Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules

Efficiency of presentation of a peptide epitope by a MHC class I molecule depends on two parameters: its binding to the MHC molecule and its generation by intracellular Ag processing. In contrast to the former parameter, the mechanisms underlying peptide selection in Ag processing are poorly understood. Peptide translocation by the TAP transporter is required for presentation of most epitopes and may modulate peptide supply to MHC class I molecules. To study the role of human TAP for peptide presentation by individual HLA class I molecules, we generated artificial neural networks capable of predicting the affinity of TAP for random sequence 9-mer peptides. Using neural network-based predictions of TAP affinity, we found that peptides eluted from three different HLA class I molecules had higher TAP affinities than control peptides with equal binding affinities for the same HLA class I molecules, suggesting that human TAP may contribute to epitope selection. In simulated TAP binding experiments with 408 HLA class I binding peptides, HLA class I molecules differed significantly with respect to TAP affinities of their ligands. As a result, some class I molecules, especially HLA-B27, may be particularly efficient in presentation of cytosolic peptides with low concentrations, while most class I molecules may predominantly present abundant cytosolic peptides.     

Substrate effects on photoelectrochemical kinetics in hydrogen production

The surface of p-Si has been treated in a number of ways, and the rate of the photoelectrochemical reduction of water to hydrogen measured on each type of surface. Correspondingly, in-situ ellipsometric determinations of thickness and refractive index of the surface films were made; corresponding XPS, ISS and SIMS studies were also carried out. The photoelectrochemical activities of the surfaces, as measured by the positive shift on the potential axis of the mid-current point of the photocurrent/potential curve, differed greatly. In treatments with HF, the chemical structure of the surface remains that of SiO₂; in treatments with aquaregia and HF, the surface becomes SiO. After hydrogen evolution, SiOH bonds appear. The degree of dependence of the photoelectrochemical activity on the surface characteristics indicates that a reaction at the semiconductor/solution interface controls the overall (consecutive) photoelectrochemical reaction. The increase in rate with change of surface structure depends on the following factors in increasing order of importance: the presence of band gap surface states, the (established) jump in the order of magnitude of conductance of SiO_x at x = 1.8, and the (argued) increasing availability of Si bonds during increasing reduction of the surface, thus causing an increase in the rate constant of a rate-determining proton transfer.     

Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules

Elucidating the interaction between major histocompatibility complex (MHC) molecules and antigenic peptides is fundamental to better understanding of the processes involved in immune responses and for the development of innovative immunotherapies. In the present study, hidden Markov models (HMM) were combined with the successive state splitting (SSS) algorithm for optimization of the HMM structure, to predict peptide binders to the human MHC class II molecule HLA-DRB1*0101. The predictive performance of our model (S-HMM) was compared with fully connected HMM and artificial neural network (ANN) methods using the relative operating characteristic (ROC) analysis. The S-HMM predictions had values of ROC > or = 0.85 which was at least as good, or better than the comparison methods. In addition, S-HMM is trained on positive data only and does not require exhaustive data preprocessing, such as peptide alignment. Our results demonstrated that S-HMM combines the high accuracy of predictions with the simplicity of implementation and is therefore useful for analyzing MHC class II binding peptides. In particular the S-HMM may be trained using only positive data and, the preprocessing of training data, such as peptide alignment and the selection of binding cores, is not required in this method.     

Accurate prediction of scorpion toxin functional properties from primary structures

Scorpion toxins are common experimental tools for studies of biochemical and pharmacological properties of ion channels. The number of functionally annotated scorpion toxins is steadily growing, but the number of identified toxin sequences is increasing at much faster pace. With an estimated 100,000 different variants, bioinformatic analysis of scorpion toxins is becoming a necessary tool for their systematic functional analysis. Here, we report a bioinformatics-driven system involving scorpion toxin structural classification, functional annotation, database technology, sequence comparison, nearest neighbour analysis, and decision rules which produces highly accurate predictions of scorpion toxin functional properties.     

2.22 The deposition by evaporation of CuAl alloy films

3hin films of CuAl alloys from pure Cu to pure Al were deposited by vacuum evaporation from single alloyed sources heated by electron bombardment. Information about the composition of the films obtained by electron microprobe was completed by lattice parameter measurements and structure information obtained by X-ray diffraction, as well as electrical resistivity measurements. The anticipated compositions of the films were calculated from the vapor pressures of the pure elements and thermodynamic data for liquid CuAl alloys at 1373 K. The agreement between the calculated values and the experimentally observed compositions is good only for alloys with low Al concentrations: less than 20 at.% Al in the source material. For the remainder of the CuAl system with more than 20 at.% Al in the source, the films were found to contain less Al than was calculated. This discrepancy might be due to too high values for the reported vapor pressures of Al.     

MHCPEP, a database of MHC-binding peptides: update 1996

MHCPEP is a curated database comprising over 9000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions and publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW, FTP or Gopher.     

Open Source in der Telekommunikation

The penguin Tux is in the news. The city council of Munich has decided to use the open source operating system GNU/Linux for its 14000 desktop and server computers. Open source software development is often seen as anarchic process and frowned upon from commercial software engineering’s point of view. The remarkable success of open source software can be explained by the evolutionary process of the development of complex systems. The first part of this article describes the open source development process and shows the justification of open source software from an economic and a legal point of view. Open source can be used in telecommunications as a simple and low cost means for prototyping. ÖFEG has built a test bed for VoIP using Asterisk as PBX software on Linux and a standard PC. The lessons learnt will be shown in the second part of this article.     

Mobile Agents in the Mobile Telephone Network Management

The paper discusses the application of mobile agents in the management of mobile telephone (cellular) networks. We propose the use of mobile agents for collecting subscriber information, such as location area identifier and cell identifier. By using a subscriber profile containing these data the signaling messages caused by location update could be reduced. We also propose a method to improve the quality of network coverage by collecting measurements data by a mobile agent in the mobile station (mobile phone) or at the mobile switching center. By analyzing these data the network provider would be able to discover areas without proper radio signal coverage (black holes), thereby avoiding expensive and time-consuming measurements done by specially equipped vehicles. In addition, we discuss the basic infrastructure requirements for deployment of the mobile agent technology in cellular networks.