Unique Composition of Intronless and Intron-Containing Type I Ifns in The
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Proteomics Provides Insights Into the Inhibition of Chinese Hamster V79
www.nature.com/scientificreports OPEN Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment Jifeng Liu1,2, Tengfei Ma1,2, Mingzhong Gao3, Yilin Liu4, Jun Liu1, Shichao Wang2, Yike Xie2, Ling Wang2, Juan Cheng2, Shixi Liu1*, Jian Zou1,2*, Jiang Wu2, Weimin Li2 & Heping Xie2,3,5 As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment afecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the efect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and diferentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable diference between the two laboratories, whereby γ ray dose rate was signifcantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g. -
A Modular Sequence Capture Probe Set for Phylogenomics And
bioRxiv preprint doi: https://doi.org/10.1101/825307; this version posted October 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC 4.0 International license. 1 FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales Carl R. Hutter1,2*, Kerry A. Cobb3, Daniel M. Portik4, Scott L. Travers1, Perry L. Wood, Jr.3 and Rafe M. Brown1 1 Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA. 2 Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. 3Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA. 4 California Academy of Sciences, San Francisco, CA 94118, USA *Corresponding author and current address: Carl R. Hutter Museum of Natural Sciences and Department of Biological Sciences Louisiana State University Baton Rouge, LA 70803, USA E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/825307; this version posted October 31, 2019. 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-NC 4.0 International license. 2 ABSTRACT Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. -
Is Dicroglossidae Anderson, 1871 (Amphibia, Anura) an Available Nomen?
Zootaxa 3838 (5): 590–594 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Correspondence ZOOTAXA Copyright © 2014 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3838.5.8 http://zoobank.org/urn:lsid:zoobank.org:pub:87DD8AF3-CB72-4EBD-9AA9-5B1E2439ABFE Is Dicroglossidae Anderson, 1871 (Amphibia, Anura) an available nomen? ANNEMARIE OHLER1 & ALAIN DUBOIS Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR7205 ISYEB, CP 30, 25 rue Cuvier, 75005 Paris 1Corresponding autho. E-mail: [email protected] Abbreviations used: BMNH, Natural History Museum, London; SVL, snout–vent length; ZMB, Zoologisch Museum, Berlin. Anderson (1871a: 38) mentioned the family nomen DICROGLOSSIDAE, without any comment, in a list of specimens of the collections of the Indian Museum of Calcutta (now the Zoological Survey of India). He referred to this family a single species, Xenophrys monticola, a nomen given by Günther (1864) to a species of MEGOPHRYIDAE from Darjeeling and Khasi Hills (India) which has a complex nomenclatural history (Dubois 1989, 1992; Deuti et al. submitted). Dubois (1987: 57), considering that the nomen DICROGLOSSIDAE had been based on the generic nomen Dicroglossus Günther, 1860, applied it to a family group taxon, the tribe DICROGLOSSINI, for which he proposed a diagnosis. The genus Dicroglossus had been erected by Günther (1860), 11 years before Anderson’s (1871a) paper, for the unique species Dicroglossus adolfi. Boulenger (1882: 17) stated that this specific nomen was a subjective junior synonym of Rana cyanophlyctis Schneider, 1799, and therefore Dicroglossus a subjective junior synonym of Rana Linnaeus, 1758 (Boulenger, 1882: 7). -
Draft Genome Assembly of the Invasive Cane Toad, Rhinella Marina
GigaScience, 7, 2018, 1–13 doi: 10.1093/gigascience/giy095 Advance Access Publication Date: 7 August 2018 Data Note Downloaded from https://academic.oup.com/gigascience/article-abstract/7/9/giy095/5067871 by Macquarie University user on 17 March 2019 DATA NOTE Draft genome assembly of the invasive cane toad, Rhinella marina † † Richard J. Edwards1, Daniel Enosi Tuipulotu1, , Timothy G. Amos1, , Denis O’Meally2,MarkF.Richardson3,4, Tonia L. Russell5, Marcelo Vallinoto6,7, Miguel Carneiro6,NunoFerrand6,8,9, Marc R. Wilkins1,5, Fernando Sequeira6, Lee A. Rollins3,10, Edward C. Holmes11, Richard Shine12 and Peter A. White 1,* 1School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia, 2Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2052, Australia, 3School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia, 4Bioinformatics Core Research Group, Deakin University, Geelong, VIC, 3216, Australia, 5Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia, 6CIBIO/InBIO, Centro de Investigac¸ao˜ em Biodiversidade e Recursos Geneticos,´ Universidade do Porto, Vairao,˜ Portugal, 7Laboratorio´ de Evoluc¸ao,˜ Instituto de Estudos Costeiros (IECOS), Universidade Federal do Para,´ Braganc¸a, Para,´ Brazil, 8Departamento de Biologia, Faculdade de Ciencias,ˆ Universidade do Porto, Porto, Portugal, 9Department of Zoology, Faculty of Sciences, University of -
Blood-Based Molecular Biomarker Signatures in Alzheimer's
bioRxiv preprint doi: https://doi.org/10.1101/481879; this version posted December 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Article Blood-based molecular biomarker signatures in Alzheimer’s disease: insights from systems biomedicine perspective Tania Islam 1,#, Md. Rezanur Rahman 2,#,*, Md. Shahjaman3, Toyfiquz Zaman2, Md. Rezaul Karim2, Julian M.W. Quinn4, R.M. Damian Holsinger5,6, and Mohammad Ali Moni 6,* 1Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh; [email protected](T.I.). 2 Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj, Bangladesh; [email protected](M.R.R.). 3 Department of Statistics, Begum Rokeya University, Rangpur, Bangladesh; [email protected] (M.S.). 4 Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia;[email protected](J.W.W.Q.). 5 Laboratory of Molecular Neuroscience and Dementia, Brain and Mind Centre, The University of Sydney, Camperdown, NSW, Australia; [email protected] (R.M.D.H.). 6 Discipline of Biomedical Science, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia; [email protected] (M.A.M.). #These two authors have made an equal contribution and hold joint first authorship for this work. * Correspondence: [email protected] (M.R.R.) or [email protected] (M.A.M.). Abstract: Background and objectives: Alzheimer’s disease (AD) is the progressive neurodegenerative disease characterized by dementia, but no peripheral biomarkers available yet that can detect the AD. -
Characterization of Genetic Aberrations in a Single Case of Metastatic Thymic Adenocarcinoma Yeonghun Lee1, Sehhoon Park2, Se-Hoon Lee2,3* and Hyunju Lee1*
Lee et al. BMC Cancer (2017) 17:330 DOI 10.1186/s12885-017-3282-9 RESEARCH ARTICLE Open Access Characterization of genetic aberrations in a single case of metastatic thymic adenocarcinoma Yeonghun Lee1, Sehhoon Park2, Se-Hoon Lee2,3* and Hyunju Lee1* Abstract Background: Thymic adenocarcinoma is an extremely rare subtype of thymic epithelial tumors. Due to its rarity, there is currently no sequencing approach for thymic adenocarcinoma. Methods: We performed whole exome and transcriptome sequencing on a case of thymic adenocarcinoma and performed subsequent validation using Sanger sequencing. Results: The case of thymic adenocarcinoma showed aggressive behaviors with systemic bone metastases. We identified a high incidence of genetic aberrations, which included somatic mutations in RNASEL, PEG10, TNFSF15, TP53, TGFB2, and FAT1. Copy number analysis revealed a complex chromosomal rearrangement of chromosome 8, which resulted in gene fusion between MCM4 and SNTB1 and dramatic amplification of MYC and NDRG1. Focal deletion was detected at human leukocyte antigen (HLA) class II alleles, which was previously observed in thymic epithelial tumors. We further investigated fusion transcripts using RNA-seq data and found an intergenic splicing event between the CTBS and GNG5 transcript. Finally, enrichment analysis using all the variants represented the immune system dysfunction in thymic adenocarcinoma. Conclusion: Thymic adenocarcinoma shows highly malignant characteristics with alterations in several cancer- related genes. Keywords: Thymic adenocarcinoma, Thymic epithelial tumors, Whole exome sequencing, Somatic mutations, Somatic copy number alterations Background With their distinct entities, thymic adenocarcinomas Thymic adenocarcinoma is an extremely rare subtype of have shown higher malignancy than other thymic epi- thymic carcinoma. Thirty-five cases have been reported thelial tumors (TETs). -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
A Draft Genome Assembly of the Eastern Banjo Frog Limnodynastes Dumerilii Dumerilii (Anura: Limnodynastidae)
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.03.971721; this version posted May 20, 2020. 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-NC-ND 4.0 International license. 1 A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii 2 dumerilii (Anura: Limnodynastidae) 3 Qiye Li1,2, Qunfei Guo1,3, Yang Zhou1, Huishuang Tan1,4, Terry Bertozzi5,6, Yuanzhen Zhu1,7, 4 Ji Li2,8, Stephen Donnellan5, Guojie Zhang2,8,9,10* 5 6 1 BGI-Shenzhen, Shenzhen 518083, China 7 2 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, 8 Chinese Academy of Sciences, Kunming 650223, China 9 3 College of Life Science and Technology, Huazhong University of Science and Technology, 10 Wuhan 430074, China 11 4 Center for Informational Biology, University of Electronic Science and Technology of China, 12 Chengdu 611731, China 13 5 South Australian Museum, North Terrace, Adelaide 5000, Australia 14 6 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide 5005, 15 Australia 16 7 School of Basic Medicine, Qingdao University, Qingdao 266071, China 17 8 China National Genebank, BGI-Shenzhen, Shenzhen 518120, China 18 9 Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 19 650223, Kunming, China 20 10 Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK- 21 2100 Copenhagen, Denmark 22 * Correspondence: [email protected] (G.Z.). -
Essential Genes Shape Cancer Genomes Through Linear Limitation of Homozygous Deletions
ARTICLE https://doi.org/10.1038/s42003-019-0517-0 OPEN Essential genes shape cancer genomes through linear limitation of homozygous deletions Maroulio Pertesi1,3, Ludvig Ekdahl1,3, Angelica Palm1, Ellinor Johnsson1, Linnea Järvstråt1, Anna-Karin Wihlborg1 & Björn Nilsson1,2 1234567890():,; The landscape of somatic acquired deletions in cancer cells is shaped by positive and negative selection. Recurrent deletions typically target tumor suppressor, leading to positive selection. Simultaneously, loss of a nearby essential gene can lead to negative selection, and introduce latent vulnerabilities specific to cancer cells. Here we show that, under basic assumptions on positive and negative selection, deletion limitation gives rise to a statistical pattern where the frequency of homozygous deletions decreases approximately linearly between the deletion target gene and the nearest essential genes. Using DNA copy number data from 9,744 human cancer specimens, we demonstrate that linear deletion limitation exists and exposes deletion-limiting genes for seven known deletion targets (CDKN2A, RB1, PTEN, MAP2K4, NF1, SMAD4, and LINC00290). Downstream analysis of pooled CRISPR/Cas9 data provide further evidence of essentiality. Our results provide further insight into how the deletion landscape is shaped and identify potentially targetable vulnerabilities. 1 Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden. 2 Broad Institute, 415 Main Street, Cambridge, MA 02142, USA. 3These authors contributed equally: Maroulio Pertesi, Ludvig Ekdahl. Correspondence and requests for materials should be addressed to B.N. (email: [email protected]) COMMUNICATIONS BIOLOGY | (2019) 2:262 | https://doi.org/10.1038/s42003-019-0517-0 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-019-0517-0 eletion of chromosomal material is a common feature of we developed a pattern-based method to identify essential genes Dcancer genomes1. -
The Axolotl Genome and the Evolution of Key Tissue Formation Regulators Sergej Nowoshilow1,2,3†*, Siegfried Schloissnig4*, Ji-Feng Fei5*, Andreas Dahl3,6, Andy W
OPEN ArtICLE doi:10.1038/nature25458 The axolotl genome and the evolution of key tissue formation regulators Sergej Nowoshilow1,2,3†*, Siegfried Schloissnig4*, Ji-Feng Fei5*, Andreas Dahl3,6, Andy W. C. Pang7, Martin Pippel4, Sylke Winkler1, Alex R. Hastie7, George Young8, Juliana G. Roscito1,9,10, Francisco Falcon11, Dunja Knapp3, Sean Powell4, Alfredo Cruz11, Han Cao7, Bianca Habermann12, Michael Hiller1,9,10, Elly M. Tanaka1,2,3† & Eugene W. Myers1,10 Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3−/− and Pax7−/− mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies. Salamanders boast an illustrious history in biological research as the 14.2 kb) using Pacific Biosciences (PacBio) instruments (Supplementary animal in which the Spemann organizer1 and Sperry’s chemoaffinity Information section 1) to avoid the read sampling bias that is often found theory of axonal guidance2 were discovered. -
Species Groups Distributed Across Elevational Gradients Reveal Convergent and Continuous Genetic Adaptation to High Elevations
Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations Yan-Bo Suna,1, Ting-Ting Fua,b,1, Jie-Qiong Jina, Robert W. Murphya,c, David M. Hillisd,2, Ya-Ping Zhanga,e,f,2, and Jing Chea,e,g,2 aState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China; bKunming College of Life Science, University of Chinese Academy of Sciences, 650204 Kunming, China; cCentre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada; dDepartment of Integrative Biology and Biodiversity Center, University of Texas at Austin, Austin, TX 78712; eCenter for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China; fState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650091 Kunming, China; and gSoutheast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar Contributed by David M. Hillis, September 7, 2018 (sent for review August 7, 2018; reviewed by John H. Malone and Fuwen Wei) Although many cases of genetic adaptations to high elevations Most previous studies of the genetic processes of HEA have have been reported, the processes driving these modifications and compared species or populations from high elevations above the pace of their evolution remain unclear. Many high-elevation 3,500 m with those from low elevations to identify sequence adaptations (HEAs) are thought to have arisen in situ as popula- variation and/or expression shifts in the high-elevation group (8– tions rose with growing mountains. -
Whole-Genome Sequence of the Tibetan Frog Nanorana Parkeri And
Whole-genome sequence of the Tibetan frog PNAS PLUS Nanorana parkeri and the comparative evolution of tetrapod genomes Yan-Bo Suna,1, Zi-Jun Xiongb,c,d,1, Xue-Yan Xiangb,c,d,e,1, Shi-Ping Liub,c,d,f, Wei-Wei Zhoua, Xiao-Long Tua,g, Li Zhongh, Lu Wangh, Dong-Dong Wua, Bao-Lin Zhanga,h, Chun-Ling Zhua, Min-Min Yanga, Hong-Man Chena, Fang Lib,d, Long Zhoub,d, Shao-Hong Fengb,d, Chao Huangb,d,f, Guo-Jie Zhangb,d,i, David Irwina,j,k, David M. Hillisl,2, Robert W. Murphya,m, Huan-Ming Yangd,n,o, Jing Chea,2, Jun Wangd,n,p,q,r,2, and Ya-Ping Zhanga,h,2 aState Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; bChina National GeneBank and cShenzhen Key Laboratory of Transomics Biotechnologies, dBGI-Shenzhen, Shenzhen 518083, China; eCollege of Life Sciences, Sichuan University, Chengdu 610064, China; fSchool of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China; gKunming College of Life Science, Chinese Academy of Sciences, Kunming 650204, China; hLaboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China; iCentre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; jDepartment of Laboratory Medicine and Pathobiology and kBanting and Best Diabetes Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada; lDepartment of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX 78712; mCentre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada; nPrincess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia; oJames D.