Showing papers by "Kyoto University published in 2007"
TL;DR: It is demonstrated that iPS cells can be generated from adult human fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc.
18,175 citations
TL;DR: KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps, and the KEGG resource is being expanded to suit the needs for practical applications.
Abstract: KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.
5,352 citations
TL;DR: The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
Abstract: We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.
4,565 citations
TL;DR: iPS cells competent for germline chimaeras can be obtained from fibroblasts, but retroviral introduction of c-Myc should be avoided for clinical application.
Abstract: We have previously shown that pluripotent stem cells can be induced from mouse fibroblasts by retroviral introduction of Oct3/4 (also called Pou5f1), Sox2, c-Myc and Klf4, and subsequent selection for Fbx15 (also called Fbxo15) expression These induced pluripotent stem (iPS) cells (hereafter called Fbx15 iPS cells) are similar to embryonic stem (ES) cells in morphology, proliferation and teratoma formation; however, they are different with regards to gene expression and DNA methylation patterns, and fail to produce adult chimaeras Here we show that selection for Nanog expression results in germline-competent iPS cells with increased ES-cell-like gene expression and DNA methylation patterns compared with Fbx15 iPS cells The four transgenes (Oct3/4, Sox2, c-myc and Klf4) were strongly silenced in Nanog iPS cells We obtained adult chimaeras from seven Nanog iPS cell clones, with one clone being transmitted through the germ line to the next generation Approximately 20% of the offspring developed tumours attributable to reactivation of the c-myc transgene Thus, iPS cells competent for germline chimaeras can be obtained from fibroblasts, but retroviral introduction of c-Myc should be avoided for clinical application
4,371 citations
TL;DR: An implementation of a rapid method to automatically assign K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies and achieving a high degree of accuracy when compared with the manually curated K EGG GENES database.
Abstract: The number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate the identification of functional properties and biological roles of genes in these genomes. In the KEGG database, genes in complete genomes are annotated with the KEGG orthology (KO) identifiers, or the K numbers, based on the best hit information using Smith-Waterman scores as well as by the manual curation. Each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy. Here, we have developed a web-based server called KAAS (KEGG Automatic Annotation Server: http://www.genome.jp/kegg/kaas/) i.e. an implementation of a rapid method to automatically assign K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.
3,220 citations
Los Alamos National Laboratory1, University of Texas at Austin2, United States Department of Energy3, Argonne National Laboratory4, Oak Ridge National Laboratory5, Case Western Reserve University6, Virginia Tech7, Doshisha University8, University of Yamanashi9, Yokohama National University10, Kyoto University11, New Energy and Industrial Technology Development Organization12, Tokyo Institute of Technology13, National Institute of Advanced Industrial Science and Technology14
TL;DR: The research focuses on the durability of polymer electrolyte fuel cells (PEFCs), in particular, membrane degradation, and he has been involved in NEDO R&D research projects on PEFC durability since 2001.
Abstract: Rod Borup is a Team Leader in the fuel cell program at Los Alamos National Lab in Los Alamos, New Mexico. He received his B.S.E. in Chemical Engineering from the University of Iowa in 1988 and his Ph.D. from the University of Washington in 1993. He has worked on fuel cell technology since 1994, working in the areas of hydrogen production and PEM fuel cell stack components. He has been awarded 12 U.S. patents, authored over 40 papers related to fuel cell technology, and presented over 50 oral papers at national meetings. His current main research area is related to water transport in PEM fuel cells and PEM fuel cell durability. Recently, he was awarded the 2005 DOE Hydrogen Program R&D Award for the most significant R&D contribution of the year for his team's work in fuel cell durability and was the Principal Investigator for the 2004 Fuel Cell Seminar (San Antonio, TX, USA) Best Poster Award. Jeremy Meyers is an Assistant Professor of materials science and engineering and mechanical engineering at the University of Texas at Austin, where his research focuses on the development of electrochemical energy systems and materials. Prior to joining the faculty at Texas, Jeremy workedmore » as manager of the advanced transportation technology group at UTC Power, where he was responsible for developing new system designs and components for automotive PEM fuel cell power plants. While at UTC Power, Jeremy led several customer development projects and a DOE-sponsored investigation into novel catalysts and membranes for PEM fuel cells. Jeremy has coauthored several papers on key mechanisms of fuel cell degradation and is a co-inventor of several patents. In 2006, Jeremy and several colleagues received the George Mead Medal, UTC's highest award for engineering achievement, and he served as the co-chair of the Gordon Research Conference on fuel cells. Jeremy received his Ph.D. in Chemical Engineering from the University of California at Berkeley and holds a Bachelor's Degree in Chemical Engineering from Stanford University. Bryan Pivovar received his B.S. in Chemical Engineering from the University of Wisconsin in 1994. He completed his Ph.D. in Chemical Engineering at the University of Minnesota in 2000 under the direction of Profs. Ed Cussler and Bill Smyrl, studying transport properties in fuel cell electrolytes. He continued working in the area of polymer electrolyte fuel cells at Los Alamos National Laboratory as a post-doc (2000-2001), as a technical staff member (2001-2005), and in his current position as a team leader (2005-present). In this time, Bryan's research has expanded to include further aspects of fuel cell operation, including electrodes, subfreezing effects, alternative polymers, hydroxide conductors, fuel cell interfaces, impurities, water transport, and high-temperature membranes. Bryan has served at various levels in national and international conferences and workshops, including organizing a DOE sponsored workshop on freezing effects in fuel cells and an ARO sponsored workshop on alkaline membrane fuel cells, and he was co-chair of the 2007 Gordon Research Conference on Fuel Cells. Minoru Inaba is a Professor at the Department of Molecular Science and Technology, Faculty of Engineering, Doshisha University, Japan. He received his B.Sc. from the Faculty of Engineering, Kyoto University, in 1984 and his M.Sc. in 1986 and his Dr. Eng. in 1995 from the Graduate School of Engineering, Kyoto University. He has worked on electrochemical energy conversion systems including fuel cells and lithium-ion batteries at Kyoto University (1992-2002) and at Doshisha University (2002-present). His primary research interest is the durability of polymer electrolyte fuel cells (PEFCs), in particular, membrane degradation, and he has been involved in NEDO R&D research projects on PEFC durability since 2001. He has authored over 140 technical papers and 30 review articles. Kenichiro Ota is a Professor of the Chemical Energy Laboratory at the Graduate School of Engineering, Yokohama National University, Japan. He received his B.S.E. in Applied Chemistry from the University of Tokyo in 1968 and his Ph.D. from the University of Tokyo in 1973. He has worked on hydrogen energy and fuel cells since 1974, working on materials science for fuel cells and water electrolysis. He has published more than 150 original papers, 70 review papers, and 50 scientific books. He is now the president of the Hydrogen Energy Systems Society of Japan, the chairman of the Fuel Cell Research Group of the Electrochemical Society of Japan, and the chairman of the National Committee for the Standardization of the Stationary Fuel Cells. ABSTRACT TRUNCATED« less
2,921 citations
University of California, Los Angeles1, United States Department of Energy2, University of Paris3, Duke University4, University of Massachusetts Medical School5, University of California, Berkeley6, Centre national de la recherche scientifique7, University of California, San Francisco8, Sun Yat-sen University9, University of Tennessee Health Science Center10, University of Minnesota11, Iowa State University12, Genetic Information Research Institute13, Salk Institute for Biological Studies14, Stanford University15, University of Liège16, University of Nebraska–Lincoln17, University of Cambridge18, Washington University in St. Louis19, University of Córdoba (Spain)20, Kyoto University21, Carnegie Institution for Science22, National Autonomous University of Mexico23, University of Münster24, École Normale Supérieure25, University of Melbourne26, University of Paris-Sud27, University of Mainz28, Scripps Research Institute29, Ohio State University30, University of Chicago31, University of Jena32, University of Arizona33, Louisiana State University34, University of New Brunswick35, University College London36, University of Potsdam37, Delaware Biotechnology Institute38, Boyce Thompson Institute for Plant Research39, Macquarie University40, Oklahoma State University Center for Health Sciences41, İzmir University of Economics42, Academy of Sciences of the Czech Republic43, Charles University in Prague44, St. Edward's University45, University of Puget Sound46, Hokkaido University47, Tsinghua University48, Washington State University49, Appalachian State University50, Marquette University51
TL;DR: Analyses of the Chlamydomonas genome advance the understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
Abstract: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
2,554 citations
TL;DR: Testing the hypothesis that long-term use of eicosapentaenoic acid (EPA) is effective for prevention of major coronary events in hypercholesterolaemic patients in Japan who consume a large amount of fish found it to be a promising treatment.
2,269 citations
TL;DR: Application of a selective Rho-associated kinase (ROCK) inhibitor, Y-27632, to hES cells markedly diminishes dissociation-induced apoptosis, increases cloning efficiency and facilitates subcloning after gene transfer, and enables SFEB-cultured hES Cells to survive and differentiate into Bf1+ cortical and basal telencephalic progenitors.
Abstract: Poor survival of human embryonic stem (hES) cells after cell dissociation is an obstacle to research, hindering manipulations such as subcloning. Here we show that application of a selective Rho-associated kinase (ROCK) inhibitor1,2, Y-27632, to hES cells markedly diminishes dissociation-induced apoptosis, increases cloning efficiency (from ∼1% to ∼27%) and facilitates subcloning after gene transfer. Furthermore, dissociated hES cells treated with Y-27632 are protected from apoptosis even in serum-free suspension (SFEB) culture3 and form floating aggregates. We demonstrate that the protective ability of Y-27632 enables SFEB-cultured hES cells to survive and differentiate into Bf1+ cortical and basal telencephalic progenitors, as do SFEB-cultured mouse ES cells.
2,094 citations
TL;DR: In this paper, a covariant generalization of the holographic entanglement entropy proposal of hep-th/0603001 is proposed to understand the time-dependence of entropy in generic quantum field theories.
Abstract: With an aim towards understanding the time-dependence of entanglement entropy in generic quantum field theories, we propose a covariant generalization of the holographic entanglement entropy proposal of hep-th/0603001. Apart from providing several examples of possible covariant generalizations, we study a particular construction based on light-sheets, motivated in similar spirit to the covariant entropy bound underlying the holographic principle. In particular, we argue that the entanglement entropy associated with a specified region on the boundary in the context of the AdS/CFT correspondence is given by the area of a co-dimension two bulk surface with vanishing expansions of null geodesics. We demonstrate our construction with several examples to illustrate its reduction to the holographic entanglement entropy proposal in static spacetimes. We further show how this proposal may be used to understand the time evolution of entanglement entropy in a time varying QFT state dual to a collapsing black hole background. Finally, we use our proposal to argue that the Euclidean wormhole geometries with multiple boundaries should be regarded as states in a non-interacting but entangled set of QFTs, one associated to each boundary.
2,047 citations
Pardis C. Sabeti1, Pardis C. Sabeti2, Patrick Varilly2, Patrick Varilly1 +255 more•Institutions (50)
TL;DR: ‘Long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population are developed.
Abstract: With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.
TL;DR: Multivariate analysis showed the expression of PD-L1 on tumor cells and intraepithelial CD8+ T lymphocyte count are independent prognostic factors and the PD-1/PD-L pathway can be a good target for restoring antitumor immunity in ovarian cancer.
Abstract: The ligands for programmed cell death 1 (PD-1), an immunoinhibitory receptor belonging to CD28/cytotoxic T lymphocyte antigen 4 family, are PD-1 ligand 1 and 2 (PD-Ls) Recent reports suggest that the aberrant expression of PD-Ls on tumor cells impairs antitumor immunity, resulting in the immune evasion of the tumor cells Although an inverse correlation between the expression level of PD-Ls and patients' prognosis has been reported for several malignant tumors, the follow-up period was limited because of the lack of the antibody (Ab) applicable to paraffin-embedded specimens Here we generated a new Ab against PD-1 ligand 1 (PD-L1) and analyzed the expression level of PD-Ls in human ovarian cancer using paraffin-embedded specimens Patients with higher expression of PD-L1 had a significantly poorer prognosis than patients with lower expression Although patients with higher expression of PD-1 ligand 2 also had a poorer prognosis, the difference was not statistically significant A significant inverse correlation was observed between PD-L1 expression and the intraepithelial CD8+ T lymphocyte count, suggesting that PD-L1 on tumor cells directly suppresses antitumor CD8+ T cells Multivariate analysis showed the expression of PD-L1 on tumor cells and intraepithelial CD8+ T lymphocyte count are independent prognostic factors The PD-1/PD-L pathway can be a good target for restoring antitumor immunity in ovarian cancer
TL;DR: Self-assembled monolayers of alkanethiols, which can provide flat and chemically well-defined surfaces, were employed as model surfaces to understand cellular interaction with artificial materials and suggest that cell adhesion is mainly determined by surface wettability, but is also affected by the surface functional group, its surface density, and the kinds of cells.
TL;DR: A novel function of LDs is revealed in the assembly of infectious HCV and a new perspective on how viruses usurp cellular functions is provided.
Abstract: The lipid droplet (LD) is an organelle that is used for the storage of neutral lipids. It dynamically moves through the cytoplasm, interacting with other organelles, including the endoplasmic reticulum (ER). These interactions are thought to facilitate the transport of lipids and proteins to other organelles. The hepatitis C virus (HCV) is a causative agent of chronic liver diseases. HCV capsid protein (Core) associates with the LD, envelope proteins E1 and E2 reside in the ER lumen, and the viral replicase is assumed to localize on ER-derived membranes. How and where HCV particles are assembled, however, is poorly understood. Here, we show that the LD is involved in the production of infectious virus particles. We demonstrate that Core recruits nonstructural (NS) proteins and replication complexes to LD-associated membranes, and that this recruitment is critical for producing infectious viruses. Furthermore, virus particles were observed in close proximity to LDs, indicating that some steps of virus assembly take place around LDs. This study reveals a novel function of LDs in the assembly of infectious HCV and provides a new perspective on how viruses usurp cellular functions.
TL;DR: Recent advances in PGE receptor research are reviewed, including studies on knock-out mice deficient in each EP subtype have defined PGE2 actions mediated by each subtype and identified the role eachEP subtype plays in various physiological and pathophysiological responses.
TL;DR: The history ofPD-1 research since its discovery and recent findings that suggest promising future for the clinical application of PD-1 agonists and antagonists to various human diseases are summarized.
Abstract: Programmed cell death-1 (PD-1, Pdcd1), an immunoreceptor belonging to the CD28/CTLA-4 family negatively regulates antigen receptor signaling by recruiting protein tyrosine phosphatase, SHP-2 upon interacting with either of two ligands, PD-L1 or PD-L2. Because of the wide range of ligand distribution in the body, its biological significance pervades almost every aspect of immune responses including autoimmunity, tumor immunity, infectious immunity, transplantation immunity, allergy and immunological privilege. In this review, we would like to summarize the history of PD-1 research since its discovery and recent findings that suggest promising future for the clinical application of PD-1 agonists and antagonists to various human diseases.
National Institute for Biological Standards and Control1, University of Sheffield2, Karolinska Institutet3, Technion – Israel Institute of Technology4, Leeds Teaching Hospitals NHS Trust5, Monash University6, Hebrew University of Jerusalem7, Thermo Fisher Scientific8, National Institutes of Health9, University of Cambridge10, University of Kansas11, University of Toronto12, Academy of Sciences of the Czech Republic13, Masaryk University14, Uppsala University15, Stanford University16, Newcastle University17, Pierre-and-Marie-Curie University18, WiCell19, University of Helsinki20, King's College London21, Kyoto University22, Hudson Institute23
TL;DR: The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide and found that despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers ofhuman embryonic stem cells.
Abstract: The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue- nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.
TL;DR: Results indicate that Tim4 and Tim1 are phosphatidylserine receptors for the engulfment of apoptotic cells, and may also be involved in intercellular signalling in which exosomes are involved.
Abstract: During programmed cell death in multicellular organisms, a large number of cells are engulfed by macrophages, thus avoiding the release of noxious materials from the dying cells. These 'apoptotic' cells expose phosphatidylserine (PS) on their surface as an 'eat-me' signal. Miyanishi et al. show that the receptors Tim4 and Tim1 are implicated in phagocyte recognition of PS, while Park et al. show that the BAI1 protein is a receptor for PS in mammalian macrophages. Apoptotic cells expose phosphatidylserine as an 'eat-me' signal for macrophages. This paper shows that the receptors Tim4 and Tim1 are implicated in phagocyte recognition of phosphatidylserine. In programmed cell death, a large number of cells undergo apoptosis, and are engulfed by macrophages to avoid the release of noxious materials from the dying cells1,2. In definitive erythropoiesis, nuclei are expelled from erythroid precursor cells and are engulfed by macrophages. Phosphatidylserine is exposed on the surface of apoptotic cells3 and on the nuclei expelled from erythroid precursor cells4; it works as an ‘eat me’ signal for phagocytes5,6. Phosphatidylserine is also expressed on the surface of exosomes involved in intercellular signalling7. Here we established a library of hamster monoclonal antibodies against mouse peritoneal macrophages, and found an antibody that strongly inhibited the phosphatidylserine-dependent engulfment of apoptotic cells. The antigen recognized by the antibody was identified by expression cloning as a type I transmembrane protein called Tim4 (T-cell immunoglobulin- and mucin-domain-containing molecule; also known as Timd4)8. Tim4 was expressed in Mac1+ cells in various mouse tissues, including spleen, lymph nodes and fetal liver. Tim4 bound apoptotic cells by recognizing phosphatidylserine via its immunoglobulin domain. The expression of Tim4 in fibroblasts enhanced their ability to engulf apoptotic cells. When the anti-Tim4 monoclonal antibody was administered into mice, the engulfment of apoptotic cells by thymic macrophages was significantly blocked, and the mice developed autoantibodies. Among the other Tim family members, Tim1, but neither Tim2 nor Tim3, specifically bound phosphatidylserine. Tim1- or Tim4-expressing Ba/F3 B cells were bound by exosomes via phosphatidylserine, and exosomes stimulated the interaction between Tim1 and Tim4. These results indicate that Tim4 and Tim1 are phosphatidylserine receptors for the engulfment of apoptotic cells, and may also be involved in intercellular signalling in which exosomes are involved.
TL;DR: Molecules that regulate the ER stress response would be potential candidates for drug targets in various conformational diseases.
Abstract: Proteins synthesized in the endoplasmic reticulum (ER) are properly folded with the assistance of ER chaperones. Malfolded proteins are disposed of by ER-associated protein degradation (ERAD). When the amount of unfolded protein exceeds the folding capacity of the ER, human cells activate a defense mechanism called the ER stress response, which induces expression of ER chaperones and ERAD components and transiently attenuates protein synthesis to decrease the burden on the ER. It has been revealed that three independent response pathways separately regulate induction of the expression of chaperones, ERAD components, and translational attenuation. A malfunction of the ER stress response caused by aging, genetic mutations, or environmental factors can result in various diseases such as diabetes, inflammation, and neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, and bipolar disorder, which are collectively known as 'conformational diseases'. In this review, I will summarize recent progress in this field. Molecules that regulate the ER stress response would be potential candidates for drug targets in various conformational diseases.
TL;DR: Detailed methods and tips for the generation of induced pluripotent stem cells, named iPS cells, can be differentiated into three germ layers and committed to chimeric mice are described.
Abstract: Clinical application of embryonic stem (ES) cells faces difficulties regarding use of embryos, as well as tissue rejection after implantation. One way to circumvent these issues is to generate pluripotent stem cells directly from somatic cells. Somatic cells can be reprogrammed to an embryonic-like state by the injection of a nucleus into an enucleated oocyte or by fusion with ES cells. However, little is known about the mechanisms underlying these processes. We have recently shown that the combination of four transcription factors can generate ES-like pluripotent stem cells directly from mouse fibroblast cultures. The cells, named induced pluripotent stem (iPS) cells, can be differentiated into three germ layers and committed to chimeric mice. Here we describe detailed methods and tips for the generation of iPS cells.
TL;DR: It is demonstrated that ATF6alpha functions as a critical regulator of ER quality control proteins in mammalian cells, in marked contrast to worm and fly cells in which IRE1 is responsible.
TL;DR: The XIS is an X-ray imaging spectrometer system, consisting of state-of-the-art charge-coupled devices (CCDs) optimized for Xray detection, camera bodies, and control electronics as mentioned in this paper.
Abstract: The XIS is an X-ray Imaging Spectrometer system, consisting of state-of-the-art charge-coupled devices (CCDs) optimized for X-ray detection, camera bodies, and control electronics. Four sets of XIS sensors are placed at the focal planes of the grazing-incidence, nested thin-foil mirrors (XRT: X-Ray Telescope) onboard the Suzaku satellite. Three of the XIS sensors have front-illuminated CCDs, while the other has a back-illuminated CCD. Coupled with the XRT, the energy range of 0.2–12keV with energy resolution of 130eV at 5.9keV, and a field of view of 18 � ×18 �
TL;DR: In this paper, the authors describe the recent experimental progress in the control of spontaneous emission by manipulating optical modes with photonic crystals, which can contribute to the evolution of a variety of applications, including illumination, display, optical communication, solar energy and even quantum information systems.
Abstract: We describe the recent experimental progress in the control of spontaneous emission by manipulating optical modes with photonic crystals. It has been clearly demonstrated that the spontaneous emission from light emitters embedded in photonic crystals can be suppressed by the so-called photonic bandgap, whereas the emission efficiency in the direction where optical modes exist can be enhanced. Also, when an artificial defect is introduced into the photonic crystal, a photonic nanocavity is produced that can interact with light emitters. Cavity quality factors, or Q factors, of up to 2 million have been realized while maintaining very small mode volumes, and both spontaneous-emission modification (the Purcell effect) and strong-coupling phenomena have been demonstrated. The use of photonic crystals and nanocavities to manipulate spontaneous emission will contribute to the evolution of a variety of applications, including illumination, display, optical communication, solar energy and even quantum-information systems.
TL;DR: A model in which dark- and light-zone cells are morphologically similar, proliferation occurs in both zones, and GC B cells compete for T cell help as well as antigen is discussed.
Massachusetts Institute of Technology1, Goddard Space Flight Center2, Kyoto University3, Nagoya University4, University of Tokyo5, Osaka University6, Ehime University7, University of Cambridge8, Hiroshima University9, Carnegie Mellon University10, Max Planck Society11, University of Miyazaki12, Franklin W. Olin College of Engineering13, Rutgers University14, Tokyo Metropolitan University15, Kobe University16, Stanford University17, Tokyo Institute of Technology18, Rikkyo University19, Kogakuin University20, Tokyo University of Science21, University of Wisconsin-Madison22, Kanazawa University23, Nihon University24, Pennsylvania State University25, European Space Research and Technology Centre26, Yale University27, Saitama University28, Chuo University29, University of Leicester30, Nihon Fukushi University31, Aoyama Gakuin University32, Iwate University33
TL;DR: In this paper, the authors summarized the spacecraft, in-orbit performance, operations, and data processing that are related to observations of the Suzaku X-ray observatory, including high-sensitivity wide-band Xray spectroscopy.
Abstract: High-sensitivity wide-band X-ray spectroscopy is the key feature of the Suzaku X-ray observatory, launched on 2005 July 10. This paper summarizes the spacecraft, in-orbit performance, operations, and data processing that are related to observations. The scientific instruments, the high-throughput X-ray telescopes, X-ray CCD cameras, non-imaging hard X-ray detector are also described.
TL;DR: Estimates of the energy flux carried by these waves and comparisons with advanced radiative magnetohydrodynamic simulations indicate that such Alfvén waves are energetic enough to accelerate the solar wind and possibly to heat the quiet corona.
Abstract: Alfven waves have been invoked as a possible mechanism for the heating of the Sun's outer atmosphere, or corona, to millions of degrees and for the acceleration of the solar wind to hundreds of kilometers per second. However, Alfven waves of sufficient strength have not been unambiguously observed in the solar atmosphere. We used images of high temporal and spatial resolution obtained with the Solar Optical Telescope onboard the Japanese Hinode satellite to reveal that the chromosphere, the region sandwiched between the solar surface and the corona, is permeated by Alfven waves with strong amplitudes on the order of 10 to 25 kilometers per second and periods of 100 to 500 seconds. Estimates of the energy flux carried by these waves and comparisons with advanced radiative magnetohydrodynamic simulations indicate that such Alfven waves are energetic enough to accelerate the solar wind and possibly to heat the quiet corona.
TL;DR: The highly ordered amide groups in the channels play an important role in the interaction with the guest molecules, which was confirmed by thermogravimetric analysis, adsorption/desorption measurements, and X-ray crystallography.
Abstract: To create a functionalized porous compound, amide group is used in porous framework to produce attractive interactions with guest molecules. To avoid hydrogen-bond formation between these amide groups our strategy was to build a three-dimensional (3D) coordination network using a tridentate amide ligand as the three-connector part. From Cd(NO3)2·4H2O and a three-connector ligand with amide groups a 3D porous coordination polymer (PCP) based on octahedral Cd(II) centers, {[Cd(4-btapa)2(NO3)2]·6H2O·2DMF}n (1a), was obtained (4-btapa = 1,3,5-benzene tricarboxylic acid tris[N-(4-pyridyl)amide]). The amide groups, which act as guest interaction sites, occur on the surfaces of channels with dimensions of 4.7 × 7.3 A2. X-ray powder diffraction measurements showed that the desolvated compound (1b) selectively includes guests with a concurrent flexible structural (amorphous-to-crystalline) transformation. The highly ordered amide groups in the channels play an important role in the interaction with the guest molec...
TL;DR: HypoFXSRT with a BED of less than 180 Gy was almost safe for stage I NSCLC, and the local control and overall survival rates in 5 years with a AED of 100 Gy or more were superior to the reported results for conventional radiotherapy.
TL;DR: The results indicate that CCR6 expression contributes to Th17 cell function in autoimmune disease, especially in autoimmune arthritis such as RA.
Abstract: This report shows that interleukin (IL) 17–producing T helper type 17 (Th17) cells predominantly express CC chemokine receptor (CCR) 6 in an animal model of rheumatoid arthritis (RA). Th17 cells induced in vivo in normal mice via homeostatic proliferation similarly express CCR6, whereas those inducible in vitro by transforming growth factor β and IL-6 additionally need IL-1 and neutralization of interferon (IFN) γ and IL-4 for CCR6 expression. Forced expression of RORγt, a key transcription factor for Th17 cell differentiation, induces not only IL-17 but also CCR6 in naive T cells. Furthermore, Th17 cells produce CCL20, the known ligand for CCR6. Synoviocytes from arthritic joints of mice and humans also produce a large amount of CCL20, with a significant correlation (P = 0.014) between the amounts of IL-17 and CCL20 in RA joints. The CCL20 production by synoviocytes is augmented in vitro by IL-1β, IL-17, or tumor necrosis factor α, and is suppressed by IFN-γ or IL-4. Administration of blocking anti-CCR6 monoclonal antibody substantially inhibits mouse arthritis. Thus, the joint cytokine milieu formed by T cells and synovial cells controls the production of CCL20 and, consequently, the recruitment of CCR6+ arthritogenic Th17 cells to the inflamed joints. These results indicate that CCR6 expression contributes to Th17 cell function in autoimmune disease, especially in autoimmune arthritis such as RA.
TL;DR: Advances in understanding the role of vascular endothelial growth factor (VEGF) in normal physiology are giving insight into the basis of adverse effects attributed to the use of VEGF inhibitors in clinical oncology.
Abstract: Advances in understanding the role of vascular endothelial growth factor (VEGF) in normal physiology are giving insight into the basis of adverse effects attributed to the use of VEGF inhibitors in clinical oncology. These effects are typically downstream consequences of suppression of cellular signalling pathways important in the regulation and maintenance of the microvasculature. Downregulation of these pathways in normal organs can lead to vascular disturbances and even regression of blood vessels, which could be intensified by concurrent pathological conditions. These changes are generally manageable and pose less risk than the tumours being treated, but they highlight the properties shared by tumour vessels and the vasculature of normal organs.