Chromosome-level genome assembly and characterization of Sophora Japonica

Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic and medicinal value. Here, we reveal a draft genome of S. japonica, which was ∼511.49 Mb long (contig N50 size of 17.34 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved N50 size of 31.32 Mb based on Hi-C data. Further investigation identified 271.76 Mb (53.13%) of repetitive sequences and 31,000 protein-coding genes, of which 30,721 (99.1%) were functionally annotated. Phylogenetic analysis indicates that S. japonica separated from Arabidopsis thaliana and Glycine max ∼107.53 and 61.24 million years ago, respectively. We detected evidence of species-specific and common-legume whole-genome duplication events in S. japonica. We further found that multiple TF families (e.g. BBX and PAL) have expanded in S. japonica, which might have led to its enhanced tolerance to abiotic stress. In addition, S. japonica harbours more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed no obvious differentiation among geographical groups and the effective population size continuously declined since 2 Ma. Our genomic data provide a powerful comparative framework to study the adaptation, evolution and active ingredients biosynthesis in S. japonica. More importantly, our high-quality S. japonica genome is important for elucidating the biosynthesis of its main bioactive components, and improving its production and/or processing.     

DeepMHADTA: Prediction of Drug-Target Binding Affinity Using Multi-Head Self-Attention and Convolutional Neural Network

Drug-target interactions provide insight into the drug-side effects and drug repositioning. However, wet-lab biochemical experiments are time-consuming and labor-intensive, and are insufficient to meet the pressing demand for drug research and development. With the rapid advancement of deep learning, computational methods are increasingly applied to screen drug-target interactions. Many methods consider this problem as a binary classification task (binding or not), but ignore the quantitative binding affinity. In this paper, we propose a new end-to-end deep learning method called DeepMHADTA, which uses the multi-head self-attention mechanism in a deep residual network to predict drug-target binding affinity. On two benchmark datasets, our method outperformed several current state-of-the-art methods in terms of multiple performance measures, including mean square error (MSE), consistency index (CI), rm2, and PR curve area (AUPR). The results demonstrated that our method achieved better performance in predicting the drug–target binding affinity.     

不同放牧制度下呼伦湖流域草原植被冠层截留

冠层截留是降雨过程中的水量分配和流域水平衡的一个重要组成部分,通过水浸泡法和降雨模拟实验研究呼伦湖流域草原3种放牧制度下(休牧、轮牧、自由放牧(超载放牧))植被冠层截留量的变化规律,并利用遥感解译植被归一化指数(NDVI),确定3种放牧制度下草原面积,估算呼伦湖流域草原降雨截留量。研究表明:在休牧、轮牧、自由放牧3种制度下,水浸泡法测定的截留量分别是0.468、0.320、0.271 mm。降雨模拟实验法测得的结果分别是0.957、0.613、0.431 mm。休牧、轮牧、自由放牧草场叶面积指数、盖度、容重、生物量等指标差异显著(P0.05),且单株植被高度、鲜重对截留量影响显著呈线性正相关关系。呼伦湖流域草原一次降雨量为大于等于30 mm全流域降雨,其植被截留量为6.462×106m3。     

土地利用/覆盖变化对中国不同季节气温的影响

近几十年中国地区土地利用/覆盖变化(LUCC)较大,在区域气候模拟中尤其需要使用更加准确的土地利用/覆盖数据。基于模式原有的USGS和新开发的LUC90两种土地利用/覆盖资料,利用区域环境集成模拟系统(RIEMS2.0)分别进行连续10a模拟,分析LUCC对中国不同季节气温的影响。结果表明:1)采用LUC90资料后,中国及东北、华北、华南夏季平均气温增加,但只有东北模拟与观测值的偏差减小,且通过显著性检验(P0.01)。中国及东北、华南冬季平均气温增加,并且模拟与观测值的偏差减少。中国及华北和华南对冬季气温年际变率的模拟改善好于夏季。2)土地利用/覆盖变化通过影响潜热通量的变化和净吸收辐射通量的变化来影响不同季节气温的变化。冬季净辐射通量变化对气温变化的贡献较夏季大,而夏季潜热通量变化对气温变化的贡献较冬季大。雨养农田转变森林、草地、灌溉农田过程造成通量变化,其对气温变化的影响也存在不同分区季节的差异。     

Discovery and SAR analysis of 5-chloro-4-((substituted phenyl)amino)pyrimidine bearing histone deacetylase inhibitors

Histone deacetylases (HDACs) are validated targets for the development of anticancer drugs in epigenetics. In the discovery of novel HDAC inhibitors with anticancer potency, the 5-chloro-4-((substituted phenyl)amino)pyrimidine fragment is assembled as a cap group into the structure of HDAC inhibitors. The SAR revealed that presence of small groups (such as methoxy substitution) is beneficial for the HDAC inhibitory activity. In the enzyme inhibitory selectivity test, compound L20 exhibited class I selectivity with IC₅₀ values of 0.684 µM (selectivity index of >1462), 2.548 µM (selectivity index of >392), and 0.217 µM (selectivity index of >4608) against HDAC1, HDAC2 and HDAC3 compared with potency against HDAC6 (IC₅₀ value of >1000 µM), respectively. In the antiproliferative assay, compound L20 showed both hematological and solid cancer inhibitory activities. In the flow cytometry, L20 promoted G0/G1 phase cell cycle arrest and apoptosis of K562 cells.     

生物启发的细菌表面人造矿物壳:通过仿生矿化保护活细胞

【目的】生物启发的细菌表面仿生矿化人造矿物壳被用于保护活细胞。【方法】将细菌限制在坚固而完整的矿物壳中,有限的物理空间和物质交换使其暂时进行休眠,降低长期保存期间的活力损失以及提高在各种极端环境中的生存能力,并且能够通过酸去除矿物壳而重新激活细菌。【结果】相较于未仿生矿化的细菌(EcN),矿化细菌(EcN@CaCO₃)在32 d的储存实验中活力最高提升262倍;在pH 2.5的强酸环境中存活率提高837倍;在pH 12.0的强碱环境中存活率提高171倍;在80 ℃的高温条件下存活率提高59.1倍;甚至在抗生素溶液中,EcN@CaCO₃中细菌的存活率是EcN的729.7倍。【结论】本研究利用仿生矿化提高了细菌的保存稳定性,使其能在酸刺激下去除涂层恢复活性,也能在极端环境下保留细菌的活力,为微生物在环境生态、食品制造和生物医药等领域的应用提供研究基础。     

TEB/POLQ plays dual roles in protecting Arabidopsis from NO-induced DNA damage

Nitric oxide (NO) is a key player in numerous physiological processes. Excessive NO induces DNA damage, but how plants respond to this damage remains unclear. We screened and identified an Arabidopsis NO hypersensitive mutant and found it to be allelic to TEBICHI/POLQ, encoding DNA polymerase θ. The teb mutant plants were preferentially sensitive to NO- and its derivative peroxynitrite-induced DNA damage and subsequent double-strand breaks (DSBs). Inactivation of TEB caused the accumulation of spontaneous DSBs largely attributed to endogenous NO and was synergistic to DSB repair pathway mutations with respect to growth. These effects were manifested in the presence of NO-inducing agents and relieved by NO scavengers. NO induced G2/M cell cycle arrest in the teb mutant, indicative of stalled replication forks. Genetic analyses indicate that Polθ is required for translesion DNA synthesis across NO-induced lesions, but not oxidation-induced lesions. Whole-genome sequencing revealed that Polθ bypasses NO-induced base adducts in an error-free manner and generates mutations characteristic of Polθ-mediated end joining. Our experimental data collectively suggests that Polθ plays dual roles in protecting plants from NO-induced DNA damage. Since Polθ is conserved in higher eukaryotes, mammalian Polθ may also be required for balancing NO physiological signaling and genotoxicity.     

High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis

Callus induction,which results in fate transition in plant cells,is considered as the first and key step for plant regeneration.This process can be stimulated in different tissues by a callus-inducing medium(CIM),which contains a high concentration of phytohormone auxin.Although a few key regulators for callus induction have been identified,the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation.Here,we find that high auxin induces callus ...     

异质水分环境下野牛草相连分株间光合同化物的生理整合及其调控

异质环境下,克隆植物通过生理整合机制使资源在分株间实现共享,提高了其对异质性环境的适应能力,具有重要的生态进化意义,研究生理整合机制及其调控机理可为进一步发掘克隆植物应用潜力提供理论依据。以野牛草3个相连分株为材料,对其中一个分株用30%聚乙二醇6000(PEG-6000)模拟水分胁迫,通过Hoagland营养液培养试验,研究了异质水分环境下光合同化物在野牛草相连分株间的生理整合及分株叶片与根系内源激素ABA与IAA含量的变化规律。结果表明,14C-光合同化物在克隆片断内存在双向运输,但以向顶运输为主,异质水分环境下,受胁迫分株光合同化物的输出率明显降低,而与其相邻分株合成的光合同化物向受胁迫分株方向运输率明显增加;异质水分环境下,各分株ABA含量均明显增加,但以受胁迫的分株叶片及根系ABA的含量增加幅度最大,各分株IAA含量较对照均显著下降(P0.05),且以受胁迫分株IAA含量下降幅度最大;各分株叶片与根系ABA/IAA均显著提高(P0.05),相邻分株ABA/IAA增加幅度低于受胁迫分株。异质水分环境影响野牛草克隆分株间光合同化物的生理整合,且ABA与IAA在分株间光合同化物运输与分配过程中具有重要的调节作用。