Artykuły w czasopismach: „Strain nomenclature”

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Fauquet, C. M., R. W. Briddon, J. K. Brown, E. Moriones, J. Stanley, M. Zerbini i X. Zhou. "Geminivirus strain demarcation and nomenclature". Archives of Virology 153, nr 4 (7.02.2008): 783–821. http://dx.doi.org/10.1007/s00705-008-0037-6.

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Zheng, Du-Ping, Tamie Ando, Rebecca L. Fankhauser, R. Suzanne Beard, Roger I. Glass i Stephan S. Monroe. "Norovirus classification and proposed strain nomenclature". Virology 346, nr 2 (marzec 2006): 312–23. http://dx.doi.org/10.1016/j.virol.2005.11.015.

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Festing, Michael F. W., Elizabeth M. Simpson, Muriel T. Davisson i Larry E. Mobraaten. "Revised nomenclature for strain 129 mice". Mammalian Genome 10, nr 8 (1.08.1999): 836. http://dx.doi.org/10.1007/s003359901099.

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Rülicke, Th, X. Montagutelli, B. Pintado, R. Thon i H. J. Hedrich. "FELASA guidelines for the production and nomenclature of transgenic rodents". Laboratory Animals 41, nr 3 (1.07.2007): 301–11. http://dx.doi.org/10.1258/002367707781282758.

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The standardized nomenclature of rodent strains, genes and mutations has long been the focus of careful attention. Its aim is to provide proper designation of laboratory animals used in research projects and to convey as much information on each strain as possible. Since the development of different techniques to mutate the genome of laboratory rodents on a large scale, the correct application of current nomenclature systems is of increased significance. It facilitates not only the accurate communication of scientific results but is indispensable in controlling the dramatically increased number of transgenic animal models in experimental units, archives and databases. It is regrettable that many publications, especially on transgenic rodents, use vague and inappropriate strain designation. This situation should definitely be improved, particularly considering the increasingly emphasized importance of genetic background on the phenotype of mutations. The aim of these guidelines is to raise awareness about specific features of production and of the current nomenclature system used for transgenic rodents.

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Ablashi, D., H. Agut, Z. Berneman, G. Campadelli-Fiume, D. Carrigan, L. Ceccerini-Nelli, B. Chandran i in. "Human herpesvirus-6 strain groups: a nomenclature". Archives of Virology 129, nr 1-4 (marzec 1993): 363–66. http://dx.doi.org/10.1007/bf01316913.

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Blake, Judith A., Richard Baldarelli, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult, Anna V. Anagnostopoulos i in. "Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology". Nucleic Acids Research 49, nr D1 (24.11.2020): D981—D987. http://dx.doi.org/10.1093/nar/gkaa1083.

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Abstract The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological reference data related to mouse genes, gene functions, phenotypes and mouse models of human disease. MGD is the primary source for official gene, allele, and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. MGD’s biocuration scientists curate information from the biomedical literature and from large and small datasets contributed directly by investigators. In this report we describe significant enhancements to the content and interfaces at MGD, including (i) improvements in the Multi Genome Viewer for exploring the genomes of multiple mouse strains, (ii) inclusion of many more mouse strains and new mouse strain pages with extended query options and (iii) integration of extensive data about mouse strain variants. We also describe improvements to the efficiency of literature curation processes and the implementation of an information portal focused on mouse models and genes for the study of COVID-19.

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Young, J. M., D. R. W. Watson i D. W. Dye. "Reconsideration of Arthrobacter ilicis (Mandel et al. 1961) Collins et al. 1982 as a plant-pathogenic species. Proposal to emend the authority and description of the species. Request for an Opinion". International Journal of Systematic and Evolutionary Microbiology 54, nr 1 (1.01.2004): 303–5. http://dx.doi.org/10.1099/ijs.0.02929-0.

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Strains now considered to represent the type strain of Arthrobacter ilicis, described as a pathogen of American holly, are not identical. The designated type strain does not represent this pathogen. However, one of the other strains sourced to the type strain of the pathogen does appear to be authentic, but is not a member of A. ilicis. It is proposed that A. ilicis is an unrelated species, not a pathogen of American holly. The nomenclature of A. ilicis can be rectified by emending the authority and by emending the species description to recognize this species as a novel species that is not a plant pathogen. The pathogen of American holly then becomes a novel pathovar, Curtobacterium flaccumfaciens pv. ilicis. The opinion of the Judicial Commission is sought.

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Tindall, B. J. "Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 has priority over Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 when the two are treated as members of the same species based on the principle of priority and Rule 23a, Note 1 as applied to the corresponding specific epithets. Opinion 94." International Journal of Systematic and Evolutionary Microbiology 64, Pt_10 (1.10.2014): 3590–92. http://dx.doi.org/10.1099/ijs.0.069203-0.

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The Judicial Commission affirms that, according to the Rules of the International Code of Nomenclature of Bacteria (including changes made to the wording), the combination Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 has priority over the combination Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 when the two are treated as members of the same species based on the principle of priority as applied to the corresponding specific epithets. The type species of the genus is Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942, even if treated as a later heterotypic synonym of Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942. Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 is typified by the strain defined on the Approved Lists of Bacterial Names and by strains known to be derived from the nomenclatural type.

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Wotjak, Carsten T. "C57BLack/BOX? The importance of exact mouse strain nomenclature". Trends in Genetics 19, nr 4 (kwiecień 2003): 183–84. http://dx.doi.org/10.1016/s0168-9525(02)00049-5.

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Lang, Elke, i Hans Reichenbach. "Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum". International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (1.11.2013): 4354–60. http://dx.doi.org/10.1099/ijs.0.056440-0.

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Ten species of the order Myxococcales with validly published names are devoid of living type strains. Four species of the genus Chondromyces are represented by dead herbarium samples as the type material. For a species of the genus Melittangium and two species of the genus Polyangium , no physical type material was assigned at the time of validation of the names or later on. In accordance with rule 18f of the International Code of Nomenclature of Bacteria the following type strains are designated for these species: strain Cm a14T ( = DSM 14605T = JCM 12615T) as the type strain of Chondromyces apiculatus , strain Cm c5T ( = DSM 14714T = JCM 12616T) as the type strain of Chondromyces crocatus , strain Sy t2T ( = DSM 14631T = JCM 12617T) as the type strain of Chondromyces lanuginosus , strain Cm p51T ( = DSM 14607T = JCM 12618T) as the type strain of Chondromyces pediculatus , strain Me b8T ( = DSM 14713T = JCM 12633T) as the type strain of Melittangium boletus , strain Pl s12T ( = DSM 14670T = JCM 12637T) as the type strain of Polyangium sorediatum and strain Pl sm5T ( = DSM 14734T = JCM 12638T) as the type strain of Polyangium spumosum . Furthermore, the type strains given for three species of the genera Cystobacter and Polyangium had been kept at one university institute and have been lost according to our investigations. In accordance with Rule 18c of the Bacteriological Code, we propose the following neotype strains: strain Cb fe18 ( = DSM 14716 = JCM 12624) as the neotype strain of Cystobacter ferrugineus , strain Cb m2 ( = DSM 14751 = JCM 12627) as the neotype strain of Cystobacter minus and strain Pl fu5 ( = DSM 14668 = JCM 12636) as the neotype strain of Polyangium fumosum . The proposals of the strains are based on the descriptions and strain proposals given in the respective chapters of Bergey’s Manual of Systematic Bacteriology (2005).

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Mehrotra, Akhil, Ajay Sharma, Swati Singh i Shubham Kacker. "Situs ambiguous with three chambered heart (single atrium), evaluation by four-dimensional X-strain color echocardiography – A case report". Indian Journal of Child Health 9, nr 7 (10.08.2022): 131–36. http://dx.doi.org/10.32677/ijch.v9i7.3534.

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Situs ambiguous accounts for 4% of all congenital heart disease (CHD) and has an incidence of 1:10,000 new born births. To standardize the nomenclature for CHD, the international nomenclature society published a globally accepted nomenclature tree for CHD with the 11th Iteration of international classification of disease. According to this publication common atrium, single atrium and atrium communis are denoted as synonyms. The incidence of common atrium among atrial septal defect (ASD) patients is 3–4% only and thus denoting it to be a rare entity. We are presenting an exceedingly rare case of a patient of situs ambiguous, left isomerism, and single atrium with a cleft on the anterior mitral leaflet, evaluated comprehensively by four-dimensional X-strain color Doppler echocardiography.

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McQueen, H. J., i S. Spigarelli. "Nomenclature for strain-induced boundaries in hot and cold working". Materials Science and Engineering: A 462, nr 1-2 (lipiec 2007): 37–44. http://dx.doi.org/10.1016/j.msea.2006.04.151.

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Pitt, Alexandra, Ulrike Koll, Johanna Schmidt i Martin W. Hahn. "Aquirufa ecclesiirivi sp. nov. and Aquirufa beregesia sp. nov., isolated from a small creek and classification of Allopseudarcicella aquatilis as a later heterotypic synonym of Aquirufa nivalisilvae". International Journal of Systematic and Evolutionary Microbiology 70, nr 8 (1.08.2020): 4602–9. http://dx.doi.org/10.1099/ijsem.0.004319.

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Two bacterial strains, 50A-KIRBAT and 50C-KIRBAT, were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to Aquirufa nivalisilvae of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the new strains represent two new species of the genus Aquirufa . Pairwise calculated whole-genome average nucleotide identity (gANI) values ranging from 85.4 to 87.5 % confirmed this conclusion. Phenotypic, chemotaxonomic and genomic traits were investigated. Like strains of other Aquirufa species, 50A-KIRBAT and 50C-KIRBAT grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented and motile, most likely by gliding. They could be distinguished by slight differences in the chemotaxonomic features. We propose to establish for strain 50A-KIRBAT (=CIP 111735T=LMG 31080T) as type strain the name Aquirufa ecclesiirivi and for strain 50C-KIRBAT (=CIP 111736T=LMG 31501T) as type strain the name Aquirufa beregesia. Furthermore, the relationship between the type strains of Aquirufa nivalisilvae (59G-WUEMPELT) and Allopseudarcicella aquatilis (HME7025T) was investigated. Results of polyphasic analyses, especially a gANI value of 97.6 %, as well as the genome-based phylogenetic reconstruction, suggested that Allopseudarcicella aquatilis is a heterotypic synonym of Aquirufa nivalisilvae . According to rule 24b of the International Code of Nomenclature of Prokaryotes we propose to classify strain HME7025 as Aquirufa nivalisilvae and provide an emended description for the latter.

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Valles, Camille, Morgane Mailhe, Davide Ricaboni, Nicholas Armstrong, Stéphane Alibar, Véronique Vitton, Jean-Christophe Lagier, Didier Raoult i Maryam Tidjani Alou. "Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample". Microbiology Research 12, nr 1 (9.02.2021): 29–42. http://dx.doi.org/10.3390/microbiolres12010004.

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A new genus, a member of the Ruminococcaceae family, was isolated from the left colon of a healthy woman. Strain Marseille P3213 was a non-motile, spore-forming, Gram-stain negative, rod-shaped bacterium. This strictly anaerobic species reached optimal growth after an incubation of 72 h at 37 °C. The 16S rRNA gene sequence of this strain shared a 93.52% similarity level with Harryflintia acetispora strain V20-281a, its closest phylogenetic neighbor with standing in the nomenclature. Its genome had a size of 2.87 Mb, with a 45.81% G + C content. We hereby propose the creation of Negativibacillus massiliensis strain P3213T as the 43rd genus within the Ruminococcaceae family.

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Coorevits, An, Anna E. Dinsdale, Jeroen Heyrman, Peter Schumann, Anita Van Landschoot, Niall A. Logan i Paul De Vos. "Lysinibacillus macroides sp. nov., nom. rev." International Journal of Systematic and Evolutionary Microbiology 62, Pt_5 (1.05.2012): 1121–27. http://dx.doi.org/10.1099/ijs.0.027995-0.

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‘Bacillus macroides’ ATCC 12905T ( = DSM 54T = LMG 18474T), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA–DNA relatedness experiments, revealed that ‘Bacillus macroides’ is genomically distinct from its closest relatives Lysinibacillus xylanilyticus , Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.8 and 98.5 %, respectively, with the type strains of these species). Further analysis showed that ‘Bacillus macroides’ shares the A4α l-Lys–d-Asp peptidoglycan type with other members of the genus Lysinibacillus and can thus be attributed to this genus. These results, combined with additional phenotypic data, justify the description of strain LMG 18474T ( = DSM 54T = ATCC 12905T) as Lysinibacillus macroides sp. nov., nom. rev.

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Assanov, Nigmetulla, Ryskeldi Bazarbayev, Assilbek Mussoyev, Bauyrzhan Otarbayev i Kairat Iskhan. "The use of RT-PCR in the diagnosis and differentiation of vaccine strains of chicken infectious bronchitis and Newcastle disease". Open Veterinary Journal 13, nr 6 (2023): 732. http://dx.doi.org/10.5455/ovj.2023.v13.i6.8.

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Background: Infectious diseases of young and adult birds with respiratory syndrome are a significant deterrent to the development of industrial poultry farming due to a decrease in productivity and significant mortality. The only effective method of combating viral diseases is timely and targeted vaccination, which largely depends on laboratory diagnostic results. Aim: The aim of this article is to study the real-time reverse transcription polymerase chain reaction, which has the prospect of more effective diagnosis of vaccine strains of chicken infectious bronchitis and Newcastle disease. Methods: The fastest and most accurate method for the differential diagnosis of pathogens in an associative viral infection is reverse transcription polymerase chain reaction. The method proposed in the article for selecting primers for amplification made it possible to use this method for the simultaneous interspecies differential diagnosis of two or more viral agents, which significantly accelerated their diagnosis. Results: The correlation of the nucleotide sequence obtained as a result of sequencing to a specific strain of the virus is complicated by the lack of a single nomenclature mechanism for separating genetic groups. Conclusion: The results of this study will allow easy and fast typing of sequences into known and databased virus strains, and avoid further confusion in the nomenclature of genetic groups in the future.

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Lázaro, Sara, Francisca Fernández-Piñas, Eduardo Fernández-Valiente, Amaya Blanco-Rivero i Francisco Leganés. "pbpB, a Gene Coding for a Putative Penicillin-Binding Protein, Is Required for Aerobic Nitrogen Fixation in the Cyanobacterium Anabaena sp. Strain PCC7120". Journal of Bacteriology 183, nr 2 (15.01.2001): 628–36. http://dx.doi.org/10.1128/jb.183.2.628-636.2001.

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ABSTRACT Transposon mutagenesis of Anabaena sp. strain PCC7120 led to the isolation of a mutant strain, SNa1, which is unable to fix nitrogen aerobically but is perfectly able to grow with combined nitrogen (i.e., nitrate). Reconstruction of the transposon mutation of SNa1 in the wild-type strain reproduced the phenotype of the original mutant. The transposon had inserted within an open reading frame whose translation product shows significant homology with a family of proteins known as high-molecular-weight penicillin-binding proteins (PBPs), which are involved in the synthesis of the peptidoglycan layer of the cell wall. A sequence similarity search allowed us to identify at least 12 putative PBPs in the recently sequencedAnabaena sp. strain PCC7120 genome, which we have named and organized according to predicted molecular size and theEscherichia coli nomenclature for PBPs; based on this nomenclature, we have denoted the gene interrupted in SNal aspbpB and its product as PBP2. The wild-type form ofpbpB on a shuttle vector successfully complemented the mutation in SNa1. In vivo expression studies indicated that PBP2 is probably present when both sources of nitrogen, nitrate and N2, are used. When nitrate is used, the function of PBP2 either is dispensable or may be substituted by other PBPs; however, under nitrogen deprivation, where the differentiation of the heterocyst takes place, the role of PBP2 in the formation and/or maintenance of the peptidoglycan layer is essential.

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Ndongo, Sokhna, Mossaab Maaloum, Magali Richez, Rachid Saile, Pierre-Edouard Fournier, Jean Christophe Lagier, Didier Raoult i Saber Khelaifia. "Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient". Current Microbiology 78, nr 8 (24.06.2021): 3313–20. http://dx.doi.org/10.1007/s00284-021-02577-8.

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AbstractStrain SN6T is a non-motile and non-spore-forming gram-negative bacterium which was isolated from the stool sample of an Amazonian patient. The optimum growth was observed at 37 °C, pH 7, and 0–5 g/l of NaCl. Based on the 16S rRNA gene sequence similarity, the strain SN6T exhibited 97.5% identity with Vitreoscilla stercoraria strain ATCC_15218 (L06174), the phylogenetically closest species with standing in nomenclature. The predominant fatty acid was hexadecenoic acid (31%). The genomic DNA G + C content of the strain SN6T was 49.4 mol %. After analysis of taxonogenomic data, phenotypic and biochemical characteristics, we concluded that strain SN6T represents a new species of the genus Vitreoscilla for which the name Vitreoscilla massiliensis sp.nov is proposed. The type strain is SN6T (=CSUR P2036 = LN870312 = DSM 100958).

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Neustupa, Jiří, Yvonne Němcová, Jana Veselá, Jana Steinová i Pavel Škaloud. "Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella-like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats". International Journal of Systematic and Evolutionary Microbiology 63, Pt_1 (1.01.2013): 377–87. http://dx.doi.org/10.1099/ijs.0.047944-0.

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The diversity of green microalgae in subaerial habitats remains largely unexplored and a number of new genus- and species-level lineages have been discovered recently. The traditional green algal genus, Chlorella, which accommodated coccoid unicellular green algal species with globular to oval cells, reproducing entirely by autospores, has been found to be polyphyletic. In this study, we provide a detailed characterization of two strains of microalgae isolated from tree bark in the Mediterranean. These algae share the general Chlorella-like morphology and their 18S rRNA and rbcL gene sequences place them in the Trebouxiophyceae. Strain CAUP H8401 forms an independent trebouxiophycean lineage, together with three previously published 18S rRNA gene environmental sequences of undescribed microalgae, which were retrieved from profoundly different habitats. In contrast, strain CAUP H7902 is related to Kalinella bambusicola in the Watanabea clade of the Trebouxiophyceae on the basis of its 18S rRNA gene sequence. This relationship is also supported by the rbcL gene sequence, acquired from the type strain of K. bambusicola. The investigated strains are described as representatives of a novel species in a new genus, Leptochlorella corticola gen. et sp. nov., and a novel species, Kalinella apyrenoidosa sp. nov., according to the International Code of Nomenclature for Algae, Fungi and Plants.

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Diop, Awa, Khoudia Diop, Enora Tomei, Nicholas Armstrong, Florence Bretelle, Didier Raoult, Florence Fenollar i Pierre-Edouard Fournier. "Collinsella vaginalis sp. nov. strain Marseille-P2666T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis". International Journal of Systematic and Evolutionary Microbiology 69, nr 4 (1.04.2019): 949–56. http://dx.doi.org/10.1099/ijsem.0.003221.

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A strictly anaerobic, Gram-stain-positive, non motile and non-spore-forming rod-shaped bacterium, strain Marseille-P2666T, was isolated using the culturomics approach from a vaginal sample of a French patient suffering from bacterial vaginosis. Cells were saccharolytic and were negative for catalase, oxidase, urease, nitrate reduction, indole production, hydrolysis of aesculin and gelatin. Strain Marseille-P2666T exhibited 97.04 % 16S rRNA sequence similarity to Collinsella tanakaei type strain YIT 12063T, the phylogenetically closest species with standing in nomenclature. The major fatty acids were C18:1ω9 (38 %), C16 : 0 (24 %) and C18 : 0 (19 %). The G+C content of the genome sequence of strain Marseille-P2666T is 64.6 mol%. On the basis of its phenotypic, phylogenetic and genomic features, strain Marseille-P2666T (=CSUR 2666T=DSM103342T) was classified as type strain of a novel species within the genus Collinsella for which the name Collinsella vaginalis sp. nov. is proposed.

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Demetriou, Victoria L., Eftychia Kyriakou i Leondios G. Kostrikis. "Near-Full Genome Characterisation of Two Natural Intergenotypic 2k/1b Recombinant Hepatitis C Virus Isolates". Advances in Virology 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/710438.

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Few natural intergenotypic hepatitis C virus (HCV) recombinants have been characterised, and only RF1_2k/1b has demonstrated widespread transmission. The near-full length genome sequences for two cases of 2k/1b recombinants (CYHCV037 and CYHCV093) sampled in Cyprus were obtained using strain-specific RT-PCR amplification and sequencing protocols. Sequence analysis confirmed their similarity with the original RF1_2k/1b strain from St. Petersburg, N687. These two isolates significantly contribute to the sequence data available on this recombinant and confirm its increasing spread among individuals from Eastern Europe, and its association with transmission through intravenous drug use. Phylogenetic analyses reveal clustering of the sequence 3′ to the recombination point, not seen in the topology of the 5′ sequences, implying a more complicated evolutionary history than that held to date. The increasing cases of HCV recombinant strains underline the requirement of their contribution to the standardised rules of HCV classification and nomenclature, molecular epidemiology, diagnosis, and treatment.

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Lindeberg, Magdalen, John Stavrinides, Jeffrey H. Chang, James R. Alfano, Alan Collmer, Jeffery L. Dangl, Jean T. Greenberg, John W. Mansfield i David S. Guttman. "Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae". Molecular Plant-Microbe Interactions® 18, nr 4 (kwiecień 2005): 275–82. http://dx.doi.org/10.1094/mpmi-18-0275.

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Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system (TTSS). Recent availability of complete genome sequences for a number of P. syringae pathovars has led to a significant increase in the rate of effector discovery. However, lack of a systematic nomenclature has resulted in multiple names being assigned to the same Hop, unrelated Hops designated by the same alphabetic character, and failure of name choices to reflect consistent standards of experimental confirmation or phylogenetic relatedness. Therefore, specific experimental and bioinformatic criteria are proposed for proteins to be designated as Hops. A generic Hop name structure, HopXY#pv strain, also is proposed, wherein family membership is indicated by the alphabetic characters, subgroup membership numerically, and source pathovar and strain in subscript. Guidelines are provided for phylogenetic characterization and name selection for Hops that are novel, related to previously characterized Hops, chimeras, pseudogenes, truncations, or nonexpressed alleles. Phylogenetic analyses of previously characterized Hops are described, the results of which have been used to guide their integration into the proposed nomenclature.

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Matthijnssens, Jelle, Max Ciarlet, Sarah M. McDonald, Houssam Attoui, Krisztián Bányai, J. Rodney Brister, Javier Buesa i in. "Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)". Archives of Virology 156, nr 8 (20.05.2011): 1397–413. http://dx.doi.org/10.1007/s00705-011-1006-z.

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Singh, Prashant, Jana Šnokhousová, Aniket Saraf, Archana Suradkar i Josef Elster. "Phylogenetic evaluation of the genus Nostoc and description of Nostoc neudorfense sp. nov., from the Czech Republic". International Journal of Systematic and Evolutionary Microbiology 70, nr 4 (1.04.2020): 2740–49. http://dx.doi.org/10.1099/ijsem.0.004102.

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Cyanobacterial strain ARC8 was isolated from seepage coming into the river Dračice, Františkov, Czech Republic, and was characterized using a polyphasic approach. Strain ARC8 showed a typical Nostoc -like morphology and in-depth morphological characterization indicated that it is a member of the genus Nostoc . Furthermore, in the 16S rRNA gene phylogeny inferred using Bayesian inference, maximum likelihood and neighbour joining methods, strain ARC8 clustered within the Nostoc sensu stricto clade. The phylogenetic distance and the positioning of strain ARC8 also indicated that it is a member of the genus Nostoc . Furthermore, the rbcL gene phylogeny along with the 16S–23S ITS secondary structure analysis also supported the findings from the 16S rRNA gene tree. In accordance with the International Code of Nomenclature for Algae, Fungi and Plants we describe a novel species of Nostoc with the name Nostoc neudorfense sp. nov.

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Saraf, Aniket, Himanshu G. Dawda, Archana Suradkar, Vaibhav Agre i Prashant Singh. "Fortiea necridiiformans sp. nov., a soil-dwelling cyanobacterium from Pachmarhi Biosphere Reserve, India". International Journal of Systematic and Evolutionary Microbiology 70, nr 8 (1.08.2020): 4714–24. http://dx.doi.org/10.1099/ijsem.0.004337.

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Cyanobacterial strain PS4G was isolated from seepage soil sampled at Pachmarhi, Madhya Pradesh, India, and was characterized using a polyphasic approach. The results of morphological analysis showed that strain PS4G had unique morphological characteristics which were not observed in the other described species of the genus Fortiea. In the 16S rRNA gene phylogenetic analysis inferred using Bayesian inference, maximum-likelihood and neighbour-joining methods, strain PS4G clustered within the clade consisting of the members of the genus Fortiea. Furthermore, in the secondary structure analysis using the D1–D1′ helix and BoxB regions of 16S–23S ITS, strain PS4G showed marked differences in comparison with other members of the genus Fortiea. Overall, the morphological, phylogenetic and folded 16S–23S ITS secondary structure examination indicated that strain PS4G represents a novel species of the genus Fortiea. In accordance with the International Code of Nomenclature of Algae, Fungi and Plants we describe a novel species of Fortiea with the name Fortiea necridiiformans sp. nov.

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Mulet, Magdalena, David Sánchez, Jorge Lalucat, Kyoung Lee i Elena García-Valdés. "Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol". International Journal of Systematic and Evolutionary Microbiology 65, Pt_11 (1.11.2015): 4013–18. http://dx.doi.org/10.1099/ijsem.0.000529.

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Pseudomonas sp. KL28T is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genus Pseudomonas. The name ‘Pseudomonas alkylphenolia’ was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28T with the Pseudomonas putida group, with Pseudomonas vranovensis DSM 16006T as the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA, gyrB, rpoD and rpoB partial gene sequences showed that isolate KL28T could be differentiated from P. vranovensis DSM 16006T (sequence similarity 93.7 %). Genomic comparisons of strain KL28T with the type strains of the species in the P. putida group using average nucleotide index based on blast (ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities with P. vranovensis DSM 16006T, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28T ( = JCM 16553T = KCTC 22206T) as the type strain of a novel species, for which the formerly proposed name, ‘P. alkylphenolia’, is correctly latinized as Pseudomonas alkylphenolica sp. nov.

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Kumar, Naresh, Aniket Saraf, Sagarika Pal i Prashant Singh. "Description of Cylindrospermum solincola sp. nov. from Jammu and Kashmir, India and Further Insights into the Ecological Distribution and Morphological Attributes of Cylindrospermum badium". Diversity 15, nr 5 (25.04.2023): 592. http://dx.doi.org/10.3390/d15050592.

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Two cyanobacterial strains KUT1-PS and 18C-PS were collected from the soil surface and vernal pool, respectively, from the Basantgarh village, Udhampur district of the union territory of Jammu and Kashmir, India and characterized by a polyphasic approach. The morphological characterization indicated that both the strains showed typical Cylindrospermum-like morphology and probably belonged to the genus Cylindrospermum. Further, phylogenetic interpretations at the genus level were made using the 16S rRNA gene while the 16S-23S ITS region phylogenetic analysis and secondary structure analysis were conducted to enhance the resolution at the species level. The results from the comparative morphological analysis, the 16S rRNA gene percent similarity and phylogenetic analyses, the 16S-23S ITS percent dissimilarity and the ITS secondary structure analyses provided enough evidence that the strain 18C-PS is a representative of Cylindrospermum badium, providing further insights into its ecological distribution and morphological attributes. Additionally, the strain KUT1-PS was a novel species of the genus Cylindrospermum and is referred to herein as Cylindrospermum solincola sp. nov., in accordance with the International Code of Nomenclature for algae, fungi and plants. This study also discusses the importance of comparing the newly sequenced strains with previously established species before making final taxonomic interpretations.

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Kläring, Karoline, Sarah Just, Ilias Lagkouvardos, Laura Hanske, Dirk Haller, Michael Blaut, Mareike Wenning i Thomas Clavel. "Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut". International Journal of Systematic and Evolutionary Microbiology 65, Pt_3 (1.03.2015): 870–78. http://dx.doi.org/10.1099/ijs.0.000030.

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Three strains of an anaerobic, Gram-stain-positive coccobacillus were isolated from the intestines of mice. These strains shared 100 % similarity in their 16S rRNA gene sequences, but were distantly related to any described members of the family Lachnospiraceae (<94 %). The most closely related species with names that have standing in nomenclature were Robinsoniella peoriensis , Ruminococcus gnavus , Blautia producta and Clostridium xylanolyticum . Phylogenetic relationships based on 16S rRNA gene sequence analysis were confirmed by partial sequencing of hsp60 genes. The use of an in-house database search pipeline revealed that the new isolates are most prevalent in bovine gut samples when compared with human and mouse samples for Ruminococcus gnavus and B. producta . All three isolated strains shared similar cellular fatty acid patterns dominated by C16 : 0 methyl ester. Differences in the proportions of C12 : 0 methyl ester, C14 : 0 methyl ester and C18 : 1 cis-11 dimethyl acetal were observed when compared with phylogenetically neighbouring species. The major short-chain fatty acid produced by strain SRB-530-5-HT was acetic acid. This strain tested positive for utilization of d-fructose, d-galacturonic acid, d-malic acid, l-alanyl l-threonine and l-glutamic acid but was negative for utilization of amygdalin, arbutin, α-d-glucose, 3-methyl d-glucose and salicin, in contrast to the type strain of the closest related species Robinsoniella peoriensis . The isolates were not able to use mannitol for growth. Based on genotypic, phenotypic and chemotaxonomic characteristics, we propose to create the new genus and species Murimonas intestini gen. nov., sp. nov. to accommodate the three strains SRB-530-5-HT ( = DSM 26524T = CCUG 63391T) (the type strain of Murimonas intestini), SRB-509-4-S-H ( = DSM 27577 = CCUG 64595) and SRB-524-4-S-H ( = DSM 27578 = CCUG 64594).

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Chongtrakool, Piriyaporn, Teruyo Ito, Xiao Xue Ma, Yoko Kondo, Suwanna Trakulsomboon, Chuntima Tiensasitorn, Mantana Jamklang, Tavinun Chavalit, Jae-Hoon Song i Keiichi Hiramatsu. "Staphylococcal Cassette Chromosome mec (SCCmec) Typing of Methicillin-Resistant Staphylococcus aureus Strains Isolated in 11 Asian Countries: a Proposal for a New Nomenclature for SCCmec Elements". Antimicrobial Agents and Chemotherapy 50, nr 3 (marzec 2006): 1001–12. http://dx.doi.org/10.1128/aac.50.3.1001-1012.2006.

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ABSTRACT A description of staphylococcal cassette chromosome mec (SCCmec) elements carried by 615 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in 11 Asian countries is reported, and a novel nomenclatural system based on their structures is proposed. The 615 strains were classified as type 3A (370 strains), type 2A (207 strains), type 2B (32 strains), type 1B (1 strain), and nontypeable (5 strains). The previously reported type III SCCmec (DDBJ/EMBL/GenBank accession no. AB037671) carried by the MRSA strain 85/2082 was ascertained to be composed of two SCC elements, type 3A SCCmec and SCCmercury. PCR analysis indicated that 310 of 370 type 3A SCCmec strains carried both SCC elements. These strains were prevalent in eight countries: Thailand, Sri Lanka, Indonesia, Vietnam, Philippines, Saudi Arabia, India, and Singapore. The remaining 60 type 3A SCCmec strains differed with respect to the left extremity polymorphism or to the presence of ccrC. Among these, two were identified as carrying only type 3A SCCmec elements, but their left extremities differed. Type 2A SCCmec strains predominated in Korea and Japan, although the frequency of the presence of ant(4′)-1 gene downstream of mecA varied (53% for Korean strains; 93% for Japanese strains). Various SCCmec elements were identified in the tested strains, and limited numbers were identified by their multilocus sequence typing genotypes. These data suggest that numerous MRSA clones are disseminated in Asian hospitals, and these consist of minor clones that are presumed to have arisen locally and major clones that are presumed to have been introduced from other countries.

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da Silva Malone, Camila Francieli, Janaína Rigonato, Haywood Dail Laughinghouse, Éder Carlos Schmidt, Zenilda Laurita Bouzon, Annick Wilmotte, Marli Fátima Fiore i Célia Leite Sant'Anna. "Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses". International Journal of Systematic and Evolutionary Microbiology 65, Pt_9 (1.09.2015): 2993–3007. http://dx.doi.org/10.1099/ijs.0.000369.

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For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically ‘intermediate’ between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants.

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Pathak, Jyoti, Gandhi Gracy Ramasamy, Aditi Agrawal, Subhi Srivastava, Bhusangar Raghavendra Basavaarya, Mohan Muthugounder, Venugopal Kundalagurki Muniyappa, Pratheepa Maria, Anil Rai i Thiruvengadam Venkatesan. "Comparative Transcriptome Analysis to Reveal Differentially Expressed Cytochrome P450 in Response to Imidacloprid in the Aphid Lion, Chrysoperla zastrowi sillemi (Esben-Petersen)". Insects 13, nr 10 (3.10.2022): 900. http://dx.doi.org/10.3390/insects13100900.

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The aphid lion, Chrysoperla zastrowi sillemi (Neuroptera: Chrysopidae) is a highly effective beneficial predator of many agricultural pests and has developed resistance to several insecticides. Understanding the molecular mechanism of insecticide resistance in the predators is crucial for its effective application in IPM programs. Therefore, transcriptomes of imidacloprid-resistant and susceptible strains have been assessed using RNA-seq. Cytochrome P450 is one of the important gene families involved in xenobiotic metabolism. Hence, our study focused on the CYP gene family where mining, nomenclature, and phylogenetic analysis revealed a total of 95 unique CYP genes with considerable expansion in CYP3 and CYP4 clans. Further, differential gene expression (DGE) analysis revealed ten CYP genes from CYP3 and CYP4 clans to be differentially expressed, out of which nine genes (CYP4419A1, CYP4XK1, CYP4416A10, CYP4416A-fragment8, CYP6YL1, CYP6YH6, CYP9GK-fragment16, CYP9GN2, CYP9GK6) were downregulated and one (CYP9GK3) was upregulated in the resistant strain as compared to the susceptible strain. Expression validation by quantitative real-time PCR (qRT-PCR) is consistent with the DGE results. The expansion and differential expression of CYP genes may be an indicator of the capacity of the predator to detoxify a particular group of insecticides.

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Kuhnert, Peter, Isabelle Brodard, Maher Alsaaod, Adrian Steiner, Michael H. Stoffel i Joerg Jores. "Treponema phagedenis (ex Noguchi 1912) Brumpt 1922 sp. nov., nom. rev., isolated from bovine digital dermatitis". International Journal of Systematic and Evolutionary Microbiology 70, nr 3 (1.03.2020): 2115–23. http://dx.doi.org/10.1099/ijsem.0.004027.

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‘ Treponema phagedenis ’ was originally described in 1912 by Noguchi but the name was not validly published and no type strain was designated. The taxon was not included in the Approved Lists of Bacterial Names and hence has no standing in nomenclature. Six Treponema strains positive in a ‘ T. phagedenis ’ phylogroup-specific PCR test were isolated from digital dermatitis (DD) lesions of cattle and further characterized and compared with the human strain ‘ T. phagedenis ’ ATCC 27087. Results of phenotypic and genotypic analyses including API ZYM, VITEK2, MALDI-TOF and electron microscopy, as well as whole genome sequence data, respectively, showed that they form a cluster of species identity. Moreover, this species identity was shared with ‘ T. phagedenis ’-like strains reported in the literature to be regularly isolated from bovine DD. High average nucleotide identity values between the genomes of bovine and human ‘ T. phagedenis ’ were observed. Slight genomic as well as phenotypic variations allowed us to differentiate bovine from human isolates, indicating host adaptation. Based on the fact that this species is regularly isolated from bovine DD and that the name is well dispersed in the literature, we propose the species Treponema phagedenis sp. nov., nom. rev. The species can phenotypically and genetically be identified and is clearly separated from other Treponema species. The valid species designation will allow to further explore its role in bovine DD. The type strain for Treponema phagedenis sp. nov., nom. rev. is B43.1T (=DSM 110455T=NCTC 14362T) isolated from a bovine DD lesion in Switzerland.

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Kretschmann, Juliane, Malte Elbrächter, Carmen Zinssmeister, Sylvia Soehner, MONIKA KIRSCH, Wolf-Henning Kusber i Marc Gottschling. "Taxonomic clarification of the dinophyte Peridinium acuminatum Ehrenb., ≡ Scrippsiella acuminata, comb. nov. (Thoracosphaeraceae, Peridiniales)". Phytotaxa 220, nr 3 (24.07.2015): 239. http://dx.doi.org/10.11646/phytotaxa.220.3.3.

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Peridinium acuminatum (Peridiniales, Dinophyceae) was described in the first half of the 19th century, but the name has been rarely adopted since then. It was used as type of Goniodoma, Heteraulacus and Yesevius, providing various sources of nomenclatural and taxonomic confusion. Particularly, several early authors emphasised that the organisms investigated by C.G. Ehrenberg and S.F.N.R. von Stein were not conspecific, but did not perform the necessary taxonomic conclusions. The holotype of P. acuminatum is an illustration dating back to 1834, which makes the determination of the species ambiguous. We collected, isolated, and cultivated Scrippsiella acuminata, comb. nov. (strain GeoB 427) from the type locality off Kiel, Germany (Baltic Sea). We barcoded the species of the Thoracosphaeraceae using rRNA sequences and investigated the morphology of the strain using light and electron microscopy. As taxonomic result, we designate an epitype for Peridinium acuminatum, as no conflict with C.G. Ehrenberg’s protologue can be stated. It is indistinguishable from Scrippsiella trochoidea (likewise described from the Kiel Fjord) that we consider a later heterotypic synonym. Our study contributes to the disentanglement of dinophyte taxonomy in a very challenging case, and we trust that C.G. Ehrenberg and S.F.N.R. von Stein investigated different species under the epithet ‘acuminatum’. The complex nomenclature and taxonomy of Goniodoma, and its type species Goniodoma acuminatum, is discussed in the Electronic Supplement. We consider Pyrrhotriadinium, with the type species Pyrrhotriadinium polyedricum (Gonyaulacales), well suited to harbour all gonyaulacalean taxa so far assigned to Goniodoma and Heteraulacus as well.

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Leonard, Susan R., Mark K. Mammel, David A. Rasko i David W. Lacher. "Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid". Applied and Environmental Microbiology 82, nr 14 (6.05.2016): 4309–19. http://dx.doi.org/10.1128/aem.01129-16.

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ABSTRACTHybrid isolates of Shiga toxin-producingEscherichia coli(STEC) and enterotoxigenicE. coli(ETEC) encoding heat-stable enterotoxin (ST) are being reported with increasing frequency from a variety of sources. However, information regarding the plasmids that these strains harbor is scarce. In this study, we sequence and characterize a plasmid, p7v, from the STEC/ETEC hybrid strain 7v. Whole-genome phylogenetic analyses of STEC/ETEC hybrid strains and prototypeE. coliisolates of other pathotypes placed 7v in theEscherichiasp. cryptic lineage 1 (CL1) clade. The complete plasmid, p7v, was determined to be 229,275 bp and encodes putative virulence factors that are typically carried on STEC plasmids as well as those often carried on ETEC plasmids, indicating that the hybrid nature of the strain extends beyond merely encoding the two toxins. Plasmid p7v carries two copies ofstawith identical sequences, which were discovered to be divergent from thestasequences found in the prototype human ETEC strains. Using a nomenclature scheme based on a phylogeny constructed fromstaandstbsequences, thestaencoded on p7v is designated STa4.In silicoanalysis determined that p7v also encodes the K88 fimbria, a colonization factor usually associated with porcine ETEC plasmids. The p7v sequence and the presence of plasmid-encoded virulence factors are compared to those of other STEC/ETEC CL1 hybrid genomes and reveal gene acquisition/loss at the strain level. In addition, the interrogation of 24 STEC/ETEC hybrid genomes for identification of plasmid replicons, colonization factors, Stx and ST subtypes, and other plasmid-encoded virulence genes highlights the diversity of these hybrid strains.IMPORTANCEHybrid Shiga toxin-producingEscherichia coli/enterotoxigenicEscherichia coli(STEC/ETEC) strains, which have been isolated from environmental, animal, and human clinical samples, may represent an emerging threat as food-borne pathogens. Characterization of these strains is important for assessing virulence potential, aiding in the development of pathogen detection methods, and understanding how the hybrid strains evolve to potentially have a greater impact on public health. This study represents, to our knowledge, both the first characterization of a closed plasmid sequence from a STEC/ETEC hybrid strain and the most comprehensive phylogenetic analysis of available STEC/ETEC hybrid genomes to date. The results demonstrate how the mobility of plasmid-associated virulence genes has resulted in the creation of a diverse plasmid repertoire within the STEC/ETEC hybrid strains.

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Gaysina, Lira A., Jeffrey R. Johansen, Aniket Saraf, Rezeda Z. Allaguvatova, Sagarika Pal i Prashant Singh. "Roholtiella volcanica sp. nov., a New Species of Cyanobacteria from Kamchatkan Volcanic Soils". Diversity 14, nr 8 (2.08.2022): 620. http://dx.doi.org/10.3390/d14080620.

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During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe our strain K7 as a novel species of the genus Roholtiella with the name Roholtiella volcanica sp. nov., in accordance with the International Code of Nomenclature for algae, fungi, and plants. This work continues the rapid expansion of the description of new taxa of cyanobacteria, and particularly demonstrates a coming phase in cyanobacterial taxonomy in which the discovery of new species in recently described genera rapidly increases our understanding of the diversity in this phylum.

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Boxberger, Manon, Sibylle Magnien, Angeline Antezack, Clara Rolland, Marine Makoa Meng, Cheikh Ibrahima Lo, Bernard La Scola i Nadim Cassir. "Leucobacter manosquensis sp. nov.—A Novel Bacterial Species Isolated from Healthy Human Skin". Microorganisms 11, nr 10 (11.10.2023): 2535. http://dx.doi.org/10.3390/microorganisms11102535.

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Extending our knowledge on human skin microbiota is a challenge to better decipher its role in health and disease. Using the culturomics method, we isolated strain Marseille-Q4368 from the healthy forehead of a 59-year-old woman. We describe here the main characteristics of this bacterium using a taxonogenomic approach. This new bacterial species is Gram-positive, non-motile, and non-spore-forming. Its 16S rRNA sequence exhibited a similarity of 99.59% with Leucobacter chromiiresistens, the most closely related species in terms of nomenclature. However, a digital DNA–DNA hybridization analysis between these two species revealed a maximum identity similarity of only 27.5%. We found phenotypical and genomic differences between strain Marseille-Q4368 and its closely related species. These findings underscore the classification of this bacterium as a distinct species. Hence, we propose the name Leucobacter manosquensis sp. nov. strain Marseille-Q4368 (=CSUR Q4368 = DSM 112403) for this newly identified bacterial species.

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Holmes, Barry, i J. Jim Farmer III. "Correction of the type strain of Aeromonas punctata (Zimmermann 1890) Snieszko 1957 and of A. punctata subsp. punctata from ATCC 15468T to NCMB 74T (=NCIMB 74T= ATCC 23309T)". International Journal of Systematic and Evolutionary Microbiology 70, nr 3 (1.03.2020): 2155–57. http://dx.doi.org/10.1099/ijsem.0.003960.

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Under Rule 23a (Note 4) of the Bacteriological Code we ask the Judicial Commission to issue an opinion that will correct two errors that were made on the original 1980 Approved Lists of Bacterial Names. We request that the type strain designations for Aeromonas punctata and Aeromonas punctata subsp. punctata be corrected from ATCC 15468T to NCMB 74T. We also ask that the opinion state the ‘correct’ or best way to write the author citations for several other Aeromonas names in order to avoid future instability in nomenclature when the citations are given.

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Kalinina, Olga, Helene Norder, Sergey Mukomolov i Lars O. Magnius. "A Natural Intergenotypic Recombinant of Hepatitis C Virus Identified in St. Petersburg". Journal of Virology 76, nr 8 (15.04.2002): 4034–43. http://dx.doi.org/10.1128/jvi.76.8.4034-4043.2002.

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ABSTRACT Hepatitis C virus (HCV) evolution is thought to proceed by mutations within the six genotypes. Here, we report on a viable spontaneous HCV recombinant and we show that recombination may play a role in the evolution of this virus. Previously, 149 HCV strains from St. Petersburg had been subtyped by limited sequencing within the NS5B region. In the present study, the core regions of 41 of these strains were sequenced to investigate the concordance of HCV genotyping for these two genomic regions. Two phylogenetically related HCV strains were found to belong to different subtypes, 2k and 1b, according to sequence analysis of the 5′ untranslated region (5′UTR)-core and the NS5B regions, respectively. By sequencing of the E2-p7-NS2 region, the crossover point was mapped within the NS2 region, probably between positions 3175 and 3176 (according to the numbering system for strain pj6CF). Sequencing of the 5′UTR-core regions of four other HCV strains, phylogenetically related to the above-mentioned two strains (based on analysis within the NS5B region), revealed that these four strains were also recombinants. Since a nonrecombinant 2k strain was found in St. Petersburg, the recombination may have taken place there around a decade ago. Since the frequency of this recombinant is now high enough to allow the detection of the recombinant in a fraction of the city's population, it seems to be actively spreading there. The reported recombinant is tentatively designated RF1_2k/1b, in agreement with the nomenclature used for HIV recombinants. Recombination between HCV genotypes must now be considered in the classification, laboratory diagnosis, and treatment of HCV infection.

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Oberste, M. Steven, David Schnurr, Kaija Maher, Suleiman al-Busaidy i Mark A. Pallansch. "Molecular identification of new picornaviruses and characterization of a proposed enterovirus 73 serotype". Journal of General Virology 82, nr 2 (1.02.2001): 409–16. http://dx.doi.org/10.1099/0022-1317-82-2-409.

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Enteroviruses (EV) have traditionally been identified by using serotype-specific antisera in a virus-neutralization test. Three EV strains isolated in California, USA, in 1955, 1964 and 1978, and a 1995 Oman isolate, were found to be antigenically related to one another; however, the strains were not neutralized by standard EV typing antisera, suggesting that they may represent a new EV serotype. The isolates were characterized genetically by RT–PCR coupled with amplicon sequencing and comparison to a database of enterovirus nucleotide sequences. The strains were 75·3 to 87·2% identical to one another in complete VP1 nucleotide sequence, but no more than 68% identical in sequence to the prototype strain of any EV serotype. Their complete capsid sequences were closely related to one another, but only distantly related to those of any EV prototype strain. The California and Oman isolates were most closely related to members of EV cluster B, suggesting that they are unclassified members (i.e. a new serotype) of cluster B. The complete genome sequence was determined for one isolate, CA55-1988, and the predicted polyprotein sequence was 86·5 to 89·2% identical to those of other cluster B EV and 56·7 to 61·9% identical to the polyprotein sequences of EV belonging to other clusters. Isolation of this new EV serotype from samples obtained on two continents and over a period of 40 years suggests continued circulation over a wide geographical area. In keeping with standard picornavirus nomenclature, we propose that this new serotype be named ‘enterovirus 73’ (EV73).

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Ping, Song, Wang Qin-Ying, Wu Hui-Xian, Lu Xiu-Jun i Wang Yong. "Identification of thecrygene inBacillus thuringiensisstrain WZ-9 and its toxicity againstHenosepilachna vigintioctomaculata". Chinese Journal of Agricultural Biotechnology 5, nr 3 (grudzień 2008): 245–50. http://dx.doi.org/10.1017/s1479236208002453.

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AbstractBacillus thuringiensisstrain WZ-9, isolated from soil in Hebei province, China, was effective againstHenosepilachna vigintioctomaculatalarvae. The strain presented bipyramidal crystals with a protein band of 130 kDa in SDS–PAGE. The pH changes of the culture media showed important fluctuations during the 24 h growth cycle. The pH varied less in log and stationary phases than it did in the exponential phase. Bioassay results showed that the WZ-9 strain was only harmful to larvae ofH. vigintioctomaculataand not to either adults ofH. vigintioctomaculataor other several lepidopteran and coleopteran insects. LC50to second-instar larvae ofH. vigintioctomaculatawas 2.95×107cells/ml after 72 h. Genotypic investigations showed that this strain possessed thecry7gene. Sequence analysis demonstrated that the encoding gene contained an open reading frame (ORF) of 3414 bp and encoded 1138 amino acid residues. The deduced amino acid sequence was 99.65% identical to that of the reported Cry7Ab2 sequences. This gene was designated by the Bt δ-endotoxin nomenclature committee as Cry7Ab3 with accession number BI 1015188 in the GenBank database.

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Papke, R. Thane, Emma White, Prajwal Reddy, Griffin Weigel, Masahiro Kamekura, Hiroaki Minegishi, Ron Usami i Antonio Ventosa. "A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales". International Journal of Systematic and Evolutionary Microbiology 61, nr 12 (1.12.2011): 2984–95. http://dx.doi.org/10.1099/ijs.0.029298-0.

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Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, the Halobacteriales is a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of the Halobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genus Haloarcula was analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within the Halobacteriales.

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Gardner, Jeffrey G., i Jorge C. Escalante-Semerena. "In Bacillus subtilis, the Sirtuin Protein Deacetylase, Encoded by the srtN Gene (Formerly yhdZ), and Functions Encoded by the acuABC Genes Control the Activity of Acetyl Coenzyme A Synthetase". Journal of Bacteriology 191, nr 6 (9.01.2009): 1749–55. http://dx.doi.org/10.1128/jb.01674-08.

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ABSTRACT This report provides in vivo evidence for the posttranslational control of the acetyl coenzyme A (Ac-CoA) synthetase (AcsA) enzyme of Bacillus subtilis by the acuA and acuC gene products. In addition, both in vivo and in vitro data presented support the conclusion that the yhdZ gene of B. subtilis encodes a NAD+-dependent protein deacetylase homologous to the yeast Sir2 protein (also known as sirtuin). On the basis of this new information, a change in gene nomenclature, from yhdZ to srtN (for sirtuin), is proposed to reflect the activity associated with the YdhZ protein. In vivo control of B. subtilis AcsA function required the combined activities of AcuC and SrtN. Inactivation of acuC or srtN resulted in slower growth and cell yield under low-acetate conditions than those of the wild-type strain, and the acuC srtN strain grew under low-acetate conditions as poorly as the acsA strain. Our interpretation of the latter result was that both deacetylases (AcuC and SrtN) are needed to maintain AcsA as active (i.e., deacetylated) so the cell can grow with low concentrations of acetate. Growth of an acuA acuC srtN strain on acetate was improved over that of the acuA + acuC srtN strain, indicating that the AcuA acetyltransferase enzyme modifies (i.e., inactivates) AcsA in vivo, a result consistent with previously reported in vitro evidence that AcsA is a substrate of AcuA.

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Skuce, Robin A., Thomas P. McCorry, Julie F. McCarroll, Solvig M. M. Roring, Alistair N. Scott, David Brittain, Stephen L. Hughes, R. Glyn Hewinson i Sydney D. Neill. "Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets". Microbiology 148, nr 2 (1.02.2002): 519–28. http://dx.doi.org/10.1099/00221287-148-2-519.

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The lack of a convenient high-resolution strain-typing method has hampered the application of molecular epidemiology to the surveillance of bacteria of the Mycobacterium tuberculosis complex, particularly the monitoring of strains of Mycobacterium bovis. With the recent availability of genome sequences for strains of the M. tuberculosis complex, novel PCR-based M. tuberculosis-typing methods have been developed, which target the variable-number tandem repeats (VNTRs) of minisatellite-like mycobacterial interspersed repetitive units (MIRUs), or exact tandem repeats (ETRs). This paper describes the identification of seven VNTR loci in M. tuberculosis H37Rv, the copy number of which varies in other strains of the M. tuberculosis complex. Six of these VNTRs were applied to a panel of 100 different M. bovis isolates, and their discrimination and correlation with spoligotyping and an established set of ETRs were assessed. The number of alleles varied from three to seven at the novel VNTR loci, which differed markedly in their discrimination index. There was positive correlation between spoligotyping, ETR- and VNTR-typing. VNTR-PCR discriminates well between M. bovis strains. Thirty-three allele profiles were identified by the novel VNTRs, 22 for the ETRs and 29 for spoligotyping. When VNTR- and ETR-typing results were combined, a total of 51 different profiles were identified. Digital nomenclature and databasing were intuitive. VNTRs were located both in intergenic regions and annotated ORFs, including PPE (novel glycine-asparigine-rich) proteins, a proposed source of antigenic variation, where VNTRs potentially code repeating amino acid motifs. VNTR-PCR is a valuable tool for strain typing and for the study of the global molecular epidemiology of the M. tuberculosis complex. The novel VNTR targets identified in this study should additionally increase the power of this approach.

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Raeburn, Candice, Shin Kasahara, Toshi Komoda, Catherine Abbott i Peter M. Smooker. "Draft genome sequence and nomenclature adjustment of Rhodococcus qingshengii CS98, a cesium-accumulating strain isolated in Japan". Biotechnology Reports 25 (marzec 2020): e00415. http://dx.doi.org/10.1016/j.btre.2019.e00415.

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Sundberg, J. P., J. M. Ward, H. HogenEsch, A. Yu Nikitin, P. M. Treuting, J. B. Macauley i P. N. Schofield. "Training Pathologists in Mouse Pathology". Veterinary Pathology 49, nr 2 (3.09.2010): 393–97. http://dx.doi.org/10.1177/0300985810381244.

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Expertise in the pathology of mice has expanded from traditional regulatory and drug safety screening (toxicologic pathology) primarily performed by veterinary pathologists to the highly specialized area of mouse research pathobiology performed by veterinary and medical pathologists encompassing phenotyping of mutant mice and analysis of research experiments exploiting inbred mouse strains and genetically engineered lines. With increasing use of genetically modified mice in research, mouse pathobiology and, by extension, expert mouse research-oriented pathologists have become integral to the success of basic and translational biomedical research. Training for today’s research-oriented mouse pathologist must go beyond knowledge of anatomic features of mice and strain-specific background diseases to the specialized genetic nomenclature, husbandry, and genetics, including the methodology of genetic engineering and complex trait analysis. While training can be accomplished through apprenticeships in formal programs, these are often heavily service related and do not provide the necessary comprehensive training. Specialty courses and short-term mentoring with expert specialists are opportunities that, when combined with active practice and publication, will lead to acquisition of the skills required for cutting-edge mouse-based experimental science.

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Roldán, M., M. Ramírez, J. del Campo, M. Hernández-Mariné i J. Komárek. "Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria ), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria". International Journal of Systematic and Evolutionary Microbiology 63, Pt_6 (1.06.2013): 2326–33. http://dx.doi.org/10.1099/ijs.0.045468-0.

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This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluorescence z-stacks, revealed a large surface area of nearly flat, arm-like thylakoidal membranes connected to each other and forming a unified structure in a way that, to our knowledge, has never been described before. Phylogenetic analyses using the 16S rRNA gene sequence showed 95 % similarity to strain Chroococcus sp. JJCM (GenBank accession no. AM710384). The diacritical phenotypic features do not correspond to any species currently described, and the genetic traits support the strain being classified as the first member of an independent genus in the order Chroococcales and the family Chroococcaceae. Hence, we propose the name Chalicogloea cavernicola gen. nov., sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. The type strain of Chalicogloea cavernicola is COLL 3T ( = CCALA 975T = CCAP 1424/1T).

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Belov, Vyacheslav, i Valery Morozov. "Fire Resistance of Non-Crack Resistant Flexural Reinforced Concrete Elements". Applied Mechanics and Materials 725-726 (styczeń 2015): 15–20. http://dx.doi.org/10.4028/www.scientific.net/amm.725-726.15.

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In developed countries only loss of property because of fire makes annually up to 2% of their national income [9, 15]. The bearing capacity of reinforced concrete structures at high temperature impact is lost within several dozens of minutes [1, 3, 5, 10, 12, 18, 25]. Disappointing statistics of increase of both the number of fires and the scope of damage due to them aggravates the actual problem of determination of reinforced concrete structures fire-endurance. The main problems and methods of evaluation of reinforced concrete structure fire resistance are stated. Within the framework of block approach to evaluation of strain of flexural reinforced concrete elements with cracks, design model of reinforced concrete thermo-force resistance is made. Extended nomenclature of influences of high temperature at fire on decrease of performance of bearing reinforced concrete structures is considered. Empirical dependencies of strength and strain characteristics of concrete and reinforcement on high temperatures are used. Proposals on specification of evaluation of fire resistance of statically indeterminate reinforced concrete structures are formulated.

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Noguera, Pedro A., i Jorge E. Ibarra. "Detection of New cry Genes of Bacillus thuringiensis by Use of a Novel PCR Primer System". Applied and Environmental Microbiology 76, nr 18 (23.07.2010): 6150–55. http://dx.doi.org/10.1128/aem.00797-10.

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ABSTRACT On the basis of the known cry gene sequences of Bacillus thuringiensis, three sets of primers were designed from four conserved blocks found in the delta-endotoxin-coding region. The primer pairs designed amplify the regions between blocks 1 and 5, 2 and 5, and 1 and 4. In silico analyses indicated that 100% of the known three-domain cry gene sequences can be amplified by these sets of primers. To test their ability to amplify known and unknown cry gene sequences, 27 strains from the CINVESTAV (LBIT series) collection showing atypical crystal morphology were selected. Their DNA was used as the template with the new primer system, and after a systematic amplification and sequencing of the amplicons, each strain showed one or more cry-related sequences, totaling 54 different sequences harbored by the 27 strains. Seven sequences were selected on the basis of their low level of identity to the known cry sequences, and once cloning and sequencing of the complete open reading frames were done, three new cry-type genes (primary ranks) were identified and the toxins that they encode were designated Cry57Aa1, Cry58Aa1, and Cry59Aa1 by the B. thuringiensis Toxin Nomenclature Committee. The rest of the seven sequences were classified Cry8Ka2, Cry8-like, Cry20Ba1, and Cry1Ma1 by the committee. The crystal morphology of the selected strains and analysis of the new Cry protein sequences showed interesting peculiarities.

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Blanco-Rivero, A., F. Leganés, E. Fernández-Valiente, P. Calle i F. Fernández-Piñas. "mrpA, a gene with roles in resistance to Na+ and adaptation to alkaline pH in the cyanobacterium Anabaena sp. PCC7120". Microbiology 151, nr 5 (1.05.2005): 1671–82. http://dx.doi.org/10.1099/mic.0.27848-0.

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Transposon mutagenesis of Anabaena sp. PCC7120 led to the isolation of a mutant strain, PHB11, which grew poorly at pH values above 10. The mutant strain exhibited pronounced Na+ sensitivity; this sensitivity was higher under basic conditions. Mutant PHB11 also showed an inhibition of photosynthesis that was much more pronounced at alkaline pH. Reconstruction of the transposon mutation of PHB11 in the wild-type strain reproduced the phenotype of the original mutant. The wild-type version of the mutated gene was cloned and the mutation complemented. In mutant strain PHB11, the transposon had inserted within an ORF that is part of a seven-ORF operon with significant sequence similarity to a family of bacterial operons that are believed to code for a novel multiprotein cation/proton antiporter primarily involved in resistance to salt stress and adaptation to alkaline pH. The Anabaena operon was denoted mrp (multiple resistance and pH adaptation) following the nomenclature of the Bacillus subtilis operon; the ORF mutated in PHB11 corresponded to mrpA. Computer analysis suggested that all seven predicted Anabaena Mrp proteins were highly hydrophobic with several transmembrane domains; in fact, the predicted protein sequences encoded by mrpA, mrpB and mrpC showed significant similarity to hydrophobic subunits of the proton pumping NADH : ubiquinone oxidoreductase. In vivo expression studies indicated that mrpA is induced with increasing external Na+ concentrations and alkaline pH; mrpA is also upregulated under inorganic carbon (Ci) limitation. The biological significance of a putative cyanobacterial Mrp complex is discussed.

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Bernáldez-Sarabia, Johanna, Andrea Figueroa-Montiel, Salvador Dueñas, Karla Cervantes-Luévano, Jesús Beltrán, Ernesto Ortiz, Samanta Jiménez i in. "The Diversified O-Superfamily in Californiconus californicus Presents a Conotoxin with Antimycobacterial Activity". Toxins 11, nr 2 (20.02.2019): 128. http://dx.doi.org/10.3390/toxins11020128.

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Californiconus californicus, previously named Conus californicus, has always been considered a unique species within cone snails, because of its molecular, toxicological and morphological singularities; including the wide range of its diet, since it is capable of preying indifferently on fish, snails, octopus, shrimps, and worms. We report here a new cysteine pattern conotoxin assigned to the O1-superfamily capable of inhibiting the growth of Mycobacterium tuberculosis (Mtb). The conotoxin was tested on a pathogen reference strain (H37Rv) and multidrug-resistant strains, having an inhibition effect on growth with a minimal inhibitory concentration (MIC) range of 3.52–0.22 μM, similar concentrations to drugs used in clinics. The peptide was purified from the venom using reverse phase high-performance liquid chromatography (RP-HPLC), a partial sequence was constructed by Edman degradation, completed by RACE and confirmed with venom gland transcriptome. The 32-mer peptide containing eight cysteine residues was named O1_cal29b, according to the current nomenclature for this type of molecule. Moreover, transcriptomic analysis of O-superfamily toxins present in the venom gland of the snail allowed us to assign several signal peptides to O2 and O3 superfamilies not described before in C. californicus, with new conotoxins frameworks.

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