Kyoto University

About: Kyoto University is a education organization based out in Kyoto, Japan. It is known for research contribution in the topics: Catalysis & Population. The organization has 85837 authors who have published 217215 publications receiving 6526826 citations. The organization is also known as: Kyōto University & Kyōto daigaku.

Corotating solar wind streams and recurrent geomagnetic activity: A review

Abstract: [1] Solar wind fast streams emanating from solar coronal holes cause recurrent, moderate intensity geomagnetic activity at Earth. Intense magnetic field regions called Corotating Interaction Regions or CIRs are created by the interaction of fast streams with upstream slow streams. Because of the highly oscillatory nature of the GSM magnetic field z component within CIRs, the resultant magnetic storms are typically only weak to moderate in intensity. CIR-generated magnetic storm main phases of intensity Dst < −100 nT (major storms) are rare. The elongated storm “recovery” phases which are characterized by continuous AE activity that can last for up to 27 days (a solar rotation) are caused by nonlinear Alfven waves within the high streams proper. Magnetic reconnection associated with the southward (GSM) components of the Alfven waves is the solar wind energy transfer mechanism. The acceleration of relativistic electrons occurs during these magnetic storm “recovery” phases. The magnetic reconnection associated with the Alfven waves cause continuous, shallow injections of plasma sheet plasma into the magnetosphere. The asymmetric plasma is unstable to wave (chorus and other modes) growth, a feature central to many theories of electron acceleration. It is noted that the continuous AE activity is not a series of substorm expansion phases. Arguments are also presented why these AE activity intervals are not convection bays. The auroras during these continuous AE activity intervals are less intense than substorm auroras and are global (both dayside and nightside) in nature. Owing to the continuous nature of this activity, it is possible that there is greater average energy input into the magnetosphere/ionosphere system during far declining phases of the solar cycle compared with those during solar maximum. The discontinuities and magnetic decreases (MDs) associated with interplanetary Alfven waves may be important for geomagnetic activity. In conclusion, it will be shown that geomagnetic storms associated with high-speed streams/CIRs will have the same initial, main, and “recovery” phases as those associated with ICME-related magnetic storms but that the interplanetary causes are considerably different.

Rational surfaces associated with affine root systems and geometry of the Painlevé equations

Abstract: We present a geometric approach to the theory of Painleve equations based on rational surfaces Our starting point is a compact smooth rational surface X which has a unique anti-canonical divisor D of canonical type We classify all such surfaces X To each X, there corresponds a root subsystem of E (1) 8 inside the Picard lattice of X We realize the action of the corresponding affine Weyl group as the Cremona action on a family of these surfaces We show that the translation part of the affine Weyl group gives rise to discrete Painleve equations, and that the above action constitutes their group of symmetries by Backlund transformations The six Painleve differential equations appear as degenerate cases of this construction In the latter context, X is Okamoto's space of initial conditions and D is the pole divisor of the symplectic form defining the Hamiltonian structure

Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice.

Abstract: New cultivars with very erect leaves, which increase light capture for photosynthesis and nitrogen storage for grain filling, may have increased grain yields. Here we show that the erect leaf phenotype of a rice brassinosteroid-deficient mutant, osdwarf4-1, is associated with enhanced grain yields under conditions of dense planting, even without extra fertilizer. Molecular and biochemical studies reveal that two different cytochrome P450s, CYP90B2/OsDWARF4 and CYP724B1/D11, function redundantly in C-22 hydroxylation, the rate-limiting step of brassinosteroid biosynthesis. Therefore, despite the central role of brassinosteroids in plant growth and development, mutation of OsDWARF4 alone causes only limited defects in brassinosteroid biosynthesis and plant morphology. These results suggest that regulated genetic modulation of brassinosteroid biosynthesis can improve crops without the negative environmental effects of fertilizers.

Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes

Abstract: RNA interference (RNAi) is a sequence-specific gene regulatory mechanism conserved among diverse eukaryotes. The sequence specificity in RNAi is determined by a family of 18- to 30-nucleotide (nt) regulatory small RNAs (for review, see Aravin and Tuschl 2005). Two major classes of endogenous small RNAs have been characterized: microRNAs (miRNAs) and small interfering RNAs (siRNAs). miRNAs—the best-characterized endogenous small RNAs in eukaryotes—have been identified in diverse plants and animals, and are mainly involved in development and differentiation. miRNAs are processed from miRNA precursors (pre-miRNAs) with a stem-loop structure and regulate gene expression through translational repression or mRNA cleavage (for reviews, see Ambros 2004; Bartel 2004; He and Hannon 2004; Du and Zamore 2005). siRNAs are generated from long double-stranded RNA (dsRNA) and are mainly involved in defense against molecular parasites including viruses, transposons, and transgenes through RNAi (Sijen and Plasterk 2003; Shi et al. 2004). Endogenous siRNAs have been classified into at least three subclasses: repeat-associated siRNAs (rasiRNAs), trans-acting siRNAs (ta-siRNAs), and siRNAs derived from natural antisense transcripts (nat-siRNAs) (Lippman and Martienssen 2004; Peragine et al. 2004; Borsani et al. 2005). rasiRNAs corresponding to repetitive elements repress the repeat sequences at the transcriptional or post-transcriptional level and maintain a centromeric heterochromatic structure (Lippman and Martienssen 2004). rasiRNAs have been cloned and sequenced in Schizosaccharomyces pombe, Trypanosoma brucei, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, and Arabidopsis thaliana, but not in mammals (for review, see Aravin and Tuschl 2005). In D. melanogaster and D. rerio, however, the lengths of rasiRNAs are longer than those of miRNAs (Ambros et al. 2003; Chen et al. 2005). ta-siRNAs are processed from dsRNAs synthesized by an endogenous RNA-dependent RNA polymerase (RdRp) utilizing endogenous mRNAs as template (Peragine et al. 2004). nat-siRNAs are processed from dsRNAs formed between endogenous sense and antisense transcripts (Borsani et al. 2005). In addition to miRNA and siRNA, several classes of small RNAs have been reported. scanRNAs (scnRNAs; 27–30 nt) in Tetrahymena thermophila are thought to be derived from dsRNA precursors and guide DNA elimination (Mochizuki et al. 2002; Lee and Collins 2006). small RNAs (23–24 nt) in T. thermophila are mapped to the genome in clusters and are oriented in the same direction (Lee and Collins 2006). X-cluster small RNAs in C. elegans are derived from a locus on Chromosome X extending ∼2 kb and are oriented in the same direction (Ambros et al. 2003). Several factors including DCR-1, Dicer-related helicase DRH-1, the RdRp RRF-1, and the exonuclease ERI-1 are reported to be required for the accumulation of X-cluster small RNAs (Duchaine et al. 2006). The roles of 23- to 24-nt small RNAs in T. thermophila and X-cluster small RNAs in C. elegans remain unknown. Key factors required for the biogenesis and function of these small RNAs are Dicer and Argonaute proteins (for review, see Tomari and Zamore 2005). Dicer is an RNaseIII-like enzyme that recognizes dsRNAs, including pre-miRNAs, and processes them into double-stranded small RNAs (Hutvagner et al. 2001). The Dicer-generated double-stranded small RNAs are recruited by Argonaute, and then a strand (called the passenger strand) is released from Argonaute and the other strand (called the guide strand) remains associated with Argonaute as a guide to regulate gene expression (Matranga et al. 2005). Based on the amino acid sequence alignments, the Argonaute protein family has been subdivided into two subfamilies, referred to as the Argonaute and Piwi families (Carmell et al. 2002). Mice have four Argonaute family genes (AGO1–4) and three Piwi family genes (Miwi, Mili, and Piwil4). AGO1–4, which are ubiquitously expressed in many tissues (Lu et al. 2005), recruit miRNAs (Liu et al. 2004). Piwi family genes are expressed predominantly in male germline cells (Kuramochi-Miyagawa et al. 2001) and have crucial roles in spermatogenesis. Disruption of Miwi causes spermatogenic arrest at the beginning of the round spermatid stage (Deng and Lin 2002). Spermatogenesis in Mili-null mice is blocked completely at the early prophase of the first meiosis (Kuramochi-Miyagawa et al. 2004). The molecular functions and associated small RNAs of Piwi family proteins remain unknown. Whether endogenous siRNAs are present in mouse is unclear for three reasons: (1) There has been no report of siRNA cloning in mammals; (2) there is no evidence for the presence of RdRp activity in mammals, which generates dsRNAs, namely the precursors of siRNAs; and (3) induction of the interferon pathway by dsRNAs usually results in cell death, suggesting that mammalian cells may not tolerate dsRNAs (Elbashir et al. 2001a). However, in mouse oocytes and preimplantation embryos the interferon response is suppressed, and injection of long dsRNAs results in specific reduction in the amount of target mRNAs (Svoboda et al. 2000; Yan et al. 2005). Furthermore, retrotransposons and their antisense transcripts are expressed in mouse preimplantation embryos (Peaston et al. 2004; Svoboda et al. 2004a), and knockdown of Dicer in mouse preimplantation embryos results in a 50% increase in IAP and MuERV-L retrotransposons (Svoboda et al. 2004a). These studies suggest that endogenous dsRNA-induced RNAi can occur in mouse oocytes and early embryos. In mammals, hundreds of miRNAs have been identified by extensive small RNA cloning and bioinformatic analyses (Lagos-Quintana et al. 2001; Houbaviy et al. 2003; Lim et al. 2003). However, other classes of small RNAs have not been studied. In this study, as a step to obtain a whole picture of the small RNA population in mammals, we have cloned and sequenced small RNAs from oocytes and testes. We identified two classes of small RNAs other than miRNAs. One class comprised ∼22-nt retrotransposon-derived siRNAs in oocytes, which showed characteristics of small RNAs associated with RNAi. The other class comprised novel 26- to 30-nt germline small RNAs (gsRNAs) that were present in male germ cells and had some interesting features that were distinct from those of siRNAs and miRNAs. The features of the two classes of small RNAs suggest their distinct origins and functions and the existence of two separate small RNA pathways in the mouse germline.