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  1. Article ; Online: A

    Aguirre-Chen, Cristina / Stec, Natalia / Ramos, Olivia Mendivil / Kim, Nuri / Kramer, Melissa / McCarthy, Shane / Gillis, Jesse / McCombie, W Richard / Hammell, Christopher M

    G3 (Bethesda, Md.)

    2020  Volume 10, Issue 5, Page(s) 1617–1628

    Abstract: Analysis of patient-derived DNA samples has identified hundreds of variants that are likely involved in neuropsychiatric diseases such as autism spectrum disorder (ASD) and schizophrenia (SCZ). While these studies couple behavioral phenotypes to ... ...

    Abstract Analysis of patient-derived DNA samples has identified hundreds of variants that are likely involved in neuropsychiatric diseases such as autism spectrum disorder (ASD) and schizophrenia (SCZ). While these studies couple behavioral phenotypes to individual genotypes, the number and diversity of candidate genes implicated in these disorders highlights the fact that the mechanistic underpinnings of these disorders are largely unknown. Here, we describe a RNAi-based screening platform that uses
    MeSH term(s) Animals ; Autism Spectrum Disorder/genetics ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Humans ; RNA Interference ; Transcription Factors/genetics
    Chemical Substances Caenorhabditis elegans Proteins ; Transcription Factors
    Language English
    Publishing date 2020-05-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.119.400925
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

    Scheben, Armin / Ramos, Olivia Mendivil / Kramer, Melissa / Goodwin, Sara / Oppenheim, Sara / Becker, Daniel J / Schatz, Michael C / Simmons, Nancy B / Siepel, Adam / McCombie, W Richard

    bioRxiv

    Abstract: Bats are exceptional among mammals for harbouring diverse pathogens and for their robust immune systems. In addition, bats are unusually long-lived and show low rates of cancer. Contiguous and complete reference genomes are needed to determine the ... ...

    Abstract Bats are exceptional among mammals for harbouring diverse pathogens and for their robust immune systems. In addition, bats are unusually long-lived and show low rates of cancer. Contiguous and complete reference genomes are needed to determine the genetic basis of these adaptations and establish bats as models for research into mammalian health. Here we sequenced and analysed the genomes of the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus). We sequenced these two species using a mix of Illumina and Oxford Nanopore Technologies (ONT), assembling draft genomes with some of the highest contig N50s (28-29Mb) of bat genomes to date. Work is in progress to increase the base-level accuracies of these genomes. We conducted gene annotation and identified a set of 10,928 orthologs from bats and mammalian outgroups including humans, rodents, horses, pigs, and dogs. To detect positively selected genes as well as lineage-specific gene gains and losses, we carried out comprehensive branch-site likelihood ratio tests and gene family size analyses. Our analysis found signatures of rapid evolution in the innate immune response genes of bats, and evidence of past infections with diverse viral clades in Artibeus jamaicensis and Pteronotus mesoamericanus. We additionally found evidence of positive selection of tumor suppressors, which may play a role in the low cancer rates, in the most recent common ancestor of bats. These new genomic resources enable insights into the extraordinary adaptations of bats, with implications for mammalian evolutionary studies and public health.
    Keywords covid19
    Publisher BioRxiv
    Document type Article ; Online
    DOI 10.1101/2020.09.09.290502
    Database COVID19

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  3. Article ; Online: (with research data) Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes.

    Fortunato, Sofia A V / Adamski, Marcin / Ramos, Olivia Mendivil / Leininger, Sven / Liu, Jing / Ferrier, David E K / Adamska, Maja

    Nature

    2014  Volume 514, Issue 7524, Page(s) 620–623

    Abstract: Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ... ...

    Abstract Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.
    MeSH term(s) Animals ; Body Patterning/genetics ; Gene Expression Regulation ; Genes, Homeobox/genetics ; Homeodomain Proteins/genetics ; Phylogeny ; Porifera/classification ; Porifera/cytology ; Porifera/genetics ; Porifera/growth & development ; Synteny
    Chemical Substances Homeodomain Proteins
    Language English
    Publishing date 2014-10-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature13881
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
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  4. Article ; Online: Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.

    Wasik, Kaja / Gurtowski, James / Zhou, Xin / Ramos, Olivia Mendivil / Delás, M Joaquina / Battistoni, Giorgia / El Demerdash, Osama / Falciatori, Ilaria / Vizoso, Dita B / Smith, Andrew D / Ladurner, Peter / Schärer, Lukas / McCombie, W Richard / Hannon, Gregory J / Schatz, Michael

    Proceedings of the National Academy of Sciences of the United States of America

    2015  Volume 112, Issue 40, Page(s) 12462–12467

    Abstract: The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of ... ...

    Abstract The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
    MeSH term(s) Animals ; Base Sequence ; Cluster Analysis ; Gene Expression Profiling/methods ; Gene Ontology ; Genes, Helminth/genetics ; Genome, Helminth/genetics ; Helminth Proteins/classification ; Helminth Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Platyhelminths/cytology ; Platyhelminths/genetics ; Platyhelminths/physiology ; Regeneration/genetics ; Sequence Homology, Nucleic Acid ; Stem Cells/metabolism ; Transcriptome/genetics
    Chemical Substances Helminth Proteins
    Language English
    Publishing date 2015-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1516718112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
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  5. Article ; Online: The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

    Chipman, Ariel D / Ferrier, David E K / Brena, Carlo / Qu, Jiaxin / Hughes, Daniel S T / Schröder, Reinhard / Torres-Oliva, Montserrat / Znassi, Nadia / Jiang, Huaiyang / Almeida, Francisca C / Alonso, Claudio R / Apostolou, Zivkos / Aqrawi, Peshtewani / Arthur, Wallace / Barna, Jennifer C J / Blankenburg, Kerstin P / Brites, Daniela / Capella-Gutiérrez, Salvador / Coyle, Marcus /
    Dearden, Peter K / Du Pasquier, Louis / Duncan, Elizabeth J / Ebert, Dieter / Eibner, Cornelius / Erikson, Galina / Evans, Peter D / Extavour, Cassandra G / Francisco, Liezl / Gabaldón, Toni / Gillis, William J / Goodwin-Horn, Elizabeth A / Green, Jack E / Griffiths-Jones, Sam / Grimmelikhuijzen, Cornelis J P / Gubbala, Sai / Guigó, Roderic / Han, Yi / Hauser, Frank / Havlak, Paul / Hayden, Luke / Helbing, Sophie / Holder, Michael / Hui, Jerome H L / Hunn, Julia P / Hunnekuhl, Vera S / Jackson, LaRonda / Javaid, Mehwish / Jhangiani, Shalini N / Jiggins, Francis M / Jones, Tamsin E / Kaiser, Tobias S / Kalra, Divya / Kenny, Nathan J / Korchina, Viktoriya / Kovar, Christie L / Kraus, F Bernhard / Lapraz, François / Lee, Sandra L / Lv, Jie / Mandapat, Christigale / Manning, Gerard / Mariotti, Marco / Mata, Robert / Mathew, Tittu / Neumann, Tobias / Newsham, Irene / Ngo, Dinh N / Ninova, Maria / Okwuonu, Geoffrey / Ongeri, Fiona / Palmer, William J / Patil, Shobha / Patraquim, Pedro / Pham, Christopher / Pu, Ling-Ling / Putman, Nicholas H / Rabouille, Catherine / Ramos, Olivia Mendivil / Rhodes, Adelaide C / Robertson, Helen E / Robertson, Hugh M / Ronshaugen, Matthew / Rozas, Julio / Saada, Nehad / Sánchez-Gracia, Alejandro / Scherer, Steven E / Schurko, Andrew M / Siggens, Kenneth W / Simmons, DeNard / Stief, Anna / Stolle, Eckart / Telford, Maximilian J / Tessmar-Raible, Kristin / Thornton, Rebecca / van der Zee, Maurijn / von Haeseler, Arndt / Williams, James M / Willis, Judith H / Wu, Yuanqing / Zou, Xiaoyan / Lawson, Daniel / Muzny, Donna M / Worley, Kim C / Gibbs, Richard A / Akam, Michael / Richards, Stephen

    PLoS biology

    2014  Volume 12, Issue 11, Page(s) e1002005

    Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not ...

    Abstract Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
    MeSH term(s) Animals ; Arthropods/genetics ; Circadian Rhythm Signaling Peptides and Proteins/genetics ; DNA Methylation ; Evolution, Molecular ; Female ; Genome ; Genome, Mitochondrial ; Hormones/genetics ; Male ; Multigene Family ; Phylogeny ; Polymorphism, Genetic ; Protein Kinases/genetics ; RNA, Untranslated/genetics ; Receptors, Odorant/genetics ; Selenoproteins/genetics ; Sex Chromosomes ; Synteny ; Transcription Factors/genetics
    Chemical Substances Circadian Rhythm Signaling Peptides and Proteins ; Hormones ; RNA, Untranslated ; Receptors, Odorant ; Selenoproteins ; Transcription Factors ; Protein Kinases (EC 2.7.-)
    Language English
    Publishing date 2014-11-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.1002005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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