatching enzyme genes in amphibians. The comprehensive investigation reported in this study will be an important basis for studying the molecular evolution of the vertebrate C6astacin genes, hatching enzyme, and its paralogous genes and for identifying these genes without the need for gene expression and functional analysis.
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Affiliation(s)
- Tatsuki Nagasawa
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Kohki Nishi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
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3
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Small CD, el-Khoury M, Deslongchamps G, Benfey TJ, Crawford BD. Matrix Metalloproteinase 13 Activity is Required for Normal and Hypoxia-Induced Precocious Hatching in Zebrafish Embryos. J Dev Biol 2020; 8:jdb8010003. [PMID: 32023839 PMCID: PMC7151336 DOI: 10.3390/jdb8010003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/11/2022] Open
Abstract
Hypoxia induces precocious hatching in zebrafish, but we do not have a clear understanding of the molecular mechanisms regulating the activation of the hatching enzyme or how these mechanisms trigger precocious hatching under unfavorable environmental conditions. Using immunohistochemistry, pharmacological inhibition of matrix metalloproteinase 13 (Mmp13), and in vivo zymography, we show that Mmp13a is present in the hatching gland just as embryos become hatching competent and that Mmp13a activity is required for both normal hatching and hypoxia-induced precocious hatching. We conclude that Mmp13a likely functions in activating the hatching enzyme zymogen and that Mmp13a activity is necessary but not sufficient for hatching in zebrafish. This study highlights the broad nature of MMP function in development and provides a non-mammalian example of extra-embryonic processes mediated by MMP activity.
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Affiliation(s)
- Christopher D. Small
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada; (C.D.S.); (M.e.-K.); (T.J.B.)
| | - Megan el-Khoury
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada; (C.D.S.); (M.e.-K.); (T.J.B.)
| | | | - Tillmann J. Benfey
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada; (C.D.S.); (M.e.-K.); (T.J.B.)
| | - Bryan D. Crawford
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada; (C.D.S.); (M.e.-K.); (T.J.B.)
- Correspondence:
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4
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Nagasawa T, Kawaguchi M, Yano T, Isoyama S, Yasumasu S, Okabe M. Translocation of promoter-conserved hatching enzyme genes with intron-loss provides a new insight in the role of retrocopy during teleostean evolution. Sci Rep 2019; 9:2448. [PMID: 30792427 PMCID: PMC6385490 DOI: 10.1038/s41598-019-38693-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/17/2018] [Indexed: 11/12/2022] Open
Abstract
The hatcing enzyme gene (HE) encodes a protease that is indispensable for the hatching process and is conserved during vertebrate evolution. During teleostean evolution, it is known that HE experienced a drastic transfiguration of gene structure, namely, losing all of its introns. However, these facts are contradiction with each other, since intron-less genes typically lose their original promoter because of duplication via mature mRNA, called retrocopy. Here, using a comparative genomic assay, we showed that HEs have changed their genomic location several times, with the evolutionary timings of these translocations being identical to those of intron-loss. We further showed that HEs maintain the promoter sequence upstream of them after translocation. Therefore, teleostean HEs are unique genes which have changed intra- (exon-intron) and extra-genomic structure (genomic loci) several times, although their indispensability for the reproductive process of hatching implies that HE genes are translocated by retrocopy with their promoter sequence.
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Affiliation(s)
- Tatsuki Nagasawa
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Research Fellow of the Japan Society for the Promotion of Science (JSPS), Tokyo, 102-0083, Japan.,Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Tohru Yano
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Sho Isoyama
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461, Japan
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5
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Cohen KL, Piacentino ML, Warkentin KM. Two types of hatching gland cells facilitate escape-hatching at different developmental stages in red-eyed treefrogs, Agalychnis callidryas (Anura: Phyllomedusidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
| | | | - Karen M Warkentin
- Department of Biology, Boston University, Boston, MA, USA
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
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6
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Nakazawa S, Shirae-Kurabayashi M, Sawada H. The role of metalloproteases in fertilisation in the ascidian Ciona robusta. Sci Rep 2019; 9:1009. [PMID: 30700775 PMCID: PMC6353882 DOI: 10.1038/s41598-018-37721-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
In the ascidian Ciona robusta (formerly C. intestinalis type A), the mechanism underlying sperm penetration through the egg investment remains unknown. We previously reported that proteins containing both an astacin metalloprotease domain and thrombospondin type 1 repeats are abundant in the sperm surface protein-enriched fraction of C. robusta. Here we investigated the involvement of those proteins in fertilisation. We refined the sequences of astacin metalloproteases, confirmed that five of them are present in the sperm, and labelled them as tunicate astacin and thrombospondin type 1 repeat-containing (Tast) proteins. Fertilisation of C. robusta eggs was potently inhibited by a metalloprotease inhibitor GM6001. The eggs cleaved normally when they were vitelline coat-free or the inhibitor was added after insemination. Furthermore, vitelline coat proteins were degraded after incubation with intact sperm. These results suggest that sperm metalloproteases are indispensable for fertilisation, probably owing to direct or indirect mediation of vitelline-coat digestion during sperm penetration. TALEN-mediated knockout of Tast genes and the presence of GM6001 impaired larval development at the metamorphic stage, suggesting that Tast gene products play a key role in late development.
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Affiliation(s)
- Shiori Nakazawa
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba, 517-0004, Mie, Japan. .,Hitachi, Ltd., Research & Development Group, Akanuma, Hatoyama, Hiki, Saitama, Japan.
| | - Maki Shirae-Kurabayashi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba, 517-0004, Mie, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba, 517-0004, Mie, Japan.
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7
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Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science 2018; 360:science.aar5780. [PMID: 29700227 DOI: 10.1126/science.aar5780] [Citation(s) in RCA: 344] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Abstract
Time series of single-cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis, we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.
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Affiliation(s)
- James A Briggs
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Wagner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sean Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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8
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Gouignard N, Schön T, Holmgren C, Strate I, Taşöz E, Wetzel F, Maccarana M, Pera EM. Gene expression of the two developmentally regulated dermatan sulfate epimerases in the Xenopus embryo. PLoS One 2018; 13:e0191751. [PMID: 29370293 PMCID: PMC5784981 DOI: 10.1371/journal.pone.0191751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/10/2018] [Indexed: 11/18/2022] Open
Abstract
Chondroitin sulfate (CS)/dermatan sulfate (DS) proteoglycans are abundant on the cell surface and in the extracellular matrix and have important functions in matrix structure, cell-matrix interaction and signaling. The DS epimerases 1 and 2, encoded by Dse and Dsel, respectively, convert CS to a CS/DS hybrid chain, which is structurally and conformationally richer than CS, favouring interaction with matrix proteins and growth factors. We recently showed that Xenopus Dse is essential for the migration of neural crest cells by allowing cell surface CS/DS proteoglycans to adhere to fibronectin. Here we investigate the expression of Dse and Dsel in Xenopus embryos. We show that both genes are maternally expressed and exhibit partially overlapping activity in the eyes, brain, trigeminal ganglia, neural crest, adenohypophysis, sclerotome, and dorsal endoderm. Dse is specifically expressed in the epidermis, anterior surface ectoderm, spinal nerves, notochord and dermatome, whereas Dsel mRNA alone is transcribed in the spinal cord, epibranchial ganglia, prechordal mesendoderm and myotome. The expression of the two genes coincides with sites of cell differentiation in the epidermis and neural tissue. Several expression domains can be linked to previously reported phenotypes of knockout mice and clinical manifestations, such as the Musculocontractural Ehlers-Danlos syndrome and psychiatric disorders.
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Affiliation(s)
- Nadège Gouignard
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Tanja Schön
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Christian Holmgren
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ina Strate
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Emirhan Taşöz
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Franziska Wetzel
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Marco Maccarana
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Edgar M. Pera
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
- * E-mail:
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9
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Cohen KL, Piacentino ML, Warkentin KM. The hatching process and mechanisms of adaptive hatching acceleration in hourglass treefrogs, Dendropsophus ebraccatus. Comp Biochem Physiol A Mol Integr Physiol 2017; 217:63-74. [PMID: 29056480 DOI: 10.1016/j.cbpa.2017.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 01/25/2023]
Abstract
Environmentally cued hatching is well documented in anurans, enabling embryos to escape diverse threats. However, knowledge of anuran hatching mechanisms is limited and based largely on aquatic-breeding species without known plasticity in hatching timing. Generally, hatching gland cells produce a hatching enzyme that degrades the vitelline membrane. We investigated hatching and its regulation in terrestrial embryos of hourglass treefrogs, Dendropsophus ebraccatus, which accelerate hatching to escape dehydration. We specifically tested if changes in hatching gland cell development or hatching enzyme gene expression are associated with accelerated hatching. We measured perivitelline chamber size of well-hydrated eggs over development as an indicator of breakdown of the vitelline membrane and found that the size of the perivitelline chamber increased steadily until hatching, suggesting gradual hatching enzyme release and vitelline membrane degradation. Hatching gland cells peaked in abundance and began regression substantially prior to hatching, but we found no developmental differences in the abundance or surface area of hatching gland cells between dry and well-hydrated embryos. Hatching enzyme gene expression also peaked early in development then declined, with no difference between hydration treatments. In D. ebraccatus breakdown of the vitelline membrane appears gradual, mediated by hatching enzyme release starting long before hatching. However, hatching acceleration is not associated with ontogenetic changes in hatching gland cell development or hatching enzyme gene expression. This hatching process contrasts with that of red-eyed treefrogs, Agalychnis callidryas, which appear to release enzyme acutely at hatching, yet both species are capable of hatching to escape acute threats.
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Affiliation(s)
- Kristina L Cohen
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
| | - Michael L Piacentino
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Karen M Warkentin
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA; Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá
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10
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Pre-oral gut contributes to facial structures in non-teleost fishes. Nature 2017; 547:209-212. [DOI: 10.1038/nature23008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/19/2017] [Indexed: 12/30/2022]
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