Global quantification of mammalian gene expression control

Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles

dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells

Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, including sequence-specific RNA interference (RNAi), sequence-independent interferon (IFN) response and editing by adenosine deaminases. To study the routing of dsRNA to these pathways in vivo, we used transgenic mice ubiquitously expressing from a strong promoter, an mRNA with a long hairpin in its 3′-UTR. The expressed dsRNA neither caused any developmental defects nor activated the IFN response, which was inducible only at high expression levels in cultured cells. The dsRNA was poorly processed into siRNAs in somatic cells, whereas, robust RNAi effects were found in oocytes, suggesting that somatic cells lack some factor(s) facilitating siRNA biogenesis. Expressed dsRNA did not cause transcriptional silencing in trans. Analysis of RNA editing revealed that a small fraction of long dsRNA is edited. RNA editing neither prevented the cytoplasmic localization nor processing into siRNAs. Thus, a long dsRNA structure is well tolerated in mammalian cells and is mainly causing a robust RNAi response in oocytes

Effect of aliskiren on post-discharge outcomes among diabetic and non-diabetic patients hospitalized for heart failure: insights from the ASTRONAUT trial

Aims The objective of the Aliskiren Trial on Acute Heart Failure Outcomes (ASTRONAUT) was to determine whether aliskiren, a direct renin inhibitor, would improve post-discharge outcomes in patients with hospitalization for heart failure (HHF) with reduced ejection fraction. Pre-specified subgroup analyses suggested potential heterogeneity in post-discharge outcomes with aliskiren in patients with and without baseline diabetes mellitus (DM). Methods and results ASTRONAUT included 953 patients without DM (aliskiren 489; placebo 464) and 662 patients with DM (aliskiren 319; placebo 343) (as reported by study investigators). Study endpoints included the first occurrence of cardiovascular death or HHF within 6 and 12 months, all-cause death within 6 and 12 months, and change from baseline in N-terminal pro-B-type natriuretic peptide (NT-proBNP) at 1, 6, and 12 months. Data regarding risk of hyperkalaemia, renal impairment, and hypotension, and changes in additional serum biomarkers were collected. The effect of aliskiren on cardiovascular death or HHF within 6 months (primary endpoint) did not significantly differ by baseline DM status (P = 0.08 for interaction), but reached statistical significance at 12 months (non-DM: HR: 0.80, 95% CI: 0.64-0.99; DM: HR: 1.16, 95% CI: 0.91-1.47; P = 0.03 for interaction). Risk of 12-month all-cause death with aliskiren significantly differed by the presence of baseline DM (non-DM: HR: 0.69, 95% CI: 0.50-0.94; DM: HR: 1.64, 95% CI: 1.15-2.33; P < 0.01 for interaction). Among non-diabetics, aliskiren significantly reduced NT-proBNP through 6 months and plasma troponin I and aldosterone through 12 months, as compared to placebo. Among diabetic patients, aliskiren reduced plasma troponin I and aldosterone relative to placebo through 1 month only. There was a trend towards differing risk of post-baseline potassium ≥6 mmol/L with aliskiren by underlying DM status (non-DM: HR: 1.17, 95% CI: 0.71-1.93; DM: HR: 2.39, 95% CI: 1.30-4.42; P = 0.07 for interaction). Conclusion This pre-specified subgroup analysis from the ASTRONAUT trial generates the hypothesis that the addition of aliskiren to standard HHF therapy in non-diabetic patients is generally well-tolerated and improves post-discharge outcomes and biomarker profiles. In contrast, diabetic patients receiving aliskiren appear to have worse post-discharge outcomes. Future prospective investigations are needed to confirm potential benefits of renin inhibition in a large cohort of HHF patients without D

SUMOylation of the brain-predominant Ataxin-3 isoform modulates its interaction with p97

BACKGROUND: Machado-Joseph Disease (MJD), a form of dominantly inherited ataxia belonging to the group of polyQ expansion neurodegenerative disorders, occurs when a threshold value for the number of glutamines in Ataxin-3 (Atx3) polyglutamine region is exceeded. As a result of its modular multidomain architecture, Atx3 is known to engage in multiple macromolecular interactions, which might be unbalanced when the polyQ tract is expanded, culminating in the aggregation and formation of intracellular inclusions, a unifying fingerprint of this group of neurodegenerative disorders. Since aggregation is specific to certain brain regions, localization-dependent posttranslational modifications that differentially affect Atx3 might also contribute for MJD. METHODS: We combined in vitro and cellular approaches to address SUMOylation in the brain-predominant Atx3 isoform and assessed the impact of this posttranslational modification on Atx3 self-assembly and interaction with its native partner, p97. RESULTS: We demonstrate that Atx3 is SUMOylated at K356 both in vitro and in cells, which contributes for decreased formation of amyloid fibrils and for increased affinity towards p97. CONCLUSIONS AND GENERAL SIGNIFICANCE: These findings highlight the role of SUMOylation as a regulator of Atx3 function, with implications on Atx3 protein interaction network and self-assembly, with potential impact for further understanding the molecular mechanisms underlying MJD pathogenesis.This work was funded by the Fundação para a Ciência e a Tecnologia (FCT, Portugal) through grants PTDC/BIA-PRO/100059/2008 and PTDC/SAU-NMC/110602/2009 (EU-FEDER funding through COMPETEFCOMP-01-0124-FEDER-009031 and FCOMP-01-0124-FEDER-015860, respectively), and by QREN — Quadro de Referência Estratégica Nacional through Programa Operacional Regional do Norte ON. 2 (Neurodegenerative Disorders — NORTE-01-0124-FEDER-000001). C.M., S.F., I.A.A. and B.A. acknowledge the financial support from FCT through fellowships SFRH/BD/47160/2008, SFRH/BPD/77009/2011, Ciência 2008 Programme, and SFRH/BPD/70783/2010, respectively

EARLINET correlative observations for CALIPSO (2006-2010)

A European Aerosol Research Lidar Network to Establish an Aerosol ClimatologyAerosols affect life on earth in several ways. They play an important role in the climate system; the effect of aerosols on the global climate system is one of the major uncertainties of present climate predictions. They play a major role in atmospheric chemistry and hence affect the concentrations of other potentially harmful atmospheric constituents, e.g. ozone. They are an important controlling factor for the radiation budget, in particular in the UV-B part of the spectrum. At ground level, they can be harmful, even toxic, to man, animals, and plants. Because of these adverse effects that aerosols can have on human life, it is necessary to achieve an advanced understanding of the processes that generate, redistribute, and remove aerosols in the atmosphere.A quantitative dataset describing the aerosol vertical, horizontal, and temporal distribution, including its variability on a continental scale, is necessary. The dataset is used to validate and improve models that predict the future state of the atmosphere and its dependence on different scenarios describing economic development, including those actions taken to preserve the quality of the environment. The EARLINET data set is the most comprehensive compilation of data available for this purpose.This project description is taken from: http://www.earlinet.org/index.php?id=earlinet_homepageSummary: Since the beginning of CALIPSO observations in June 2006 EARLINET has performed correlative measurements during nearby overpasses of the satellite at individual stations following a dedicated observational strategy. The EARLINET-CALIPSO correlative measurement plan considers the criteria established in the CALIPSO validation plan (http://calipsovalidation.hamptonu.edu). Participating EARLINET stations perform measurements, as close in time as possible and for a period of at least 30 min up to several hours, when CALIPSO overpasses their location within a horizontal radius of 100 km. Within the 16-day observational cycle of CALIPSO each station is overpassed within this distance 1-2 times during daytime (typically between 1100 and 1400 UTC) and 1-2 times during night time (typically between 0000 and 0300 UTC). Additional measurements are performed, mainly on a non-regular basis, when CALIPSO overpasses a neighboring station in order to study the horizontal variability of the aerosol distribution. The time schedule for correlative observations is calculated starting from the high-resolution ground-track data provided by NASA, and is updated and distributed to whole network weekly. The EARLINET-CALIPSO correlative dataset represents a statistically significant data set to be used for the validation and full exploitation of the CALIPSO mission, for studying the representativeness of cross sections along an orbit against network observations on a continental scale, and for supporting the continuous, harmonized observation of aerosol and clouds with remote-sensing techniques from space over long time periods