The Genetic Diversity of Helicobacter pylori Virulence Genes Is Not Associated with Gastric Atrophy Progression

Atrophy of the gastric mucosa is a precursor of intestinal-type gastric cancer, and Helicobacter pylori infection causes atrophic gastritis. The aim of this study was to determine whether the genetic diversity of H. pylori virulence genes is associated with the development and progression of gastric atrophy in humans. We isolated and cultured H. pylori strains from patients with gastric ulcer and duodenal ulcer accompanied by atrophic gastritis in background mucosa. H. pylori strains were stored at －80℃ prior to the experiments being carried out. We analyzed iceA, babA, vacA, cagA, and cagE genes by PCR. The cagA gene was analyzed through sequencing of the C-terminal region containing the EPIYA motif, which is related to tyrosine phosphorylation. Severe atrophy was observed in patients with gastric ulcer. The major phenotype of the vacA gene was s1c/m1 (93ｵ). The cagA gene was detected in all strains. The cagE gene was not detected in 2 and 5 strains from the mild cases and severe cases, respectively. The major cagA EPIYA motif, which is amino acids repeat in the C terminus, was the A-B-D type (44 of 58 strains). The virulence genes were not statistically associated with the severity of atrophy in the background gastric mucosa in humans. Not only identification of bacterial virulence factors but also studies of the host response will be necessary to investigate the progression of gastric atrophy and subsequent cancer development in humans

PRELIMINARY SURVEY OF WATER ENVIRONMENT PROBLEMS IN HCMC

Joint Research on Environmental Science and Technology for the Eart

Immune Reactions Against Elongation Factor 2 Kinase: Specific Pathogenesis of Gastric Ulcer from Helicobacter pylori Infection

Helicobacter pylori (H. pylori) infection is a definite causative factor for gastric ulcers (GUs). In the present study we detected a specific antigen of gastric epithelial cells (HGC-27) using cell ELISA, which was recognized by the sera of GU patients (n = 20) but not in patients with chronic gastritis (CG; n = 20) or in healthy volunteers (HC; n = 10). This antigen was over-expressed by a stressful (heat-stressed) environment, and was identified as elongation factor 2 kinase (EF-2K) by western blotting. The GU patients' lymphocytes stimulated by H. pylori specifically disrupted heat-stressed HGC-27 cells in a cytotoxic assay. In flow cytometry, the effector cells (lymphocytes) from GU patients were significantly differentiated to T helper type 1 lymphocyte (Th1) and cytotoxic T lymphocyte (CTL) as opposed to those from CG patients. The target cells (HGC-27) expressed EF-2K and MHC-class I together with costimulatory molecules from heat stress. This antigen specific immune mechanism could have a prominent role in the pathogenesis of GU

Inter-rater reliability of streetscape audits using online observations: Microscale Audit of Pedestrian Streetscapes (MAPS) global in Japan

This study aimed to evaluate the inter-rater reliability of streetscape audits among online observations using the Microscale Audit of Pedestrian Streetscapes-Global version (MAPS-Global) in Japan. MAPS-Global observations were conducted on routes with distances ranging from 400 to 725 m from a residence toward a non-residential destination. Google Street View audits were independently conducted by two trained raters on each route. A tiered scoring system was applied to summarize the items at multiple levels of aggregation. Positive and negative valence scores were created based on the expected association with physical activity. Inter-rater reliability analyses were performed using kappa statistics or intraclass correlation coefficients (ICC). Of the 32 older adults participating in an intervention study in the community-wide physical activity promotion project in Fujisawa City, 19 addresses were used, excluding those with nearby addresses. Results demonstrated “excellent” agreement for most of the summary scores analyzed (kappa or ICC values of 0.75 or higher [80.4 %]), while 6.5 % of items exhibited “good” agreement (ICC = 0.60–0.74). By contrast, only 13.0 % of the scales had ICC values lower than 0.60 (“fair” or “poor” reliability). The results illustrated high reliability for the grand summary scores and composite subscale measures. However, caution should be exercised when interpreting subscale scores for less frequently observed negative attributes and aesthetic/social characteristics. The results presented in this study support the application of online observations using MAPS-Global in urban areas of Japan, which could be implemented to inform decisions related not only to physical activity but also to traffic safety

Spontaneous Nicking in the Nontoxic-Nonhemagglutinin Component of the costridium botulinum Toxin Conplex

Clostiridium botulinum D型4947株によって産生された毒素複合体から非毒素ー非血球凝集素（NTNHA）標品を蛋白分解酵素フリーの条件下で、単独の形と神経毒(NT)/NTNHA複合体の形で調製できた。両調製物質のNTNHAはスポンテニアスにニックの入ったNTNHAとなり、15-と115-kDaフラグメント及び特異的部分でいくつかのアミノ酸の削除を生じることが長時間培養のSDS-PAGEで認められた。しかし、NT/NTNHA/血球凝集素(HA)複合体は同じ条件下でニックの入らない一本鎖のペプチドのままであった。NTNHA調製物に少量のニック型の物が含まれていることから、NTNHAのニック型は精製の残物と/あるいはNTNHAがインタクトNTNHAをそれ自身との切断酵素活性によってニックを入れたことが考えられる

Role of C-Terminal Region of HA-33 Component of Botulinum Toxin in Hemagglutination

Clostridium botulinum D型1873株とC型Yoichi株の産生するプロジェニター毒素から得られた1種類のサブコンポーネントである血球凝集素（HA-33）は、C及びD型参照株のそれより少し小さい分子サイズであるが、他のコンポーネントのの大きさに違いがないことが、SDS-PAGEを用いて見いだされた。すなわち、HA-33のN-及びC-末端シーケンス分析に基つき、両株のHA-33淡白において特異的なサイトでC-末端から33アミノ酸残基の欠落があることが見いだされた。両株のプロジェニター毒素は、参照株毒素の血球凝集力価2かそれ以下の弱い血球凝集活性を示すが、赤血球に吸着することはできない。これらの結果はHA-33の短いC-末端部分が、ボツリヌスプロジェンター毒素の血球凝集活性において重要な役割を果たしていることを示す。さらに、シーケンスモチーフの探索により、HA-33のC-末端部分は炭化水素認識サブドメインを持っていることが推測された

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

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

Assessment of canopy photosynthetic capacity and estimation of GPP by using spectral vegetation indices and the light–response function in a larch forest

Integration of CO2 flux observations with remote sensing technique and ecosystem modeling is expected to be useful for estimation of gross primary production (GPP). We focused on the changes in the two main parameters for the canopy-scale light-response curve-Pmax (maximum GPP at light saturation) and φ (initial slope)-as indicators to represent canopy photosynthetic capacity. We hypothesized that Pmax and φ could be evaluated by using spectral reflectance related to the changes in the levels of canopy nitrogen and chlorophyll. We analyzed the relationships between Pmax and φ, derived from tower-based CO2 flux observations, and ground-based spectral vegetation indices (VIs) in a temperate deciduous coniferous forest. The canopy-scale Pmax and φ showed clear seasonal changes accompanying phenological stages. Both the variations in Pmax and φ were strongly correlated with VIs, especially with the ratio vegetation index (RVI) and enhanced vegetation index (EVI), independent of the growth stages. Moreover, day-to-day short-term variations of Pmax and φ were affected by meteorological conditions such as vapor pressure deficit (VPD) and relative solar radiation which was calculated as the ratio of monitored radiation per theoretical maximum radiation. Thus, seasonal changes of Pmax and φ were effectively assessed by RVI or EVI, and their short-term variations were evaluated by the empirical relationships with VPD and relative solar radiation. We propose a new simple method for estimating GPP with good precision; by fitting the light-response function with the evaluated parameters, the estimated GPP reflects 3 types of temporal variation: diurnal, day-to-day, and seasonal