An X-ray diffraction study on a single rod outer segment from frog retina

X-ray diffraction was recorded from retinal rod outer segments of frog using a microbeam

Resurrection of a Bull by Cloning from Organs Frozen without Cryoprotectant in a −80°C Freezer for a Decade

Frozen animal tissues without cryoprotectant have been thought to be inappropriate for use as a nuclear donor for somatic cell nuclear transfer (SCNT). We report the cloning of a bull using cells retrieved from testicles that had been taken from a dead animal and frozen without cryoprotectant in a −80°C freezer for 10 years. We obtained live cells from defrosted pieces of the spermatic cords of frozen testicles. The cells proliferated actively in culture and were apparently normal. We transferred 16 SCNT embryos from these cells into 16 synchronized recipient animals. We obtained five pregnancies and four cloned calves developed to term. Our results indicate that complete genome sets are maintained in mammalian organs even after long-term frozen-storage without cryoprotectant, and that live clones can be produced from the recovered cells

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

Growth and age composition of northern shrimp Pandalus eous estimated by multiple length frequency analysis

We examined growth of northern shrimp Pandalus eous in the Sea of Japan, off western Hokkaido, to improve estimations of catch-at-age for stock assessment. Multiple length frequency analysis based on length frequency data collected by a scientific research vessel was conducted to examine length-at-age in the shrimp population. Multi-normal distributions estimated using maximum likelihood indicated a good fit to length distributions. AIC values and regression analyses revealed annual growth variation and a decreasing trend in the length at several age classes in the shrimp population. We revised the method for estimating catch-at-age from the age-conversion table (ACT), which is a simple method for age determination, to age-length keys (ALK) calculated from the results of multiple length frequency analysis. Abundant year classes caught successively year after year could be more easily identified from the catch-at-age data computed using ALK than by using ACT. Our results suggested not only that the mean size of commercial landings fluctuated based on changes in age composition but also that a decrease in the length-at-age in the population influenced the consistent size decrease of commercial landings.北海道西部日本海海域におけるホッコクアカエビの成長と年齢別漁獲尾数を推定するため，調査船標本にもとづく甲長組成解析を行い，年齢別サイズを調べた。解析結果から，成長の年変動と年齢別サイズの減少傾向が認められた。年齢別漁獲尾数の推定方法を，従来の甲長－年齢変換テーブル（ACT）から，age-length key（ALK）による方法に改良した。また，近年の漁獲物の小型化は，年齢組成の変動だけではなく，年齢別サイズの減少の影響を受けていることを明らかにした

われわれのUreaplasma urealyticum検出率について

Ureaplasma urealyticumの検出率は尿道炎から25.5%, 前立腺炎から12.9%であった.非淋菌性尿道炎からの検出率が淋菌性尿道炎からのそれより高かった.通常, 尿からの検出率は10%位といわれているが, 症状のある患者からはやや高率に見出されるのであろうUreaplasma urealyticum was isolated in 25.5% of the patients with urethritis and in 12.9% of the patients with prostatitis. The organism was isolated more frequently in non-gonococcal urethritis than in gonorrheal urethritis. It may thus be said that the isolation rate was higher among patients with overt signs or symptoms as compared with the common isolation rate in urine reportedly being about 10%