Relatedness between numerically small Dutch Red dairy cattle populations and possibilities for multibreed genomic prediction

Red dairy breeds are a valuable cultural and historical asset, and often a source of unique genetic diversity. However, they have difficulties competing with other, more productive, dairy breeds. Improving competitiveness of Red dairy breeds, by accelerating their genetic improvement using genomic selection, may be a promising strategy to secure their long-term future. For many Red dairy breeds, establishing a sufficiently large breed-specific reference population for genomic prediction is often not possible, but may be overcome by adding individuals from another breed. Relatedness between breeds strongly decides the benefit of adding another breed to the reference population. To prioritize among available breeds, the effective number of chromosome segments (M_e) can be used as an indicator of relatedness between individuals from different breeds. The M_e is also an important parameter in determining the accuracy of genomic prediction. The M_e can be estimated both within a population and between 2 populations or breeds, as the reciprocal of the variance of genomic relationships. We investigated relatedness between 6 Dutch Red cattle breeds, Groningen White Headed (GWH), Dutch Friesian (DF), Meuse-Rhine-Yssel (MRY), Dutch Belted (DB), Deep Red (DR), and Improved Red (IR), focusing primarily on the M_e, to predict which of those breeds may benefit from including reference animals of the other breeds. All of these breeds, except MRY, are under high risk of extinction. Our results indicated high variability of M_e, especially between M_e ranging from ～3,500 to ～17,400, indicating different levels of relatedness between the breeds. Two clusters are especially important, one formed by MRY, DR, and IR, and the other comprising DF and DB. Although relatedness between breeds within each of these 2 clusters is high, across-breed genomic prediction is still limited by the current number of genotyped individuals, which for many breeds is low. However, adding MRY individuals would increase the reference population of DR substantially. We estimated that between 11 and 133 individuals from other breeds are needed to achieve accuracy of genomic prediction equivalent to using one additional individual from the same breed. Given the variation in size of the breeds in this study, the benefit of a multibreed reference population is expected to be lower for larger breeds than for the smaller ones.     

Induction of Oxidative Stress and Antioxidative Mechanisms in Arabidopsis thaliana after Uranium Exposure at pH 7.5

To evaluate the environmental impact of uranium (U) contamination, it is important to investigate the effects of U at ecologically relevant conditions. Since U speciation, and hence its toxicity, strongly depends on environmental pH, the present study aimed to investigate dose-dependent effects of U at pH 7.5. Arabidopsis thaliana plants (Mouse-ear Cress) were exposed for three days to different U concentrations at pH 7.5. In the roots, the increased capacities of ascorbate peroxidase and glutathione reductase indicate an important role for the ascorbate-glutathione cycle during U-induced stress. However, a significant decrease in the ascorbate redox state was observed after exposure to 75 and 100 µM U, indicating that those roots are severely stressed. In accordance with the roots, the ascorbate-glutathione cycle plays an important role in the antioxidative defence systems in A. thaliana leaves exposed to U at pH 7.5 as the ascorbate and glutathione biosynthesis were upregulated. In addition, small inductions of enzymes of the antioxidative defence system were observed at lower U concentrations to counteract the U-induced stress. However, at higher U concentrations it seems that the antioxidative defence system of the leaves collapses as reductions in enzyme activities and gene expression levels were observed.     

Sound black-box checking in the LearnLib

Innovations in Systems and Software Engineering - In black-box checking (BBC) incremental hypotheses on the behavior of a system are learned in the form of finite automata, using information from a...     

Benefit and Implementation of Groundwater Protection Zoning in South Africa

Groundwater studies in several African countries show that the contamination of water-supply aquifers is mainly due to improper placement of land-based activities such as agriculture, industries, waste disposal. In South Africa, groundwater pollution is also of increasing concern due to fast population growth and accompanying development. Groundwater protection zoning is a supplemental methodology for groundwater management that incorporates land use planning. The land is managed to minimize the potential of groundwater contamination by human activities that occur on or below the land surface. The various benefits associated with implementation of protection zoning are discussed for stakeholders such as communities, water supply companies, ecosystems and policy makers. A South African case study is presented comparing the cost of protection with the cost incurred due to the treatment of sick and dying people due to contaminated drinking water. These benefits must be communicated to the stakeholders to start the implementation at all management levels. Implementation steps of groundwater protection zones are discussed and can be tested even with low budgets and little data available. Monitoring and reassessment of protection zones are important to test the effectiveness and prove to decision makers that the money was well spent. The legal framework for implementation of groundwater protection zoning in a South African context is described, where the water law makes provision for tools like differentiated protection, licensing and recovery of cost. Challenges regarding implementation of groundwater protection are discussed with some action steps on how to move forward.     

Optical and electrical properties and phonon drag effect in low temperature TEP measurements of AgSbSe2 thin films

Polycrystalline thin films of silver antimony selenide have been deposited using a reactive evaporation technique onto an ultrasonically cleaned glass substrate at a vacuum of 10-5 torr. The preparative parameters, like substrate temperature and incident fluxes, have been properly controlled in order to get stoichiometric, good quality and reproducible thin film samples. The samples are characterized by XRD, SEM, AFM and a UV-vis-NIR spectrophotometer. The prepared sample is found to be polycrystalline in nature. From the XRD pattern, the average particle size and lattice constant are calculated. The dislocation density, strain and number of crystallites per unit area are evaluated using the average particle size. The dependence of the electrical conductivity on the temperature has also been studied and the prepared AgSbSe2 samples are semiconducting in nature. The AgSbSe2 thin films exhibited an indirect allowed optical transition with a band gap of 0.64 eV. The compound exhibits promising thermoelectric properties, a large Seebeck coefficient of 30 mV/K at 48 K due to strong phonon electron interaction. It shows a strong temperature dependence on thermoelectric properties, including the inversion of a dominant carrier type from p to n over a low temperature range 9-300 K, which is explained on the basis of a phonon drag effect.     

Verification of a sliding window protocol in μCRL and PVS

We prove the correctness of a sliding window protocol with an arbitrary finite window size n and sequence numbers modulo 2n. The correctness consists of showing that the sliding window protocol is branching bisimilar to a queue of capacity 2n. The proof is given entirely on the basis of an axiomatic theory, and has been checked in the theorem prover PVS. Received November 2004 Revised June 2005 Accepted July 2005 by J. V. Tucker     

Atomic force microscopy of collagen structure in bone and dentine revealed by osteoclastic resorption

Mineralised tissues such as bone consist of two material phases: collagen protein fibrils, secreted by osteoblasts, form model structures for subsequent deposition of mineral, calcium hydroxyapatite. Collagen and mineral are removed in a three-dimensional manner by osteoclasts during bone turnover in skeletal growth or repair. Bone active drugs have recently been developed for skeletal diseases, and there is revived interest in changes in the structure of mineralised tissues seen in disease and upon treatment. The resolution of atomic force microscopy and use of unmodified samples has enabled us to image bone and dentine collagen exposed by the natural process of cellular dissolution of mineralised matrix. The morphology of bone and dentine has been analysed when fully mineralised and after osteoclast-mediated bone resorption, and compared with results from other microscopy techniques. Banded type I collagen, with 66.5+/-1.4 nm axial D-periodicity and 62.2+/-7.0 nm diameter, has been identified within resorption lacunae in bone and 69.4+/-4.3 nm axial D-periodicity and 140.6+/-12.4 nm diameter in dentine substrates formed by human and rabbit osteoclasts, respectively. This observation suggests a route by which the material and morphological properties of bone collagen can be analysed in situ, compared with collagen from non-skeletal sites, and contrasted in diseases of medical importance, such as osteoporosis, where skeletal tissue is mechanically weakened.     

A calculus for four-valued sequential logic

We present a complete axiomatisation for four-valued sequential logic. It consists of nine axioms, from which all valid laws can be derived by equational reasoning. These nine axioms are independent of each other.     

On the axiomatizability of priority II

This paper contributes to the study of the equational theory of the priority operator of Baeten, Bergstra and Klop in the setting of the process algebra BCCSP. It is shown that, in the presence of at least two actions, the collection of process equations over BCCSP with the priority operator that are valid modulo bisimilarity, irrespective of the chosen priority order over actions, is not finitely based. This holds true even if one restricts oneself to the collection of valid process equations that do not contain occurrences of process variables.