University of Tokyo

About: University of Tokyo is a education organization based out in Tokyo, Japan. It is known for research contribution in the topics: Population & Gene. The organization has 134564 authors who have published 337567 publications receiving 10178620 citations. The organization is also known as: Todai & Universitas Tociensis.

Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies.

Abstract: In the last two decades, considerable progress has been made in the field of molecular biology, which has enabled a molecular-level understanding of a number of interesting biological events. In particular, the discovery of a family of moving proteins and their assemblies has attracted particular attention not only of biologists but also of chemists and physicists.1-5 In response to certain biological stimuli, these proteins perform directed or programmed motions, similar to many tools and machines used in our daily life. Such biological molecular machines play essential roles in a wide variety of biological events, particularly those related to the activities of cells,1 and realize specific functions through their stimuliresponsive mechanical motions. Cytoplasmic proteins such as myosins, kinesins, and dyneins are called “molecular motors” and are the most extensively studied molecular machines.2-5 These protein-based supramolecular conjugates are known to switch back and forth along linear tracks of actin filaments or microtubules and transport substrates at the expense of adenosine triphosphate (ATP) as fuel. The flagellum is a huge protein conjugate that controls the swimming motion of bacteria.6 The bacterial flagellar motor consists of (1) flagellar filaments that are 15 μm long and 120-250 Å in diameter and a (2) motor domain that rotates the flagellar filaments alternately in clockwise and anticlockwise directions. This unique behavior of rotation allows bacteria to swim desirably. ATP synthase is a different type of a molecular machine, which synthesizes and hydrolyzes ATP through its rotary motion.7-9 ATP synthase is built up of two different machinery components, that is, F1 and F0, where the rotation of the former is driven by the free energy released from the hydrolysis of ATP to adenosine diphosphate (ADP); the latter rotates by a flux of ions passing through a membrane and synthesizes ATP. This huge protein complex has a shaft, which rotates just like real rotary motors. Since the rotary motion of ATP synthase occurs in a stepwise manner in response to the hydrolysis of ATP, it is regarded as a biological stepping motor. In addition to these molecular motors, some other biological machines are known, where the hydrolysis of ATP triggers different types of mechanical motions. Representative examples include the family of chap† The University of Tokyo. ‡ PRESTO. 1377 Chem. Rev. 2005, 105, 1377−1400

Remote Sensing of Tropospheric Aerosols from Space: Past, Present, and Future.

Abstract: Aerosol particles originate from man-made sources such as urban/industrial activities,rurning associated with land use processes, wind-blown dust, and natural sources. Their interaction with sunlight and their effect on cloud microphysics forms a major uncertainty in predicting climate change. Furthermore, the lifetime of only a few days causes high spatial variability in aerosol optical and radiative properties that requires global observations from space. Remote sensing of aerosol properties from space is reviewed both for present and planned national and international satellite sensors. Techniques that are being used to enhance our ability to characterize the global distribution of aerosol properties include well-calibrated multispectral radiometers, multispectral polarimeters, and multi-angle spectroradiometers. Though most of these sensor systems rely primarily on visible to mid-infrared spectral channels, the availability of of thermal channels to aid in cloud screening is an important additional piece of information that is not always incorporated into the sensor design. In this paper we describe the various satellite sensor systems being developed by Europe, Japan, and the U.S., and highlight the advantages and disadvantages of each of these systems for aerosol applications. An important underlying theme is that the remote sensing of aerosol properties, especially aerosol size distribution and single scattering albedo, is exceedingly difficult. As a consequence, no one sensor system is capable of providing totally unambiguous information, and hence a careful intercomparison of derived products from different sensors, together with a comprehensive network of ground-based sun-photometer and sky radiometer systems, are required to advance our quantitative understanding of global aerosol characteristics.

Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9.

Abstract: Histone H3 Lys 9 (H3-K9) methylation is a crucial epigenetic mark for transcriptional silencing. G9a is the major mammalian H3-K9 methyltransferase that targets euchromatic regions and is essential for murine embryogenesis. There is a single G9a-related methyltransferase in mammals, called GLP/Eu-HMTase1. Here we show that GLP is also important for H3-K9 methylation of mouse euchromatin. GLP-deficiency led to embryonic lethality, a severe reduction of H3-K9 mono- and dimethylation, the induction of Mage-a gene expression, and HP1 relocalization in embryonic stem cells, all of which were phenotypes of G9a-deficiency. Furthermore, we show that G9a and GLP formed a stoichiometric heteromeric complex in a wide variety of cell types. Biochemical analyses revealed that formation of the G9a/GLP complex was dependent on their enzymatic SET domains. Taken together, our new findings revealed that G9a and GLP cooperatively exert H3-K9 methyltransferase function in vivo, likely through the formation of higher-order heteromeric complexes.

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

Abstract: Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project ‘‘Assembling the Fungal Tree of Life’’ (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

Association of p19ARF with Mdm2 inhibits ubiquitin ligase activity of Mdm2 for tumor suppressor p53

Abstract: We have demonstrated previously that the oncoprotein Mdm2 has a ubiquitin ligase activity for the tumor suppressor p53 protein. In the present study, we characterize this ubiquitin ligase activity of Mdm2. We first demonstrate the ubiquitination of several p53 point mutants and deletion mutants by Mdm2. The point mutants, which cannot bind to Mdm2, are not ubiquitinated by Mdm2. The ubiquitination of the C-terminal deletion mutants, which contain so-called Mdm2-binding sites, is markedly decreased, compared with that of wild-type p53. The binding of Mdm2 to p53 is essential for ubiquitination, but p53's tertiary structure and/or C-terminal region may also be important for this reaction. DNA-dependent protein kinase is known to phosphorylate p53 on Mdm2-binding sites, where DNA damage induces phosphorylation, and p53 phosphorylated by this kinase is not a good substrate for Mdm2. This suggests that DNA damage-induced phosphorylation stabilizes p53 by inhibiting its ubiquitination by Mdm2. We further investigated whether the tumor suppressor p19(ARF) affects the ubiquitin ligase activity of Mdm2 for p53. The activity of p19(ARF)-bound Mdm2 was found to be lower than that of free Mdm2, suggesting that p19(ARF) promotes the stabilization of p53 by inactivating Mdm2.