Adaptive double self-organizing maps for clustering gene expression profiles

This paper introduces a new model of self-organizing map (SOM) known as adaptive double self-organizing map (ADSOM). ADSOM has a flexible topology and performs data partitioning and cluster visualization simultaneously without requiring a priori knowledge about the number of clusters. It combines features of the popular SOM with two-dimensional position vectors, which serve as a visualization tool to detect the number of clusters present in the data. ADSOM updates its free parameters and allows convergence of its position vectors to a fairly consistent number of clusters provided its initial number of nodes is greater than the expected number of clusters. A novel index is introduced based on hierarchical clustering of the final locations of position vectors. The index allows automated detection of the number of clusters, thereby reducing human error that could be incurred from counting clusters visually. To test ADSOM's consistency in data partitioning, we examine the number of common profiles found in the clusters that were obtained by varying the initial number of nodes. This provides a confidence measure for the clusters formed by ADSOM and illustrates the effect of different initial number of nodes on data partitioning. The reliance of ADSOM in identifying number of clusters is demonstrated by applying it to publicly available yeast gene expression data.

Di- and tetranuclear ruthenium(II) and/or osmium(II) complexes of polypyridyl ligands bridged by a fully conjugated aromatic spacer: synthesis, characterization, and electrochemical and photophysical studies

A series of mono-, di-, and tetranuclear homo/heterometallic complexes of Ru(II) and Os(II) based on the bridging ligand dppz(11-11')dppz (where dppz = dipyrido[3,2-a:2',3'-c]phenazine) (BL) have been synthesized and characterized. This bridging ligand is a long rigid rod with only one rotational degree of freedom and provides complete conjugation between the chromophores. The complexes synthesized are of general formula [(bpy)(2)Ru-BL](2+), [(phen)(2)/(bpy)(2)M-BL-M(bpy)(2)/(phen)(2)](4+) (M = Ru(II) and Os(II)), [(bpy)(2)Ru-BL-Os(bpy)(2)](4+), and [((bpy)(2)Ru-BL)(3)M](8+). Detailed (1)H NMR studies of these complexes revealed that each chiral center does not influence its neighbor because of the long distance between the metal centers and the superimposed resonances of the diastereoisomers, which allowed the unambiguous assignment of the signals, particularly for homonuclear complexes. Concentration-dependent (1)H NMR studies show molecular aggregation of the mono- and dinuclear complexes in solution by pi-pi stacking. Electrospray mass spectrometry data are consistent with dimerization of mono- and dinuclear complexes in solution. Electrochemical studies show oxidations of Ru(II) and Os(II) in the potential ranges +1.38 to +1.40 and +0.92 to +1.01 V, respectively. The bridging ligand exhibits two one-electron reductions, and it appears that the added electrons are localized on the phenazene moieties of the spacer. All of these complexes show strong metal-to-ligand charge-transfer (MLCT) absorption and (3)MLCT luminescence at room temperature. Quantum yields have been calculated, and the emission lifetimes of all complexes have been measured by laser flash photolysis experiments. The luminescence intensity and lifetime data suggest that the emission due to the Ru center of the heteronuclear complexes is strongly quenched (>90%) compared to that of the corresponding model complexes. This quenching is attributed to intramolecular energy transfer from the Ru(II) center to the Os(II) center (k = (3-5) x 10(7) s(-1)) across the bridging ligand.

Macrophage colony stimulating factor (M-CSF) within cord blood sera may be partially responsible for the reduced proliferation of cord blood T cells

We show that there are differences in the soluble factors in cord blood (CB) and adult serum and that these differences play a role in T cell function. Thus, the mitogen and alloantigen-specific proliferative response of adult T cells was enhanced with increasing concentrations of adult serum and CB serum, but to a lesser extent with CB serum. In addition, proliferation of T cells induced by stimulation through the T cell receptor alone (via CD3 stimulation), could be enhanced with adult but not CB serum. However, CB serum enhanced the IL-2-specific proliferative response of pure T cells whereas adult serum did not. To determine whether there was an anti-inflammatory cytokine within CB serum which could induce these results, we assayed our serum samples for anti-inflammatory cytokines. IL-13 could not be detected in any serum sample, whereas IL-10 could be detected in adult but not CB serum (P < 0.002). However, there was a significant difference in the levels of macrophage colony stimulating factor (M-CSF) detected in adult and CB serum samples (P < 0.01). M-CSF was detected in 6/7 CB serum samples (mean +/- SD was 3.8 +/- 2.3 ng/ml) and 0/5 adult serum samples. Furthermore, anti-M-CSF antibody restored the reduced allo-response of T cells incubated in CB serum. Thus, M-CSF may act as a suppressor factor in CB serum. Whether this is sufficient to explain the lack of an allo-response by the foetus to the mother, or the reduced graft-versus-host disease when CB is used instead of bone marrow in stem cell transplantation, is yet to be determined.

Paper-based archiving of mammalian and plant samples for RNA analysis

The ability to archive biological samples for subsequent nucleic acid analysis is essential for tissue specimens and forensic samples. FTA Card is a chemically treated filter paper designed for the collection and room temperature storage of biological samples for subsequent DNA analysis. Its usefulness for the preservation of biological samples for subsequent RNA analysis was tested. Here, we demonstrate that RNA in biological samples stored on FTA Cards is stable and can be used successfully for RT-PCR and northern blot analysis. RNA stability depends on the storage temperature and the type of biological specimen. RNA in mammalian cells stored on FTA Cards is stable for over one year at temperatures at or below -20 degrees C and for two to three months in samples stored at room temperature. For plant leaf, longer storage times (> 5 days) require temperatures at or below -70 degrees C following sample application. FTA Cards may constitute a method not only for convenient collection and storage of biological samples but also for rapid RT-PCR analysis of tissue and cell samples.