Mammalian microRNAs predominantly act to decrease target mRNA levels

MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.National Institutes of Health (U.S.

Characterization of microRNAs Identified in a Table Grapevine Cultivar with Validation of Computationally Predicted Grapevine miRNAs by miR-RACE

BACKGROUND: Alignment analysis of the Vv-miRNAs identified from various grapevine cultivars indicates that over 30% orthologous Vv-miRNAs exhibit a 1-3 nucleotide discrepancy only at their ends, suggesting that this sequence discrepancy is not a random event, but might mainly derive from divergence of cultivars. With advantages of miR-RACE technology in determining precise sequences of potential miRNAs from bioinformatics prediction, the precise sequences of vv-miRNAs predicted computationally can be verified with miR-RACE in a different grapevine cultivar. This presents itself as a new approach for large scale discovery of precise miRNAs in different grapevine varieties. METHODOLOGY/PRINCIPAL FINDINGS: Among 88 unique sequences of Vv-miRNAs from bioinformatics prediction, 83 (96.3%) were successfully validated with MiR-RACE in grapevine cv. 'Summer Black'. All the validated sequences were identical to their corresponding ones obtained from deep sequencing of the small RNA library of 'Summer Black'. Quantitative RT-PCR analysis of the expressions levels of 10 Vv-miRNA/target gene pairs in grapevine tissues showed some negative correlation trends. Finally, comparison of Vv-miRNA sequences with their orthologs in Arabidopsis and study on the influence of divergent bases of the orthologous miRNAs on their targeting patterns in grapevine were also done. CONCLUSION: The validation of precise sequences of potential Vv-miRNAs from computational prediction in a different grapevine cultivar can be a new way to identify the orthologous Vv-miRNAs. Nucleotide discrepancy of orthologous Vv-miRNAs from different grapevine cultivars normally does not change their target genes. However, sequence variations of some orthologous miRNAs in grapevine and Arabidopsis can change their targeting patterns. These precise Vv-miRNAs sequences validated in our study could benefit some further study on grapevine functional genomics

Identification and Characterization of MicroRNAs in Normal Equine Tissues by Next Generation Sequencing

The role of microRNAs (miRNAs) as a post-transcriptional gene regulator has been elucidated in a broad range of organisms including domestic animals. Characterization of miRNAs in normal tissues is an important step to investigate the functions of miRNAs in various physiological and pathological conditions. Using Illumina Next Generation Sequencing (NGS) technology, we identified a total of 292 known and 329 novel miRNAs in normal horse tissues including skeletal muscle, colon and liver. Distinct sets of miRNAs were differentially expressed in a tissue-specific manner. The miRNA genes were distributed across all the chromosomes except chromosomes 29 and 31 in the horse reference genome. In some chromosomes, multiple miRNAs were clustered and considered to be polycistronic transcript. A base composition analysis showed that equine miRNAs had a higher frequency of A+U than G+C. Furthermore, U tended to be more frequent at the 59 end of miRNA sequences. This is the first experimental study that identifies and characterizes the global miRNA expression profile in normal horse tissues. The present study enriches the horse miRNA database and provides useful information for further research dissecting biological functions of miRNAs in horse.open2

Correction to: Cluster identification, selection, and description in Cluster randomized crossover trials: the PREP-IT trials

An amendment to this paper has been published and can be accessed via the original article

Work-life balance, management practices and productivity

Do “Anglo-Saxon” management practices generate higher productivity only at the expense of lousy work-life balance (WLB) for workers? Many critics of “neo-libéralisme sauvage” have argued that increased competition from globalisation is damaging employees’ quality of life. Others have argued the opposite that improving work-life balance is actually a competitive tool that companies can use to raise productivity. We try to shed some empirical light on these issues using an innovative survey tool to collect new data on management and work-life balance practices from 732 medium sized manufacturing firms in the US, France, Germany and the UK. First, we show that our measure of work-life balance is a useful summary of a range of policies in the firm – family-friendly policies, flexible working, shorter hours, more holidays, subsidised childcare, etc. We show that this worklife balance measure is significantly associated with better management. Firms in environments that are more competitive and/or who are more productive, however, do not have significantly worse work-life balance for their workers. These findings are inconsistent with the view that competition, globalisation and “Anglo-Saxon” management practices are intrinsically bad for the work-life balance of workers. On the other hand, neither are these findings supportive of the optimistic “winwin” view that work-life balance improves productivity in its own right. Rather we find support for a “hybrid” theory that work-life balance is a choice for managers that is compatible with low or high productivity

Virtual Developmental Screening After Invasive Mechanical Ventilation in Children: A Prospective Cohort Pilot Study

OBJECTIVES: With decreasing PICU mortality, survivor morbidity has increased. This study aims to evaluate feasibility of virtual PICU-led follow-up of patients at risk for pediatric postintensive care syndrome. DESIGN: Prospective cohort study. SETTING: Single-center, quaternary children's hospital. PATIENTS: Children less than or equal to 4 years without known preexisting neurodevelopmental deficits requiring greater than or equal to 12 hours mechanical ventilation. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Age-appropriate Ages and Stages Questionnaires, Third Edition (ASQ-3) were administered via a web-based system at 3, 6, and 12 months following PICU discharge. Primary-care physicians were notified of results; at-risk patients were referred to early developmental intervention. Forty-eight patients enrolled with median age 11.5 months (interquartile range [IQR], 2-19.5 mo) and median mechanical ventilation duration 92.5 hours (IQR, 40.5-147 hr). Fifty-eight percent completed greater than or equal to 1 ASQ-3. Lower caregiver educational achievement, lower income, and single-caregiver status were associated with lower ASQ-3 completion rates. Of those completing any ASQ-3, 50% flagged as at-risk for developmental delay and referred to early developmental intervention. There was no association between patient characteristics and abnormal ASQ-3. CONCLUSIONS: Virtual caregiver-completed surveillance is a promising method to screen children for neurodevelopmental abnormalities following PICU hospitalization and facilitate early referral for developmental intervention, but special attention must be dedicated to families with limited resources for follow-up

Regulation of vascular leak and recovery from ischemic injury by general and VE-cadherin-restricted miRNA antagonists of miR-27

Please see erratum at DOI: 10.1182/blood-2014-09-604066 The errors have been corrected in the online version, which now differs from the print version.Cellular junctions are essential to the normal functioning of the endothelium and control angiogenesis, tissue leak, and inflammation. From a screen of micro RNAs (miRNAs) altered in in vitro angiogenesis, we selected a subset predicted to target junctional molecules. MiR-27a was rapidly downregulated upon stimulation of in vitro angiogenesis, and its level of expression is reduced in neovessels in vivo. The downregulation of miR-27a was essential for angiogenesis because ectopic expression of miR-27a blocked capillary tube formation and angiogenesis. MiR-27a targets the junctional, endothelial-specific cadherin, VE-cadherin. Consistent with this, vascular permeability to vascular endothelial growth factor in mice is reduced by administration of a general miR-27 inhibitor. To determine that VE-cadherin was the dominant target of miR-27a function, we used a novel technology with “Blockmirs,” inhibitors that bind to the miR-27 binding site in VE-cadherin. The Blockmir CD5-2 demonstrated specificity for VE-cadherin and inhibited vascular leak in vitro and in vivo. Furthermore, CD5-2 reduced edema, increased capillary density, and potently enhanced recovery from ischemic limb injury in mice. The Blockmir technology offers a refinement in the use of miRNAs, especially for therapy. Further, targeting of endothelial junctional molecules by miRNAs has clinical potential, especially in diseases associated with vascular leak.Jennifer A. Young, Ka Ka Ting, Jia Li, Thorleif Moller, Louise Dunn, Ying Lu, Joshua Moses, Leonel Prado-Lourenço, Levon M. Khachigian, Martin Ng, Philip A. Gregory, Gregory J. Goodall, Anna Tsykin, Ilana Lichtenstein, Christopher N. Hahn, Nham Tran, Nicholas Shackel, James G. Kench, Geoffrey McCaughan, Mathew A. Vadas, and Jennifer R. Gambl