Parashorea chinensis is an endemic tree species in China and an endangered species of the Dipterocarpaceae family. This study contributes to the understanding of soil fertility management during the relocation and conservation of P. chinensis and the restoration of its natural communities by doing an ecological chemometric investigation of the factors limiting soil nutrients in P. chinensis plantations. To investigate the variation in rhizosphere and non-rhizosphere soil nutrients, microbial biomass, and extracellular enzyme activities, we chose pure plantation stands of 6 ages in the subtropics and calculated stoichiometric ratios. The results show that (1) soil pH is strongly acidic (pH < 4.6) and is less influenced by the stand age, and the soil carbon (C), nitrogen (N), and phosphorus (P) content limit soil microorganisms at all stand ages; (2) the availability of soil N, P, and K elements is an essential factor driving P limitation in the growth of P. chinensis and its soil microbes; (3) stand age has a significant effect on the soil C/N, C/P, N/P, C/K, N/K, and P/K, the stoichiometry of microbial biomass C, N, and P, and the stoichiometry of C, N, and P acquisition enzyme activity. Soil microbial biomass C, N, and P stoichiometry are more sensitive indicators of nutrient limitations than the stoichiometry of enzyme activity and nutrient content; and (4) there was a significant correlation between microbial biomass C, N, and P stoichiometry and soil C/P and N/P, as well as a highly significant (p < 0.01) correlation between the stoichiometry of the enzyme activity and Vector L and Vector A. In conclusion, the plantations of P. chinensis in this study area were established on acidic phosphorus-poor soil, and the ecological stoichiometry of the soil reveals nutrient limitations and its variation with the stand age. P availability plays a key role in the growth of P. chinensis and in improving the rhizosphere microbial community. Therefore, soil effectiveness should be dynamically assessed during the cultivation and relocation conservation of P. chinensis, and a soluble P fertilizer should be supplemental over time in the trees’ root distribution area.
Background Eucalyptus is the main plantation wood species, mostly grown in aluminized acid soils. To understand the response of Eucalyptus clones to aluminum (Al) toxicity, the Al-tolerant Eucalyptus grandis × E. urophylla clone GL-9 (designated “G9”) and the Al-sensitive E. urophylla clone GL-4 (designated “W4”) were employed to investigate the production and secretion of citrate and malate by roots. Results Eucalyptus seedlings in hydroponics were exposed to the presence or absence of 4.4 mM Al at pH 4.0 for 24 h. The protein synthesis inhibitor cycloheximide (CHM) and anion channel blocker phenylglyoxal (PG) were applied to explore possible pathways involved in organic acid secretion. The secretion of malate and citrate was earlier and greater in G9 than in W4, corresponding to less Al accumulation in G9. The concentration of Al in G9 roots peaked after 1 h and decreased afterwards, corresponding with a rapid induction of malate secretion. A time-lag of about 6 h in citrate efflux in G9 was followed by robust secretion to support continuous Al-detoxification. Malate secretion alone may alleviate Al toxicity because the peaks of Al accumulation and malate secretion were simultaneous in W4, which did not secrete appreciable citrate. Enhanced activities of citrate synthase (CS) and phosphoenolpyruvate carboxylase (PEPC), and reduced activities of isocitrate dehydrogenase (IDH), aconitase (ACO) and malic enzyme (ME) were closely associated with the greater secretion of citrate in G9. PG effectively inhibited citrate and malate secretion in both Eucalyptus clones. CHM also inhibited malate and citrate secretion in G9, and citrate secretion in W4, but notably did not affect malate secretion in W4. Conclusions G9 immediately secrete malate from roots, which had an initial effect on Al-detoxification, followed by time-delayed citrate secretion. Pre-existing anion channel protein first contributed to malate secretion, while synthesis of carrier protein appeared to be needed for citrate excretion. The changes of organic acid concentrations in response to Al can be achieved by enhanced CS and PEPC activities, but was supported by changes in the activities of other enzymes involved in organic acid metabolism. The above information may help to further explore genes related to Al-tolerance in Eucalyptus.
Aluminized acidic soil can damage Eucalyptus roots and limit tree growth, hindering the productivity of Eucalyptus plantations. At present, the negative impacts of elevated aluminum (Al) on the cell morphology and cell wall properties of Eucalyptus root tip are still unclear. In order to investigate the responses of two different tolerant clones, Eucalyptus urophylla (G4) and Eucalyptus grandis × Eucalyptus urophylla (G9), to Al toxicity, seedling roots were treated hydroponically with an Al solution, and the polysaccharide content in the root tip cell wall and the characteristics of programmed cell death were studied. The results show that the distribution of Al was similar in both clones, although G9 was found to be more tolerant to Al toxicity than G4. The Al3+ uptake of pectin in root tip cell walls was significantly higher in G4 than in G9. The root tip in G4 was obviously damaged, enlarged, thickened, and shorter; the root crown cells were cracked and fluffy; and the cell elongation area was squeezed. The lower cell wall polysaccharide content and PME activity may result in fewer carboxylic groups in the root tip cell wall to serve as Al-binding sites, which may explain the stronger Al resistance of G9 than G4. The uptake of nitrogen and potassium in G4 was significantly reduced after aluminum application and was lower than in G9. Al-resistant Eucalyptus clones may have synergistic pleiotropic effects in resisting high aluminum–low phosphorus stress, and maintaining higher nitrogen and potassium levels in roots may be an important mechanism for effectively alleviating Al toxicity.
Background Eucalyptus is the main timber species, most of which are hybrid clones, and usually grow in aluminized acid soil in China. The exudation of organic acids from roots may contribute to detoxification of Al and lead to the Al-tolerance in Eucalyptus genotypes. To further understand the organic acid response in Al tolerance in Eucalyptus, the Al-tolerant Eucalyptus grandis × E. urophylla clone GL-9 (marked as “G9”) and the Al-sensitive Eucalyptus urophylla clone GL-4 (marked as “W4”) were used to investigate the secretion and metabolism of citrate and malate in roots. Results Eucalyptus seedlings in hydroponics were exposed to the presence or absence of 4.4 mM Al at pH 4.0 for 24 hours. The protein synthesis inhibitor cycloheximide (CHM) and the anion channel blocker phenylglyoxal (PG) were applied to explore possible pathways involved in organic acid secretion. The Al treatments caused higher Al accumulation in roots of both clones. The secretion of malate and citrate was greater in G9 than in W4, corresponding to the relatively higher tolerance in G9 to Al. The peak Al concentration occurred after 1 h in G9 roots and declined afterward, indicating the activation of detoxification to alleviate Al accumulation. After 6 h of Al exposure, the efflux of citrate dramatically increased in G9 after a substantial lag phase, while both peak Al accumulation in roots and peak malate secretion occurred and there was no induction of citrate secretion in W4. Enhanced activity for citrate synthase and phosphoenolpyruvate carboxylase, and reduced activity for NADP-isocitrate dehydrogenase, aconitase and NADP-malic enzyme were closely associated with the greater secretion of citrate in G9. Both PG and CHM were effective inhibitors of citrate and malate secretion in both Eucalyptus clones, except the malate secretion in W4 was not affected by CHM. Conclusions In two different Al-tolerant Eucalyptus clones, both secretion and internal accumulation of citrate and malate in roots were involved in Al detoxification. An anion channel on the plasma membrane could be an important mode of organic acid secretion. Citrate and relevant metabolizing enzymes led more important role in the response to Al in E. grandis × E. urophylla.
The identification of T cell neo-epitopes is fundamental and computational challenging in tumor immunotherapy study. As the binding of pMHC - T cell receptor (TCR) is the essential condition for neo-epitopes to trigger the cytotoxic T cell reactivity, several computational studies have been proposed to predict neo-epitopes from the perspective of pMHC-TCR binding recognition. However, they often failed with the inaccurate binding prediction for a single pMHC -TCR pair due to the highly diverse TCR space. In this study, we proposed a novel weakly-supervised learning framework,i.e.,TCRBagger, to facilitate the personalized neo-epitope identification with weakly-supervised peptide-TCR binding prediction by bagging a sample-specific TCR profile.TCRBaggerintegrates three carefully designed learning strategies,i.e. a self-supervised learning strategy, a denoising learning strategy and a Multi-Instance Learning (MIL) strategy in the modeling of peptide-TCR binding. Our comprehensive tests revealed thatTCRBaggerexhibited great advances over existing tools by modeling interactions between peptide and TCR profiles. We further appliedTCRBaggerin different clinical settings, including (1) facilitating the peptide-TCR binding prediction under MIL using single-cell TCR-seq data. (2) improving the patient-specific neoantigen prioritization compared to the existing neoantigen identification tools. Collectively,TCRBaggerprovides novel perspectives and contributions for identifying neo-epitopes as well as discovering potential pMHC-TCR interactions in personalized tumor immunotherapy.
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