Optimizing filter trap assay for the detection of aggregated alpha-synuclein in brain samples

No abstract availabl

Growth under cold conditions in a wide perennial ryegrass panel is under tight physiological control

Background Perennial ryegrass is a cool-season grass species from the family Poaceae and is widely cultivated in temperate regions because it exhibits rapid growth and establishment, and possesses high forage quality. The extension of the growing season in Ireland in spring and autumn is a breeding target to make farming more profitable since a grass-fed diet based on grazing is the cheapest way of nutrition for ruminants. Methods Fifty-seven perennial ryegrass accessions were screened for their ability to grow under typical Irish spring conditions as taken from long term temperature records in controlled climate chambers. They were grown in low temperature (8 °C/2 °C day/night) and control conditions (15 °C/8 °C day/night) in three consecutive independent experiments. Fresh weight, height, chlorophyll content and electrolyte leakage were measured, and these parameters were used to rank plant performance under low temperature growth conditions. Results The results showed that height, yield and electrolyte leakage are excellent measures for the impact of cold stress tolerance. Little variation in growth was seen under cold stress, but a wide variety of responses were observed under control conditions. Discussion Our results suggest that cold stress is under tight physiological control. Interestingly, the various genotypes responded differentially to more amenable control conditions, indicating that a quick response to more amenable growth conditions is a better target for breeding programmes

Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass.

peer-reviewedPrior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach

Genomic prediction of crown rust resistance in Lolium perenne

peer-reviewedBackground Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.This work received funding from the Irish Department of Agriculture Food and the Marine DAFM (RSF 11/S/109) and Teagasc core funding. SKA is supported by a Teagasc PhD Walsh Fellowship. SLB has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 658031

Tau expression and phosphorylation in enteroendocrine cells

Background and objectiveThere is mounting evidence to suggest that the gut-brain axis is involved in the development of Parkinson’s disease (PD). In this regard, the enteroendocrine cells (EEC), which faces the gut lumen and are connected with both enteric neurons and glial cells have received growing attention. The recent observation showing that these cells express alpha-synuclein, a presynaptic neuronal protein genetically and neuropathologically linked to PD came to reinforce the assumption that EEC might be a key component of the neural circuit between the gut lumen and the brain for the bottom-up propagation of PD pathology. Besides alpha-synuclein, tau is another key protein involved in neurodegeneration and converging evidences indicate that there is an interplay between these two proteins at both molecular and pathological levels. There are no existing studies on tau in EEC and therefore we set out to examine the isoform profile and phosphorylation state of tau in these cells.MethodsSurgical specimens of human colon from control subjects were analyzed by immunohistochemistry using a panel of anti-tau antibodies together with chromogranin A and Glucagon-like peptide-1 (two EEC markers) antibodies. To investigate tau expression further, two EEC lines, namely GLUTag and NCI-H716 were analyzed by Western blot with pan-tau and tau isoform specific antibodies and by RT-PCR. Lambda phosphatase treatment was used to study tau phosphorylation in both cell lines. Eventually, GLUTag were treated with propionate and butyrate, two short chain fatty acids known to sense EEC, and analyzed at different time points by Western blot with an antibody specific for tau phosphorylated at Thr205.ResultsWe found that tau is expressed and phosphorylated in EEC in adult human colon and that both EEC lines mainly express two tau isoforms that are phosphorylated under basal condition. Both propionate and butyrate regulated tau phosphorylation state by decreasing its phosphorylation at Thr205.Conclusion and inferenceOur study is the first to characterize tau in human EEC and in EEC lines. As a whole, our findings provide a basis to unravel the functions of tau in EEC and to further investigate the possibility of pathological changes in tauopathies and synucleinopathies

Improving phenotyping in winter barley cultivars towards waterlogging tolerance by combining field trials under natural conditions with controlled growth condition experiments

Additional rainfall in Northern Europe due to global climate change is increasing the incidences of field flooding. Flooding causes hypoxic stress that results in a reduced capacity for photosynthesis, reduction in nutrient availability and uptake, increased production of toxic metabolites by anaerobic bacteria in the soil, and ultimately yield losses and crop death. To overcome hypoxic environmental conditions, new cultivars need to be bred and tested for waterlogging tolerance. We scored 403 winter barley cultivars from the ‘Association Genetics of UK Elite Barley’ (AGOUEB) population, taking advantage of the phenotypic changes associated with hypoxic stress. This enabled us to identify an initial set of waterlogging sensitive and tolerant cultivars. Comparative analysis of a subset of 65 cultivars exposed to waterlogging stress under field and growth cabinet environments showed variability in scores due to varying sensitivity to waterlogging over multi-season field trials. In field trials, we observed waterlogging damage resulting in reductions in biomass, grain yield and crop height. However, the effects varied between seasons and the severity of waterlogging due to differences in the topography of the field and the amount of rainfall. To overcome the seasonal variations in environmental conditions in multi-season field trials, we developed in parallel, an enhanced phenotyping method by complementing field experiments with phenotyping under controlled growth conditions. The phenotyping scoring method allows for the grouping of cultivars by sensitivity and tolerance to waterlogging, with limited variance between cultivars scored in the field and controlled conditions. Together, these two complementary approaches maximise the data available to breeders, allowing for the reliable selection of more tolerant cultivars able to grow under flooding conditions

Is mutational meltdown a threat to the mega diverse genus Begonia?

Begonia is one of the most species-rich angiosperm genera, studied for its rapid species radiation in tropical regions, and high morphological diversity. Typical populations are isolated and many display characteristics of narrow endemism. Endemic populations are prone to inbreeding and vulnerable to anthropogenic disturbance, while being isolated and difficult to access for population size estimation. For these rare species, herbarium specimens are the most accessible material available, even though the number of specimens collected for a single population is few. We have developed a pipeline to use genomic data recovered from a single herbarium specimen to estimate the degree of inbreeding and the demographic history of the population. This pipeline has been designed to process low-coverage ancient DNA datasets from non-model organisms and assess the inbreeding coefficient using several genomic homozygosity estimators. The pipeline integrate several tools to manage ancient DNA (aDNA) damage patterns, duplicated genes, problematic baits, and to determine homozygosity patterns in fresh and historical specimens. The pipeline includes mapDamage, a tool to quantify nucleotides substitution A to G or C to T in the set of data, and recalibrate the quality score of the alignment files, minimizing the bias due to aDNA patterns of damages. Target capture baits matching multiple regions of the genome have been identified, characterised, and removed from the analysis as well to prevent subsequent incorrect variant call. Many paralogous genes are found in Begonia genomes due to an early whole genome duplication event in the history of the genus. As this can introduce a bias in the variant calling step of the pipeline, we have implemented a step to detect baits capturing sequences from paralogous genes in our analysis. Three methods have been considered for this: deviation of the genotype frequencies expected in a mapping population, detection of a unexpected level of heterozygosity (HDplot tool), or segregating multiple contigs aligning to the same bait (pipeline HybPiper). This analysis used genome skims from a mapping population to test the approaches. The study showed low overlap between the baits detected as capturing paralogs between the three methods with only 73 detected in all of them. Herbarium historical specimens from a single population are scarce, and at one time point considered we can expect to find a reduced number of specimens available for analysis. In a lot of cases, only a unique specimen is available and represent the whole population. Therefore, rather than using inbreeding coefficients based on alleles frequencies, we are using Runs of Homozygosity (ROH) to estimate inbreeding and need only a single sample to be measured. To be able to measure ROH with Hyb-Seq data, we needed to know what part of the genome the Begonia baits are capturing with contiguous baits. The length of genome captured by the bait set has been calculated for the four most complete Begonia genomes available to determine the length of syntenic regions which can be captured. This was a key point to establish the last part of the pipeline to calculate the size of ROH. We used PLINK to detect and quantify ROHs from VCF files produced by variant calling. The estimators derived are the total length of ROH in the dataset (SROH), the total number of ROH in the dataset (NROH), and the frequency of ROH for each sample (FROH). The confrontation of the SROH and NROH scores on a scatter plot provide an estimation of the relative size of the population, and give clues about an admixture with another population, a bottleneck event, or consanguinity are provided by this plot. The FROH estimator is less informative but follows linearly the size of the population estimated by the NROH/SROH plot. It has been used to study the biogeography of the specimens and mapped to their phylogenetic reconstruction to investigate the patterns of homozygosity. We have analysed two sets of target-capture data with the pipeline, one with Arabian Begonia, and the second with Begonia from Papua New Guinea. The first set is composed of 43 specimens of Arabian Begonia specimens from the Socotran archipelago including the species B. socotrana and B. samhaensis and with silica-dried and herbarium-dried historical specimens. Examination of the Hyb-Seq Socotran dataset revealed uneven coverage across the baits. This capture has been used to show the limitation of the pipeline, as phylogenetic reconstruction has not been successful beyond species level, and the ROH estimations were not significant. The second set of target capture data included 160 samples from the New Guinea Highlands, from silica-dried and herbarium-dried historical specimens. As output of the pipeline, 10 specimens showed high homozygosity levels indicating a bottleneck in their demographic history, 3 outliers were suspected to be inbred, 60 were found to be from a large population or showing introgression, and 87 did not display homozygosity patterns significant enough and were filtered out by the pipeline. Mapping FROH metrics to the phylogeny shows a group within section Petermannia with consistently high homozygosity levels. Biogeographical analysis of the distribution of the samples did not reveal any clear relation between patterns of homozygosity and geographic location of the populations sampled. The data analysis has revealed a higher genetic diversity than expected in the Papua New Guinea Begonia collected and has given clues about the origin of the homozygosity patterns observed which seem more related to phylogenetic relationship rather than microevolution at population level

On algebraic extra-stress models for the simulation of viscoelastic flows

A methodology is presented for the formulation of an algebraic extra-stress model derivable from the Oldroyd-B constitutive equation for a viscoelastic fluid. An implicit algebraic tensor relation is derived directly from the differential constitutive relation by involving a slow variation condition on the evolution of the deviatoric part of the extra-stress tensor. An explicit solution to this algebraic constitutive equation is then obtained using representation bases developed previously for the turbulent flow of Newtonian fluids. A series of validation flows are then studied to assess the accuracy and range of applicability of the algebraic extra-stress model. (C) 1998 Elsevier Science B.V. All rights reserved

Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass.

Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach