Comparative assessment of performance and genome dependence among phylogenetic profiling methods

BACKGROUND: The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced eukaryotic genomes comes a need for bioinformatic techniques to aid in functional annotation. Ideally, genome context based techniques such as proximity, fusion, and phylogenetic profiling, which have been so successful in prokaryotes, could be utilized in eukaryotes. Here we explore the application of phylogenetic profiling, a method that exploits the evolutionary co-occurrence of genes in the assignment of functional linkages, to eukaryotic genomes. RESULTS: In order to evaluate the performance of phylogenetic profiling in eukaryotes, we assessed the relative performance of commonly used profile construction techniques and genome compositions in predicting functional linkages in both prokaryotic and eukaryotic organisms. When predicting linkages in E. coli with a prokaryotic profile, the use of continuous values constructed from transformed BLAST bit-scores performed better than profiles composed of discretized E-values; the use of discretized E-values resulted in more accurate linkages when using S. cerevisiae as the query organism. Extending this analysis by incorporating several eukaryotic genomes in profiles containing a majority of prokaryotes resulted in similar overall accuracy, but with a surprising reduction in pathway diversity among the most significant linkages. Furthermore, the application of phylogenetic profiling using profiles composed of only eukaryotes resulted in the loss of the strong correlation between common KEGG pathway membership and profile similarity score. Profile construction methods, orthology definitions, ontology and domain complexity were explored as possible sources of the poor performance of eukaryotic profiles, but with no improvement in results. CONCLUSION: Given the current set of completely sequenced eukaryotic organisms, phylogenetic profiling using profiles generated from any of the commonly used techniques was found to yield extremely poor results. These findings imply genome-specific requirements for constructing functionally relevant phylogenetic profiles, and suggest that differences in the evolutionary history between different kingdoms might generally limit the usefulness of phylogenetic profiling in eukaryotes

Measurement of Intervertebral Motion Using Quantitative Fluoroscopy: Report of an International Forum and Proposal for Use in the Assessment of Degenerative Disc Disease in the Lumbar Spine

Quantitative fluoroscopy (QF) is an emerging technology for measuring intervertebral motion patterns to investigate problem back pain and degenerative disc disease. This International Forum was a networking event of three research groups (UK, US, Hong Kong), over three days in San Francisco in August 2009. Its aim was to reach a consensus on how best to record, analyse, and communicate QF information for research and clinical purposes. The Forum recommended that images should be acquired during regular trunk motion that is controlled for velocity and range, in order to minimise externally imposed variability as well as to correlate intervertebral motion with trunk motion. This should be done in both the recumbent passive and weight bearing active patient configurations. The main recommended outputs from QF were the true ranges of intervertebral rotation and translation, neutral zone laxity and the consistency of shape of the motion patterns. The main clinical research priority should initially be to investigate the possibility of mechanical subgroups of patients with chronic, nonspecific low back pain by comparing their intervertebral motion patterns with those of matched healthy controls

Getting to know you: Engagement and relationship building: First interim national positive futures case study research report

This report represents the culmination of the first phase of the Positive Futures (PF) Case Studies Research Project rather than a definitive set of findings as such. Rather like the PF programme itself it is very much a work in progress which is evolving all the time in the context of the action research approach we have adopted. This approach involves a cycle of action and reflection, with both the projects and research adapting in relation to the themes that emerge from the study as it progresses. Nevertheless whilst this element of the research has been concerned as much with the establishment of relations with projects and participants as investigating the relationships between them, we have begun to identify a number of tentative themes and findings. These themes are presented in a fashion which is intended to guide the future direction of projects every bit as much as to gain abstract theoretical insight. Yet this recognition of the importance of practicality and direction should not distract from the importance of gaining a wider contextual feel for the programme. For whilst this summary is intended to highlight the key themes emerging from the research and the policy and practice issues associated with them, it is in the detail of the main report that a full appreciation of the PF approach emerges. It is from the more narrative accounts in these subsequent parts that we have drawn the conclusions and recommendations presented here and which will provide the baselines against which we assess future progress. Indeed these accounts are themselves drawn from three regional reports focused on the seven case studies that constitute the overall national research project

The effect of electro-hydrodynamic shockwaves on the quality of striploin and brisket beef muscles during long-term storage

Shockwaves generate instantaneous high pressures, which could affect meat shelf-life or quality. This study assessed microbiological counts, pH, drip, cook and moisture loss and texture of striploin (longissimus lumborum) and brisket (pectoralis profundus) treated with electrical shockwave (25 kV, 8 pulses) and subsequently stored (−0.5 °C) for 0, 4, 8, 12, 16 and 20 weeks. Shockwave did not affect total viable counts (p>0.05), with all samples considered microbiologically acceptable (0.05). Shockwave × storage time increased moisture losses in striploin (p<0.01) and brisket (p<0.01) at week 0 but this decreased over subsequent storage weeks. Shockwave technology did not affect meat shelf-life and has potential for beef tenderisation

Environmental drivers of Culicoides phenology: how important is species-specific variation when determining disease policy?

Since 2006, arboviruses transmitted by Culicoides biting midges (Diptera: Ceratopogonidae) have caused significant disruption to ruminant production in northern Europe. The most serious incursions involved strains of bluetongue virus (BTV), which cause bluetongue (BT) disease. To control spread of BTV, movement of susceptible livestock is restricted with economic and animal welfare impacts. The timing of BTV transmission in temperate regions is partly determined by the seasonal presence of adult Culicoides females. Legislative measures therefore allow for the relaxation of ruminant movement restrictions during winter, when nightly light-suction trap catches of Culicoides fall below a threshold (the ‘seasonally vector free period’: SVFP). We analysed five years of time-series surveillance data from light-suction trapping in the UK to investigate whether significant inter-specific and yearly variation in adult phenology exists, and whether the SVFP is predictable from environmental factors. Because female vector Culicoides are not easily morphologically separated, inter-specific comparisons in phenology were drawn from male populations. We demonstrate significant inter-specific differences in Culicoides adult phenology with the season of Culicoides scoticus approximately eight weeks shorter than Culicoides obsoletus. Species-specific differences in the length of the SVFP were related to host density and local variation in landscape habitat. When the Avaritia Culicoides females were modelled as a group (as utilised in the SFVP), we were unable to detect links between environmental drivers and phenological metrics. We conclude that the current treatment of Avaritia Culicoides as a single group inhibits understanding of environmentally-driven spatial variation in species phenology and hinders the development of models for predicting the SVFP from environmental factors. Culicoides surveillance methods should be adapted to focus on concentrated assessments of species-specific abundance during the start and end of seasonal activity in temperate regions to facilitate refinement of ruminant movement restrictions thereby reducing the impact of Culicoides-borne arboviruses

Expert consensus on low-calorie sweeteners:facts, research gaps and suggested actions

A consensus workshop on low-calorie sweeteners (LCS) was held in November 2018 where seventeen experts (the panel) discussed three themes identified as key to the science and policy of LCS: (1) weight management and glucose control; (2) consumption, safety and perception; (3) nutrition policy. The aims were to identify the reliable facts on LCS, suggest research gaps and propose future actions. The panel agreed that the safety of LCS is demonstrated by a substantial body of evidence reviewed by regulatory experts and current levels of consumption, even for high users, are within agreed safety margins. However, better risk communication is needed. More emphasis is required on the role of LCS in helping individuals reduce their sugar and energy intake, which is a public health priority. Based on reviews of clinical evidence to date, the panel concluded that LCS can be beneficial for weight management when they are used to replace sugar in products consumed in the diet (without energy substitution). The available evidence suggests no grounds for concerns about adverse effects of LCS on sweet preference, appetite or glucose control; indeed, LCS may improve diabetic control and dietary compliance. Regarding effects on the human gut microbiota, data are limited and do not provide adequate evidence that LCS affect gut health at doses relevant to human use. The panel identified research priorities, including collation of the totality of evidence on LCS and body weight control, monitoring and modelling of LCS intakes, impacts on sugar reduction and diet quality and developing effective communication strategies to foster informed choice. There is also a need to reconcile policy discrepancies between organisations and reduce regulatory hurdles that impede low-energy product development and reformulation

A single amino acid distorts the Fc γ receptor IIIb/CD16b structure upon binding immunoglobulin G1 and reduces affinity relative to CD16a

Therapeutic mAbs engage Fc γ receptor III (CD16) to elicit a protective cell-mediated response and destroy the target tissue. Newer drugs designed to bind CD16a with increased affinity surprisingly also elicit protective CD16b-mediated responses. However, it is unclear why IgG binds CD16a with more than 10-fold higher affinity than CD16b even though these receptors share more than 97% identity. Here we identified one residue, Gly-129, that contributes to the greater IgG binding affinity of CD16a. The CD16b variant D129G bound IgG1 Fc with 2-fold higher affinity than CD16a and with 90-fold higher affinity than the WT. Conversely, the binding affinity of CD16a-G129D was decreased 128-fold relative to WT CD16a and comparably to that of WT CD16b. The interaction of IgG1 Fc with CD16a, but not with CD16b, is known to be sensitive to the composition of the asparagine-linked carbohydrates (N-glycans) attached to the receptor. CD16a and CD16b-D129G displaying minimally processed oligomannose N-glycans bound to IgG1 Fc with about 5.2-fold increased affinity compared with variants with highly processed complex-type N-glycans. CD16b and the CD16a-G129D variant exhibited a smaller 1.9-fold affinity increase with oligomannose N-glycans. A model of glycosylated CD16b bound to IgG1 Fc determined to 2.2 Å resolution combined with a 250-ns all-atom molecular dynamics simulation showed that the larger Asp-129 residue deformed the Fc-binding surface. These results reveal how Asp-129 in CD16b affects its binding affinity for IgG1 Fc and suggest that antibodies engineered to engage CD16b with high affinity must accommodate the Asp-129 side chain

Lifeform indicators reveal large-scale shifts in plankton across the North-West European shelf

Increasing direct human pressures on the marine environment, coupled with climate-driven changes, is a concern to marine ecosystems globally. This requires the development and monitoring of ecosystem indicators for effective management and adaptation planning. Plankton lifeforms (broad functional groups) are sensitive indicators of marine environmental change and can provide a simplified view of plankton biodiversity, building an understanding of change in lower trophic levels. Here, we visualize regional-scale multi-decadal trends in six key plankton lifeforms as well as their correlative relationships with sea surface temperature (SST). For the first time, we collate trends across multiple disparate surveys, comparing the spatially and temporally extensive Continuous Plankton Recorder (CPR) survey (offshore) with multiple long-term fixed station-based time-series (inshore) from around the UK coastline. These analyses of plankton lifeforms showed profound long-term changes, which were coherent across large spatial scales. For example, ‘diatom’ and ‘meroplankton’ lifeforms showed strong alignment between surveys and coherent regional-scale trends, with the 1998–2017 decadal average abundance of meroplankton being 2.3 times that of 1958–1967 for CPR samples in the North Sea. This major, shelf-wide increase in meroplankton correlated with increasing SSTs, and contrasted with a general decrease in holoplankton (dominated by small copepods), indicating a changing balance of benthic and pelagic fauna. Likewise, inshore-offshore gradients in dinoflagellate trends, with contemporary increases inshore contrasting with multi-decadal decreases offshore (approx. 75% lower decadal mean abundance), urgently require the identification of causal mechanisms. Our lifeform approach allows the collation of many different data types and time-series across the NW European shelf, providing a crucial evidence base for informing ecosystem-based management, and the development of regional adaptation plans