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  • 11
    Publikationsdatum: 2022-08-19
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Albertin, C. B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z. Y., Grimwood, J., Rosenthal, J. J. C., Ragsdale, C. W., Simakov, O., & Rokhsar, D. S. Genome and transcriptome mechanisms driving cephalopod evolution. Nature Communications, 13(1), (2022): 2427, https://doi.org/10.1038/s41467-022-29748-w.
    Beschreibung: Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing.
    Beschreibung: We thank the Marine Resources Center and the Cephalopod program at the Marine Biological Laboratory for supplying D. pealeii, R. Hanlon for the image in Fig. 1a, R. Hanlon and S. Senft for help with tissue dissection, Dr. Chuck Winkler for supplying O. bimaculoides, B. Burford and W. Gilly for assistance with D. opalescens collection, and the Vienna Zoo (Tiergarten Schönbrunn), particularly R. Halbauer, A. Weissenbacher, and the aquarist team for E. scolopes husbandry. Computation was done using the Life Science Cluster at the University of Vienna. This project began with generous funding from the Grass Foundation, administered by the MBL through J.J.R. It was also supported by Austrian Science fund FWF (P30686-B29) to H.S. and O.S., the Whitman Center Early Career Fellowship to O.S., the Okinawa Institute of Science and Technology Molecular Genetics Unit, Chan-Zuckerberg BioHub, and the Marthella Foskett Brown Chair in Computational Biology to D.S.R, NSF grant (IOS-1354898) to C.W.R, and the Hibbitt Early Career Fellowship to C.B.A. Sequencing at the University of Chicago Functional Genomics Facility was partially supported by the NIH (5UL1TR002389-02 and UL1 TR000430).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
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  • 12
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 33, doi:10.1186/s13742-016-0138-1.
    Beschreibung: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (〉10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
    Beschreibung: Bioinformatic analysis was performed in part on computing resources at the University of Puerto Rico (UPR) Puerto Rico Center for Environmental Neuroscience (PRCEN)’s High Performance Computing Facility, which is supported by: Institutional Development Award Networks of Biomedical Research Excellent (INBRE) grant P20GM103475 from the National Institute of General Medical Sciences, National Institutes of Health; the Institute for Functional Nanomaterials (IFN) award from the Experimental Program to Stimulate Competitive Research (EPSCoR) Track 1 program of the National Science Foundation (NSF); and EPSCoR Track 2 awards for computational nanoscience (EPS 1002410, EPS 1010094). Funding and support of the research was provided by PRCEN thanks to an NSF Centers of Research Excellent in Science and Technology (CREST) award, number HRD-1137725.
    Schlagwort(e): Porites astreoides ; Calcification ; Biomineralization ; Coral ; Symbiodinium ; Dinoflagellate ; Zooxanthellae ; Symbiosis ; Swimming larvae ; Larval settlement
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 13
    Publikationsdatum: 2022-05-26
    Beschreibung: Author Posting. © Company of Biologists, 2019. This article is posted here by permission of Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Experimental Biology 223(3), (2019): jeb.218081, doi: 10.1242/jeb.218081.
    Beschreibung: An important aspect of the performance of many fast muscle fiber types is rapid excitation. Previous research on the cross-striated muscle fibers responsible for the rapid tentacle strike in squid has revealed the specializations responsible for high shortening velocity, but little is known about excitation of these fibers. Conventional whole-cell patch recordings were made from tentacle fibers and the slower obliquely striated muscle fibers of the arms. The fast-contracting tentacle fibers show an approximately 10-fold greater sodium conductance than that of the arm fibers and, unlike the arm fibers, the tentacle muscle fibers produce action potentials. In situ hybridization using an antisense probe to the voltage-dependent sodium channel present in this squid genus shows prominent expression of sodium channel mRNA in tentacle fibers but undetectable expression in arm fibers. Production of action potentials by tentacle muscle fibers and their absence in arm fibers is likely responsible for the previously reported greater twitch–tetanus ratio in the tentacle versus the arm fibers. During the rapid tentacle strike, a few closely spaced action potentials would result in maximal activation of transverse tentacle muscle. Activation of the slower transverse muscle fibers in the arms would require summation of excitatory postsynaptic potentials over a longer time, allowing the precise modulation of force required for supporting slower movements of the arms.
    Beschreibung: This work was supported by the National Science Foundation (IOS 1557754 to W.F.G. and IOS 0951067 to W.M.K.).
    Beschreibung: 2021-01-03
    Schlagwort(e): Calcium current ; Cephalopod muscle ; Current clamp ; Patch clamp ; Sodium current ; Voltage clamp
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
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  • 14
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 41095, doi:10.1038/srep41095.
    Beschreibung: Adenosine-to-inosine RNA editing in transcripts encoding the voltage-gated potassium channel Kv1.1 converts an isoleucine to valine codon for amino acid 400, speeding channel recovery from inactivation. Numerous Kv1.1 mutations have been associated with the human disorder Episodic Ataxia Type-1 (EA1), characterized by stress-induced ataxia, myokymia, and increased prevalence of seizures. Three EA1 mutations, V404I, I407M, and V408A, are located within the RNA duplex structure required for RNA editing. Each mutation decreased RNA editing both in vitro and using an in vivo mouse model bearing the V408A allele. Editing of transcripts encoding mutant channels affects numerous biophysical properties including channel opening, closing, and inactivation. Thus EA1 symptoms could be influenced not only by the direct effects of the mutations on channel properties, but also by their influence on RNA editing. These studies provide the first evidence that mutations associated with human genetic disorders can affect cis-regulatory elements to alter RNA editing.
    Beschreibung: This work was supported by the Vanderbilt Molecular Endocrinology Training Program (T32DK007563; E.A.F.K.), a Ruth L. Kirschstein National Research Service Award (F31NS087911; E.A.F.K), a Vanderbilt Dissertation Enhancement Grant (E.A.F.K.), and the Vanderbilt Joel G. Hardman Chair in Pharmacology (R.B.E). Additional support for J.J.C.R. included NINDS (R0111223855, R01NS64259) and the Cystic Fibrosis Foundation Therapeutics (Rosent14XXO). Infrastructural support for J.J.C.R. was provided by NIGMS (P20GM103642), NIMH (G12-MD007600), and NSF (DBI 0115825, DBI 1337284).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 15
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Authors, 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Williams, T. L., Senft, S. L., Yeo, J., Martin-Martinez, F. J., Kuzirian, A. M., Martin, C. A., DiBona, C. W., Chen, C., Dinneen, S. R., Nguyen, H. T., Gomes, C. M., Rosenthal, J. J. C., MacManes, M. D., Chu, F., Buehler, M. J., Hanlon, R. T., & Deravi, L. F. (2019). Dynamic pigmentary and structural coloration within cephalopod chromatophore organs. Nature Communications, 10, (2019): 1004, doi:10.1038/s41467-019-08891-x.
    Beschreibung: Chromatophore organs in cephalopod skin are known to produce ultra-fast changes in appearance for camouflage and communication. Light-scattering pigment granules within chromatocytes have been presumed to be the sole source of coloration in these complex organs. We report the discovery of structural coloration emanating in precise register with expanded pigmented chromatocytes. Concurrently, using an annotated squid chromatophore proteome together with microscopy, we identify a likely biochemical component of this reflective coloration as reflectin proteins distributed in sheath cells that envelop each chromatocyte. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules. These findings offer fresh perspectives on the intricate biophotonic interplay between pigmentary and structural coloration elements tightly co-located within the same dynamic flexible organ - a feature that may help inspire the development of new classes of engineered materials that change color and pattern.
    Beschreibung: We thank Professor Daniel Morse and Dr. Wendy Crookes-Goodson for providing the reflectin antibodies used in this report and Dr. Lydia Mäthger for the photograph in Fig. 4C. They also thank Dr. Amrita Kumar for her SEMs of the granules and pigment-extracted granules in Fig. 4 and Robert Chalkley and Al Burlingame for access to a developmental version of the Protein Prospector software. We also acknowledge that they have complied with all relevant ethical regulations in this study. We gratefully acknowledge support from the National Science Foundation (DMR-1700720, T.L.W., L.F.D., and F.C.) and the Barnett Institute of Chemical and Biological Analysis and the Department of Chemistry and Chemical Biology at Northeastern University (T.L.W., L.F.D). J.J.C.R. was supported by NSF IOS 1557748 and 1664767, NSF HRD-1137725, BSF 2013094 and the Frank R. Lillie and Herbert Rand Summer Research Fellowship from the Marine Biological Laboratory. R.T.H., S.L.S., and A.M.K. are grateful for support from AFOSR grant FA9550–14–1–0134 and the Sholley Foundation. F.J.M.M. and M.J.B acknowledge support from the US Department of Defense, Office of Naval Research (N00014–16–1–233). J.Y., F.J.M.M., and M.J.B. are grateful for support from the National Institutes of Health (U01 EB014976). J.Y. also acknowledges support from Singapore’s Agency for Science, Technology, and Research (A1786a0031). This work was supported by Singapore’s A*STAR Computational Resource Center and the National Supercomputing Center through the use of their high-performance computing facilities.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 16
    Publikationsdatum: 2007-04-29
    Print ISSN: 1545-9993
    Digitale ISSN: 1545-9985
    Thema: Biologie , Medizin
    Publiziert von Springer Nature
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  • 17
    Publikationsdatum: 2004-09-07
    Print ISSN: 1545-9993
    Digitale ISSN: 1545-9985
    Thema: Biologie , Medizin
    Publiziert von Springer Nature
    Standort Signatur Erwartet Verfügbarkeit
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  • 18
    Publikationsdatum: 2015-01-08
    Beschreibung: RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.
    Digitale ISSN: 2050-084X
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 19
  • 20
    Publikationsdatum: 2016-08-23
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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