Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana

Background: Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits. Results: A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait. Conclusions: We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation

Missing the peacock - arts, sciences, creativity, and chronic environmental conflicts

Debate on conflicts and disputes over environmental issues has intensified due to climate change and other global pressing problems becoming ever more pronounced. Simultaneously, there is little evidence of natural or social sciences helping transform even local conflicts, some of them lasting decades, gradually becoming chronic and having severe and pervasive effects on people’s lives. On the contrary, natural sciences often become part of the conflicts while social sciences remain distant observers. Conflict management requires creativity: imagining new solutions, relating to, thinking and acting in new ways. Hence, stimulation of creative thinking might offer avenues for coping with conflicting situations. We tested new forms of interaction and opportunities of creative work in managing prolonged conflicts in a series of meetings between natural scientists, social scientists, artists and conflict mediation professionals. This article discusses the experiences emerging from this experimental process. Experimenting with creative working methods provided us with new tools to facilitate interaction in the conflicts we intervene in or study. However, we don't see arts-science collaborations as a panacea to resolving conflict situations. More than interactive skills and tools that would lead to a clear-cut end of conflicts, we emphasize the ability to reflect on our own practice and role in environmental conflicts. Creative experiments can be valuable in pointing out open questions, such as what is the role that scientists, artists and mediators take and should take in controversial situations

Decellularized Matrix from Tumorigenic Human Mesenchymal Stem Cells Promotes Neovascularization with Galectin-1 Dependent Endothelial Interaction

BACKGROUND: Acquisition of a blood supply is fundamental for extensive tumor growth. We recently described vascular heterogeneity in tumours derived from cell clones of a human mesenchymal stem cell (hMSC) strain (hMSC-TERT20) immortalized by retroviral vector mediated human telomerase (hTERT) gene expression. Histological analysis showed that cells of the most vascularized tumorigenic clone, -BD11 had a pericyte-like alpha smooth muscle actin (ASMA+) and CD146+ positive phenotype. Upon serum withdrawal in culture, -BD11 cells formed cord-like structures mimicking capillary morphogenesis. In contrast, cells of the poorly tumorigenic clone, -BC8 did not stain for ASMA, tumours were less vascularized and serum withdrawal in culture led to cell death. By exploring the heterogeneity in hMSC-TERT20 clones we aimed to understand molecular mechanisms by which mesenchymal stem cells may promote neovascularization. METHODOLOGY/PRINCIPAL FINDINGS: Quantitative qRT-PCR analysis revealed similar mRNA levels for genes encoding the angiogenic cytokines VEGF and Angiopoietin-1 in both clones. However, clone-BD11 produced a denser extracellular matrix that supported stable ex vivo capillary morphogenesis of human endothelial cells and promoted in vivo neovascularization. Proteomic characterization of the -BD11 decellularized matrix identified 50 extracellular angiogenic proteins, including galectin-1. siRNA knock down of galectin-1 expression abrogated the ex vivo interaction between decellularized -BD11 matrix and endothelial cells. More stable shRNA knock down of galectin-1 expression did not prevent -BD11 tumorigenesis, but greatly reduced endothelial migration into -BD11 cell xenografts. CONCLUSIONS: Decellularized hMSC matrix had significant angiogenic potential with at least 50 angiogenic cell surface and extracellular proteins, implicated in attracting endothelial cells, their adhesion and activation to form tubular structures. hMSC -BD11 surface galectin-1 expression was required to bring about matrix-endothelial interactions and for xenografted hMSC -BD11 cells to optimally recruit host vasculature

Effect of postweaning nadling strategies on welfare and productive traits in lambs

Postweaning management strategies that include an element of social enrichment may reduce weaning stress and improve welfare and productive performance. We analyzed the effect of postweaning handling strategies on welfare and production traits in lambs. After weaning, 36 lambs were assigned to 3 experimental groups with 12 lambs each (control [C], fattening with gentle human female contact [H], and fattening with 2 adult ewes [E]). The average daily gain (ADG) was estimated. Blood samples were taken, and infrared thermography was used to estimate stress variables. There were significant differences among treatments (in favor of alternative strategies) regarding production and stress variables (cortisol, glucose, and creatine kinase). The results suggest that the lambs handled gently during the fattening were less reactive and better able to modulate their physiological stress. The E group adapted better to acute stress than the C group but was less efficient in modulating chronic stress. Both treatments showed higher slaughter live weights and better ADGs compared with the control. The use of social enrichment at weaning, especially to establish a positive human–nonhuman animal bond, alleviates lamb weaning stress and improves welfare and performance

Agricultural economics and transition: What was expected, what we observed, the lessons learned Proceedings (Volume I / II)

Over fifteen years have elapsed since the transition from the centrally planned economic system started in the early 1990’s. During this time agricultural and rural areas of Central and Eastern Europe have undergone profound structural changes with wide variations in the degree of transformation and in the rate of success in creating a competitive market and private ownership based food and agricultural system. By becoming member of the European Union the "transition" in its traditional interpretation has been concluded in ten of the Central East European countries. The transition to market based agriculture, however, is far from completion in Southern and Eastern Europe and especially in the CIS countries. International Association of Agricultural Economists (IAAE) and European Association of Agricultural Economists (EAAE) in collaboration with the Corvinus University of Budapest and with a number of other institutions in Hungary organized an inter-conference seminar on the subject of agricultural transition in Central and Eastern Europe and Central Asia. The major objective of the seminar was to discuss and draw conclusions on the role of agricultural policy in the transition process in the light of actual progress and current situation in Central and East European countries and in formal Soviet States. In addition the contribution of agricultural economics – both from the West and from the East – as a discipline and a profession to the transition process in agriculture were discussed. A specific objective was to identify priorities and means to strengthen the agricultural economics profession in the transition countries and determine research and educational priorities for the future. The seminar was attended by 118 participants representing 26 countries from Europe, North America and Asia. The Seminar was the largest professional meeting organized by the two associations in 2007. Over 110 abstracts were submitted and evaluated by the International Program Committee. In the two day program of the meeting, 8 presentations were made during the 3 plenary sessions, 66 papers were presented in the 15 contributed paper sessions in 8 subject categories. In addition there were 15 posters discussed in the poster session and the findings of a World Bank study on distortions of agricultural incentives in the region was the subject of a pre-conference workshop. Plenary speakers included Ulrich Koester, Johan Swinnen, Jerzy Wilkin, Zvi Lerman, Eugenia Serova and József Popp-Gábor Udovecz. At the end of the seminar David Colman, President of IAAE gave a global assessment of the status of agricultural economics discipline and profession, while Csaba Csáki, former President of IAAE made summary comments on major issues discussed during the seminar. This volume includes the plenary and contributed papers presented at the seminar and submitted for publications by the authors as well as the abstracts of the poster papers discussed. The seminar was supported and sponsored by a number of organizations and persons. All of their contributions have to be greatly acknowledged. First the two international organizations IAAE and EAAE have to be mentioned, which provided overall organizational framework and logistical support. The IAAE provided in addition a generous grant to support the participation of young agricultural economists from Central and Eastern Europe on the seminar. On the Hungarian side the Corvinus University of Budapest, the Szent István University of Gödöllő, the Research Institute for Agricultural Economics, the Hungarian Agricultural Economics Association, the Hungarian Association of Agricultural Sciences and the Hungarian Ministry of Agriculture and Rural Development were the major material and organizational supporters. The International Program committee was chaired by David Colman and Csaba Csáki and included Ulrich Koester, Joe Swinnen, Eugenia Serova and Jerzy Wilkin. The local Organizing committee was chaired by Csaba Forgács and István Szűcs and included Zoltán Lakner, András Nábrádi, József Popp, József Tóth, Gábor Udovecz, László Vajda, László Villányi, Krisztina Fodor, Attila Jámbor and Tamás Mizik. Finally IAMO, Halle facilitated the publication of this proceedings