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.     

The Ultrastructure of Tetrasporogenesis in the Marine Red Alga Chondria tenuissima (Good, et Woodw.) (Ceramiales, Rhodomelaceae)

Tetraspore development has been studied in Chondria tenuissimausing light and electron microscopy. The transformation of tetrasporangialmother cells into mature tetrasporangia involves a series ofstructural changes, especially of dictyosomes and of the nucleus.The youngest stage of tetrasporogenesis consists of a uninucleatetetraspore mother cell with synaptonemal complexes present duringearly prophase of meiosis I. Mitochondria are aggregated aroundthe nucleus, dictyosome activity is low, and proplastids occurin the peripheral cytoplasm. The cleavage furrows are initiatedalmost concomitantly with commencement of meiosis. When thecleavage furrows are initiated, spherical bodies bounded bytwo membranes are found within the cytoplasm; they develop intovacuoles with fibrillar contents (fv₁), which increase in sizeduring tetraspore development by fusing with each other andwith Golgi vesicles. The Golgi vesicles and the vacuoles withfibrillar contents (fv₁) contribute material to the developingtetraspore wall. During the middle stage of tetraspore formationthe vacuoles with fibrillar contents (fv₁) are dominant, dictyosomeactivity increases, as well as the number of plastids and mitochondria;starch formation also increases. Stacked cisternae of the endoplasmicreticulum are found within the peripheral part of the nucleus.The same nuclear structures are also observed in tetrasporangiaof the marine red alga Gastroclonium clavalum. The final stageis characterized by the disappearance of vacuoles with fibrillarcontents (fv₁) and of the stacked ER within the nucleus, presenceof straight, large dictyosomes which produce cored vesicles,an abundance of starch grains and by the formation of fullydeveloped chlorqplasts. The cored vesicles contain Thiéry-positivematerial and contribute to the formation of vacuoles with fibrouscontents (fv₂) as they are dominant in the tetraspores beforetheir liberation. Rhodophlyla, Chondria, tetrasporogenesis, ultrastructure, Golgi apparatus     

The inhibition of phospholipase A2 by manoalide and manoalide analogues

Manoalide, a natural product from sponge, displays anti-inflammatory activity in vivo. Previous work has shown that manoalide is also a potent covalent inhibitor of the extracellular phospholipase A2 from cobra venom and that the inhibition correlated with a pH-dependent change in manoalide (Lombardo and Dennis (1985) J. Biol. Chem. 260, 7234-7240). Manoalide contains two rings and the opening of either would produce an alpha,beta-unsaturated aldehyde. The cobra venom phospholipase A2 may be able to catalyze the opening or isomerization of one of these rings, raising the possibility that manoalide is acting as a suicide substrate. To ascertain the role of the gamma-lactone ring in the inhibition, we have now investigated a synthetic manoalide analogue, 3(cis,cis-7,10)-hexadecadienyl-4-hydroxy-2-butenolide (HDHB) which contains only the alpha,beta-unsaturated gamma-lactone ring. We have found that the closed and open forms are in rapid equilibrium between pH 4 and 9 with the cyclic form being preferred at acidic pH values and the open cis form preferred at pH 9.5. When the pH is raised above 12, the alpha,beta double bond isomerizes to form trans-HDHB. Once the trans compound is formed, it is stable at all pH values and does not recyclize to the gamma-lactone ring. The observed pKa of 7.7 found for the inhibition of manoalide agrees well with the transition of the closed to the cis form of the gamma-lactone ring. Kinetic experiments with the HDHB compound show that under conditions in which the cis and closed form of the inhibitor are present in equal molar ratios, HDHB is not an irreversible inhibitor, but reversibly competes with substrate. However, the kinetics of this inhibition are complex and do not follow either pure competitive or non-competitive inhibition. The trans-HDHB exhibits similar complex kinetic but is several times more potent. The distinct differences between the behavior of manoalide and HDHB clearly indicate that while the gamma-lactone ring may play an important role in manoalide inhibition, it alone does not produce irreversible inhibition.     

Is the mitochondrial precursor protein apocytochrome c able to pass a lipid barrier?

To obtain insight into the role of lipids in the translocation of extramitochondrially synthesized proteins, we studied the ability of apocytochrome c to pass lipid bilayers. With polyacrylamide gel electrophoresis, the digestion of externally added apocytochrome c by trypsin, enclosed in lipid vesicles, was followed. The experiments demonstrate that apocytochrome c is able to pass a lipid barrier and this process shows both a lipid- and protein specificity. The most probable molecular mechanisms involved in this phenomenon are 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.     

Views on the wisdom of using antioxidant vitamin supplements

In the Forum that follows, four authorities in nutrition and vitaminology present their divergent views on the use of antioxidant vitamin supplements. In this introduction, the basic dilemma between setting RDAs that insure an absence of deficiency symptoms and those that insure optimal health is discussed, as well as other factors that must be considered to reach a consensus on this controversial topic.