Generalized approach for enabling multimode quantum optics

We develop a universal approach enabling the study of any multimode quantum optical system evolving under a quadratic Hamiltonian. Our strategy generalizes the standard symplectic analysis and permits the treatment of multimode systems even in situations where traditional theoretical methods cannot be applied. This enables the description and investigation of a broad variety of key-resources for experimental quantum optics, ranging from optical parametric oscillators, to silicon-based micro-ring resonator, as well as opto-mechanical systems

Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5], 12:i:- Strains Isolated from Wild Griffon Vultures in Eastern Spain

[EN] Monophasic Salmonella enterica subsp. enterica serovar Typhimurium is one of the most common zoonotic pathogens. Salmonella species reside in a wide variety of hosts, including wild animals. Thus, we report here the genome sequences of 12 monophasic S. Typhimurium strains isolated from healthy wild vultures to gain better insight into their epidemiology and host-pathogen interactions.This work was funded by Generalitat Valenciana (Government of Valencia) and by CEU-UCH (Consolidacion de Indicadores INDI15/16, INDI16/20, and INDI17/25).Marín, C.; D'auria, G.; Martínez-Priego, L.; Marco-Jiménez, F. (2019). Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5], 12:i:- Strains Isolated from Wild Griffon Vultures in Eastern Spain. Microbiology Resource Announcements. 8(42):1-3. https://doi.org/10.1128/MRA.00570-19S13842Blanco, G. (2018). Supplementary feeding as a source of multiresistantSalmonellain endangered Egyptian vultures. Transboundary and Emerging Diseases, 65(3), 806-816. doi:10.1111/tbed.12806Krawiec, M., Kuczkowski, M., Kruszewicz, A., & Wieliczko, A. (2015). Prevalence and genetic characteristics of Salmonella in free-living birds in Poland. BMC Veterinary Research, 11(1), 15. doi:10.1186/s12917-015-0332-xMolina-López, R. A., Vidal, A., Obón, E., Martín, M., & Darwich, L. (2015). Multidrug-resistantSalmonella entericaSerovar Typhimurium Monophasic Variant 4,12:i:- Isolated from Asymptomatic Wildlife in a Catalonian Wildlife Rehabilitation Center, Spain. Journal of Wildlife Diseases, 51(3), 759-763. doi:10.7589/2015-01-019Marin, C., Torres, C., Marco-Jiménez, F., Cerdà-Cuéllar, M., Sevilla, S., Ayats, T., & Vega, S. (2018). Supplementary feeding stations for conservation of vultures could be an important source of monophasic Salmonella typhimurium 1,4,[5],12:i:-. Science of The Total Environment, 636, 449-455. doi:10.1016/j.scitotenv.2018.04.310Marin, C., Palomeque, M.-D., Marco-Jiménez, F., & Vega, S. (2014). Wild Griffon Vultures (Gyps fulvus) as a Source of Salmonella and Campylobacter in Eastern Spain. PLoS ONE, 9(4), e94191. doi:10.1371/journal.pone.0094191Schmieder, R., & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27(6), 863-864. doi:10.1093/bioinformatics/btr026Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. doi:10.1093/bioinformatics/btu170Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. doi:10.1093/bioinformatics/btq033Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics, 30(14), 2068-2069. doi:10.1093/bioinformatics/btu153Lima, T., Auchincloss, A. H., Coudert, E., Keller, G., Michoud, K., Rivoire, C., … Bairoch, A. (2009). HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Research, 37(Database), D471-D478. doi:10.1093/nar/gkn661Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., … Bateman, A. (2015). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 44(D1), D279-D285. doi:10.1093/nar/gkv1344Seribelli, A. A., Frazão, M. R., Gonzales, J. C., Cao, G., Leon, M. S., Kich, J. D., … Falcão, J. P. (2018). Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil. Genome Announcements, 6(16), e00232-18. doi:10.1128/genomea.00232-1

Draft genome sequence of Mycobacterium brumae ATCC 51384

Here, we report the draft genome sequence of Mycobacterium brumae type strain ATCC 51384. This is the first draft genome sequence of M. brumae, a nonpathogenic, rapidly growing, nonchromogenic mycobacterium, with immunotherapeutic capacities

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

BACKGROUND: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes. DESCRIPTION: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information. CONCLUSION: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at

The Active Human Gut Microbiota Differs from the Total Microbiota

The human gut microbiota is considered one of the most fascinating reservoirs of microbial diversity hosting between 400 to 1000 bacterial species distributed among nine phyla with Firmicutes, Bacteroidetes and Actinobacteria representing around of the diversity. One of the most intriguing issues relates to understanding which microbial groups are active players in the maintenance of the microbiota homeostasis

Legionella pneumophila pangenome reveals strain-specific virulence factors

<p>Abstract</p> <p>Background</p> <p><it>Legionella pneumophila </it>subsp. <it>pneumophila </it>is a gram-negative <it>γ-Proteobacterium </it>and the causative agent of Legionnaires' disease, a form of epidemic pneumonia. It has a water-related life cycle. In industrialized cities <it>L. pneumophila </it>is commonly encountered in refrigeration towers and water pipes. Infection is always via infected aerosols to humans. Although many efforts have been made to eradicate <it>Legionella </it>from buildings, it still contaminates the water systems. The town of Alcoy (Valencian Region, Spain) has had recurrent outbreaks since 1999. The strain "Alcoy 2300/99" is a particularly persistent and recurrent strain that was isolated during one of the most significant outbreaks between the years 1999-2000.</p> <p>Results</p> <p>We have sequenced the genome of the particularly persistent <it>L. pneumophila </it>strain Alcoy 2300/99 and have compared it with four previously sequenced strains known as Philadelphia (USA), Lens (France), Paris (France) and Corby (England).</p> <p>Pangenome analysis facilitated the identification of strain-specific features, as well as some that are shared by two or more strains. We identified: (1) three islands related to anti-drug resistance systems; (2) a system for transport and secretion of heavy metals; (3) three systems related to DNA transfer; (4) two CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems, known to provide resistance against phage infections, one similar in the Lens and Alcoy strains, and another specific to the Paris strain; and (5) seven islands of phage-related proteins, five of which seem to be strain-specific and two shared.</p> <p>Conclusions</p> <p>The dispensable genome disclosed by the pangenomic analysis seems to be a reservoir of new traits that have mainly been acquired by horizontal gene transfer and could confer evolutionary advantages over strains lacking them.</p

Manihot Esculenta (Euphorbiaceae), A New Alien Species In Italy

Abstract In the present work the presence of Manihot esculenta Crantz is reported for the first time for Italy and Europe, a neophyte native to South America: ecology and invasive status are presented

Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein

<p>Abstract</p> <p>Background</p> <p>The repeats in toxin (Rtx) are an important pathogenicity factor involved in host cells invasion of <it>Legionella pneumophila </it>and other pathogenic bacteria. Its role in escaping the host immune system and cytotoxic activity is well known. Its repeated motives and modularity make Rtx a multifunctional factor in pathogenicity.</p> <p>Results</p> <p>The comparative analysis of <it>rtx </it>gene among 6 strains of <it>L. pneumophila </it>showed modularity in their structures. Among compared genomes, the N-terminal region of the protein presents highly dissimilar repeats with functionally similar domains. On the contrary, the C-terminal region is maintained with a fashionable modular configuration, which gives support to its proposed role in adhesion and pore formation. Despite the variability of <it>rtx </it>among the considered strains, the flanking genes are maintained in synteny and similarity.</p> <p>Conclusion</p> <p>In contrast to the extracellular bacteria <it>Vibrio cholerae</it>, in which the <it>rtx </it>gene is highly conserved and flanking genes have lost synteny and similarity, the gene region coding for the Rtx toxin in the intracellular pathogen <it>L. pneumophila </it>shows a rapid evolution. Changes in the <it>rtx </it>could play a role in pathogenicity. The interplay of the Rtx toxin with host membranes might lead to the evolution of new variants that are able to escape host cell defences.</p