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From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases. -
Facklamia Sourekii Sp. Nov., Isolated F Rom 1 Human Sources
International Journal of Systematic Bacteriology (1999), 49, 635-638 Printed in Great Britain Facklamia sourekii sp. nov., isolated f rom NOTE 1 human sources Matthew D. Collins,' Roger A. Hutson,' Enevold Falsen2 and Berit Sj6den2 Author for correspondence : Matthew D. Collins. Tel : + 44 1 18 935 7226. Fax : + 44 1 18 935 7222. e-mail : [email protected] 1 Department of Food Two strains of a Gram-positive catalase-negative, facultatively anaerobic Science and Technology, coccus originating from human sources were characterized by phenotypic and University of Reading, Whiteknights, molecular taxonomic methods. The strains were found to be identical to each Reading RG6 6AP, other based on 165 rRNA gene sequencing and constitute a new subline within UK the genus Facklamia. The unknown bacterium was readily distinguished from * Culture Collection, Facklamis hominis and Facklamia ignava by biochemicaltests and Department of Clinical electrophoretic analysis of whole-cell proteins. Based on phylogenetic and Bacteriology, University of Goteborg, Sweden phenotypic evidence it is proposed that the unknown bacterium be classified as Facklamia sourekii sp. nov., the type strain of which is CCUG 28783AT. Keywords : Facklamia sourekii, taxonomy, phylogeny, 16s rRNA The Gram-positive catalase-negative cocci constitute a Gram-positive coccus-shaped organisms, which con- phenotypically heterogeneous group of organisms stitute a third species of the genus Facklamia, Fack- which belong to the Clostridium branch of the Gram- lamia sourekii sp. nov. This report adds to the many positive bacteria. This broad group of organisms new taxa and the diversity of Gram-positive catalase- includes many human and animal pathogens (e.g. -
Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances. -
Facklamia Sourekii Sp. Nov., Isolated F Rom 1 Human Sources
International Journal of Systematic Bacteriology (1999), 49, 635-638 Printed in Great Britain Facklamia sourekii sp. nov., isolated f rom NOTE 1 human sources Matthew D. Collins,' Roger A. Hutson,' Enevold Falsen2 and Berit Sj6den2 Author for correspondence : Matthew D. Collins. Tel : + 44 1 18 935 7226. Fax : + 44 1 18 935 7222. e-mail : [email protected] 1 Department of Food Two strains of a Gram-positive catalase-negative, facultatively anaerobic Science and Technology, coccus originating from human sources were characterized by phenotypic and University of Reading, Whiteknights, molecular taxonomic methods. The strains were found to be identical to each Reading RG6 6AP, other based on 165 rRNA gene sequencing and constitute a new subline within UK the genus Facklamia. The unknown bacterium was readily distinguished from * Culture Collection, Facklamis hominis and Facklamia ignava by biochemicaltests and Department of Clinical electrophoretic analysis of whole-cell proteins. Based on phylogenetic and Bacteriology, University of Goteborg, Sweden phenotypic evidence it is proposed that the unknown bacterium be classified as Facklamia sourekii sp. nov., the type strain of which is CCUG 28783AT. Keywords : Facklamia sourekii, taxonomy, phylogeny, 16s rRNA The Gram-positive catalase-negative cocci constitute a Gram-positive coccus-shaped organisms, which con- phenotypically heterogeneous group of organisms stitute a third species of the genus Facklamia, Fack- which belong to the Clostridium branch of the Gram- lamia sourekii sp. nov. This report adds to the many positive bacteria. This broad group of organisms new taxa and the diversity of Gram-positive catalase- includes many human and animal pathogens (e.g. -
Molecular Characterization of the Penile Microbiome of Dorper Rams (Ovis Aries)
Molecular characterization of the penile microbiome of Dorper rams (Ovis aries) by Auberi Marie Madeleine Courchay Thesis presented in fulfilment of the requirements for the degree of Masters in the Faculty of Science at Stellenbosch University Supervisor: Dr H. Lambrecths Co-supervisor: Prof J.T. Burger March 2017 Stellenbosch University https://scholar.sun.ac.za DECLARATION By submitting this thesis electronically, I declare that the entirety of the work contained therein is my own, original work, that I am the sole author thereof (save to the extent explicitly otherwise stated), that reproduction and publication thereof by Stellenbosch University will not infringe any third party rights and that I have not previously in its entirety or in part submitted it for obtaining any qualification. March 2017 Copyright © 2017 Stellenbosch University All rights reserved i Stellenbosch University https://scholar.sun.ac.za ABSTRACT Characterizing the bacterial community inhabiting the penile environment of Dorper rams may provide insight into the aetiology of ulcerative balanoposthitis (UB), a venereal disease of unknown aetiology, which occurs predominantly in this breed, and that is of great economic importance to the mutton industry in South Africa. Profiling of the bacteria present in the penile environment of healthy and diseased rams was carried out previously using culture-based methods. These culture-based studies identified Mycoplasma mycoides mycoides large colony (MMMLC) and Trueperella pyogenes as potentially contributing to the incidence of UB. Although cultured-based methods have been described as the gold standard for identification of bacteria, many bacteria are uncultivable or grow slowly and poorly in-vitro. The advent of high throughput next generation sequencing (HT-NGS), a culture-independent bacterial identification approach, has offered high coverage and depths in determining the bacterial penile community. -
Ignavigranum Ruoffiae, a Rare Pathogen That Caused a Skin Abscess
CASE REPORT De Paulis et al., JMM Case Reports 2018;5 DOI 10.1099/jmmcr.0.005137 Ignavigranum ruoffiae, a rare pathogen that caused a skin abscess Adriana N. De Paulis,1 Eugenia Bertona,1 Miguel A. Gutierrez, 1 María S. Ramírez,2 Carlos A. Vay3 and Silvia C. Predari1,* Abstract Introduction. Ignavigranum ruoffiae is an extremely rare cause of human infections. Case presentation. An 83-year-old male with a painless, ten-day-old, erythematous skin abscess on his left flank, which had showed a purulent discharge for 48 h, was admitted to the Emergency service. He was treated with cephalexin, disinfection with Codex water and spray of rifampicin. Five days later, surgical drainage of the abscess was proposed due to the torpid evolution of the patient. Samples were taken for culture, and antibiotic treatment with trimethoprim-sulfamethoxazole was established. The patient returned after 10 days showing healing of the abscess. Microbiological studies showed a few Gram-positive cocci present as single cells and short chains that grew after 72 h of incubation at 35 C with CO2 on 5 % sheep blood agar. Colonies presented a strong sauerkraut odour. Initial biochemical test results were negative for catalase, aesculin and bile-aesculin, and positive for pyrrolidonyl arylamidase, leucine aminopeptidase and growth in 6.5 % NaCl broth, which prompted the preliminary identification of Facklamia species or I. ruoffiae. The positive result for arginine deamination and negative result for hippurate hydrolysis, failure to produce acid from mannitol, sucrose, sorbitol or trehalose, plus the distinctive sauerkraut odour identified the organism as I. ruoffiae. -
Generating Subunit of Ribonucleotide Reductase
bioRxiv preprint doi: https://doi.org/10.1101/373563; this version posted July 20, 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. Fusion of a functional glutaredoxin to the radical- generating subunit of ribonucleotide reductase Inna Rozman Grinberg1, Daniel Lundin1, Margareta Sahlin1, Mikael Crona1,2, Gustav Berggren3, Anders Hofer4, Britt-Marie Sjöberg1* From the 1Department of Biochemistry and Biophysics, Stockholm University, Sweden; 2Swedish Orphan Biovitrum AB, Stockholm, Sweden; 3Department of Chemistry, Uppsala University, Uppsala, Sweden; 4Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden. Running title: Glutaredoxin and ATP-cone fusions to ribonucleotide reductase *To whom correspondence should be addressed: Britt-Marie Sjöberg, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden; britt- [email protected]; Tel +46-8-164150; Fax +46 8-155597 Keywords: allosteric regulation, ATP-cone, dATP inhibition, dimanganese, dithiol, monothiol mechanism, tetramers, radical mechanism, redox activity, ribonucleotide reductase Abstract Class I ribonucleotide reductase (RNR) consists of a catalytic subunit (NrdA) and a radical- generating subunit (NrdB) that together catalyse reduction of the four ribonucleotides to their corresponding deoxyribonucleotides. Facklamia ignava NrdB is an unprecedented fusion protein with N-terminal add-ons of a glutaredoxin (Grx) domain followed by an ATP-cone. Grx, which in general is encoded elsewhere in the genome than is the RNR operon, is a known physiological reductant of RNRs. Here we show that the fused Grx domain functions as an efficient reductant of the F. ignava class I RNR via the common dithiol mechanism and interestingly also via a monothiol mechanism, although less efficiently.