Constraint line methods and the applications in ecology北大核心CSCD

With increasing data availability in the big data era, many traditional statistical analyses based on the mean or median are insufficient or inappropriate to elucidate the complex patterns of variation. This is particularly the case when multiple factors are involved and the bivariate scatter occurs as scatter clouds. In such circumstances, constraint line (or envelope) method could be an alternative and effective tool to extract the data boundaries, thus improves our understanding of the complex relationships between limiting factor and response factor. Here, we synthesize the major findings and achievements in the field of applying the constraint line method in ecology. Specifically, we first describe the history and development of the constraint line method. We then discuss the techniques to establish the constraint lines with examples, and discuss the applications and implications of the constraint lines in species distribution, population performance, and optimization problem. We suggest simultaneously application of both constraint lines and regression techniques to the same datasets to achieve a comprehensive understanding of ecological process and underlying mechanisms. Such combined methods should be used with special attention to the role of spatial heterogeneity and scale dependency. We also discuss in detail the potential applicability of the constraint line method in studying the linkages between ecosystem services, and land system design.     

生境异质性对鼎湖山常绿阔叶林群落功能多样性的影响

物种共存机制一直以来是群落生态学的研究热点。为了探讨异质生境条件下鼎湖山常绿阔叶林群落功能多样性变化,找到其变化的主要环境驱动因子,该研究利用位于鼎湖山20 hm~2监测样地第2次群落调查数据并选择代表不同生境(海拔和地形)的27个样方(20 m×20 m),于2013年夏季在样地内所选样方中测定所有胸径≥1 cm树种的叶片功能性状。所测性状包括形态学性状(比叶面积、叶片干物质含量、叶面积以及叶片长宽比)和化学计量学性状(叶片碳、氮、磷的含量),结合地形和土壤数据并通过分析功能多样性随环境梯度的变化,探讨了环境过滤和竞争在鼎湖山群落物种共存中的相对重要性。结果表明:功能分歧度和群落权重平均值与环境因素关系密切,尤其是海拔、凹凸度和土壤养分。环境条件较好区域(微尺度高海拔、高凹凸度和土壤养分含量)的植物采取统一的养分有效保存(低SLA,高LDMC)的适应策略(功能分歧度低),环境过滤所起作用更强;植物在相反的环境条件下,采取快速生长策略(高SLA,低LDMC),能够更好地适应环境的变化,且性状变化是多样的(功能分歧度高),在该条件下竞争作用更为显著。叶面积和叶片氮含量的分歧度在环境条件较好的区域增大,这与其他功能性状不一致,说明不同生态位轴(环境因素)影响不同性状的分歧度变化,并且在局域尺度上植物为了更好地适应环境变化采取了多样的适应策略。     

氧化鱼油对草鱼肠道黏膜抗氧化应激通路基因表达水平的影响

为了探讨氧化鱼油对草鱼肠道黏膜损伤后, 参与抗氧化应激的基因通路及其通路基因表达活性的变化,以草鱼为试验对象, 灌喂氧化鱼油7d后, 采集肠道黏膜组织并提取总RNA, 采用RNA-seq方法, 进行了氧化鱼油组和正常鱼油组草鱼肠道黏膜基因注释、IPA基因通路分析和基因表达活性差异分析。结果显示, 组织切片观察发现氧化鱼油导致草鱼肠道黏膜出现严重的损伤; 肠道黏膜中具有较为完整的Keap1-Nrf2-ARE基因调控通路。肠道黏膜在受到氧化鱼油的氧化损伤作用后, 激活了细胞的抗氧化损伤保护机制, 使NRF2介导的氧化应激反应通路基因差异表达显著性地上调, 并导致了下游的GSH/GSTs通路基因差异表达显著性上调, 促进了GSH的生物合成和GSTs的抗氧化作用; 导致Keap1-Nrf2-ARE信号通路下游的热休克蛋白和泛素-蛋白酶体通路基因差异表达显著性上调, 清除受损伤蛋白质, 保护细胞结构完整性。研究表明, 上述三类抗氧化应激通路构成了对肠道黏膜损伤细胞、损伤蛋白质的降解系统和清除系统, 显示其对肠道黏膜组织和黏膜细胞的保护、修复发挥了重要的作用。     

5-氨基乙酰丙酸对苹果叶片耐弱光能力的影响

为了探讨5-氨基乙酰丙酸(ALA)对苹果耐弱光性的影响,以‘润太2号’和‘郑优3号’两个品种苹果为材料,设置露天对照(CK)、轻度遮荫(LS)和重度遮荫(SS)3种光照条件,通过根际浇灌法研究了10mg·L~(-1) ALA处理对弱光条件下苹果叶片活性氧代谢与叶绿素荧光特性的影响。结果显示:(1)与CK相比,弱光胁迫显著降低了两品种苹果叶片的超氧化物歧化酶(SOD)与过氧化物酶(POD)的活性,增大了超氧阴离子(O_2~(-·))产生速率以及过氧化氢(H2O2)和丙二醛(MDA)含量,且‘郑优3号’的活性氧产生速率及MDA含量在弱光下的升高幅度更大;ALA处理显著提高了弱光胁迫下两品种的保护酶活性,降低了活性氧产生速率和MDA含量,并以耐弱光性较差的‘郑优3号’的变化更显著。(2)在弱光胁迫下,苹果叶片的叶绿素含量和叶绿素b/a升高,而ALA处理使二者进一步显著升高。(3)弱光胁迫下,苹果叶片的叶绿素荧光参数V_J、M_o、DI_o/RC显著升高,而ψ_o、ψE_o、ψR_o、PI_(ABS)、PI_(CS)和PI_(total)显著降低;ALA处理抑制了叶绿素荧光参数在弱光胁迫下的变化,甚至使其达到优于对照的水平。研究表明,弱光条件下苹果的抗氧化能力较差,受到明显的氧化伤害,且‘郑优3号’的耐弱光能力比‘润太2号’差;ALA处理提高了苹果在弱光下的抗氧化能力,降低了弱光对苹果叶片的氧化伤害,同时还提高了弱光条件下苹果叶片捕捉、传递和转化光能的效率,改善了光合电子传递情况,增大了苹果叶片在弱光胁迫下的光能利用效率,改善了光合性能;根灌ALA可以明显提高苹果的耐弱光性。     

Genome‐wide association study of callus induction variation to explore the callus formation mechanism of rice

Rice(Oryza sativa) is one of the most widely cultivated food crops, worldwide. Tissue culture is extensively used in rice breeding and functional genome research. The ability to induce callus determines whether a particular rice variety can be subjected to tissue culture and Agrobacterium-mediated transformation. Over the past two decades, many quantitative trait loci(QTLs)related to callus induction traits have been identified;however, individual genes associated with rice callus induction have not been reported. In this study, we characterized three callus-induction traits in a global collection of 510 rice accessions. A genome-wide association study of the rice population in its entirety as well as subpopulations revealed 21 significant loci located in rice callus induction QTLs. We identified three candidate callus induction genes, namely CRL1, Os BMM1, and Os SET1, which Rese are orthologs of Arabidopsis LBD17/LBD29, BBM, and SWN,respectively, which are known to affect callus formation.Furthermore, we predicted that 14 candidate genes might be involved in rice callus induction and showed that RNA interference(RNAi)-mediated disruption of Os IAA10 inhibited callus formation on tissue culture medium.Embryo growth in the Os IAA10 RNAi line was not inhibited by synthetic auxin(2,4-D) treatment, suggesting that Os IAA10 may perceive auxin and activate the expression of downstream genes, such as CRL1, to induce callus formation. The significant loci and candidate genes identified here may provide insight into the mechanism underlying callus formation in rice.     

马氏珠母贝(Pinctada fucata martensii)PmHEXL基因的分子特征与表达分析

几丁质作为有机框架主要成分参与贝壳的形成。β-N-乙酰-己糖胺酶(Beta-hexosaminidase/Beta-N-acetylhexosaminidase, HEX)属于糖苷水解酶家族20,在几丁质水解过程发挥重要作用。为了探究Pm HEXL在马氏珠母贝贝壳形成中的作用,本研究利用RACE技术克隆获得Pm HEXL基因c DNA全长序列并检测其在不同组织的表达模式。研究显示,Pm HEXL基因序列全长2 760 bp,其中5'UTR为167 bp,3'UTR为268 bp,开放阅读框(ORF)为2 325 bp,编码774个氨基酸;预测其相对分子量为89.59 kD,理论等电点为5.93;SMART软件分析PmHEXL蛋白质序列,发现它具有典型的GH20、GH20b结构域和CHB-HEX结构域;多序列比对结果显示Pm HEXL与其它物种的HEX具有较高的保守性;qPCR表达分析显示Pm HEXL在外套膜套膜区表达量最高,边缘区次之。综上所述,Pm HEXL可能参与马氏珠母贝贝壳的形成过程。     

Synthetic genome with recoding

<正>With the development of DNA synthesis techniques, synthetic biology has enabled redesign and construction of genome on purposes (Luo et al., 2018). The whole-genome recoding of Escherichia coli could be used to enhance incorporation of non-natural amino acids into proteins and to construct safer and multi-virus-resistant strains, which has always been a long-cherished wish in synthetic biology. In recent years, many research teams around the world have been engaged in genetic recoding. The Church group in