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

Observation of Plasma Turbulence in a Hall Thruster Using Microwave Interferometry

To understand anomalous electron transport in a Hall thruster, plasma turbulence inside the acceleration channel was observed using a 76 GHz microwave interferometer. The dependence of the amplitude of the 100–500 kHz turbulence on magnetic flux density, and the relationships between the turbulence and other plasma instabilities and between the turbulence and the discharge current were investigated through spectral density and bicoherence analysis. The amplitude of electron number density fluctuations of the turbulence, integrating the spectral density from 100 to 500 kHz, is [Formula: see text], or almost 10% of the time-averaged electron number density. The amplitude of the turbulence decreases with increase in weak magnetic field strength (coil current less than 0.6 A) and then increases with increase in magnetic field strength. The amplitude of the turbulence has a positive relation to the discharge current, leads to anomalous electron transport inside the acceleration channel, and is coupled with ionization instability. In addition, low-frequency perturbations of several hundred hertz were observed, with a positive relation to the turbulence and coupled with both ionization instability and turbulence

Lanthanide ion-doped silica nanohelix: a helical inorganic network acts as a chiral source for metal ions dagger

We demonstrate that lanthanide ions doped in nanometrical silica helices with a chirally arranged siloxane network without any organic mediates show induced chiroptical properties such as circular dichroism and circularly polarized luminescence

Thermal <i>E</i>/<i>Z</i> Isomerization in First Generation Molecular Motors

Determination of a thermal <i>E</i>/<i>Z</i> isomerization barrier of first generation molecular motors is reported. Stable (<i>E</i>)-<b>1a</b> directly converts to stable (<i>Z</i>)-<b>1c</b> without photochemical <i>E</i>/<i>Z</i> isomerization. The activation Gibbs energy of the isomerization was determined to be 123 kJ mol^–1 by circular dichroism spectral changes. Density functional theory calculations show that (<i>Z</i>)-<b>1c</b> is ∼11.4 kJ mol^–1 more stable than (<i>E</i>)-<b>1a</b>

TiNbSn stems with gradient changes of Young’s modulus and stiffness reduce stress shielding compared to the standard fit-and-fill stems

Abstract Background The difference between Young’s moduli of the femur and the stem causes stress shielding (SS). TiNbSn (TNS) stem has a low Young’s modulus and strength with gradient functional properties during the change in elastic modulus with heat treatment. The aim of this study was to investigate the inhibitory effect of TNS stems on SS and their clinical outcomes compared to conventional stems. Methods This study was a clinical trial. Primary THA was performed using a TNS stem from April 2016 to September 2017 for patients in the TNS group. Unilateral THA was performed using a Ti6Al4V alloy stem from January 2007 to February 2011 for patients in the control group. The TNS and Ti6Al4V stems were matched in shape. Radiographs were obtained at the 1- and 3-year follow-ups. Two surgeons independently checked the SS grade and appearance of cortical hypertrophy (CH). The Japanese Orthopaedic Association (JOA) scores before and 1 year after surgery were assessed as clinical scores. Results None of the patients in the TNS group had grade 3 or 4 SS. In contrast, in the control group, 24% and 40% of patients had grade 3 and 4 SS at the 1- and 3-year follow-ups, respectively. The SS grade was lower in the TNS group than in the control group at the 1- and 3-year follow-ups (p < 0.001). The frequencies of CH in both groups were no significant difference at the 1- and 3-year follow-ups. The JOA scores of the TNS group significantly improved at 1 year after surgery and were comparable to control group. Conclusion The TNS stem reduced SS at 1 and 3 years after THA compared to the proximal-engaging cementless stem, although the shapes of the stems matched. The TNS stem could reduce SS, stem loosening, and periprosthetic fractures. Trial registration: Current Controlled Trials. ISRCTN21241251. https://www.isrctn.com/search?q=21241251 . The date of registration was October 26, 2021. Retrospectively registered