The utility of NBS profiling for plant systematics: a first study in tuber-bearing Solanum species

Systematic relationships are important criteria for researchers and breeders to select materials. We evaluated a novel molecular technique, nucleotide binding site (NBS) profiling, for its potential in phylogeny reconstruction. NBS profiling produces multiple markers in resistance genes and their analogs (RGAs). Potato (Solanum tuberosum L.) is a crop with a large secondary genepool, which contains many important traits that can be exploited in breeding programs. In this study we used a set of over 100 genebank accessions, representing 49 tuber-bearing wild and cultivated Solanum species. NBS profiling was compared to amplified fragment length polymorphism (AFLP). Cladistic and phenetic analyses showed that the two techniques had similar resolving power and delivered trees with a similar topology. However, the different statistical tests used to demonstrate congruency of the trees were inconclusive. Visual inspection of the trees showed that, especially at the lower level, many accessions grouped together in the same way in both trees; at the higher level, when looking at the more basal nodes, only a few groups were well supported. Again this was similar for both techniques. The observation that higher level groups were poorly supported might be due to the nature of the material and the way the species evolved. The similarity of the NBS and AFLP results indicate that the role of disease resistance in speciation is limite

Punitive sanctions and the transition from welfare to work

social welfare;employment;labour policy;job search

Inleiding tot die belangrikste metodes in die moderne literatuurwetenskap - 'n Metodologiese benadering

The article opens with a brief discussion of the development of literary theory as an independent discipline in the twentieth century. The author then provides some theoretical background and discussion of two main streams of modern literary method: Positivism and Hermeneutics

Allele mining in solanum: conserved homologues of Rpi-blb 1 are identified in Solanum stoloniferum

Allele mining facilitates the discovery of novel resistance (R) genes that can be used in breeding programs and sheds light on the evolution of R genes. Here we focus on two R genes, Rpi-blb1 and Rpi-blb2, originally derived from Solanum bulbocastanum. The Rpi-blb1 gene is part of a cluster of four paralogues and is flanked by RGA1-blb and RGA3-blb. Highly conserved RGA1-blb homologues were discovered in all the tested tuber-bearing (TB) and non-tuber-bearing (NTB) Solanum species, suggesting RGA1-blb was present before the divergence of TB and NTB Solanum species. The frequency of the RGA3-blb gene was much lower. Interestingly, highly conserved Rpi-blb1 homologues were discovered not only in S. bulbocastanum but also in Solanum stoloniferum that is part of the series Longipedicellata. Resistance assays and genetic analyses in several F1 populations derived from the relevant late blight resistant parental genotypes harbouring the conserved Rpi-blb1 homologues, indicated the presence of four dominant R genes, designated as Rpi-sto1, Rpi-plt1, Rpi-pta1 and Rpi-pta2. Furthermore, Rpi-sto1 and Rpi-plt1 resided at the same position on chromosome VIII as Rpi-blb1 in S. bulbocastanum. Segregation data also indicated that an additional unknown late blight resistance gene was present in three populations. In contrast to Rpi-blb1, no homologues of Rpi-blb2 were detected in any material examined. Hypotheses are proposed to explain the presence of conserved Rpi-blb1 homologues in S. stoloniferum. The discovery of conserved homologues of Rpi-blb1 in EBN 2 tetraploid species offers the possibility to more easily transfer the late blight resistance genes to potato varieties by classical breeding

Reconstruction of sea surface temperatures from the oxygen isotope composition of fossil planktic foraminifera.

Knowledge of the historic surface temperature of sea water is of importance for the calibration of climate models. The oxygen isotope composition of the shells of several species of planktic foraminifera can be used as a measure for this sea surface temperature. In this paper we investigate how mathematical models can contribute to the process of extracting information about the temperature at which the foraminifera lived from measurement of the oxygen isotope composition of their shells. A simple model is proposed which captures both the average and the variability of the temperature. Preliminary findings suggest that this model forms a solid basis for future research

Bias-based modeling and entropy analysis of PUFs

Physical Unclonable Functions (PUFs) are increasingly becoming a well-known security primitive for secure key storage and anti-counterfeiting. For both applications it is imperative that PUFs provide enough entropy. The aim of this paper is to propose a new model for binary-output PUFs such as SRAM, DFF, Latch and Buskeeper PUFs, and a method to accurately estimate their entropy. In our model the measurable property of a PUF is its set of cell biases. We determine an upper bound on the ‘extractable entropy’, i.e. the number of key bits that can be robustly extracted, by calculating the mutual information between the bias measurements done at enrollment and reconstruction. In previously known methods only uniqueness was studied using information-theoretic measures, while robustness was typically expressed in terms of error probabilities or distances. It is not always straightforward to use a combination of these two metrics in order to make an informed decision about the performance of different PUF types. Our new approach has the advantage that it simultaneously captures both of properties that are vital for key storage: uniqueness and robustness. Therefore it will be possible to fairly compare performance of PUF implementations using our new method. Statistical validation of the new methodology shows that it clearly captures both of these properties of PUFs. In other words: if one of these aspects (either uniqueness or robustness) is less than optimal, the extractable entropy decreases. Analysis on a large database of PUF measurement data shows very high entropy for SRAM PUFs, but rather poor results for all other memory-based PUFs in this database

Convex treemaps with bounded aspect ratio

Treemaps are a popular technique to visualize hierarchical data. The input is a weighted tree T where the weight of each node is the sum of the weights of its children. A treemap for T is a hierarchical partition of a rectangle into simply connected regions, usually rectangles. Each region represents a node of T and the area of each region is proportional to the weight of the corresponding node. An important quality criterium for treemaps is the aspect ratio of its regions. Unfortunately, one cannot bound the aspect ratio if the regions are restricted to be rectangles. Hence Onak and Sidiropoulos introduced polygonal partitions, which use convex polygons. We are the first to obtain convex partitions with optimal aspect ratio O(depth(T )). We also consider the important special case that depth(T ) = 1, that is, single-level treemaps. We show how to construct convex single-level treemaps that use only four simple shapes for the regions and have aspect ratio at most 34/7

A role for age-related changes in TGFβ signaling in aberrant chondrocyte differentiation and osteoarthritis

Transforming growth factor beta (TGFβ) is a growth factor with many faces. In our osteoarthritis (OA) research we have found that TGFβ can be protective as well as deleterious for articular cartilage. We postulate that the dual effects of TGFβ on chondrocytes can be explained by the fact that TGFβ can signal via different receptors and related Smad signaling routes. On chondrocytes, TGFβ not only signals via the canonical type I receptor ALK5 but also via the ALK1 receptor. Notably, signaling via ALK5 (Smad2/3 route) results in markedly different chondrocyte responses than ALK1 signaling (Smad1/5/8), and we postulate that the balance between ALK5 and ALK1 expression on chondrocytes will determine the overall effect of TGFβ on these cells. Importantly, signaling via ALK1, but not ALK5, stimulates MMP-13 expression by chondrocytes. In cartilage of ageing mice and in experimental OA models we have found that the ALK1/ALK5 ratio is significantly increased, favoring TGFβ signaling via the Smad1/5/8 route, changes in chondrocyte differentiation and MMP-13 expression. Moreover, human OA cartilage showed a significant correlation between ALK1 and MMP-13 expression. In this paper we summarize concepts in OA, its link with ageing and disturbed growth factor responses, and a potential role of TGFβ signaling in OA development