Multiple RNA interactions position Mrd1 at the site of the small subunit pseudoknot within the 90S pre-ribosome

Ribosomal subunit biogenesis in eukaryotes is a complex multistep process. Mrd1 is an essential and conserved small (40S) ribosomal subunit synthesis factor that is required for early cleavages in the 35S pre-ribosomal RNA (rRNA). Yeast Mrd1 contains five RNA-binding domains (RBDs), all of which are necessary for optimal function of the protein. Proteomic data showed that Mrd1 is part of the early pre-ribosomal complexes, and deletion of individual RBDs perturbs the pre-ribosomal structure. In vivo ultraviolet cross-linking showed that Mrd1 binds to the pre-rRNA at two sites within the 18S region, in helix 27 (h27) and helix 28. The major binding site lies in h27, and mutational analyses shows that this interaction requires the RBD1-3 region of Mrd1. RBD2 plays the dominant role in h27 binding, but other RBDs also contribute directly. h27 and helix 28 are located close to the sequences that form the central pseudoknot, a key structural feature of the mature 40S subunit. We speculate that the modular structure of Mrd1 coordinates pseudoknot formation with pre-rRNA processing and subunit assembly.     

Male nest building but not display behaviour directly influences mating success in the polygynous Red Bishop,Euplectes orix

Previous studies of the highly polygynous and strikingly sexually dimorphic Red Bishop, Euplectes orix (Ploceinae, weaverbirds), have suggested random female settlement patterns and no correlates of male reproductive success except the number of nest frames (‘cock's nests’) built by the male. Although this confirms the central role of the nest in weaverbird courtship it also contrasts with demonstrated sexual selection on male morphology and behaviour in several closely related Euplectes species. Two major aspects of male sexual advertising have not been included in previous studies; display behaviour and territory size. In this study we use multivariate selection analysis, with the number of active nests in a territory as the fitness measure, to identify direct and indirect sexual selection on male sexual behaviour, territory size and nest building. In accor–dance with previous findings, mating success was not strongly skewed among the territorial males, and females appeared to settle randomly with respect to available nests. The number of cock𠀧s nest built was the only determinant of male breeding success, even when controlling for male display activity and territory size. We argue that, despite their conspicuous sexual dimorphism, females settle independently of both male or territory quality, and that variance in male reproductive success is a consequence of male–male competition.     

The Shaft of the Type 1 Fimbriae Regulates an External Force to Match the FimH Catch Bond

Type 1 fimbriae mediate adhesion of uropathogenic Escherichia coli to host cells. It has been hypothesized that due to their ability to uncoil under exposure to force, fimbriae can reduce fluid shear stress on the adhesin-receptor interaction by which the bacterium adheres to the surface. In this work, we develop a model that describes how the force on the adhesin-receptor interaction of a type 1 fimbria varies as a bacterium is affected by a time-dependent fluid flow mimicking in vivo conditions. The model combines in vivo hydrodynamic conditions with previously assessed biomechanical properties of the fimbriae. Numerical methods are used to solve for the motion and adhesion force under the presence of time-dependent fluid profiles. It is found that a bacterium tethered with a type 1 pilus will experience significantly reduced shear stress for moderate to high flow velocities and that the maximum stress the adhesin will experience is limited to ∼120 pN, which is sufficient to activate the conformational change of the FimH adhesin into its stronger state but also lower than the force required for breaking it under rapid loading. Our model thus supports the assumption that the type 1 fimbria shaft and the FimH adhesin-receptor interaction are optimized to each other, and that they give piliated bacteria significant advantages in rapidly changing fluidic environments.     

Using forest history and spatial patterns to identify potential high conservation value forests in Romania

Naturally dynamic forests have a high proportion of biotopes with old large trees, diverse vertical and horizontal structure at multiple scales, and much dead wood. As such, they provide habitat to species and ecosystem processes that forests managed for wood production cannot provide to the same degree. Whether termed old-growth, ancient, virgin, intact, primeval or continuity forests, a major challenge and need is to map such potential high conservation value forest for subsequent inclusion in functional habitat networks for biodiversity conservation in forest landscapes. Given that the delivery time of natural forest properties is much longer than of industry wood, we explore the usefulness of using historical maps to identify forests that have been continuously present for 220 years (potential old-growth) versus 140 years (potential aging forest) in a case study in the Romanian Carpathian Mountains (see Online Resource 1). While the total forest cover increased by 35 % over the past two centuries, the area of potential aging and potential old-growth forest declined by 56 and 34 %, respectively. Spatial modelling of edge effects and patch size for virtual species with different requirements indicated an even greater decrease in the area of functional habitat networks of old-growth and ageing forest. Our analyses show that compared to simple mapping of potential high conservation forests, the area of functional habitat patches is severely overestimated, and caution is needed when estimating the area of potential high conservation value forests that form functional habitat networks, i.e. a green infrastructure. In addition, the landscape and regional scale connectivity of patches needs to be considered. We argue that the use of historical maps combined with assessment of spatial patterns is an effective tool for identifying and analyzing potential high conservation value forests in a landscape context.     

The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes

Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.     

Estimating the proportion cured of cancer: Some practical advice for users

BackgroundCure models can provide improved possibilities for inference if used appropriately, but there is potential for misleading results if care is not taken. In this study, we compared five commonly used approaches for modelling cure in a relative survival framework and provide some practical advice on the use of these approaches.Patients and methodsData for colon, female breast, and ovarian cancers were used to illustrate these approaches. The proportion cured was estimated for each of these three cancers within each of three age groups. We then graphically assessed the assumption of cure and the model fit, by comparing the predicted relative survival from the cure models to empirical life table estimates.ResultsWhere both cure and distributional assumptions are appropriate (e.g., for colon or ovarian cancer patients aged <75 years), all five approaches led to similar estimates of the proportion cured. The estimates varied slightly when cure was a reasonable assumption but the distributional assumption was not (e.g., for colon cancer patients ≥75 years). Greater variability in the estimates was observed when the cure assumption was not supported by the data (breast cancer).ConclusionsIf the data suggest cure is not a reasonable assumption then we advise against fitting cure models. In the scenarios where cure was reasonable, we found that flexible parametric cure models performed at least as well, or better, than the other modelling approaches. We recommend that, regardless of the model used, the underlying assumptions for cure and model fit should always be graphically assessed.     

Single Nucleotide Polymorphisms in the Wilms’ Tumour Gene 1 in Clear Cell Renal Cell Carcinoma

The Wilms’ tumour gene 1 (WT1) single nucleotide polymorphism (SNP) rs16754 has recently been described as an independent prognostic factor in acute myeloid leukaemia (AML) patients. It is of great interest to test whether WT1 SNPs can be used as a molecular marker in other cancer types in order to improve risk and treatment stratification. We performed sequencing analysis on all 10 exons of the WT1 gene in a total of 182 patients with clear cell renal cell carcinoma (ccRCC). Six different SNPs were identified, in descending order for minor allele frequency: rs2234582, rs16754, rs1799925, rs5030315, rs2234583, and rs2234581. At least one minor allele for WT1 SNP was identified in 61% of ccRCC patients. In the entire study population, only 6% carried two copies of the minor allele. The genotypes of WT1 SNPs in 78 tumour-free kidney tissue specimens were found to be in 95% concordance with corresponding tumour samples. No correlation was observed between WT1 SNP genotypes and RNA expression level. WT1 SNP genotypes did not associate with clinical and pathological characteristics. We found favourable outcomes associated with the homozygous minor allele for WT1 SNP. However, SNP genotypes did not show to be of prognostic significance when comparing wild-type versus homozygous or heterozygous for the minor allele in the entire cohort. None of the previously reported WT1 mutations in AML was found in the present study. A novel WT1 missense mutation was identified in only one patient. Our data suggest that common WT1 mutations are not involved in ccRCC. Due to too few cases harbouring the homozygous minor allele, the prognostic impact needs to be verified in larger study populations.