A novel superior factor widely controlling the rice grain quality

Synthesis of storage starch and protein accumulation is the main action of endosperm organogenesis in term of the economic importance of rice. This event is strongly disturbed by abiotic stresses such as high temperature; thus, the upcoming global warming will cause a crisis with a great impact on food production^1,2^. The enzymes for the protein storage and starch synthesis pathway should work in concert to carry out the organogenesis of rice endosperm^3-5^, but the regulatory mechanism is largely unknown. Here we show that a novel regulatory factor, named OsCEO1, acts as the conductor of endosperm organogenesis during the rice grain filling stage. The physiological properties of _floury-endosperm-2_ (_flo2_) mutants showed many similarities to symptoms of grains developed under high-temperature conditions, suggesting important roles of the responsible gene in sensitivity to high-temperature stress. Our map-based cloning identified the responsible gene for the _flo2_ mutant, _OsCEO1_, which has no homology to any genes of known function. The _OsCEO1_ belongs to a novel conserved gene family and encodes a protein composed of 1,720 amino acid residues containing a TPR (tetratricopeptide repeat) motif, which is considered to mediate a protein-protein interaction. The yeast two-hybrid analysis raised an unknown protein showing homology to a late embryogenesis abundant protein and a putative basic helix-loop-helix protein as candidates for the direct interactor for _OsCEO1_, whereas no enzyme genes for the synthesis of storage substances were detected. The _flo2_ mutant exhibited reduced expression of several genes for putative regulatory proteins as well as many enzymes involved in storage starch and proteins. These results suggest that _OsCEO1_ is a superior conductor of the novel regulatory cascade of endosperm organogenesis and may have important roles in the response to high-temperature stress

The Intricacies of Identifying Equatorial Waves

Equatorial waves (EWs) are synoptic- to planetary-scale propagating disturbances at low latitudes with periods from a few days to several weeks. Here, this term includes Kelvin waves, equatorial Rossby waves, mixed Rossby–gravity waves, and inertio-gravity waves, which are well described by linear wave theory, but it also other tropical disturbances such as easterly waves and the intraseasonal Madden–Julian Oscillation with more complex dynamics. EWs can couple with deep convection, leading to a substantial modulation of clouds and rainfall. EWs are amongst the dynamic features of the troposphere with the longest intrinsic predictability, and models are beginning to forecast them with an exploitable level of skill. Most of the methods developed to identify and objectively isolate EWs in observations and model fields rely on (or at least refer to) the adiabatic, frictionless linearized primitive equations on the sphere or the shallow-water system on the equatorial -plane. Common ingredients to these methods are zonal wave-number–frequency filtering (Fourier or wavelet) and/or projections onto predefined empirical or theoretical dynamical patterns. This paper gives an overview of six different methods to isolate EWs and their structures, discusses the underlying assumptions, evaluates the applicability to different problems, and provides a systematic comparison based on a case study (February 20–May 20, 2009) and a climatological analysis (2001–2018). In addition, the influence of different input fields (e.g., winds, geopotential, outgoing long-wave radiation, rainfall) is investigated. Based on the results, we generally recommend employing a combination of wave-number–frequency filtering and spatial-projection methods (and of different input fields) to check for robustness of the identified signal. In cases of disagreement, one needs to carefully investigate which assumptions made for the individual methods are most probably not fulfilled. This will help in choosing an approach optimally suited to a given problem at hand and avoid misinterpretation of the results

AsiaPEX:Challenges and Prospects in Asian Precipitation Research

The Asian Precipitation Experiment (AsiaPEX) was initiated in 2019 to understand terrestrial precipitation over diverse hydroclimatological conditions for improved predictions, disaster reduction, and sustainable development across Asia under the framework of the Global Hydroclimatology Panel (GHP)/Global Energy and Water Exchanges (GEWEX). AsiaPEX is the successor to GEWEX Asian Monsoon Experiment (GAME; 1995-2005) and Monsoon Asian Hydro-Atmosphere Scientific Research and Prediction Initiative (MAHASRI; 2006-16). While retaining the key objectives of the aforementioned projects, the scientific targets of AsiaPEX focus on land-atmosphere coupling and improvements to the predictability of the Asian hydroclimatological system. AsiaPEX was designed for both fine-scale hydroclimatological processes occurring at the land surface and the integrated Asian hydroclimatological system characterized by multiscale interactions. We adopt six approaches including observation, process studies, scale interactions, high-resolution hydrological modeling, field campaigns, and climate projection, which bridge gaps in research activities conducted in different regions. Collaboration with mesoscale and global modeling researchers is one of the core methods in AsiaPEX. We review these strategies based on the literature and our initial outcomes. These include the estimation and validation of highresolution satellite precipitation, investigations of extreme rainfall mechanisms, field campaigns over the Maritime Continent and Tibetan Plateau, areas of significant impact on the entire AsiaPEX region, process studies on diurnal- to interdecadal-scale interactions, and evaluation of the predictabilities of climate models for long-term variabilities. We will conduct integrated observational and modeling initiative, the Asian Monsoon Year (AMY)-II around 2025-28, whose strategies are the subregional observation platforms and integrated global analysis.</p

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

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