Development of a high-resolution NGS-based HLA-typing and analysis pipeline

The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions

ERP and four dimensions of absorptive capacity: lessons from a developing country

Enterprise resource planning systems can grant crucial strategic, operational and information-based benefits to adopting firms when implemented successfully. However, a failed implementation can often result in financial losses rather than profits. Until now, the research on the failures and successes were focused on implementations in large manufacturing and service organizations firms located in western countries, particularly in USA. Nevertheless, IT has gained intense diffusion to developing countries through declining hardware costs and increasing benefits that merits attention as much as developed countries. The aim of this study is to examine the implications of knowledge transfer in a developing country, Turkey, as a paradigm in the knowledge society with a focus on the implementation activities that foster successful installations. We suggest that absorptive capacity is an important characteristic of a firm that explains the success level of such a knowledge transfer.Publicad

Sharing responsibilities in fisheries management; Part 2 - Annex: case studies

This report focuses on the evaluation of the process of devolution of responsibilities in the current institutional landscape in European fisheries management. In particular the analysis focuses on how the present management systems contribute to good governance. We follow the criteria as suggested in the EU communication on governance (EU 2001): Openness, Participation, Accountability, Effectiveness and Coherence. The analysis of the various proposed fisheries management models confirms what would then be the hypothesis: There is no definitive alternative management model that can be applied - given the wide spectrum of circumstances surrounding fisheries activity in the six countries included in the study (Norway, Denmark, the United Kingdom, France, The Netherlands and Spain), or at least, none as clear-cut as the models proposed for regionalisation/devolution a decade ago. There are significant differences between these proposals for more decentralised fisheries management systems and the various alternative fisheries management systems proposed require improved efficiency in the application of policies and highlight the importance of local level involvement, whilst providing the opportunity to confer greater legitimacy on policies through improved participation

Numerical Solution Of The Polymer System By Front Tracking

. The paper describes the application of front tracking to the polymer system, an example of a nonstrictly hyperbolic system. Front tracking computes piecewise constant approximations based on approximate Riemann solutions and exact tracking of waves. It is well--known that the front tracking method may introduce a blowup of the initial total variation for initial data along the curve where the two eigenvalues of the hyperbolic system are identical. It is demonstrated by numerical examples that the method converges to the correct solution after a finite time that decreases with the discretization parameter. For multidimensional problems, front tracking is combined with dimensional splitting and numerical experiments indicate that large splitting steps can be used without loss of accuracy. Typical CFL numbers are in the range 10 to 20, and comparisons with Riemann free, high--resolution methods confirm that the high efficiency of front tracking. The polymer system, coupled with an ellip..

An Oxidized Tryptophan Facilitates Copper Binding in Methylococcus Capsulatus Secreted Protein Mope

Proteins can coordinate metal ions with endogenous nitrogen and oxygen ligands through backbone amino and carbonyl groups, but the amino acid side chains coordinating metals do not include tryptophan. Here we show for the first time the involvement of the tryptophan metabolite kynurenine in a protein metal binding site. The crystal structure to 1.35 of MopE from the methane oxidizing Methylococcus capsulatus Bath provided detailed information about its structure and mononuclear copper binding site. MopE contains a novel protein fold of which only one third of the structure displays similarities to other known folds. The geometry around the copper ion is distorted tetrahedral with one oxygen ligand from a water molecule, two histidine imidazoles His 132 and His 203 , and at the fourth distorted tetrahedral position, the N1 atom of the kynurenine, an oxidation product of Trp 130. Trp 130 was not oxidized to kynurenine in MopE heterologously expressed in Escherichia coli, nor did this protein bind copper. Our findings indicate that the modification of tryptophan to kynurenine and its involvement in copper binding is an innate property of M. capsulatus Mop