Imaging of isotope diffusion using atomic-scale vibrational spectroscopy

The spatial resolutions of even the most sensitive isotope analysis techniques based on light or ion probes are limited to a few hundred nanometres. Although vibration spectroscopy using electron probes has achieved higher spatial resolution, the detection of isotopes at the atomic level has been challenging so far. Here we show the unambiguous isotopic imaging of 12C carbon atoms embedded in 13C graphene and the monitoring of their self-diffusion via atomic level vibrational spectroscopy. We first grow a domain of 12C carbon atoms in a preexisting crack of 13C graphene, which is then annealed at 600C for several hours. Using scanning transmission electron microscopy electron energy loss spectroscopy, we obtain an isotope map that confirms the segregation of 12C atoms that diffused rapidly. The map also indicates that the graphene layer becomes isotopically homogeneous over 100 nanometre regions after 2 hours. Our results demonstrate the high mobility of carbon atoms during growth and annealing via selfdiffusion. This imaging technique can provide a fundamental methodology for nanoisotope engineering and monitoring, which will aid in the creation of isotope labels and tracing at the nanoscale

Correlations Among Consistency, Computed Tomography Values, and Histopathological Subtypes of Spinal Meningioma

The consistency of spinal meningiomas is important to consider when performing tumor removal surgery. This study evaluated the correlations between spinal meningioma consistency and both preoperative computed tomography (CT) values and histopathological subtypes. Fifteen consecutive patients who underwent surgical resection of spinal meningioma at our institution were identified, and preoperative CT values and the signal intensity of T2-weighted magnetic resonance images of the tumor were determined retrospectively. The consistency of the spinal meningioma was defined based on the ultrasonic surgical aspirator output during tumor debulking. Patients were assigned to 2 groups: a soft group (n=4) and a hard group (n=11). The T2 signal intensity was significantly higher in the soft group than in the hard group (p=0.001). While the CT values were considerably higher in the hard group, the difference was not significant (p=0.19). Regarding the histopathological subtypes, psammomatous meningioma exhibited significantly higher CT values than meningothelial meningioma (p=0.019); however, there was a higher frequency of hard tumors in meningothelial meningioma cases than in psammomatous meningioma cases. Although neither robust correlations between tumor consistency and CT values nor a relationship between tumor consistency and histopathological subtype has been established, these results might help with the perioperative manegement of spinal tumors

Relationship between mitochondrial DNA polymorphism and postnatal growth of Japanese beef cattle

Correlation coefficients (r) between mitochondrial DNA (mtDNA) haplotypes, maternal lineage (ML), birth weight (BWT), preweaning average daily gain (PREADG), weaning weight (WT6), post weaning average daily gain (POSTADG) and yearling weight (WT12) were computed in Japanese Black beef cattle within the same herd and management. The objective was to study the relationship between maternal and postnatal growth traits and to investigate if postnatal growth of calves to yearling age could be accurately predicted from mtDNA genotype at an early age. Blood samples and phenotypic records from 129 cattle which were part of a QTL mapping herd were utilized. mtDNA from the displacement-loop (D-loop) region (496 bp) was genotyped and classified into sub-groups 2 and 3 haplotypes and sequenced. General linear models procedure was utilized to adjust for genetic and non-genetic effects on postnatal growth traits. Simple and multiple linear regressions were fitted to predict postnatal growth traits from mtDNA haplotypes and the coefficients of determination (R2 ) were computed. Results revealed 19 maternal lineages and four mtDNA types (1, 11, 73 and a new hitherto unreported one). There were strong, positive and highly significant (P0.05) ranging from -0.05 to 0.1. Prediction of postnatal growth from mtDNA yielded very low R2 values ranging from 0.002 for BWT to 0.019 for WT6. The addition of ML, sub-group 2 and sub-group 3 haplotype information did not lead to any appreciable improvement in prediction accuracy. It was concluded that mtDNA polymorphism has no significant association with postnatal growth from birth to yearling age, and by implication, nuclear rather than cytoplasmic DNA, is most likely responsible for genetic variation observed in postnatal growth of Japanese Black cattle. Therefore, mtDNA genotyping at an early age has no bearing on future growth performance of calves

SILVERRUSH. VII. Subaru/HSC Identifications of 42 Protocluster Candidates at z~6-7 with the Spectroscopic Redshifts up to z=6.574: Implications for Cosmic Reionization

We report fourteen and twenty-eight protocluster candidates at z=5.7 and 6.6 over 14 and 19 deg^2 areas, respectively, selected from 2,230 (259) Lya emitters (LAEs) photometrically (spectroscopically) identified with Subaru/Hyper Suprime-Cam (HSC) deep images (Keck, Subaru, and Magellan spectra and the literature data). Six out of the 42 protocluster candidates include 1-12 spectroscopically confirmed LAEs at redshifts up to z=6.574. By the comparisons with the cosmological Lya radiative transfer (RT) model reproducing LAEs with the reionization effects, we find that more than a half of these protocluster candidates are progenitors of the present-day clusters with a mass of > 10^14 M_sun. We then investigate the correlation between LAE overdensity delta and Lya rest-frame equivalent width EW_Lya^rest, because the cosmological Lya RT model suggests that a slope of EW_Lya^rest-delta relation is steepened towards the epoch of cosmic reionization (EoR), due to the existence of the ionized bubbles around galaxy overdensities easing the escape of Lya emission from the partly neutral intergalactic medium (IGM). The available HSC data suggest that the slope of the EW_Lya^rest-delta correlation does not evolve from the post-reionization epoch z=5.7 to the EoR z=6.6 beyond the moderately large statistical errors. There is a possibility that we would detect the evolution of the EW_Lya^rest - delta relation from z=5.7 to 7.3 by the upcoming HSC observations providing large samples of LAEs at z=6.6-7.3

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