Volatile hydrocarbons inhibit methanogenic crude oil degradation

Methanogenic degradation of crude oil in subsurface sediments occurs slowly, but without the need for exogenous electron acceptors, is sustained for long periods and has enormous economic and environmental consequences. Here we show that volatile hydrocarbons are inhibitory to methanogenic oil biodegradation by comparing degradation of an artificially weathered crude oil with volatile hydrocarbons removed, with the same oil that was not weathered. Volatile hydrocarbons (nC5-nC10, methylcyclohexane, benzene, toluene, and xylenes) were quantified in the headspace of microcosms. Aliphatic (n-alkanes nC12-nC34) and aromatic hydrocarbons (4-methylbiphenyl, 3-methylbiphenyl, 2-methylnaphthalene, 1-methylnaphthalene) were quantified in the total hydrocarbon fraction extracted from the microcosms. 16S rRNA genes from key microorganisms known to play an important role in methanogenic alkane degradation (Smithella and Methanomicrobiales) were quantified by quantitative PCR. Methane production from degradation of weathered oil in microcosms was rapid (1.1 ± 0.1 μmol CH4/g sediment/day) with stoichiometric yields consistent with degradation of heavier n-alkanes (nC12-nC34). For non-weathered oil, degradation rates in microcosms were significantly lower (0.4 ± 0.3 μmol CH4/g sediment/day). This indicated that volatile hydrocarbons present in the non-weathered oil inhibit, but do not completely halt, methanogenic alkane biodegradation. These findings are significant with respect to rates of biodegradation of crude oils with abundant volatile hydrocarbons in anoxic, sulphate-depleted subsurface environments, such as contaminated marine sediments which have been entrained below the sulfate-reduction zone, as well as crude oil biodegradation in petroleum reservoirs and contaminated aquifers

Moving from Trust to Trustworthiness: Experiences of public engagement in the Scottish Health Informatics Programme

The Scottish Health Informatics Programme (SHIP) was a Scotland-wide research programme exploring ways of collecting, managing and analysing electronic patient records for health research. As part of the SHIP public engagement work stream, a series of eight focus groups and a stakeholder workshop were conducted to explore perceptions of the role, relevance and functions of trust (or trustworthiness) in relation to research practices. The findings demonstrate that the public’s relationships of trust and/or mistrust in science and research are not straightforward. This paper aims to move beyond simple descriptions of whether publics trust researchers, or in whom members of the public place their trust, and to explore more fully the bases of public trust/mistrust in science, what trust implies and equally what it means for research/researchers to be trustworthy. This has important implications for public engagement in interdisciplinary projects

Exploration of chronic kidney disease prevalence estimates using new measures of kidney function in the health survey for England

Background: chronic kidney disease (CKD) diagnosis relies on glomerular filtration rate (eGFR) estimation, traditionally using the creatinine-based Modification of Diet in Renal Disease (MDRD) equation. The Chronic Kidney Disease Epidemiology Collaboration (CKDEPI) equation performs better in estimating eGFR and predicting mortality and CKD progression risk. Cystatin C is an alternative glomerular filtration marker less influenced by muscle mass. CKD risk stratification is improved by combining creatinine eGFR with cystatin C and urinary albumin to creatinine ratio (uACR). We aimed to identify the impact of introducing CKDEPI and cystatin C on the estimated prevalence and risk stratification of CKD in England and to describe prevalence and associations of cystatin C.Methods and findings: cross sectional study of 5799 people in the nationally representative 2009 and 2010 Health Surveys for England. Primary outcome measures: prevalence of MDRD, CKDEPI and cystatin C-defined eGFR&lt;60ml/min/1.73m2; prevalence of CKD biomarker combinations (creatinine, cystatin C, uACR). Using CKDEPI instead of MDRD reduced the prevalence of eGFR&lt;60ml/min/1.73m2 from 6.0% (95% CI 5.4–6.6%) to 5.2% (4.7–5.8%) equivalent to around 340,000 fewer individuals in England. Those reclassified as not having CKD evidenced a lower risk profile. Prevalence of cystatin C eGFR&lt;60ml/min/1.73m2 was 7.7% and independently associated with age, lack of qualifications, being an ex-smoker, BMI, hypertension, and albuminuria. Measuring cystatin C in the 3.9% people with CKDEPI-defined eGFR&lt;60ml/min/1.73m2 without albuminuria (CKD Category G3a A1) reclassified about a third into a lower risk group with one of three biomarkers and two thirds into a group with two of three. Measuring cystatin C in the 6.7% people with CKDEPI eGFR &gt;60ml/min/1.73m2 with albuminuria (CKD Category G1-2) reclassified almost a tenth into a higher risk group.Limitations: cross sectional study, single eGFR measure, no measured (‘true’) GFR.Conclusions: introducing the CKDEPI equation and targeted cystatin C measurement reduces estimated CKD prevalence and improves risk stratification<br/

Validity of estimated prevalence of decreased kidney function and renal replacement therapy from primary care electronic health records compared with national survey and registry data in the United Kingdom.

BACKGROUND: Anonymous primary care records are an important resource for observational studies. However, their external validity is unknown in identifying the prevalence of decreased kidney function and renal replacement therapy (RRT). We thus compared the prevalence of decreased kidney function and RRT in the Clinical Practice Research Datalink (CPRD) with a nationally representative survey and national registry. METHODS: Among all people ≥25 years of age registered in the CPRD for ≥1 year on 31 March 2014, we identified patients with an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2, according to their most recent serum creatinine in the past 5 years using the Chronic Kidney Disease Epidemiology Collaboration equation and patients with recorded diagnoses of RRT. Denominators were the entire population in each age-sex band irrespective of creatinine measurement. The prevalence of eGFR <60 mL/min/1.73 m2 was compared with that in the Health Survey for England (HSE) 2009/2010 and the prevalence of RRT was compared with that in the UK Renal Registry (UKRR) 2014. RESULTS: We analysed 2 761 755 people in CPRD [mean age 53 (SD 17) years, men 49%], of whom 189 581 (6.86%) had an eGFR <60 mL/min/1.73 m2 and 3293 (0.12%) were on RRT. The prevalence of eGFR <60 mL/min/1.73 m2 in CPRD was similar to that in the HSE and the prevalence of RRT was close to that in the UKRR across all age groups in men and women, although the small number of younger patients with an eGFR <60 mL/min/1.73 m2 in the HSE might have hampered precise comparison. CONCLUSIONS: UK primary care data have good external validity for the prevalence of decreased kidney function and RRT

Translation elongation can control translation initiation on eukaryotic mRNAs

Synonymous codons encode the same amino acid, but differ in other biophysical properties. The evolutionary selection of codons whose properties are optimal for a cell generates the phenomenon of codon bias. Although recent studies have shown strong effects of codon usage changes on protein expression levels and cellular physiology, no translational control mechanism is known that links codon usage to protein expression levels. Here, we demonstrate a novel translational control mechanism that responds to the speed of ribosome movement immediately after the start codon. High initiation rates are only possible if start codons are liberated sufficiently fast, thus accounting for the observation that fast codons are overrepresented in highly expressed proteins. In contrast, slow codons lead to slow liberation of the start codon by initiating ribosomes, thereby interfering with efficient translation initiation. Codon usage thus evolved as a means to optimise translation on individual mRNAs, as well as global optimisation of ribosome availability

The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes

Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace) and Marinobacter sp. (Gammaproteobacteria) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g(cell-C)/g(alkane-C)], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g(cell-C)/g(alkane-C)] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales). Enrichment of hydrogen-oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella

Accommodation or political identity:Scottish members of the UK Parliament

Phonetic variation among Scottish Members of the UK Parliament may be influenced by\ud convergence to Southern English norms (Carr & Brulard 2006) or political identity (e.g.,\ud Hall-Lew, Coppock & Starr 2010). Drawing on a year’s worth of political speeches (2011-\ud 2012) from ten Scottish Members of the UK Parliament (MPs), we find no acoustic evidence\ud for the adoption of a Southern English low vowel system; rather, we find that vowel height is\ud significantly correlated with political party: Scottish Labour Party MPs produce a higher\ud ‘CAT’ vowel (Johnston 1997) than do Scottish National Party MPs. The results contradict\ud claims that Scottish MPs acquire ‘Anglo-English’ features while at UK Parliament. Rather,\ud we suggest that the variation indexes political meaning, with a subset of individuals drawing\ud on that indexicality in production

Methanogenic crude oil-degrading microbial consortia are not universally abundant in anoxic environments

Crude oil-amended microcosms were prepared with inocula from eleven anoxic environments (4 river sediments, 3 lake sediments, and 4 sludges from wastewater treatment reactors) to determine their ability to produce methane from the biodegradation of crude oil. Over incubation periods of up to 1150 days, oil-stimulated methanogenesis and concomitant loss of alkanes occurred in microcosms prepared with five of the inocula whereas six of the inocula did not show oil-stimulated methane production. Bacterial and archaeal communities from microcosms exhibiting high levels of oil-stimulated methanogenesis were distinct from communities where methanogenic crude oil degradation was not detected. Successional changes were consistent with the quantitative enrichment of syntrophic hydrocarbon degrading bacteria and methanogens over time. In conclusion, in oil-impacted environments methanogenic crude oil-degrading microbial consortia are present in relatively low abundance and exhibit slow growth, and while they may be ubiquitously distributed they may not be present at sufficiently high abundance to be detected