Biomedical subjects

Akio Kobayashi

Publications and source records attributed to Akio Kobayashi.

At least 19 recordsLinked to original sources

PubMed2007

Prediction of Japanese green tea ranking by gas chromatography/mass spectrometry-based hydrophilic metabolite fingerprinting.

An innovative technique for green tea's quality determination was developed by means of metabolomics. Gas-chromatography coupled with time-of-flight mass spectrometry and multivariate data analysis was employed to evaluate the quality of green tea. Alteration of green tea varieties and manufacturing processes effects a variation in green tea metabolites, which leads to a classification of the green tea's grade. Therefore, metabolic fingerprinting of green tea samples of different qualities was studied. A set of ranked green tea samples from a Japanese commercial tea contest was analyzed with the aim of creating a reliable quality-prediction model. Several multivariate algorithms were performed. Among those, the partial least-squares projections to latent structures (PLS) analysis with the spectral filtering technique, orthogonal signal correction (OCS), was found to be the most practical approach. In addition, metabolites that play an important role in green tea's grade classification were identified.

Algorithms↗

PubMed2006

Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment.

Salt stress is one of the most important factors limiting plant cultivation. Many investigations of plant response to high salinity have been performed using conventional transcriptomics and/or proteomics approaches. However, transcriptomics and proteomics techniques are not all-encompassing methods that can achieve exclusive insights into the metabolite networks contributing to biochemical reactions. Hence, the functions of the complex stress response pathways are yet to be determined, especially at the metabolic level. A time-course metabolic profiling with Arabidopsis thaliana cell cultures after the imposition of salt stress is reported in this study. Analyses of primary metabolites, especially small polar metabolites such as amino acids, sugars, sugar alcohols, organic acids, and amines, was performed by GC/MS and LC/MS at 0.5, 1, 2, 4, 12, 24, 48, and 72 h after a salt-stress treatment with 100 mM NaCl being the final concentration. The mass chromatographic data were converted into matrix data sets, which were subjected to data mining processes, including principal component analysis (PCA) and batch-learning self-organizing mapping analysis (BL-SOM). The mining results suggest that the methylation cycle for the supply of methyl groups, the phenylpropanoid pathway for lignin production, and glycinebetaine biosynthesis are synergetically induced as a short-term response against salt-stress treatment. The results also suggest the the co-induction of glycolysis and sucrose metabolism as well as co-reduction of the methylation cycle as long-term responses to salt stress.

Amines↗

PubMed2006

Fgf9 and Wnt4 act as antagonistic signals to regulate mammalian sex determination.

The genes encoding members of the wingless-related MMTV integration site (WNT) and fibroblast growth factor (FGF) families coordinate growth, morphogenesis, and differentiation in many fields of cells during development. In the mouse, Fgf9 and Wnt4 are expressed in gonads of both sexes prior to sex determination. Loss of Fgf9 leads to XY sex reversal, whereas loss of Wnt4 results in partial testis development in XX gonads. However, the relationship between these signals and the male sex-determining gene, Sry, was unknown. We show through gain- and loss-of-function experiments that fibroblast growth factor 9 (FGF9) and WNT4 act as opposing signals to regulate sex determination. In the mouse XY gonad, Sry normally initiates a feed-forward loop between Sox9 and Fgf9, which up-regulates Fgf9 and represses Wnt4 to establish the testis pathway. Surprisingly, loss of Wnt4 in XX gonads is sufficient to up-regulate Fgf9 and Sox9 in the absence of Sry. These data suggest that the fate of the gonad is controlled by antagonism between Fgf9 and Wnt4. The role of the male sex-determining switch--Sry in the case of mammals--is to tip the balance between these underlying patterning signals. In principle, sex determination in other vertebrates may operate through any switch that introduces an imbalance between these two signaling pathways.

Animals↗

PubMed2006

Gene expression profiles in developing nephrons using Lim1 metanephric mesenchyme-specific conditional mutant mice.

BACKGROUND: Lim1 is a homeobox gene that is essential for nephrogenesis. During metanephric kidney development, Lim1 is expressed in the nephric duct, ureteric buds, and the induced metanephric mesenchyme. Conditional ablation of Lim1 in the metanephric mesenchyme blocks the formation of nephrons at the nephric vesicle stage, leading to the production of small, non-functional kidneys that lack nephrons. METHODS: In the present study, we used Affymetrix probe arrays to screen for nephron-specific genes by comparing the expression profiles of control and Lim1 conditional mutant kidneys. Kidneys from two developmental stages, embryonic day 14.5 (E14.5) and 18.5 (E18.5), were examined. RESULTS: Comparison of E18.5 kidney expression profiles generated a list of 465 nephron-specific gene candidates that showed a more than 2-fold increase in their expression level in control kidney versus the Lim1 conditional mutant kidney. Computational analysis confirmed that this screen enriched for kidney-specific genes. Furthermore, at least twenty-eight of the top fifty (56%) candidates (or their vertebrate orthologs) were previously reported to have a nephron-specific expression pattern. Our analysis of E14.5 expression data yielded 41 candidate genes that are up-regulated in the control kidneys compared to the conditional mutants. Three of them are related to the Notch signaling pathway that is known to be important in cell fate determination and nephron patterning. CONCLUSION: Therefore, we demonstrate that Lim1 conditional mutant kidneys serve as a novel tissue source for comprehensive expression studies and provide a means to identify nephron-specific genes.

Animals↗

PubMed2006

A novel microsurgery method for intact plant tissue at the single cell level using ArF excimer laser microprojection.

A novel microsurgery technique for the partial removal of rigid cell-walls in intact plant tissue is established. Using a size-variable slit, an ArF excimer laser was microprojected on the surface of the targeted cell, and this method enabled the area- and depth-controllable processing of the cortical structure of plant cells including the cuticle and cell wall layer. In epidermal cells of all tested plants, viabilities of more than 90% were retained 24 h after irradiation. Scanning electron microscope (SEM) observation revealed that the cuticle layer of the irradiated region was completely ablated, and the cellulose microfibrils of the secondary cell wall were partially removed; furthermore, 4 days after laser treatment, the regeneration of cell wall fibrils was observed. As a model experiment, the transient expression of synthetic green fluorescent protein (sGFP) was performed by the microinjection of cauliflower mosaic virus (CMV) 35S promoter-derived sGFP gene through an "aperture" in the treated cell surface. Moreover, micron-sized fluorescent beads were successfully introduced by the same method into the onion cells indicating that this method can be used to introduce foreign materials as large as organelles.

Caulimovirus↗

PubMed2006

Guidelines for the treatment of Crohn's disease in children.

This paper shows guidelines for the treatment of Crohn's disease in children by the Working Group of the Japanese Society for Pediatric Gastroenterology, Hepatology and Nutrition (Chair: Yuichiro Yamashiro) and the Japanese Society for Pediatric Inflammatory Bowel Disease (Chair: Akio Kobayashi). The points in which these guidelines differ from those for adult patients are as follows. (i) Total enteral nutrition in the form of an elemental formula is indicated as primary therapy for children with Crohn's disease at onset as well as the active stage. Oral mesalazine is used together. (ii) Total parenteral nutrition (TPN) with oral mesalazine is required for children with serious illness. The use of a corticosteroid should be withheld for at least 1 week after TPN has been started. (iii) When TPN is not considered to be effective, additional corticosteroid is used. Full doses of corticosteroid should be used for at least 2 weeks after clinical improvement has been achieved, and then the dose of the corticosteroid should be tapered carefully. (iv) When surgery is indicated in pediatric patients with stricture or fistula formation and complicated by persistent growth failure despite medical therapy, the optimum time for surgery is thought to be before epiphyseal plates have been closed.

Child↗

PubMed2006

Pressure-assisted capillary electrophoresis mass spectrometry using combination of polarity reversion and electroosmotic flow for metabolomics anion analysis.

We have developed a method based on capillary electrophoresis (CE) coupled to mass spectrometry (MS) that is a powerful tool for metabolome analysis. In this paper, a simple method for the simultaneous analysis of anionic metabolites such as sugar phosphates, organic acids, nucleotides and CoA compounds based on pressure-assisted capillary electrophoresis coupled to electrospray ionization mass spectrometry (PACE/ESI-MS) is described. The feature of this method is that CE polarity, where the inlet of the capillary is at the anode and the outlet at the cathode, is inverted from conventional CE analysis for anions. Moreover, an ordinary fused silica capillary was chosen instead of a specific cationic polymer-coated capillary (SMILE (+) capillary). A robust and inexpensive analytical method was established from the above-mentioned CE polarity and noncoated fused silica capillary. A trimethylamine acetate electrolyte, pH 10.0, provides a high resolution between isomers. Electrolyte flow using an air pump after electrophoresis enables the comprehensive and simultaneous analyses of sugar phosphates, organic acids, nucleotides and a CoA compound that to date have been impossible to analyze. Our method can be used as a de facto standard for metabolome analysis.

Anions↗

PubMed2006

A polymerase chain reaction-mediated yeast artificial chromosome-splitting technology for generating targeted yeast artificial chromosomes subclones.

The yeast artificial chromosomes (YAC) system makes it possible not only to clone large DNA fragments but also to simplify the physical mapping and functional analysis of chromosomes and genomes through YAC manipulation. To manipulate large DNA fragments cloned into YACs, YAC fragmentation has been developed and also a new method called the YAC-splitting method was developed recently. Although the YAC fragmentation method can be used to delete DNA from one side of a YAC, the YAC-splitting method generates two smaller YACs, both of which are transmitted to daughter cells during mitotic growth. This chapter describes the YAC-splitting method improved by incorporating polymerase chain reaction-mediated chromosome splitting (PCS) technique and by adding yeast autonomously replicating sequence (ARS) to the system. The PCS method combines a streamlined procedure (two-step PCR and one transformation per splitting event) with the Cre/loxP system for marker rescue. The improved YAC-splitting method can convert a targeted region of a eukaryotic chromosome within a YAC into a new replicating YAC.

Chromosomes, Artificial, Yeast↗

PubMed2006

Transformation of yeast using bioactive beads with surface-immobilized yeast artificial chromosomes.

Yeast artificial chromosomes (YACs) are useful cloning vectors with the capacity to carry large DNA inserts. The largest barrier using such large DNA molecules in transformation experiments has been their physical instability in a solution. We developed a new method for transforming yeast with chromosome-sized DNA. The method uses bioactive beads composed of calcium alginate to immobilize yeast chromosomal DNAs. Chromosomal DNA immobilized on bioactive beads is physically stable when compared with naked chromosomal DNAs. The bead-mediated transformation performed well, not only with respect to the transformation frequency, but also in successful transformation using split chromosomal DNA that exceeded 450 kb in size. In this chapter we introduce a new method for transforming yeast using bioactive beads. In conjunction with genomic YAC libraries and the yeast chromosome-splitting method, this technique will pave the way to stable and effective transfer of YACs into yeast cells.

Alginates↗

PubMed2005

Historical aspects for the control of soil-transmitted helminthiases.

Japan has been one of the very few countries that operated the nationwide control programme against soil-transmitted helminths (STH) infections and gained a great success. On the basis of researches and operational studies, periodical mass-examination using cellophane thick smear (Kato technique) and selective mass-treatment targeted at school children were employed as the most useful control measure. In later years, Japan's experience and the strategy for STH control programme were transferred to Asian countries through Asian Parasite Control Organization (APCO) and also to countries of Asia, Africa and Latin-America through seminar at a modified form of the integration programme (IP) of STH control with family planning and nutritional improvement. The parasitologists group conducted studies in all aspects to seek effective STH control measures for respective countries and obtained many successful results.

Adolescent↗

PubMed2005

A versatile and general splitting technology for generating targeted YAC subclones.

Yeast artificial chromosomes (YAC) splitting technology was developed as a means to subclone any desired region of eukaryotic chromosomes from one YAC into new YACs. In the present study, the conventional YAC splitting technology was improved by incorporating PCR-mediated chromosome splitting technique and by adding autonomously replicating sequence (ARS) to the system. To demonstrate the performance of the improved method, a 60-kb region from within a 590-kb YAC (clone CIC9e2 from Arabidopsis thaliana chromosome 5) that could not be subcloned using the original method was split to convert into a replicating YAC. Two template plasmids, pSK-KCA and pSKCLY, were used to generate two splitting fragments by PCR. Two splitting fragments consisted of telomeric (C(4)A(2))(6) repeats, 400-bp target region, CEN4, H4ARS and Km(r) (selective marker for plant transformants), or CgLEU2. These splitting fragments were introduced into Saccharomyces cerevisiae harboring the 100-kb split YAC generated by splitting of the 590-kb YAC and containing the 60-kb region. Among 12 Leu(+) transformants, four exhibited the expected karyotype in which two newly split 40- and 60-kb chromosomes were generated. These results demonstrate that the improved method can convert a targeted region of a eukaryotic chromosome within a YAC into a replicating YAC.

Arabidopsis↗

PubMed2005

Separation of polyprenol and dolichol by monolithic silica capillary column chromatography.

We attempted an analysis of naturally occurring polyprenol and dolichol using a monolithic silica capillary column in HPLC. First, the separation of the polyprenol mixture alone was performed using a 250 x 0.2 mm inner diameter (ID) octadecylsilyl (ODS)-monolithic silica capillary column. The resolution of the separation between octadecaprenol (prenol 18) and nonadecaprenol (prenol 19) exceeded by >or=2-fold the level recorded when using a conventional ODS-silica particle-packed column (250 x 4.6 mm ID) under the same elution conditions. Next, the mixture of the prenol type (polyprenol) and dolichol type (dihydropolyprenol) was subjected to this capillary HPLC system, and the separation of each homolog was successfully achieved. During the analysis of polyprenol fraction derived from Eucommia ulmoides leaves, dolichols were found as a single peak, including all-trans-polyprenol and cis-polyprenol previously identified. This sensitive high-resolution system is very useful for the analysis of compounds that are structurally close to polyprenols and dolichols and that have a low content.

Chromatography, High Pressure Liquid↗

PubMed2005

A novel crude oil emulsifier excreted in the culture supernatant of a marine bacterium, Myroides sp. strain SM1.

A marine bacterium, Myroides sp. SM1, can grow on weathered crude oil and show emulsification of it. The biosurfactant able to emulsify crude oil was excreted in culture supernatant of Myroides sp. SM1 grown on marine broth, which was extracted with chloroform/methanol (1:1) at pH 7 and purified by normal and reverse phase silica gel column chromatographies. The compound was ninhydrin-positive, and the chemical structure was elucidated by nuclear magnetic resonance (NMR), infrared spectroscopy (IR), fast atom bombardment mass spectrometry, and gas chromatography-mass spectrometry (GC-MS) to be a mixture of L: -ornithine lipids, which were composed of L: -ornithine and a different couple of iso-3-hydroxyfatty acid (C(15)-C(17)) and iso-fatty acid (C(15) or C(16)) in a ratio of 1:1:1. The critical micelle concentration for a mixture of ornithine lipids was measured to be approximately 40 mg/l. A mixture of ornithine lipids exhibited emulsifying activity for crude oil in a broad range of pH, temperature, and salinity and showed higher surface activity for oil displacement test than other several artificial surfactants and a biosurfactant, surfactin.

Culture Media, Conditioned↗

PubMed2005

Enzymatic and structural characterization of type II isopentenyl diphosphate isomerase from hyperthermophilic archaeon Thermococcus kodakaraensis.

Enzymatic and thermodynamic characteristics of type II isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase (Tk-IDI) from Thermococcus kodakaraensis, which catalyzes the interconversion of IPP and DMAPP, were examined. FMN was tightly bound to Tk-IDI, and the enzyme required NADPH and Mg2+ for the isomerization in both directions. The melting temperature (Tm), the change of enthalpy (deltaH(m)), and the heat capacity change (deltaC(p)) of Tk-IDI were 88.0 degrees C, 444 kJ mol(-1), and 13.2 kJ mol(-1) K(-1), respectively, indicating that Tk-IDI is fairly thermostable. Kinetic parameters dramatically changed when the temperature crossed 80 degrees C even though its native overall structure was stably maintained up to 90 degrees C, suggesting that local conformational change would occur around 80 degrees C. This speculation was supported by the result of the circular dichroism analysis that showed the shift of the alpha-helical content occurred at 80 degrees C.

Amino Acid Sequence↗

PubMed2005

Cloning of a cryptochrome homologue from the holoparasitic plant Orobanche minor Sm.

Orobanche minor is a non-photosynthetic root holoparasitic plant. Although it is known that photosynthesis-related genes are inactivated or have been eliminated from the plastid genomes of holoparasites, little is known about the alterations in their genes involved in the signaling networks by which light regulates photosynthesis. Cryptochromes (crys), which are blue-light receptors, appear to control both photosynthesis-related and non-photosynthetic responses to light in higher plants. Because we are interested in to what extent a cry-mediated light signaling network remains in the holoparasites, we cloned CRY homologous cDNA from O. minor (OmCRY1) and used real-time RT-PCR to compare its expression under natural daylight and darkness. We found that the OmCRY1 has a high degree of homology with CRY1 s from photosynthetic plants. Expression of the OmCRY1 gene was higher in plants grown in the dark than that in the plants grown under natural daylight. This is the first report of the gene expression of a blue-light receptor in non-photosynthetic plants.

Cloning, Molecular↗

PubMed2005

Preparation of the flexion gap affects the extension gap in total knee arthroplasty.

Changes in the extension gap caused by the preparation of the flexion gap were measured in 50 varus osteoarthritic knees undergoing total knee arthroplasty. The extension gap was first prepared and then measured before and after preparation of the flexion gap. The extension gap increased significantly on both the medial and lateral sides (19.3 +/- 0.3 to 22.0 +/- 0.3 and 21.9 +/- 0.3 to 24.0 +/- 0.3 mm, respectively, mean +/- SE, both P < .0001). The increase was greater medially (P = .0014), and in the knees with more varus deformities (> or = 10 degrees, P = .0075). Thus, preparation of the flexion gap resulted in significant widening of the extension gap, especially on the medial side. The medial release should be stepwise and conservative to achieve adequate soft tissue balance.

Aged↗

PubMed2005

Polyethylene wear particle generation in vivo in an alumina medial pivot total knee prosthesis.

Polyethylene wear particle generation is one of the most important factors affecting mid- to long-term results of total knee arthroplasties. It has been reported that the medial pivot total knee prosthesis (MP) design and alumina ceramic femoral component reduce polyethylene wear. The aim of this study is to evaluate in vivo polyethylene wear particle generation in the newly introduced alumina MP, in comparison with a metal MP. Synovial fluid was obtained from 11 knees with alumina MP and 15 knees with metal MP at nine months after the operation. Polyethylene particles were isolated, and examined using scanning electron microscope and image analyzer. Total number of particles in each knee was 7.10+/-2.86x10(6) in alumina (mean+/-standard error), and 5.70+/-2.82x10(7) in metal MP (p=0.048). Particle size (equivalent circle diameter) was 0.78+/-0.04 microm in alumina, and 0.66+/-0.06 microm in metal MP (p=0.120). Particle shape (aspect ratio) was 1.52+/-0.05 in alumina, and 1.88+/-0.11 in metal MP (p=0.014). Apart from the femoral component, the material and manufacturing method of polyethylene insert differed between the two groups, although the sterilization method was the same. Alumina MP generated fewer and rounder polyethylene wear particles than metal MP in early clinical stage, and could potentially reduce prevalence of osteolysis and aseptic loosening.

Aged↗

PubMed2005

Rotational deformity in varus osteoarthritis of the knee: analysis with computed tomography.

UNLABELLED: Rotational deformities in varus osteoarthritis of the knee were evaluated with computed tomography. Preoperative computed tomography scans of 150 knees (114 patients) having total knee arthroplasty and 31 control knees (20 patients) were included. The femorotibial rotation was quantified using the clinical epicondylar axis of the femur and the tibial tuberosity (patella tendon) as the references. The knees with osteoarthritis were divided into three groups according to the femorotibial angle (Group 1, 0 degrees -9 degrees varus, n = 87; Group 2, 10 degrees -19 degrees varus, n = 51; Group 3, 20 degrees or greater varus, n = 12) and statistically analyzed. Rotational deformities (external rotation of the tibia) existed in knees with osteoarthritis and were larger in knees with increased varus deformities (mean +/- standard deviation, -2.24 degrees +/- 4.19 degrees in Group 1; 0.33 degrees +/- 4.14 degrees in Group 2; and 5.33 degrees +/- 5.71 degrees in Group 3). When the femorotibial rotation of each knee was stratified by the corresponding femorotibial angle, we found a correlation. The information should help minimize the rotational mismatch between the femoral and the tibial components in total knee arthroplasty and elucidate the pathogenesis of varus osteoarthritis of the knee. LEVEL OF EVIDENCE: Diagnostic study, Level III-1 (study of nonconsecutive patients--no consistently applied reference gold standard). See the Guidelines for Authors for a complete description of levels of evidence.

Aged↗