Crystal Structures of the 43 Kda Atpase Domain of Xanthomonas Oryzae Pv. Oryzae Topoisomerase IV Pare Subunit and Its Complex with Novobiocin
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Seres Health, 160 First Street Suite 1A, Cambridge MA 02142 1
Genetics: Early Online, published on September 27, 2013 as 10.1534/genetics.113.152306 1 Tolerance of Escherichia coli to fluoroquinolone antibiotics depends on specific 2 components of the SOS response pathway 3 4 Alyssa Theodore, Kim Lewis, Marin Vulić1 5 Antimicrobial Discovery Center, Department of Biology, Northeastern University, 6 Boston, Massachusetts 02115 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 1Present Address: Seres Health, 160 First Street Suite 1A, Cambridge MA 02142 1 Copyright 2013. 32 Fluoroquinolone Tolerance in Escherichia coli 33 34 Keywords: SOS response, Persisters, Tolerance, DNA repair, fluoroquinolones 35 36 Corresponding Author: 37 Marin Vulić 38 Current Address: Seres Health 39 160 First Street Suite 1A 40 Cambridge MA 02142 41 [email protected] 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 2 65 ABSTRACT 66 67 Bacteria exposed to bactericidal fluoroquinolone (FQ) antibiotics can survive without 68 becoming genetically resistant. Survival of these phenotypically resistant cells, 69 commonly called persisters, depends on the SOS gene network. We have examined 70 mutants in all known SOS-regulated genes to identify functions essential for tolerance in 71 Escherichia coli. The absence of DinG and UvrD helicases and Holliday junction 72 processing enzymes RuvA and RuvB lead to a decrease in survival. Analysis of the 73 respective mutants indicates that in addition to repair of double strand breaks, tolerance 74 depends on the repair of collapsed replication forks and stalled transcription complexes. -
Management of E. Coli Sister Chromatid Cohesion in Response to Genotoxic Stress
ARTICLE Received 1 Oct 2016 | Accepted 13 Jan 2017 | Published 6 Mar 2017 DOI: 10.1038/ncomms14618 OPEN Management of E. coli sister chromatid cohesion in response to genotoxic stress Elise Vickridge1,2,3, Charlene Planchenault1, Charlotte Cockram1, Isabel Garcia Junceda1 & Olivier Espe´li1 Aberrant DNA replication is a major source of the mutations and chromosomal rearrange- ments associated with pathological disorders. In bacteria, several different DNA lesions are repaired by homologous recombination, a process that involves sister chromatid pairing. Previous work in Escherichia coli has demonstrated that sister chromatid interactions (SCIs) mediated by topological links termed precatenanes, are controlled by topoisomerase IV. In the present work, we demonstrate that during the repair of mitomycin C-induced lesions, topological links are rapidly substituted by an SOS-induced sister chromatid cohesion process involving the RecN protein. The loss of SCIs and viability defects observed in the absence of RecN were compensated by alterations in topoisomerase IV, suggesting that the main role of RecN during DNA repair is to promote contacts between sister chromatids. RecN also modulates whole chromosome organization and RecA dynamics suggesting that SCIs significantly contribute to the repair of DNA double-strand breaks (DSBs). 1 Center for Interdisciplinary Research in Biology (CIRB), Colle`ge de France, UMR CNRS-7241, INSERM U1050, PSL Research University, 11 place Marcelin Berthelot, 75005 Paris, France. 2 Universite´ Paris-Saclay, 91400 Orsay, France. 3 Ligue Nationale Contre le Cancer, 75013 Paris, France. Correspondence and requests for materials should be addressed to O.E. (email: [email protected]). NATURE COMMUNICATIONS | 8:14618 | DOI: 10.1038/ncomms14618 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14618 ll cells must accurately copy and maintain the integrity of or cohesin-like activities26,27. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
Molecular and Immunological Sd0100025 Characterization of Mycobacteria Associated with Bovine Farcy
MOLECULAR AND IMMUNOLOGICAL SD0100025 CHARACTERIZATION OF MYCOBACTERIA ASSOCIATED WITH BOVINE FARCY. Thesis submitted in accordance with requirements of the University of Khartoum for the Degree of Doctor of Philosophy (Ph.D). By Victor Loku Kwajok B.V.Med. 1978, University of Cairo/Egypt. M.V.Sc.1992, University of Khartoum/Sudan. Supervisor: Dr. Maowia M. Mukhtar. Institute of Endemic Diseases, University of Khartoum. Department of Preventive Medicine and Veterinary Public Health. Faculty of Veterinary Science, University of Khartoum. 2000. 32/27 SOME PAGES ARE MISSING IN THE ORIGINAL DOCUMENT LIST OF CONTENTS DEDICATION. * ii v ACKNOWLEDGEMENTS vi ABBREVIATIONS viii ABSTRACT. xi CHAPTER ONE. REVIEW OF LITERATURE. 1. General Introduction. 1. 1.1. Molecular Systematics of genus Mycobacterium. 2. 1.2. Molecular taxonomy of M. farcinogenese and M. senegalense 11. 1.3. Immunology of bovine farcy agents. 36. CHAPTER TWO. MATERIALS AND METHODOLOGY 41. Isolation, identification and characterization of M. farcinogenes. 2.1 Phenotypic characterization. 41. 2.1.1. Morphological and biochemical tests. 2.1.2. Degradation tests. 2.1.3. Rapid fluorogenic enzyme tests. 2.1.4. Nutritional tests. 2.1.5. Physiological tests. 2.2. Molecular characterization. 52. 2.2.1. DNA extraction and purification 2.2.2. PCR amplification and application. 2.2.3. DNA sequencing of 16SrDNA. 2.2.4. PCR-based restriction fragment length polymorphism. 2.3 Imrmmological analyses of bovine farcy agents. 71. 2.3.1 .EL1SA technique for sera diagnosis. 2.3.2 Animal pathogenicity Tests. 2.3.3 Protein antigen profiles determination using. CHAPTER THREE: RESULTS. 78. CHAPTER. FOUR: DISCUSSION. 124. REFERENCES. 133. -
Supporting Information
Supporting Information Barshis et al. 10.1073/pnas.1210224110 SI Materials and Methods and “ssu-parc.fasta” downloaded on September 14, 2011 from mRNA Extraction. Total RNA was extracted from each sample www.arb-silva.de), and potential Symbiodinium contamination using a modified TRIzol (GibcoBRL/Invitrogen) protocol. Ap- was removed based significant nucleotide similarity (BLASTN, proximately 150–200 mg of coral tissue and skeleton was placed ≥100 bp and ≥70% identity) to ESTs from Symbiodinium sp. in 1 mL of TRIzol and homogenized for 2 min by vortexing with KB8 (clade A) and Symbiodinium sp. MF1.04b (clade B) (6) ∼100 μL of 0.5-mm Zirconia/Silica Beads (BioSpec Products). and the related dinoflagellate Polarella glacialis. Finally, the re- Resulting tissue/TRIzol slurry was removed by centrifugation, sulting contigs were compared (via BLASTX) to the NCBI non- and the standard TRIzol extraction was performed according to redundant protein database (nr; downloaded on June 7, 2011 manufacturer’s specifications with the replacement of 250 μLof from www.ncbi.nlm.nih.gov). The nonredundant (nr) results were 100% (vol/vol) isopropanol with 250 μL of high-salt buffer (0.8 used to remove any additional sequences likely to be noncoral, M Na citrate, 1.2 M NaCl) during the final precipitation step. based on similarity to alveolates, fungi, bacteria, or Archaea, as Resulting RNA pellet was resuspended in 12 μL of diethylpyro- determined using the metagenome analyzer (MEGAN) Version 4 = = = carbonate (DEPC)-treated H2O. mRNA was isolated from total (min. support 1, min. score 200, top percent 20) (7). RNA using the Micro-FastTrack mRNA isolation kit (In- The remaining, putatively coral, contigs were then “meta- vitrogen) and an overnight precipitation at −80 °C. -
Interaction of Silver Atomic Quantum Clusters With
Chemical Volume 6 Number 12 December 2015 Pages 6681–7356 Science www.rsc.org/chemicalscience ISSN 2041-6539 EDGE ARTICLE B. García, F. Dominguez et al. Interaction of silver atomic quantum clusters with living organisms: bactericidal eff ect of Ag3 clusters mediated by disruption of topoisomerase–DNA complexes Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Interaction of silver atomic quantum clusters with living organisms: bactericidal effect of Ag3 clusters Cite this: Chem. Sci.,2015,6,6717 mediated by disruption of topoisomerase–DNA complexes† a b a b a b J. Neissa,‡ C. Perez-Arnaiz,´ ‡ V. Porto, N. Busto, E. Borrajo, J. M. Leal, c b a M. A. Lopez-Quintela,´ B. Garc´ıa* and F. Dominguez* Essential processes for living cells such as transcription and replication depend on the formation of specific protein–DNA recognition complexes. Proper formation of such complexes requires suitable fitting between the protein surface and the DNA surface. By adopting doxorubicin (DOX) as a model probe, we report here that Ag3 atomic quantum clusters (Ag-AQCs) inhibit the intercalation of DOX into DNA and have considerable influence on the interaction of DNA-binding proteins such as topoisomerase IV, Escherichia coli DNA gyrase and the restriction enzyme HindIII. Ag-AQCs at nanomolar Creative Commons Attribution-NonCommercial 3.0 Unported Licence. concentrations inhibit enzyme activity. The inhibitory effect of Ag-AQCs is dose-dependent and occurs by intercalation into DNA. All these effects, not observed in the presence of Ag+ ions, can explain the Received 5th June 2015 powerful bactericidal activity of Ag-AQCs, extending the knowledge of silver bactericidal properties. -
Antibiotic Sensitivity of Bacterial Pathogens Isolated from Bovine Mastitis Milk
Content of Research Report A. Project title: Antibiotic Sensitivity of Bacterial Pathogens Isolated From Bovine Mastitis Milk B. Abstract: Antibiotic sensitivity of bacteria isolated from bovine milk samples was investigated. The 18 antibiotics that were evaluated (e.g., penicillin, novobiocin, gentamicin) are commonly used to treat various diseases in cattle, including mastitis, an inflammation of the udder of dairy cows. A common concern in using antibiotics is the increase in drug resistance with time. This project studies if antibiotic resistance is a threat to consumers of raw milk products and if these antibiotics are still effective against mastitis pathogens. The study included isolating and culturing bacteria from quarter milk samples (n=205) collected from mastitic dairy cows from farms in Chino and Ontario, CA. The isolated bacteria were tested for sensitivity to antibiotics using the Kirby Bauer disk diffusion method. The prevalence (%) of resistance to the individual antibiotics was reported. Resistance to penicillin was 45% which may support previous data on penicillin-resistant bacteria, especially Staphylococcus and Streptococcus. Resistance rates (%) for oxytetracycline (26.8%) and tetracycline (22.9%) were low compared to previous studies but a trend was seen in our results that may support concerns of emerging resistance to tetracyclines in both gram- positive and gram-negative bacteria. Similarly, 31.9% of bacterial isolates showed resistance to erythromycin which is at least 30% less than in reported literature concerning emerging resistance to macrolides. More numbers (%) that should be noted are cefazolin (26.3%), ampicillin (29.7%), novobiocin (33.0%), polymyxin B (31.5%), and resistance ranging from 9 18% for the other antibiotics. -
Unexpected Drug Residuals in Human Milk in Ankara, Capital of Turkey Ayşe Meltem Ergen1 and Sıddıka Songül Yalçın2*
Ergen and Yalçın BMC Pregnancy and Childbirth (2019) 19:348 https://doi.org/10.1186/s12884-019-2506-1 RESEARCH ARTICLE Open Access Unexpected drug residuals in human milk in Ankara, capital of Turkey Ayşe Meltem Ergen1 and Sıddıka Songül Yalçın2* Abstract Background: Breast milk is a natural and unique nutrient for optimum growth and development of the newborn. The aim of this study was to investigate the presence of unpredictable drug residues in mothers’ milk and the relationship between drug residues and maternal-infant characteristics. Methods: In a descriptive study, breastfed infants under 3 months of age and their mothers who applied for child health monitoring were enrolled for the study. Information forms were completed for maternal-infant characteristics, breastfeeding problems, crying and sleep characteristics of infants. Maternal and infant anthropometric measurements and maternal milk sample were taken. Edinburgh Postpartum Depression Scale was applied to mothers. RANDOX Infiniplex kit for milk was used for residual analysis. Results: Overall, 90 volunteer mothers and their breastfed infants were taken into the study and the mean age of the mothers and their infants was 31.5 ± 4.2 years and 57.8 ± 18.1 days, respectively. Anti-inflammatory drug residues in breast milk were detected in 30.0% of mothers and all had tolfenamic acid. Overall, 94.4% had quinolone, 93.3% beta-lactam, 31.1% aminoglycoside and 13.3% polymycin residues. Drugs used during pregnancy or lactation period were not affected by the presence of residues. Edinburgh postpartum depression scores of mothers and crying and sleeping problems of infants were similar in cases with and without drug residues in breast milk. -
Fostering Research Into Antimicrobial Resistance in India
ANTIMICROBIAL RESISTANCE IN SOUTH EAST ASIA Fostering research into antimicrobial resistance BMJ: first published as 10.1136/bmj.j3535 on 6 September 2017. Downloaded from in India Bhabatosh Das and colleagues discuss research and development of new antimicrobials and rapid diagnostics, which are crucial for tackling antimicrobial resistance in India ndia is among the world’s largest Box 1: Examples of the impact of antimicrobial resistance research and interventions consumers of antibiotics.1 The efficacy globally of several antibiotics is threatened by the emergence of resistant microbial • In 2011, the Chinese Ministry of Health implemented a campaign for rational use of pathogens. Multiple factors, such antibiotics in healthcare, accompanied by supervision audits and inspections. Over a year, Ias a high burden of disease, poor public superfluous prescription of antimicrobials was reduced by 10-12% for patients in hospital 45 health infrastructure, rising incomes, and and for outpatients, as were drug sales for antimicrobials. unregulated sales of cheap antibiotics, • The Swedish Strategic Programme against Antibiotic Resistance (STRAMA) led to a decrease have amplified the crisis of antimicrobial in antibiotic use for outpatients from 15.7 to 12.6 daily doses per 1000 inhabitants and from resistance (AMR) in India.2 536 to 410 prescriptions per 1000 inhabitants per year from 1995 to 2004.6 The decrease The Global Action Plan on AMR was most evident for macrolides (65%) emphasises the need to increase • The effect of WHO essential medicines policies was studied in 55 countries. These policies knowledge through surveillance and were linked to reductions in antibiotic use of ≥20% in upper respiratory tract infections. -
Anew Drug Design Strategy in the Liht of Molecular Hybridization Concept
www.ijcrt.org © 2020 IJCRT | Volume 8, Issue 12 December 2020 | ISSN: 2320-2882 “Drug Design strategy and chemical process maximization in the light of Molecular Hybridization Concept.” Subhasis Basu, Ph D Registration No: VB 1198 of 2018-2019. Department Of Chemistry, Visva-Bharati University A Draft Thesis is submitted for the partial fulfilment of PhD in Chemistry Thesis/Degree proceeding. DECLARATION I Certify that a. The Work contained in this thesis is original and has been done by me under the guidance of my supervisor. b. The work has not been submitted to any other Institute for any degree or diploma. c. I have followed the guidelines provided by the Institute in preparing the thesis. d. I have conformed to the norms and guidelines given in the Ethical Code of Conduct of the Institute. e. Whenever I have used materials (data, theoretical analysis, figures and text) from other sources, I have given due credit to them by citing them in the text of the thesis and giving their details in the references. Further, I have taken permission from the copyright owners of the sources, whenever necessary. IJCRT2012039 International Journal of Creative Research Thoughts (IJCRT) www.ijcrt.org 284 www.ijcrt.org © 2020 IJCRT | Volume 8, Issue 12 December 2020 | ISSN: 2320-2882 f. Whenever I have quoted written materials from other sources I have put them under quotation marks and given due credit to the sources by citing them and giving required details in the references. (Subhasis Basu) ACKNOWLEDGEMENT This preface is to extend an appreciation to all those individuals who with their generous co- operation guided us in every aspect to make this design and drawing successful. -
Cytoplasmic Localized Ubiquitin Ligase Cullin 7 Binds to P53 and Promotes Cell Growth by Antagonizing P53 Function
Oncogene (2006) 25, 4534–4548 & 2006 Nature Publishing Group All rights reserved 0950-9232/06 $30.00 www.nature.com/onc ORIGINAL ARTICLE Cytoplasmic localized ubiquitin ligase cullin 7 binds to p53 and promotes cell growth by antagonizing p53 function P Andrews1,2,YJHe1 and Y Xiong1,2,3 1Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA; 2Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA and 3Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC, USA Cullins are a family of evolutionarily conserved proteins monomeric manner (monoubiquitination) to cause that bind to the small RING fingerprotein,ROC1, to conformational change to the substrate or in a constitute potentially a large number of distinct E3 polyubiquitin chain which signals the substrate to be ubiquitin ligases. CUL7 mediates an essential function degraded by the 26S proteasome. Both ubiquitin formouse embryodevelopment and has been linked with activating and conjugating enzymes are well character- cell transformation by its physical association with the ized and contain highly conserved functional domains. SV40 large T antigen. We report here that, like its closely The identity and mechanism of E3 ubiquitin ligases, on related homolog PARC, CUL7 is localized predominantly the other hand, has been elusive and long postulated as in the cytoplasm and binds directly to p53. In contrast to an activity responsible for both recognizing substrates PARC, however, CUL7, even when overexpressed, did not and for catalysing polyubiquitin chain formation sequesterp53 in the cytoplasm. We have identified a (Hershko and Ciechanover, 1998). sequence in the N-terminal region of CUL7 that is highly Currently, two major families of E3 ligases have been conserved in PARC and a sequence spanning the described. -
Visual Data Mining : Background, Techniques, and Drug Discovery
Visual Data Mining: Background, Techniques, and Drug Discovery Applications Mihael Ankerst The Boeing Company Georges Grinstein UMass Lowell and AnVil Inc. Daniel Keim AT&T Research and University of Konstanz A color version of the tutorial notes can be found via http://www.fmi.uni-konstanz.de/~keim KDD’2002 Conference Emails and URLs Data Exploration • Definition Mihael Ankerst – [email protected] Data Exploration is the process of searching and analyzing – http://www.visualclassification.com/ankerst databases to find implicit but potentially useful information Daniel A. Keim – [email protected] • more formally – [email protected] Data Exploration is the process of finding a – http://www.fmi.uni-konstanz.de/~keim • subset D‘ of the database D and George Grinstein – [email protected] • hypotheses Hu(D‘,C) – http://genome.uml.edu that a user U considers useful in an application context C – http://www.anvilinfo.com Mihael Ankerst, The Boeing Company -- Daniel A. Keim, AT&T and Univ. of Konstanz Mihael Ankerst, The Boeing Company -- Daniel A. Keim, AT&T and Univ. of Konstanz Georges Grinstein, UMass Lowell and AnVil Inc. 2 Georges Grinstein, UMass Lowell and AnVil Inc. 5 Overview Abilities of Humans and Computers Part I: Visualization Techniques 1. Introduction 2. Visual Data Exploration Techniques abilities of Data Storage 3. Distortion and Interaction Techniques the computer Numerical Computation 4. Visual Data Mining Systems Searching Part II: Specific Visual Data Mining Techniques 1. Association Rules Planning 2. Classification Diagnosis Logic 3. Clustering Prediction 4. Text Mining 5. Tightly Integrated Visualization Perception Part III: Drug Discovery Applications Creativity 1.