Classification of heterogeneous microarray data by maximum entropy kernel

Background  

There is a large amount of microarray data accumulating in public databases, providing various data waiting to be analyzed jointly. Powerful kernel-based methods are commonly used in microarray analyses with support vector machines (SVMs) to approach a wide range of classification problems. However, the standard vectorial data kernel family (linear, RBF, etc.) that takes vectorial data as input, often fails in prediction if the data come from different platforms or laboratories, due to the low gene overlaps or consistencies between the different datasets.     

Novel agents combining platelet activating factor (PAF) receptor antagonist with thromboxane synthase inhibitor (TxSI)

Compounds 1 or 2 which possess dual-acting PAF antagonist/TxSI in a previous paper were modified and evaluated for the dual-acting activity. It was found that several compounds were potent dual-acting PAF antagonist/TxSI in and ex vivo. 6-(2-Chlorophenyl)-3-[4-[(E/Z)-6-ethoxycarbonyl-1-(3-pyridyl)-1-hexenyl]phenylmethyl]-8,11-dimethyl-2,3,4,5-tetrahydro-8H-pyrido[4',3': 4,5]thieno[3,2-f]triazolo[4,3-a]diazepine (12) is excellent orally dual-acting PAF antagonist/TxSI.     

A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters

The availability of computerized knowledge on biochemical pathways in the KEGG database opens new opportunities for developing computational methods to characterize and understand higher level functions of complete genomes. Our approach is based on the concept of graphs; for example, the genome is a graph with genes as nodes and the pathway is another graph with gene products as nodes. We have developed a simple method for graph comparison to identify local similarities, termed correlated clusters, between two graphs, which allows gaps and mismatches of nodes and edges and is especially suitable for detecting biological features. The method was applied to a comparison of the complete genomes of 10 microorganisms and the KEGG metabolic pathways, which revealed, not surprisingly, a tendency for formation of correlated clusters called FRECs (functionally related enzyme clusters). However, this tendency varied considerably depending on the organism. The relative number of enzymes in FRECs was close to 50% for Bacillus subtilis and Escherichia coli, but was <10% for Synechocystis and Saccharomyces cerevisiae. The FRECs collection is reorganized into a collection of ortholog group tables in KEGG, which represents conserved pathway motifs with the information about gene clusters in all the completely sequenced genomes.     

Approach to dual-acting platelet activating factor (PAF) receptor antagonist/thromboxane synthase inhibitor (TxSI) based on the link of PAF antagonists and TxSIs

A series of compounds (22-36) which possess dual-acting PAF antagonist/TxSI have been generated by the approach of linking the known PAF antagonists and TxSIs, such as Ridogrel (1).     

Expression and phosphorylation of TOPK during spermatogenesis

Among normal organs and tissues, the MAPKK-like mitotic protein kinase TOPK is expressed exclusively in the testis. We analyzed the expression and phosphorylation of TOPK to address the functional role of this kinase during spermatogenesis. TOPK protein is expressed mainly in the cytosol of spermatocytes and spermatids, but not in spermatids and spermatogonia in situ. TOPK-Thr-9, a cdk1/cyclin B target residue, was specifically phosphorylated during mitotic and meiotic phases, while TOPK-Thr-198, a key amino acid for the ATP pocket, was constantly phosphorylated irrespective of the cell cycle. These data indicate that spermatogenic germ cells with vital proliferation activity express TOPK. As TOPK-Thr-9 was phosphorylated during both mitosis and meiosis, TOPK was indicted to play a role in cytokinesis and/or chromosomal segregation but not in DNA replication.     

Characterization of a MAPKK-like protein kinase TOPK

A MAPKK-like protein kinase TOPK expresses in a wide range of proliferating cells and tissues such as cancer cells and testis. However, details of this kinase are still uncovered. We investigated the intracellular distribution of TOPK and its association with cdk1/cyclin B and microtubules. In interphase cells, TOPK expresses in cytosol and nucleus without any significant association with microtubule networks. During mitosis, TOPK-Thr-9 was phosphorylated by cdk1/cyclin B and TOPK significantly associates with mitotic spindles. When TOPK expression was suppressed, formation of spindle midzone was thinned and dimmed and cytokinesis was disturbed. We propose that TOPK plays a role in the formation of spindle midzone and in cytokinesis.