In mammalian mitochondria, 22 species of tRNAs encoded in mitochondrial DNA play crucial roles in the translation of 13 essential subunits of the respiratory chain complexes involved in oxidative ...phosphorylation. Following transcription, mitochondrial tRNAs are modified by nuclear-encoded tRNA-modifying enzymes. These modifications are required for the proper functioning of mitochondrial tRNAs (mt tRNAs), and the absence of these modifications can cause pathological consequences. To date, however, the information available about these modifications has been incomplete. To address this issue, we isolated all 22 species of mt tRNAs from bovine liver and comprehensively determined the post-transcriptional modifications in each tRNA by mass spectrometry. Here, we describe the primary structures with post-transcriptional modifications of seven species of mt tRNAs which were previously uncharacterized, and provide revised information regarding base modifications in five other mt tRNAs. In the complete set of bovine mt tRNAs, we found 15 species of modified nucleosides at 118 positions (7.48% of total bases). This result provides insight into the molecular mechanisms underlying the decoding system in mammalian mitochondria and enables prediction of candidate tRNA-modifying enzymes responsible for each modification of mt tRNAs.
We introduce a cluster extension of multipole moments to discuss the anomalous Hall effect (AHE) in both ferromagnetic (FM) and antiferromagnetic (AFM) states in a unified framework. We first derive ...general symmetry requirements for the AHE in the presence or absence of the spin-orbit coupling by considering the symmetry of the Berry curvature in k space. The cluster multipole (CMP) moments are then defined to quantify the macroscopic magnetization in noncollinear AFM states as a natural generalization of the magnetization in FM states. We identify the macroscopic CMP order which induces the AHE. The theoretical framework is applied to the noncollinear AFM states of Mn3Ir , for which an AHE was predicted in a first-principles calculation, and Mn3Z (Z = Sn, Ge) , for which a large AHE was recently discovered experimentally. We further compare the AHE in Mn3Z and bcc Fe in terms of the CMP. We show that the AHE in Mn3Z is characterized by the magnetization of a cluster octupole moment in the same manner as that in bcc Fe characterized by the magnetization of the dipole moment.
We have performed a 2.5-dimensional magnetohydrodynamic simulation that resolves the propagation and dissipation of Alfvén waves in the solar atmosphere. Alfvénic fluctuations are introduced on the ...bottom boundary of the extremely large simulation box that ranges from the photosphere to far above the solar wind acceleration region. Our model is ab initio in the sense that no corona and no wind are assumed initially. The numerical experiment reveals the quasi-steady solution that has the transition from the cool to the hot atmosphere and the emergence of the high speed wind. The global structure of the resulting hot wind solution fairly well agrees with the coronal and the solar wind structure inferred from observations. The purpose of this study is to complement the previous paper by Matsumoto & Suzuki and describe the more detailed results and the analysis method. These results include the dynamics of the transition region and the more precisely measured heating rate in the atmosphere. Particularly, the spatial distribution of the heating rate helps us to interpret the actual heating mechanisms in the numerical simulation. Our estimation method of heating rate turned out to be a good measure for dissipation of Alfvén waves and low beta fast waves.
We propose a systematic method to generate a complete orthonormal basis set of multipole expansion for magnetic structures in arbitrary crystal structure. The key idea is the introduction of a ...virtual atomic cluster of a target crystal on which we can clearly define the magnetic configurations corresponding to symmetry-adapted multipole moments. The magnetic configurations are then mapped onto the crystal so as to preserve the magnetic point group of the multipole moments, leading to the magnetic structures classified according to the irreducible representations of the crystallographic point group. We apply the present scheme to pyrochlore and hexagonal ABO3 crystal structures and demonstrate that the multipole expansion is useful to investigate the macroscopic responses of antiferromagnets.
Genome engineering using programmable nucleases enables homologous recombination (HR)-mediated gene knock-in. However, the labour used to construct targeting vectors containing homology arms and ...difficulties in inducing HR in some cell type and organisms represent technical hurdles for the application of HR-mediated knock-in technology. Here, we introduce an alternative strategy for gene knock-in using transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) mediated by microhomology-mediated end-joining, termed the PITCh (Precise Integration into Target Chromosome) system. TALEN-mediated PITCh, termed TAL-PITCh, enables efficient integration of exogenous donor DNA in human cells and animals, including silkworms and frogs. We further demonstrate that CRISPR/Cas9-mediated PITCh, termed CRIS-PITCh, can be applied in human cells without carrying the plasmid backbone sequence. Thus, our PITCh-ing strategies will be useful for a variety of applications, not only in cultured cells, but also in various organisms, including invertebrates and vertebrates.
Peptide:N-glycanase (PNGase) is a de-N-glycosylating enzyme that cleaves intact N-glycans from glycoproteins/glycopeptides. The activity of the cytoplasmic PNGase in several mammalian-derived ...cultured cells was first reported in 1993, and 7 years later, the gene encoding the enzyme was identified in budding yeast. Although the gene-PNG1 in budding yeast and NGLY1/Ngly1 in mammalian cells-appears to be well conserved throughout eukaryotes, the biological significance of this enzyme has remained elusive until recently. However, discovery of a human genetic disorder involving the NGLY1 gene clearly indicates that this enzyme plays a critical role in human biology. This review summarizes the research history of cytoplasmic PNGase. The importance of curiosity-driven, pure 'basic science' will also be discussed.
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