Influence of pH and calcium nutrition on the coffee wilt caused by fusarium oxysporum

Em mudas de Coffea arabica L. cv. Mundo Novo, cultivadas em solução nutritiva analisaram- se os efeitos da nutrição de Ca e pH no crescimento, estado nutriticional e colonização dos tecidos vasculares por Fusarium oxysporum f. sp. coffeae. Os tratamentos consistiram em cinco doses de Ca (0, 10, 100, 200 e 400 µg ml-1), combinadas com dois níveis de pH (4,5 e 6,5). Utilizou-se uma técnica de inoculação do patógeno na região do colo, realizada 105 dias após a emissão das cotiledonares. Observou-se um aumento significativo no desenvolvimento das plantas quando os níveis de Ca na solução foram de 0 a 100 µg ml-1, e uma redução quando os níveis se situaram entre 200 e 400 µg Ca ml-1. Os tratamentos com Ca aumentaram as absorções de Ca e N e diminuíram as de P, K, Mg, Mn e Fe, não afetando, porém, as de Cu e Zn. A progressão do patógeno nos tecidos vasculares foi maior com pH 6,5 que 4,5. A percentagem de tecidos da raiz e caule colonizados aumentou com a diminuição das doses de Ca na solução (0 e 10 µg de Ca ml-1). A severidade da doença geralmente diminuiu com o aumento de Ca de 200 e 400 µg ml-1.A greenhouse solution experiment was conducted with coffee seedlings to investigate the effects of Ca nutrition and pH on growth, plant nutrient content, and the incidence of Fusarium oxysporum f. sp. coffeae. Five concentrations of Ca (0, 10, 100, 200 and 400 µg ml-1) were maintained in combination with two pH levels (4.5 and 6.5). Suspensions of the fungus were inoculated at the colon region of seedlings after 105 days of cotyledon emergency. Dry weight yields increased with increasing Ca levels up to 100 µg ml-1 followed by a marked decrease when Ca concentration was raised to 200 - 400 µg ml-1' of Ca. Plant tissue analysis showed that increasing Ca levels in solution increased the uptake of Ca and N, decreased P, K, Mg, Mn and Fe, and had no effect on Cu and Zn. The extent of colonization of the vascular tissues by the fungus was greater at pH 6.5 than 4.5. The percentage of root and stem tissues incited by the fungus mycelium was increased at low Ca treatments (0 and 10µg of Ca ml-1). The severity of disease generally decreased with increasing Ca in solution up to 200 and 400µg ml-1.

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