Coexistence of emerging bacterial pathogens in ixodes ricinus ticks in Serbia

The list of tick-borne pathogens is long, varied and includes viruses, bacteria, protozoa and nematodes. As all of these agents can exist in ticks, their co-infections hove been previously reported. We studied co-infections of emerging bacterial pathogens (Borrelia burgdorferi sensu lato, Ana plasma phagocytophilum and Francisella tularensis) in Ixodes ricinus ticks in Serbia. Using PCR technique, we detected species-specific sequences, rrf-rrl rDNA intergenic spacer for B. burgdorferi s.l., p44/msp2 paralogs for A. phagocytophilum, and the 17 kDa lipoprotein gene, TUL4, for F tularensis, respectively, in total DNA extracted from the ticks. Common infections with more than one pathogen were detected in 42 (28.8 %) of 146 infected l. ricinus ticks. Co-infections with two pathogens were present in 39 (26.7 %) of infected ticks. Simultaneous presence of A. phagocytophilum and different genospecies of B. burgdorferi s.l. complex was recorded in 16 ticks, co-infection with different B. burgdorferi s. l. genospecies was found in 15 ticks and eight ticks harbored mixed infections with F tularensis and B. burgdorferi s.l. genospecies. Less common were triple pathogen species infections, detected in three ticks, one infected with A. phagocytophilum / B. burgdorferi s.s. / B. lusitaniae and two infected with F tularensis / B. burgdorferi s.s. / B. lusitaniae. No mixed infections of A. phagocytophilum and F. tularensis were detected

余呉湖・湖沼堆積物解析から推定される後期完新世の湖沼: 流域系水文環境変動

金沢大学環日本海域環境研究センターHydro-environmental fluctuations in the central Japan during the Late Holocene have been imprinted in the sediment cores from Lake Yogo, where hydrological conditions changed at c.700 AD; from low water regime to high water regime. An abrupt change in ^Pb concentration of the cores shows that rapid increase in the sedimentation rate may have been connected to artificial channel construction in 1960. Temporal fluctuation in mineral particle size of sediment corresponds to yearly averaged precipitation observed near the lake before the construction (1896-1960), leading to that an annual precipitation around Lake Yogo in the Little Ice Age may be estimated about 2,200 mm and in the late part of Medieval Warm Episode about 2,500 mm, larger than during the past 30 years (about 2,000 mm)

Leptospirosis in Squirrels Imported from United States to Japan

We diagnosed leptospirosis in 2 patients exposed to southern flying squirrels imported from the United States to Japan. Patients worked with exotic animals in their company. Leptospira isolates from 1 patient and 5 of 10 squirrels at the company were genetically and serologically identical and were identified as Leptospira kirschneri

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

(Table 1) Sediment chemistry and Sulphur isotope ratios of ODP Site 127-795

Sixty sediment samples collected every 10 m from Holes 795A and 795B in the northern Japan Sea were analyzed for 27 major and trace elements using instrumental neutron activation analysis, and for total organic carbon (TOC), total nitrogen, and total sulfur (TS). Sulfur isotope ratio (d34S CDT) was measured on sedimentary framboidal pyrite isolated from sediments with a high sulfur content. The changes in redox condition of the bottom water of the sea are estimated from vertical variations of redox sensitive elements (TOC, TS, Mn, Sb, U, and As) and from TOC-TS and TS-d34S CDT relationships. These data were compared to those from a piston core (KH77-3-L4') collected near Site 795. The estimated changes in the redox condition are: a variation between less oxic and less euxinic in Units 5,4B, 4A, and 3 (ca. 13-15 to 6-7 Ma); oxic but less so than that of the present Japan Sea with diagenetic sulfate reduction under very high biological productivity in Unit 2 (ca. 6-7 to 2.4 Ma); and a drastic variation between oxic, similar to the present bottom water, and euxinic, similar to that during the last glacial period in the sea, in Units IB (ca. 2.4-1.2 Ma) and 1A (ca. 1.2 Ma to the present)

海洋科学における高精度AMSの利用

第2世代タンデトロン(4130-AMS)は, ^C, ^C, ^Cを同時に測定する, 現代炭素で20分の測定で^Cで200,000カウントの測定が可能, 59試料の連続測定が可能, など多くの利点を有している。このことは, 第1に多数の試料を同一条件でを短時間で測定が可能となることを意味し, 海水中の溶存無機態炭素の年代測定など, 多数の試料を同一条件で迅速に測定することを可能とし, 海洋での2次元または3次元分布を求めることが可能となる。第2には, 現在鉄触媒水素還元法では安定な結果を得るには試料として炭素1mgを用いるのが標準となっているが, もし0.1mgでも測定が可能となれば, 海水の無機炭素であれば4ml海水で,有孔虫であれば1mgでまた堆積物中の有機態炭素であれば堆積物5mg(Corp=2%)で測定が可能となり, その応用範囲の拡大ははかりしれない。さらにこれまで測定が難しかった海水中の溶存有機態炭素や溶存メタンの^Cの測定が現実のものとなりうる。この装置を有効に活用するためには, 効率的かつ安定したターゲット調整法・システムの構築, 0.1mgオーダーの少量炭素試料での測定の実現, カウント数だけではなく実質的測定精度の評価と向上手法開発等が求められる。実際に応用が想定される海洋科学における幾つかの研究課題について議論した。A second generation TANDETRON AMS has advantages of simultaneous measurements of ^C, ^C, and ^C, high counting rates such as 200,000 counts of ^C for a modern carbon sample by 20 minutes measurements, and continuous measurements of 59 samples on a sample holder. These advantages indicate that many samples will be measured for a short time at the same condition and it will make it possible to draw 2- or 3-dimension distributions of seawater DIC in the ocean effectively. Now we use 1mg carbon for the preparation of graphite target by the iron-catalytic hydrogen reduction method to get an acceptable result with the present AMS. If the amount of carbon for the graphite target preparation would be reduced to 0.1mg, we will need only 4ml of seawater for DIC, 1mg of foraminifera, or 5mg of sediment sample for POC, and the AMS ^C method will be applied to great many kinds of new samples, such as DOC in seawater, methane in seawater, etc. To get good results with a second generation AMS, the construction of effective target preparation system, the reduction of sample size, the development of an evaluation method of "real" accuracy will be needed. Several topics relating AMS ^C measurements in marine sciences were discussed.名古屋大学タンデトロン加速器質量分析計シンポジウム(平成8年(1996年度)報告 ｢第2世代タンデトロン加速器質量分析計(加速器年代測定システム)による高精度･高分解能14C年代測定の利用分野･方法の開拓｣ Proceedings of Symposium on Researches with a Tandetron Accelerator Mass Spectrometer at Nagoya University in 1996“Studies on New Fields and New Methods of Applications of High-Precision and High-Accuracy Radiocarbon Dating with a Second-Generation Tandetron Accelerator Mass Spectrometer at Nagoya University”日時:1997 (平成9)年3月10日 場所:名古屋大学年代測定資料研究センター古川総合研究資料館講義