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Biogenesis, delivery, and function of extracellular RNA
(2015)Journal of Extracellular VesiclesThe Extracellular RNA (exRNA) Communication Consortium was launched by the National Institutes of Health to focus on the extent to which RNA might function in a non-cell-autonomous manner. With the availability of increasingly sensitive tools, small amounts of RNA can be detected in serum, plasma, and other bodily fluids. The exact mechanism(s) by which RNA can be secreted from cells and the mechanisms for the delivery and uptake by ...Journal Article -
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REDEMPTION: reduced dimension ensemble modeling and parameter estimation
(2015)BioinformaticsJournal Article -
Cross-disciplinary research: What configurations of fields of science are found in grant proposals today?
(2015)Research EvaluationJournal Article -
Short loop-targeting oligoribonucleotides antagonize Lin28 and enable pre-let-7 processing and suppression of cell growth in let-7-deficient cancer cells
(2015)Nucleic Acids ResearchMicroRNAs (miRNAs) originate from stem-loop-containing precursors (pre-miRNAs, pri-miRNAs) and mature by means of the Drosha and Dicer endonucleases and their associated factors. The let-7 miRNAs have prominent roles in developmental differentiation and in regulating cell proliferation. In cancer, the tumor suppressor function of let-7 is abrogated by overexpression of Lin28, one of several RNA-binding proteins that regulate let-7 biogenesis ...Journal Article -
How to assess the effectiveness of development aid projects: evaluation ratings versus project indicators
(2015)Journal of International DevelopmentMost studies on project-based aid effectiveness rely on subjective evaluation ratings to measure projects' performance. Using the example of drinking water projects, this study compares evaluation ratings to objective, quantitative project indicators based on water supply to better understand the drivers of evaluation ratings. We find that evaluation ratings are only weakly correlated with improvements in water supply. Whereas the water ...Journal Article -
Properties of short double-stranded RNAs carrying randomized base pairs: Toward better controls for RNAi experiments
(2015)RNAShort interfering RNAs (siRNAs) are mediators of RNA interference (RNAi), a commonly used technique for selective down-regulation of target gene expression. Using an equimolar mixture of A, G, C, and U phosphoramidites during solid-phase synthesis, we introduced degenerate positions into RNA guide and passenger strands so that, when annealed, a large pool of distinct siRNA duplexes with randomized base pairs at defined sites was created. ...Journal Article -
Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: A comprehensive view in Enterococcus faecalis
(2015)RNAEnterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5′ RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search ...Journal Article -
Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing
(2015)RNAThe human hnRNP C is a ubiquitous cellular protein involved in mRNA maturation. Recently, we have shown that this protein specifically recognizes uridine (U) pentamers through its single RNA recognition motif (RRM). However, a large fraction of natural RNA targets of hnRNP C consists of much longer contiguous uridine stretches. To understand how these extended sites are recognized, we studied the binding of the RRM to U-tracts of 8–11 ...Journal Article -
Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
(2015)Genome ResearchIn animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the Caenorhabditis elegans miR-58 miRNA family, composed primarily of the four highly abundant members miR-58.1, miR-80, miR-81, and miR-82, as a model to investigate the redundancy of miRNA family ...Journal Article