Location, morphology and size distribution of solid particles in an ice core retrieved from NEEM, Greenland

The Tenth Symposium on Polar Science/Ordinary sessions: [OM] Polar Meteorology and Glaciology, Thu. 5 Dec. / 2F Auditorium , National Institute of Polar Researc

Spatial variation of surface mass balance and seasonal variation of dust deposition at EGRIP, Greenland

The Tenth Symposium on Polar Science/Ordinary sessions: [OM] Polar Meteorology and Glaciology, Wed. 4 Dec. / Entrance Hall (1st floor) , National Institute of Polar Researc

eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

[Background] Bioinformatics capability to analyze spatio–temporal dynamics of gene expression is essential in understanding animal development. Animal cells are spatially organized as functional tissues where cellular gene expression data contain information that governs morphogenesis during the developmental process. Although several computational tissue reconstruction methods using transcriptomics data have been proposed, those methods have been ineffective in arranging cells in their correct positions in tissues or organs unless spatial information is explicitly provided. [Results] This study demonstrates stochastic self-organizing map clustering with Markov chain Monte Carlo calculations for optimizing informative genes effectively reconstruct any spatio–temporal topology of cells from their transcriptome profiles with only a coarse topological guideline. The method, eSPRESSO (enhanced SPatial REconstruction by Stochastic Self-Organizing Map), provides a powerful in silico spatio–temporal tissue reconstruction capability, as confirmed by using human embryonic heart and mouse embryo, brain, embryonic heart, and liver lobule with generally high reproducibility (average max. accuracy = 92.0%), while revealing topologically informative genes, or spatial discriminator genes. Furthermore, eSPRESSO was used for temporal analysis of human pancreatic organoids to infer rational developmental trajectories with several candidate ‘temporal’ discriminator genes responsible for various cell type differentiations. [Conclusions] eSPRESSO provides a novel strategy for analyzing mechanisms underlying the spatio–temporal formation of cellular organizations

Microstructure in the EastGRIP ice core, Greenland

Behavior of Earth’s ice sheets is intensely monitored via surface and remote sensing techniques to improve predictions of sea level evolution. Radio echo sounding along with drilling ice cores are currently used to monitor the Earth’s ice sheets behaviour not only from the surface but in the 3rd dimension. Particularly the ice material properties can only be accessed via ice drilling. These properties control the deformation in general, and particularly strain localization such as observed in ice streams, which supply the major discharges into the oceans. Currently the first ice core on an active ice stream, the North-East Greenland Ice Stream (NEGIS) is being drilled. EastGRIP (East Greenland Ice-Core Project, http://eastgrip.org) drilling started in 2016 and will be ongoing until 2019. This is the first chance to study ice microstructure from a dynamically active region (www.awi.de/en/focus/eisschilde/eis-ist-ein-heisses-material.html), with a deformation regime differing from the usual locations of previous long ice cores. Those were usually placed on domes or on ice divides due to straightforward kinematics and deformation rates which is advantageous for paleo-climate reconstruction from ice core records. We present CPO (c-axes fabric) and the grain size measurements of the uppermost 350m, the depth to which the ice core has been processed for analysis so far (275 thin sections discontinuous with 10m depth resolution). The CPO patterns found in the upper 350m at EastGRIP show (1) a more rapid evolution of c-axes anisotropy with depth compared to other ice cores and (2) partly novel characteristics in the caxes distributions. (Remark: This is an invited poster.

Microstructural analysis of the NEEM ice core, Greenland by using electron backscatter diffraction (EBSD)

Mass loss of the Greenland ice sheet is accelerating, which is attributed to increased ice stream discharge and changes in surface mass balance including increased runoff. Ice stream discharge is caused by both ice deformation and basal sliding. For better projection of future mass loss, it is important to understand deformation mechanisms of polycrystalline ice in ice sheet. Deformation properties of polycrystalline material are related to its microstructure (e.g. crystal grain orientation and size). As recrystallization and recovery are occurring together in ice sheet, analysis of microstructure of ice is essential. Electron backscatter diffraction (EBSD) is a method for measuring crystal lattice orientation with high angular and spatial resolutions. Both c- and a-axes of ice can be measured. We analyzed Greenland NEEM ice core and the preliminary result shows that most subgrain boundaries (SGBs) observed by optical microscopy have lattice misorientations < 4°. This result is in accordance with analyses of Antarctic EDML ice core by X-ray diffractometry while it differs from threshold angle of SGB/GB estimated with a dislocation theory. The observation results from ice sheet ice could contribute to better estimations of strain rate by models based on microstructural processes

後方散乱電子回折（EBSD）による氷結晶中の微小方位差測定

第6回極域科学シンポジウム[OM] 極域気水圏11月16日（月）　国立極地研究所１階交流アトリウ

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target