Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency

The Japanese wrinkled frog (Glandirana rugosa) is unique in having both XX-XY and ZZ-ZW types of sex chromosomes within the species. The genome sequencing and comparative genomics with other frogs should be important to understand mechanisms of turnover of sex chromosomes within one species or during a short period. In this study, we analyzed the newly sequenced genome of G. rugosa using a batch-learning self-organizing map which is unsupervised artificial intelligence for oligonucleotide compositions. To clarify genome characteristics of G. rugosa, we compared its short oligonucleotide compositions in all 1-Mb genomic fragments with those of other six frog species (Pyxicephalus adspersus, Rhinella marina, Spea multiplicata, Leptobrachium leishanense, Xenopus laevis, and Xenopus tropicalis). In G. rugosa, we found an Mb-level large size of repeat sequences having a high identity with the W chromosome of the African bullfrog (P. adspersus). Our study concluded that G. rugosa has unique genome characteristics with a high CG frequency, and its genome is assumed to heterochromatinize a large size of genome via methylataion of CG

Seasonal variation of paralytic and amnesic shellfish toxicities in bivalves and microalgae in Haiphong area, Vietnam

Monitoring survey was conducted to know the distribution and seasonal variation of PSP and ASP toxicities in bivalves and the abundance of toxic microalgae in Haiphong area, Vietnam. Sampling was carried out at the stations in Cat Ba and Do Son every two weeks from February 2002 to March 2004. Low levels of PSP and DA were detected in shellfish samples from both stations, showing seasonal and yearly variation. Toxicity of plankton samples also showed fluctuation, though the clear correlation could not be observed with the shellfish toxicities. HPLC or LC-MSMS analysis provided clear evidence of shellfish contamination with these toxins and indicated the existence of causative microalgae for these toxicities in this area. Several species of Alexandrium such as A. minutum, A. tamiyavanichii, A. ostenfeldii, A. tamarense were found, though the abundance of them was very low. On the other hand, massive bloom of Pseudo-nitzschia occurred in January at both stations. However, these blooms did not always cause the increase of DA level both in plankton and shellfish samples

Seasonal variation of paralytic and amnesic shellfish toxicities in bivalves and microalgae in Haiphong area, Vietnam

Monitoring survey was conducted to know the distribution and seasonal variation of PSP and ASP toxicities in bivalves and the abundance of toxic microalgae in Haiphong area, Vietnam. Sampling was carried out at the stations in Cat Ba and Do Son every two weeks from February 2002 to March 2004. Low levels of PSP and DA were detected in shellfish samples from both stations, showing seasonal and yearly variation. Toxicity of plankton samples also showed fluctuation, though the clear correlation could not be observed with the shellfish toxicities. HPLC or LC-MSMS analysis provided clear evidence of shellfish contamination with these toxins and indicated the existence of causative microalgae for these toxicities in this area. Several species of Alexandrium such as A. minutum, A. tamiyavanichii, A. ostenfeldii, A. tamarense were found, though the abundance of them was very low. On the other hand, massive bloom of Pseudo-nitzschia occurred in January at both stations. However, these blooms did not always cause the increase of DA level both in plankton and shellfish samples

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

Repercussions of the Great East Japan Earthquake tsunami on ellipsoidal Alexandrium cysts (Dinophyceae) in Ofunato Bay, Japan

Shellfish aquaculture in Ofunato Bay, Northeast Japan, was seriously damaged by a tsunami generated by the Great East Japan Earthquake, March 11th, 2011, accompanied by paralytic shellfish poisoning (PSP) outbreaks caused by Alexandrium tamarense (Dinophyceae). To understand longer future trends of PSP, an investigation was made of the historical occurrence and causes of Alexandrium outbreaks after the tsunami. Vertical distributions of Alexandrium cysts in two sediment-cores from Ofunato Bay revealed that the sediments above ca. 25 cm were eroded, re-suspended and re-deposited, and they included unusually abundant Alexandrium cysts. This abundance of cysts was due to re-deposition of older sediments by the tsunami. The first Ofunato Bay PSP incident was in 1961 after the Chilean Earthquake tsunami and was probably caused by similar unusual blooms of Alexandrium germinated from older sediments as the Great East Japan tsunami, together with nutrient enrichment because of population increase at the start of shellfish aquaculture