Improving interoperability between microbial information and sequence databases

BACKGROUND: Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distribution of biological resources and related data collected by 28 European culture collections. Linking this information to bioinformatics databanks can make the collections' holdings more visible after a search in molecular biology databanks and vice-versa. Identification of links to sequence databases can be useful, but annotation and indexing problems, together with compilation errors, immediately arise. In this paper, we present our efforts for the identification of cross-references between CABRI catalogues and the EMBL Data Library and related results. RESULTS: An SRS site with both EMBL and CABRI catalogues has been set up. Ad-hoc changes in indexing scripts allowed to achieve homogeneous index keys and SRS link features have been used to identify links between databases. After manual checking and comparison with an alternative procedure, about 67,500 valid cross-references were identified, added to the EMBL Data Library and are now distributed with it. HTML links can be established from EMBL to CABRI network service. Procedures can be executed whenever needed. CONCLUSION: Links between EMBL and CABRI catalogues constitute an improved access to micro-organisms of certified quality and can produce positive effects on biomedical research. Further links between CABRI catalogues and other bioinformatics databases can now easily be defined by using these cross-references. Linking genetic information onto natural resources information may stand model for the integration of other databases containing empirical data on these materials

Waddlia chondrophila induces systemic infection, organ pathology, and elicits Th1-associated humoral immunity in a murine model of genital infection.

Waddlia chondrophila is a known bovine abortigenic Chlamydia-related bacterium that has been associated with adverse pregnancy outcomes in human. However, there is a lack of knowledge regarding how W. chondrophila infection spreads, its ability to elicit an immune response and induce pathology. A murine model of genital infection was developed to investigate the pathogenicity and immune response associated with a W. chondrophila infection. Genital inoculation of the bacterial agent resulted in a dose-dependent infection that spread to lumbar lymph nodes and successively to spleen and liver. Bacterial-induced pathology peaked on day 14, characterized by leukocyte infiltration (uterine horn, liver, and spleen), necrosis (liver) and extramedullary hematopoiesis (spleen). Immunohistochemistry demonstrated the presence of a large number of W. chondrophila in the spleen on day 14. Robust IgG titers were detected by day 14 and remained high until day 52. IgG isotypes consisted of high IgG2a, moderate IgG3 and no detectable IgG1, indicating a Th1-associated immune response. This study provides the first evidence that W. chondrophila genital infection is capable of inducing a systemic infection that spreads to major organs, induces uterus, spleen, and liver pathology and elicits a Th1-skewed humoral response. This new animal model will help our understanding of the mechanisms related to intracellular bacteria-induced miscarriages, the most frequent complication of pregnancy that affects one in four women

Antibacterial activity of a combination of cysteine and ciprofloxacin and its relationship with the generation of oxidative stress in extended-spectrum betalactamase-producing escherichia coli strains

The aim of the present work was to evaluate whether L-cysteine enhances theantibiotic susceptibility of extended-spectrum beta-lactamase (ESBL) Escherichia coli strains to ciprofloxacin and to identify the role of Reactive oxygen species (ROS) in the antimicrobial activity.The combined ef5fect of L-cysteine and ciprofloxacin was investigated by the macrodilution broth method and chemiluminescence assay. ESBL 1 and ESBL 2 strains presented a growth inhibition when they were incubated with 0.4 or 0.2 mM of cysteine, respectively compared to the control without antibiotic. Both strains at sub-inhibitory concentration of ciprofloxacin were combined withcysteine, and a clear growth inhibition respect to the control was observed. An increase of 68% in ROS occurred respect to the control when ESBL 1 was treated with a combination of ciprofloxacin and cysteine, while for ESBL 2 there was a rice of 127 %. The combination of ciprofloxacin with cysteine had the capacity to undergo redox cycling and ROS production with subsequent cellularinjury.Fil: Martínez, S. R.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Bongiovanni, M. E.. Hospital Privado Centro Medico de Córdoba; ArgentinaFil: Piersigilli, Andrea Laura. Sanatorio Aconcagua; ArgentinaFil: Albesa, Inés. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; ArgentinaFil: Becerra, María Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; Argentin

The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation

We thank Manuel Kulagin for technical help, Pierre Bonnaventure for portal vein blood sampling, Francisco Sepulveda for technical assistance in GS-MS acquisition, and Dorothee Hahne (Metabolomics Australia, University of Western Australia) for human samples SCFA isolation, acquisition, and analysis. We also thank Cristina Cartoni (Phenotyping Unit, EPFL) for Milliplex analysis, Jessica Dessimoz and her team from the Histology Core Facility (EPFL), Miguel Garcia and his team from the Flow Cytometry Core Facility (EPFL), and staff from the EPFL CPG animal house for excellent animal care. The computations were partially performed at the Vital-IT Center for high-performance computing of the SIB Swiss Institute of Bioinformatics (http://www.vital-it.ch). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement n. 310948. Funding for A.W.W. and a subset of the 16S rRNA gene sequencing was provided by the Wellcome Trust (grant number WT 098051). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Bartonella henselae Persistence within Mesenchymal Stromal Cells Enhances Endothelial Cell Activation and Infectibility That Amplifies the Angiogenic Process (*Scutera S and Mitola S co-first authors; Sozzani S and Musso T co-last authors)

Some bacterial pathogens can manipulate the angiogenic response, suppressing or inducing it for their own ends. In humans, Bartonella henselae is associated with cat-scratch disease and vasculoproliferative disorders such as bacillary angiomatosis and bacillary peliosis. Although endothelial cells (ECs) support the pathogenesis of B. henselae, the mechanisms by which B. henselae induces EC activation are not completely clear, as well as the possible contributions of other cells recruited at the site of infection. Mesenchymal stromal cells (MSCs) are endowed with angiogenic potential and play a dual role in infections, exerting antimicrobial properties but also acting as a shelter for pathogens. Here, we delved into the role of MSCs as a reservoir of B. henselae and modulator of EC functions. B. henselae readily infected MSCs and survived in perinuclearly bound vacuoles for up to 8 days. Infection enhanced MSC proliferation and the expression of epidermal growth factor receptor (EGFR), Toll-like receptor 2 (TLR2), and nucleotide-binding oligomerization domain-containing protein 1 (NOD1), proteins that are involved in bacterial internalization and cytokine production. Secretome analysis revealed that infected MSCs secreted higher levels of the proangiogenic factors vascular endothelial growth factor (VEGF), fibroblast growth factor 7 (FGF-7), matrix metallopeptidase 9 (MMP-9), placental growth factor (PIGF), serpin E1, thrombospondin 1 (TSP-1), urokinase-type plasminogen activator (uPA), interleukin 6 (IL-6), platelet-derived growth factor D (PDGF-D), chemokine ligand 5 (CCL5), and C-X-C motif chemokine ligand 8 (CXCL8). Supernatants from B. henselae-infected MSCs increased the susceptibility of ECs to B. henselae infection and enhanced EC proliferation, invasion, and reorganization in tube-like structures. Altogether, these results indicate MSCs as a still underestimated niche for persistent B. henselae infection and reveal MSC-EC cross talk that may contribute to exacerbate bacterium-induced angiogenesis and granuloma formation