Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies
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Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya Gossypii
Chalmers Publication Library Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii This document has been downloaded from Chalmers Publication Library (CPL). It is the author´s version of a work that was accepted for publication in: Biotechnology and Bioengineering (ISSN: 0006-3592) Citation for the published paper: Ledesma-Amaro, R. ; Kerkhoven, E. ; Revuelta, J. (2014) "Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii". Biotechnology and Bioengineering, vol. 111(6), pp. 1191-1199. http://dx.doi.org/10.1002/bit.25167 Downloaded from: http://publications.lib.chalmers.se/publication/200098 Notice: Changes introduced as a result of publishing processes such as copy-editing and formatting may not be reflected in this document. For a definitive version of this work, please refer to the published source. Please note that access to the published version might require a subscription. Chalmers Publication Library (CPL) offers the possibility of retrieving research publications produced at Chalmers University of Technology. It covers all types of publications: articles, dissertations, licentiate theses, masters theses, conference papers, reports etc. Since 2006 it is the official tool for Chalmers official publication statistics. To ensure that Chalmers research results are disseminated as widely as possible, an Open Access Policy has been adopted. The CPL service is administrated and maintained by Chalmers Library. (article starts on next page) ARTICLE Genome Scale Metabolic Modeling of the -
A CRISPR-Cas9–Engineered Mouse Model for GPI-Anchor Deficiency Mirrors Human Phenotypes and Exhibits Hippocampal Synaptic Dysfunctions
A CRISPR-Cas9–engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions Miguel Rodríguez de los Santosa,b,c,d, Marion Rivalane,f, Friederike S. Davidd,g, Alexander Stumpfh, Julika Pitschi,j, Despina Tsortouktzidisi, Laura Moreno Velasquezh, Anne Voigth, Karl Schillingk, Daniele Matteil, Melissa Longe,f, Guido Vogta,c, Alexej Knausd, Björn Fischer-Zirnsaka,c, Lars Wittlerm, Bernd Timmermannn, Peter N. Robinsono,p, Denise Horna, Stefan Mundlosa,c, Uwe Kornaka,c,q, Albert J. Beckeri, Dietmar Schmitzh, York Wintere,f, and Peter M. Krawitzd,1 aInstitute for Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, 13353 Berlin, Germany; bBerlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; cResearch Group Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; dInstitute for Genomic Statistics and Bioinformatics, University of Bonn, 53127 Bonn, Germany; eAnimal Outcome Core Facility of the NeuroCure Center, Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany; fInstitute of Cognitive Neurobiology, Humboldt University, 10117 Berlin, Germany; gInstitute of Human Genetics, Faculty of Medicine, University Hospital Bonn, 53127 Bonn, Germany; hNeuroscience Research Center, Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany; iSection for Translational Epilepsy Research, Department of Neuropathology, University Hospital Bonn, 53127 Bonn, Germany; jDepartment of Epileptology, -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Comparative Genomics of Biotechnologically Important Yeasts Supplementary Appendix
Comparative genomics of biotechnologically important yeasts Supplementary Appendix Contents Note 1 – Summary of literature on ascomycete yeasts used in this study ............................... 3 CUG-Ser yeasts ................................................................................................................................................................ 3 Other Saccharomycotina ............................................................................................................................................. 5 Taphrinomycotina ....................................................................................................................................................... 10 Note 2 – Genomes overview .................................................................................................11 Yeast culturing, identification, DNA and total RNA extraction ................................................................. 12 Genome sequencing and assembly ....................................................................................................................... 12 Transcriptome sequencing and assembly ......................................................................................................... 13 Table S1. Genome statistics ..................................................................................................................................... 14 Table S2. Annotation statistics .............................................................................................................................. -
High Mutation Frequency of the PIGA Gene in T Cells Results In
High Mutation Frequency of the PIGA Gene in T Cells Results in Reconstitution of GPI A nchor−/CD52− T Cells That Can Give Early Immune Protection after This information is current as Alemtuzumab-Based T Cell−Depleted of October 1, 2021. Allogeneic Stem Cell Transplantation Floris C. Loeff, J. H. Frederik Falkenburg, Lois Hageman, Wesley Huisman, Sabrina A. J. Veld, H. M. Esther van Egmond, Marian van de Meent, Peter A. von dem Borne, Hendrik Veelken, Constantijn J. M. Halkes and Inge Jedema Downloaded from J Immunol published online 2 February 2018 http://www.jimmunol.org/content/early/2018/02/02/jimmun ol.1701018 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2018/02/02/jimmunol.170101 Material 8.DCSupplemental Why The JI? Submit online. by guest on October 1, 2021 • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2018 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published February 2, 2018, doi:10.4049/jimmunol.1701018 The Journal of Immunology High Mutation Frequency of the PIGA Gene in T Cells Results in Reconstitution of GPI Anchor2/CD522 T Cells That Can Give Early Immune Protection after Alemtuzumab- Based T Cell–Depleted Allogeneic Stem Cell Transplantation Floris C. -
Comparing Spatial Expression Dynamics of Bovine
Comparing spatial expression dynamics of bovine blastocyst under three different procedures : in-vivo, in-vitro derived, Title and somatic cell nuclear transfer embryos Nagatomo, Hiroaki; Akizawa, Hiroki; Sada, Ayari; Kishi, Yasunori; Yamanaka, Ken-ichi; Takuma, Tetsuya; Sasaki, Author(s) Keisuke; Yamauchi, Nobuhiko; Yanagawa, Yojiro; Nagano, Masashi; Kono, Tomohiro; Takahashi, Masashi; Kawahara, Manabu Citation Japanese Journal of Veterinary Research, 63(4), 159-171 Issue Date 2015-11 DOI 10.14943/jjvr.63.4.159 Doc URL http://hdl.handle.net/2115/60304 Type bulletin (article) Additional Information There are other files related to this item in HUSCAP. Check the above URL. File Information JJVR63-4 p.159-171 Suppl. Table 3.pdf (Supplemental Table 3) Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Supplemental table 3. Genes that were differentially expressed in the ICM relative to the TE in in SCNT blastocyst (SCNT list). Gene Symbol Probe Set ID Regulation Fold change ([ICM] / [TE]) Gene Title EEF1A1 AFFX-Bt-ef1a-3_at UP 1.2092365 eukaryotic translation elongation factor 1 alpha 1 IGFBP3 Bt.422.1.S2_at UP 2.5323892 insulin-like growth factor binding protein 3 IGFBP3 Bt.422.1.S1_at UP 3.7850845 insulin-like growth factor binding protein 3 SULT1A1 Bt.3537.1.S1_at UP 2.7092714 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1 SPP1 Bt.2632.1.S1_at UP 5.6928325 secreted phosphoprotein 1 SCARB1 Bt.4520.1.S1_at UP 3.106944 scavenger receptor class B, member 1 TSPO Bt.3988.1.S1_at -
Complement and Inflammasome Overactivation Mediates Paroxysmal Nocturnal Hemoglobinuria with Autoinflammation
Complement and inflammasome overactivation mediates paroxysmal nocturnal hemoglobinuria with autoinflammation Britta Höchsmann, … , Peter M. Krawitz, Taroh Kinoshita J Clin Invest. 2019. https://doi.org/10.1172/JCI123501. Research Article Hematology Inflammation Graphical abstract Find the latest version: https://jci.me/123501/pdf The Journal of Clinical Investigation RESEARCH ARTICLE Complement and inflammasome overactivation mediates paroxysmal nocturnal hemoglobinuria with autoinflammation Britta Höchsmann,1,2 Yoshiko Murakami,3,4 Makiko Osato,3,5 Alexej Knaus,6 Michi Kawamoto,7 Norimitsu Inoue,8 Tetsuya Hirata,3 Shogo Murata,3,9 Markus Anliker,1 Thomas Eggermann,10 Marten Jäger,11 Ricarda Floettmann,11 Alexander Höllein,12 Sho Murase,7 Yasutaka Ueda,5 Jun-ichi Nishimura,5 Yuzuru Kanakura,5 Nobuo Kohara,7 Hubert Schrezenmeier,1 Peter M. Krawitz,6 and Taroh Kinoshita3,4 1Institute of Transfusion Medicine, University of Ulm, Ulm, Germany. 2Institute of Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service and University Hospital Ulm, Ulm, Germany. 3Research Institute for Microbial Diseases and 4WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan. 5Department of Hematology and Oncology, Graduate School of Medicine, Osaka University, Osaka, Japan. 6Institute for Genomic Statistics and Bioinformatics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany. 7Department of Neurology, Kobe City Medical Center General Hospital, Kobe, Japan. 8Department of Tumor Immunology, Osaka -
Ashbya Gossypii
A role of actin-regulatory proteins in the formation of needle-shaped spores in the filamentous fungus Ashbya gossypii Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) Fachbereich Biologie/Chemie der Universität Osnabrück vorgelegt von Manuela Lickfeld Osnabrück, im März 2012 Table of contents 1 Summary 1 2 Introduction 3 2.1 Ashbya gossypii - a model for the investigation of cell biological processes 3 2.2 Sporulation in ascomycetes 7 2.3 The role of actin in spore development 11 2.4 Aims of this study 14 3 Results 21 3.1 A Bnr-like formin links actin to the spindle pole body during sporulation in the 23 filamentous fungus Ashbya gossypii M. Kemper, L. Mohlzahn, M. Lickfeld, C. Lang, S. Wählisch & H.P. Schmitz, (2011) Molecular Microbiology 80: 1276-1295 3.2 Selection of STOP-free sequences from random mutagenesis for 51 ދloss of interactionތ two-hybrid studies Lickfeld, M. & H.P. Schmitz, (2011) Yeast 28: 535-545. 3.3 A network involving Rho-type GTPases, a Paxillin and a Formin homolog 65 regulates spore length and spore wall integrity in the filamentous fungus Ashbya gossypii Lickfeld, M. & H.P. Schmitz, (2012) manuscript submitted 3.4 Dissection of Rho-GTPase function in polar growth and sporulation of 111 Ashbya gossypii Lickfeld, M. & H.P. Schmitz, (2012) manuscript in preparation 4 Concluding remarks 141 5 Appendix 145 5.1 The AgPXL1 deletion and overexpression strains show septation defects 145 5.2 AgPrk1 is essential in A. gossypii 146 6 Abbreviations 149 7 Anlage 1 151 8 Danksagung 153 1 Summary 1 Summary Spore formation is an essential step in the fungal life cycle that contributes to the dispersal of the organism and also to survival under harsh environmental conditions. -
Genome Sequence of the Lignocellulose-Bioconverting and Xylose-Fermenting Yeast Pichia Stipitis
ARTICLES Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis Thomas W Jeffries1,2,8, Igor V Grigoriev3,8, Jane Grimwood4, Jose´ M Laplaza1,5, Andrea Aerts3, Asaf Salamov3, Jeremy Schmutz4, Erika Lindquist3, Paramvir Dehal3, Harris Shapiro3, Yong-Su Jin6, Volkmar Passoth7 & Paul M Richardson3 Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. http://www.nature.com/naturebiotechnology The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions. Xylose is a five-carbon sugar abundant in hardwoods and agri- RESULTS cultural residues1, so its fermentation is essential for the economic The 15.4-Mbp genome of P. stipitis was sequenced using a shotgun conversion of lignocellulose to ethanol2. Pichia stipitis Pignal (1967) is approach and finished to high quality (o1 error in 100,000). The a haploid, homothallic, hemiascomycetous yeast3,4 that has the eight chromosomes range in size from 3.5 to 0.97 Mbp, as previously highest native capacity for xylose fermentation of any known reported16. -
NGS Catalog: a Database of Next Generation Sequencing Studies in Humans
HUMAN MUTATION Database in Brief 33: E2341-E2355 (2012) Online DATABASE IN BRIEF HUMAN MUTATION OFFICIAL JOURNAL NGS Catalog: A Database of Next Generation Sequencing Studies in Humans www.hgvs.org Junfeng Xia1,†, Qingguo Wang1,†, Peilin Jia1, Bing Wang1, William Pao2,3, and Zhongming Zhao1,3,4,* 1Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA,2Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA,3Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA,4Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA †These authors contributed equally to this work. *Correspondence to Zhongming Zhao, Ph.D., Department of Biomedical Informatics, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, Nashville, TN, 37203, USA; Phone: +1-615-343-9158; FAX: +1-615-936-8545; E-mail: [email protected]. Contract grant sponsor: This study was partially supported by the Stand Up To Cancer-American Association for Cancer Research Innovative Research Grant (SU2C-AACR-IRG0109) and the VICC Cancer Center Core grant P30CA68485 from National Institutes of Health. Communicated by Johan T. den Dunnen ABSTRACT: Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. -
Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases LÁSZLÓ G
Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases LÁSZLÓ G. NAGY,1 RENÁTA TÓTH,2 ENIKŐ KISS,1 JASON SLOT,3 ATTILA GÁCSER,2 and GÁBOR M. KOVÁCS4,5 1Synthetic and Systems Biology Unit, Institute of Biochemistry, HAS, Szeged, Hungary; 2Department of Microbiology, University of Szeged, Szeged, Hungary; 3Department of Plant Pathology, Ohio State University, Columbus, OH 43210; 4Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary; 5Plant Protection Institute, Center for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary ABSTRACT The fungal lineage is one of the three large provides an overview of some of the most important eukaryotic lineages that dominate terrestrial ecosystems. fungal traits, how they evolve, and what major genes They share a common ancestor with animals in the eukaryotic and gene families contribute to their development. The supergroup Opisthokonta and have a deeper common ancestry traits highlighted here represent just a sample of the with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among characteristics that have evolved in fungi, including po- all living organisms. This article provides an overview of some of larized multicellular growth, fruiting body development, the most important fungal traits, how they evolve, and what dimorphism, secondary metabolism, wood decay, and major genes and gene families contribute to their development. mycorrhizae. However, a great deal of other important The traits highlighted here represent just a sample of the traits also underlie the evolution of the taxonomically characteristics that have evolved in fungi, including polarized and phenotypically hyperdiverse fungal kingdom, which multicellular growth, fruiting body development, dimorphism, could fill up a volume on its own. -
A New Entrez Database Transitioning from Locuslink to Entrez
NCBI News National Center for Biotechnology Information National Library of Medicine National Institutes of Health Spring 2004 Department of Health and Human Services Transitioning from LocusLink to Entrez Gene Cancer Chromosomes: a New Entrez Database A gene-based view of annotated The Entrez Gene help document genomes is essential to capitalize on provides tips to ease the transition Three databases, the NCI/NCBI the increase in the sequencing and for LocusLink users to the current SKY (Spectral Karyotyping)/M- analysis of model genomes. The Entrez Gene database. FISH (Multiplex-FISH) and CGH Entrez Gene database has been (Comparative Genomic The default display format for developed to supply key connections Hybridization) Database, the NCI Entrez Gene is the graphics display between maps, sequences, expression Mitelman Database of Chromosome shown in Figure 1 for BMP7, which profiles, structure, function, homolo- Aberrations in Cancer, and the NCI resembles the traditional view of a gy data, and the scientific literature. Recurrent Chromosome Aberrations LocusLink record. The array of col- Unique identifiers are assigned to in Cancer databases are now integrat- ored boxes at the head of LocusLink genes with defining sequence, genes ed into NCBI’s Entrez system as the reports that provide links to gene- with known map positions, and “Cancer Chromosomes” database. related resources is replaced by the genes inferred from phenotypic Cancer Chromosomes supports “Links” menu in Gene, which information. These gene identifiers searches for cytogenetic, clinical, or includes additional links, such as are tracked, and functional informa- reference information using the flexi- those to Books, GEO, UniSTS, and tion is added when available.