Alterations in blood microbiota after colonic cancer surgery.

BACKGROUND: Mechanisms contributing to the perioperative stress response remain poorly understood. This study investigated changes in the amount of bacterial DNA in blood and the diversity of blood microbiota in the perioperative period in patients undergoing minimally invasive surgery for colonic cancer in an enhanced recovery after surgery setting. METHODS: DNA encoding the bacterial 16S ribosomal RNA gene (16S rDNA) in whole blood obtained the day before surgery, and on postoperative day (POD) 1 and POD 10-14 was amplified and quantified by PCR before sequencing for taxonomic assignment. Richness, evenness and similarity measures were calculated to compare microbiota between days. Differences in relative abundance were analysed using the linear discriminant analysis effect size (LEfSe) algorithm. RESULTS: Thirty patients were included between January and July 2016. The concentration of bacterial 16S rDNA in blood increased between the day before surgery and POD 1 (P = 0.025). Bacterial richness was lower on POD 10-14 than on the day before surgery and POD 1 (both P < 0·001). LEfSe analysis comparing the day before surgery and POD 10-14 identified changes in the abundance of several bacteria, including Fusobacterium nucleatum, which was relatively enriched on POD 10-14. CONCLUSION: These findings suggest that the blood of patients with colonic cancer harbours bacterial 16S rDNA, which increases in concentration after surgery.

ANTECEDENTES: Los mecanismos que contribuyen a la respuesta al estrés perioperatorio siguen siendo poco conocidos. Este estudio investigó los cambios en la cantidad de ADN bacteriano en la sangre y la diversidad de la microbiota sanguínea en el período perioperatorio en pacientes sometidos a cirugía mínimamente invasiva por cáncer de colon en el contexto de un programe de recuperación mejorada después de la cirugía. MÉTODOS: El ADN que codifica el gen de ARN ribosómico (rNDA) 16S bacteriano en sangre completa obtenido el día antes de la cirugía, el día 1 del postoperatorio y el día 10-14 del postoperatorio se amplificó y cuantificó mediante qPCR antes de la secuenciación para la asignación taxonómica. Se calcularon medidas de riqueza, uniformidad y similitud para comparar la microbiota entre los diferentes días. Las diferencias en la abundancia relativa se analizaron mediante un algoritmo de análisis discriminante lineal de tamaño de efecto (linear discriminant analysis effect size, LEfSe). RESULTADOS: De enero a julio de 2016 se incluyeron 30 pacientes. La concentración de 16S rNDA bacteriano en sangre aumentó desde el día antes de la operación al día 1 del postoperatorio. La riqueza bacteriana disminuyó en el día 10-14 del postoperatorio en comparación con el preoperatorio y el día 1 del postoperatorio. La comparación del preoperatorio y del día 10-14 postoperatorio por LEfSe identificó cambios en la abundancia de varias bacterias, incluida Fusobacterium nucleatum que mostró un enriquecimiento relativo el día 10-14 del postoperatorio. CONCLUSIÓN: Estos hallazgos sugieren que la sangre de los pacientes con cáncer de colon alberga 16S rNDA bacteriano cuya concentración aumenta tras la cirugía.

Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time.

Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.

Observation of vortex coalescence in the anisotropic spin-triplet superconductor Sr2RuO4.

We present direct imaging of magnetic flux structures over the ab face of the anisotropic, spin-triplet superconductor Sr2RuO4 using a scanning microSQUID force microscope. Individual vortices with a single flux quantum were observed at low magnetic fields applied along the out-of-pane direction. At intermediate fields, the direct imaging revealed coalescing of vortices and the formation of flux domains. Our observations imply the existence of a mechanism in this material for bringing vortices together overcoming the conventional repulsive vortex-vortex interaction.

Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.

The CluSTr database (http://www.ebi.ac.uk/clustr/) offers an automatic classification of SWISS-PROT+TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pair-wise sequence comparisons between proteins using the Smith-Waterman algorithm. The analysis, carried out on different levels of protein similarity, yields a hierarchical organization of clusters. Information about domain content of the clustered proteins is provided via the InterPro resource. The introduced InterPro 'condensed graphical view' simplifies the visual analysis of represented domain architectures. Integrated applications allow users to visualize and edit multiple alignments and build sequence divergence trees. Links to the relevant structural data in Protein Data Bank (PDB) and Homology derived Secondary Structure of Proteins (HSSP) are also provided.

Interactive InterPro-based comparisons of proteins in whole genomes.

MOTIVATION: The SWISS-PROT group at the EBI has developed the Proteome Analysis Database utilizing existing resources and providing comprehensive and integrated comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes. The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

InterPro--an integrated documentation resource for protein families, domains and functional sites.

MOTIVATION: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. RESULTS: Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.