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Showing papers by "Osaka University published in 2003"


Journal ArticleDOI
TL;DR: This unit discusses mammalian Toll receptors (TLR1‐10) that have an essential role in the innate immune recognition of microorganisms and are discussed are TLR‐mediated signaling pathways and antibodies that are available to detect specific TLRs.
Abstract: The innate immune system in drosophila and mammals senses the invasion of microorganisms using the family of Toll receptors, stimulation of which initiates a range of host defense mechanisms. In drosophila antimicrobial responses rely on two signaling pathways: the Toll pathway and the IMD pathway. In mammals there are at least 10 members of the Toll-like receptor (TLR) family that recognize specific components conserved among microorganisms. Activation of the TLRs leads not only to the induction of inflammatory responses but also to the development of antigen-specific adaptive immunity. The TLR-induced inflammatory response is dependent on a common signaling pathway that is mediated by the adaptor molecule MyD88. However, there is evidence for additional pathways that mediate TLR ligand-specific biological responses.

5,915 citations


Journal ArticleDOI
01 Aug 2003-Science
TL;DR: It is shown that TRIF is essential for TLR3- and TLR4-mediated signaling pathways facilitating mammalian antiviral host defense and complete loss of nuclear factor kappa B activation in response toTLR4 stimulation is demonstrated.
Abstract: Stimulation of Toll-like receptors (TLRs) triggers activation of a common MyD88-dependent signaling pathway as well as a MyD88-independent pathway that is unique to TLR3 and TLR4 signaling pathways leading to interferon (IFN)-beta production. Here we disrupted the gene encoding a Toll/IL-1 receptor (TIR) domain-containing adaptor, TRIF. TRIF-deficient mice were defective in both TLR3- and TLR4-mediated expression of IFN-beta and activation of IRF-3. Furthermore, inflammatory cytokine production in response to the TLR4 ligand, but not to other TLR ligands, was severely impaired in TRIF-deficient macrophages. Mice deficient in both MyD88 and TRIF showed complete loss of nuclear factor kappa B activation in response to TLR4 stimulation. These findings demonstrate that TRIF is essential for TLR3- and TLR4-mediated signaling pathways facilitating mammalian antiviral host defense.

2,969 citations


Journal ArticleDOI
TL;DR: The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform, and provides a mechanism to ensure consistent data for software developers and users worldwide.
Abstract: mentation will be kept publicly available and the distribution sites will mirror the PDB archive using identical contents and subdirectory structure. However, each member of the wwPDB will be able to develop its own web site, with a unique view of the primary data, providing a variety of tools and resources for the global community. An Advisory Board consisting of appointees from the wwPDB, the International Union of Crystallography and the International Council on Magnetic Resonance in Biological Systems will provide guidance through annual meetings with the wwPDB consortium. This board is responsible for reviewing and determining policy as well as providing a forum for resolving issues related to the wwPDB. Specific details about the Advisory Board can be found in the wwPDB charter, available on the wwPDB web site. The RCSB is the ‘archive keeper’ of wwPDB. It has sole write access to the PDB archive and control over directory structure and contents, as well as responsibility for distributing new PDB identifiers to all deposition sites. The PDB archive is a collection of flat files in the legacy PDB file format 3 and in the mmCIF 4 format that follows the PDB exchange dictionary (http://deposit.pdb.org/ mmcif/). This dictionary describes the syntax and semantics of PDB data that are processed and exchanged during the process of data annotation. It was designed to provide consistency in data produced in structure laboratories, processed by the wwPDB members and used in bioinformatics applications. The PDB archive does not include the websites, browsers, software and database query engines developed by researchers worldwide. The members of the wwPDB will jointly agree to any modifications or extensions to the PDB exchange dictionary. As data technology progresses, other data formats (such as XML) and delivery methods may be included in the official PDB archive if all the wwPDB members concur on the alteration. Any new formats will follow the naming and description conventions of the PDB exchange dictionary. In addition, the legacy PDB format would not be modified unless there is a compelling reason for a change. Should such a situation occur, all three wwPDB members would have to agree on the changes and give the structural biology community 90 days advance notice. The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform. It provides a mechanism to ensure consistent data for software developers and users worldwide. We hope that this will encourage individual creativity in developing tools for presenting structural data, which could benefit the scientific research community in general.

2,431 citations


Journal ArticleDOI
Shizuo Akira1
TL;DR: Current understanding of the TLR signaling pathways is reviewed, which shows that individual TLRs can activate overlapping as well as distinct signaling pathways, ultimately giving rise to distinct biological effects.

1,806 citations


Journal ArticleDOI
TL;DR: NOD2 mediates the host response to bacterial muropeptides derived from peptidoglycan, an activity that is important for protection against Crohn's disease and has implications for understanding adjuvant function and effective vaccine development.

1,652 citations


Journal ArticleDOI
TL;DR: This report examines how dectin-1, a lectin family receptor for β-glucans, collaborates with TLRs in recognizing microbes and demonstrates that collaborative recognition of distinct microbial components by different classes of innate immune receptors is crucial in orchestrating inflammatory responses.
Abstract: Toll-like receptors (TLRs) mediate recognition of a wide range of microbial products including lipopolysaccharides, lipoproteins, flagellin, and bacterial DNA, and signaling through TLRs leads to the production of inflammatory mediators. In addition to TLRs, many other surface receptors have been proposed to participate in innate immunity and microbial recognition, and signaling through some of these receptors is likely to cooperate with TLR signaling in defining inflammatory responses. In this report we have examined how dectin-1, a lectin family receptor for β-glucans, collaborates with TLRs in recognizing microbes. Dectin-1, which is expressed at low levels on macrophages and high levels on dendritic cells, contains an immunoreceptor tyrosine-based activation motif–like signaling motif that is tyrosine phosphorylated upon activation. The receptor is recruited to phagosomes containing zymosan particles but not to phagosomes containing immunoglobulin G–opsonized particles. Dectin-1 expression enhances TLR-mediated activation of nuclear factor κB by β-glucan–containing particles, and in macrophages and dendritic cells dectin-1 and TLRs are synergistic in mediating production of cytokines such as interleukin 12 and tumor necrosis factor α. Additionally, dectin-1 triggers production of reactive oxygen species, an inflammatory response that is primed by TLR activation. The data demonstrate that collaborative recognition of distinct microbial components by different classes of innate immune receptors is crucial in orchestrating inflammatory responses.

1,565 citations


Journal ArticleDOI
TL;DR: Male patients with hypoadiponectinemia had a significant 2-fold increase in CAD prevalence, independent of well-known CAD risk factors.
Abstract: Background— Adiponectin is an adipocyte-derived plasma protein that accumulates in the injured artery and has potential antiatherogenic properties. This study was designed to determine whether a decreased plasma adiponectin level (hypoadiponectinemia) can be independently associated with the prevalence of coronary artery disease (CAD). Methods and Results— The consecutive 225 male patients were enrolled from inpatients who underwent coronary angiography. Voluntary blood donors (n=225) matched for age served as controls. Plasma adiponectin levels in the CAD patients were significantly lower than those in the control subjects. Multiple logistic regression analysis including plasma adiponectin level, diabetes mellitus, dyslipidemia, hypertension, smoking habits, and body mass index revealed that hypoadiponectinemia was significantly and independently correlated with CAD ( P Conclusions— Male patients with hypoadiponectinemia (

1,379 citations


Journal ArticleDOI
Suyong Choi1, S. L. Olsen, Kazuo Abe, T. Abe  +172 moreInstitutions (46)
TL;DR: In this article, a narrow charmonium-like state produced in the exclusive decay process B+/--->K+/-pi(+)pi(-)J/psi has been observed, which has a mass of 3872.0+/-0.6(stat)+/- 0.5(syst) MeV.
Abstract: We report the observation of a narrow charmoniumlike state produced in the exclusive decay process B+/--->K+/-pi(+)pi(-)J/psi. This state, which decays into pi(+)pi(-)J/psi, has a mass of 3872.0+/-0.6(stat)+/-0.5(syst) MeV, a value that is very near the M(D0)+M(D(*0)) mass threshold. The results are based on an analysis of 152M B-Bmacr; events collected at the Upsilon(4S) resonance in the Belle detector at the KEKB collider. The signal has a statistical significance that is in excess of 10sigma.

1,294 citations


Journal ArticleDOI
TL;DR: It is reported that NOD1 mediates selective recognition of bacteria through detection of iE-DAP-containing peptidoglycan derived primarily from Gram-negative bacteria.
Abstract: Nucleotide-binding oligomerization domain protein 1 (NOD1) belongs to a family that includes multiple members with NOD and leucine-rich repeats in vertebrates and plants. NOD1 has been suggested to have a role in innate immune responses, but the mechanism involved remains unknown. Here we report that NOD1 mediates the recognition of peptidoglycan derived primarily from Gram-negative bacteria. Biochemical and functional analyses using highly purified and synthetic compounds indicate that the core structure recognized by NOD1 is a dipeptide, γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP). Murine macrophages deficient in NOD1 did not secrete cytokines in response to synthetic iE-DAP and did not prime the lipopolysaccharide response. Thus, NOD1 mediates selective recognition of bacteria through detection of iE-DAP-containing peptidoglycan. *Note: In the version of this article initially published online, one author's first name and last name were reversed. The correct author name should be Su Qiu. This mistake has been corrected for the HTML and print versions of the article.

1,267 citations


Journal ArticleDOI
TL;DR: A map of GFP distribution in the knock‐in mouse brain is constructed and many medium‐sized spherical somata emitting intense GFP fluorescence were observed in layer I, in accord with unidentified GFP‐positive cells.
Abstract: Gamma-aminobutyric acid (GABA)ergic neurons in the central nervous system regulate the activity of other neurons and play a crucial role in information processing. To assist an advance in the research of GABAergic neurons, here we produced two lines of glutamic acid decarboxylase-green fluorescence protein (GAD67-GFP) knock-in mouse. The distribution pattern of GFP-positive somata was the same as that of the GAD67 in situ hybridization signal in the central nervous system. We encountered neither any apparent ectopic GFP expression in GAD67-negative cells nor any apparent lack of GFP expression in GAD67-positive neurons in the two GAD67-GFP knock-in mouse lines. The timing of GFP expression also paralleled that of GAD67 expression. Hence, we constructed a map of GFP distribution in the knock-in mouse brain. Moreover, we used the knock-in mice to investigate the colocalization of GFP with NeuN, calretinin (CR), parvalbumin (PV), and somatostatin (SS) in the frontal motor cortex. The proportion of GFP-positive cells among NeuN-positive cells (neocortical neurons) was approximately 19.5%. All the CR-, PV-, and SS-positive cells appeared positive for GFP. The CR-, PV, and SS-positive cells emitted GFP fluorescence at various intensities characteristics to them. The proportions of CR-, PV-, and SS-positive cells among GFP-positive cells were 13.9%, 40.1%, and 23.4%, respectively. Thus, the three subtypes of GABAergic neurons accounted for 77.4% of the GFP-positive cells. They accounted for 6.5% in layer I. In accord with unidentified GFP-positive cells, many medium-sized spherical somata emitting intense GFP fluorescence were observed in layer I.

1,214 citations


Journal ArticleDOI
TL;DR: A novel mechanism whereby the genomic DNA of a virus can engage TLR9 and result in the secretion of IFN-α by pDCs is demonstrated.
Abstract: Plasmacytoid dendritic cells (pDCs) have been identified as a potent secretor of the type I interferons (IFNs) in response to CpG as well as several viruses. In this study, we examined the molecular mechanism of virus recognition by pDCs. First, we demonstrated that the CD11c+Gr-1intB220+ pDCs from mouse bone marrow secreted high levels of IFN-α in response to either live or UV-inactivated Herpes simplex virus-2 (HSV-2). Next, we identified that IFN-α secretion by pDCs required the expression of the adaptor molecule MyD88, suggesting the involvement of a Toll-like receptor (TLR) in HSV-2 recognition. To test whether a TLR mediates HSV-2–induced IFN-α secretion from pDCs, various knockout mice were examined. These experiments revealed a clear requirement for TLR9 in this process. Further, we demonstrated that purified HSV-2 DNA can trigger IFN-α secretion from pDCs and that inhibitory CpG oligonucleotide treatment diminished HSV-induced IFN-α secretion by pDCs in a dose-dependent manner. The recognition of HSV-2 by TLR9 was mediated through an endocytic pathway that was inhibited by chloroquine or bafilomycin A1. The strict requirement for TLR9 in IFN-α secretion was further confirmed by the inoculation of HSV-2 in vivo. Therefore, these results demonstrate a novel mechanism whereby the genomic DNA of a virus can engage TLR9 and result in the secretion of IFN-α by pDCs.

Journal ArticleDOI
TL;DR: Results indicate that TLR3, TLR7 and TLR9 may play an important role in detecting and combating viral infections.

Journal ArticleDOI
TL;DR: TRAM provides specificity for the MyD88-independent component of TLR4 signaling, and is identified as a fourth TIR domain–containing adaptor, TRIF-related adaptor molecule (TRAM), and analyzed its physiological function by gene targeting.
Abstract: Recognition of pathogens by Toll-like receptors (TLRs) triggers innate immune responses through signaling pathways mediated by Toll–interleukin 1 receptor (TIR) domain–containing adaptors such as MyD88, TIRAP and TRIF. MyD88 is a common adaptor that is essential for proinflammatory cytokine production, whereas TRIF mediates the MyD88-independent pathway from TLR3 and TLR4. Here we have identified a fourth TIR domain–containing adaptor, TRIF-related adaptor molecule (TRAM), and analyzed its physiological function by gene targeting. TRAM-deficient mice showed defects in cytokine production in response to the TLR4 ligand, but not to other TLR ligands. TLR4- but not TLR3-mediated MyD88-independent interferon-β production and activation of signaling cascades were abolished in TRAM-deficient cells. Thus, TRAM provides specificity for the MyD88-independent component of TLR4 signaling.

Journal ArticleDOI
TL;DR: This finding explains clinical features of V parahaemolyticus infections, which commonly include inflammatory diarrhoea and in some cases systemic manifestations such as septicaemia, distinct from those of V cholerae infections,Which are generally associated with non-inflammatory diarrhoeA.

Journal ArticleDOI
TL;DR: In this paper, a review of the results of these research activities with respect to the catalytic use of unreactive CH bonds in organic synthesis can be found, as well as a survey of catalytic reactions involving carbon-hydrogen bond cleavage.
Abstract: The development of catalytic reactions involving carbon-hydrogen bond cleavage is currently one of the most attractive research subjects in organic and organometallic chemistry. About 40 years have past since the pioneering report of the cleavage of CH bonds with transition metal complexes. Since that time, a vast number of studies of the cleavage of CH bonds, using stoichiometric amounts of transition metal complexes has appeared. In the last decade, a variety of catalytic reactions involving CH bond cleavage has been reported. In this review we briefly survey the results of these research activities with respect to the catalytic use of unreactive CH bonds in organic synthesis.

Journal ArticleDOI
TL;DR: The reciprocal association of adiponectin and CRP levels in both human plasma and adipose tissue might participate in the development of atherosclerosis.
Abstract: Background— High-sensitive C-reactive protein (hs-CRP) is a well-known risk factor for coronary artery disease (CAD). Recently, we have demonstrated that adiponectin served as an antiatherogenic plasma protein which was secreted specifically from adipocytes. The present study investigated the association between adiponectin and CRP in the blood stream and adipose tissue. Methods and Results— We studied a total of 101 male patients, 71 of whom had angiographically documented coronary atherosclerosis. As a control group, 30 patients with normal coronary angiogram were included. The plasma hs-CRP levels were negatively correlated with the plasma adiponectin levels ( r =−0.29, P r =−0.89, P Conclusions— The reciprocal association of adiponectin and CRP levels in both human plasma and adipose tissue might participate in the development of atherosclerosis.

Journal ArticleDOI
TL;DR: GPC3 is specifically overexpressed in most HCCs and is elevated in the serum of a large proportion of patients with HCC, suggesting that the simultaneous determination of GPC3 and AFP may significantly increase the sensitivity for diagnosis of HCC.

Journal ArticleDOI
TL;DR: Analysis of rat L6 myotubes treated with the PPARδ subtype-selective agonist, GW501516, by the Affymetrix oligonucleotide microarrays revealed that PPAR Δ is pivotal to control the program for fatty acid oxidation in the skeletal muscle, thereby ameliorating obesity and insulin resistance through its activation in obese animals.
Abstract: In this study, we defined the role of peroxisome proliferator-activated receptor beta/delta (PPARdelta) in metabolic homeostasis by using subtype selective agonists. Analysis of rat L6 myotubes treated with the PPARdelta subtype-selective agonist, GW501516, by the Affymetrix oligonucleotide microarrays revealed that PPARdelta controls fatty acid oxidation by regulating genes involved in fatty acid transport, beta-oxidation, and mitochondrial respiration. Similar PPARdelta-mediated gene activation was observed in the skeletal muscle of GW501516-treated mice. Accordingly, GW501516 treatment induced fatty acid beta-oxidation in L6 myotubes as well as in mouse skeletal muscles. Administration of GW501516 to mice fed a high-fat diet ameliorated diet-induced obesity and insulin resistance, an effect accompanied by enhanced metabolic rate and fatty acid beta-oxidation, proliferation of mitochondria, and a marked reduction of lipid droplets in skeletal muscles. Despite a modest body weight change relative to vehicle-treated mice, GW501516 treatment also markedly improved diabetes as revealed by the decrease in plasma glucose and blood insulin levels in genetically obese ob/ob mice. These data suggest that PPARdelta is pivotal to control the program for fatty acid oxidation in the skeletal muscle, thereby ameliorating obesity and insulin resistance through its activation in obese animals.

Journal ArticleDOI
TL;DR: SOCS3 selectively blocks signaling by IL-6, thereby preventing its ability to inhibit LPS signaling, and is shown to be a key regulator of the divergent action of these two cytokines.
Abstract: Whereas interleukin-6 (IL-6) is a proinflammatory cytokine, IL-10 is an anti-inflammatory cytokine. Although signal transducer and activator of transcription 3 (STAT3) is essential for the function of both IL-6 and IL-10, it is unclear how these two cytokines have such opposing functions. Here we show that suppressor of cytokine signaling 3 (SOCS3) is a key regulator of the divergent action of these two cytokines. In macrophages lacking the Socs3 gene or carrying a mutation of the SOCS3-binding site in gp130, the lipopolysaccharide-induced production of tumor necrosis factor (TNF) and IL-12 is suppressed by both IL-10 and IL-6. SOCS3 specifically prevents activation of STAT3 by IL-6 but not IL-10. Taken together, these data indicate that SOCS3 selectively blocks signaling by IL-6, thereby preventing its ability to inhibit LPS signaling.

Journal ArticleDOI
01 Jul 2003-Diabetes
TL;DR: The results indicate that PPAR-gamma and LRH-1 play significant roles in the transcriptional activation of adiponectin gene via the PPRE and theLRH-RE in its promoter.
Abstract: Adiponectin is a fat-derived hormone with antidiabetic and antiatherogenic properties. Hypoadiponectinemia seen in obesity is associated with insulin-resistant diabetes and atherosclerosis. Thiazolidinediones, peroxisome proliferator-activated receptor-gamma (PPAR-gamma) agonists, have been shown to increase plasma adiponectin levels by the transcriptional induction in adipose tissues. However, the precise mechanism of such action is unknown. In this study, we have identified a functional PPAR-responsive element (PPRE) in human adiponectin promoter. PPAR-gamma/retinoid X receptor (RXR) heterodimer directly bound to the PPRE and increased the promoter activity in cells. In adipocytes, point mutation of the PPRE markedly reduced the basal transcriptional activity and completely blocked thiazolidinedione-induced transactivation of adiponectin promoter. We have also identified a responsive element of another orphan nuclear receptor, liver receptor homolog-1 (LRH-1), in adiponectin promoter. LRH-1 was expressed in 3T3-L1 cells and rat adipocytes. LRH-1 bound specifically to the identified responsive element (LRH-RE). LRH-1 augmented PPAR-gamma-induced transactivation of adiponectin promoter, and point mutation of the LRH-RE significantly decreased the basal and thiazolidinedione-induced activities of adiponectin promoter. Our results indicate that PPAR-gamma and LRH-1 play significant roles in the transcriptional activation of adiponectin gene via the PPRE and the LRH-RE in its promoter.

Journal ArticleDOI
TL;DR: It is demonstrated that TRIF associates with TRAF6 and TBK1 independently, and activates two distinct transcription factors, NF-κB and IFN regulatory factor-3, respectively.
Abstract: We previously reported a new Toll/IL-1R (TIR)-containing molecule, named TIR domain-containing adaptor inducing IFN-β (TRIF). Although initial study indicated that TRIF possesses the ability to activate not only the NF-κB-dependent but also the IFN-β promoters, the molecular mechanisms of TRIF-induced signaling are poorly understood. In this study, we investigated the signaling cascades through TRIF. TNF receptor-associated factor (TRAF)6 interacted with TRIF through the TRAF domain of TRAF6 and TRAF6-binding motifs found in the N-terminal portion of TRIF. Disruption of TRAF6-binding motifs of TRIF disabled it from associating with TRAF6, and resulted in a reduction in the TRIF-induced activation of the NF-κB-dependent but not IFN-β promoter. TANK-binding kinase (TBK)-1, which was recently reported to be a kinase of IFN regulatory factor-3, which is an essential transcription factor for IFN-β expression, also associated with the N-terminal region of TRIF. Moreover, the association between TRIF and TBK1 appeared to require the kinase activity of TBK1, as well as phosphorylation of TRIF. Because TRAF6 and TBK1 bind close the region of TRIF, it seems that TRAF6 physically prevents the association between TRIF and TBK1. Taken together, these results demonstrate that TRIF associates with TRAF6 and TBK1 independently, and activates two distinct transcription factors, NF-κB and IFN regulatory factor-3, respectively.

Journal ArticleDOI
TL;DR: Adiponectin is an endogenous biologically relevant modulator of vascular remodeling linking obesity and vascular disease, and acts as an anti-inflammatory and anti-atherogenic plasma protein.
Abstract: Purpose of review Obesity is the most common risk factor for cardiovascular diseases in industrial countries. It is now clear that adipose tissue secretes various bioactive substances, conceptualized as adipocytokines, and that dysregulation of adipocytokines directly contributes to obesity-related diseases. Chronic inflammatory processes contribute to the development of atherosclerosis. In this review, the authors focus on the relationship between adiponectin, a recently discovered anti-atherogenic adipocytokine, and vascular inflammation. Recent findings Plasma concentrations of adiponectin, an adipocyte-specific protein, are reduced in obese subjects and in patients with type 2 diabetes and coronary artery disease. Adiponectin inhibits the expression of tumor necrosis factor-alpha-induced endothelial adhesion molecules, macrophage-to-foam cell transformation, tumor necrosis factor-alpha expression in macrophages and adipose tissues, and smooth muscle cell proliferation. In addition, adenovirus-expressed adiponectin reduces atherosclerotic lesions in a mouse model of atherosclerosis, and adiponectin-deficient mice exhibit an excessive vascular remodeling response to injury. Clinically, hypoadiponectinemia is closely associated with increased levels of inflammatory markers such as C-reactive protein and interleukin-6. Summary Adiponectin acts as an anti-inflammatory and anti-atherogenic plasma protein. Adiponectin is an endogenous biologically relevant modulator of vascular remodeling linking obesity and vascular disease.

Journal ArticleDOI
07 Nov 2003-Science
TL;DR: The dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quin one-analog inhibitor, and a novel heme are bound.
Abstract: The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.

Journal ArticleDOI
TL;DR: It is demonstrated that the mouse Apg12-Apg5 conjugate forms a ∼800 kDa protein complex containing a novel WD-repeat protein, which is concluded to be the functional counterpart of the yeast Apg16.
Abstract: Macroautophagy is the major intracellular degradation system delivering cytoplasmic components to the lysosome/vacuole. We have shown that, in yeast and mammalian cells, the Apg12-Apg5 protein conjugate, which is formed by a ubiquitin-like system, is essential for autophagosome formation. In yeast, the Apg12-Apg5 conjugate interacts with a small coiled-coil protein, Apg16, to form a approximately 350 kDa multimeric complex. We demonstrate that the mouse Apg12-Apg5 conjugate forms a approximately 800 kDa protein complex containing a novel WD-repeat protein. Because the N-terminal region of this novel protein shows homology with yeast Apg16, we have designated it mouse Apg16-like protein (Apg16L). Apg16L, however, has a large C-terminal domain containing seven WD repeats that is absent from yeast Apg16. Apg16L interacts with both Apg5 and additional Apg16L monomers; neither interaction, however, depends on the WD-repeat domain. In conjunction with Apg12-Apg5, Apg16L associates with the autophagic isolation membrane for the duration of autophagosome formation. Because these features are similar to yeast Apg16, we concluded Apg16L is the functional counterpart of the yeast Apg16. We also found that membrane targeting of Apg16L requires Apg5 but not Apg12. Because WD-repeat proteins provide a platform for protein-protein interactions, the approximately 800 kDa complex is expected to function in autophagosome formation, further interacting with other proteins in mammalian cells.

Journal ArticleDOI
02 May 2003-Cell
TL;DR: It is shown that DDB2 and CSA are each integrated into nearly identical complexes via interaction with DDB1, suggesting that the distinct UV response of the DDB-CSA complexes is involved in diverse mechanisms of NER.

Journal ArticleDOI
07 Aug 2003-Nature
TL;DR: A complete atomic model of the R-type filament by electron cryomicroscopy reveals intricate molecular packing and an α-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament.
Abstract: The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in two distinct conformations, L- and R-type, for supercoiling. The X-ray crystal structure of a flagellin fragment lacking about 100 terminal residues revealed the protofilament structure, but the full filament structure is still essential for understanding the mechanism of supercoiling and polymerization. Here we report a complete atomic model of the R-type filament by electron cryomicroscopy. A density map obtained from image data up to 4 A resolution shows the feature of α-helical backbone and some large side chains. The atomic model built on the map reveals intricate molecular packing and an α-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament.

Journal ArticleDOI
S. Fukuda1, Y. Fukuda1, T. Hayakawa1, E. Ichihara1  +183 moreInstitutions (28)
TL;DR: Super-Kamiokande is the world's largest water Cherenkov detector, with net mass 50,000 tons as discussed by the authors, which collected 1678 live-days of data, observing neutrinos from the Sun, Earth's atmosphere, and the K2K long-baseline neutrino beam with high efficiency.
Abstract: Super-Kamiokande is the world's largest water Cherenkov detector, with net mass 50,000 tons. During the period April, 1996 to July, 2001, Super-Kamiokande I collected 1678 live-days of data, observing neutrinos from the Sun, Earth's atmosphere, and the K2K long-baseline neutrino beam with high efficiency. These data provided crucial information for our current understanding of neutrino oscillations, as well as setting stringent limits on nucleon decay. In this paper, we describe the detector in detail, including its site, configuration, data acquisition equipment, online and offline software, and calibration systems which were used during Super-Kamiokande I.

Journal ArticleDOI
TL;DR: The gain-of-function mutations of PDGFR alpha appear to play an important role in development of GISTs without KIT mutations.

Journal ArticleDOI
TL;DR: The gamman-->K(+)K(-)n reaction on 12C has been studied by measuring both K+ and K- at forward angles and a sharp baryon resonance peak was observed, consistent with an antidecuplet of baryons predicted by the chiral soliton model.
Abstract: The $\ensuremath{\gamma}n\ensuremath{\rightarrow}{K}^{+}{K}^{\ensuremath{-}}n$ reaction on $^{12}\mathrm{C}$ has been studied by measuring both ${K}^{+}$ and ${K}^{\ensuremath{-}}$ at forward angles. A sharp baryon resonance peak was observed at $1.54\ifmmode\pm\else\textpm\fi{}0.01\text{ }\text{ }\mathrm{G}\mathrm{e}\mathrm{V}/{c}^{2}$ with a width smaller than $25\text{ }\text{ }\mathrm{M}\mathrm{e}\mathrm{V}/{c}^{2}$ and a Gaussian significance of $4.6\ensuremath{\sigma}$. The strangeness quantum number ($S$) of the baryon resonance is $+1$. It can be interpreted as a molecular meson-baryon resonance or alternatively as an exotic five-quark state ($uudd\overline{s}$) that decays into a ${K}^{+}$ and a neutron. The resonance is consistent with the lowest member of an antidecuplet of baryons predicted by the chiral soliton model.

Book ChapterDOI
TL;DR: In this paper, a signal orchestration model was proposed to explain how IL-6 can elicit proinflammatory or anti-inflammatory effects, depending on the in vivo environmental circumstances, which can be seen as a consequence of the orchestration of diverse signaling pathways generated by a given ligand.
Abstract: Interleukin (IL)-6 is a pleiotropic cytokine that not only affects the immune system, but also acts in other biological systems and many physiological events in various organs. In a target cell, IL-6 can simultaneously generate functionally distinct or sometimes contradictory signals through its receptor complex, IL-6Rα and gp130. One good illustration is derived from the in vitro observations that IL-6 promotes the growth arrest and differentiation of M1 cells through gp130-mediated STAT3 activation, whereas the Y759/SHP-2-mediated cascade by gp130 stimulation has growth-enhancing effects. The final physiological output can be thought of as a consequence of the orchestration of the diverse signaling pathways generated by a given ligand. This concept, the signal orchestration model, may explain how IL-6 can elicit proinflammatory or anti-inflammatory effects, depending on the in vivo environmental circumstances. Elucidation of the molecular mechanisms underlying this issue is a challenging subject for future research. Intriguingly, recent in vivo studies indicated that the SHP-2-binding site- and YXXQ-mediated pathways through gp130 are not mutually exclusive but affect each other: a mutation at the SHP-2-binding site prolongs STAT3 activation, and a loss of STAT activation by gp130 truncation leads to sustained SHP-2/ERK MAPK phosphorylation. Although IL-6/gp130 signaling is a promising target for drug discovery for many human diseases, the interdependence of each signaling pathway may be an obstacle to the development of a nonpeptide orally active small molecule to inhibit one of these IL-6 signaling cascades, because it would disturb the signal orchestration. In mice, a consequence of the imbalanced signals causes unexpected results such as gastrointestinal disorders, autoimmune diseases, and/or chronic inflammatory proliferative diseases. However, lessons learned from IL-6 KO mice indicate that IL-6 is not essential for vital biological processes, but a significant impact on disease progression in many experimental models for human disorders. Thus, IL-6/gp130 signaling will become a more attractive therapeutic target for human inflammatory diseases when a better understanding of IL-6 signaling, including the identification of the conductor for gp130 signal transduction, is achieved.