Accuracy of radiological staging in identifying high-risk colon cancer patients suitable for neoadjuvant chemotherapy: a multicentre experience.

AIM: A pilot study was undertaken to determine the accuracy of computed tomography (CT) staging in identifying patients with high-risk colon cancers who would be considered as candidates for a neoadjuvant therapy trial (FOxTROT) and those at low risk (T1/T2) who would be excluded. METHOD: Participating radiologists from 19 centres attended workshops for standardization of image interpretation according to previously defined prognostic criteria: good prognosis tumours, including, T1/T2; intermediate prognosis, T3 < 5 mm tumour invasion beyond the muscularis propria (MP); and poor prognosis tumours, including T3 with tumour extension ≥ 5 mm beyond the MP or T4. The CT findings were compared with histopathology as the reference standard. RESULTS: Of 94 patients with radiological and pathological data, 71% were categorized by CT as having a poor prognosis. The sensitivity and specificity of CT in identifying these tumours were 87% (95% CI, 74-94) and 49% (95% CI, 33-65). Sensitivity and specificity for tumour infiltration beyond the MP (T3/T4 vs T1/T2) were 95% (95% CI, 87-98) and 50% (95% CI, 22-77), respectively. Including all CT-staged T3 and T4 patients in the trial would have increased the proportion eligible for entry to 89% (n = 84) without affecting the false-positive rate of 7%. Some 20% of T3/T4 patients would have been ineligible for FOxTROT because of synchronous metastases. CONCLUSION: In a multicentre setting, CT scanning identified high-risk (T3/4) colon cancers with minimal overstaging of T1/T2 tumours, thus establishing the feasibility of radiologically guided neoadjuvant chemotherapy.

Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool.

Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin-Benson-Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium.

Freshwater cyanobacterial blooms have increased worldwide, channeling organic carbon into these systems, and threatening animal health through the production of cyanotoxins. Both toxic and nontoxic Microcoleus proliferations usually occur when there are moderate concentrations of dissolved inorganic nitrogen, but when phosphorus is scarce. In order to understand how Microcoleus establishes thick biofilms (or mats) on riverbeds under phosphorus-limiting conditions, we collected Microcoleus-dominated biofilms over a 19-day proliferation event for proteogenomics. A single pair of nitrogen-dependent Microcoleus species were consistently present in relatively high abundance, although each followed a unique metabolic trajectory. Neither possessed anatoxin gene clusters, and only very low concentrations of anatoxins (~2 µg kg-1) were detected, likely originating from rarer Microcoleus species also present. Proteome allocations were dominated by photosynthesizing cyanobacteria and diatoms, and data indicate biomass was actively recycled by Bacteroidetes and Myxococcales. Microcoleus likely acquired nutrients throughout the proliferation event by uptake of nitrate, urea, and inorganic and organic phosphorus. Both species also harbored genes that could be used for inorganic phosphate solubilization with pyrroloquinoline quinone cofactors produced by cohabiting Proteobacteria. Results indicate that Microcoleus are equipped with diverse mechanisms for nitrogen and phosphorus acquisition, enabling them to proliferate and out-compete others in low-phosphorus waters.

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill.

The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.

Biogeochemical controls on microbial diversity in seafloor sulphidic sediments.

The ultimate fate of hydrothermal sulphides on the seafloor depends on the nature and rate of abiotic and microbially catalysed reactions where sulphide minerals are exposed to oxic seawater. This study combines organic and inorganic geochemical with microbiological measurements across a suboxic transition zone of highly altered sulphidic sediments from the Trans-Atlantic Geotransverse hydrothermal field to characterize the reaction products and microbial communities present. There is distinct biogeochemical zonation apparent within the sediment sequence from oxic surface layers through a suboxic transition zone into the sulphide material. The microbial communities in the sediment differ significantly between the biogeochemical horizons sampled, with the identified microbes inferred to be associated with Fe and S redox cycling. In particular, Marinobacter species, organisms associated with circumneutral Fe oxidation, are dominant in a sulphide lens present in the lower core. The dominance of Marinobacter-related sequences within the relict sulphide lens implies that these organisms play an important role in the alteration of sulphides at the seafloor once active venting has ceased.

Correlates of health care utilization among HIV-seropositive injection drug users.

This study sought to identify correlates of poor health care utilization among HIV-positive injection drug users (IDUs) using Andersen's behavioural health model. We used baseline data from INSPIRE, a study of HIV-positive IDUs (n=1161) to identify predisposing, enabling, and need factors related to poor utilization (defined as fewer than two outpatient visits in the past six months, or identification of emergency room (ER) as the usual place for care). Using bivariate and multivariate models, we found a number of enabling factors that could facilitate the use of health care services such as having health insurance, having seen a case manager, and better engagement with health care providers. These enabling factors could be modified through interventions targeting HIV-positive IDUs. In addition, health insurance and case management appear to be important factors to address because they contributed in making other factors (e.g. lower education, lack of stable housing) non-significant barriers to outpatient care utilization. In the future, these findings may be used to inform the development of interventions that maximize use of scarce HIV resources and improve health care utilization among HIV-positive IDUs.