Zooplankton diversity analysis through single-gene sequencing of a community sample

<p>Abstract</p> <p>Background</p> <p>Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited because of their fragile nature, small body size, and the large number of species from various taxonomic phyla. Here we present the results of single-gene zooplankton community analysis using a method that determines a large number of mitochondrial <it>COI </it>gene sequences from a bulk zooplankton sample. This approach will enable us to estimate the species richness of almost the entire zooplankton community.</p> <p>Results</p> <p>A sample was collected from a depth of 721 m to the surface in the western equatorial Pacific off Pohnpei Island, Micronesia, with a plankton net equipped with a 2-m²mouth opening. A total of 1,336 mitochondrial <it>COI </it>gene sequences were determined from the cDNA library made from the sample. From the determined sequences, the occurrence of 189 species of zooplankton was estimated. BLASTN search results showed high degrees of similarity (>98%) between the query and database for 10 species, including holozooplankton and merozooplankton.</p> <p>Conclusion</p> <p>In conjunction with the Census of Marine Zooplankton and Barcode of Life projects, single-gene zooplankton community analysis will be a powerful tool for estimating the species richness of zooplankton communities.</p

Molecular characterization of buckwheat major immunoglobulin E-reactive proteins in allergic patients

ABSTRACTBuckwheat extract was analyzed by immunoblotting experiments using sera from nine allergic and three non-allergic individuals. Major IgE-reactive bands were 73, 70, 62, 58 and 54kDa under non-reducing conditions and were detected in allergic subjects, but not in non-allergic ones. Under reducing conditions, the 73, 70, 62 and 58kDa bands split to 56 and 24, 52 and 24, 45 and 24, and 43 and 24kDa, respectively. The 24kDa molecule was the most prominent band recognized with IgE as well as IgG or IgA. The FA02 cDNA clone, encoding the α and β subunits of the legumin-like storage protein, was isolated from a cDNA library made of immature buckwheat seeds. The deduced amino acid sequence of the cDNA clone is substantially identical to the N-terminal amino acid sequence of the 24kDa molecule, which may be identical to that of BW24KD reported by Urisu et al. Consistent with these results, the translation product of the cDNA encoding the putative β subunit was strongly recognized with serum IgE, IgG and IgA from buckwheat-allergic patients. These results suggested that the 24kDa molecule may be the β subunit of the legumin-like storage molecule of buckwheat

AGN number fraction in galaxy groups and clusters at z < 1.4 from the Subaru Hyper Suprime-Cam survey

One of the key questions on active galactic nuclei (AGN) in galaxy clusters is how AGN could affect the formation and evolution of member galaxies and galaxy clusters in the history of the Universe. To address this issue, we investigate the dependence of AGN number fraction ($f_{\rm AGN}$) on cluster redshift ($z_{\rm cl}$) and distance from the cluster center ($R/R_{\rm 200}$). We focus on more than 27,000 galaxy groups and clusters at $0.1 < z_{\rm cl} < 1.4$ with more than 1 million member galaxies selected from the Subaru Hyper Suprime-Cam. By combining various AGN selection methods based on infrared (IR), radio, and X-ray data, we identify 2,688 AGN. We find that (i) $f_{\rm AGN}$ increases with $z_{\rm cl}$ and (ii) $f_{\rm AGN}$ decreases with $R/R_{\rm 200}$. The main contributors to the rapid increase of $f_{\rm AGN}$ towards high-$z$ and cluster center are IR- and radio-selected AGN, respectively. Those results indicate that the emergence of the AGN population depends on the environment and redshift, and galaxy groups and clusters at high-$z$ play an important role in AGN evolution. We also find that cluster-cluster mergers may not drive AGN activity in at least the cluster center, while we have tentative evidence that cluster-cluster mergers would enhance AGN activity in the outskirts of (particularly massive) galaxy clusters.Comment: 16 pages, 21 figures, and 2 tables, accepted for publication in PAS

Optical IFU Observations of GOALS Sample with KOOLS-IFU on Seimei Telescope: Initial results of 9 U/LIRGs at z<z < 0.04

We present ionized gas properties of 9 local ultra/luminous infrared galaxies (U/LIRGs) at $z <$ 0.04 through IFU observations with KOOLS-IFU on Seimei Telescope. The observed targets are drawn from the Great Observatories All-sky LIRG Survey (GOALS), covering a wide range of merger stages. We successfully detect emission lines such as H$\beta$, [OIII]$\lambda$5007, H$\alpha$, [NII]$\lambda\lambda$6549,6583, and [SII]$\lambda\lambda$6717,6731 with a spectral resolution of $R$ = 1500-2000, which provides (i) spatially-resolved ($\sim$200-700 pc) moment map of ionized gas and (ii) diagnostics for active galactic nucleus (AGN) within the central $\sim$3--11 kpc in diameter for our sample. We find that [OIII] outflow that is expected to be driven by AGN tends to be stronger (i) towards the galactic center and (ii) as a sequence of merger stage. In particular, the outflow strength in the late-stage (stage D) mergers is about 1.5 times stronger than that in the early-state (stage B) mergers, which indicates that galaxy mergers could induce AGN-driven outflow and play an important role in the co-evolution of galaxies and supermassive black holes.Comment: 12 pages, 8 figures, and 2 tables, accepted for publication in PAS

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

Analysis of the structure and neuritogenic activity of chondroitin sulfate/dermatan sulfate hybrid chains from porcine fetal membranes

The amniotic membrane (AM) is the innermost layer of fetal membranes and possesses various biological activities. Although the mechanism underlying these biological activities remains unclear, unique components seem to be involved. AM contains various extracellular matrix components such as type I collagen, laminin, fibronectin, hyaluronic acid, and proteoglycans bearing chondroitin sulfate/dermatan sulfate (CS/DS) glycosaminoglycan side chains. To elucidate the function of CS/DS in AM, the structure and bioactivity of the CS/DS chains from porcine fetal membranes (FM-CS/DS) were investigated. A compositional analysis using various chondroitinases revealed that the characteristic DS domain comprised of iduronic acid-containing disaccharide units is embedded in FM-CS/DS, along with predominant disaccharide units, GlcA-GalNAc, GlcA-GalNAc(4-O-sulfate), and GlcA-GalNAc (6-O-sulfate), where GlcA and GalNAc represent D-glucuronic acid and N-acetyl-D-galactosamine, respectively. The average molecular size of FM-CS/DS chains was unusually large and estimated to be 250 - 300 kDa. The FM-CS/DS chains showed neurite outgrowth-promoting activity with a dendrite-like morphology, which was eliminated by digestion with chondroitinase ABC of the CS/DS chains. This activity was suppressed by antibodies against growth factors including pleiotrophin, midkine, and fibroblast growth factor-2. The binding of these growth factors to FM-CS/DS was also demonstrated by surface plasmon resonance spectroscopy

Demonstration of the hepatocyte growth factor signaling pathway in the in vitro neuritogenic activity of chondroitin sulfate from ray fish cartilage

Chondroitin sulfate (CS) was isolated from ray fish cartilage, an industrial waste, after protease digestion, and its structure and neurite outgrowth-promoting (NOP) activity were analyzed to investigate a potential application to nerve regeneration. A disaccharide analysis using chondroitinase ABC revealed that the major unit in the CS preparation was GlcUA-GalNAc(6-O-sulfate) (63%), where GlcUA and GalNAc represent D-glucuronic acid and N-acetyl-D-galactosamine, respectively. Small proportions of other disaccharide units, GlcUA-GalNAc(4-O-sulfate) (25%), GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate) (7%), and GlcUA-GalNAc (5%), were also detected. The average molecular mass of CS was estimated to be 142 kDa by gel-filtration chromatography. The prepration showed NOP activity in vitro, which was eliminated by digestion with chondroitinase ABC, suggesting that a polymeric structure is required for the activity. Antibodies against hepatocyte growth factor (HGF) and its receptor c-Met suppressed the NOP activity, suggesting the involvement of the HGF signaling pathway in the in vitro NOP activity of the CS preparation. Since the specific binding of HGF to the CS preparation was also demonstrated by surface plasmon resonance spectroscopy, the CS chains were fractionated using an HGF-immobilized column into unbound and bound fractions accounting for 44 and 56% of the total yield, respectively. The latter contained a higher proportion of the GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate) unit, and showed greater NOP activity than the former, indicating that the HGF-binding domain contains GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate) and is involved in the NOP activity. CS from ray cartilage may have potential pharmaceutical applications