PADLS User Guide
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Phylogenetic Analysis Reveals an Ancient Gene Duplication As The
1 Phylogenetic analysis reveals an ancient gene duplication as 2 the origin of the MdtABC efflux pump. 3 4 Kamil Górecki1, Megan M. McEvoy1,2,3 5 1Institute for Society & Genetics, 2Department of MicroBiology, Immunology & Molecular 6 Genetics, and 3Molecular Biology Institute, University of California, Los Angeles, CA 90095, 7 United States of America 8 Corresponding author: [email protected] (M.M.M.) 9 1 10 Abstract 11 The efflux pumps from the Resistance-Nodulation-Division family, RND, are main 12 contributors to intrinsic antibiotic resistance in Gram-negative bacteria. Among this family, the 13 MdtABC pump is unusual by having two inner membrane components. The two components, 14 MdtB and MdtC are homologs, therefore it is evident that the two components arose by gene 15 duplication. In this paper, we describe the results obtained from a phylogenetic analysis of the 16 MdtBC pumps in the context of other RNDs. We show that the individual inner membrane 17 components (MdtB and MdtC) are conserved throughout the Proteobacterial species and that their 18 existence is a result of a single gene duplication. We argue that this gene duplication was an ancient 19 event which occurred before the split of Proteobacteria into Alpha-, Beta- and Gamma- classes. 20 Moreover, we find that the MdtABC pumps and the MexMN pump from Pseudomonas aeruginosa 21 share a close common ancestor, suggesting the MexMN pump arose by another gene duplication 22 event of the original Mdt ancestor. Taken together, these results shed light on the evolution of the 23 RND efflux pumps and demonstrate the ancient origin of the Mdt pumps and suggest that the core 24 bacterial efflux pump repertoires have been generally stable throughout the course of evolution. -
Metabolic and Genetic Basis for Auxotrophies in Gram-Negative Species
Metabolic and genetic basis for auxotrophies in Gram-negative species Yara Seifa,1 , Kumari Sonal Choudharya,1 , Ying Hefnera, Amitesh Ananda , Laurence Yanga,b , and Bernhard O. Palssona,c,2 aSystems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122; bDepartment of Chemical Engineering, Queen’s University, Kingston, ON K7L 3N6, Canada; and cNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark Edited by Ralph R. Isberg, Tufts University School of Medicine, Boston, MA, and approved February 5, 2020 (received for review June 18, 2019) Auxotrophies constrain the interactions of bacteria with their exist in most free-living microorganisms, indicating that they rely environment, but are often difficult to identify. Here, we develop on cross-feeding (25). However, it has been demonstrated that an algorithm (AuxoFind) using genome-scale metabolic recon- amino acid auxotrophies are predicted incorrectly as a result struction to predict auxotrophies and apply it to a series of the insufficient number of known gene paralogs (26). Addi- of available genome sequences of over 1,300 Gram-negative tionally, these methods rely on the identification of pathway strains. We identify 54 auxotrophs, along with the corre- completeness, with a 50% cutoff used to determine auxotrophy sponding metabolic and genetic basis, using a pangenome (25). A mechanistic approach is expected to be more appropriate approach, and highlight auxotrophies conferring a fitness advan- and can be achieved using genome-scale models of metabolism tage in vivo. We show that the metabolic basis of auxotro- (GEMs). For example, requirements can arise by means of a sin- phy is species-dependent and varies with 1) pathway structure, gle deleterious mutation in a conditionally essential gene (CEG), 2) enzyme promiscuity, and 3) network redundancy. -
Biofilm Formation and Cellulose Expression by Bordetella Avium 197N, the Causative Agent of Bordetellosis in Birds and an Opportunistic Respiratory Pathogen in Humans
Accepted Manuscript Biofilm formation and cellulose expression by Bordetella avium 197N, the causative agent of bordetellosis in birds and an opportunistic respiratory pathogen in humans Kimberley McLaughlin, Ayorinde O. Folorunso, Yusuf Y. Deeni, Dona Foster, Oksana Gorbatiuk, Simona M. Hapca, Corinna Immoor, Anna Koza, Ibrahim U. Mohammed, Olena Moshynets, Sergii Rogalsky, Kamil Zawadzki, Andrew J. Spiers PII: S0923-2508(17)30017-7 DOI: 10.1016/j.resmic.2017.01.002 Reference: RESMIC 3563 To appear in: Research in Microbiology Received Date: 17 November 2016 Revised Date: 16 January 2017 Accepted Date: 16 January 2017 Please cite this article as: K. McLaughlin, A.O. Folorunso, Y.Y. Deeni, D. Foster, O. Gorbatiuk, S.M. Hapca, C. Immoor, A. Koza, I.U. Mohammed, O. Moshynets, S. Rogalsky, K. Zawadzki, A.J. Spiers, Biofilm formation and cellulose expression by Bordetella avium 197N, the causative agent of bordetellosis in birds and an opportunistic respiratory pathogen in humans, Research in Microbiologoy (2017), doi: 10.1016/j.resmic.2017.01.002. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Page 1 of 25 ACCEPTED MANUSCRIPT 1 For Publication 2 Biofilm formation and cellulose expression by Bordetella avium 197N, 3 the causative agent of bordetellosis in birds and an opportunistic 4 respiratory pathogen in humans 5 a* a*** a b 6 Kimberley McLaughlin , Ayorinde O. -
Yersinia Ruckeri Sp. Nov., the Redmouth (RM) Bacterium
0020-7713/78/0028-0037$02-00/0 INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1978, p. 37-44 Vol. 28, No. 1 Copyright 0 1978 International Association of Microbiological Societies Printed in U.S. A. Yersinia ruckeri sp. nov., the Redmouth (RM) Bacterium W. H. EWING,? A. J. ROSS,?t DON J. BRENNER,??? AND G. R. FANNING Division of Biochemistry, Walter Reed Army Institute of Research, Washington, D.C. 20012 Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine(G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteri- aceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. -
Insights Into the Pathogenicity of Burkholderia Pseudomallei
REVIEWS Melioidosis: insights into the pathogenicity of Burkholderia pseudomallei W. Joost Wiersinga*, Tom van der Poll*, Nicholas J. White‡§, Nicholas P. Day‡§ and Sharon J. Peacock‡§ Abstract | Burkholderia pseudomallei is a potential bioterror agent and the causative agent of melioidosis, a severe disease that is endemic in areas of Southeast Asia and Northern Australia. Infection is often associated with bacterial dissemination to distant sites, and there are many possible disease manifestations, with melioidosis septic shock being the most severe. Eradication of the organism following infection is difficult, with a slow fever-clearance time, the need for prolonged antibiotic therapy and a high rate of relapse if therapy is not completed. Mortality from melioidosis septic shock remains high despite appropriate antimicrobial therapy. Prevention of disease and a reduction in mortality and the rate of relapse are priority areas for future research efforts. Studying how the disease is acquired and the host–pathogen interactions involved will underpin these efforts; this review presents an overview of current knowledge in these areas, highlighting key topics for evaluation. Melioidosis is a serious disease caused by the aerobic, rifamycins, colistin and aminoglycosides), but is usually Gram-negative soil-dwelling bacillus Burkholderia pseu- susceptible to amoxicillin-clavulanate, chloramphenicol, domallei and is most common in Southeast Asia and doxycycline, trimethoprim-sulphamethoxazole, ureido- Northern Australia. Melioidosis is responsible for 20% of penicillins, ceftazidime and carbapenems2,4. Treatment all community-acquired septicaemias and 40% of sepsis- is required for 20 weeks and is divided into intravenous related mortality in northeast Thailand. Reported cases are and oral phases2,4. Initial intravenous therapy is given likely to represent ‘the tip of the iceberg’1,2, as confirmation for 10–14 days; ceftazidime or a carbapenem are the of disease depends on bacterial isolation, a technique that drugs of choice. -
Identification of Bordetella Spp. in Respiratory Specimens From
504 Clinical Microbiology and Infection, Volume 14 Number 5, May 2008 isolates of extended-spectrum-beta-lactamase-producing Original Submission: 27 October 2007; Revised Sub- Shigella sonnei. Ann Trop Med Parasitol 2007; 101: 511–517. mission: 5 December 2007; Accepted: 19 December 21. Rice LB. Controlling antibiotic resistance in the ICU: 2007 different bacteria, different strategies. Cleve Clin J Med 2003; 70: 793–800. Clin Microbiol Infect 2008; 14: 504–506 22. Boyd DA, Tyler S, Christianson S et al. Complete nucleo- 10.1111/j.1469-0691.2008.01968.x tide sequence of a 92-kilobase plasmid harbouring the CTX-M-15 extended spectrum b-lactamase involved in an outbreak in long-term-care facilities in Toronto, Canada. Cystic fibrosis (CF) is an autosomal recessive Antimicrob Agents Chemother 2004; 48: 3758–3764. disease, characterised by defective chloride ion channels that result in multi-organ dysfunction, most notably affecting the respiratory tract. The RESEARCH NOTE alteration in the pulmonary environment is asso- ciated with increased susceptibility to bacterial infection. Recent advances in bacterial taxonomy and improved microbial identification systems Identification of Bordetella spp. in have led to an increasing recognition of the respiratory specimens from individuals diversity of bacterial species involved in CF lung with cystic fibrosis infection. Many such species are opportunistic T. Spilker, A. A. Liwienski and J. J. LiPuma human pathogens, some of which are rarely found in other human infections [1]. Processing Department of Pediatrics and Communicable of CF respiratory cultures therefore employs Diseases, University of Michigan Medical selective media and focuses on detection of School, Ann Arbor, MI, USA uncommon human pathogens. -
Mouse Anti-Bacteria Yersinia Ruckeri Monoclonal Antibody, Clone 8G6/G7 (DMAB6804) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Mouse anti-Bacteria Yersinia Ruckeri Monoclonal antibody, clone 8G6/G7 (DMAB6804) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Mouse anti-bacteria yersinia ruckeri monoclonal antibody. Yersinia Ruckeri IgG fraction obtained by immunizing mice with five Chilean isolates of Yersinia ruckeri (whole bacterial cells). The IgG fraction was purified using Protein G-Sepharose. Antigen Description Y. ruckeri is a Gram-negative, rod-shaped bacterium that shows a variable motility due to the presence of flagella. These flagella are not always observed. It is the causative agent of enteric redmouth disease (ERM) which is characterized by a chronic or acute enterosepticemia with high morbidity and mortality rates in salmonids and non-salmonids species. Six serovars have been described according to whole-cell serological typing. Isotype IgG2b Source/Host Mouse Clone 8G6/G7 Conjugate Unconjugated Applications ELISA, WB, IF Stability Stable at least one year at -20oC. Avoid repeated freezing and thawing. Format Solution at 1.0 mg/ml in PBS. Size 100 μg Preservative None Storage Store at -20ºC. BACKGROUND Introduction Yersinia is a genus of bacteria in the family Enterobacteriaceae. Yersinia are Gram-negative rod shaped bacteria, a few micrometers long and fractions of a micrometer in diameter, and are facultative anaerobes. Some members of Yersinia are pathogenic in humans; in particular, Y. 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved pestis is the causative agent of the plague. -
Iron Transport Strategies of the Genus Burkholderia
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2015 Iron transport strategies of the genus Burkholderia Mathew, Anugraha Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-113412 Dissertation Published Version Originally published at: Mathew, Anugraha. Iron transport strategies of the genus Burkholderia. 2015, University of Zurich, Faculty of Science. Iron transport strategies of the genus Burkholderia Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Anugraha Mathew aus Indien Promotionskomitee Prof. Dr. Leo Eberl (Vorsitz) Prof. Dr. Jakob Pernthaler Dr. Aurelien carlier Zürich, 2015 2 Table of Contents Summary .............................................................................................................. 7 Zusammenfassung ................................................................................................ 9 Abbreviations ..................................................................................................... 11 Chapter 1: Introduction ....................................................................................... 14 1.1.Role and properties of iron in bacteria ...................................................................... 14 1.2.Iron transport mechanisms in bacteria ..................................................................... -
Gallibacterium Anatis: an Emerging Pathogen of Poultry Birds And
ary Scien in ce r te & e T V e f c h o Journal of Veterinary Science & n n l o o a a l l n n o o r r g g u u Singh, et al., J Veterinar Sci Techno 2016, 7:3 y y o o J J Technology DOI: 10.4172/2157-7579.1000324 ISSN: 2157-7579 Review Article Open Access Gallibacterium anatis: An Emerging Pathogen of Poultry Birds and Domiciled Birds Shiv Varan Singh, Bhoj R Singh*, Dharmendra K Sinha, Vinodh Kumar OR, Prasanna Vadhana A, Monika Bhardwaj and Sakshi Dubey Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar-243 122, Uttar Pradesh, India *Corresponding author: Dr. Bhoj R Singh, Acting Head of Division of Epidemiology, ICAR-IVRI, Izatnagar-243122, Uttar Pradesh, India, Tel: +91-8449033222; E-mail: [email protected] Rec date: Feb 09, 2016; Acc date: Mar 16, 2016; Pub date: Mar 18, 2016 Copyright: © 2016 Singh SV, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Gallibacterium anatis though known since long as opportunistic pathogen of intensively reared poultry birds has emerged in last few years as multiple drug resistance pathogen causing heavy mortality outbreaks not only in poultry birds but also in other domiciled or domestic birds. Due to its fastidious nature, commensal status and with no pathgnomonic lesions in diseased birds G. anatis infection often remains obscure for diagnosis. -
Structural and Functional Effects of Bordetella Avium Infection in the Turkey Respiratory Tract William George Van Alstine Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1987 Structural and functional effects of Bordetella avium infection in the turkey respiratory tract William George Van Alstine Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Animal Sciences Commons, and the Veterinary Medicine Commons Recommended Citation Van Alstine, William George, "Structural and functional effects of Bordetella avium infection in the turkey respiratory tract " (1987). Retrospective Theses and Dissertations. 11655. https://lib.dr.iastate.edu/rtd/11655 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS While the most advanced technology has been used to photograph and reproduce this manuscript, the quality of the reproduction is heavily dependent upon the quality of the material submitted. For example: • Manuscript pages may have indistinct print. In such cases, the best available copy has been filmed. • Manuscripts may not always be complete. In such cases, a note will indicate that it is not possible to obtain missing pages. • Copyrighted material may have been removed from the manuscript. In such cases, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, and charts) are photographed by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Unraveling the Biotechnological Potential of the Secretome of Burkholderia Cepacia Complex, with Focus on Its Antimicrobial Activity
Unraveling the biotechnological potential of the secretome of Burkholderia cepacia complex, with focus on its antimicrobial activity Carina Andreia Ribeiro Galhofa Thesis to obtain the Master of Science Degree in Biotechnology Supervisors: Prof. Doctor Isabel Maria de Sá Correia Leite de Almeida; Doctor Patrick de Oliveira Freire Examination Committee Chairperson: Doctor Arsénio do Carmo Sales Mendes Fialho Supervisor: Prof. Doctor Isabel Maria de Sá Correia Leite de Almeida Members of the Committee: Doctor Inês Batista Guinote December 2017 Acknowledgements The wish to become a future microbiologist and to study the “little bugs” that were able to cause diseases in individuals way bigger than them has been present since I was a child. As such, I would like to acknowledge those that helped me from the beginning to the end of this work, making this possible. To Prof. Dr.Isabel Sá Correia, I would like to express my gratitude not only for advising, but also for accepting me in this project which I enjoyed to do so much. To Dr. Patrick Freire, my advisor within BioMimetx, not only for all the guidance and patience but, most of all, for the motivation and believing in my work and Dr. Carla Coutinho for the support, for bearing my inexperience and for all the tips given that prevented me from exploding the laboratory…and the centrifuge. To the funding of IBB (Institute for Bioengineering and Biosciences) and BioMimetx, that gave me all the resources and conditions that enabled the conduction of my work. To Amir Hassan, for staying up late at the lab waiting for me to finish my work and for the “Goooooodddd woooorkkkkk” motivational screams. -
A Further Characterization of Yersinia Ruckeri (Enteric Redmouth Bacterium)
‹›•aŒ¤‹† Fish Pathology 14 (2) 71-78, 1979. 9 A further Characterization of Yersinia ruckeri (Enteric Redmouth Bacterium) P. J. O'LEARY, J. S. ROHOVEC and J. L. FRYER Department of Microbiology, Oregon State University, Corvallis, OR 97331 (Received May 22, 1979) Seventeen cultures of Enteric Redmouth Bacterium were examined biochemically at selected temperatures. Incubation temperature altered the motility of the bacterium. At 9•Ž non functional peritrichous flagella were produced, while at 18, 22, and 27•Ž the bacterium was motile. The cells were nonmotile at 37•Ž due to a lack of flagellar production. The percent guanine plus cytosine was determined to be 47.95•}0.45 (P=0.05). This work supports the proposal of Yersinia ruckeri as the genus and species designation of the Entric Redmouth Bacterium. hynchus tshawytscha) and coho (O. kisutch) Introduction salmon, and rainbow trout (Salmo gairdneri). In the early 1950's, Rucker isolated a gram Each isolate was stored on Brain Heart In- negative, oxidase negative, motile bacterium fusion (BHI: Difco) slants under sterile mineral from moribund rainbow trout (Salmo gaird oil. neri). The first publication concerning this Biochemical tests bacterium did not appear until 1966 (Ross et The methods used to study most of the al., 1966) in which the definitive taxonomic biochemical properties of this organism have position of the bacterium could not be defined, been described previously (EDWARDSand EWING although it was placed in the family Entero 1972; LENETTE et al., 1974). For carbohydrate bacteriaceae. Hence the name Enteric Red utilization tests, sugars were incorporated into mouth Bacterium (ERMB) arose.