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

Nocturnal moths as potential pollinators of Marsdenia formosana (Apocynaceae: Asclepiadoideae)

Asclepiad flowers transfer the pollinaria, including pollen masses, to diverse body parts of flower visitors in various ways. In this study, we observed the insects visiting the flowers of Marsdenia formosana (Apocynaceae: Asclepiadoideae) at a forest in Taiwan in early May, 2016. Nocturnal moths of ten species (Lepidoptera: Pyralidae, Crambidae, Geometridae, Erebidae, and Noctuidae) were observed visiting M. formosana flowers. A pollinarium was found attached to the proboscis’ tip of a Bertula hadenalis persimilis (Lepidoptera: Erebidae) specimen. This suggests that nectar-seeking moths visit M. formosana flowers and involuntarily transfer the pollinaria on the tip of the proboscis

Dolichogenidea ultor

D. ultor (Reinhard, 1880): Antenna light brown; propodeum with complete areola, including transverse carinae; T 2 smooth; legs mostly yellow.Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 174, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/369917

Data from: A diverse assemblage of moths feeding on aphid honeydew

Sakagami, K., Sugiura, S., 2018. A diverse assemblage of moths feeding on aphid honeydew. Journal of Asia-Pacific Entomology DOI: 10.1016/j.aspen.2018.01.01

Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera)

Fernandez-Triana, Jose, Sakagami, Kota, Shimizu, So (2018): Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera). Acta Entomologica Musei Nationalis Pragae 58 (1): 167-175, DOI: 10.2478/aemnp-2018-001

Predicted Absorption Performance of Cylindrical and Rectangular Permeable Membrane Space Sound Absorbers Using the Three-Dimensional Boundary Element Method

Three-dimensional, permeable membrane space sound absorbers have been proposed as practical and economical alternatives to three-dimensional, microperforated panel space sound absorbers. Previously, the sound absorption characteristics of a three-dimensional, permeable membrane space sound absorber were predicted using the two-dimensional boundary element method, but the prediction accuracy was impractical. Herein, a more accurate prediction method is proposed using the three-dimensional boundary element method. In the three-dimensional analysis, incident waves from the elevation angle direction and reflected waves from the floor are considered, using the mirror image. In addition, the dissipated energy ratio is calculated based on the sound absorption of a surface with a unit sound absorption power. To validate the three-dimensional numerical method, and to estimate the improvement in prediction accuracy, the results are compared with those of the measurements and two-dimensional analysis. For cylindrical and rectangular space sound absorbers, three-dimensional analysis provides a significantly improved prediction accuracy for any shape and membrane sample that is suitable for practical use

Revisiting the host use and phylogeny of Colastomion Baker (Hymenoptera, Braconidae, Rogadinae), with a new host record from Japan

We report the solitary parasitism by Colastomion formosanum (Watanabe) (Hymenoptera, Braconidae, Rogadinae) on the larva of Nevrina procopia (Stoll) (Lepidoptera, Crambidae) feeding on Turpinia ternata Nakai (Staphyleaceae) in Amami Ôshima Is., Japan. This is the first host record for the genus Colastomion Baker outside of Papua New Guinea. We have also inferred the phylogenetic relationships of Colastomion species using Bayesian and maximum likelihood approaches, based on the mitochondrial cytochrome oxidase 1 gene. The results indicate two major clades–solitary and gregarious parasitoids–within Colastomion. Colastomion formosanum belongs to the clade of solitary parasitoids that specifically parasitize the crambid subfamily Spilomelinae. Plant-host-parasitoid associations and the evolutionary scenario of the host use of Colastomion are discussed

A Basic Study on a Rectangular Plane Space Sound Absorber Using Permeable Membranes

In this communication, the sound absorption characteristics of rectangular-shaped plane space sound absorbers without any backing structure using permeable membranes (PMs) are measured by reverberation room method. First, three types of PMs, in this study woven fabrics, are selected with different flow resistances and surface densities. They are prepared in the plane rectangular-shaped space absorbers of two different sizes. The measured results are discussed through comparison with the existing theoretical and measured results for absorbers of the other shapes or configurations. The present results and discussion demonstrate that the reverberation absorption coefficients of the proposed absorbers are low at low frequencies and converge to a moderately high value at high frequencies. Especially, ones with higher flow resistance than the air impedance converge to a value greater than 0.5, which is a theoretically estimated maximum absorption coefficient of infinite single-leaf PM. This is inferred to be attributed mainly to area effect. From these results the proposed absorbers can be used effectively despite of their very simple structure. Also it is found that the proposed absorber can offer higher sound absorption than permeable membrane absorbers of other shapes or configuration. Regarding the effect of the size, the absorbers of smaller size offer higher absorption coefficients regardless of material properties of the PMs used in the experiments