DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples

Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato

Quinone-mediated extracellular electron transfer processes in ex situ biomethanation reactors

Redox mediators are used in a wide diversity of systems including biological ones. We investigated the effect of adding an artificial quinone (2,7-AQDS) as external redox molecule to an anaerobic digester system dominated by hydrogenotrophic methanogens. When oxidized AQDS was present, the methanogens diverted electrons from H2 to reduce AQDS instead of CO2. The AQDS reduction process was accompanied by a temporary CH4 inhibition, which was re-established several days after the full reduction of AQDS to AH2QDS. The presence of AQDS furthermore resulted in a community shift from Methanobacterium as the dominant methanogen to a more diverse community of methanogens. Protein expression profiles showed a shift in cofactor preference of the adapted community, as a potential response mechanism to AQDS inhibition. AH2QDS was only used as electron donor to a limited extent. Stable isotope incorporation experiments here indicated that the acetogen Acetoanaerobium used AH2QDS to reduce CO2 into acetate.</p

Evaluation of serum ARGS neoepitope as an osteoarthritis biomarker using a standardized model for exercise-induced cartilage extra cellular matrix turnover

Summary: Objective: To propose a standardized model for exercise-induced cartilage turnover and investigate residual levels and dynamics of biomarker serum ARGS (sARGS) in primary osteoarthritis (OA) patients and a supportive group of young healthy subjects. Method: The trial is a randomized, cross-over, exploratory study with interventions of exercise and inactivity. 20 subjects with knee OA, as well as 20 young healthy subjects (mean age 25.7 years (range; 19–30), 50% male), underwent cycling, running and resting interventions on separate days one week apart. Blood samples were taken at baseline, immediately, 1, 2, 3 and 24 h after activity start. sARGS was measured by sandwich ELISA. Results: Intraclass correlation between visits were 0.97 and 0.77 for the OA and healthy group, respectively. An acute drop in sARGS in response to high-intensity exercise was observed in both groups. Minute acute sARGS increase was observed in OA subjects in response to moderate intensity running and cycling, which normalized within 24 h. In healthy subjects an acute drop in sARGS was seen immediately after running, but not cycling, and no other changes were observed. A negative correlation between baseline Kellgren-Lawrence (KL) grade and baseline sARGS (r = −0.69, p = 0.002) in OA was found. A negative correlation between age and sARGS was found in healthy subjects (r = −0.67, p = <0.002). Conclusion: sARGS sensitivity to physical activity is considered low and sARGS is a reproducible and stable marker. Minute acute increases in sARGS were observed in the hours following moderate intensity exercise

Armenia: What drives first movers and how can their efforts be scaled up?

The paper examines ways to expand the contribution of the Armenian diaspora to Armenia’s long-term development agenda. It identifies factors that could explain the involvement and dynamics of a small group of entrepreneurs from the diaspora who have been active in and with Armenia. Based on these findings, it develops recommendations, consistent with the diaspora’s institutional capabilities, for increasing the number of such business activists and transforming diaspora efforts from humanitarian relief campaigns to business initiatives and development projects. The findings are based on detailed interviews with a group of prominent diaspora activists

Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma

CD8+ T cell reactivity towards tumor mutation-derived neoantigens is widely believed to facilitate the antitumor immunity induced by immune checkpoint blockade (ICB). Here we show that broadening in the number of neoantigen-reactive CD8+ T cell (NART) populations between pre-treatment to 3-weeks post-treatment distinguishes patients with controlled disease compared to patients with progressive disease in metastatic urothelial carcinoma (mUC) treated with PD-L1-blockade. The longitudinal analysis of peripheral CD8+ T cell recognition of patient-specific neopeptide libraries consisting of DNA barcode-labelled pMHC multimers in a cohort of 24 patients from the clinical trial NCT02108652 also shows that peripheral NARTs derived from patients with disease control are characterised by a PD1+ Ki67+ effector phenotype and increased CD39 levels compared to bystander bulk- and virus-antigen reactive CD8+ T cells. The study provides insights into NART characteristics following ICB and suggests that early-stage NART expansion and activation are associated with response to ICB in patients with mUC

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats

Blob dynamics in the TORPEX experiment:a multi-code validation

Three-dimensional and two-dimensional seeded blob simulations are performed with five different fluid models, all based on the drift-reduced Braginskii equations, and the numerical results are compared among themselves and validated against experimental measurements provided by the TORPEX device (Fasoli et al 2006 Phys. Plasmas 13 055902). The five models are implemented in four simulation codes, typically used to simulate the plasma dynamics in the tokamak scrape-off layer, namely BOUT++ (Dudson et al 2009 Comput. Phys. Commun. 180 1467), GBS (Ricci et al 2012 Plasma Phys. Control. Fusion 54 124047), HESEL (Nielsen et al 2015 Phys. Lett. A 379 3097), and TOKAM3X (Tamain et al 2014 Contrib. Plasma Phys. 54 555). Three blobs with different velocities and different stability properties are simulated. The differences observed among the simulation results and the different levels of agreement with experimental measurements are investigated, increasing our confidence in our simulation tools and shedding light on the blob dynamics. The comparisons demonstrate that the radial blob dynamics observed in the three-dimensional simulations is in good agreement with experimental measurements and that, in the present experimental scenario, the two-dimensional model derived under the assumption of ${{k}_{\parallel}}=0$ is able to recover the blob dynamics observed in the three-dimensional simulations. Moreover, it is found that an accurate measurement of the blob temperature is important to perform reliable seeded blob simulations

Association of alcohol use with years lived without major chronic diseases: A multicohort study from the IPD-Work consortium and UK Biobank

BACKGROUND: Heavy alcohol consumption increases the risk of several chronic diseases. In this multicohort study, we estimated the number of life-years without major chronic diseases according to different characteristics of alcohol use. METHODS: In primary analysis, we pooled individual-level data from up to 129,942 adults across 12 cohort studies with baseline data collection on alcohol consumption, drinking patterns, and history between 1986 and 2005 (the IPD-Work Consortium). Self-reported alcohol consumption was categorised according to UK guidelines – non-drinking (never or former drinkers); moderate consumption (1–14 units); heavy consumption (>14 units per week). We further subdivided moderate and heavy drinkers by binge drinking pattern (alcohol-induced loss of consciousness). In addition, we assessed problem drinking using linked data on hospitalisations due to alcohol abuse or poisoning. Follow-up for chronic diseases for all participants included incident type 2 diabetes, coronary heart disease, stroke, cancer, and respiratory disease (asthma and chronic obstructive pulmonary disease) as ascertained via linkage to national morbidity and mortality registries, repeated medical examinations, and/or self-report. We estimated years lived without any of these diseases between 40 and 75 years of age according to sex and characteristics of alcohol use. We repeated the main analyses using data from 427,621 participants in the UK Biobank cohort study. FINDINGS: During 1·73 million person-years at risk, 22,676 participants in IPD-Work cohorts developed at least one chronic condition. From age 40 to 75 years, never-drinkers [men: 29·3 (95%CI 27·9–30·8) years, women 29·8 (29·2–30·4) years)] and moderate drinkers with no binge drinking habit [men 28·7 (28·4–29·0) years, women 29·6 (29·4–29·7) years] had the longest disease-free life span. A much shorter disease-free life span was apparent in participants who experienced alcohol poisoning [men 23·4 (20·9–26·0) years, women 24·0 (21·4–26·5) years] and those with self-reported heavy overall consumption and binge drinking [men: 26·0 (25·3–26·8), women 27·5 (26·4–28·5) years]. The pattern of results for alcohol poisoning and self-reported alcohol consumption was similar in UK Biobank. In IPD-Work and UK Biobank, differences in disease-free years between self-reported moderate drinkers and heavy drinkers were 1·5 years or less. INTERPRETATION: Individuals with alcohol poisonings or heavy self-reported overall consumption combined with a binge drinking habit have a marked 3- to 6-year loss in healthy longevity. Differences in disease-free life between categories of self-reported weekly alcohol consumption were smaller. FUNDING: Medical Research Council, National Institute on Aging, NordForsk, Academy of Finland, Finnish Work Environment Fund