Transfer of rice mitochondrial ribosomal protein L6 gene to the nucleus: acquisition of the 5'-untranslated region via a transposable element

<p>Abstract</p> <p>Background</p> <p>The mitochondria of contemporary organisms contain fewer genes than the ancestral bacteria are predicted to have contained. Because most of the mitochondrial proteins are encoded in the nucleus, the genes would have been transferred from the mitochondrion to the nucleus at some stage of evolution and they must have acquired cis-regulatory elements compatible with eukaryotic gene expression. However, most of such processes remain unknown.</p> <p>Results</p> <p>The ribosomal protein L6 gene (<it>rpl6</it>) has been lost in presently-known angiosperm mitochondrial genomes. We found that each of the two rice <it>rpl6 </it>genes (<it>OsRpl6-1 </it>and <it>OsRpl6-2</it>) has an intron in an identical position within the 5'-untranslated region (UTR), which suggests a duplication of the <it>rpl6 </it>gene after its transfer to the nucleus. Each of the predicted RPL6 proteins lacks an N-terminal extension as a mitochondrial targeting signal. Transient assays using green fluorescent protein indicated that their mature N-terminal coding regions contain the mitochondrial targeting information. Reverse transcription-PCR analysis showed that <it>OsRpl6-2 </it>expresses considerably fewer transcripts than <it>OsRpl6-1</it>. This might be the result of differences in promoter regions because the 5'-noncoding regions of the two <it>rpl6 </it>genes differ at a point close to the center of the intron. There are several sequences homologous to the region around the 5'-UTR of <it>OsRpl6-1 </it>in the rice genome. These sequences have characteristics similar to those of the transposable elements (TE) belonging to the <it>PIF</it>/Harbinger superfamily.</p> <p>Conclusion</p> <p>The above evidences suggest a novel mechanism in which the 5'-UTR of the transferred mitochondrial gene was acquired via a TE. Since the 5'-UTRs and introns within the 5'-UTRs often contain transcriptional and posttranscriptional cis-elements, the transferred rice mitochondrial <it>rpl6 </it>gene may have acquired its cis-element from a TE.</p

Fluctuation Dissipation Relation for a Langevin Model with Multiplicative Noise

A random multiplicative process with additive noise is described by a Langevin equation. We show that the fluctuation-dissipation relation is satisfied in the Langevin model, if the noise strength is not so strong.Comment: 11 pages, 6 figures, other comment

Response Rate Is Associated with Prolonged Survival in Patients with Advanced Non-small Cell Lung Cancer Treated with Gefitinib or Erlotinib

Introduction:Gaining a higher response rate (RR) has usually been determined as a primary end point in phase II trials evaluating the efficacy of new molecular targeted drugs. However, a relationship between clinical response and survival benefit has not been well studied in the patients treated with molecular targeted agents.Methods:Prospective trials of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) monotherapy in non-small cell lung cancer were extracted from MEDLINE, EMBASE, and the annual meetings in 2007 of the American Society of Clinical Oncology, European Cancer Conference, and World Conference on Lung Cancer.Correlation between clinical response and survival was examined using linear regression analysis. We also tried to compare the significance of RR as surrogate markers for survival with that of disease control rate (DCR) by calculating the area under their receiver operating characteristic (ROC) curves.Results:We identified 24 phase II trials and 4 phase III trials with a total of 6171 patients and 30 treatment arms, including 22 arms for the gefitinib group and 8 arms for the erlotinib group. Both RR and DCR strongly correlated with median survival time (MST; p < 0.0001 and p = 0.003, respectively). In an ROC analysis, the area under the ROC curve predicting MST prolongation by RR was 0.918, which was higher than the area under the ROC curve by DCR.Conclusions:We found a significant relationship between RR and MST in clinical trials with EGFR-TKIs. RR could be an independent surrogate marker for MST in the current response criteria in the clinical trials of EGFR-TKIs

Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

京の伝統野菜ミブナの育種の歴史を解明. 京都大学プレスリリース. 2021-06-02.Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna

Five-dimensional Black Hole and Particle Solution with Non-Abelian Gauge Field

We study the 5-dimensional Einstein-Yang-Mills system with a cosmological constant. Assuming a spherically symmetric spacetime, we find a new analytic black hole solution, which approaches asymptotically "quasi-Minkowski", "quasi anti-de Sitter", or "quasi de Sitter" spacetime depending on the sign of a cosmological constant. Since there is no singularity except for the origin which is covered by an event horizon, we regard it as a localized object. This solution corresponds to a magnetically charged black hole. We also present a singularity-free particle-like solution and a non-trivial black hole solution numerically. Those solutions correspond to the Bartnik-McKinnon solution and a colored black hole with a cosmological constant in the 4-dimensions. We analyze their asymptotic behaviors, spacetime structures and thermodynamical properties. We show that there is a set of stable solutions if a cosmological constant is negative.Comment: 17 pages, 17 figures, submitted to PR

High frequency ESR investigation on dynamical charge disproportionation and spin gap excitation in NaV_2O_5

A significant frequency dependence of the ESR line width is found in NaV_2O_5 between 34-100 K and the line width increases as the resonance frequency is increased from 95 GHz to 760 GHz. The observed frequency dependence is qualitatively explained in terms of the dynamical charge disproportionation. The present results show the essential role of the internal charge degree of freedom in a V-O-V bond. We have also proposed the existence of the Dzyaloshinsky-Moriya interaction in the low temperature charge ordered phase considering the breaking of the selection rule of ESR realized as the direct observation of the spin gap excitation.Comment: 9 figures submitted to J. Phys.Soc. Jp

Resonant X-ray Scattering in Manganites - Study of Orbital Degree of Freedom -

Orbital degree of freedom of electrons and its interplay with spin, charge and lattice degrees of freedom are one of the central issues in colossal magnetoresistive manganites. The orbital degree of freedom has until recently remained hidden, since it does not couple directly to most of experimental probes. Development of synchrotron light sources has changed the situation; by the resonant x-ray scattering (RXS) technique the orbital ordering has successfully been observed . In this article, we review progress in the recent studies of RXS in manganites. We start with a detailed review of the RXS experiments applied to the orbital ordered manganites and other correlated electron systems. We derive the scattering cross section of RXS where the tensor character of the atomic scattering factor (ASF) with respect to the x-ray polarization is stressed. Microscopic mechanisms of the anisotropic tensor character of ASF is introduced and numerical results of ASF and the scattering intensity are presented. The azimuthal angle scan is a unique experimental method to identify RXS from the orbital degree of freedom. A theory of the azimuthal angle and polarization dependence of the RXS intensity is presented. The theoretical results show good agreement with the experiments in manganites. Apart from the microscopic description of ASF, a theoretical framework of RXS to relate directly to the 3d orbital is presented. The scattering cross section is represented by the correlation function of the pseudo-spin operator for the orbital degree of freedom. A theory is extended to the resonant inelastic x-ray scattering and methods to observe excitations of the orbital degree of freedom are proposed.Comment: 47 pages, 24 figures, submitted to Rep. Prog. Phy

Spectroscopy of 32Ne and the Island of Inversion

We report on the first spectroscopic study of the N=22 nucleus 32Ne at the newly completed RIKEN Radioactive Ion Beam Factory. A single gamma-ray line with an energy of 722(9) keV was observed in both inelastic scattering of a 226 MeV/u 32Ne beam on a Carbon target and proton removal from 33Na at 245 MeV/u. This transition is assigned to the de-excitation of the first J^pi = 2+ state in 32Ne to the 0+ ground state. Interpreted through comparison with state-of-the-art shell model calculations, the low excitation energy demonstrates that the Island of Inversion extends to at least N=22 for the Ne isotopes.Comment: Accepted for publication in Phys. Rev. Lett. 11 pages, 3 figure

Identification of 45 New Neutron-Rich Isotopes Produced by In-Flight Fission of a 238U Beam at 345 MeV/nucleon

A search for new isotopes using in-flight fission of a 345 MeV/nucleon 238U beam has been carried out at the RI Beam Factory at the RIKEN Nishina Center. Fission fragments were analyzed and identified by using the superconducting in-flight separator BigRIPS. We observed 45 new neutron-rich isotopes: 71Mn, 73,74Fe, 76Co, 79Ni, 81,82Cu, 84,85Zn, 87Ga, 90Ge, 95Se, 98Br, 101Kr, 103Rb, 106,107Sr, 108,109Y, 111,112Zr, 114,115Nb, 115,116,117Mo, 119,120Tc, 121,122,123,124Ru, 123,124,125,126Rh, 127,128Pd, 133Cd, 138Sn, 140Sb, 143Te, 145I, 148Xe, and 152Ba

One-dimensional dynamics of the d-electrons in α′\alpha'-NaV2_{2}O5_{5}

We have studied the electronic properties of the ladder compound $\alpha'$-NaV$_{2}$O$_{5}$, adopting a joint experimental and theoretical approach. The momentum-dependent loss function was measured using electron energy-loss spectroscopy in transmission. The optical conductivity derived from the loss function by a Kramers-Kronig analysis agrees well with our results from LSDA+U band-structure calculations upon application of an antiferromagnetic alignment of the V~3$d_{xy}$ spins along the legs and an on-site Coulomb interaction U of between 2 and 3 eV. The decomposition of the calculated optical conductivity into contributions from transitions between selected energy regions of the DOS reveals the origin of the observed anisotropy of the optical conductivity. In addition, we have investigated the plasmon excitations related to transitions between the vanadium states within an effective 16 site vanadium cluster model. Good agreement between the theoretical and experimental loss function was obtained using the hopping parameters derived from the tight binding fit to the band-structure and moderate Coulomb interactions between the electrons within the ab plane.Comment: 23 pages, 8 figures; submitted to PR