The common data acquisition platform in the Helmholtz Association

Various centres of the German Helmholtz Association (HGF) started in 2012 to developa modular data acquisition (DAQ) platform, covering the entire range from detector readout todata transfer into parallel computing environments. This platform integrates generic hardwarecomponents like the multi-purpose HGF-Advanced Mezzanine Card or a smart scientific cameraframework, adding user value with Linux drivers and board support packages. Technically the scopecomprises the DAQ-chain from FPGA-modules to computing servers, notably frontend-electronicsinterfaces, microcontrollers and GPUs with their software plus high-performance data transmissionlinks. The core idea is a generic and component-based approach, enabling the implementationof specific experiment requirements with low effort. This so called DTS-platform will supportstandards like MTCA.4 in hard- and software to ensure compatibility with commercial components.Its capability to deploy on other crate standards or FPGA-boards with PCI express or Ethernetinterfaces remains an essential feature.Competences of the participating centres are coordinated in order to provide a solid technological basis for both research topics in the Helmholtz Programme “Matter and Technology”:“Detector Technology and Systems” and “Accelerator Research and Development”. The DTSplatform aims at reducing costs and development time and will ensure access to latest technologiesfor the collaboration. Due to its flexible approach, it has the potential to be applied in other scientificprograms

The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference

HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8+ T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8+ T cell epitopes.Fil: Trolle, Thomas. Technical University of Denmark; DinamarcaFil: McMurtrey, Curtis. Oklahoma State University; Estados UnidosFil: Sidney, John. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Bardet, Wilfried. Oklahoma State University; Estados UnidosFil: Osborn, Sean C.. Oklahoma State University; Estados UnidosFil: Kaever, Thomas. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Sette, Alessandro. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Hildebrand, Willliam H.. Oklahoma State University; Estados UnidosFil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas ; Argentina. Universidad Nacional de San Martín; ArgentinaFil: Peters, Bjoern. La Jolla Institute for Allergy and Immunology; Estados Unido

The Common Data Acquisition Platform in the Helmholtz Association

Various centres of the German Helmholtz Association (HGF) started in 2012 to developa modular data acquisition (DAQ) platform, covering the entire range from detector readout todata transfer into parallel computing environments. This platform integrates generic hardwarecomponents like the multi-purpose HGF-Advanced Mezzanine Card or a smart scientific cameraframework, adding user value with Linux drivers and board support packages. Technically the scopecomprises the DAQ-chain from FPGA-modules to computing servers, notably frontend-electronicsinterfaces, microcontrollers and GPUs with their software plus high-performance data transmissionlinks. The core idea is a generic and component-based approach, enabling the implementationof specific experiment requirements with low effort. This so called DTS-platform will supportstandards like MTCA.4 in hard- and software to ensure compatibility with commercial components.Its capability to deploy on other crate standards or FPGA-boards with PCI express or Ethernetinterfaces remains an essential feature.Competences of the participating centres are coordinated in order to provide a solid technological basis for both research topics in the Helmholtz Programme “Matter and Technology”:“Detector Technology and Systems” and “Accelerator Research and Development”. The DTSplatform aims at reducing costs and development time and will ensure access to latest technologiesfor the collaboration. Due to its flexible approach, it has the potential to be applied in other scientificprograms

The Gac/Rsm and cyclic-di-GMP signaling networks coordinately regulate iron uptake in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a versatile bacterial pathogen capable of occupying diverse ecological niches. To cope with iron limitation, P. aeruginosa secretes two siderophores, pyoverdine and pyochelin, whose ability to deliver iron to the cell is crucial for biofilm formation and pathogenicity. In this study, we describe a link between iron uptake and the Gac/Rsm system, a conserved signal transducing pathway of P. aeruginosa that controls the production of extracellular products and virulence factors, as well as the switch from planktonic to biofilm lifestyle. We have observed that pyoverdine and pyochelin production in P. aeruginosa is strongly dependent on the activation state of the Gac/Rsm pathway, which controls siderophore regulatory and biosynthetic genes at the transcriptional level, in a manner that does not involve regulation of ferric uptake regulator (Fur) expression. Gac/Rsm-mediated regulation of iron uptake genes appears to be conserved in different P. aeruginosa strains. Further experiments led to propose that the Gac/Rsm system regulates siderophore production through modulation of the intracellular levels of the second messenger c-di-GMP, indicating that the c-di-GMP and the Gac/Rsm regulatory networks essential for biofilm formation can also coordinately control iron uptake in P. aeruginosa