PP2Acα promotes macrophage accumulation and activation to exacerbate tubular cell death and kidney fibrosis through activating Rap1 and TNFα production

Macrophage accumulation and activation play an essential role in kidney fibrosis; however, the underlying mechanisms remain to be explored. By analyzing the kidney tissues from patients and animal models with kidney fibrosis, we found a large induction of PP2Acα in macrophages. We then generated a mouse model with inducible macrophage ablation of PP2Acα. The knockouts developed less renal fibrosis, macrophage accumulation, or tubular cell death after unilateral ureter obstruction or ischemic reperfusion injury compared to control littermates. In cultured macrophages, PP2Acα deficiency resulted in decreased cell motility by inhibiting Rap1 activity. Moreover, co-culture of PP2Acα^−/− macrophages with tubular cells resulted in less tubular cell death attributed to downregulated Stat6-mediated tumor necrosis factor α (TNFα) production in macrophages. Together, this study demonstrates that PP2Acα promotes macrophage accumulation and activation, hence accelerates tubular cell death and kidney fibrosis through regulating Rap1 activation and TNFα production.Subject terms: Cell biology, Inflammation     

In-depth assessment of the PAM compatibility and editing activities of Cas9 variants

A series of Cas9 variants have been developed to improve the editing fidelity or targeting range of CRISPR–Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated sequencing to analyze the editing efficiency, specificity and protospacer adjacent motif (PAM) compatibility of a dozen of SpCas9 variants at multiple target sites in depth, and our findings validate the high fidelity or broad editing range of these SpCas9 variants. With regard to the PAM-flexible SpCas9 variants, we detect significantly increased levels of off-target activity and propose a trade-off between targeting range and editing specificity for them, especially for the near-PAM-less SpRY. Moreover, we use a deep learning model to verify the consistency and predictability of SpRY off-target sites. Furthermore, we combine high-fidelity SpCas9 variants with SpRY to generate three new SpCas9 variants with both high fidelity and broad editing range. Finally, we also find that the existing SpCas9 variants are not effective in suppressing genome instability elicited by CRISPR–Cas9 editing, raising an urgent issue to be addressed.     

同义密码子通过精微翻译选择机制实现对基因的表达调控

自然界中,同义密码子的存在使得众多氨基酸能够同时被多种密码子编码合成。随着研究的深入,同义密码子使用偏嗜性发挥出的生物学功能已经渗透到了基因复制、转录、翻译以及化学修饰等生命活动过程中。基于同义密码子使用偏嗜性的生物学特性,陆续发现密码子对(codon pair)和密码子共现(codon co-occurrence)同样在使用模式上存在明显的偏嗜性。在基因表达的过程中,针对编码序列的密码子优化能够显著提升基因的表达水平,这在生物工程领域对于蛋白表达有着重要的生物学意义。此外,同义密码子使用模式在调控基因转录、化学修饰以及翻译过程中间接控制着细胞内生命活动的有序性。而这些与同义密码子使用模式有着千丝万缕联系的生命过程主要是受精微翻译选择压力来调控运行的。本文中,我们结合当前同义密码子使用模式介导的精微翻译选择压力,简述密码子使用模式如何从转录、化学修饰以及翻译等方面来影响基因表达及蛋白产物生物学功能。这将为今后生物工程学领域如何优化蛋白高效表达以及深入研究重要生物学活动中基因表达调控提供可参考的思路与理念。     

受油菜素内酯调控的水稻幼苗地上部膜蛋白的鉴定及功能分析

油菜素内酯(brassinosteroids,BRs)对水稻株高、叶夹角等重要农艺性状具有明显的调控作用,鉴定水稻中受BR调控的蛋白质对揭示BR调控水稻生长发育特定生化过程的潜在机制具有重要的意义。该研究以日本晴水稻(Oryza sativa L.ssp.japanica cv.Nipponbare)为研究材料,用明显影响水稻地上部生长的BR浓度处理,提取地上部膜蛋白,经双向电泳及质谱分析,鉴定到7个受BR调控的蛋白质:光系统II稳定因子HCF136、PMRP(putative membrane related protein,gi|113565516)、ATP synthase(gi|113611230)、gi|113594641、gi|22831029、gi|47497322和gi|56784135,对这些蛋白的功能鉴定可以为阐明BR调控水稻生长发育的机理提供新的思路和途径。其中功能未知的膜蛋白PMRP受BR下调,经亚细胞定位,PMRP定位在细胞质膜上,经生物信息学分析,PMRP具有磷脂酰胆碱结合位点,可能影响膜的组分进而参与水稻抗逆性调控;PMRP RNAi转基因拟南芥对冷害的抵抗能力增强,说明BR可通过调控PMRP的表达提高植物的抗冷性。     

A Hidden Markov Model for Urban-Scale Traffic Estimation Using Floating Car Data

Urban-scale traffic monitoring plays a vital role in reducing traffic congestion. Owing to its low cost and wide coverage, floating car data (FCD) serves as a novel approach to collecting traffic data. However, sparse probe data represents the vast majority of the data available on arterial roads in most urban environments. In order to overcome the problem of data sparseness, this paper proposes a hidden Markov model (HMM)-based traffic estimation model, in which the traffic condition on a road segment is considered as a hidden state that can be estimated according to the conditions of road segments having similar traffic characteristics. An algorithm based on clustering and pattern mining rather than on adjacency relationships is proposed to find clusters with road segments having similar traffic characteristics. A multi-clustering strategy is adopted to achieve a trade-off between clustering accuracy and coverage. Finally, the proposed model is designed and implemented on the basis of a real-time algorithm. Results of experiments based on real FCD confirm the applicability, accuracy, and efficiency of the model. In addition, the results indicate that the model is practicable for traffic estimation on urban arterials and works well even when more than 70% of the probe data are missing.     

纳米基因载体在植物遗传转化中的应用

纳米基因载体已成功地应用于生物医学领域并显示了优越的转染效率、良好的生物相容性和有效的基因保护作用。近年来,纳米颗粒作为基因载体在植物转导中的应用潜力越来越受到关注,也为植物遗传工程提供了新的可能性。在阐述纳米载体的特性、在植物细胞中的转导机制及转导优势的基础上,重点讨论了纳米载体在植物转基因中的应用,并对其前景进行了展望。     

水稻核不育系4个柱头性状的遗传分析

为改良水稻(Oryza sativa)核不育系柱头性状提供遗传信息, 调查了粳型核不育系7001S、籼型核不育系Z913S及其杂交、自交获得的F₁、F₂和F_2:3群体的4个柱头性状, 分析了4个性状间的相关性, 并利用主基因+多基因遗传模型对2个世代4个性状进行遗传分析。结果表明, 4个性状两两间呈极显著正相关, 相关系数介于0.274-0.897之间。除F_2:3群体中花柱长度和柱头外露率分别表现出受2对加性-显性主基因和1对负等效加性-显性主基因+多基因控制外, F₂和F_2:3群体的柱头长度、花柱长度、柱头-花柱总长度以及柱头外露率均表现出受2对主基因和多基因控制, 且F_2:3群体中控制花柱长度的主基因表现出加性-显性效应, 其余均表现出加性-显性-上位性效应。2个世代中4个性状均以主基因遗传为主。     

Substituted indolin-2-ones as p90 ribosomal S6 protein kinase 2 (RSK2) inhibitors: Molecular docking simulation and structure–activity relationship analysis

A series of novel indolin-2-ones inhibitors against p90 ribosomal S6 protein kinase 2 (RSK2) were designed and synthesized and their structure–activity relationship (SAR) was studied. The most potent inhibitor, compound 3s, exhibited potent inhibition against RSK2 with an IC₅₀ value of 0.5 μM and presented a satisfactory selectivity against 23 kinases. The interactions of these inhibitors with RSK2 were investigated based on the proposed binding poses with molecular docking simulation. Four compounds and six compounds exhibited moderate anti-proliferation activities against PC 3 cells and MCF-7 cells, respectively.