Mayday - integrative analytics for expression data

Background  

DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files.     

Pentazocine-induced agranulocytosis.

A 46-year-old man with pentazocine-induced agranulocytosis is described. In previously reported cases of a complete absence of mature neutrophils in the peripheral blood and bone marrow the patients had undergone marrow-depressing treatment with radiation and antineoplastic drugs. This case is unique in that the patient had complete agranulocytosis without predisposing factors.     

T-cell responsiveness in Mycobacterium lepraemurium infections in a "resistant" (CBA) and a "susceptible" (BALB/c) mouse strain

Antigen-specific and mitogen-nonspecific T-lymphocyte proliferation and lymphokine release (interleukin 2 and macrophage activation factor) were studied in BALB/c and CBA mice infected intravenously with 10(8) Mycobacterium lepraemurium organisms. The responsiveness of spleen cells from infected animals to Con A and specific MLM antigen declined as the infection progressed. Thus, the decreased responsiveness appeared earlier and was more profound in the relatively susceptible BALB/c strain than in the relatively resistant CBA strain. Nylon-wool-purified, T-cell-enriched spleen cells from both strains, however, responded to both M. lepraemurium antigen and Con A until the later stages of infection (17 weeks postinfection). The relevance of nonspecific immunodepression mediated by nylon-wool-adherent spleen cells to the progressive nature of this infection is discussed.     

Immunochemical cross-reactivity between cyanogen bromide fragments of human serum albumin

The antigenic structure of human albumin was investigated in order to establish whether or not there was any similarity between its antigenic sites. Using immunoadsorbent columns prepared with cyanogen bromide fragments of human serum albumin, antibodies directed against different portions of the albumin molecules were isolated. Measurement of the amount of the antibodies isolated and study of their specificity by inhibition techniques show that these subpopulations of antibodies reacted not only with the fragment used for their isolation (homologous) but also with the other fragments (heterologous). Heterologous fragments were inhibiting only at a very high concentration with regard to the homologous ones. These results show that there is a weak cross-reactivity between different portions of the albumin molecule. This reaction is most probably due to the homology existing in the sequence of the human albumin molecule which has arisen by gene duplication. The same type of behavior can be predicted to extent to other molecules which have evolved by similar mechanisms.     

There are two gene sequences for human apolipoprotein CI (apo CI) on chromosome 19, one of which is 4 kb from the gene for apo E

A cDNA probe corresponding to the mRNA sequence for apolipoprotein E (apo E) was used to screen two independently-constructed human genomic libraries. Two recombinants (lambda E-2, and lambda E2-1), isolated using the apo E cDNA probe, also contain part or all of the apo CI gene. Hybridisation studies using both apo E and apo CI cDNA probes show that these two genes are in the same orientation and separated by 4 kb.     

Monoclonal anti-idiotypic antibodies that recognize the binding site for nicotine on rat brain receptor

Anti-idiotypic monoclonal antibodies have been prepared that represent the internal image of nicotine and are specific for the nicotine binding site on rat brain receptor. Specificity of these antibodies for the combining site on anti-nicotine was demonstrated by their ability to inhibit binding of monoclonal anti-nicotine to immobilized nicotine-polylysine. Furthermore, purified rat brain nicotine receptor but not acetylcholine receptor from fish electric organ effectively competed with anti-nicotine for immobilized nicotine and for immobilized anti-idiotype. Only 9 pmoles of naturally occurring (-)-nicotine inhibited idiotype-anti-idiotype binding by 50% whereas 11 times more (+)-nicotine was required. Acetylcholine, several cholinergic agonists and antagonists, nicotine metabolites, and other structurally related compounds were poor inhibitors.     

The primary structure of histone H3 from the nematode Caenorhabditis elegans

The complete amino acid sequence of histone H3 (135 residues) from the nematode Caenorhabditis elegans has been established. Microheterogeneity occurs at positions 96 and 100 of the chain. The sequences of the nematode H3 isoforms are very similar to the major chain of calf thymus H3 with which they show 4 substitutions in total. The major variant has cysteine in position 96. This is the first report of cysteine in this position in H3 from non-mammalian tissue. An exceptional methylation site has been detected at position 79. Various other sites of secondary modification are of a conservative nature.     

Fitness comparison inPhytoseiulus persimilis strains resistant and susceptible to methidathion

The effect of selection for methidathion resistance on fitness components of aP. persimilis strain was analysed by different means. The resistant strain was compared with the susceptible one from which it was selected. The life history and some parameters essential to the successful use of this species in biological control (voracity, resistance to starvation and drought) were analysed. Methidathion resistance was followed for 6 months under rearing conditions free of insecticide in the resistant and in a mixed strain. The investigations showed that the fitness of resistant mites did not seem altered by methidathion selection. It thus appears possible to increase pesticide resistance in beneficial arthropods without adversely affecting their main fitness components.