Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.)

BACKGROUND: The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium. RESULTS: A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r(2)). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r(2 )> 0.05, or up to 10 cM with r(2 )> 0.2. Few loci mapping to different chromosomes showed significant LD with r(2 )> 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r(2 )> 0.05 and had higher values of r(2), although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations. CONCLUSION: A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley

Great Sumatra Earthquake Registers on Electrostatic Sensor

Strong electrical signals that correspond to the Mw = 9.3 earthquake of 26 December 2004, which occurred at 0058:50.7 UTC off the west coast of northern Sumatra, Indonesia, were recorded by an electrostatic sensor (a device that detects short-term variations in Earth’s electrostatic fi eld) at a seismic station in Italy, which had been installed to study the infl uence of local earthquakes on a new landslide monitoring system. Electrical signals arrived at the station practically instantaneously and were detected up to several hours before the onset of the Sumatra earthquake (Figure 1) as well as before local quakes. The corresponding seismic signals (p-waves) arrived 740 seconds after the start of the earthquake. Because the electrical signals travel at the speed of light, electrical monitoring for the global detection of very strong earthquakes could be an important tool in signifi cantly increasing the hazard alert window

Evaluation of laboratory and on-farm tests to estimate colostrum quality for dairy cows

The objectives of this study were to evaluate different analytical methods to determine colostrum quality in dairy cattle, including one laboratory-based method (ELISA) and 4 on-farm tests. We hypothesized that the colostral IgG concentration using different analytical methods, such as ELISA (mg/mL), digital Brix refractometer (% Brix), colostrometer (specific gravity and mg/mL), an outflow funnel (seconds), and a lateral flow assay (mg/mL), were highly correlated with the reference method, radial immunodiffusion (RID; mg/mL) and would generate comparable results. Colostrum samples were collected from 209 Holstein Friesian cows on 2 commercial dairy farms in Germany. Colostrum weight and colostrum temperature were measured. Test characteristics, such as optimum thresholds, sensitivity, specificity, and area under the curve (AUC) were determined using a receiver operating characteristic curve analyses for each test. Out of 209 colostrum samples assessed by RID, 186 (89%) samples had high quality (≥50 mg IgG/mL), while 23 colostrum samples (11%) showed poor quality with IgG concentrations less than 50 mg/mL. The mean IgG concentration (±SD) was 101.3 ± 45.9 mg/mL and the range was 6.0 to 244.3 mg/mL. The Pearson correlation coefficient (r) between RID and ELISA was r = 0.78. In comparison to RID, Pearson correlation coefficients for the on-farm tests were: r = 0.79 (digital Brix refractometry), r = 0.58 (colostrometer: specific gravity), r = 0.61 (colostrometer: temperature corrected), r = 0.26 (outflow funnel) and r = 0.43 (lateral flow assay), respectively. The optimal threshold to identify high-quality colostrum using ELISA was 50.8 mg/mL with sensitivity 91.3%, specificity 92.3%, and AUC of 0.94. For the on-farm tests sensitivity ranged from 95.7% (Brix refractometry) to 60.9% (lateral flow assay). Specificity ranged from 88.6% (lateral flow assay) to 75.9% (colostrometer: temperature corrected). The AUC ranged from 0.93 (Brix refractometry) to 0.73 (outflow funnel). Based on the AUC, ELISA (0.94) and Brix refractometry (0.93) can be considered highly accurate. In conclusion, the ELISA is accurate to assess colostrum quality. Regarding the on-farm tests only the digital Brix refractometer and the colostrometer were adequate to determine colostrum quality

Maternal stress, child behavior and the promotive role of older siblings

Abstract Background: In the first years of their lives, children develop the cognitive, social and emotional skills that will provide the foundations for their lifelong health and achievements. To increase their life prospects and reduce the long-term effects of early aversive conditions, it is therefore crucial to understand the risk factors that negatively affect child development and the factors that are instead beneficial. In this study, we tested (i) the effects of different social and environmental stressors on maternal stress levels, (ii) the dynamic relationship between maternal stress and child behavior problems during development, and (iii) the potential promotive (i.e. main) or protective (i.e. buffering) effect of siblings on child behavior problems during development.Methods: We used longitudinal data from 373 mother–child pairs (188 daughters, 185 sons) from pregnancy until 10 years of age. We assessed maternal stress and child behavior problems (internalizing and externalizing) with vali-dated questionnaires, and then used linear mixed models, generalized linear mixed models and longitudinal cross-lagged models to analyze the data.Results: Our results showed that higher maternal stress levels were predicted by socio-environmental stressors (i.e. the lack of sufficient social areas in the neighborhood). Moreover, prenatal maternal stress reliably predicted the occurrence of behavior problems during childhood. Finally, the presence of older siblings had a promotive function, by reducing the likelihood that children developed externalizing problems.Conclusions: Overall, our results confirm the negative effects that maternal stress during pregnancy may have on the offspring, and suggest an important main effect of older siblings in promoting a positive child development

Towards a simulation of minibuses in South Africa

After private cars, minibus taxis are the most common transport mode in South Africa. Especially for low-income citizens living in townships, minibus services are often the only possibility for mobility. Despite the great importance of the mode, there is very little knowledge of routes, fares, and the number of minibuses. Hence, it is difficult to simulate and to understand the influence of this mode on other modes and on transport planning in general.. is article presents the development of the first "close-to-reality" minibus supply model based on demand and street network only The approach adopts the survival-of-the-fittest principle, using a co-evolutionary algorithm that is integrated into a microscopic multi-agent simulation framework The successful application of the approach to a large-scale, real-world scenario in the Nelson Mandela Bay Area Municipality in South Africa shows that it is able to identify the main minibus corridors as well as to find robust service coverage in lower-demand areas The resulting minibus supply model can then be used for planning purposes (e.g., to investigate aspects of strategic, operational, or regulatory changes)

First Model-Independent Measurement of the Spin Triplet pΛp\Lambda Scattering Length from Final State Interaction in the p⃗p→pK+Λ\vec{p}p \rightarrow pK^{+}\Lambda Reaction

The $\vec{p}p \rightarrow pK^{+}\Lambda$ reaction has been measured with the COSY-TOF detector at a beam momentum of $2.7\,\mathrm{GeV}/c$. The polarized proton beam enables the measurement of the beam analyzing power by the asymmetry of the produced kaon ($A_N^{K}$). This observable allows the $p\Lambda$ spin triplet scattering length to be extracted for the first time model independently from the final-state interaction in the reaction. The obtained value is $a_{t} = (-2.55 ^{+0.72}_{-1.39} {}_{\textrm{stat.}} \pm 0.6_{\textrm{syst.}} \pm 0.3_{\textrm{theo.}})\mathrm{fm}$. This value is compatible with theoretical predictions and results from model-dependent analyses.Comment: Revised version as accepted for publication in PR

Effective one-band electron-phonon Hamiltonian for nickel perovskites

Inspired by recent experiments on the Sr-doped nickelates, $La_{2-x}Sr_xNiO_4$, we propose a minimal microscopic model capable to describe the variety of the observed quasi-static charge/lattice modulations and the resulting magnetic and electronic-transport anomalies. Analyzing the motion of low-spin (s=1/2) holes in a high-spin (S=1) background as well as their their coupling to the in-plane oxygen phonon modes, we construct a sort of generalized Holstein t-J Hamiltonian for the $NiO_2$ planes, which contains besides the rather complex ``composite-hole'' hopping part non-local spin-spin and hole-phonon interaction terms.Comment: 12 pages, LaTeX, submitted to Phys. Rev.

High precision measurement of the associated strangeness production in proton proton interactions

A new high precision measurement of the reaction pp -> pK+Lambda at a beam momentum of 2.95 GeV/c with more than 200,000 analyzed events allows a detailed analysis of differential observables and their inter-dependencies. Correlations of the angular distributions with momenta are examined. The invariant mass distributions are compared for different regions in the Dalitz plots. The cusp structure at the N Sigma threshold is described with the Flatt\'e formalism and its variation in the Dalitz plot is analyzed.Comment: accepted for publication in Eur. Phys. J.

Disorder Induced Quantum Phase Transition in Random-Exchange Spin-1/2 Chains

We investigate the effect of quenched bond-disorder on the anisotropic spin-1/2 (XXZ) chain as a model for disorder induced quantum phase transitions. We find non-universal behavior of the average correlation functions for weak disorder, followed by a quantum phase transition into a strongly disordered phase with only short-range xy-correlations. We find no evidence for the universal strong-disorder fixed point predicted by the real-space renormalization group, suggesting a qualitatively different view of the relationship between quantum fluctuations and disorder.Comment: 4 pages, 4 postscript figures, needs RevTeX

Observation of two time scales in the ferromagnetic manganite La(1-x)Ca(x)MnO(3), x = 0.3

We report new zero-field muon spin relaxation and neutron spin echo measurements in ferromagnetic (FM) (La,Ca)MnO3 which taken together suggest two spatially separated regions in close proximity possessing very different Mn-ion spin dynamics. One region corresponds to an extended cluster which displays 'critical slowing down' near Tc and an increasing volume fraction below Tc. The second region possesses more slowly fluctuating spins and a decreasing volume fraction below Tc. These data are discussed in terms of the growth of small polarons into overlapping regions of correlated spins below Tc, resulting in a microscopically inhomogeneous FM transition.Comment: 10 pages, 3 figure