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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 -
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 -
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 -
REDEMPTION: reduced dimension ensemble modeling and parameter estimation
(2015)BioinformaticsJournal Article -
Connexin 43 expression predicts poor progression-free survival in patients with non-muscle invasive urothelial bladder cancer
(2015)Journal of Clinical PathologyObjectives: To evaluate the protein expression of connexin 43 (Cx43) in primary urothelial bladder cancer and test its association with the histopathological characteristics and clinical outcome. Methods: A tissue microarray containing 348 tissue samples from 174 patients with primary urothelial carcinomas of the bladder was immunohistochemically stained for Cx43. The intensity of staining was semiquantitatively evaluated (score 0, 1+, ...Journal Article -
A Falsification of the Citation Impediment in the Taxonomic Literature
(2015)Systematic BiologyCurrent science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) ...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 -
Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies
(2015)Systematic BiologyTens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees, inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: Empirical trees show very different imbalance between the ...Journal Article -
Assessment of the 3D Pore Structure and Individual Components of Preshaped Catalyst Bodies by X-Ray Imaging
(2015)ChemCatChemPorosity in catalyst particles is essential because it enables reactants to reach the active sites and it enables products to leave the catalyst. The engineering of composite-particle catalysts through the tuning of pore-size distribution and connectivity is hampered by the inability to visualize structure and porosity at critical-length scales. Herein, it is shown that the combination of phase-contrast X-ray microtomography and high-resolution ...Journal Article