Role of the cytosolic loop C2 and the C-terminus of YidC in ribosome binding and insertion activity

Members of the YidC/Oxa1/Alb3 protein family mediate membrane protein insertion, and this process is initiated by the assembly of YidC·ribosome nascent chain complexes at the inner leaflet of the lipid bilayer. The positively charged C terminus of Escherichia coli YidC plays a significant role in ribosome binding but is not the sole determinant because deletion does not completely abrogate ribosome binding. The positively charged cytosolic loops C1 and C2 of YidC may provide additional docking sites. We performed systematic sequential deletions within these cytosolic domains and studied their effect on the YidC insertase activity and interaction with translation-stalled (programmed) ribosome. Deletions within loop C1 strongly affected the activity of YidC in vivo but did not influence ribosome binding or substrate insertion, whereas loop C2 appeared to be involved in ribosome binding. Combining the latter deletion with the removal of the C terminus of YidC abolished YidC-mediated insertion. We propose that these two regions play an crucial role in the formation and stabilization of an active YidC·ribosome nascent chain complex, allowing for co-translational membrane insertion, whereas loop C1 may be involved in the downstream chaperone activity of YidC or in other protein-protein interactions

Can the use of an inclinometer improve acetabular cup inclination in total hip arthroplasty? A review of the literature

Introduction: The angle of acetabular (cup) radiographic inclination is an important measurement in total hip arthroplasty (THA) procedures. Abnormal radiographic inclination is associated with dislocation, edge loading and higher failure rates. Consistently achieving a satisfactory radiographic inclination remains a challenge. Inclinometers have been increasingly used over the last decade. This paper reviews the literature to determine whether using an inclinometer improves the accuracy of acetabular cup inclination in THA. Methods: A systematic literature search was performed. The following search terms were used: ('hip' OR 'hip replacement' OR 'hip arthroplasty' OR 'primary hip replacement' OR 'THR' OR 'THA' OR 'Acetabular cup Inclination') AND ('Inclinometer'). Titles and abstracts were screened for relevance. Both radiographic and operative inclination comparisons were included. Results: 7 studies met the inclusion criteria. 2 were randomised control trials with level I evidence, and the remaining studies were cohort studies with level III/IV evidence. 5 were clinical and 2 experimental. In total there were 16 cohorts: 7 using an inclinometer, 6 freehand, and 3 using MAG techniques. All studies comparing radiographic inclination and 1 of 2 studies comparing operative inclination showed an improvement in the attainment of the optimal inclination. Similarly, the use of an inclinometer showed a reduction in the number of outliers when compared to MAG and freehand techniques. Discussion: This review demonstrates that using an inclinometer improved the surgeon's ability to achieve their intended inclination (both operative and radiographic) and reduced the incidence of positioning outside the safe-zone. However, only 2 of the studies were randomised control trials and these resulted in opposing conclusions. Therefore, further studies looking at the use of inclinometers would prove useful in understanding their true benefit

Developing observational methods to drive future hydrological science: can we make a start as a community?

Hydrology is still, and for good reasons, an inexact science, even if evolving hydrological understanding has provided a basis for improved water management for at least the last three millennia. The limitations of that understanding have, however, become much more apparent and important in the last century as the pressures of increasing populations, and the anthropogenic impacts on catchment forcing and responses, have intensified. At the same time, the sophistication of hydrological analyses and models has been developing rapidly, often driven more by the availability of computational power and geographical data sets than any real increases in understanding of hydrological processes. This sophistication has created an illusion of real progress but a case can be made that we are still rather muddling along, limited by the significant uncertainties in hydrological observations, knowledge of catchment characteristics and related gaps in conceptual understanding, particularly of the sub-surface. These knowledge gaps are illustrated by the fact that for many catchments we cannot close the water balance without significant uncertainty, uncertainty that is often neglected in evaluating models for practical applications

Individual common variants exert weak effects on the risk for autism spectrum disorders.

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest

Novel Protein Kinase Signaling Systems Regulating Lifespan Identified by Small Molecule Library Screening Using Drosophila

Protein kinase signaling cascades control most aspects of cellular function. The ATP binding domains of signaling protein kinases are the targets of most available inhibitors. These domains are highly conserved from mammals to flies. Herein we describe screening of a library of small molecule inhibitors of protein kinases for their ability to increase Drosophila lifespan. We developed an assay system which allowed screening using the small amounts of materials normally present in commercial chemical libraries. The studies identified 17 inhibitors, the majority of which targeted tyrosine kinases associated with the epidermal growth factor receptor (EGFR), platelet-derived growth factor (PDGF)/vascular endothelial growth factor (VEGF) receptors, G-protein coupled receptor (GPCR), Janus kinase (JAK)/signal transducer and activator of transcription (STAT), the insulin and insulin-like growth factor (IGFI) receptors. Comparison of the protein kinase signaling effects of the inhibitors in vitro defined a consensus intracellular signaling profile which included decreased signaling by p38MAPK (p38), c-Jun N-terminal kinase (JNK) and protein kinase C (PKC). If confirmed, many of these kinases will be novel additions to the signaling cascades known to regulate metazoan longevity

SIGNATURE: A workbench for gene expression signature analysis

<p>Abstract</p> <p>Background</p> <p>The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise.</p> <p>Results</p> <p>We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access.</p> <p>Conclusions</p> <p>SIGNATURE is available for public use at <url>http://genepattern.genome.duke.edu/signature/</url>.</p

Inclination estimates from off-axis GRB afterglow modelling

For gravitational wave (GW) detected neutron star mergers, one of the leading candidates for electromagnetic (EM) counterparts is the afterglow from an ultra-relativistic jet. Where this afterglow is observed, it will likely be viewed off-axis, such as the afterglow following GW170817/GRB 170817A. The temporal behaviour of an off-axis observed GRB afterglow can be used to reveal the lateral jet structure, and statistical model fits can put constraints on the various model free-parameters. Amongst these parameters is the inclination of the system to the line of sight. Along with the GW detection, the afterglow modelling provides the best constraint on the inclination to the line-of-sight and can improve the estimates of cosmological parameters, for example, the Hubble constant, from GW-EM events. However, modelling of the afterglow depends on the assumed jet structure and—often overlooked—the effects of lateral spreading. Here we show how the inclusion of lateral spreading in the afterglow models can affect the estimated inclination of GW-EM events