Comments on selected fundamental aspects of microarray analysis

Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.     

Atomic control of water interaction with biocompatible surfaces: the case of SiC(001)

The interaction of water with Si- and C- terminated beta-SiC(001) surfaces was investigated by means of ab initio molecular dynamics simulations. Irrespective of coverage, varied from 1/4 to 1 monolayer, we found that water dissociates on the Si-terminated surface, substantially modifying the clean surface reconstruction, while the C-terminated surface is nonreactive and hydrophobic. Based on our results, we propose that STM images and photoemission experiments may detect specific changes induced by water on both the structural and electronic properties of SiC(001) surfaces.     

Methane activation by silica-supported Zr(IV) hydrides: the dihydride [(triple bond)SiO)2ZrH2] is much faster than the monohydride [(triple bond)SiO)3ZrH

The silica-supported Zr(iv) dihydride [(triple bond)SiO)2ZrH2] reacts quickly and completely with methane to yield [(triple bond)SiO)2ZrMe2] through the intermediate [(triple bond)SiO)2ZrHMe], while its monohydride analogue [(triple bond)SiO)3ZrH] yields the monomethylated product [(triple bond)SiO)3ZrMe] slowly and incompletely.     

Oxidative coupling of 17beta-estradiol: inventory of oligomer products and configuration assignment of atropoisomeric c4-linked biphenyl-type dimers and trimers

The oxidation chemistry of 17beta-estradiol (1) is of central relevance to the nongenomic effects of estrogens and offers valuable prospects in the search for novel steroidal scaffolds of academic and industrial interest. Herein, we report the results of a detailed investigation into the nature of the oligomer products formed by phenolic oxidation of 1. Of the oxidants tested, the peroxidase/H2O2 system proved to be the most effective in inducing conversion of 1 to a complex mixture of oligomer species. Repeated chromatographic fractionation followed by extensive 2D NMR and mass spectrometric analysis allowed identification of a series of phenolic coupling products comprising, besides the C2-symmetric dimers 2 and 3, a 2,4' dimer (4), two O-linked dimers (5, 6), and the novel trimers 7-9. All 4-linked biphenyl-type oligomers, i.e., 3 and 7-9, occurred as couples of atropoisomers, reflecting steric hindrance at biphenyl linkages. For all atropoisomers, absolute configuration was established by the exciton chirality method and the interconversion energy was determined by dynamic NMR. These results provide the first systematic inventory of oxidative coupling products of 1 and lay the foundation for future studies aimed to develop novel estrogen derivatives based on oligomeric scaffolds.     

Smooth solutions to a class of free boundary parabolic problems

We establish existence, uniqueness, and regularity results for solutions to a class of free boundary parabolic problems, including the free boundary heat equation which arises in the so-called ``focusing problem' in the mathematical theory of combustion. Such solutions are proved to be smooth with respect to time for positive , if the data are smooth.

     

Widely tunable continuous-wave diode-pumped 2-microm Tm-Ho:KYF4 laser

Continuous-wave laser action at approximately 2 microm is demonstrated in a Tm-Ho:KYF4 single crystal at room temperature. Crystal growth, spectroscopic measurements, and laser results are presented. An output power in excess of 250 mW is obtained with a tuning range of 99 nm, the largest ever published, to our knowledge, for Tm-Ho in any crystalline host.     

Electron density investigation of a push-pull ethylene (C14H24N2O2.H2O) by X-ray diffraction at T = 21 K

The electron charge distribution in a strongly twisted push-pull ethylene [PPE, 3-(1,3-diisopropyl-2-imidazolidinylidene)-2,4-pentanedione] has been determined by low temperature (T = 21 K) single-crystal X-ray diffraction analysis. The derived electronic properties are consistent with a zwitterionic molecule, as indicated by a charge transfer of 0.82(16) e from the push to the pull moieties and a charge polarization of 0.29(7) e on the olefinic bond. A dipole moment of 12(3) D has been determined, which compares well with ab initio theoretical results in terms of both modulus and orientation. The second moments, which have also been obtained with good precision, characterize PPE as a highly quadrupolar molecule. The special electronic features of the molecule confer particular topological properties to the electron density distribution, as evidenced by comparison with "standard" organic molecules. The crystallographic asymmetric unit of the present system includes one water molecule, which is hydrogen bonded to PPE. Its topological properties have also been investigated, together with an analysis of the hydrogen bonds involved.