Showing papers by "Kyoto University published in 2004"

Functional porous coordination polymers.

Abstract: The chemistry of the coordination polymers has in recent years advanced extensively, affording various architectures, which are constructed from a variety of molecular building blocks with different interactions between them. The next challenge is the chemical and physical functionalization of these architectures, through the porous properties of the frameworks. This review concentrates on three aspects of coordination polymers: 1). the use of crystal engineering to construct porous frameworks from connectors and linkers ("nanospace engineering"), 2). characterizing and cataloging the porous properties by functions for storage, exchange, separation, etc., and 3). the next generation of porous functions based on dynamic crystal transformations caused by guest molecules or physical stimuli. Our aim is to present the state of the art chemistry and physics of and in the micropores of porous coordination polymers.

The KEGG resource for deciphering the genome

Abstract: A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.

Naturally Arising CD4+ Regulatory T Cells for Immunologic Self-Tolerance and Negative Control of Immune Responses

Abstract: ▪ Abstract Naturally occurring CD4+ regulatory T cells, the majority of which express CD25, are engaged in dominant control of self-reactive T cells, contributing to the maintenance of immunologic self-tolerance. Their depletion or functional alteration leads to the development of autoimmune disease in otherwise normal animals. The majority, if not all, of such CD25+CD4+ regulatory T cells are produced by the normal thymus as a functionally distinct and mature subpopulation of T cells. Their repertoire of antigen specificities is as broad as that of naive T cells, and they are capable of recognizing both self and nonself antigens, thus enabling them to control various immune responses. In addition to antigen recognition, signals through various accessory molecules and via cytokines control their activation, expansion, and survival, and tune their suppressive activity. Furthermore, the generation of CD25+CD4+ regulatory T cells in the immune system is at least in part developmentally and genetically contro...

Funktionale poröse Koordinationspolymere

Abstract: Die Chemie der Koordinationspolymere hat sich in den vergangenen Jahren rasant entwickelt. Strukturen aus einer Vielzahl molekularer Bausteine mit unterschiedlichen Wechselwirkungen sind mittlerweile zuganglich. Die nachste Stufe ist die chemische und physikalische Funktionalisierung dieser Architekturen durch Einstellung ihrer Porositaten. Dieser Aufsatz konzentriert sich auf drei Aspekte von Koordinationspolymeren: 1) Anwendung von Kristall-Engineering zum Aufbau poroser Geruste aus Konnektoren und Linkern (“Nanospace-Engineering”), 2) Charakterisierung und Katalogisierung poros-struktureller Funktionalitat fur Anwendungen in Speicherungs-, Austausch-, Trennprozessen etc. und 3) poros-strukturelle Funktionalitat auf der Basis dynamischer Kristallumwandlungen durch Gastmolekule oder physikalische Reize. Ziel ist es, den aktuellen Stand der Forschung zur Chemie und Physik von und in den Mikroporen poroser Koordinationspolymere vorzustellen.

Principles, techniques, and limitations of near infrared spectroscopy.

Abstract: In the last decade the study of the human brain and muscle energetics underwent a radical change, thanks to the progressive introduction of noninvasive techniques, including near-infrared (NIR) spectroscopy (NIRS). This review summarizes the most recent literature about the principles, techniques, advantages, limitations, and applications of NIRS in exercise physiology and neuroscience. The main NIRS instrumentations and measurable parameters will be reported. NIR light (700-1000 m) penetrates superficial layers (skin, subcutaneous fat, skull, etc.) and is either absorbed by chromophores (oxy- and deoxyhemoglobin and myoglobin) or scattered within the tissue. NIRS is a noninvasive and relatively low-cost optical technique that is becoming a widely used instrument for measuring tissue O2 saturation, changes in hemoglobin volume and, indirectly, brain/muscle blood flow and muscle O2 consumption. Tissue O2 saturation represents a dynamic balance between O2 supply and O2 consumption in the small vessels such as the capillary, arteriolar, and venular bed. The possibility of measuring the cortical activation in response to different stimuli, and the changes in the cortical cytochrome oxidase redox state upon O2 delivery changes, will also be mentioned.

Real-Space Observation of Current-Driven Domain Wall Motion in Submicron Magnetic Wires

Abstract: We report direct observation of current-driven magnetic domain wall (DW) displacement by using a well-defined single DW in a microfabricated magnetic wire with submicron width. Magnetic force microscopy visualizes that a single DW introduced in a wire is displaced back and forth by positive and negative pulsed current, respectively. The direct observation gives quantitative information on the DW displacement as a function of the intensity and the duration of the pulsed current. The result is discussed in terms of the spin-transfer mechanism.

The Arabidopsis cytochrome P450 CYP707A encodes ABA 8′‐hydroxylases: key enzymes in ABA catabolism

Abstract: The hormonal action of abscisic acid (ABA) in plants is controlled by the precise balance between its biosynthesis and catabolism. In plants, ABA 8′-hydroxylation is thought to play a predominant role in ABA catabolism. ABA 8′-hydroxylase was shown to be a cytochrome P450 (P450); however, its corresponding gene had not been identified. Through phylogenetic and DNA microarray analyses during seed imbibition, the candidate genes for this enzyme were narrowed down from 272 Arabidopsis P450 genes. These candidate genes were functionally expressed in yeast to reveal that members of the CYP707A family, CYP707A1–CYP707A4, encode ABA 8′-hydroxylases. Expression analyses revealed that CYP707A2 is responsible for the rapid decrease in ABA level during seed imbibition. During drought stress conditions, all CYP707A genes were upregulated, and upon rehydration a significant increase in mRNA level was observed. Consistent with the expression analyses, cyp707a2 mutants exhibited hyperdormancy in seeds and accumulated six-fold greater ABA content than wild type. These results demonstrate that CYP707A family genes play a major regulatory role in controlling the level of ABA in plants.

Highly Efficient Dye-Sensitized Solar Cells with a Titania Thin-Film Electrode Composed of a Network Structure of Single-Crystal-like TiO2 Nanowires Made by the “Oriented Attachment” Mechanism

Abstract: In this study, single-crystal-like anatase TiO(2) nanowires were formed in a network structure by surfactant-assisted self-assembling processes at low temperature. The crystal lattice planes of the nanowires and networks of such wires composed of many nanoparticles were almost perfectly aligned with each other due to the "oriented attachment" mechanism, resulting in the high rate of electron transfer through the TiO(2) nanonetwork with single-crystal-like anatase nanowires. The direction of crystal growth of oriented attachment was controlled by changing the mole ratio of acetylacetone to Ti, that is, regulating both the adsorption of surfactant molecules via control of the reaction rate and the surface energy. A single-crystalline anatase exposing mainly the [101] plane has been prepared, which adsorbed ruthenium dye over 4 times higher as compared to P-25. A high light-to-electricity conversion yield of 9.3% was achieved by applying the titania nanomaterials with network structure as the titania thin film of dye-sensitized solar cells.

Stereotactic hypofractionated high-dose irradiation for stage I nonsmall cell lung carcinoma: clinical outcomes in 245 subjects in a Japanese multiinstitutional study.

Abstract: BACKGROUND Stereotactic irradiation (STI) has been actively performed using various methods to achieve better local control of Stage I nonsmall cell lung carcinoma (NSCLC) in Japan. The authors retrospectively evaluated results from a Japanese multiinstitutional study. METHODS Patients with Stage I NSCLC (n = 245; median age, 76 years; T1N0M0, n=155; T2N0M0, n=90) were treated with hypofractionated high-dose STI in 13 institutions. Stereotactic three-dimensional treatment was performed using noncoplanar dynamic arcs or multiple static ports. A total dose of 18–75 gray (Gy) at the isocenter was administered in 1–22 fractions. The median calculated biologic effective dose (BED) was 108 Gy (range, 57–180 Gy). RESULTS During follow-up (median, 24 months; range, 7–78 months), pulmonary complications of National Cancer Institute-Common Toxicity Criteria Grade > 2 were observed in only 6 patients (2.4%). Local progression occurred in 33 patients (14.5%), and the local recurrence rate was 8.1% for BED ≥ 100 Gy compared with 26.4% for < 100 Gy (P < 0.05). The 3-year overall survival rate of medically operable patients was 88.4% for BED ≥ 100 Gy compared with 69.4% for < 100 Gy (P < 0.05). CONCLUSIONS Hypofractionated high-dose STI with BED < 150 Gy was feasible and beneficial for curative treatment of patients with Stage I NSCLC. For all treatment methods and schedules, local control and survival rates were better with BED ≥ 100 Gy compared with < 100 Gy. Survival rates in selected patients (medically operable, BED ≥ 100 Gy) were excellent, and were potentially comparable to those of surgery. Cancer 2004. © 2004 American Cancer Society.

Cyclic electron flow around photosystem I is essential for photosynthesis

Abstract: Photosynthesis provides at least two routes through which light energy can be used to generate a proton gradient across the thylakoid membrane of chloroplasts, which is subsequently used to synthesize ATP. In the first route, electrons released from water in photosystem II (PSII) are eventually transferred to NADP+ by way of photosystem I (PSI)1. This linear electron flow is driven by two photochemical reactions that function in series. The cytochrome b6f complex mediates electron transport between the two photosystems and generates the proton gradient (ΔpH). In the second route, driven solely by PSI, electrons can be recycled from either reduced ferredoxin or NADPH to plastoquinone, and subsequently to the cytochrome b6f complex2,3,4,5. Such cyclic flow generates ΔpH and thus ATP without the accumulation of reduced species. Whereas linear flow from water to NADP+ is commonly used to explain the function of the light-dependent reactions of photosynthesis, the role of cyclic flow is less clear. In higher plants cyclic flow consists of two partially redundant pathways. Here we have constructed mutants in Arabidopsis thaliana in which both PSI cyclic pathways are impaired, and present evidence that cyclic flow is essential for efficient photosynthesis.

Crucial role of FOXP3 in the development and function of human CD25+CD4+ regulatory T cells

Abstract: Naturally occurring CD25 1 CD4 1 regulatory T cells are engaged in the maintenance of immunological self-tolerance and down-regulation of various immune responses. Recent studies with mice showed that Foxp3, which encodes the transcription factor Scurfin, is a master regulatory gene for the development and function of CD25 1 CD4 1 regulatory T cells. Here we examined the role of FOXP3 in human CD25 1 CD4 1 regulatory T cells. The FOXP3 gene and its protein product were preferentially expressed in peripheral CD25 1 CD4 1 T cells, in particular CD25 1 CD45RO 1 CD4 1 T cells in normal individuals and, interestingly, in some human T cell leukemia virus type 1-infected T cell lines, which

PD-L1/B7H-1 Inhibits the Effector Phase of Tumor Rejection by T Cell Receptor (TCR) Transgenic CD8+ T Cells

Abstract: Although increased circulating tumor antigen-specific CD8+ T cells can be achieved by vaccination or adoptive transfer, tumor progression nonetheless often occurs through resistance to effector function. To develop a model for identifying mechanisms of resistance to antigen-specific CTLs, poorly immunogenic B16-F10 melanoma was transduced to express the Kb-binding peptide SIYRYYGL as a green fluorescent protein fusion protein that should be recognized by high-affinity 2C TCR transgenic T cells. Although B16.SIY cells expressed high levels of antigen and were induced to express Kb in response to IFN-γ, they were poorly recognized by primed 2C/RAG2−/− T cells. A screen for candidate inhibitory ligands revealed elevated PD-L1/B7H-1 on IFN-γ-treated B16-F10 cells and also on eight additional mouse tumors and seven human melanoma cell lines. Primed 2C/RAG2−/−/PD-1−/− T cells showed augmented cytokine production, proliferation, and cytolytic activity against tumor cells compared with wild-type 2C cells. This effect was reproduced with anti-PD-L1 antibody present during the effector phase but not during the priming culture. Adoptive transfer of 2C/RAG2−/−/PD-1−/− T cells in vivo caused tumor rejection under conditions in which wild-type 2C cells or CTLA-4-deficient 2C cells did not reject. Our results support interfering with PD-L1/PD-1 interactions to augment the effector function of tumor antigen-specific CD8+ T cells in the tumor microenvironment.

Health-related quality of life associated with chronic conditions in eight countries: results from the International Quality of Life Assessment (IQOLA) Project.

Abstract: Context: Few studies and no international comparisons have examined the impact of multiple chronic conditions on populations using a comprehensive health-related quality of life (HRQL) questionnaire Objective: The impact of common chronic conditions on HRQL among the general populations of eight countries was assessed Design: Cross-sectional mail and interview surveys were conducted Participants and setting: Sample representatives of the adult general population of eight countries (Denmark, France, Germany, Italy, Japan, the Netherlands, Norway and the United States) were evaluated Sample sizes ranged from 2031 to 4084 Main outcome measures: Self-reported prevalence of chronic conditions (including allergies, arthritis, congestive heart failure, chronic lung disease, hypertension, diabetes, and ischemic heart disease), sociodemographic data and the SF-36 Health Survey were obtained The SF-36 scale and summary scores were estimated for individuals with and without selected chronic conditions and compared across countries using multivariate linear regression analyses Adjustments were made for age, gender, marital status, education and the mode of SF-36 administration Results: More than half (551%) of the pooled sample reported at least one chronic condition, and 302% had more than one Hypertension, allergies and arthritis were the most frequently reported conditions The effect of ischemic heart disease on many of the physical health scales was noteworthy, as was the impact of diabetes on general health, or arthritis on bodily pain scale scores Arthritis, chronic lung disease and congestive heart failure were the conditions with a higher impact on SF-36 physical summary score, whereas for hypertension and allergies, HRQL impact was low (comparing with a typical person without chronic conditions, deviation scores were around −4 points for the first group and −1 for the second) Differences between chronic conditions in terms of their impact on SF-36 mental summary score were low (deviation scores ranged between −1 and −2) Conclusions: Arthritis has the highest HRQL impact in the general population of the countries studied due to the combination of a high deviation score on physical scales and a high frequency Impact of chronic conditions on HRQL was similar roughly across countries, despite important variation in prevalence The use of HRQL measures such as the SF-36 should be useful to better characterize the global burden of disease

Gamma-Ray Burst Formation Rate Inferred from the Spectral Peak Energy-Peak Luminosity Relation

Abstract: We estimate a gamma-ray burst (GRB) formation rate based on the new relation between the spectral peak energy (Ep) and the peak luminosity. The new relation is derived by combining the data of Ep and the peak luminosities by BeppoSAX and BATSE, and it looks considerably tighter and more reliable than the relations suggested by the previous works. Using the new Ep-luminosity relation, we estimate redshifts of the 689 GRBs without known distances in the BATSE catalog and derive a GRB formation rate as a function of the redshift. For the redshift range of 0 ≤ z ≤ 2, the GRB formation rate increases and is well correlated with the star formation rate, while it keeps constant toward z ~ 12. We also discuss the luminosity function and the redshift dependence of the intrinsic luminosity (luminosity evolution).

Germinal center dark and light zone organization is mediated by CXCR4 and CXCR5.

Abstract: Germinal center (GC) dark and light zones segregate cells undergoing somatic hypermutation and antigen-driven selection, respectively, yet the factors guiding this organization are unknown. We report here that GC organization was absent from mice deficient in the chemokine receptor CXCR4. Centroblasts had high expression of CXCR4 and GC B cells migrated toward the CXCR4 ligand SDF-1 (CXCL12), which was more abundant in the dark zone than in the light zone. CXCR4-deficient cells were excluded from the dark zone in the context of a wild-type GC. These findings establish that GC organization depends on sorting of centroblasts by CXCR4 into the dark zone. In contrast, CXCR5 helped direct cells to the light zone and deficiency in CXCL13 was associated with aberrant light zone localization.

Specific induction of neuronal cells from bone marrow stromal cells and application for autologous transplantation

Abstract: Bone marrow stromal cells (MSCs) have the capability under specific conditions of differentiating into various cell types such as osteocytes, chondrocytes, and adipocytes. Here we demonstrate a highly efficient and specific induction of cells with neuronal characteristics, without glial differentiation, from both rat and human MSCs using gene transfection with Notch intracellular domain (NICD) and subsequent treatment with bFGF, forskolin, and ciliary neurotrophic factor. MSCs expressed markers related to neural stem cells after transfection with NICD, and subsequent trophic factor administration induced neuronal cells. Some of them showed voltage-gated fast sodium and delayed rectifier potassium currents and action potentials compatible with characteristics of functional neurons. Further treatment of the induced neuronal cells with glial cell line-derived neurotrophic factor (GDNF) increased the proportion of tyrosine hydroxylase-positive and dopamine-producing cells. Transplantation of these GDNF-treated cells showed improvement in apomorphine-induced rotational behavior and adjusting step and paw-reaching tests following intrastriatal implantation in a 6-hydroxy dopamine rat model of Parkinson disease. This study shows that a population of neuronal cells can be specifically generated from MSCs and that induced cells may allow for a neuroreconstructive approach.

Interactions between Sox9 and β-catenin control chondrocyte differentiation

Abstract: Chondrogenesis is a multistep process that is essential for endochondral bone formation. Previous results have indicated a role for β-catenin and Wnt signaling in this pathway. Here we show the existence of physical and functional interactions between β-catenin and Sox9, a transcription factor that is required in successive steps of chondrogenesis. In vivo, either overexpression of Sox9 or inactivation of β-catenin in chondrocytes of mouse embryos produces a similar phenotype of dwarfism with decreased chondrocyte proliferation, delayed hypertrophic chondrocyte differentiation, and endochondral bone formation. Furthermore, either inactivation of Sox9 or stabilization of β-catenin in chondrocytes also produces a similar phenotype of severe chondrodysplasia. Sox9 markedly inhibits activation of β-catenin-dependent promoters and stimulates degradation of β-catenin by the ubiquitination/proteasome pathway. Likewise, Sox9 inhibits β-catenin-mediated secondary axis induction in Xenopus embryos. β-Catenin physically interacts through its Armadillo repeats with the C-terminal transactivation domain of Sox9. We hypothesize that the inhibitory activity of Sox9 is caused by its ability to compete with Tcf/Lef for binding to β-catenin, followed by degradation of β-catenin. Our results strongly suggest that chondrogenesis is controlled by interactions between Sox9 and the Wnt/β-catenin signaling pathway.

Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut

Abstract: The mechanism to maintain homeostasis of the gut microbiota remains largely unknown despite its critical role in the body defense. In the intestines of mice with deficiency of activation-induced cytidine deaminase (AID), the absence of hypermutated IgA is partially compensated for by the presence of large amounts of unmutated IgM and normal expression levels of defensins and angiogenins. We show here a predominant and persistent expansion of segmented filamentous bacteria throughout the small intestine of AID–/– mice. Reconstitution of lamina propria IgA production in AID–/– mice recovered the normal composition of gut flora and abolished the local and systemic activation of the immune system. The results indicate that secretions of IgAs rather than innate defense peptides are critical to regulation of commensal bacterial flora and that the segmented filamentous bacteria antigens are strong stimuli of the mucosal immune system.

XBP1: a link between the unfolded protein response, lipid biosynthesis, and biogenesis of the endoplasmic reticulum

Abstract: When the protein folding capacity of the endoplasmic reticulum (ER) is challenged, the unfolded protein response (UPR) maintains ER homeostasis by regulating protein synthesis and enhancing expression of resident ER proteins that facilitate protein maturation and degradation. Here, we report that enforced expression of XBP1(S), the active form of the XBP1 transcription factor generated by UPR-mediated splicing of XBP1 mRNA, is sufficient to induce synthesis of phosphatidylcholine, the primary phospholipid of the ER membrane. Cells overexpressing XBP1(S) exhibit elevated levels of membrane phospholipids, increased surface area and volume of rough ER, and enhanced activity of the cytidine diphosphocholine pathway of phosphatidylcholine biosynthesis. These data suggest that XBP1(S) links the mammalian UPR to phospholipid biosynthesis and ER biogenesis.

Identified charged particle spectra and yields in Au + Au collisions at √sNN = 200 GeV

Abstract: The centrality dependence of transverse momentum distributions and yields for ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}},{K}^{\ifmmode\pm\else\textpm\fi{}},p$, and $\overline{p}$ in $\text{Au}+\text{Au}$ collisions at $\sqrt{{s}_{NN}}=200\phantom{\rule{0.3em}{0ex}}\text{GeV}$ at midrapidity are measured by the PHENIX experiment at the Relativistic Heavy Ion Collider. We observe a clear particle mass dependence of the shapes of transverse momentum spectra in central collisions below $\ensuremath{\sim}2\phantom{\rule{0.3em}{0ex}}\text{GeV}∕c$ in ${p}_{T}$. Both mean transverse momenta and particle yields per participant pair increase from peripheral to midcentral and saturate at the most central collisions for all particle species. We also measure particle ratios of ${\ensuremath{\pi}}^{\ensuremath{-}}∕{\ensuremath{\pi}}^{+}$, ${K}^{\ensuremath{-}}∕{K}^{+}$, $\overline{p}∕p$, $K∕\ensuremath{\pi}$, $p∕\ensuremath{\pi}$, and $\overline{p}∕\ensuremath{\pi}$ as a function of ${p}_{T}$ and collision centrality. The ratios of equal mass particle yields are independent of ${p}_{T}$ and centrality within the experimental uncertainties. In central collisions at intermediate transverse momenta $\ensuremath{\sim}1.5--4.5\phantom{\rule{0.3em}{0ex}}\text{GeV}∕c$, proton and antiproton yields constitute a significant fraction of the charged hadron production and show a scaling behavior different from that of pions.

A plant vacuolar protease, VPE, mediates, virus-induced hypersensitive cell death

Abstract: Programmed cell death (PCD) in animals depends on caspase protease activity. Plants also exhibit PCD, for example as a response to pathogens, although a plant caspase remains elusive. Here we show that vacuolar processing enzyme (VPE) is a protease essential for a virus-induced hypersensitive response that involves PCD. VPE deficiency prevented virus-induced hypersensitive cell death in tobacco plants. VPE is structurally unrelated to caspases, although VPE has a caspase-1 activity. Thus, plants have evolved a regulated cellular suicide strategy that, unlike PCD of animals, is mediated by VPE and the cellular vacuole.