Spiral Tissue Microarrays as Next Evolutionary Step in the High-density Tissue Microarray Technology

Tissue microarray (TMA) is a well-established technique that connects basic research with clinical applications that allow the validation of many pathobiologic events from gene expression dysregulation to genomic aberrations. However, conventional TMAs have several limitations such as limited representation of tissue heterogeneity, destruction of donor tissue blocks due to coring and usage of particular specimens that have limited evaluable material (tissue from thin specimens or needle biopsies). We have developed a novel method, which we termed "Spiral TMA" that generates TMAs that allow for improved representation of the donor tissue while keeping the architectural details of the donor block intact. This technology is ideal for specimens with limited tissue without the need to punch holes into the original block and therefore preserving the tissue integrity. In this report, we describe the methodology of constructing Spiral TMA and demonstrate the validation of tumor representation and tissue heterogeneity by comparing Spiral TMA to conventional TMA using immunohistochemical staining to EGFR and CK7

Optical follow-up observation of Fast Radio Burst 151230

The origin of fast radio bursts (FRBs), bright millisecond radio transients, is still somewhat of a mystery. Several theoretical models expect that the FRB accompanies an optical afterglow (e.g., Totani 2013; Kashiyama et al. 2013). In order to investigate the origin of FRBs, we perform $gri$-band follow-up observations of FRB~151230 (estimated $z \lesssim 0.8$) with Subaru/Hyper Suprime-Cam at $8$, $11$, and $14$~days after discovery. The follow-up observation reaches a $50\%$ completeness magnitude of $26.5$~mag for point sources, which is the deepest optical follow-up of FRBs to date. We find $13$ counterpart candidates with variabilities during the observation. We investigate their properties with multicolor and multi-wavelength observations and archival catalogs. Two candidates are excluded by the non-detection of FRB~151230 in the other radio feed horns that operated simultaneously to the detection, as well as the inconsistency between the photometric redshift and that derived from the dispersion measure of FRB~151230. Eight further candidates are consistent with optical variability seen in AGNs. Two more candidates are well fitted with transient templates (Type IIn supernovae), and the final candidate is poorly fitted with all of our transient templates and is located off-center of an extended source. It can only be reproduced with rapid transients with a faint peak and rapid decline and the probability of chance coincidence is $\sim3.6\%$. We also find that none of our candidates are consistent with Type Ia supernovae, which rules out the association of Type Ia supernovae to FRB~151230 at $z\leq0.6$ and limits the dispersion measure of the host galaxy to $\lesssim300$~pc~cm$^{-3}$ in a Type Ia supernova scenario.Comment: 22 pages, 11 figures. Accepted for publication in PASJ (Publications of the Astronomical Society of Japan

A search for optical transients associated with fast radio burst 150418†‡

We have searched for optical variability in the host galaxy of the radio variable source possibly associated with fast radio burst (FRB) 150418. We compare images of the galaxy taken 1 day after the burst using Subaru/Suprime-Cam with images taken ∼1 yr after the burst using Gemini-South/GMOS. No optical variability is found between the two epochs with a limiting absolute magnitude ≳ -19 (AB). This limit applies to the optical variability of the putative active galactic nucleus in the galaxy on a timescale of ∼1 yr, and also to the luminosity of an optical counterpart of FRB 150418 one day after the burst should it have occurred in this galaxy

Magnetic thickness measurement for various iron steels using magnetic sensor and effect of electromagnetic characteristics

The diagnosis and prevention of the deterioration of iron-steel infrastructure has become an important social issue in recent years. The thickness measurement technique (extremely low-frequency eddy current testing (ELECT)) using a magnetic sensor for detecting steel corrosion at extreme frequency ranges has been previously reported. Using the calibration curves based on the correlation between the phase of the detected magnetic signal and the plate thickness, the plate thickness reduction caused by corrosion can be estimated from the detected phase signal. Iron-steel materials have large changes in electromagnetic characteristics; therefore, the reference calibration data for each type of iron-steel are required for plate thickness estimation. In this study, the effect of electromagnetic characteristics on the magnetic thickness measurement was investigated to improve the thickness estimation. Four types of iron-steel plates (SS400, SM400A, SM490A, and SMA400AW) with thicknesses ranging from 1 mm to 18 mm were measured by ELECT, and the phase change at multiple frequencies of each plate were analyzed. The shift in the phase and linearity regions of the calibration curves for each type of steel plate was observed. To analyze this shift phenomenon, the electromagnetic characteristics (permeability μ and conductivity σ) of each type of steel were measured. Compared with the permeability μ and conductivity σ of each steel plate in the applied magnetic field strength range, the product (σμ) for various steel plates decreased in the following order: SM400 > SS400 >SMA400AW > SM490A. The product of μ and σ is related to the skin depth, indicating the electromagnetic wave attenuation and eddy current phase shift in the material. Therefore, each shift in the calibration curve of each type of iron steel is explained by the changes in the parameters σ and μ

Circadian protection against bacterial skin infection by epidermal CXCL14-mediated innate immunity

体内時計は夜間に自然免疫を発動 --皮膚ケモカインによる自然免疫機構--. 京都大学プレスリリース. 2022-06-16.Biological clocks set for skin immunity. 京都大学プレスリリース. 2022-06-21.The epidermis is the outermost layer of the skin and the body’s primary barrier to external pathogens; however, the early epidermal immune response remains to be mechanistically understood. We show that the chemokine CXCL14, produced by epidermal keratinocytes, exhibits robust circadian fluctuations and initiates innate immunity. Clearance of the skin pathogen Staphylococcus aureus in nocturnal mice was associated with CXCL14 expression, which was high during subjective daytime and low at night. In contrast, in marmosets, a diurnal primate, circadian CXCL14 expression was reversed. Rhythmically expressed CXCL14 binds to S. aureus DNA and induces inflammatory cytokine production by activating Toll-like receptor (TLR)9-dependent innate pathways in dendritic cells and macrophages underneath the epidermis. CXCL14 also promoted phagocytosis by macrophages in a TLR9-independent manner. These data indicate that circadian production of the epidermal chemokine CXCL14 rhythmically suppresses skin bacterial proliferation in mammals by activating the innate immune system

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