Showing papers by "University of Tokyo published in 2007"

KEGG for linking genomes to life and the environment

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.

Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer

Abstract: Improvement in the clinical outcome of lung cancer is likely to be achieved by identification of the molecular events that underlie its pathogenesis. Here we show that a small inversion within chromosome 2p results in the formation of a fusion gene comprising portions of the echinoderm microtubule-associated protein-like 4 (EML4) gene and the anaplastic lymphoma kinase (ALK) gene in non-small-cell lung cancer (NSCLC) cells. Mouse 3T3 fibroblasts forced to express this human fusion tyrosine kinase generated transformed foci in culture and subcutaneous tumours in nude mice. The EML4-ALK fusion transcript was detected in 6.7% (5 out of 75) of NSCLC patients examined; these individuals were distinct from those harbouring mutations in the epidermal growth factor receptor gene. Our data demonstrate that a subset of NSCLC patients may express a transforming fusion kinase that is a promising candidate for a therapeutic target as well as for a diagnostic molecular marker in NSCLC.

Spins in few-electron quantum dots

Abstract: The canonical example of a quantum-mechanical two-level system is spin. The simplest picture of spin is a magnetic moment pointing up or down. The full quantum properties of spin become apparent in phenomena such as superpositions of spin states, entanglement among spins, and quantum measurements. Many of these phenomena have been observed in experiments performed on ensembles of particles with spin. Only in recent years have systems been realized in which individual electrons can be trapped and their quantum properties can be studied, thus avoiding unnecessary ensemble averaging. This review describes experiments performed with quantum dots, which are nanometer-scale boxes defined in a semiconductor host material. Quantum dots can hold a precise but tunable number of electron spins starting with 0, 1, 2, etc. Electrical contacts can be made for charge transport measurements and electrostatic gates can be used for controlling the dot potential. This system provides virtually full control over individual electrons. This new, enabling technology is stimulating research on individual spins. This review describes the physics of spins in quantum dots containing one or two electrons, from an experimentalist’s viewpoint. Various methods for extracting spin properties from experiment are presented, restricted exclusively to electrical measurements. Furthermore, experimental techniques are discussed that allow for 1 the rotation of an electron spin into a superposition of up and down, 2 the measurement of the quantum state of an individual spin, and 3 the control of the interaction between two neighboring spins by the Heisenberg exchange interaction. Finally, the physics of the relevant relaxation and dephasing mechanisms is reviewed and experimental results are compared with theories for spin-orbit and hyperfine interactions. All these subjects are directly relevant for the fields of quantum information processing and spintronics with single spins i.e., single spintronics.

El Niño Modoki and its possible teleconnection

Abstract: [1] Using observed data sets mainly for the period 1979–2005, we find that anomalous warming events different from conventional El Nino events occur in the central equatorial Pacific. This unique warming in the central equatorial Pacific associated with a horseshoe pattern is flanked by a colder sea surface temperature anomaly (SSTA) on both sides along the equator. empirical orthogonal function (EOF) analysis of monthly tropical Pacific SSTA shows that these events are represented by the second mode that explains 12% of the variance. Since a majority of such events are not part of El Nino evolution, the phenomenon is named as El Nino Modoki (pseudo-El Nino) (“Modoki” is a classical Japanese word, which means “a similar but different thing”). The El Nino Modoki involves ocean-atmosphere coupled processes which include a unique tripolar sea level pressure pattern during the evolution, analogous to the Southern Oscillation in the case of El Nino. Hence the total entity is named as El Nino–Southern Oscillation (ENSO) Modoki. The ENSO Modoki events significantly influence the temperature and precipitation over many parts of the globe. Depending on the season, the impacts over regions such as the Far East including Japan, New Zealand, western coast of United States, etc., are opposite to those of the conventional ENSO. The difference maps between the two periods of 1979–2004 and 1958–1978 for various oceanic/atmospheric variables suggest that the recent weakening of equatorial easterlies related to weakened zonal sea surface temperature gradient led to more flattening of the thermocline. This appears to be a cause of more frequent and persistent occurrence of the ENSO Modoki event during recent decades.

Ubiquity and dominance of oxygenated species in organic aerosols in anthropogenically-influenced Northern Hemisphere midlatitudes

Abstract: Organic aerosol (OA) data acquired by the Aerosol Mass Spectrometer (AMS) in 37 field campaigns were deconvolved into hydrocarbon-like OA (HOA) and several types of oxygenated OA (OOA) components. HOA has been linked to primary combustion emissions (mainly from fossil fuel) and other primary sources such as meat cooking. OOA is ubiquitous in various atmospheric environments, on average accounting for 64%, 83% and 95% of the total OA in urban, urban downwind, and rural/remote sites, respectively. A case study analysis of a rural site shows that the OOA concentration is much greater than the advected HOA, indicating that HOA oxidation is not an important source of OOA, and that OOA increases are mainly due to SOA. Most global models lack an explicit representation of SOA which may lead to significant biases in the magnitude, spatial and temporal distributions of OA, and in aerosol hygroscopic properties.

Genome-wide detection and characterization of positive selection in human populations

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.

DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response

Abstract: Central to innate immunity is the sensing of pathogen-associated molecular patterns by cytosolic and membrane-associated receptors. In particular, DNA is a potent activator of immune responses during infection or tissue damage, and evidence indicates that, in addition to the membrane-associated Toll-like receptor 9, an unidentified cytosolic DNA sensor(s) can activate type I interferon (IFN) and other immune responses. Here we report on a candidate DNA sensor, previously named DLM-1 (also called Z-DNA binding protein 1 (ZBP1)), for which biological function had remained unknown; we now propose the alternative name DAI (DNA-dependent activator of IFN-regulatory factors). The artificial expression of otherwise IFN-inducible DAI (DLM-1/ZBP1) in mouse fibroblasts selectively enhances the DNA-mediated induction of type I IFN and other genes involved in innate immunity. On the other hand, RNA interference of messenger RNA for DAI (DLM-1/ZBP1) in cells inhibits this gene induction programme upon stimulation by DNA from various sources. Moreover, DAI (DLM-1/ZBP1) binds to double-stranded DNA and, by doing so, enhances its association with the IRF3 transcription factor and the TBK1 serine/threonine kinase. These observations underscore an integral role of DAI (DLM-1/ZBP1) in the DNA-mediated activation of innate immune responses, and may offer new insight into the signalling mechanisms underlying DNA-associated antimicrobial immunity and autoimmune disorders.

TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity

Abstract: The cytoplasmic receptor RIG-I recognizes viral RNAs and initiates a protective innate immune response against a number of important viruses. Here, it is shown that RIG-I is regulated by ubiquitination. Retinoic-acid-inducible gene-I (RIG-I; also called DDX58) is a cytosolic viral RNA receptor that interacts with MAVS (also called VISA, IPS-1 or Cardif) to induce type I interferon-mediated host protective innate immunity against viral infection1,2,3,4,5,6. Furthermore, members of the tripartite motif (TRIM) protein family, which contain a cluster of a RING-finger domain, a B box/coiled-coil domain and a SPRY domain, are involved in various cellular processes, including cell proliferation and antiviral activity7. Here we report that the amino-terminal caspase recruitment domains (CARDs) of RIG-I undergo robust ubiquitination induced by TRIM25 in mammalian cells. The carboxy-terminal SPRY domain of TRIM25 interacts with the N-terminal CARDs of RIG-I; this interaction effectively delivers the Lys 63-linked ubiquitin moiety to the N-terminal CARDs of RIG-I, resulting in a marked increase in RIG-I downstream signalling activity. The Lys 172 residue of RIG-I is critical for efficient TRIM25-mediated ubiquitination and for MAVS binding, as well as the ability of RIG-I to induce antiviral signal transduction. Furthermore, gene targeting demonstrates that TRIM25 is essential not only for RIG-I ubiquitination but also for RIG-I-mediated interferon-β production and antiviral activity in response to RNA virus infection. Thus, we demonstrate that TRIM25 E3 ubiquitin ligase induces the Lys 63-linked ubiquitination of RIG-I, which is crucial for the cytosolic RIG-I signalling pathway to elicit host antiviral innate immunity.

Distinct Roles of Autophagy in the Heart During Ischemia and Reperfusion: Roles of AMP-Activated Protein Kinase and Beclin 1 in Mediating Autophagy

Abstract: Autophagy is an intracellular bulk degradation process for proteins and organelles. In the heart, autophagy is stimulated by myocardial ischemia. However, the causative role of autophagy in the survival of cardiac myocytes and the underlying signaling mechanisms are poorly understood. Glucose deprivation (GD), which mimics myocardial ischemia, induces autophagy in cultured cardiac myocytes. Survival of cardiac myocytes was decreased by 3-methyladenine, an inhibitor of autophagy, suggesting that autophagy is protective against GD in cardiac myocytes. GD-induced autophagy coincided with activation of AMP-activated protein kinase (AMPK) and inactivation of mTOR (mammalian target of rapamycin). Inhibition of AMPK by adenine 9-beta-d-arabinofuranoside or dominant negative AMPK significantly reduced GD-induced autophagy, whereas stimulation of autophagy by rapamycin failed to cause an additive effect on GD-induced autophagy, suggesting that activation of AMPK and inhibition of mTOR mediate GD-induced autophagy. Autophagy was also induced by ischemia and further enhanced by reperfusion in the mouse heart, in vivo. Autophagy resulting from ischemia was accompanied by activation of AMPK and was inhibited by dominant negative AMPK. In contrast, autophagy during reperfusion was accompanied by upregulation of Beclin 1 but not by activation of AMPK. Induction of autophagy and cardiac injury during the reperfusion phase was significantly attenuated in beclin 1(+/-) mice. These results suggest that, in the heart, ischemia stimulates autophagy through an AMPK-dependent mechanism, whereas ischemia/reperfusion stimulates autophagy through a Beclin 1-dependent but AMPK-independent mechanism. Furthermore, autophagy plays distinct roles during ischemia and reperfusion: autophagy may be protective during ischemia, whereas it may be detrimental during reperfusion.

New Non-Oxide Photocatalysts Designed for Overall Water Splitting under Visible Light

Abstract: Overall water splitting to form hydrogen and oxygen over a heterogeneous photocatalyst using solar energy is a promising process for clean and recyclable hydrogen production in large-scale. In recent years, numerous attempts have been made for the development of photocatalysts that work under visible-light irradiation to efficiently utilize solar energy. This article presents recent research progress in the development of visible-light-driven photocatalysts, focusing on the refinement of non-oxide-type photocatalysts such as (oxy)nitrides and oxysulfides.

Mesoscale iron enrichment experiments 1993-2005 : Synthesis and future directions

Abstract: Since the mid-1980s, our understanding of nutrient limitation of oceanic primary production has radically changed. Mesoscale iron addition experiments (FeAXs) have unequivocally shown that iron supply limits production in one-third of the world ocean, where surface macronutrient concentrations are perennially high. The findings of these 12 FeAXs also reveal that iron supply exerts controls on the dynamics of plankton blooms, which in turn affect the biogeochemical cycles of carbon, nitrogen, silicon, and sulfur and ultimately influence the Earth climate system. However, extrapolation of the key results of FeAXs to regional and seasonal scales in some cases is limited because of differing modes of iron supply in FeAXs and in the modern and paleo-oceans. New research directions include quantification of the coupling of oceanic iron and carbon biogeochemistry.

Targeted disruption of AdipoR1 and AdipoR2 causes abrogation of adiponectin binding and metabolic actions.

Abstract: Adiponectin plays a central role as an antidiabetic and antiatherogenic adipokine. AdipoR1 and AdipoR2 serve as receptors for adiponectin in vitro, and their reduction in obesity seems to be correlated with reduced adiponectin sensitivity. Here we show that adenovirus-mediated expression of AdipoR1 and R2 in the liver of Lepr(-/-) mice increased AMP-activated protein kinase (AMPK) activation and peroxisome proliferator-activated receptor (PPAR)-alpha signaling pathways, respectively. Activation of AMPK reduced gluconeogenesis, whereas expression of the receptors in both cases increased fatty acid oxidation and lead to an amelioration of diabetes. Alternatively, targeted disruption of AdipoR1 resulted in the abrogation of adiponectin-induced AMPK activation, whereas that of AdipoR2 resulted in decreased activity of PPAR-alpha signaling pathways. Simultaneous disruption of both AdipoR1 and R2 abolished adiponectin binding and actions, resulting in increased tissue triglyceride content, inflammation and oxidative stress, and thus leading to insulin resistance and marked glucose intolerance. Therefore, AdipoR1 and R2 serve as the predominant receptors for adiponectin in vivo and play important roles in the regulation of glucose and lipid metabolism, inflammation and oxidative stress in vivo.

Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum - Part 1: experiments and large-scale features

Abstract: . A set of coupled ocean-atmosphere simulations using state of the art climate models is now available for the Last Glacial Maximum and the Mid-Holocene through the second phase of the Paleoclimate Modeling Intercomparison Project (PMIP2). This study presents the large-scale features of the simulated climates and compares the new model results to those of the atmospheric models from the first phase of the PMIP, for which sea surface temperature was prescribed or computed using simple slab ocean formulations. We consider the large-scale features of the climate change, pointing out some of the major differences between the different sets of experiments. We show in particular that systematic differences between PMIP1 and PMIP2 simulations are due to the interactive ocean, such as the amplification of the African monsoon at the Mid-Holocene or the change in precipitation in mid-latitudes at the LGM. Also the PMIP2 simulations are in general in better agreement with data than PMIP1 simulations.

The use of clinical risk factors enhances the performance of BMD in the prediction of hip and osteoporotic fractures in men and women.

Abstract: BMD and clinical risk factors predict hip and other osteoporotic fractures. The combination of clinical risk factors and BMD provide higher specificity and sensitivity than either alone. To develop a risk assessment tool based on clinical risk factors (CRFs) with and without BMD. Nine population-based studies were studied in which BMD and CRFs were documented at baseline. Poisson regression models were developed for hip fracture and other osteoporotic fractures, with and without hip BMD. Fracture risk was expressed as gradient of risk (GR, risk ratio/SD change in risk score). CRFs alone predicted hip fracture with a GR of 2.1/SD at the age of 50 years and decreased with age. The use of BMD alone provided a higher GR (3.7/SD), and was improved further with the combined use of CRFs and BMD (4.2/SD). For other osteoporotic fractures, the GRs were lower than for hip fracture. The GR with CRFs alone was 1.4/SD at the age of 50 years, similar to that provided by BMD (GR = 1.4/SD) and was not markedly increased by the combination (GR = 1.4/SD). The performance characteristics of clinical risk factors with and without BMD were validated in eleven independent population-based cohorts. The models developed provide the basis for the integrated use of validated clinical risk factors in men and women to aid in fracture risk prediction.

Identification of Tim4 as a phosphatidylserine receptor.

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.

The medaka draft genome and insights into vertebrate genome evolution

Abstract: The medaka fish (Oryzias latipes) is a popular pet in Japan and more recently a laboratory model organism for developmental genetics and evolutionary biology. Now the medaka's genome has been sequenced and analysed by a large Japanese consortium. Cichlids and stickleback, which are emerging model systems for understanding the genetic basis of vertebrate speciation, are evolutionarily closer to medaka than zebrafish, so the medaka's genome sequence will yield valuable insights into 400 million years of vertebrate genome evolution. The medaka fish (Oryzias latipes) has long been a popular pet in Japan and more recently a laboratory model organism; it now has its genome sequenced and analysed by a Japanese consortium. Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats1. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published2,3, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination4,5,6 and developmental genetics7. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including ∼2,900 new genes, using 5′-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of ∼50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.

Schemas and memory consolidation

Abstract: Memory encoding occurs rapidly, but the consolidation of memory in the neocortex has long been held to be a more gradual process. We now report, however, that systems consolidation can occur extremely quickly if an associative "schema" into which new information is incorporated has previously been created. In experiments using a hippocampal-dependent paired-associate task for rats, the memory of flavor-place associations became persistent over time as a putative neocortical schema gradually developed. New traces, trained for only one trial, then became assimilated and rapidly hippocampal-independent. Schemas also played a causal role in the creation of lasting associative memory representations during one-trial learning. The concept of neocortical schemas may unite psychological accounts of knowledge structures with neurobiological theories of systems memory consolidation.

Phase transition between the quantum spin Hall and insulator phases in 3D: emergence of a topological gapless phase

Abstract: Phase transitions between the quantum spin Hall (QSH) and the insulator phases in three dimensions (3D) are studied. We find that in inversion-asymmetric systems there appears a gapless phase between the QSH and insulator phases in 3D which is in contrast with the 2D case. Existence of this gapless phase stems from a topological nature of gapless points (diabolical points) in 3D, but not in 2D.

Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice

Abstract: The OsNAC6 gene is a member of the NAC transcription factor gene family in rice. Expression of OsNAC6 is induced by abiotic stresses, including cold, drought and high salinity. OsNAC6 gene expression is also induced by wounding and blast disease. A transactivation assay using a yeast system demonstrated that OsNAC6 functions as a transcriptional activator, and transient localization studies with OsNAC6-sGFP fusion protein revealed its nuclear localization. Transgenic rice plants over-expressing OsNAC6 constitutively exhibited growth retardation and low reproductive yields. These transgenic rice plants showed an improved tolerance to dehydration and high-salt stresses, and also exhibited increased tolerance to blast disease. By utilizing stress-inducible promoters, such as the OsNAC6 promoter, it is hoped that stress-inducible over-expression of OsNAC6 in rice can improve stress tolerance by suppressing the negative effects of OsNAC6 on growth under normal growth conditions. The results of microarray analysis revealed that many genes that are inducible by abiotic and biotic stresses were upregulated in rice plants over-expressing OsNAC6. A transient transactivation assay showed that OsNAC6 activates the expression of at least two genes, including a gene encoding peroxidase. Collectively, these results indicate that OsNAC6 functions as a transcriptional activator in response to abiotic and biotic stresses in plants. We conclude that OsNAC6 may serve as a useful biotechnological tool for the improvement of stress tolerance in various kinds of plants.

The WASP-WAVE protein network: connecting the membrane to the cytoskeleton.

Abstract: Membrane-binding and membrane-deforming proteins have emerged as binding partners of the Wiskott–Aldrich syndrome protein (WASP) and WASP-family verprolin-homologous protein (WAVE) family proteins that regulate the actin cytoskeleton. Membrane deformation and cytoskeletal reorganization might be coupled in processes that require alteration of membrane shapes, including endocytosis and membrane protrusion. Wiskott–Aldrich syndrome protein (WASP) and WASP-family verprolin-homologous protein (WAVE) family proteins are scaffolds that link upstream signals to the activation of the ARP2/3 complex, leading to a burst of actin polymerization. ARP2/3-complex-mediated actin polymerization is crucial for the reorganization of the actin cytoskeleton at the cell cortex for processes such as cell movement, vesicular trafficking and pathogen infection. Large families of membrane-binding proteins were recently found to interact with WASP and WAVE family proteins, therefore providing a new layer of membrane-dependent regulation of actin polymerization.

Room-temperature reversible spin Hall effect.

Abstract: Reversible spin Hall effect comprising the direct and inverse spin Hall effects was electrically detected at room temperature. A platinum wire with a strong spin-orbit interaction is used not only as a spin current absorber but also as a spin-current source in the specially designed lateral structure. The obtained spin Hall conductivities are $2.4\ifmmode\times\else\texttimes\fi{}{10}^{4}\text{ }\text{ }(\ensuremath{\Omega}\mathrm{m}{)}^{\ensuremath{-}1}$ at room temperature, ${10}^{4}$ times larger than the previously reported values of semiconductor systems. Spin Hall conductivities obtained from both the direct and inverse spin Hall effects are experimentally confirmed to be the same, demonstrating the Onsager reciprocal relations between spin and charge currents.

AAindex: amino acid index database, progress report 2008

Abstract: AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section. Accordingly AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid substitution matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. The database can be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.jp/dbget-bin/www_bfind?aaindex) or downloaded by anonymous FTP (ftp://ftp.genome.jp/pub/db/community/aaindex/).

The X-Ray Observatory Suzaku

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.

Giant thermoelectric Seebeck coefficient of a two-dimensional electron gas in SrTiO3

Abstract: Enhancement of the Seebeck coefficient (S ) without reducing the electrical conductivity (sigma) is essential to realize practical thermoelectric materials exhibiting a dimensionless figure of merit (ZT=S2 x sigma x T x kappa-1) exceeding 2, where T is the absolute temperature and kappa is the thermal conductivity. Here, we demonstrate that a high-density two-dimensional electron gas (2DEG) confined within a unit cell layer thickness in SrTiO(3) yields unusually large |S|, approximately five times larger than that of SrTiO(3) bulks, while maintaining a high sigma2DEG. In the best case, we observe |S|=850 microV K-1 and sigma2DEG=1.4 x 10(3) S cm-1. In addition, by using the kappa of bulk single-crystal SrTiO(3) at room temperature, we estimate ZT approximately 2.4 for the 2DEG, corresponding to ZT approximately 0.24 for a complete device having the 2DEG as the active region. The present approach using a 2DEG provides a new route to realize practical thermoelectric materials without the use of toxic heavy elements.

The infrared astronomical mission AKARI

Abstract: AKARI, the first Japanese satellite dedicated to infrared astronomy, was launched on 2006 February 21, and started observations in May of the same year. AKARI has a 68.5 cm cooled telescope, together with two focal-plane instruments, which survey the sky in six wavelength bands from mid- to far-infrared. The instruments also have a capability for imaging and spectroscopy in the wavelength range 2-180 mu m in the pointed observation mode, occasionally inserted into a continuous survey operation. The in-orbit cryogen lifetime is expected to be one and a half years. The All-Sky Survey will cover more than 90% of the whole sky with a higher spatial resolution and a wider wavelength coverage than that of the previous IRAS all-sky survey. Point-source catalogues of the All-Sky Survey will be released to the astronomical community. Pointed observations will be used for deep surveys of selected sky areas and systematic observations of important astronomical targets. These will become an additional future heritage of this mission.

Non-volcanic tremor and low-frequency earthquake swarms

Abstract: Extended-duration seismic signals occur episodically on some major faults, often in conjunction with aseismic or 'slow-slip' earthquake events. The mechanism underlying this tremor and its relationship to the aseismic slip are as yet unresolved. David Shelley et al. demonstrate that tremor beneath Shikoku, Japan can be explained as a swarm of small, low-frequency earthquakes, each of which occurs as shear faulting on the subduction zone plate interface. This suggests that tremor and slow slip are different manifestations of a single process. Tremor beneath Shikoku, Japan can be explained as a swarm of small, low-frequency earthquakes, each of which occurs as shear faulting on the subduction zone plate interface. This suggests that tremor and slow slip are different manifestations of a single process. Non-volcanic tremor is a weak, extended duration seismic signal observed episodically on some major faults, often in conjunction with slow slip events1,2,3,4. Such tremor may hold the key to understanding fundamental processes at the deep roots of faults, and could signal times of accelerated slip and hence increased seismic hazard. The mechanism underlying the generation of tremor and its relationship to aseismic slip are, however, as yet unresolved. Here we demonstrate that tremor beneath Shikoku, Japan, can be explained as a swarm of small, low-frequency earthquakes, each of which occurs as shear faulting on the subduction-zone plate interface. This suggests that tremor and slow slip are different manifestations of a single process.

The Fifth Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through 2005 June and represents the completion of the SDSS-I project (whose successor, SDSS-II, will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 deg^2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg^2 of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus Cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.