Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity

The proteome is the second axis of the microbiome:host interactome and proteases are a significant aspect in this interaction. They interact with a large variety of host proteins and structures and in many situations are implicated in pathogenesis. Furthermore faecal samples are commonly collected and stored frozen so they can be analysed at a later date. So we were interested to know whether long term storage affected the integrity of proteases and total protein and whether historical native faecal samples were still a viable option for answering research questions around the functional proteome

The stability of microbially reduced U(IV); impact of residual electron donor and sediment ageing

AbstractThe stimulation of microbial U(VI) reduction to precipitate insoluble U(IV) has been proposed as a means of remediating mobile uranium groundwater contamination. Crucial to the success of such a remediation strategy is determining the longevity of U(IV) biominerals in the subsurface, particularly if the groundwater becomes oxidising. Here we describe experiments to assess the susceptibility of microbially-reduced U(IV) to oxidative remobilisation both via aeration and by the addition of nitrate at environmentally-relevant conditions. Additional factors examined include the possibility of biogenic U(IV) becoming more crystalline (and potentially more recalcitrant) during a period of ageing, and the role played by residual electron donor in controlling the long-term fate of the uranium. Biogenic U(IV) was precipitated as a non-crystalline U(IV) or “monomeric” phase, with a small but increasing contribution to the EXAFS spectra from nanocrystalline uraninite occurring during 15months of ageing. Despite this, no evidence was observed for an increase in recalcitrance to oxidative remobilisation. However, the presence of residual electron donor post-biostimulation was shown to exert a strong control on U(IV) reoxidation kinetics, highlighting the importance of maintaining the presence of electron donor in the subsurface, in order to protect biogenic U(IV) from oxidative remobilisation

Carbon cycling in a Patagonian fjord: Strength of biological vs. physical pump

Póster presentado en la 2nd International Ocean Research Conference, celebrada en Barcelona del 17 al 21 de noviembre de 2014.Understanding the role of the pelagic “biological and physical pump” in carbon cycling is critical to climate change adaptation and mitigation efforts especially in coastal areas characterized by intense biogeochemical cycling. Fjords are among the few coastal regions that appear to be net annual sinks for atmosphericCO2. Vertical profiles of temperature and salinity were collected with a CTD revealing intense vertical structure in the water column that could be summarised as 2 layers with a transition-mixing region .Spatio-temporal sampling of physical and biogeochemical (C system, nutrients, Phyto- and Zooplankton, in situ dissolved pCO2) parameters was conducted in Comau Fjord (Puerto Montt-Chile) during Austral spring from the surface and deep layers. Spatial variation in water column structure in the fjord was minimal, however the depth of the upper layer varies probably depending on the surface-water inputs. Surface waters had significantly lower pCO2 values compared to the atmosphere and deeper water. Concentrations of suspended material and chlorophyll a were higher deeper in the water column, suggesting concentration process of material across the halocline. Overall, concentrations of particulate matter and mesozooplankton (during the study period), were low compared to many mid-latitude regions, and near absent in the vicinity of the 2 rivers entering the fjord. The low surface water pCO2 values suggest negative air-water CO2fluxes predominates within Comau Fjord during Austral spring. This preliminary study suggests that the geochemical properties of watershed and the low [DIC] of surface-water inputs, i.e., the physical pump, seems to play an important role in this region.This work was supported by the project 2013CL0013 funded by the CSIC, Fundacion Endesa and Fundación San Ignacio del Huinay. Funding was also provided by the Spanish Ministry of Sciences and Innovation (JAE DOCTORES 2010 contract for E.P.M., JAE PREDOCTORAL scholarship for S.T. and S.F.) and part-funded bythe European Union (European Social Fund, ESF2007-2013) and the Spanish Ministry for Economy and Competitiveness.Peer Reviewe

The Scavenger Receptor MARCO Modulates TLR-Induced Responses in Dendritic Cells

The scavenger receptor MARCO mediates macrophage recognition and clearance of pathogens and their polyanionic ligands. However, recent studies demonstrate MARCO expression and function in dendritic cells, suggesting MARCO might serve to bridge innate and adaptive immunity. To gain additional insight into the role of MARCO in dendritic cell activation and function, we profiled transcriptomes of mouse splenic dendritic cells obtained from MARCO deficient mice and their wild type counterparts under resting and activating conditions. In silico analysis uncovered major alterations in gene expression in MARCO deficient dendritic cells resulting in dramatic alterations in key dendritic cell-specific pathways and functions. Specifically, changes in CD209, FCGR4 and Complement factors can have major consequences on DC-mediated innate responses. Notably, these perturbations were magnified following activation with the TLR-4 agonist lipopolysaccharide. To validate our in silico data, we challenged DC‘s with various agonists that recognize all mouse TLRs and assessed expression of a set of immune and inflammatory marker genes. This approach identified a differential contribution of MARCO to TLR activation and validated a major role for MARCO in mounting an inflammatory response. Together, our data demonstrate that MARCO differentially affects TLR-induced DC activation and suggest targeting of MARCO could lead to different outcomes that depend on the inflammatory context encountered by DC

Randomized phase II study investigating pazopanib versus weekly paclitaxel in relapsed or progressive urothelial cancer

Purpose: Two previous single-arm trials have drawn conflicting conclusions regarding the activity of pazopanib in urothelial cancers after failure of platinum-based chemotherapy. Patients and Methods: This randomized (1:1) open-label phase II trial compared the efficacy of pazopanib 800 mg orally with paclitaxel (80 mg/m2 days 1, 8, and 15 every 28 days) in the second-line setting. The primary end point was overall survival (OS). Results: Between August 2012 and October 2014, 131 patients, out of 140 planned, were randomly assigned. The study was terminated early on the recommendation of the independent data monitoring committee because of futility. Final analysis after the preplanned number of deaths (n = 110) occurred after a median follow-up of 18 months. One hundred fifteen deaths had occurred at the final data extract presented here. Median OS was 8.0 months for paclitaxel (80% CI, 6.9 to 9.7 months) and 4.7 months for pazopanib (80% CI, 4.2 to 6.4 months). The hazard ratio (HR) adjusted for baseline stratification factors was 1.28 (80% CI, 0.99 to 1.67; one-sided P = .89). Median progression-free survival was 4.1 months for paclitaxel (80% CI, 3.0 to 5.6 months) and 3.1 months for pazopanib (80% CI, 2.7 to 4.6 months; HR, 1.09; 80% CI, 0.85 to 1.40; one-sided P = .67). Discontinuations for toxicity occurred in 7.8% and 23.1% for paclitaxel and pazopanib, respectively. Conclusion: Pazopanib did not have greater efficacy than paclitaxel in the second-line treatment of urothelial cancers. There was a trend toward superior OS for paclitaxel

A quality-of-life measure for adults with primary ciliary dyskinesia: QOL-PCD

Primary ciliary dyskinesia (PCD) is characterised by chronic suppurative lung disease, rhino-sinusitis, hearing impairment and sub-fertility. We have developed the first multidimensional measure to assess health-related quality of life (HRQoL) in adults with PCD (QOL-PCD). Following a literature review and expert panel meeting, open-ended interviews with patients investigated the impact of PCD on HRQoL in the UK and North America (n=21). Transcripts were content analysed to derive saturation matrices. Items were rated for relevance by patients (n=49). Saturation matrices, relevance scores, literature review, evaluation of existing measures, and expert opinion contributed to development of a preliminary questionnaire. The questionnaire was refined following cognitive interviews (n=18). Open-ended interviews identified a spectrum of issues unique to adults with PCD. Saturation matrices confirmed comprehensive coverage of content. QOL-PCD includes 48 items covering the following seven domains: Physical Functioning, Emotional Functioning, Treatment Burden, Respiratory and Sinus Symptoms, Ears and Hearing, Social Functioning, and Vitality and Health Perceptions. Cognitive testing confirmed that content was comprehensive and the items were well-understood by respondents. Content validity and cognitive testing supported the items and structure. QOL-PCD has been translated into other languages and is awaiting psychometric testing

Molecular Epidemiology of Eastern Equine Encephalitis Virus, New York

Southern strains are undergoing amplification, perpetuation, and overwintering in New York

Linguistics

Contains research summary and abstracts for nine theses

Two-stage study designs combining genome-wide association studies, tag single-nucleotide polymorphisms, and exome sequencing: accuracy of genetic effect estimates

Genome-wide association studies (GWAS) test for disease-trait associations and estimate effect sizes at tag single-nucleotide polymorphisms (SNPs), which imperfectly capture variation at causal SNPs. Sequencing studies can examine potential causal SNPs directly; however, sequencing the whole genome or exome can be prohibitively expensive. Costs can be limited by using a GWAS to detect the associated region(s) at tag SNPs followed by targeted sequencing to identify and estimate the effect size of the causal variant. Genetic effect estimates obtained from association studies can be inflated because of a form of selection bias known as the winner’s curse. Conversely, estimates at tag SNPs can be attenuated compared to the causal SNP because of incomplete linkage disequilibrium. These two effects oppose each other. Analysis of rare SNPs further complicates our understanding of the winner’s curse because rare SNPs are difficult to tag and analysis can involve collapsing over multiple rare variants. In two-stage analysis of Genetic Analysis Workshop 17 simulated data sets, we find that selection at the tag SNP produces upward bias in the estimate of effect at the causal SNP, even when the tag and causal SNPs are not well correlated. The bias similarly carries through to effect estimates for rare variant summary measures. Replication studies designed with sample sizes computed using biased estimates will be under-powered to detect a disease-causing variant. Accounting for bias in the original study is critical to avoid discarding disease-associated SNPs at follow up