The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells.

Transfer RNAs (tRNAs) function in translational machinery and further serves as a source of short non-coding RNAs (ncRNAs). tRNA-derived ncRNAs show differential expression profiles and play roles in many biological processes beyond translation. Molecular mechanisms that shape and regulate their expression profiles are largely unknown. Here, we report the mechanism of biogenesis for tRNA-derived Piwi-interacting RNAs (td-piRNAs) expressed in Bombyx BmN4 cells. In the cells, two cytoplasmic tRNA species, tRNAAspGUC and tRNAHisGUG, served as major sources for td-piRNAs, which were derived from the 5\u27-part of the respective tRNAs. cP-RNA-seq identified the two tRNAs as major substrates for the 5\u27-tRNA halves as well, suggesting a previously uncharacterized link between 5\u27-tRNA halves and td-piRNAs. An increase in levels of the 5\u27-tRNA halves, induced by BmNSun2 knockdown, enhanced the td-piRNA expression levels without quantitative change in mature tRNAs, indicating that 5\u27-tRNA halves, not mature tRNAs, are the direct precursors for td-piRNAs. For the generation of tRNAHisGUG-derived piRNAs, BmThg1l-mediated nucleotide addition to -1 position of tRNAHisGUG was required, revealing an important function of BmThg1l in piRNA biogenesis. Our study advances the understanding of biogenesis mechanisms and the genesis of specific expression profiles for tRNA-derived ncRNAs

Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells.

Piwi proteins and their bound Piwi-interacting RNAs (piRNAs) are predominantly expressed in the germline and play crucial roles in germline development by silencing transposons and other targets. Bombyx mori BmN4 cells are culturable germ cells that equip the piRNA pathway. Because of the scarcity of piRNA-expressing culturable cells, BmN4 cells are being utilized for the analyses of piRNA biogenesis. We here report that the piRNA biogenesis in BmN4 cells is regulated by cell density. As cell density increased, the abundance of Piwi proteins and piRNA biogenesis factors was commonly upregulated, resulting in an increased number of perinuclear nuage-like granules where Piwi proteins localize. Along with these phenomena, the abundance of mature piRNAs also globally increased, whereas levels of long piRNA precursor and transposons decreased, suggesting that increasing cell density promotes piRNA biogenesis pathway and that the resultant accumulation of mature piRNAs is functionally significant for transposon silencing. Our study reveals a previously uncharacterized link between cell density and piRNA biogenesis, designates cell density as a critical variable in piRNA studies using BmN4 cell system, and suggests the alteration of cell density as a useful tool to monitor piRNA biogenesis and function

Slippage detection for grasping force control of robotic hand using force sensing resistors

This paper presents the formulation of a nonlinear adaptive backstepping force control in grasping weight-varying objects using robotic hand driven by Pneumatic Artificial Muscle (PAM). The modelling and control problems arise from the high nonlinear PAM dynamics and the inherent hysteresis leading to a lack of robustness in the hand’s performance. The robotic finger and the PAM actuator been mathematically modelled as a nonlinear second order system based on an empirical approach. An adaptive backstepping controller has been designed for force control of the pneumatic hand. The estimator of the system uncertainty is incorporated into the proposed control law and a slip detection strategy is introduced to grasp objects with changing weights. The simulation and experimental results show that the robotic hand can maintain grasping an object and stop further slippage when its weight is increased up to 500 g by detecting the slip signal from the force sensor. The results also have proven that the adaptive backstepping controller is capable to compensate the uncertain coulomb friction force of PAM actuator with maximum hysteresis error 0.18◦

Generation of 2′,3′-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome

Cellular RNA molecules contain phosphate or hydroxyl ends. A 2′,3′-cyclic phosphate (cP) is one of the 3′-terminal forms of RNAs mainly generated from RNA cleavage by ribonucleases. Although transcriptome profiling using RNA-seq has become a ubiquitous tool in biological and medical research, cP-containing RNAs (cP-RNAs) form a hidden transcriptome layer, which is infrequently recognized and characterized, because standard RNA-seq is unable to capture them. Despite cP-RNAs’ invisibility in RNA-seq data, increasing evidence indicates that they are not accumulated simply as non-functional degradation products; rather, they have physiological roles in various biological processes, designating them as noteworthy functional molecules. This review summarizes our current knowledge of cP-RNA biogenesis pathways and their catalytic enzymatic activities, discusses how the cP-RNA generation affects biological processes, and explores future directions to further investigate cP-RNA biology

Effective theory for universal seesaw model and FCNC

We study the quark sector of the universal seesaw model with SU(2)$_L$ $\times$ SU(2)$_R$ $\times$ $U(1)$.The model incorporates the seesaw mechanism with the vector-like quarks (VLQs). The purpose of this work is to study the model with the effective theory. After integrating the heavy five VLQs, we derive the effective theory with four up-type quark and three down type quark. In this work, the FCNC of Z boson for top quark and top$^\prime$ quark is derived.Comment: 4 pages, Contribution to the proceedings for International Conference on Kaon Physics 202

Loading orientation dependence of the formation behavior of deformation kink bands in the Mg-based long-period stacking ordered (LPSO) phase

The variation in the deformation behavior of a directionally solidified (DS) Mg-based long-period stacking ordered (LPSO)-phase crystal depending on the loading orientation was examined. The frequency of formation of the beak-like shape of the deformation band, which is known as one of the important deformation mechanisms in the LPSO phase, monotonically decreased as the inclination angle of the loading orientation with respect to the crystal growth direction in the DS crystal increased, and was accompanied by a decrease in the yield stress due to the activation of basal slip. Deformation bands formed along a direction approximately perpendicular to the grain boundary independent of the loading orientation. The crystal rotation axes selected in the deformation bands were perpendicular to [0001] in almost all grains, independent of the loading orientation. However, the rotation axes in the bands were not fixed but varied between h1010 - i and h1120 - i; this variation was correlated with the loading axis. These observed features strongly suggest that the deformation bands formed in the LPSO phase are predominantly deformation kink bands and that the formation mechanism itself does not vary with the loading orientation but instead its details. The selectivity of the crystal rotation axis in the kink band is strongly affected by the loading orientation.Hagihara K., Okamoto T., Ueyama R., et al. Loading orientation dependence of the formation behavior of deformation kink bands in the Mg-based long-period stacking ordered (LPSO) phase. Materials Transactions 61, 1821 (2020); https://doi.org/10.2320/matertrans.MT-MM2019001