Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

La biophotonique au service de l'identification de marqueurs pronostiques intracellulaires

International audienceUsing biophotonics techniques to retrieve prognostic intracellular signatures : IHMO project aims at developing a multimodal microscopy platform that includes in a single machine Raman micro spectroscopy and multispectral imaging used for tumor diagnosis and prognosis. Lymphocytes from 24 leukaemic patients suffering from hyper leukocytosis Chronic Lymphoid Leukemia and from 11 healthy individual have been studied, using around 90 cells per blood sample. Blood smears were prepared on microscopy slides; cells were localized by optical microscopy, and Raman microspectroscopy spectra were acquired on cell nuclei. Afterward multi-Z stacks images of each cell were acquired for eight bands distributed in the visible spectrum. Raman data's were classified using a Support Vector Machine algorithm that provided a molecular signature that allowed for distinguishing lymphocytes from other nucleated blood components with 99.6% sensibility and 98.8% specificity. Then the algorithm was used for developing a classification model splitting leukaemic and healthy smears; sensibility was 95% and specificity was 87.5% among the spectra used for evaluation: 1540 from 11 leukaemic patients and 516 from seven healthy individual. IHMO project has demonstrated the power of Raman microspectroscopy for cell classification. Morphological descriptors obtained from multi-Z and multispectral images provide another independent classification that still needs to be assessed. The microscopy platform can be used more generally in the field of cytohaematology, however application to cytological and histological pathology would need further developments

HS2ST1-dependent signaling pathways determine breast cancer cell viability, matrix interactions, and invasive behavior

Heparan sulfate proteoglycans (HSPGs) act as signaling co-receptors by interaction of their sulfated glycosaminoglycan chains with numerous signaling molecules. In breast cancer, the function of heparan sulfate 2-O-sulfotransferase (HS2ST1), the enzyme mediating 2-O-sulfation of HS, is largely unknown. Hence, a comparative study on the functional consequences of HS2ST1 overexpression and siRNA knockdown was performed in the breast cancer cell lines MCF-7 and MDA-MB-231. HS2ST1 overexpression inhibited Matrigel invasion, while its knockdown reversed the phenotype. Likewise, cell motility and adhesion to fibronectin and laminin were affected by altered HS2ST1 expression. Phosphokinase array screening revealed a general decrease in signaling via multiple pathways. Fluorescent ligand binding studies revealed altered binding of fibroblast growth factor 2 (FGF-2) to HS2ST1-expressing cells compared with control cells. HS2ST1-overexpressing cells showed reduced MAPK signaling responses to FGF-2, and altered expression of epidermal growth factor receptor (EGFR), E-cadherin, Wnt-7a, and Tcf4. The increased viability of HS2ST1-depleted cells was reduced to control levels by pharmacological MAPK pathway inhibition. Moreover, MAPK inhibitors generated a phenocopy of the HS2ST1-dependent delay in scratch wound repair. In conclusion, HS2ST1 modulation of breast cancer cell invasiveness is a compound effect of altered E-cadherin and EGFR expression, leading to altered signaling via MAPK and additional pathways