Jutta Bachmann

SYFPEITHI: database for MHC ligands and peptide motifs

Abstract The first version of the major histocompatibility complex (MHC) databank SYFPEITHI: database for MHC ligands and peptide motifs, is now available to the general public. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. All motifs currently available are accessible as individual entries. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database content is restricted to published data only.

MHC ligands and peptide motifs

1. History and Overview -- 2. The MHC Genes -- 3. The Structure -- 4. The Function -- 5. Recognition by Immune Cells -- Appendix A: Useful Internet Addresses -- Appendix B: Computer Programs -- Appendix C: Abbreviations.

Genomic Differentiation of Neanderthals and Anatomically Modern Man Allows a Fossil-DNA-Based Classification of Morphologically Indistinguishable Hominid Bones

Southern blot hybridizations of genomic DNA were introduced as a relatively simple fossil-DNA-based approach to classify remains of Neanderthals. When hybridized with genomic DNA of either human or Neanderthal origin, DNA extracted from two Neanderthal finds-the Os parietale, from Warendorf-Neuwarendorf, Germany, and a clavicula, from Krapina, Croatia-was shown to yield hybridization signals that differ by at least a factor of two compared to the signals obtained with the use of fossil DNA of an early Homo sapiens from the Vogelherd cave (Stetten I), Germany. When labeled chimpanzee DNA was used as a probe, Neanderthal and human DNA, however, revealed hybridization signals of similar intensity. Thus, the genome of Neanderthals is expected to differ significantly from the genome of anatomically modern man, because of the contrasting composition of repetitive DNA. These data support the hypothesis that Neanderthals were not ancestors of anatomically modern man.

Protein biochips: the calm before the storm

The growth of protein biochip technology is on a different trajectory than other drug discovery and development technologies, such as DNA sequencing and high-throughput screening, where output per experiment has grown exponentially. By contrast, experimentation with protein biochips immediately hit barriers in output because of the limited availability of content and the challenges of running biochemical experiments on the surface of a biochip. Nevertheless, the industry has been making significant progress recently by launching new platforms with focused content and new multiplexed biochemical assays. However, this success might only represent the calm before the storm. Over the long-term, protein biochips have the potential to change the drug discovery and development process at the molecular level. The output and throughput of protein biochips could enable researchers to change from the traditional model of one target-one drug to a new model of evaluating one or more potential drugs against a panel of relevant molecular targets from a complex disease state.

History and Overview

The traits of MHC genes have been noticed as early as in the beginning of the 20th century: a tumor grafted from a mouse to a genetically different mouse was rejected, whereas a tumor transplanted to a mouse of the same strain was not rejected. Thus, the tumor was not rejected on account of tumor-specific antigens but rather because of genetic differences between the mouse strains involved.1 It was not until 1936, however, that what is now known as the MHC was discovered by Peter Gorer, then in London.2 He had produced a rabbitanti-mouse serum for the sake of blood group studies. The reactivity of this serum, called Nr. II, showed a striking correlation with tumor rejection: a tumor of the mouse strain A was rejected by C57 mice and in a certain proportion of (A × C57)F1 × C57 backcross mice. All mice not reactive with the serum rejected the tumor. On the other hand, those mice rejecting the tumor developed antibodies with the same reactivity as rabbit serum Nr. II. Thus, it appeared that what caused tumor rejection was a blood-group like antigen shared by normal and tumor cells.2 Since this antigen was originally discovered because of its recognition by rabbit anti-mouse serum Nr. II and because it resulted in tumor rejection, it was called histocompatibility antigen 2 or H-2—not immediately, however, but about 10 years later by George Snell and Gorer.1

Protein Microarrays: Technologies And Applications

Protein microarray technology has been successfully applied for the identification, quantification, and functional analysis of proteins in basic and applied proteome research. It can be shown that these miniaturized and parallelized assay s ystems have the potential of replacing the singleplex analysis systems. However, robustness and automation need to be demonstrated before this technology can be used reliably for high throughput and routine applications. In this review we summarize the current stage of protein microarray technology. Recent applications used for the simultaneous determination of a variety of parameters from a minute amount of sample will be described and future challenges of this cutting-edge technology will be discussed.

Recognition by Immune Cells

Natural killer cells have a different way of looking at MHC molecules as compared to T-cells. The relationship between NK cells and MHC molecules was originally proposed by Klaas Karre’s ‘missing self’ hypothesis which assumed that NK cells screen other cells for the absence of MHC molecules.1–5 This hypothesis has been proven correct in essence.’ NK cells express group-specific receptors for MHC molecules.6 These receptors can be either inhibitory (killer inhibitory receptors, KIR), or activatory. In addition, NK cells express activatory receptors that recognize structures expressed on many cell types. If an NK cell binds to a normal MHC expressing cell, both inhibitory and activatory receptors are engaged. This leads to a dominant inhibitory effect so that no activation takes place. If a target cell has lost MHC expression, however, the inhibitory receptor does not find its ligand, and as a consequence, the target cell is killed. A number of KIRs both on human and mouse cells have been identified.7,8 Originally, receptors of different gene families were discovered in mice and humans and only recently evidence that the two families exist in both species has been provided.b6,8–11 Therefore, the best known mouse receptors are of the lectin receptor type, whereas the most intensively studied human ones belong to the immunoglobulin superfamily. Each of the mouse receptors, Ly49 A, B, C, D, E, F, G, and H, is specific for a different selection of H-2 molecules (see Table 5.1). Similarly, each of the human receptors, NKAT1 through NKAT4, recognizes a certain epitope on the HLA class I molecule that defines its recognition pattern (Table 5.1).8,12–14 Each NK cell expresses several KIRs; their combination, relative density, and functional significance is dependent on inheritance and selection processes during their ontogeny, details of which are not well known, however.15–19

PROTEIN MICROARRAY TECHNOLOGIES: AN ARRAY OF APPLICATIONS

Publisher Summary Microarrays are solid phase-based assay systems consisting of an array of miniaturized test sites arranged in rows and columns. These microspots are usually less than 250μm in diameter. Protein microarray technologies generate an enormous amount of quantitative information with considerable savings in labor and sample volumes. In protein arrays, capture molecules need to be immobilized in a functional state on a solid support. Capture molecules can be printed onto chip surfaces with contact printing arrayers equipped with tiny needles to place sub-nanoliter sample volumes directly onto the surface. Alternatively, non-contact deposition technologies, which employ capillaries or ink jet technology to deposit nanoliter to picoliter droplets onto the surface can be used. Micropatterned protein arrays have also been produced with photolithographic methods. As far as microarray detection is concerned, captured targets are mainly detected by fluorescence using CCD cameras or laser scanners with confocal detection optics. In todays world, microarrays are robust, reliable research tools with which a multitude of parameters can be screened from minimal amounts of sample. The acceptance of protein microarrays, due to the efficiency of sandwich immunoassays, is constantly growing, and they have become useful screening tools in biomarker screening programs, where panels of disease-specific biomarkers are generated.