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Comparative Proteomic Analysis of Erythropoiesis Tissue Head Kidney Among Three Antarctic Fish Species
Comparative Proteomic Analysis of Erythropoiesis Tissue Head Kidney Among three Antarctic Fish Species Ruonan Jia Shanghai Ocean University Shaojun Huang Shanghai Ocean University Wanying Zhai Shanghai Ocean University Shouwen Jiang Shanghai Ocean University Wenhao Li Shanghai Ocean University Faxiang Wang Shanghai Ocean University Qianghua Xu ( [email protected] ) Shanghai Ocean University https://orcid.org/0000-0003-0351-1765 Research Article Keywords: Antarctic icesh, erythropoiesis, hematopoiesis, head kidney, immunity Posted Date: June 15th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-504121/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Antarctic icesh is the only known vertebrate species that lacks oxygen-carrying hemoglobin and functional erythrocytes. To reveal the unique hematopoietic process of icesh, we used an integrated approach including tandem mass tag (TMT) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify the dynamic changes in the head kidney whole proteome of a white-blooded icesh, Chionodraco hamatus, compared to those in two other red-blooded Antarctic sh, Trematomus bernacchii and Notothenia coriiceps. Of the 4,672 identied proteins, in the Antarctic ice sh head kidney, 123 proteins were signicantly up-regulated and 95 proteins were down-regulated. The functional grouping of differentially expressed proteins based on KEGG pathway analysis shows that white blood sh and red blood sh have signicant differences in erythropoiesis, heme biogenesis, leucocyte and platelet cell development. The proteins involved in the hematopoietic process in icesh showed a clear trend of downregulation of erythroid lineage marker proteins and upregulation of lymphoid and megakaryocytic lineage marker proteins, including CD9, ITGB2, and MTOR, which suggests a shift in hematopoiesis in the icesh head kidney due to the loss of erythrocytes. -
Mitochondrial DNA, Morphology, and the Phylogenetic Relationships of Antarctic Icefishes
MOLECULAR PHYLOGENETICS AND EVOLUTION Molecular Phylogenetics and Evolution 28 (2003) 87–98 www.elsevier.com/locate/ympev Mitochondrial DNA, morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae) Thomas J. Near,a,* James J. Pesavento,b and Chi-Hing C. Chengb a Center for Population Biology, One Shields Avenue, University of California, Davis, CA 95616, USA b Department of Animal Biology, 515 Morrill Hall, University of Illinois, Urbana, IL 61801, USA Received 10 July 2002; revised 4 November 2002 Abstract The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence be- tween existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony- based version of the Shimodaira–Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylo- genetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. -
Downloaded from Transcriptome Shotgun Assembly (TSA) Database on 29 November 2020 (Ftp://Ftp.Ddbj.Nig.Ac.Jp/Ddbj Database/Tsa/, Table S3)
viruses Article Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing Xin-Xin Chen, Wei-Chen Wu and Mang Shi * School of Medicine, Sun Yat-sen University, Shenzhen 518107, China; [email protected] (X.-X.C.); [email protected] (W.-C.W.) * Correspondence: [email protected] Abstract: In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray- finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. -
Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function
GBE Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function Alessandro Coppe1,y, Cecilia Agostini2,y, Ilaria A.M. Marino2, Lorenzo Zane2, Luca Bargelloni1, Stefania Bortoluzzi2,*, and Tomaso Patarnello1 1Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Legnaro (Padova), Italy 2Department of Biology, University of Padova, Padova, Italy yThese authors contributed equally to this work. *Corresponding author: E-mail: [email protected]. Accepted: November 23, 2012 Abstract Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modi- fications, including high mitochondrial densities in aerobic tissues. A genomic expansion accompanying the evolution of these fish was reported, but paucity of genomic information limits the understanding of notothenioid cold adaptation. We reconstructed and annotated the first skeletal muscle transcriptome of the icefish Chionodraco hamatus providing a new resource for icefish genomics (http://compgen.bio.unipd.it/chamatusbase/, last accessed December 12, 2012). We exploited deep sequencing of this energy- dependent tissue to test the hypothesis of selective duplication of genes involved in mitochondrial function. We developed a bio- informatic approach to univocally assign C. hamatus transcripts to orthology groups extracted from phylogenetic trees of five model species. Chionodraco hamatus duplicates were recorded for each orthology group allowing the identification of duplicated genes specific to the icefish lineage. Significantly more duplicates were found in the icefish when transcriptome data were compared with whole-genome data of model species. -
Draft Genome Assembly and Transcriptome Data of The
ARTICLE https://doi.org/10.1038/s42003-019-0685-y OPEN Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures 1234567890():,; Luca Bargelloni 1,2,3*, Massimiliano Babbucci1, Serena Ferraresso1, Chiara Papetti3,4, Nicola Vitulo 5, Roberta Carraro1, Marianna Pauletto 1, Gianfranco Santovito3, Magnus Lucassen6, Felix Christopher Mark 6, Lorenzo Zane 2,3 & Tomaso Patarnello1,3 Antarctic fish belonging to Notothenioidei represent an extraordinary example of radiation in the cold. In addition to the absence of hemoglobin, icefish show a number of other striking peculiarities including large-diameter blood vessels, high vascular densities, mitochondria- rich muscle cells, and unusual mitochondrial architecture. In order to investigate the bases of icefish adaptation to the extreme Southern Ocean conditions we sequenced the complete genome of the icefish Chionodraco myersi. Comparative analyses of the icefish genome with those of other teleost species, including two additional white-blooded and five red-blooded notothenioids, provided a new perspective on the evolutionary loss of globin genes. Muscle transcriptome comparative analyses against red-blooded notothenioids as well as temperate fish revealed the peculiar regulation of genes involved in mitochondrial function in icefish. Gene duplication and promoter sequence divergence were identified as genome-wide pat- terns that likely contributed to the broad transcriptional program underlying the unique features of icefish mitochondria. 1 Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy. 2 Department of Land, Environment, Agriculture, and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy. -
Biogeographic Atlas of the Southern Ocean
Census of Antarctic Marine Life SCAR-Marine Biodiversity Information Network BIOGEOGRAPHIC ATLAS OF THE SOUTHERN OCEAN CHAPTER 7. BIOGEOGRAPHIC PATTERNS OF FISH. Duhamel G., Hulley P.-A, Causse R., Koubbi P., Vacchi M., Pruvost P., Vigetta S., Irisson J.-O., Mormède S., Belchier M., Dettai A., Detrich H.W., Gutt J., Jones C.D., Kock K.-H., Lopez Abellan L.J., Van de Putte A.P., 2014. In: De Broyer C., Koubbi P., Griffiths H.J., Raymond B., Udekem d’Acoz C. d’, et al. (eds.). Biogeographic Atlas of the Southern Ocean. Scientific Committee on Antarctic Research, Cambridge, pp. 328-362. EDITED BY: Claude DE BROYER & Philippe KOUBBI (chief editors) with Huw GRIFFITHS, Ben RAYMOND, Cédric d’UDEKEM d’ACOZ, Anton VAN DE PUTTE, Bruno DANIS, Bruno DAVID, Susie GRANT, Julian GUTT, Christoph HELD, Graham HOSIE, Falk HUETTMANN, Alexandra POST & Yan ROPERT-COUDERT SCIENTIFIC COMMITTEE ON ANTARCTIC RESEARCH THE BIOGEOGRAPHIC ATLAS OF THE SOUTHERN OCEAN The “Biogeographic Atlas of the Southern Ocean” is a legacy of the International Polar Year 2007-2009 (www.ipy.org) and of the Census of Marine Life 2000-2010 (www.coml.org), contributed by the Census of Antarctic Marine Life (www.caml.aq) and the SCAR Marine Biodiversity Information Network (www.scarmarbin.be; www.biodiversity.aq). The “Biogeographic Atlas” is a contribution to the SCAR programmes Ant-ECO (State of the Antarctic Ecosystem) and AnT-ERA (Antarctic Thresholds- Ecosys- tem Resilience and Adaptation) (www.scar.org/science-themes/ecosystems). Edited by: Claude De Broyer (Royal Belgian Institute -
Dottorato Di Ricerca in Biochimica E Biologia Cellulare E Molecolare
UNIVERSITA’ DEGLI STUDI DI NAPOLI FEDERICO II DOTTORATO DI RICERCA IN BIOCHIMICA E BIOLOGIA CELLULARE E MOLECOLARE TESI DI DOTTORATO, 2006 GENOMA E AMBIENTE: TEMPERATURA E METILAZIONE DOTTORANDA: ANNALISA VARRIALE LABORATORIO DI EVOLUZIONE MOLECOLARE STAZIONE ZOOLOGICA ANTON DOHRN RELATORE: Prof. GIUSEPPE GERACI CORRELATORE: Prof. GIORGIO BERNARDI COORDINATORE: Prof. GIUSEPPE D’ALESSIO INDICE pagina SOMMARIO i ABSTRACT ii 1-INTRODUZIONE 1 1.1 -I pesci 7 1.2 -I rettili 8 1.6 -Ambiente e termostabilità dell’RNA ribosomale (rRNA) 18S 9 2-MATERIALI E METODI 12 2.1 DNA e campioni di tessuto biologico 12 2.2 Estrazione del DNA genomico e analisi per ultracentrifugazione 12 2.3 Idrolisi enzimatica del DNA 12 2.4 Analisi con RP-HPLC 13 2.5 Analisi dei geni ortologhi 14 2.6 Analisi delle sequenze di RNA ribosomale 18S in vertebrati 15 3-RISULTATI 16 3.1.1 Analisi del livello di metilazione in pesci 16 3.1.2 Analisi del livello di metilazione nei rettili 22 I 3.1.3 Analisi del livello di metilazione nei mammiferi 25 3.2 Correlazione del livello di metilazione con la lunghezza del genoma 28 3.3 Livello di CpG in geni ortologhi 29 3.4 Correlazione del livello di metilazione con tassonomia e filogenia 32 3.5 Correlazione tra livello di metilazione e temperatura corporea 32 3.6 Correlazione tra livello di GC derivante dall’analisi dei nucleosidi e dalla centrifugazione in gradiente di densità di cloruro di cesio (CsCl) 33 3.7 Analisi dell’RNA ribosomale 18S endotermi ed endotermi 35 4.DISCUSSIONE 37 5.CONCLUSIONE 41 3-RINGRAZIAMENTI 42 3-BIBLIOGRAFIA 43 II Sommario La temperatura è un fattore ambientale che influenza la vita degli organismi. -
Adaptation of Proteins to the Cold in Antarctic Fish: a Role for Methionine?
bioRxiv preprint doi: https://doi.org/10.1101/388900; this version posted August 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Cold fish 1 Article: Discoveries 2 Adaptation of proteins to the cold in Antarctic fish: A role for Methionine? 3 4 Camille Berthelot1,2, Jane Clarke3, Thomas Desvignes4, H. William Detrich, III5, Paul Flicek2, Lloyd S. 5 Peck6, Michael Peters5, John H. Postlethwait4, Melody S. Clark6* 6 7 1Laboratoire Dynamique et Organisation des Génomes (Dyogen), Institut de Biologie de l'Ecole 8 Normale Supérieure ‐ UMR 8197, INSERM U1024, 46 rue d'Ulm, 75230 Paris Cedex 05, France. 9 2European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome 10 Campus, Hinxton, Cambridge, CB10 1SD, UK. 11 3University of Cambridge, Department of Chemistry, Lensfield Rd, Cambridge CB2 1EW, UK. 12 4Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA. 13 5Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 14 Nahant, MA 01908, USA. 15 6British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, 16 Cambridge, CB3 0ET, UK. 17 18 *Corresponding Author: Melody S Clark, British Antarctic Survey, Natural Environment Research 19 Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK. Email: [email protected] 20 21 bioRxiv preprint doi: https://doi.org/10.1101/388900; this version posted August 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Near2009chap45.Pdf
Notothenioid fi shes (Notothenioidei) Thomas J. Near and A lled vacant niches aJ er the onset of polar condi- Department of Ecology and Evolutionary Biology & Peabody tions ~35 Ma (2). 7 e fossil A shes preserved in the Eocene Museum of Natural History, Yale University, New Haven, CT 06520, La Meseta Formation on Seymour Island at the tip of the USA ([email protected]) Antarctic Peninsula indicate that before the development of polar conditions the nearshore A sh fauna of Antarctica Abstract was diverse, cosmopolitan, and not dominated by noto- thenioids (5). 7 e only documented notothenioid fossil Notothenioids are a clade of acanthomorph teleosts that is a well-preserved neurocranium of the extinct species represent a rare example of adaptive radiation among mar- Proeleginops grandeastmanorum from the La Meseta ine fi shes. The notothenioid Antarctic Clade is character- Formation that is dated to ~40 Ma (6–10). ized by extensive morphological and ecological variation Ecologically, Antarctic notothenioids have diversiA ed and adaptations to avoid freezing in the ice-laden water of into both benthic and water column habitats (2). Several Southern Ocean marine habitats. A recent analysis of noto- lineages are able to utilize water column habitats des- thenioid divergence times indicates that the clade dates to pite lacking a swim bladder by modiA cation of buoyancy the Cretaceous (125 million years ago, Ma), but the Antarctic through the reduction of ossiA cation and the evolution of Clade diversifi ed near the Oligocene–Miocene boundary intra- and intermuscular lipid deposits (11, 12). A notable (23 Ma). These age estimates are consistent with paleogeo- group of notothenioid species is the Channichthyidae, graphic events in the Southern Ocean that drove climate or iceA shes (Fig. -
Biological Characteristics of Antarctic Fish Stocks in the Southern Scotia Arc Region
CCAMLR Science, Vol. 7 (2000): 141 BIOLOGICAL CHARACTERISTICS OF ANTARCTIC FISH STOCKS IN THE SOUTHERN SCOTIA ARC REGION K.-H. Kock Institut fur Seefischerei Bundesforschungsanstalt fiir Fischerei Palmaille 9, D-22767 Hamburg, Germany C.D. Jones National Oceanic and Atmospheric Administration National Marine Fisheries Service US Antarctic Marine Living Resources Program PO Box 271, La Jolla, Ca. 92038, USA S. Wilhelms HelenenstraBe 16 D-22765 Hamburg, Germany Abstract Commercial exploitation of finfish in the southern Scotia Arc took place from 1977/78 to 1989/90, and was in its heyday from 1977/78 to 1981/82. Except for Elephant Island, the state of fish stocks of the southern Scotia Arc region has been accorded little attention until 1998, despite substantial catches in the first four years of the fishery and ample opportunity to sample these catches. The only scientific surveys of these stocks during these years were conducted by Germany in 1985, and by Spain in 1987 and 1991. More recently, the US Antarctic Marine Living Resources (US AMLR) Program carried out two extensive surveys around Elephant Island and the lower South Shetland Islands in March 1998 and around the South Orkney Islands in March 1999. In this paper, the authors present new data on species composition, species groups, length compositions, length-weight relationships, length at sexual maturity and length at first spawning, gonadosomatic indices and oocyte diameter. Lesser Antarctic or peri-Antarctic species predominated in the fish fauna. Species groups differed by up to 55-60% from one shelf area to the other, mostly due to differences in the abundance of the predominant species on each shelf area and the increase in the number of high-Antarctic species in the South Orkney Islands. -
Investigating the Larval/Juvenile Notothenioid Fish Species Assemblage in Mcmurdo Sound, Antarctica Using Phylogenetic Reconstruction
INVESTIGATING THE LARVAL/JUVENILE NOTOTHENIOID FISH SPECIES ASSEMBLAGE IN MCMURDO SOUND, ANTARCTICA USING PHYLOGENETIC RECONSTRUCTION BY KATHERINE R. MURPHY THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology with a concentration in Ecology, Ethology, and Evolution in the Graduate College of the University of Illinois at Urbana-Champaign, 2015 Urbana, Illinois Master’s Committee: Professor Chi-Hing Christina Cheng, Director of Research Professor Emeritus Arthur L. DeVries Professor Ken N. Paige ABSTRACT Aim To investigate and identify the species found within the little-known larval and juvenile notothenioid fish assemblage of McMurdo Sound, Antarctica, and to compare this assemblage to the well-studied local adult community. Location McMurdo Sound, Antarctica. Methods We extracted genomic DNA from larval and juvenile notothenioid fishes collected from McMurdo Sound during the austral summer and used mitochondrial ND2 gene sequencing with phylogenetic reconstruction to make definitive species identifications. We then surveyed the current literature to determine the adult notothenioid communities of McMurdo Sound, Terra Nova Bay, and the Ross Sea, and subsequently compared them to the species identified in our larval/juvenile specimens. Results Of our 151 larval and juvenile fishes, 142 specimens or 94.0% represented seven species from family Nototheniidae. Only one specimen was not matched directly to a reference sequence but instead was placed as sister taxon to Pagothenia borchgrevinki with a bootstrap value of 100 and posterior probability of 1.0. The nine non-nototheniid specimens represented the following six ii species: Pogonophryne scotti, Pagetopsis maculatus, Chionodraco myersi, Chionodraco hamatus, Neopagetopsis ionah, and Psilodraco breviceps. -
The Role of Notothenioid Fish in the Food Web of the Ross Sea Shelf Waters
Polar Biol (2004) 27: 321–338 DOI 10.1007/s00300-004-0599-z REVIEW M. La Mesa Æ J. T. Eastman Æ M. Vacchi The role of notothenioid fish in the food web of the Ross Sea shelf waters: a review Received: 27 June 2003 / Accepted: 23 January 2004 / Published online: 12 March 2004 Ó Springer-Verlag 2004 Abstract The Ross Sea, a large, high-latitude (72–78°S) are benthic predators on fish while smaller species feed embayment of the Antarctic continental shelf, averages mainly on benthic crustaceans. Channichthyids are less 500 m deep, with troughs to 1,200 m and the shelf break dependent on the bottom for food than other notothe- at 700 m. It is covered by pack ice for 9 months of the nioids. Some species combine benthic and pelagic life year. The fish fauna of about 80 species includes pri- styles; others are predominantly pelagic and all consume marily 4 families and 53 species of the endemic perci- euphausiids and/or fish. South polar skuas, Antarctic form suborder Notothenioidei. This review focuses on petrels, Ade´lie and emperor penguins, Weddell seals and the diet and role in the food web of notothenioids and minke and killer whales are the higher vertebrate com- top-level bird and mammal predators, and also includes ponents of the food web, and all prey on notothenioids new information on the diets of artedidraconids and to some extent. Based on the frequency of occurrence of bathydraconids. Although principally a benthic group, prey items in the stomachs of fish, bird and mammal notothenioids have diversified to form an adaptive predators, P.