Effect of X-Irradiation at Different Stages in the Cell Cycle on Individual Cell?Based Kinetics in an Asynchronous Cell Population

Using an asynchronously growing cell population, we investigated how X-irradiation at different stages of the cell cycle influences individual cell-based kinetics. To visualize the cellcycle phase, we employed the fluorescent ubiquitination-based cell cycle indicator (Fucci). After 5 Gy irradiation, HeLa cells no longer entered M phase in an order determined by their previous stage of the cell cycle, primarily because green phase (S and G2) was less prolonged in cells irradiated during the red phase (G1) than in those irradiated during the green phase. Furthermore, prolongation of the green phase in cells irradiated during the red phase gradually increased as the irradiation timing approached late G1 phase. The results revealed that endoreduplication rarely occurs in this cell line under the conditions we studied. We next established a method for classifying the green phase into early S, mid S, late S, and G2 phases at the time of irradiation, and then attempted to estimate the duration of G2 arrest based on certain assumptions. The value was the largest when cells were irradiated in mid or late S phase and the smallest when they were irradiated in G1 phase. In this study, by closely following individual cells irradiated at different cell-cycle phases, we revealed for the first time the unique cell-cycle kinetics in HeLa cells that follow irradiation

On the origin and evolution of the asteroid Ryugu: A comprehensive geochemical perspective

Presented here are the observations and interpretations from a comprehensive analysis of 16 representative particles returned from the C-type asteroid Ryugu by the Hayabusa2 mission. On average Ryugu particles consist of 50% phyllosilicate matrix, 41% porosity and 9% minor phases, including organic matter. The abundances of 70 elements from the particles are in close agreement with those of CI chondrites. Bulk Ryugu particles show higher δ18O, Δ17O, and ε54Cr values than CI chondrites. As such, Ryugu sampled the most primitive and least-thermally processed protosolar nebula reservoirs. Such a finding is consistent with multi-scale H-C-N isotopic compositions that are compatible with an origin for Ryugu organic matter within both the protosolar nebula and the interstellar medium. The analytical data obtained here, suggests that complex soluble organic matter formed during aqueous alteration on the Ryugu progenitor planetesimal (several 10’s of km), <2.6 Myr after CAI formation. Subsequently, the Ryugu progenitor planetesimal was fragmented and evolved into the current asteroid Ryugu through sublimation

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

Dose-dependency of prolongation of red and green phase after irradiation.

<p>(A) Schematic presentation of irradiation timing and measurement of the duration of green (a) or red (b) phase. Black square represents M phase. In panel b, the two daughter cells did not exhibit exactly the same red-phase duration; therefore, each value was separately measured and mean values were calculated. (B) Dose-dependency of prolongation of red and green phases after irradiation. Data represent means ± S.D. of values obtained from at least four different fields for each dose. Each field contained at least 10 cells. *, p < 0.05; **, p < 0.01 vs. control values at 0 Gy (one way ANOVA with post hoc Dunnett’s test).</p

Estimation of G2 arrest durations in cells irradiated in G1, early/mid/late S, and G2 phases.

<p>(A) Pedigree analysis of cells irradiated in green phase. a: Distribution of total green-phase durations in cells irradiated in each phase, sorted according to green fluorescence intensities. Two straight lines represent the remaining S-phase durations at irradiation (maximal 7 h for the leftmost cell in early S phase) (lower dashed line) and plus elongation of S phase (maximal 2 h for the leftmost cell in early S phase) (upper dashed line) in each phase. b: Distribution of G2-arrest durations after subtraction of the corresponding S phase and its elongation from the left panel a. (B) Comparisons of G2-arrest durations in cells irradiated in each phase. Data are represented as box-and-whisker plots as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128090#pone.0128090.g003" target="_blank">Fig 3E</a>. Cell number in each sub-phase is equivalent to that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128090#pone.0128090.g005" target="_blank">Fig 5C</a>. *, p < 0.05; **, p < 0.01 by Mann–Whitney U test.</p

Durations (h) of each cell-cycle phase in exponentially growing HeLa-Fucci cells.

<p>1) From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128090#pone.0128090.g001" target="_blank">Fig 1A</a>, G1-phase duration was determined from the red-phase duration. S+G2-phase duration was determined from the green-phase duration. Values represent means from 150 cells. Mitotic cells were identified morphologically. Total cell-cycle time was calculated from the duration between one M phase and the next M phase, as determined by time-lapse imaging.</p><p>2) Each cell-cycle phase duration was calculated from the proportion of each cell cycle phase (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128090#pone.0128090.g001" target="_blank">Fig 1B</a>), assuming an exponential distribution according to the equations as described by Watanabe and Okada [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128090#pone.0128090.ref029" target="_blank">29</a>]. Values in parenthesis were derived from Fucci analysis.</p><p>3) Durations of S and G2 phases were directly determined from the curve in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128090#pone.0128090.g001" target="_blank">Fig 1C</a>, as described in Materials and Methods. G1-phase duration was determined by subtracting the S+G2+M duration from the total cell-cycle time.</p><p>4) The actual culture doubling time obtained from growth curves was 17–18 h.</p><p>Durations (h) of each cell-cycle phase in exponentially growing HeLa-Fucci cells.</p