Radiation damage to nucleoprotein complexes in macromolecular crystallography

Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses

From Models to Simulations

This book analyses the impact computerization has had on contemporary science and explains the origins, technical nature and epistemological consequences of the current decisive interplay between technology and science: an intertwining of formalism, computation, data acquisition, data and visualization and how these factors have led to the spread of simulation models since the 1950s. Using historical, comparative and interpretative case studies from a range of disciplines, with a particular emphasis on the case of plant studies, the author shows how and why computers, data treatment devices and programming languages have occasioned a gradual but irresistible and massive shift from mathematical models to computer simulations

The distribution and re-distribution of income of selfemployed as freelancers and entrepreneurs in Europe

The economic transformations of modern industrial societies have changed the labor markets in terms of industrial relations and occupational structure. The transformation of the traditional welfare state, the deregulation of the labor markets, the technological change and the reorganization of industrial structures influenced strongly the attitude of individuals towards their preferred labor contract. The structural change of the occupational structure was one of the results of this tendency. In particular the self-employed and freelancers have been affected and are a driving factor of labor market changings. On the one side the value of autonomy regarding industrial relations is becoming more important for employees. On the other side employers want to get rid of social security contributions. As a result the multitudinousness of these professions increased. The increasing varieties of occupations among the self-employed and freelancers influenced strongly their income distribution. Recent studies for Germany have shown a great dispersion and a heterogeneous structure of earnings in particular of freelancers (liberal professions) and self-employed. Though there are a variety of international income distribution studies, but – as to the best to our knowledge – no study focusing on the self-employed and freelancers within the total labor force. In our study we concentrate on the income distribution of self-employed and freelancers in different European countries. Based on the Luxembourg Income Study (LIS) we analyze five different European countries and the United States structured by different types of welfare states according to Esping Anderson. We analyze income distributional aspects, an occupational decomposition à la Shorrocks, and re-distributional effects of the tax and transfer systems.Europe, Income distribution of freelancers and self-employed, decomposition of inequality, redistribution, LIS microdata

CrossFlow: Cross-Organizational Workflow Management for Service Outsourcing in Dynamic Virtual Enterprises

In this report, we present the approach to cross-organizational workflow management of the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual enterprises is based on dynamic service outsourcing specified in electronic contracts. Service enactment is performed by dynamically linking the workflow management infrastructures of the involved organizations. Extended service enactment support is provided in the form of cross-organizational transaction management and process control, advanced quality of service monitoring, and support for high-level flexibility in service enactment. CrossFlow technology is realized on top of a commercial workflow management platform and applied in two real-world scenarios in the contexts of a logistics and an insurance company

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays