Neo-Formation of Chromosomes in Bacteria
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Characterization of Stress Tolerance and Metabolic Capabilities of Acidophilic Iron-Sulfur-Transforming Bacteria and Their Relevance to Mars
Characterization of stress tolerance and metabolic capabilities of acidophilic iron-sulfur-transforming bacteria and their relevance to Mars Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften – Dr. rer. nat. – vorgelegt von Anja Bauermeister aus Leipzig Im Fachbereich Chemie der Universität Duisburg-Essen 2012 Die vorliegende Arbeit wurde im Zeitraum von März 2009 bis Dezember 2012 im Arbeitskreis von Prof. Dr. Hans-Curt Flemming am Biofilm Centre (Fakultät für Chemie) der Universität Duisburg-Essen und in der Abteilung Strahlenbiologie (Institut für Luft- und Raumfahrtmedizin, Deutsches Zentrum für Luft- und Raumfahrt, Köln) durchgeführt. Tag der Einreichung: 07.12.2012 Tag der Disputation: 23.04.2013 Gutachter: Prof. Dr. H.-C. Flemming Prof. Dr. W. Sand Vorsitzender: Prof. Dr. C. Mayer Erklärung / Statement Hiermit versichere ich, dass ich die vorliegende Arbeit mit dem Titel „Characterization of stress tolerance and metabolic capabilities of acidophilic iron- sulfur-transforming bacteria and their relevance to Mars” selbst verfasst und keine außer den angegebenen Hilfsmitteln und Quellen benutzt habe, und dass die Arbeit in dieser oder ähnlicher Form noch bei keiner anderen Universität eingereicht wurde. Herewith I declare that this thesis is the result of my independent work. All sources and auxiliary materials used by me in this thesis are cited completely. Essen, 07.12.2012 Table of contents Abbreviations ....................................................................................... -
FUNCTIONAL STUDIES on Csis and Csps
FUNCTIONAL STUDIES ON CSIs AND CSPs FUNCTIONAL SIGNIFICANCE OF NOVEL MOLECULAR MARKERS SPECIFIC FOR DEINOCOCCUS AND CHLAMYDIAE SPECIES BY F M NAZMUL HASSAN, B.Sc. A Thesis Submitted to the School of Graduate Studies in Partial Fulfillment of the Requirements for the Degree Master of Science McMaster University © Copyright by F M Nazmul Hassan, December, 2017 MASTER OF SCIENCE (2017) McMaster University (Biochemistry) Hamilton, Ontario TITLE: Functional Significance of Novel Molecular Markers Specific for Deinococcus and Chlamydiae Species AUTHOR: F M Nazmul Hassan, B.Sc. (Khulna University) SUPERVISOR: Professor Radhey S. Gupta NUMBER OF PAGES: xv, 108 ii This thesis is dedicated to my mom and dad. I lost my mother when I was a high school student. She always liked to share stories about science and inspired me to do something for the beneficial of human being. Her dream was guided by my father. I was always encouraged by my father to do higher education. I have lost my father this year. It was most critical moment of my life. But, I have continued to do research because of fulfill his dream. iii THESIS ABSTRACT The Deinococcus species are highly resistant to oxidation, desiccation, and radiation. Very few characteristics explain these unique features of Deinococcus species. This study reports the results of detailed comparative genomics, structural and protein-protein interactions studies on the DNA repair proteins from Deinococcus species. Comparative genomics studies have identified a large number of conserved signature indels (CSIs) in the DNA repair proteins that are specific for Deinococcus species. In parallel, I have carried out the structural and protein-protein interactions studies of CSIs which are present in nucleotide excision repair (NER), UV damage endonuclease (UvsE)-dependent excision repair (UVER) and homologous recombination (HR) pathways proteins. -
Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3. -
Universidade Estadual De Campinas Instituto De Biologia
UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso. -
Experimental and Statistical Analysis of Nutritional Requirements for the Growth of the Extremophile Deinococcus Geothermalis DSM 11300
Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300 Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gorret To cite this version: Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gor- ret. Experimental and statistical analysis of nutritional requirements for the growth of the ex- tremophile Deinococcus geothermalis DSM 11300. Extremophiles, Springer Verlag, 2014, 18 (6), pp.1009-1021. 10.1007/s00792-014-0671-8. hal-01268947 HAL Id: hal-01268947 https://hal.archives-ouvertes.fr/hal-01268947 Submitted on 11 Mar 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible This is an author’s version published in: http://oatao.univ-toulouse.fr/22999 Official URL: https://doi.org/10.1007/s00792-014-0671-8 To cite this version: Bornot, Julie and Aceves-Lara, César-Arturo and Molina-Jouve, Carole and Uribelarrea, Jean-Louis and Gorret, Nathalie Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300. -
Molecular Subtypes of Diffuse Large B-Cell Lymphoma Arise by Distinct Genetic Pathways
Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways Georg Lenza, George W. Wrightb, N. C. Tolga Emrea, Holger Kohlhammera, Sandeep S. Davea, R. Eric Davisa, Shannon Cartya, Lloyd T. Lama, A. L. Shaffera, Wenming Xiaoc, John Powellc, Andreas Rosenwaldd, German Ottd,e, Hans Konrad Muller-Hermelinkd, Randy D. Gascoynef, Joseph M. Connorsf, Elias Campog, Elaine S. Jaffeh, Jan Delabiei, Erlend B. Smelandj,k, Lisa M. Rimszal, Richard I. Fisherm,n, Dennis D. Weisenburgero, Wing C. Chano, and Louis M. Staudta,q aMetabolism Branch, bBiometric Research Branch, cCenter for Information Technology, and hLaboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892; dDepartment of Pathology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany; eDepartment of Clinical Pathology, Robert-Bosch-Krankenhaus, 70376 Stuttgart, Germany; fBritish Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4E6; gHospital Clinic, University of Barcelona, 08036 Barcelona, Spain; iPathology Clinic and jInstitute for Cancer Research, Rikshospitalet Hospital, Oslo, Norway; kCentre for Cancer Biomedicine, Faculty Division the Norwegian Radium Hospital, N-0310, Oslo, Norway; lDepartment of Pathology, University of Arizona, Tucson, AZ 85724; mSouthwest Oncology Group, 24 Frank Lloyd Wright Drive, Ann Arbor, MI 48106 ; nJames P. Wilmot Cancer Center, University of Rochester, Rochester, NY 14642; and oDepartments of Pathology and Microbiology, University of Nebraska, Omaha, NE 68198 Edited by Ira -
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A Tertiary-Branched Tetra-Amine, N4-Aminopropylspermidine Is A
Journal of Japanese Society for Extremophiles (2010) Vol.9 (2) Journal of Japanese Society for Extremophiles (2010) Vol. 9 (2), 75-77 ORIGINAL PAPER a a b Hamana K , Hayashi H and Niitsu M NOTE 4 A tertiary-branched tetra-amine, N -aminopropylspermidine is a major cellular polyamine in an anaerobic thermophile, Caldisericum exile belonging to a new bacterial phylum, Caldiserica a Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan. b Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0290, Japan. Corresponding author: Koei Hamana, [email protected] Phone: +81-27-234-4611, Fax: +81-27-234-4611 Received: November 17, 2010 / Revised: December 8, 2010 /Accepted: December 8, 2010 Abstract Acid-extractable cellular polyamines of Anaerobic, moderately thermophilic, filamentous, thermophilic Caldisericum exile belonging to a new thiosulfate-reducing Caldisericum exile was isolated bacterial phylum, Caldiserica were analyzed by HPLC from a terrestrial hot spring in Japan for the first and GC. The coexistence of an unusual tertiary cultivated representative of the candidate phylum OP5 4 brancehed tetra-amine, N -aminopropylspermidine with and located in the newly validated bacterial phylum 19,20) spermine, a linear tetra-amine, as the major polyamines Caldiserica (order Caldisericales) . The in addition to putrescine and spermidine, is first reported temperature range for growth is 55-70°C, with the 20) in the moderate thermophile isolated from a terrestrial optimum growth at 65°C . The optimum growth 20) hot spring in Japan. Linear and branched penta-amines occurs at pH 6.5 and with the absence of NaCl . T were not detected. -
Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
Tyrosine Kinase Oncogenes in Normal Hematopoiesis and Hematological Disease
Oncogene (2002) 21, 3314 ± 3333 ã 2002 Nature Publishing Group All rights reserved 0950 ± 9232/02 $25.00 www.nature.com/onc Tyrosine kinase oncogenes in normal hematopoiesis and hematological disease Blanca Scheijen1,2 and James D Grin*,1,2 1Department of Adult Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts, MA 02115, USA; 2Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA Tyrosine kinase oncogenes are formed as a result of Adaptors do not contain intrinsic catalytic activity but mutations that induce constitutive kinase activity. Many consist of independent functioning interaction modules of these tyrosine kinase oncogenes that are derived from like SH2-domain (mediates binding to phosphotyrosine genes, such as c-Abl, c-Fes, Flt3, c-Fms, c-Kit and residues), SH3-domain (interacts with polyproline-rich PDGFRb, that are normally involved in the regulation of PXXP stretch) or pleckstrin homology (PH) domain hematopoiesis or hematopoietic cell function. Despite (binds to inositol lipids). dierences in structure, normal function, and subcellular The ®rst tyrosine kinase oncogene associated with location, many of the tyrosine kinase oncogenes signal human hematologic disease, Bcr ± Abl, was identi®ed through the same pathways, and typically enhance almost twenty years ago, and there is now evidence for proliferation and prolong viability. They represent involvement of multiple tyrosine kinase oncogenes in excellent potential drug targets, and it is likely that acute and chronic leukemias, lymphomas, and myelo- additional mutations will be identi®ed in other kinases, mas. In each case, the tyrosine kinase activity of the their immediate downstream targets, or in proteins oncogene is constitutively activated by mutations that regulating their function. -
A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules Natasha L
www.nature.com/scientificreports OPEN A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules Natasha L. Patel-Murray1, Miriam Adam2, Nhan Huynh2, Brook T. Wassie2, Pamela Milani2 & Ernest Fraenkel 2,3* High-throughput screening and gene signature analyses frequently identify lead therapeutic compounds with unknown modes of action (MoAs), and the resulting uncertainties can lead to the failure of clinical trials. We developed an approach for uncovering MoAs through an interpretable machine learning model of transcriptomics, epigenomics, metabolomics, and proteomics. Examining compounds with benefcial efects in models of Huntington’s Disease, we found common MoAs for compounds with unrelated structures, connectivity scores, and binding targets. The approach also predicted highly divergent MoAs for two FDA-approved antihistamines. We experimentally validated these efects, demonstrating that one antihistamine activates autophagy, while the other targets bioenergetics. The use of multiple omics was essential, as some MoAs were virtually undetectable in specifc assays. Our approach does not require reference compounds or large databases of experimental data in related systems and thus can be applied to the study of agents with uncharacterized MoAs and to rare or understudied diseases. Unknown modes of action of drug candidates can lead to unpredicted consequences on efectiveness and safety. Computational methods, such as the analysis of gene signatures, and high-throughput experimental methods have accelerated the discovery of lead compounds that afect a specifc target or phenotype1–3. However, these advances have not dramatically changed the rate of drug approvals. Between 2000 and 2015, 86% of drug can- didates failed to earn FDA approval, with toxicity or a lack of efcacy being common reasons for their clinical trial termination4,5. -
Anti-GRAP Antibody (ARG63124)
Product datasheet [email protected] ARG63124 Package: 100 μg anti-GRAP antibody Store at: -20°C Summary Product Description Goat Polyclonal antibody recognizes GRAP Tested Reactivity Hu Predict Reactivity Ms, Rat, Cow Tested Application WB Host Goat Clonality Polyclonal Isotype IgG Target Name GRAP Antigen Species Human Immunogen C-GFFPRSYVQPVHL Conjugation Un-conjugated Alternate Names GRB2-related adapter protein Application Instructions Application table Application Dilution WB 0.3 - 1 µg/ml Application Note WB: Recommend incubate at RT for 1h. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 25 kDa Properties Form Liquid Purification Purified from goat serum by ammonium sulphate precipitation followed by antigen affinity chromatography using the immunizing peptide. Buffer Tris saline (pH 7.3), 0.02% Sodium azide and 0.5% BSA Preservative 0.02% Sodium azide Stabilizer 0.5% BSA Concentration 0.5 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/2 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Database links GeneID: 10750 Human Swiss-port # Q13588 Human Background This gene encodes a member of the GRB2/Sem5/Drk family and functions as a cytoplasmic signaling protein which contains an SH2 domain flanked by two SH3 domains.