Yasuhiro Futamura

A method for finding optimal RNA secondary structures using a new entropy model (vsfold)

We are developing a program to calculate optimal RNA secondary structures. The model uses di-nucleotide pairing energies as with most traditional approaches. However, for long-range entropy interactions, the approach uses an entropy-loss model based on the accumulated sum of the entropy of bonding between each base-pair weighted inversely by the correlation of the RNA sequence (the Kuhn length). Stiff RNA forms very different structures from flexible RNA. The results demonstrate that the long-range folding is largely governed by this entropy and the Kuhn length.

Evaluation of Anti-Inflammatory Drug-Conjugated Silicon Quantum Dots: Their Cytotoxicity and Biological Effect

Silicon quantum dots (Si-QDs) have great potential for biomedical applications, including their use as biological fluorescent markers and carriers for drug delivery systems. Biologically inert Si-QDs are less toxic than conventional cadmium-based QDs, and can modify the surface of the Si-QD with covalent bond. We synthesized water-soluble alminoprofen-conjugated Si-QDs (Ap-Si). Alminoprofen is a non-steroid anti-inflammatory drug (NSAID) used as an analgesic for rheumatism. Our results showed that the “silicon drug” is less toxic than the control Si-QD and the original drug. These phenomena indicate that the condensed surface integration of ligand/receptor-type drugs might reduce the adverse interaction between the cells and drug molecules. In addition, the medicinal effect of the Si-QDs (i.e., the inhibition of COX-2 enzyme) was maintained compared to that of the original drug. The same drug effect is related to the integration ratio of original drugs, which might control the binding interaction between COX-2 and the silicon drug. We conclude that drug conjugation with biocompatible Si-QDs is a potential method for functional pharmaceutical drug development.

Statistics of trinucleotides in coding sequences and evolution

The aim of this paper is to give measurements indicative of evolutional stages of the species. Two types of statistics of trinucleotides in coding regions are analysed for 27 species. The first one is the codon space, the nucleotide ratio for each of the three codon positions. We apply principal component analysis on this space and extract two principal components faithfully describing the original distribution of the codon space. The first principal component corresponds to the GC content. The second principal component classifies the species into three evolutional groups, Archaea, Bacteria and Eukaryota. The second statistics is the real and theoretical frequency of amino acids. The real frequency of an amino acid in a coding sequence is its frequency in the translated protein. The theoretical frequency is the expected frequency calculated from the ratio of nucleotides. We introduce the discrepancy between these two frequencies as an index of non-randomness of nucleotides in the sequence. This index of non-randomness divides the species into two groups: eukaryotes having smaller non-randomness (i.e. being more random) and prokaryotes having higher non-randomness.

Amino Acid Synthesis in a Supercritical Carbon Dioxide - Water System

Mars is a CO2-abundant planet, whereas early Earth is thought to be also CO2-abundant. In addition, water was also discovered on Mars in 2008. From the facts and theory, we assumed that soda fountains were present on both planets, and this affected amino acid synthesis. Here, using a supercritical CO2/liquid H2O (10:1) system which mimicked crust soda fountains, we demonstrate production of amino acids from hydroxylamine (nitrogen source) and keto acids (oxylic acid sources). In this research, several amino acids were detected with an amino acid analyzer. Moreover, alanine polymers were detected with LC-MS. Our research lights up a new pathway in the study of life’s origin.

Novel Production Method for Plant Polyphenol from Livestock Excrement Using Subcritical Water Reaction

Plant polyphenol, including vanillin, is often used as the intermediate materials of the medicines and vanilla flavoring. In agriculture generally vanillin is produced from vanilla plant and in industry from lignin of disposed wood pulp. We have recently developed a method for the production of plant polyphenol with the excrement as a natural resource of lignin, of the herbivorous animals, by using the subcritical water. The method for using the subcritical water is superior to that of the supercritical water because in the latter complete decomposition occurs. We have successfully produced the vanillin, protocatechuic acid, vanillic acid, and syringic acid in products. Our method is simpler and more efficient not only because it requires the shorter treatment time but also because it releases less amount of carbon dioxide into the atmosphere.

Silicon nanocrystals as handy biomarkers

Quantum dots (QDs) have brighter and longer fluorescence than organic dyes. Therefore, QDs can be applied to biotechnology, and have capability to be applied to medical technology. Currently, among the several types of QDs, CdSe with a ZnS shell is one of the most popular QDs to be used in biological experiments. However, when the CdSe QDs were applied to clinical technology, potential toxicological problems due to CdSe core should be considered. To eliminate the problem, silicon nanocrystals, which have the potential of biocompatibility, could be a candidate of alternate probes. Silicon nanocrystals have been synthesized using several techniques such as aerosol, electrochemical etching, laser pyrolysis, plasma deposition, and colloids. Recently, the silicon nanocrystals were reported to be synthesized in inverse micelles and also stabilized with 1-heptene or allylamine capping. Blue fluorescence of the nanocrystals was observed when excited with a UV light. The nanocrystals covered with 1-heptene are hydrophobic, whereas the ones covered with allylamine are hydrophilic. To test the stability in cytosol, the water-soluble nanocrystals covered with allylamine were examined with a Hela cell incorporation experiment. Bright blue fluorescence of the nanocrystals was detected in the cytosol when excited with a UV light, implying that the nanocrystals were able to be applied to biological imaging. In order to expand the application range, we synthesized and compared a series of silicon nanocrystals, which have variable surface modification, such as alkyl group, alcohol group, and odorant molecules. This study will provide a wider range of optoelectronic applications and bioimaging technology.