Search

Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5′-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model of PhopRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available. Here, this information was combined to orient the crystallographic structures of the proteins relative to their RNA binding sites in the PhopRNA model. Some alterations were made to the PhopRNA model to improve the fit. In the resulting structure, a heterotetramer composed of PhoPop5 and PhoRpp30 bridges helices P3 and P16 in the PhopRNA C-domain, thereby probably stabilizing a double-stranded RNA structure (helix P4) containing catalytic Mg2+ ions, while a heterodimer of PhoRpp21 and PhoRpp29 locates on a single-stranded loop connecting helices P11 and P12 in the specificity domain (S-domain) in PhopRNA, probably forming an appropriate conformation of the precursor tRNA (pre-tRNA) binding site. The fifth protein PhoRpp38 binds each kink-turn (K-turn) motif in helices P12.1, P12.2, and P16 in PhopRNA. Comparison of the structure of the resulting 3-D model with that of bacterial RNase P suggests transition from RNA-RNA interactions in bacterial RNase P to protein-RNA interactions in archaeal RNase P. The proposed 3-D model of P. horikoshii RNase P will serve as a framework for further structural and functional studies on archaeal, as well as eukaryotic, RNase Ps.

We investigate a differentiated mixed duopoly with two cities where a public firm and a private firm are located in different cities. We find that in most cases the privatization level is higher under centralization (the national or regional government owns the public firm) than under decentralization (a city government owns the public firm). In particular, under decentralization, the public firm is fully owned by the city government if the substitutability of differentiated goods is relatively high. While the social welfare is higher under centralization, the welfare of the city with the public firm is higher under decentralization in most cases.

Ribonuclease P (RNase P) is a ribonucleoprotein that catalyzes the processing of 5′ leader sequences of precursor tRNAs (pre-tRNA). RNase P proteins PhoRpp21 and PhoRpp29 in the hyperthermophilic archaeon Pyrococcus horikoshii, homologs of human nuclear RNase P proteins Rpp21 and Rpp29 respectively, fold into a heterodimeric structure and synergistically function in the activation of the specificity domain (S-domain) in RNase P RNA (PhopRNA). To elucidate the molecular basis for their cooperativity, we first analyzed binding ability to PhopRNA using a pull-down assay. The result showed that PhoRpp21 is able to bind to PhopRNA in the absence of PhoRpp29, whereas PhoRpp29 alone has reduced affinity to PhopRNA, suggesting that PhoRpp21 primarily functions as a binding element for PhopRNA in the PhoRpp21-PhoRpp29 complex. Mutational analyses suggested that although individual positively charged clusters contribute little to the PhopRNA binding, Lys53, Lys54, and Lys56 at the N-terminal helix (α2) in PhoRpp21 and 10 C-terminal residues in PhoRpp29 are essential for PhopRNA activation. Moreover, deletion of a single stranded loop linking P11 and P12 helices in the PhopRNA S-domain impaired the PhoRpp21-PhoRpp29 complex binding to PhopRNA. Collectively, the present results suggest that PhoRpp21 binds the loop between P11 and P12 helices through overall positively charged clusters on the surface of the complex and serves as a scaffold for PhoRpp29 to optimize structural conformation of its N-terminal helix (α2) in PhoRpp21, as well as C-terminal residues in PhoRpp29, for RNase P activity.

Introduction: Interhospital transfer to endovascular-capable centers (ECCs) is reported to correlate with worse clinical outcome after endovascular stroke reperfusion therapy (ESRT). The aim of this study was to investigate the relationship between admission mode and functional outcome after ESRT in real clinical setting in Japan. Methods: The RICOVERY study retrospectively registered 575 patients with large vessel occlusion who were admitted to and underwent ESRT at 16 ECCs in Ibaraki prefecture, located just northeast of Tokyo, within 24 hours of onset between January 2015 and December 2017. We extracted patients without in-hospital stroke onset or recurrence and divided them into two groups: those with interhospital transfer (I group) and with direct admission to ECCs (D group). Favorable outcome (FO) was defined as a mRS of 0-2 at discharge. We additionally performed a subgroup analysis with patients with premorbid mRS of 0-2 and who underwent ESRT within 6 hours of onset. Results: A total of 483 patients (198 women, 75±11 years) was included. Intravenous thrombolysis was performed in 289 patients (60%). In the I group (n=69), median baseline NIHSS score was lower (17 vs 19, p=0.025) and the proportion of large-artery atherosclerosis was higher (19% vs 10%, p=0.025) compared with the D group (n=414). The rates of reperfusion (mTICI grade 2b/3) were similarly high in both groups (88% and 86%, respectively). Although median onset-to-puncture time (OPT) was longer in the I group than in the D group (240 min vs 185 min, p=0.01), no significant difference was shown in the rate of FO between the groups (28% vs 36%, p=0.197). In subgroup analysis, baseline NIHSS scores and stroke subtypes were similar between the I group (n=51) and the D group (n=273). Median OPT was longer in the I group than in the D group (220 min vs 160 min, p=0.005) as with the entire study cohort, and the rate of FO in the I group was lower than in the D group (24% vs 43%, p=0.01). After multivariate adjustment, interhospital transfer was a negative predictor of FO (Odds ratio, 0.343; 95% confidence interval, 0.158-0.747). Conclusion: In this Japanese real-world study, interhospital transfer was associated with delays of ESRT and lower chance of FO within a 6-hour time window.

Public-Private Partnerships (PPP) include various governance structures which distribute tasks and ownership of facility differently. Many earlier theoretical studies using the incomplete contracts theory assume two tasks, building and operation, for the projects of public services. This may be too simple, however, to consider complicated projects such as prisons. Critics argue that those studies could not fully explain the reality. In addition, Those models are not suitable for comparing different PPP approaches such as Private Finance Initiative (PFI) and private management. The present paper divides the task of operation into two (maintenance and security). This enables us to compare four relevant governance structures in a single framework, and to suggest the conditions for successful PPP prison projects. The main findings are that the tasks of maintenance and security should be conducted by different parties (private consortium and civil servant) under certain conditions, while unbundling construction and operation stages is desirable in other cases.

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of the 5′-leader sequence of precursor tRNA (pre-tRNA) and other small RNAs in all phylogenetic domains. A characteristic feature of archaeal RNase P RNAs is that they alone have, unlike bacterial counterparts, little pre-tRNA cleavage activity, but the interaction with protein components activates their catalytic activity. In addition, it has not yet been confirmed whether archaeal RNase P, like its bacterial and eukaryotic counterparts, has additional substrates in vivo. We have found that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. Biochemical and structural studies over the past 10 years have revealed that PhoPop5 and PhoRpp30 form a heterotetrameric complex and cooperatively activates a catalytic domain (C-domain), while PhoRpp21 and PhoRpp29 form a heterodimer and function together to activate a specificity domain (S-domain) in PhopRNA. As for the fifth protein, PhoRpp38 is involved in elevation of the optimum temperature of RNase P activity, binding to two peripheral stem-loops, including helices P12.1/12.2 and P16. Moreover, comparative analysis of the RNase P RNA sequences and existing crystallographic structural information of the bacterial RNase P RNAs were combined to generate a phylogenetically supported three-dimensional (3D) model of PhopRNA. Recent biochemical data on the protein-PhopRNA interactions localized the protein binding sites on PhopRNA. Moreover, a comparative transcriptome on the hyperthermophilic archaeon Thermococcus kodakarensis suggested the presence of additional substrates for archaeal RNase Ps. Here, we review biochemical information on archaeal RNase Ps, mainly focusing on recent studies that allow us to generate a structural and mechanistic model for the PhopRNA activation by the protein cofactors.

The protein component PhoRpp38 of Pyrococcus horikoshii ribonuclease P (RNase P) is known to be a multifunctional RNA-binding protein. Previous biochemical data indicate that it binds to two stem-loops in RNase P RNA (PhopRNA). Thermodynamic analysis revealed that PhoRpp38 and PhopRNA interact with each other with an association constant (Ka) of 1.56 × 107 M−1. It was further found that PhoRpp38 simultaneously binds two stem-loop structures in PhopRNA with approximately equal affinity. Crystals of PhoRpp38 in complex with the stem-loop were grown and diffracted to a resolution of 7.0 A on a synchrotron X-ray source.

The assumption of separate tax bases on which the literature of preferential tax regimes has been based is not necessarily the case. In this paper we assume a single type of capital, or money, invested in different industries as well as in different countries. Tax elasticities can differ across industries depending on production technologies and therefore governments have incentives to provide preferential tax treatment to certain industries. Then it is shown that preferential regimes may not be desirable in different senses from the literature. Resumen La suposicion de bases fiscales separadas en las que se ha basado la literatura de regimenes fiscales preferenciales no es necesariamente asi. En este articulo asumimos un unico tipo de capital, o dinero, invertido en industrias diferentes asi como en paises diferentes. Las elasticidades fiscales pueden diferir entre industrias dependiendo de las tecnologias de la produccion y por tanto los gobiernos tienen incentivos para proporcionar un trato fiscal preferencial a ciertas industrias. Se muestra entonces que los regimenes preferenciales podrian no ser deseables en sentidos diferentes de los de la literatura.

International audience; In this chapter, we propose methods for correcting gate-level designs by identifying appropriate logic functions for internal gates. We introduce programmable circuits, such as look up table (LUT) and multiplexer (MUX) to the circuits under debugging, in order to formulate the correction processes mathematically. There are two steps in the proposed methods. The first one is to identify sets of gates and their appropriate inputs whose functions are to be modified. The second one is to actually identify logic functions for the correction by solving QBF (Quantified Boolean Formula) problems with repeated application of SAT solvers. There are a number of bugs which cannot be corrected unless the inputs of the gates to be modified are changed from the original ones, and the selection of such additional inputs is a key for effective debugging. We show a couple of methods by which appropriate inputs to the gates can be efficiently identified. Experimental results for each such a method as well as their combinations targeting benchmark circuits as well as industrial ones are shown.

As the verification and debugging of complicated VLSI designs are dominating the chip development time, automated debugging becomes more and more important. In this paper, we propose a method to correct buggy gate-level designs by introducing programmable circuits, such as look up table (LUT) and multiplexer (MUX), that are inserted in order to formulate the debugging processes mathematically. We first replace sets of gates with programmable circuits and try to find a configuration for correction. Some bugs, however, cannot be fixed with only the replacement. In such cases, we add another input to a LUT, where the selection of such additional input is a key for effective debugging. We introduce a necessary condition by which many unusable signals as input to the LUTs can be efficiently eliminated. The experimental results on industrial designs having real bugs show that our proposed method can automatically correct the designs.