Noise Analysis of Duplicated Data on Microarrays Using Mixture Distribution Modeling

We propose a technique for estimating gene expression values for duplicated data on cDNA microarrays. In the scatter plots, the distribution is constructed from a mixture of normal two-dimensional distributions, which represent fluctuations in gene expression values due to noise. An expectation-maximization (EM) algorithm is used for estimating the modeling parameters. The probability that duplicated data is shifted by noise is calculated using Bayesian estimation. Six data sets of rice cDNA microarray assays were used to test the proposed technique. Genes in the data sets were subjected to clustering based on probability of true value. Clustering successfully identified candidate genes regulated by circadian rhythms in rice.     

Axial ligand substituted nonheme FeIV=O complexes: observation of near-UV LMCT bands and Fe=O Raman vibrations

Axial ligand substitution of a mononuclear nonheme oxoiron(IV) complex, [FeIV(O)(TMC)(NCCH3)]2+ (1) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), leads to the formation of new FeIV=O species with relatively intense electronic absorption features in the near-UV region. The presence of these near-UV features allowed us to make the first observation of Fe=O vibrations of S = 1 mononuclear nonheme oxoiron(IV) complexes by resonance Raman spectroscopy. We have also demonstrated that the reactivity of nonheme oxoiron(IV) intermediates is markedly influenced by the axial ligands.     

Studies aimed at the total synthesis of azadirachtin. A modeled connection of C-8 and C-14 in azadirachtin

[reaction: see text] Studies on the connection between the right and left segments of azadirachtin are described. The Ireland-Claisen rearrangement of Li-enolate of the modeled ester with dichlorodimethylsilane in toluene afforded the desired limonoid framework stereoselectively in good yield.     

Seed polymerization of tetraethyl ortho-silicate in the presence of rod-like colloidal particles of anionic palygorskite and cationic β-FeO(OH)

Kinetic analyses were made of the seed polymerization of tetraethyl ortho-silicate (TEOS) in the presence of rod-like colloidal particles of palygorskite and cationic -FeO(OH) by turbidity and dynamic light-scattering measurements. Transmission electron microscopic measurements supported the formation of core-shell particles. The seed polymerization of TEOS took place exclusively on the surfaces of palygorskite. The main cause of the observation is due to the fact that the main component of palygorskite is SiO₂ and the affinity between palygorskite and TEOS is high, though the electrostatic repulsion between them is not favorable for shell formation. The shell formation of silica on a -FeO(OH) particle also proceeded. The electrostatic attraction forces between the anionic polar TEOS monomers and cationic -FeO(OH) particles played an important role in shell formation. These results are consistent with a polymerization mechanism consisting of the formation of small preliminary particles followed by their coalescence on the surfaces of the seeds to give the final large particles coated with silica layers.     

Comparison of potassium ion preference of potassium-sensing oligonucleotides,PSO-1 and PSO-2, carrying the human and Oxytricha telomeric sequence,respectively

Human [G(3)(TTAG(3))(3)] and Oxytricha [G(4)(T(4)G(4))(3)] telomere model oligonucleotides, PSO-1 and PSO-2, bearing two fluorophores, 6-carboxyfluorescein (6-FAM) and 6-carboxytetramethylrhodamine (6-TAMRA) at their 5'- and 3'-termini, respectively, were synthesized. Both of them can form an intramolecular antiparallel tetraplex upon addition of K(+), and an enhanced fluorescence resonance energy transfer (FRET) was observed. PSO-1 showed a 43,000 times higher selectivity for K(+) against Na(+). Fluorometric and circular dichroism spectrophotometric studies revealed that this system is useful for the evaluation of the interaction of different telomeric repeat oligonucleotide sequences with metal ions.     

Synthesis of novel macrocyclic peroxides by bis(sym-collidine)iodine (I) hexafluorophosphate-mediated cyclization of unsaturated hydroperoxides and unsaturated alcohols

Bis(sym-collidine)iodine (I) hexafluorophosphate-mediated cyclization of unsaturated hydroperoxides, prepared by a variety of different methods, afforded the corresponding 10- to 20-membered macrocyclic peroxides having two or three peroxide units located within one ring in moderate yields. By analogy, cyclization of unsaturated alcohols having one or two peroxide bond in the chain afforded the corresponding cyclic ethers. The efficiency of the latter reactions were found to be a function of the structure of the alcohols.     

Resonance raman investigation of the specific sensing mechanism of a target molecule by gas sensory proteins

Specific sensing of gas molecules such as CO, NO, and O2 is a unique function of gas sensory hemoproteins, while hemoproteins carry out a wide variety of functions such as oxygen storage/transport, electron transfer, and catalysis as enzymes. It is important in gas sensory proteins that the heme domain not only recognizes its target molecule but also discriminates against other gases having similar molecular structures. Coordination of a target molecule to the heme is assumed to alter the protein conformation in the vicinity of heme, and the conformation change is propagated to the effector domain where substrate turnover, DNA binding, or interaction with a signal transduction protein is performed differently than the binding of other gases. To understand the appearance of such a specificity, we focus our attention on the ligand-protein interactions in the distal side of heme. In practice, the metal-ligand vibrations as well as internal modes of ligand and heme are measured with resonance Raman spectroscopy for wild-type and some mutant proteins with full-length or limited sensory regions. On the basis of such observations together with the knowledge currently available, we discuss the mechanism of specific sensing of a diatomic molecule in gas sensory proteins.     

A synthesis of heteroaromatic analogues of 1-methyl-1,2,3,4-tetrahydroisoquinoline using the Pummerer-type cyclization reaction: observation of tandem cyclization reaction

The sulfoxides 7b and 7d carrying thiophene or benzothiophene as heteroaromatic nucleophiles, when treated with trifluoroacetic anhydride at room temperature (Pummerer reaction), underwent an intramolecular alkylation in an exclusive manner to yield 4,5,6,7-tetrahydro-7-methyl-4-phenylsulfanylthieno[2,3-c]pyridine-6-carbaldehyde (10) and the corresponding benzothiophene derivative (12b) in high yields, respectively. Thus, this route provides biologically interesting nitrogen heterocycles (1b) and (2b). On the other hand, the sulfoxide (7c) carrying benzofuran as a nucleophile on reaction with TFAA yielded not only the Pummerer-type cyclization product (12a), but also the diastereoisomeric tandem cyclization products (13) and (14) having a noble 11-aza-2-oxa-7-thiatricyclo[4.3.3.0(1,5)]dodecane ring system (B). The formation of these products can be readily rationalized by the intervention of the oxonium ion intermediate (21).     

Diastereoselective synthesis of Pro-Phe phosphinyl dipeptide isosteres

The diastereoselective synthesis of Pro-Phe phosphinyl dipeptide isosteres in protected form was achieved by starting from optically active 1,1-diethoxyethyl(aminomethyl)phosphinate. Our methodology involves diastereoselective α-alkylation and β′-alkylation of phosphinate derivatives with an asymmetric center at the phosphorus atom.