A new species of Cybaeus L. Koch, 1868 (Araneae, Cybaeidae) with simple genitalia from central Japan is the sister species of C. melanoparvus Kobayashi, 2006 with elongated genitalia

Spiders of the genus Cybaeus L. Koch, 1868 exhibit two major centers of diversity: Western North America and Japan. Several Japanese Cybaeus possess an elongated embolus in the male palp and elongated tubular spermathecae in the female genitalia. Here we describe Cybaeus koikei sp. nov. from central Honshu, Japan, which has an unelongated embolus and bulbous spermathecae. Phylogenetic analyses using nuclear and mitochondrial gene markers clearly support the monophyly of C. koikei sp. nov. and Cybaeus melanoparvus Kobayashi, 2006, a species with elongated genitalia. Both species share a similar habitus and a cluster of robust setae on the lateral surface of the male palpal patella. The latter is considered a synapomorphy for C. koikei sp. nov. and C. melanoparvus. A supplementary description of the spermathecae of C. melanoparvus is also provided

The subterranean spider Cybaeus fujisanus (Araneae: Cybaeidae) revisited: the first description of a male from Mt. Fuji, Japan

A taxonomic account of the spider Cybaeus fujisanus Yaginuma, 1972, which was described on the basis of only a female holotype from a cave at the foot of Mt. Fuji, Japan, is revisited. A male specimen was collected near the type locality and is described for the first time. A redescription of the female using the holotype and other newly collected specimens is also provided. The conspecificity of the present male and female specimens was confirmed using nuclear ITS-1 and mitochondrial COI sequences

Integrative taxonomy reveals multiple lineages of the spider genus Cybaeus endemic to the Ryukyu Islands, Japan (Arachnida : Araneae : Cybaeidae)

The epigean spiders of the genus Cybaeus L. Koch, 1868 are known to have diversified in western North America and the Japanese Archipelago. To date, ~80 species of Cybaeus are known from Japan, but they have not previously been recorded from the Ryukyu Islands that harbour a diversity of endemic species. Here we describe eight new species of Cybaeus from the Ryukyu Islands, extending the range of Cybaeus southward to the central Ryukyus. Both sexes of each of the new species are described, and their phylogenetic relationships are estimated using nuclear and mitochondrial gene markers. Although Cybaeus okumurai, sp. nov. and C. kumadori, sp. nov. possess genital features that are common in the other Japanese congeners, the other six species (C. yakushimensis, sp. nov., C. kodama, sp. nov., C. amamiensis, sp. nov., C. aikana, sp. nov., C. tokunoshimensis, sp. nov., and C. hikidai, sp. nov.) are characterised by an elongated embolus and tubular spermathecae. These unique genital characteristics and the phylogeny recovered here suggest that these features evolved independently among the Japanese and Ryukyu Cybaeus species. Phylogenetic analyses highlight an unusual biogeographical pattern in which C. yakushimensis and C. kodama endemic to Yakushima Island in the northern Ryukyus are related to species distributed in the central Ryukyus. In contrast, our phylogeny suggests that C. okumurai from Tanegashima Island in the northern Ryukyus is sister to C. ashikitaensis (Komatsu, 1968), distributed in Kyushu of the Japanese Archipelago. The retreat constructs and sympatric distribution of Cybaeus found among the Ryukyus are also briefly discussed

Two new species of Arcuphantes (Araneae: Linyphiidae: Micronetinae) from Owase, Kii Peninsula, Japan

Two new linyphiid species, Arcuphantes shiozakii sp. nov. and A. yakiyama sp. nov., from Owase, eastern Kii Peninsula, Japan, are described based on both sexes. Given the fact that the two new species share almost identical mitochondrial cytochrome c oxidase subunit I sequences, they may represent closely related sister species, but nonetheless, they are clearly distinguishable from each other by the genital characters. Additionally, the new species are closely related to A. osugiensis (Oi 1960) and A. yamakawai (Oi 1960), but they are also distinguished by the morphology of genitalia

Oral delivery of Lactococcus lactis that secretes bioactive heme oxygenase-1 alleviates development of acute colitis in mice

Background: Mucosal delivery of therapeutic proteins using genetically modified strains of lactic acid bacteria (gmLAB) is being investigated as a new therapeutic strategy. Methods: We developed a strain of gmLAB, Lactococcus lactis NZ9000 (NZ-HO), which secretes the anti-inflammatory molecule recombinant mouse heme oxygenase-1 (rmHO-1). The effects of short-term continuous oral dosing with NZ-HO were evaluated in mice with dextran sulfate sodium (DSS)-induced acute colitis as a model of inflammatory bowel diseases (IBD). Results: We identified the secretion of rmHO-1 by NZ-HO. rmHO-1 was biologically active as determined with spectroscopy. Viable NZ-HO was directly delivered to the colon via oral administration, and rmHO-1 was secreted onto the colonic mucosa in mice. Acute colitis in mice was induced by free drinking of 3 % DSS in water and was accompanied by an increase in the disease activity index score and histopathological changes. Daily oral administration of NZ-HO significantly improved these colitis-associated symptoms. In addition, NZ-HO significantly increased production of the anti-inflammatory cytokine interleukin (IL)-10 and decreased the expression of pro-inflammatory cytokines such as IL-1 alpha and IL-6 in the colon compared to a vector control strain. Conclusions: Oral administration of NZ-HO alleviates DSS-induced acute colitis in mice. Our results suggest that NZ-HO may be a useful mucosal therapeutic agent for treating IBD.ArticleMICROBIAL CELL FACTORIES. 14:189 (2015)journal articl

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

Taxonomic Reassessment of Cybaeus communis and Cybaeus maculosus (Araneae: Cybaeidae) from Central Honshu, Japan

The taxonomic status of the two Japanese species of the spider genus Cybaeus L. Koch, 1868, viz., C. communis Yaginuma, 1972 and C. maculosus Yaginuma, 1972, is revisited on the basis of male and female specimens, which were collected from each type locality and the adjacent areas, along with the holotypes of both species. Mitochondrial cytochrome c oxidase subunit I and nuclear internal transcribed spacer 1 sequence data confirmed that C. communis and C. maculosus are conspecific, and C. maculosus is synonymized with C. communis. The obtained molecular phylogenies corroborate the monophyly of C. communis, C. kirigaminensis Komatsu, 1963, C. shinkaii (Komatsu, 1970), and C. daimonji Matsuda, Ihara, and Nakano, 2020

Description of a new species of Cybaeus (Araneae: Cybaeidae) from central Honshu, Japan

A new spider species, Cybaeus daimonji, from Kyoto, western-central Honshu, Japan is described based on both sexes. The shape of epigyne indicates that this new species is close to C. communis Yaginuma, 1972, C. kirigaminensis Komatsu, 1963, C. maculosus Yaginuma, 1972 and C. shinkaii (Komatsu, 1970), which are distributed in eastern to central Honshu. Nuclear internal transcribed spacer 1, 28S ribosomal RNA and histone H3 as well as mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA and 16S ribosomal RNA sequences of the new species are provided for future phylogenetic studies