Practical Data Processing Approach for RNA Sequencing of Microorganisms

The rapid evolvement of sequencing technology has generated huge amounts of DNA/RNA sequences, even with the continuous performance acceleration. Due to the wide variety of basic studies and applications derived from the huge number of species and the microorganism diversity, the targets to be sequenced are also expanding. The huge amounts of data generated by recently developed high-throughput sequencers have required highly efficient data analysis algorithms using recently developed high-performance computers. We have developed a highly accurate and cost-effective mapping strategy that includes the exclusion of unreliable base calls and correction of the reference sequence through provisional mapping of RNA sequencing reads. The use of mapping software tools, such as HISAT and STAR, precisely aligned RNA-Seq reads to the genome of a filamentous fungus considering exon-intron boundaries. The accuracy of the expression analysis through the refinement of gene models was achieved by the results of mapped RNA-Seq reads in combination with ab initio gene finding tools using generalized hidden Markov models (GHMMs). Visualization of the mapping results greatly helps evaluate and improve the entire analysis in terms of both wet experiment and data processing. We believe that at least a portion of our approach is useful and applicable to the analysis of any microorganism

Predicting Long-Term Effects of Infrastructure Development Projects in Continental South East Asia: IDE Geographical Simulation Model

It is important to develop a rigorous economic geography model for predicting changes in the location of population and industries across regions in the process of economic integration. The IDE Geographical Simulation Model (IDE-GSM) has been developed for two major objectives: (1) to determine the dynamics of locations of population and industries in East Asia in the long term, and (2) to analyze the impact of specific infrastructure projects on the regional economy at sub-national levels. The basic structure of the IDE-GSM is introduced in this article and accompanied with results of test analyses on the effects of the East West Economic Corridor on regions in Continental South East Asia. Results indicate that border costs appear to play a big role in the location choice of populations and industries, often a more important role than physical infrastructures themselves.Economic geography; Infrastructure development; Custom clearance

Economic impacts of economic corridors in Mongolia : an application of IDE-GSM

In this paper, we tried to estimate the economic impacts of the Central Asia Regional Economic Cooperation (CAREC) Economic Corridor 4a, 4b, and 4c projects, which enhance the connectivity between Mongolia and its surrounding countries, using a computational general equilibrium model based on spatial economics. The estimation results show that the economic impacts for Corridor 4b, which connects China and Russia through Ulaanbaatar, the capital of Mongolia, are the highest compared with the other two corridors. Apart from Mongolia, Corridor 4b also economically impacts China, EU, and Russia; thus, cooperation among these four parties might be a suitable arrangement for development. The evaluation of large-scale economic development of corridors is not very easy without proper evaluation tools

The IDE geographical simulation model : predicting long-term effects of infrastructure development projects

It is important to be able to predict changes in the location of populations and industries in regions that are in the process of economic integration. The IDE Geographical Simulation Model (IDE-GSM) has been developed with two major objectives: (1) to determine the dynamics of locations of populations and industries in East Asia in the long-term, and (2) to analyze the impact of specific infrastructure projects on the regional economy at sub-national levels. The basic structure of the IDE-GSM is introduced in this article and accompanied with results of test analyses on the effects of the East West Economic Corridor on regions in Continental South East Asia. Results indicate that border costs appear to play a big role in the location choice of populations and industries, often a more important role than physical infrastructures themselves

Economic impacts of the US-China trade war on the asian economy : an applied analysis of IDE-GSM

In this paper, we try to estimate the economic impacts of the US–China trade war that began in 2018. We used IDE-GSM, a computational general equilibrium simulation model, to estimate the economic impacts of a “full-confrontation” scenario wherein both countries impose 25% additional tariffs on all goods imported from each other for three years 2019 onwards. In our calculation, the economic impact for the US is -0.4% and -0.6% for China. Some Asian countries actually benefit from the trade war. As far as it remains bilateral, the trade war is only an issue for the concerned parties. We also ran the US–world trade war scenario, wherein the US and all other countries impose a 25% additional tariff on all goods. The negative impact on the global economy is 1.7%, much greater than the 0.1% impact from the US–China trade war. Thus, it is clear that the world cannot afford to engage in a multilateral trade war

China-Kyrgyzstan railway meets IDE-GSM

The impact of connecting Kashgar, Trougart, Uzgen, and Karasuu and facilitating customs at the national border between China and Kyrgyzstan are examined by using IDE-GSM (Institute of Developing Economies, JETRO Geographical Simulation Model). We found that the railway connection has a positive impact in southern Kyrgyzstan and a negative impact in regions of northern Kyrgyzstan, neither of which are the capital city of Kyrgyzstan

Comparing the economic impacts of Asian integration by computational simulation analysis

The Geographical Simulation Model developed by IDE-JETRO (IDE-GSM) is a computer simulation model based on spatial economics. IDE-GSM enables us to predict the economic impacts of various trade and transport facilitation measures. Here, we mainly compare the prioritized projects of the Master Plan on ASEAN Connectivity (MPAC) and the Comprehensive Asia Development Plan (CADP). MPAC focus on specific hard or soft infrastructure projects that connect one ASEAN member state to another while the CADP emphasizes the importance of economic corridors or linkages between a large cluster and another cluster. As compared with MPAC projects, the simulation analysis shows that CADP projects have much larger positive impacts on ASEAN countries

Inverse Magnetic Susceptibility Fabrics in Pelagic Sediment: Implications for Magnetofossil Abundance and Alignment

金沢大学理工研究域地球社会基盤学系Single-domain magnetite particles exhibit minimum susceptibility along their elongation, resulting in so-called inverse fabric of the anisotropy of magnetic susceptibility (AMS). We report the discovery of inverse AMS fabrics from pelagic clay recovered by a ∼12 m long piston core from the western North Pacific. A previous study identified fossil single-domain magnetite produced by magnetotactic bacteria (magnetofossils) as the dominant ferrimagnetic mineral in the sediment. The inverse AMS fabrics were found in a ∼2 m zone. The ∼6 and ∼4 m of sediment above and below this zone showed normal, horizontal AMS fabrics. Rock magnetic data and ferromagnetic resonance spectroscopy indicated that magnetofossils account for most of the mean susceptibility regardless of normal or inverse AMS. This was explained by the mixing models where the inverse fabric from magnetofossils is nearly balanced by the normal fabrics of terrigenous minerals. The corrected degree of AMS carried by magnetofossils in the sediment was estimated to be ∼1.01, which is comparable to that of typical pelagic sediment at shallow depth. On the other hand, terrigenous minerals in the sediment were estimated to have higher degree of anisotropy, possibly reflecting burial and subsequent erosion of >80 m of sediment, which was also suggested by a subbottom acoustic stratigraphy. This suggests that inverse AMS fabrics due to magnetofossils may be widespread in pelagic clay without strong compaction. ©2019. American Geophysical Union. All Rights Reserved

Simulating the decoupling world under Russia\u27s invasion of Ukraine: an application of IDE-GSM

The world appears to be divided into three blocs: the Chinese–Russian bloc, the Western alliance, and the rest of the world that remains neutral in the conflict between the former camps. This study estimates the economic impacts of “decoupling” scenarios on each country and region using a computable general equilibrium (CGE)-type simulation model called the geographical simulation model developed by the Institute of Developing Economies (IDE-GSM). Simulation results indicate that 1) the decoupling of Russia will not have a significant impact on the global economy, except i n the mining sector, and 2) if China joins the Russian camp, the impact will be s ignificant on the world economy, especially for Asian countries

Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata

KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain