Error-enhanced augmented proprioceptive feedback in stroke rehabilitation training:a pilot study

Augmented feedback plays an essential role in stroke rehabilitation therapy. When a force is applied to the arm, an augmented sensory (proprioceptive) cue is provided. The question was to find out if stroke patients can learn reach-and retrieval movements with error-enhanced augmented sensory feedback. The movements were performed over a predefined path, and when deviating of the path a force is provided, as colliding to a wall of a tunnel. Two chronic stroke survivors (FM of 53 and 49) performed reach and retrieval movements in a virtual tunnel. When two consecutive series of 15 repetitions of the same movements were performed, there was a consistent decrease of collisions to the wall in the second series of movements. This indicates that these patients were able to learn the predefined trajectory by means of augmented proprioceptive feedback. Despite the small number of patients tested, this finding is promising for the usage of error-enhanced augmented proprioceptive feedback in rehabilitation therapy

Inter-molecular structure factors of macromolecules in solution: integral equation results

The inter-molecular structure of semidilute polymer solutions is studied theoretically. The low density limit of a generalized Ornstein-Zernicke integral equation approach to polymeric liquids is considered. Scaling laws for the dilute-to-semidilute crossover of random phase (RPA) like structure are derived for the inter-molecular structure factor on large distances when inter-molecular excluded volume is incorporated at the microscopic level. This leads to a non-linear equation for the excluded volume interaction parameter. For macromolecular size-mass scaling exponents, $\nu$, above a spatial-dimension dependent value, $\nu_c=2/d$, mean field like density scaling is recovered, but for $\nu<\nu_c$ the density scaling becomes non-trivial in agreement with field theoretic results and justifying phenomenological extensions of RPA. The structure of the polymer mesh in semidilute solutions is discussed in detail and comparisons with large scale Monte Carlo simulations are added. Finally a new possibility to determine the correction to scaling exponent $\omega_{12}$ is suggested.Comment: 11 pages, 5 figures; to be published in Phys. Rev. E (1999

Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

Article purchased; Published online: 3 August 2017Cassava (Manihot esculenta (L.) Crantz) is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and micronutrient density, particularly of provitamin A, traits that are negatively correlated, are among the primary selection objectives in cassava breeding. This study aimed at identifying genetic markers associated with these traits and uncovering the potential underlying cause of their negative correlation - whether linkage and/or pleiotropy. A genome-wide association mapping using 672 clones genotyped at 72,279 SNP loci was carried out. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness was identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that co-located with the 24.1 Mbp peak for carotenoid content was identified. Haplotypes at these loci explained a large proportion of the phenotypic variability. Evidence of mega-base-scale linkage disequilibrium around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid (phytoene synthase) and starch biosynthesis (UDP-glucose pyrophosphorylase and sucrose synthase) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate on the genetic architecture of carotenoids and dry matter in cassava and provides an opportunity to accelerate genetic improvement of these traits

Genome-wide association study of resistance to cassava green mite pest and related traits in cassava

Published: 26 July 2018Cassava green mite [CGM, Mononychellus tanajoa (Bondar)] is a dry-season pest that usually feeds on the underside of young leaves causing leaf chlorosis, stunted growth, and root yield reduction by 80%. Since cassava (Manihot esculenta Crantz) leaves and roots serve as a primary staple food source, a decline in cassava yield can lead to household food, nutrition, and income insecurity. To evaluate the existence of CGM resistance alleles in the available germplasm, a diversity panel of 845 advanced breeding lines obtained from IITA, CIAT, and the National Root Crops Research Institute (NRCRI) were evaluated for CGM severity (CGMS), leaf pubescence (LP), leaf retention (LR), stay green, shoot tip compactness, and shoot tip size. A genome-wide association mapping detected 35 single-nucleotide polymorphisms (SNPs) markers significantly associated with CGMS, LP, and LR on chromosome 8. Colocalization of the most significant SNP associated with CGMS, LP, and LR on chromosome 8 is possibly an indication of pleiotropy or the presence of closely linked genes that regulate these traits. Seventeen candidate genes were found to be associated to CGM resistance. These candidate genes were subdivided into seven categories according to their protein structure namely, Zn finger, pentatricopeptide, MYB, MADS, homeodomain, trichome birefringence-related protein, and ethylene-responsive transcription factor genes. This study revealed significant loci associated with CGM, not previously reported, which together represent potential sources for the ongoing effort to develop multiple pest- and disease-resistant cassava cultivars

Reproducibility of microvessel counts in breast cancer specimens

Assessment of tumour vascularity in core biopsy specimens may be a useful predictor of response to primary therapy. This study addresses practical methodological issues regarding accuracy of tumour vascularity assessments in different breast cancer specimens. Issues addressed in the study are variation caused by (i) inherent observer variation in the method, (ii) tumour heterogeneity and (iii) previous surgical manipulation of tumours. Microvessel counts were performed by two observers on separate occasions and by two different observers. Counts were performed on core biopsies and tumour sections taken simultaneously (n = 16) and with an intervening time interval (n = 21). In addition core biopsies were obtained from the same tumour on two separate occasions (n = 10). A highly significant correlation was found in counts performed by the same observers at different times and between two different observers. No significant correlation was found in counts of core biopsies and tumour sections taken either simultaneously or subsequently. No correlation was found between counts of sequential core biopsies. Study findings suggest that, although microvessel counts may be assessed reproducibly by the same and different observers, counts performed in core biopsies do not accurately reflect those of overall tumour, limiting their potential as predictive or prognostic markers. © 1999 Cancer Research Campaig

QTL linkage analysis of connected populations using ancestral marker and pedigree information

The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals’ genotype probability without significantly increasing computational demand

Population structure and linkage disequilibrium unravelled in tetraploid potato

Association mapping is considered to be an important alternative strategy for the identification of quantitative trait loci (QTL) as compared to traditional QTL mapping. A necessary prerequisite for association analysis to succeed is detailed information regarding hidden population structure and the extent of linkage disequilibrium. A collection of 430 tetraploid potato cultivars, comprising two association panels, has been analysed with 41 AFLP® and 53 SSR primer combinations yielding 3364 AFLP fragments and 653 microsatellite alleles, respectively. Polymorphism information content values and detected number of alleles for the SSRs studied illustrate that commercial potato germplasm seems to be equally diverse as Latin American landrace material. Genome-wide linkage disequilibrium (LD)—reported for the first time for tetraploid potato—was observed up to approximately 5 cM using r2 higher than 0.1 as a criterion for significant LD. Within-group LD, however, stretched on average twice as far when compared to overall LD. A Bayesian approach, a distance-based hierarchical clustering approach as well as principal coordinate analysis were adopted to enquire into population structure. Groups differing in year of market release and market segment (starch, processing industry and fresh consumption) were repeatedly detected. The observation of LD up to 5 cM is promising because the required marker density is not likely to disable the possibilities for association mapping research in tetraploid potato. Population structure appeared to be weak, but strong enough to demand careful modelling of genetic relationships in subsequent marker-trait association analyses. There seems to be a good chance that linkage-based marker-trait associations can be identified at moderate marker densities

Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato

Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ≤ 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ≤ 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed

Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

<p>Abstract</p> <p>Background</p> <p>Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102) assembled at the start of the Barley Coordinated Agricultural Project (CAP). This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608.</p> <p>Results</p> <p>Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without <it>a priori </it>knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We then conducted association analyses - with SNP data only - in the larger germplasm arrays. For both vernalization sensitivity and inflorescence type, the most significant associations in the larger data sets were found with SNPs coincident with the synthetic markers used in the CAP Core and with SNPs detected via interaction analysis in the CAP Core.</p> <p>Conclusions</p> <p>Small and highly structured collections of germplasm, such as the CAP Core, are cost-effectively phenotyped and genotyped with high-throughput markers. They are also useful for characterizing allelic diversity at loci in germplasm of interest. Our results suggest that discovery-oriented exercises in AM in such small arrays may generate a large number of false-positives. However, if haplotypes in candidate genes are available, they may be used as anchors in an analysis of interactions to identify other candidate regions harboring genes determining target traits. Using larger germplasm arrays, genome regions where the principal genes determining vernalization sensitivity and row type are located were identified.</p