Reforestation following harvesting of conifer plantations in Japan: Current issues from silvicultural and ecological perspectives

Following the Second World War, the number of Cupressaceae plantations in Japan increased, in accordance with government policy for the restoration of timber resources and conservation of soil and water. Currently, these even-aged plantations occupy approximately 44% of the forested area and 24% of the national land area of Japan. Although many of these plantations have become available as timber resources, there are several silviculture-related problems associated with reforestation following clear-cutting of these plantations. The abundant annual precipitation in Japan allows for dominance by competitive vegetation, which makes natural regeneration difficult and increases the cost of silvicultural operations during and after the planting of seedlings. Because the number of seedling producers has decreased, there has been little incentive to keep seedling production techniques up to date. Additionally, damage to planted seedlings by the overabundant sika deer (Cervus nippon) population has increased dramatically in the last dozen years or so. To determine how to overcome these difficulties, various studies are underway in Japan. For example, seedling studies have examined the relationship between seedling size and competitive ability with other species in reforested areas, and have led to the development of lower-cost systems to produce customized Cupressaceae seedlings, as well as measures to minimize transplanting damage to seedlings. Previous studies have shown that no-weeding operations might lower the risk of sika deer browsing seedlings, although this silvicultural countermeasure may potentially reduce seedling growth. Studies have also examined the types of physical protection against sika deer browsing that are most efficient. We must combine these findings into a unified silvicultural system for successful restoration via lower-cost plantations

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

Growth and photosynthetic traits of hybrid larch F1 (Larix gmelinii var. japonica x L. kaempferi) under elevated CO2 concentration with low nutrient availability

The hybrid larch F1 (Larix gmelinii var. japonica x Larix kaempferi) is considered as one of the most important tree species not only for timber production but also as an afforestation material for severe conditions such as infertile soil. To predict the ability of hybrid larch F1 as an afforestation material under potential climates in the future, it is important to understand the response of hybrid larch F1 to elevated CO2 concentration ([CO2]) under low nutrient availability. Three-year-old seedlings of hybrid larch F1 were grown under two different levels of [CO2], 360 (ambient) and 720 μmol mol^[-1] (elevated), in combination with two different levels of nitrogen (N) supply (0 and 30 kg ha^[-1]) for one growing season. Elevated [CO2] reduced the maximum rates of carboxylation and electron transport in the needles. Net photosynthetic rates at growth [CO2] (i.e., 360 and 720 μmol mol^[-1] for ambient and elevated treatment, respectively) did not differ between the two CO2 treatments. Reductions in the N content and the N use efficiency to perform photosynthetic functions owing to the deficiency of nutrients other than N, such as P and K, and/or increase of cell wall mass were considered as the factors of photosynthetic down-regulation under elevated [CO2], whereas stomatal closure little affected the photosynthetic down-regulation. Although we observed strong down-regulation of photosynthesis, the dry matter increase of hybrid larch F1 seedlings was enhanced under elevated [CO2]. This is mainly attributable to the increase in the amount of needles with increasing the number of sylleptic branches. These results suggest that elevated CO2 may increase growth of hybrid larch F1 even under low nutrient availability, and that this increase may be regulated by both changes in crown architecture and in needle photosynthesis, which is mainly affected by not stomatal limitation but by biochemical limitation

High nitrogen and elevated [CO2] effects on the growth, defense and photosynthetic performance of two eucalypt species

Atmospheric nitrogen deposition and [CO2] are increasing and represent environmental problems. Planting fast-growing species is prospering to moderate these environmental impacts by fixing CO2. Therefore, we examined the responses of growth, photosynthesis, and defense chemical in leaves of Eucalyptus urophylla (U) and the hybrid of E. deglupta x E. camadulensis (H) to different CO2 and nitrogen levels. High nitrogen load significantly increased plant growth, leaf N, photosynthetic rate (A_[growth]), and photosynthetic water use efficiency (WUE). High CO2 significantly increased A_[growth], photosynthetic nitrogen use efficiency (PNUE) and WUE. Secondary metabolite (SM, i.e. total phenolics and condensed tannin) was specifically altered; as SM of U increased by high N load but not by elevated [CO2], and vice versa for SM of H

Comparison of growth characteristics and tolerance to serpentine soil of three ectomycorrhizal spruce seedlings in northern Japan

Picea glehnii is distributed widely on serpentine soils in northern Japan. Serpentine soil is characterised by the presence of heavy metals (Ni, Cr) and excessive Mg; these elements often suppress plant growth. We have examined the tolerance to serpentine soil and its effects on growth of P. glehnii, P. jezoensis (distributed in the same region) and P. abies (planted for timber production). The dry mass of each organ was not reduced in P. glehnii planted in serpentine soil contained nursery (serpentine nursery). In contrast, growth of P. jezoensis and P. abies was suppressed. Concentrations of Ni and Mg in needles and roots of P. glehnii planted in serpentine nursery were the lowest of the three species. Moreover, the photosynthetic rate of P. glehnii planted in the serpentine nursery was not reduced. P. glehnii has high capability to maintain low concentration of Ni, and ectomycorrhizal symbiosis may have a positive effect to excluding Ni. As a result, P. glehnii has a high tolerance against Ni toxicity, and its photosynthetic capacity is not suppressed by accumulation of Ni.The original publication is available at www.springerlink.com