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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 -
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 -
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 -
Ammonia-oxidizing bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing archaea in oligotrophic surface sediments near the South Atlantic Gyre
(2015)Environmental Microbiology ReportsSediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA ...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 -
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 -
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity
(2015)Human MutationPrioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A large number of in silico tools have been employed for the task of pathogenicity prediction, including PolyPhen-2, SIFT, FatHMM, MutationTaster-2, MutationAssessor, Combined Annotation Dependent Depletion, LRT, phyloP, and GERP++, as well as optimized methods of combining ...Journal Article