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Katsutoshi Takahashi

Publications and source records attributed to Katsutoshi Takahashi.

15 recordsLinked to original sources
PubMed2006

Infrared multiphoton dissociation spectroscopic analysis of peptides and oligosaccharides by using fourier transform ion cyclotron resonance mass spectrometry with a midinfrared free-electron laser.

The fragmentation of peptides and oligosaccharides in the gas phase was investigated by means of electrospray ionization Fourier transform ion cyclotron resonance (FTICR) mass spectrometry coupled with dissociation by a laser-cleavage infrared multiphoton dissociation (IRMPD) technique. In this technique, an IR free-electron laser is used as a tunable source of IR radiation to cause cleavage of the ionized samples introduced into the FTICR cell. The gas-phase IRMPD spectra of protonated peptides (substance P and angiotensin II) and two sodiated oligosaccharides (sialyl Lewis X and lacto-N-fucopentaose III) were obtained over the IR scan range of 5.7-9.5 microm. In the IRMPD spectra for the peptide, fragment ions are observed as y/b-type fragment ions in the range 5.7-7.5 microm, corresponding to cleavage of the backbone of the parent amino acid sequence, whereas the spectra of the oligosaccharides have major peaks in the range 8.4-9.5 microm, corresponding to photoproducts of the B/Y type.

Electrons↗
PubMed2006

A computational study of structure-reactivity relationships in Na-adduct oligosaccharides in collision-induced dissociation reactions.

Elucidating the fragmentation mechanisms in oligosaccharides using theoretical calculations is useful in analyzing the experimentally obtained mass spectra. Semi-empirical and ab initio quantum mechanics calculations were used to study the relationship between the structure and reactivity and the chemical properties of oligosaccharides. In these calculations, sodium-cationized oligosaccharides were investigated to determine Na+ ion affinity at several binding positions; in addition, the dependence of the glycosidic bond cleavage on the Na+ position was examined. The calculated structures reported in this study are directed at interpreting experimentally observed fragment ions, resulting from the cleavage of the glycosidic bonds. The calculated results for oligosaccharides containing between three and five monosaccharide units (27 oligosaccharides) were compared with experimental data generated by matrix-assisted laser-desorption/ionization (MALDI) using a quadrupole ion trap (QIT) with a time-of-flight (TOF) mass spectrometer (MS).

Carbohydrate Sequence↗
PubMed2006

High-throughput and high-resolution two dimensional mapping of pI and m/z using a microchip in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer.

We have developed a high-throughput, two-dimensional-mapping (isoelectric point [pI], mass-to-charge ratio [m/z]) method by combining a capillary isoelectric focusing chip sealed with removable resin tape and a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. Sample proteins are separated in a meandering channel on the chip and immediately frozen. The tape is then removed and the proteins are freeze-dried. The freeze-drying maintains the separation state of the proteins and prevents movement of the sample solution, which can reduce pI resolution. A matrix solution is then applied and mass spectrometry is carried out by laser irradiation. The whole process takes less than 70 min, more than 10 times faster than with two-dimensional, polyacrylamide gel electrophoresis.

Isoelectric Focusing↗
PubMed2005

A strategy for identification of oligosaccharide structures using observational multistage mass spectral library.

Glycosylation is the most widespread posttranslational modification in eukaryotes; however, the role of oligosaccharides attached to proteins has been little studied because of the lack of a sensitive and easy analytical method for oligosaccharide structures. Recently, tandem mass spectrometric techniques have been revealing that oligosaccharides might have characteristic signal intensity profiles. We describe here a strategy for the rapid and accurate identification of the oligosaccharide structures on glycoproteins using only mass spectrometry. It is based on a comparison of the signal intensity profiles of multistage tandem mass (MSn) spectra between the analyte and a library of observational mass spectra acquired from structurally defined oligosaccharides prepared using glycosyltransferases. To smartly identify the oligosaccharides released from biological materials, a computer suggests which ion among the fragment ions in the MS/MS spectrum should yield the most informative MS3 spectrum to distinguish similar oligosaccharides. Using this strategy, we were able to identify the structure of N-linked oligosaccharides in immunoglobulin G as an example.

Amino Acid Sequence↗
PubMed2005

Statistical evaluation of a bottom-up clustering for single particle molecular images.

We examined the statistical performance of clustering single particle molecular images by bottom-up clustering, a hierarchical algorithm, using simulated protein images with a low signal-to-noise ratio. Using covariance for the measure of similarity together with the iterative alignment, our method was found to be fairly robust against noise. Clustering tests of four known protein structures were performed at three levels of noise and with three levels of smoothing. A significant effect of smoothing was confirmed in our results for images with noise suggesting an effective degree of smoothing depending on the noise and structural features of the target molecule. The consistency of clustering results was evaluated by the average solid angle of projection, and the precision of our clustering results was checked by the average image correlation between the obtained cluster image and the true projection. Once image features are extracted appropriately, the average solid angle also represents the degree of clustering precision.

Algorithms↗
PubMed2004

Clinico-molecular study of dedifferentiation in well-differentiated liposarcoma.

Well-differentiated liposarcoma (WD) acquires fully malignant potential when the histological progression named dedifferentiation occurs. This progression is supposed to occur in a time-dependent manner but this is still a debated issue. Clinically, the prediction of dedifferentiation for WD is very important from the therapeutic point of view. To identify genes that are predictive of dedifferentiation and to understand the mechanism of dedifferentiation, we investigated clinical information of 50 cases and studied the gene expression profiles of 36 lipomatous tumors using cDNA microarray. The clinical study showed that the dedifferentiation did not always seem to occur in a time-dependent manner. Interestingly, from the gene expression study, unsupervised hierarchical clustering analysis of well-differentiated lesions obtained from dedifferentiated liposarcoma (DD) cases that were indistinguishable from WD pathologically showed a clearly distinct gene expression pattern from WD. Using the pattern-matching program, 1687 genes including 487 known genes were identified, which discriminated WD cases from well-differentiated lipomatous lesions obtained from DD cases. These results suggest that the dedifferentiation may arise from different types of WD that could be distinguished from gene expression profiling but could hardly be classified by the pathological studies.

Base Sequence↗
PubMed2004

Endogenous adrenomedullin protects against vascular response to injury in mice.

BACKGROUND: In our previous study, adrenomedullin (AM) overexpression could limit the arterial intimal hyperplasia induced by cuff injury in rats. However, it remains to be elucidated whether endogenous AM plays a role against vascular injury. METHODS AND RESULTS: We used the AM knockout mice to investigate the effect of endogenous AM. Compared with wild-type (AM+/+) mice, heterozygous AM knockout (AM+/-) mice had the increased intimal thickening of the cuff-injured femoral artery, concomitantly with lesser AM staining. In AM+/- mice, cuff placement increased both the production of superoxide anions (O2-) measured by coelentarazine chemiluminescence and the immunostaining of p67phox and gp91phox, subunits of NAD(P)H oxidase in the adventitia, associated with the increment of CD45-positive leukocytes, suggesting that the stimulated formation of radical oxygen species accompanied chronic adventitial inflammation. Not only the AM gene transfection but also the treatment of NAD(P)H oxidase inhibitor apocynin and membrane-permeable superoxide dismutase mimetic tempol could limit cuff-induced intimal hyperplasia in AM+/- mice, associated with the inhibition of O2- formation in cuff-injured artery. CONCLUSIONS: The overproduction of oxidative stress induced by the increased NAD(P)H oxidase activity might be involved in cuff-injured arterial intimal hyperplasia in AM+/- mice. Thus, it is suggested that endogenous AM possesses a protective action against the vascular response to injury, possibly through the inhibition of oxidative stress production.

Acetophenones↗
PubMed2004

Fragmentation study of peptides using Fourier transform ion cyclotron resonance with infrared multiphoton dissociation: experiment and simulation.

In this study, the fragmentation of gas-phase protonated Angiotensin II is investigated using electrospray ionization (ESI), Fourier-transform ion cyclotron resonance (FT-ICR), and mass spectrometry (MS) with a laser cleavage infrared multiphoton dissociation (IRMPD) technique. The experimental results show that the spectra peaks for the photoproducts are y2/b6- and y7-type ions, corresponding to the cleavage of His-Pro and Asp-Arg in the parent amino acid sequence. The fragmentation of the peptide under collision-free vacuum conditions is modeled using molecular dynamics simulations (MD). The binding energy for the peptide bonds (C'-N bond) of Angiotensin II is estimated from ab initio calculations. The calculations are directed at predicting experimental measurements of the product ions from the photodissociation of the peptide. The product distributions simulated by the MD dissociation trajectories include predominantly y7/b1 and y2/b6 pair ions.

Angiotensin II↗
PubMed2004

Two cases of renovascular hypertension and ischemic renal dysfunction: reliable choice of examinations and treatments.

We experienced two aged patients with atherosclerotic renovascular stenosis associated with hypertension and ischemic nephropathy. Both patients exhibited sudden rise in blood pressure (BP) and progressive aggravation of renal dysfunction. In these patients, the use of contrast medium to screen for renal artery stenosis (RAS) ran the risk of further deterioration of renal function. We therefore used magnetic resonance angiography (MRA), which is less conducive to renal damage, to screen for RAS. One-sided RAS was treated by percutaneous transluminal angioplasty of the renal artery (PTRA) and stenting. As a result, BP decreased in both patients. Serum creatinine (Cr) decreased slightly in one patient, whereas, in the other, serum Cr increased transiently and then decreased and stabilized to pre-treatment levels. Thus, although it is unclear whether the combination of PTRA and stenting is among the best treatments for patients with RAS and moderate-to-severe renal dysfunction, PTRA and stenting are clearly of benefit in selected patients. In addition, recent progress in characterizing the pathophysiology of ischemic nephropathy associated with renovascular hypertension has created interest in the therapeutic potential of angiotensin II receptor antagonists, sympatholytic agents, and antioxidants. Therefore, we discuss the therapeutic utility of PTRA and stenting and the above-mentioned medications in patients with RAS and renal dysfunction.

Angioplasty, Balloon↗
PubMed2003

Dynamic modeling of genetic networks using genetic algorithm and S-system.

MOTIVATION: The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused on the estimation of only network structures, and they were ineffective in inferring a network structure with feedback loops. We previously proposed a method to predict not only the network structure but also its dynamics using a Genetic Algorithm (GA) and an S-system formalism. However, it could predict only a small number of parameters and could rarely obtain essential structures. In this work, we propose a unified extension of the basic method. Notable improvements are as follows: (1) an additional term in its evaluation function that aims at eliminating futile parameters; (2) a crossover method called Simplex Crossover (SPX) to improve its optimization ability; and (3) a gradual optimization strategy to increase the number of predictable parameters. RESULTS: The proposed method is implemented as a C program called PEACE1 (Predictor by Evolutionary Algorithms and Canonical Equations 1). Its performance was compared with the basic method. The comparison showed that: (1) the convergence rate increased about 5-fold; (2) the optimization speed was raised about 1.5-fold; and (3) the number of predictable parameters was increased about 5-fold. Moreover, we successfully inferred the dynamics of a small genetic network constructed with 60 parameters for 5 network variables and feedback loops using only time-course data of gene expression.

Algorithms↗
PubMed2003

Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure.

We applied a method based on Akaike's information criterion (AIC) to detect genes whose expression profile is considerably different in some tissue(s) than in others. Such observations are detected as outliers, and the method we used was originally developed to detect outliers. The main advantage of the method is that objective decisions are possible because the procedure is independent of a significance level. We applied the method to 48 expression ratios corresponding to various tissues in each of 14,610 clones obtained from the RIKEN Expression Array Database (READ; http://read.gsc.riken.go.jp). As a result, for several tissues (e.g., muscle, heart, and tongue tissues that contain similar cell types) we objectively obtained specific clones without any "thresholding." Our study demonstrates the feasibility of the method for detecting tissue-specific gene expression patterns.

Algorithms↗
PubMed2003

Inference of Euler angles for single-particle analysis by means of evolutionary algorithms.

Single-particle analysis is one of the methods for structural studies of protein and macromolecules; it requires advanced image analysis of electron micrographics. Reconstructing three-dimensional (3D) structure from microscope images is not an easy analysis because of the low image resolution of images and lack of the directional information of images in 3D structure. To improve the resolution, different projections are aligned, classified, and averaged. Inferring the orientations of these images is so difficult that the task of reconstructing 3D structures depends upon the experience of researchers. But recently, a method to reconstruct 3D structures was automatically devised. In this paper, we propose a new method for determining Euler angles of projections by applying genetic algorithms. We empirically show that the proposed approach has improved the previous one in terms of computational time and acquired precision.

Algorithms↗
PubMed2003

DNA aptamers that recognize fluorophore using on-chip screening in combination with an in silico evolution.

We successfully developed a novel screening method for the acquisition of DNA aptamers. The technique selectively recognizes resorufin using on-chip screening in combination with an in silico evolution method. This method proved efficient for screening for DNA aptamers of single-stranded oligo-DNAs. A genetic algorithm was applied to make oligonucleotide sequences for the combinatorial library. A fluorophore, resorufin was applied to the ligand screening as a target. The affinity of the library was analyzed by the DNA microarray. This method for screening DNA ligands includes on-chip selection and a computer-evolved sequence, where the highest affinity was chosen. The fluorescence intensity of the library on the DNA microarray increased after three repetitions of the selection round.

Base Sequence↗
PubMed2002

Inference of Euler angles for single particle analysis by using Genetic Algorithms.

Single particle analysis is one of the methods for structural studies of protein and macromolecules developed in image analysis on electron microscopy. Reconstructing 3D structure from microscope images is not an easy analysis because of the low resolution of images and lack of the directional information of images in 3D structure. To improve the resolution, different projections are aligned, classified and averaged. Inferring the orientations of these images is so difficult that the task of reconstructing 3D structures depends upon the experience of researchers. But recently, a method to reconstruct 3D structures is automatically devised. In this paper, we propose a new method for determining Euler angles of projections by applying Genetic Algorithms (i.e., GAs). We empirically show that the proposed approach has improved the previous one in terms of computational time and acquired precision.

Algorithms↗