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Background: The term triple-negative breast cancer (TNBC) is used to describe breast cancers without expression of estrogen receptor, progesterone receptor or HER2 amplification. To advance targeted treatment options for TNBC, it is critical that the subtypes within this classification be described in regard to their characteristic biology and gene expression. The Cancer Genome Atlas (TCGA) dataset provides not only clinical and mRNA expression data but also expression data for microRNAs.Results: In this study, we applied the Lehmann classifier to TCGA-derived TNBC cases which also contained microRNA expression data and derived subtype-specific microRNA expression patterns. Subsequent analyses integrated known and predicted microRNA-mRNA regulatory nodes as well as patient survival data to identify key networks. Notably, basal-like 1 (BL1) TNBCs were distinguished from basal-like 2 TNBCs through up-regulation of members of the miR-17-92 cluster of microRNAs and suppression of several known miR-17-92 targets including inositol polyphosphate 4-phosphatase type II, INPP4B.Conclusions: These data demonstrate TNBC subtype-specific microRNA and target mRNA expression which may be applied to future biomarker and therapeutic development studies.

BackgroundDespite their importance as vectors of zoonotic parasites that can impact human and animal health, Culicoides species distribution across different habitat types is largely unknown. Here we document the community composition of Culicoides found in an urban environment including developed and natural sites in east central Texas, a region of high vector diversity due to subtropical climates, and report their infection status with haemoparasites.ResultsA total of 251 individual Culicoides were collected from May to June 2016 representing ten Culicoides species, dominated by C. neopulicaris followed by C. crepuscularis. We deposited 63 sequences to GenBank among which 25 were the first deposition representative for six Culicoides species: C. arboricola (n = 1); C. nanus (n = 4); C. debilipalpis (n = 2); C. haematopotus (n = 14); C. edeni (n = 3); and C. hinmani (n = 1). We also record for the first time the presence of C. edeni in Texas, a species previously known to occur in the Bahamas, Florida and South Carolina. The urban environments with natural area (sites 2 and 4) had higher species richness than sites more densely populated or in a parking lot (sites 1 and 3) although a rarefaction analysis suggested at least two of these sites were not sampled sufficiently to characterize species richness. We detected a single C. crepuscularis positive for Onchocercidae gen. sp. DNA and another individual of the same species positive for Haemoproteus sacharovi DNA, yielding a 2.08% prevalence (n = 251) for both parasites in this species.ConclusionsWe extend the knowledge of the Culicoides spp. community in an urban environment of Texas, USA, and contribute to novel sequence data for these species. Additionally, the presence of parasite DNA (Onchocercidae gen. sp. and H. sacharovi) from C. crepuscularis suggests the potential for this species to be a vector of these parasites.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-3283-9) contains supplementary material, which is available to authorized users.

Soil and sediment samples from several intertidal environment exposed to different types of contamination were studied to investigate the importance of grain size in relation to the capacity of the substrates to retain trace metals. The unfractionated samples (referred to as bulk samples) were separated into the following grain/size fractions: fine-coarse sand (2-0.100 mm), very fine sand (0.100-0.050 mm), silt (0.050-0.002 mm), and clay (0.002 mm). The sample into its fractions was carried out was in a glove box under high-purity N2 atmosphere in order to minimize any alterations to the samples. The bulk samples were characterized in terms of physicochemical properties such as pH, redox potential, and grain size. The total organic carbon (TOC), total sulfur (S), iron (Fe) pyrite, Fe, and manganese (Mn), and trace metals lead (Pb), mercury (Hg), chromium (Cr), and nickel (Ni) were analyzed in the bulk samples and in each fraction. The sand fractions were also examined by scanning electron microscopy (SEM). Comparisons of the above parameters were made between fractions and between each fraction and the corresponding bulk sample. The fine-coarse sand fraction contained high levels of the primary elements of the geochemical processes that occur in marine sedimentary environments such as TOC, total Fe, Mn, and S. The net concentrations of these four elements were higher in the fine-coarse sand fraction than in the very fine sand fraction and were similar to the net concentrations in the silt and clay fractions. Detailed SEM analysis of the sand coarse fraction revealed the presence of Fe and aluminum oxyhydroxide coatings in the oxic layers, whereas the framboidal pyrites and coatings observed in the anoxic layers were Fe sulfides. The presence of the various coatings explains why the trace metal concentrations in the sand fine-coarse fraction were similar to those in the clay fraction and higher than those in the very fine sand fraction. The present results highlight the importance of the sand fraction, which is generally disregarded in geochemical and environmental studies of sedimentary layers.