The Joint Center for Advanced High Performance Computing (JCAHPC), which is jointly operated under the collaboration between the Center for Computational Sciences, University of Tsukuba, and the Information Technology Center, the University of Tokyo, has named its new supercomputer system “Miyabi,” which is planned to start its entire operation in January 2025.
筑波大学計算科学研究センターと東京大学情報基盤センターが共同運営する、最先端共同HPC基盤施設（JCAHPC：Joint Center for Advanced High Performance Computing、施設長：朴泰祐）は、2025年1月に稼働を開始する次期スーパーコンピュータシステムの名称を “Miyabi”（みやび）に決定しました。
Title: Climate Change Research: Insights from KAUST Speaker: Prof Ibrahim Hoteit（King Abdullah University of Science and Technology） Date: 2 April 2024 Time: 13:30-14:15 Venue: Center for Computational Sciences, Workshop Room Language: English
*After the invited presentation, the following seminar is scheduled.
13:30-14:15 Climate Change Research: Insights from KAUST Prof Ibrahim Hoteit, King Abdullah University of Science and Technology
14:15-14:45 Urban Climate Modeling for urban and district scales: WRF-UCM and City-LES Prof Hiroyuki Kusaka, University of Tsukuba
14:45-15:15 Urban Extreme Weather and Climate Change Asst Prof Quang-Van Doan, University of Tsukuba
講演タイトル:Climate Change Research: Insights from KAUST 講演者: Prof Ibrahim Hoteit（King Abdullah University of Science and Technology） 日時: 2024年4月2日（火） 13:30-14:15 場所: 計算科学研究センター ワークショップ室 言語: English
＊計算科学コロキウムに続けて、セミナーが開催されます。 全体のスケジュールは以下の通りです。
13:30-14:15 Climate Change Research: Insights from KAUST Prof Ibrahim Hoteit, King Abdullah University of Science and Technology
14:15-14:45 Urban Climate Modeling for urban and district scales: WRF-UCM and City-LES Prof Hiroyuki Kusaka, University of Tsukuba
14:45-15:15 Urban Extreme Weather and Climate Change Asst Prof Quang-Van Doan, University of Tsukuba
Researchers led by University of Tsukuba have discovered rdxPolA, a putative DNA polymerase involved in replicating ancestral mitochondrial genomes, in diverse eukaryotic lineages. Based on the phylogenetic distribution of rdxPolA among eukaryotes, they proposed an evolutionary scenario of DNA polymerases for mitochondrial genome maintenance in the early evolution of eukaryotes.
Tsukuba, Japan—Mitochondria are intracellular organelles that evolved from a bacterium belonging to Alpharoteobacteria, which was taken up as an endosymbiont by the common ancestor of eukaryotes. Mitochondria possess their own highly reduced genomes (known as mitochondrial genomes), which are principally the descendants of the genome of the α-proteobacterial symbiont. Phylogenetically diverse eukaryotes use a type of DNA polymerase called “POP” to maintain their mitochondrial genomes.
In this study, the researchers identified 10 novel types of DNA polymerase that are distinct from the previously known types, including POPs, across diverse eukaryotic lineages. The evolutionary origin and subcellular localization of each novel DNA polymerase were investigated. Intriguingly, one of the DNA polymerases identified in this study, rdxPolA, was found to be involved in mitochondrial DNA maintenance and is a direct descendant of the DNA polymerase in the α-proteobacterial symbiont that gave rise to the first mitochondrion. The researchers proposed a scenario for the evolution of DNA polymerases involved in mitochondrial DNA maintenance from primitive to extant eukaryotes.
These findings provide critical insights into the early evolution of the machinery for mitochondrial DNA maintenance and the establishment of mitochondria in primitive eukaryotic cells.
### This research was supported by the Japan Society for Promotion of Sciences projects 18KK0203, 19H03280, 23H02535, and BPI05044 (to Y. Inagaki), 22J11104 (to R. Harada), and 19H03274 (to R. Kamikawa).
Original Paper
Title of original paper:
Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion
Professor INAGAKI Yuji HARADA Ryo (JSPS Research Fellowship for Young Scientists DC2) Center for Computational Sciences (CCS), University of Tsukuba
Senior Researcher YABUKI Akinori Deep-Sea Biodiversity Research Group, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Resercher YAZAKI Euki Research Center for Advanced Analysis, National Agriculture and Food Research Organization
Associate Professor KAMIKAWA Ryoma Graduate School of Agriculture, Kyoto University
NASA Deep Space Network (DSN)の1つであるオーストラリアのキャンベラ深宇宙通信施設（Canberra Deep Space Communication Complex、CDSCC)とオーストラリアの電波望遠鏡を活用して2015年に小惑星のレーダー観測を開始し、現在までに３０以上もの地球接近小惑星の検出に成功した。小惑星のレーダー観測は、それまでアメリカのGoldstoneやプエルトリコのAreciboなど、主に北半球で行われていた。しかし地球に再接近する小惑星のおよそ５％は南半球からしか観測できないので、ギャップを埋められるようになったことは、小惑星の探査・プラネタリーディフェンス・利用など、多岐にわたる分野で注目されている。講演では、レーダー観測により小惑星の軌道が精度良く決定され、また小惑星の形状や自転、表面物質の素性、表面状態などの情報が得られることを紹介し、またアストロバイオロジーへの応用の可能性についても議論する。
Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion. （オルガネラ局在ファミリーA DNAポリメラーゼ百科：原始ミトコンドリア共生体をふくむ細菌からの進化的貢献について）
Purple sulfur bacteria (PSB) convert light energy into chemical energy through photosynthesis. Interestingly, certain species can photosynthesize even in environments with low-calcium levels. Using cryo-electron microscopy, researchers from University of Tsukuba unveiled the structure of light-harvesting complexes and elucidated the mechanism that facilitates photosynthesis under low-calcium conditions.
Tsukuba, Japan—Photosynthetic bacteria, unlike plants, do not generate oxygen as a photosynthetic byproduct because they use hydrogen sulfide instead of water to convert solar energy into chemical energy (electrons). This process is orchestrated by a protein complex, the light-harvesting 1-reaction center (LH1-RC). Numerous PSB thrive in calcium-rich environments, such as hot springs and seawater. In the three-dimensional LH1-RC structure, the LH1 antenna protein is typically associated with calcium. However, the photosynthetic mechanism remains elusive in Allochromatium vinosum, a model species of autotrophic bacteria capable of thriving in low-calcium or soft-water environments, as hypothetically, calcium is not involved in the photosynthetic process in this model.
Using cryo-electron microscopy, the researchers revealed the LH1-RC structures of this model species at a resolution that enabled individual amino acid visualization. These observations revealed calcium binding only at six specific sites in the LH1 subunit. In contrast, the closely related thermophilic bacterium Thermochromatium tepidum displayed calcium attachment across all 16 LH1 subunits, indicating a calcium binding dependence on the amino acid sequence pattern. These results imply an evolutionary adaptation in this species, enabling it to bind trace amounts of calcium in low-calcium environments, thereby improving its thermal stability for photosynthesis.
These findings would potentially advance the efficient use of solar energy, and contribute to environmental protection, and highlight the capability of certain species to conduct photosynthesis in freshwater while detoxifying hydrogen sulfide, which is toxic to numerous organisms, into sulfur.
### This research was partially supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Numbers JP21am0101118 and JP21am0101116, and JP23ama121004
Original Paper
Title of original paper:
High-Resolution Structure and Biochemical Properties of the LH1-RC Photocomplex from the Model Purple Sulfur Bacterium, Allochromatium vinosum
