Keiichi Nagai

HUNT: launch of a full-length cDNA database from the Helix Research Institute

The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project principally funded by the Japanese Ministry of International Trade and Industry, and the clones were sequenced in the governmental New Energy and Industrial Technology Development Organization (NEDO) Human cDNA Sequencing Project. The HUNT database contains an extensive amount of annotation from advanced analysis and represents an essential bioinformatics contribution towards understanding of the gene function. The HRI human cDNA clones were obtained from full-length enriched cDNA libraries constructed with the oligo-capping method and have resulted in novel full-length cDNA sequences. A large fraction has little similarity to any proteins of known function and to obtain clues about possible function we have developed original analysis procedures. Any putative function deduced here can be validated or refuted by complementary analysis results. The user can also extract information from specific categories like PROSITE patterns, PFAM domains, PSORT localization, transmembrane helices and clones with GENIUS structure assignments. The HUNT database can be accessed at http://www.hri.co.jp/HUNT.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants.

Cooling Effects of CO2, CO2-N2 and CO2-He Gases by Absorption of Q-Switched Laser Radiations

Transient cooling of CO 2 and mixtures of CO 2 –N 2 , CO 2 –He was investigated in the pressure range of range of 5–460 Torr, using different wavelength radiations of the CO 2 laser, i.e. the P and R branches of 10.6 µm and 9.6 µm radiation. Temperature variations of the irradiated gases were detected by a condenser microphone through the pressure changes. Observed experimental results are explained, based on the variation of the vibrational relaxation times of the CO 2 molecule under different physical conditions.

Interaction between cationic fluorocarbon surfactant and polyoxyethylated surfactants having a sulfate group

Abstract Interaction between a cationic fluorocarbon surfactant, bis(2-hydroxyethyl)(2-hydroxy-3-perfluorooctylpropyl)-methylammonium chloride (DEFUMAC) and sodium dodecyl poly(oxyethylene)sulfate (SDEnS, n = 3, 5, 8) in dilute aqueous solutions has been investigated by means of surface tension, fluorescence probing, solubilization, and static and dynamic light scattering measurements. The same systems in concentrated aqueous solutions have been characterized from the phase diagram. In the concentrated solution no crystals are formed at any molar fraction in the DEFUMAC-SDE8S system, whereas precipitation of crystals is observed over wide regions in the DEFUMAC-SDE3S or SDE5S systems. On the other hand, in the dilute solution, the mixed critical micelle concentration (CMC), the surface tension at the CMC, an interaction parameter β (from regular solution theory), the apparent aggregation number and the diffusion coefficient of the mixed micelles all depend on the oxyethylene chain length of SDEnS. These characteristics change markedly with decreasing value of n. This is predominantly due to the strong electrostatic attractive interaction between the surfactants in spite of the mutual phobicity of hydrocarbon and fluorocarbon chains.

Infrared photochemical reaction of C2F3 C1 induced by a tea CO2 laser

Abstract An infrared photochemical reaction of C 2 F 3 Cl induced by a TEA CO 2 laser was observed. Main reaction products were C 2 F 4 and ClFCCFCl(trans), being quite different from those obtained by thermal or ultraviolet photochemical reactions.

Infrared multiphoton dissociation of C2F3Cl.

The mechanism of infrared multiphoton dissociation of C2F3Cl was investigated by observing CO2 laser power dependences of a number of absorbed photon/molecule and reaction rate. A phenomenological model calculation shows that the absorbed energy is localized in two vibrational modes in quasicontinuum state.

DNA sequence comparison considering both amino acid and nucleotide insertions/deletions because of evolution and experimental error.

Amino acid similarity often needs to be considered in DNA sequence comparison to elucidate gene functions. We propose a Smith-Waterman-like algorithm which considers amino acid similarity and insertions/deletions in sequences at the DNA level and at the protein level in a hybrid manner. The algorithm is applied to cDNA sequences of Oryza sativa and those of Arabidopsis thaliana. The results are compared with the results of application of NCBIs tblastx program (which compares the sequences in the BLAST manner after translation). It is shown that the present algorithm is very helpful in discovering nucleotide insertions/deletions originating from experimental errors as well as amino acid insertions/deletions due to evolutionary reasons.

REAL-TIME DNA DETECTION SYSTEMS

Publisher Summary This chapter focuses on two real-time DNA fragment detection systems, detecting β ray and fluorescence. As visible light produces only a small amount of fluorescence in gels, a visible light-emitting fluorophore is used as a labeling compound. Only one kind of fluorophore is used because of several drawbacks of the multicolor label method. Fluoresceine isothicyanate (FITC) is used as the labeling compound. It gives strong fluorescence and, therefore, a high detecting sensitivity. For a high-sensitivity detection, it is necessary to carry out simultaneous irradiation of all electrophoresis lanes and simultaneous detection of fluorescence from every lane. To achieve this, a side-entry laser irradiation method is employed. It is also used as fluorescence line-image sensing by means of a TV camera system. The real-time fluorescence detection method is a very promising method for rapid DNA sequencing. Its capability is enhanced by improving data acquisition system and electrophoresis condition. A capability of gel reuse is also demonstrated, which is another feature of the fluorescence method.