Adaptive evolution of Toll-like receptor 5 in domesticated mammals

<p>Abstract</p> <p>Background</p> <p>Previous studies have proposed that mammalian toll like receptors (TLRs) have evolved under diversifying selection due to their role in pathogen detection. To determine if this is the case, we examined the extent of adaptive evolution in the TLR5 gene in both individual species and defined clades of the mammalia.</p> <p>Results</p> <p>In support of previous studies, we find evidence of adaptive evolution of mammalian TLR5. However, we also show that TLR5 genes of domestic livestock have a concentration of single nucleotide polymorphisms suggesting a specific signature of adaptation. Using codon models of evolution we have identified a concentration of rapidly evolving codons within the TLR5 extracellular domain a site of interaction between host and the bacterial surface protein flagellin.</p> <p>Conclusions</p> <p>The results suggest that interactions between pathogen and host may be driving adaptive change in TLR5 by competition between species. In support of this, we have identified single nucleotide polymorphisms (SNP) in sheep and cattle TLR5 genes that are co-localised and co-incident with the predicted adaptive codons suggesting that adaptation in this region of the TLR5 gene is on-going in domestic species.</p

Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance

<p>Abstract</p> <p>Background</p> <p>There is accumulating evidence that polymorphism in Toll-like receptor (<it>TLR) </it>genes might be associated with disease resistance or susceptibility traits in livestock. Polymorphic sites affecting TLR function should exhibit signatures of positive selection, identified as a high ratio of non-synonymous to synonymous nucleotide substitutions (ω). Phylogeny based models of codon substitution based on estimates of ω for each amino acid position can therefore offer a valuable tool to predict sites of functional relevance. We have used this approach to identify such polymorphic sites within the bovine <it>TLR2 </it>genes from ten <it>Bos indicus </it>and <it>Bos taurus </it>cattle breeds. By analysing <it>TLR2 </it>gene phylogeny in a set of mammalian species and a subset of ruminant species we have estimated the selective pressure on individual sites and domains and identified polymorphisms at sites of putative functional importance.</p> <p>Results</p> <p>The ω were highest in the mammalian TLR2 domains thought to be responsible for ligand binding and lowest in regions responsible for heterodimerisation with other TLR-related molecules. Several positively-selected sites were detected in or around ligand-binding domains. However a comparison of the ruminant subset of <it>TLR2 </it>sequences with the whole mammalian set of sequences revealed that there has been less selective pressure among ruminants than in mammals as a whole. This suggests that there have been functional changes during ruminant evolution. Twenty newly-discovered non-synonymous polymorphic sites were identified in cattle. Three of them were localised at positions shaped by positive selection in the ruminant dataset (Leu227Phe, His305Pro, His326Gln) and in domains involved in the recognition of ligands. His326Gln is of particular interest as it consists of an exchange of differentially-charged amino acids at a position which has previously been shown to be crucial for ligand binding in human TLR2.</p> <p>Conclusion</p> <p>Within bovine TLR2, polymorphisms at amino acid positions 227, 305 and 326 map to functionally important sites of TLR2 and should be considered as candidate SNPs for immune related traits in cattle. A final proof of their functional relevance requires further studies to determine their functional effect on the immune response after stimulation with relevant ligands and/or their association with immune related traits in animals.</p

Timber gridshells: beyond the drawing board

In March 2011, a week-long workshop that invited participation from all architecture and architectural technology students at Sheffield Hallam University, UK was organised with the objective of enhancing students’ thinking and experience by construction thinking. It was aimed at creating a sense of realness to realise a design project collectively. Timber was set as the material of exploration. The students had to make use of bending to design and create a timber gridshell structure. This made use of a quality traditionally felt to be a structural weakness of the material. To do this, students form-found non-mathematically and non-digitally using paper gridmats. This paper describes the aims, activity and outcome of the timber gridshell workshop as a way of preparing architects and technologists of the future and introducing the challenges of architectural design in terms of economics and construction process, aesthetics, effective communication and structural intuition by working with a given material – all important aspects in achieving effective architecture

Intragenic haplotypes at the bovine CSN1S1 locus

A new alternative genotyping method based on PCR-SSCP was developed for direct differentiation of the CSN1S1 alleles B and C in the coding region. In addition a PCR-RFLP test based on a MaeIII restriction site in the promoter region of CSN1S1, reported in the literature as an alternative test for the differentiation of CSN1S1*B and C was used and the alleles named b and c. Genotyping of 649 animals belonging to 17 European and Turkish cattle breeds showed differences in occurrence and frequency of the alleles. CSN1S1*B occurred in all breeds with frequencies varying from 0.50 in Anatolian Blackup to 1.0 in e.g. Ayrshire. CSN1S1*b on the other hand varied from 0.63 in Jersey, 0.97 in Ayrshire to 1.0 in e.g. Angler. Comparison of the results from both typing methods and positions in the gene showed that both mutations do not always occur together. From the resulting four intragenic haplotypes (B-b, B-c, C-c and C-b) B-b is predominant in all breeds with frequencies varying from 0.3450 in Anatolian Black to 1.0 in Angler and Scottish Highland. The number of haplotypes varied from only one in Angler and Scottish Highland, two in Ayrshire, three in Asturian Valley and Turkish Grey Steppe to all four in the other 12 breeds. Correlation between allele frequencies and the geographic origin of the breeds was significant for the MaeIII promoter polymorphism.O. Jann, E.-M. Prinzenberg, H. Brandt, J. L. Williams, P. Ajmone-Marsan, P. Zaragoza, C. Özbeyaz, and G. Erhard

High-Resolution Motor State Detection in Parkinson's Disease Using Convolutional Neural Networks

Patients with advanced Parkinson's disease regularly experience unstable motor states. Objective and reliable monitoring of these fluctuations is an unmet need. We used deep learning to classify motion data from a single wrist-worn IMU sensor recording in unscripted environments. For validation purposes, patients were accompanied by a movement disorder expert, and their motor state was passively evaluated every minute. We acquired a dataset of 8,661 minutes of IMU data from 30 patients, with annotations about the motor state (OFF,ON, DYSKINETIC) based on MDS-UPDRS global bradykinesia item and the AIMS upper limb dyskinesia item. Using a 1-minute window size as an input for a convolutional neural network trained on data from a subset of patients, we achieved a three-class balanced accuracy of 0.654 on data from previously unseen subjects. This corresponds to detecting the OFF, ON, or DYSKINETIC motor state at a sensitivity/specificity of 0.64/0.89, 0.67/0.67 and 0.64/0.89, respectively. On average, the model outputs were highly correlated with the annotation on a per subject scale (r = 0.83/0.84;p < 0.0001), and sustained so for the highly resolved time windows of 1 minute (r = 0.64/0.70;p < 0.0001). Thus, we demonstrate the feasibility of long-term motor-state detection in a free-living setting with deep learning using motion data from a single IMU

Changes in catastrophic health expenditure in post-conflict Sierra Leone: an Oaxaca-blinder decomposition analysis.

BACKGROUND: At the end of the eleven-year conflict in Sierra Leone, a wide range of policies were implemented to address both demand- and supply-side constraints within the healthcare system, which had collapsed during the conflict. This study examines the extent to which households' exposure to financial risks associated with seeking healthcare evolved in post-conflict Sierra Leone. METHOD: This study uses the 2003 and 2011 cross-sections of the Sierra Leone Integrated Household Survey to examine changes in catastrophic health expenditure between 2003 and 2011. An Oaxaca-Blinder decomposition approach is used to quantify the extent to which changes in catastrophic health expenditure are attributable to changes in the distribution of determinants (distributional effect) and to changes in the impact of these determinants on the probability of incurring catastrophic health expenditure (coefficient effect). RESULTS: The incidence of catastrophic health expenditure decreased significantly by 18% from approximately 50% in 2003 t0 32% in 2011. The decomposition analysis shows that this decrease represents net effects attributable to the distributional and coefficient effects of three determinants of catastrophic health expenditure - ill-health, the region in which households reside and the type of health facility used. A decrease in the incidence of ill-health and changes in the regional location of households contributed to a decrease in catastrophic health expenditure. The distributional effect of health facility types observed as an increase in the use of public health facilities, and a decrease in the use of services in facilities owned by non-governmental organizations (NGOs) also contributed to a decrease in the incidence of catastrophic health expenditure. However, the coefficient effect of public health facilities and NGO-owned facilities suggests that substantial exposure to financial risk remained for households utilizing both types of health facilities in 2011. CONCLUSION: The findings support the need to continue expanding current demand-side policies in Sierra Leone to reduce the financial risk of exposure to ill health

The Financial Burden of Non-Communicable Chronic Diseases in Rural Nigeria: Wealth and Gender Heterogeneity in Health Care Utilization and Health Expenditures

Objectives Better insights into health care utilization and out-of-pocket expenditures for non-communicable chronic diseases (NCCD) are needed to develop accessible health care and limit the increasing financial burden of NCCDs in Sub-Saharan Africa. Methods A household survey was conducted in rural Kwara State, Nigeria, among 5,761 individuals. Data were obtained using biomedical and socio-economic questionnaires. Health care utilization, NCCD-related health expenditures and distances to health care providers were compared by sex and by wealth quintile, and a Heckman regression model was used to estimate health expenditures taking selection bias in health care utilization into account. Results The prevalence of NCCDs in our sample was 6.2%. NCCD-affected individuals from the wealthiest quintile utilized formal health care nearly twice as often as those from the lowest quintile (87.8% vs 46.2%, p = 0.002). Women reported foregone formal care more often than men (43.5% vs. 27.0%, p = 0.058). Health expenditures relative to annual consumption of the poorest quintile exceeded those of the highest quintile 2.2-fold, and the poorest quintile exhibited a higher rate of catastrophic health spending (10.8% among NCCD-affected households) than the three upper quintiles (4.2% to 6.7%). Long travel distances to the nearest provider, highest for the poorest quintile, were a significant deterrent to seeking care. Using distance to the nearest facility as instrument to account for selection into health care utilization, we estimated out-of-pocket health care expenditures for NCCDs to be significantly higher in the lowest wealth quintile compared to the three upper quintiles. Conclusions Facing potentially high health care costs and poor accessibility of health care facilities, many individuals suffering from NCCDs—particularly women and the poor—forego formal care, thereby increasing the risk of more severe illness in the future. When seeking care, the poor spend less on treatment than the rich, suggestive of lower quality care, while their expenditures represent a higher share of their annual household consumption. This calls for targeted interventions that enhance health care accessibility and provide financial protection from the consequences of NCCDs, especially for vulnerable populations