RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here

Turicibacter and Acidaminococcus predict immune-related adverse events and efficacy of immune checkpoint inhibitor

IntroductionImmune checkpoint inhibitors have had a major impact on cancer treatment. Gut microbiota plays a major role in the cancer microenvironment, affecting treatment response. The gut microbiota is highly individual, and varies with factors, such as age and race. Gut microbiota composition in Japanese cancer patients and the efficacy of immunotherapy remain unknown. MethodsWe investigated the gut microbiota of 26 patients with solid tumors prior to immune checkpoint inhibitor monotherapy to identify bacteria involved in the efficacy of these drugs and immune-related adverse events (irAEs).ResultsThe genera Prevotella and Parabacteroides were relatively common in the group showing efficacy towards the anti-PD-1 antibody treatment (effective group). The proportions of Catenibacterium (P = 0.022) and Turicibacter (P = 0.049) were significantly higher in the effective group than in the ineffective group. In addition, the proportion of Desulfovibrion (P = 0.033) was significantly higher in the ineffective group. Next, they were divided into irAE and non-irAE groups. The proportions of Turicibacter (P = 0.001) and Acidaminococcus (P = 0.001) were significantly higher in the group with irAEs than in those without, while the proportions of Blautia (P = 0.013) and the unclassified Clostridiales (P = 0.027) were significantly higher in the group without irAEs than those with. Furthermore, within the Effective group, Acidaminococcus and Turicibacter (both P = 0.001) were more abundant in the subgroup with irAEs than in those without them. In contrast, Blautia (P = 0.021) and Bilophila (P= 0.033) were statistically significantly more common in those without irAEs.DiscussionOur Study suggests that the analysis of the gut microbiota may provide future predictive markers for the efficacy of cancer immunotherapy or the selection of candidates for fecal transplantation for cancer immunotherapy

A flexible representation of omic knowledge for thorough analysis of microarray data

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site

GJETC report 2020 : German-Japanese cooperation in energy research ; supporting the closure of implementation gaps ; key results and policy recommendations

The German-Japanese Energy Transition Council (GJETC) was established in 2016 by experts from research institutions, energy policy think tanks, and practitioners in Germany and Japan. The objectives and main activities of the Council and the supporting secretariats are to identify and analyze current and future issues regarding policy frameworks, markets, infrastructure, and technological developments in the energy transition, and to hold Council meetings to exchange ideas and propose better policies and strategies. In its second project phase (2018-2020), the GJETC had six members from academia on the Japanese side, and eight members on the German side, with one Co-Chair from each country. From October 2018 to March 2020, the GJETC worked on and debated six topics: 1) Digitalization and the energy transition. 2) Hydrogen society. 3) Review of German and Japanese long-term energy scenarios and their evaluation mechanism. 4) Buildings, energy efficiency, heating/cooling. 5) Integration costs of renewable energies. 6) Transport and sector coupling. The outputs and the recommendations of the second phase of the GJETC are summarized in this report

GJETC report 2018 : intensified German-Japanese cooperation in energy research ; key results and policy recommendations

The challenges and also potentials of the energy transition are tremendous in Germany, as well as in Japan. Sometimes, structures of the old energy world need "creative destruction" to clear the way for innovations for a decarbonized, low-risk energy system. In these times of disruptive changes, a constructive and sometimes controversial dialog within leading industrial nation as Japan and Germany over the energy transition is even more important. The German-Japanese Energy Transition Council (GJETC) released a summarizing report for the first project phase 2016-2018. It includes jointly formulated recommendations for politics as well as a controversial dialogue part. The Council jointly states and recommends that: Ambitious long-term targets and strategies for a low-carbon energy system must be defined and ambitiously implemented; Germany and Japan as high technology countries need to take the leadership. Both countries will have to restructure their energy systems substantially until 2050 while maintaining their competitiveness and securing energy supply. Highest priority is given to the forced implementation of efficiency technologies and renewable energies, despite different views on nuclear energy. In both countries all relevant stakeholders - but above all the decision-makers on all levels of energy policy - need to increase their efforts for a successful implementation of the energy transition. Design of the electricity market needs more incentives for flexibility options and for the extensive expansion of variable power generation, alongside with strategies for cost reduction for electricity from photovoltaic and wind energy. The implementation gap of the energy efficiency needs to be closed by an innovative energy policy package to promote the principle of "Energy Efficiency First". Synergies and co-benefits of an enhanced energy and resource efficiency policy need to be realized. Co-existence of central infrastructure and the growing diversity of the activities for decentralization (citizens funding, energy cooperatives, establishment of public utility companies) should be supported. Scientific cooperation can be intensified by a joint working group for scenarios and by the establishment of an academic exchange program

Is 1+1 more than 2? : The German-Japanese Energy Transition Council (GJETC), a role model for bi-national cooperation

In spite of differences in energy policies and supply, Japan and Germany have to master similar challenges: To reorganize the energy supply system towards - in the long term - being reliable, affordable, low in risks and resource use, and climate-neutral. At the same time, the ecological modernization should maintain or even strengthen international competitiveness. To better address these challenges, a bi-national expert council has been established between the two high-tech countries in 2016 - the GJETC. The aim of the GJETC is to show that despite different starting points, a national energy transition can be more successful, if both countries learn from their strengths and also weaknesses, to avoid the latter. If the implementation of an energy transition in the two countries is socially and economically sound and advances technology innovation and deployment, it may not only double success, but can also serve as blue prints for other countries, especially due to learning from similarities and differences. For example: Why is per capita energy consumption higher in transport in Germany, but energy intensity higher in Japan's building sector? How can variable renewable energies be integrated in an efficient energy system at lowest costs? The Council meets twice a year, holds stakeholder dialogues and outreach events, and prepares policy papers on strategic topics of mutual interest. Four comprehensive studies, each in cooperation of a German and a Japanese research institute, have been the basis for 15 joint key recommendations during the 1st phase. The 2nd phase to 2020 will study the role of hydrogen and digitalisation for the energy transition, as well as other topics. The paper presents the findings and recommendations of the GJETC of the first phase 2016-18 as well as first results of the second phase. It also reviews the setup of the GJETC and the way it works, to assess if and how it can serve as a role model of bilateral cooperation on the energy transition

Unidirectionally Aligned Donor–Acceptor Semiconducting Polymers in Floating Films for High‐Performance Unipolar n‐Channel Organic Transistors

Abstract The orientational control of semiconducting polymers (SCPs) in floating films offers several advantages over conventional solution‐processing methods for device fabrication, and the unidirectional floating film transfer method (UFTM) has been applied to fabricate large‐area oriented p‐type SCP films. Here, UFTM can be used to prepare high‐performance n‐type SCP films of P(NDI2OD‐T2) is reported. A strong correlation between the degree of polymer orientation and the solvent used for the preparation of P(NDI2OD‐T2) floating films is observed. In particular, the size of the nanofibers aligned along the orientation direction prepared using chloroform is dramatically increased by adding a small amount of chlorobenzene. Microstructural characterization reveals that the P(NDI2OD‐T2) floating films are uniaxially aligned with edge‐on orientation, whereas the spin‐coated films are isotropic with face‐on orientation. Notably, the floating films of P(NDI2OD‐T2) prepared with solvent blending have higher electron mobility with ambipolar‐like device characteristics and high threshold voltage (VTH) of ≈25 V. Finally, using the one‐step immersion process, the introduction of an interlayer of hexa(ethylene glycol)‐dithiol between the source/drain contacts and P(NDI2OD‐T2) film results in a drastic improvement in device, giving unipolar n‐channel transistor characteristics with a VTH of ≈0 V, on/off ratio of >105, and mobility reliability factor of almost 100%

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences

We mapped RIKEN Arabidopsis full-length (RAFL) cDNAs to the Arabidopsis thaliana genome to search for alternative splicing events. We used 278 734 full-length and 3′/5′ terminal reads of the sequences of 220 214 RAFL cDNA clones for the analysis. Eighty-nine percent of the cDNA sequences could be mapped to the genome and were clustered in 17 130 transcription units (TUs). Alternative splicing events were found in 1764 out of 15 214 TUs (11.6%) with multiple sequences. We collected full-length cDNA clones from plants grown under various environmental conditions or from various organs. We then analyzed the correlation between alternative splicing events and environmental stress conditions. Alternative splicing profiles changed according to environmental stress conditions and the various developmental stages of plant organs. In particular, cold-stress conditions affected alternative splicing profiles. The change in alternative splicing profiles under cold stress may be mediated by alternative splicing and transcriptional regulation of splicing factors

Can Human Embryonic Stem Cell-Derived Stromal Cells Serve a Starting Material for Myoblasts?

A large number of myocytes are necessary to treat intractable muscular disorders such as Duchenne muscular dystrophy with cell-based therapies. However, starting materials for cellular therapy products such as myoblasts, marrow stromal cells, menstrual blood-derived cells, and placenta-derived cells have a limited lifespan and cease to proliferate in vitro. From the viewpoints of manufacturing and quality control, cells with a long lifespan are more suitable as a starting material. In this study, we generated stromal cells for future myoblast therapy from a working cell bank of human embryonic stem cells (ESCs). The ESC-derived CD105+ cells with extensive in vitro proliferation capability exhibited myogenesis and genetic stability in vitro. These results imply that ESC-derived CD105+ cells are another cell source for myoblasts in cell-based therapy for patients with genetic muscular disorders. Since ESCs are immortal, mesenchymal stromal cells generated from ESCs can be manufactured at a large scale in one lot for pharmaceutical purposes

Biochemical Characterization of a Novel Indole Prenyltransferase from Streptomyces sp. SN-593▿ †

Genome sequencing of Streptomyces species has highlighted numerous potential genes of secondary metabolite biosynthesis. The mining of cryptic genes is important for exploring chemical diversity. Here we report the metabolite-guided genome mining and functional characterization of a cryptic gene by biochemical studies. Based on systematic purification of metabolites from Streptomyces sp. SN-593, we isolated a novel compound, 6-dimethylallylindole (DMAI)-3-carbaldehyde. Although many 6-DMAI compounds have been isolated from a variety of organisms, an enzyme catalyzing the transfer of a dimethylallyl group to the C-6 indole ring has not been reported so far. A homology search using known prenyltransferase sequences against the draft sequence of the Streptomyces sp. SN-593 genome revealed the iptA gene. The IptA protein showed 27% amino acid identity to cyanobacterial LtxC, which catalyzes the transfer of a geranyl group to (−)-indolactam V. A BLAST search against IptA revealed much-more-similar homologs at the amino acid level than LtxC, namely, SAML0654 (60%) from Streptomyces ambofaciens ATCC 23877 and SCO7467 (58%) from S. coelicolor A3(2). Phylogenetic analysis showed that IptA was distinct from bacterial aromatic prenyltransferases and fungal indole prenyltransferases. Detailed kinetic analyses of IptA showed the highest catalytic efficiency (6.13 min−1 μM−1) for l-Trp in the presence of dimethylallyl pyrophosphate (DMAPP), suggesting that the enzyme is a 6-dimethylallyl-l-Trp synthase (6-DMATS). Substrate specificity analyses of IptA revealed promiscuity for indole derivatives, and its reaction products were identified as novel 6-DMAI compounds. Moreover, ΔiptA mutants abolished the production of 6-DMAI-3-carbaldehyde as well as 6-dimethylallyl-l-Trp, suggesting that the iptA gene is involved in the production of 6-DMAI-3-carbaldehyde