Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants

Evidence is emerging that t RNA-derived fragments(t RFs) are regulatory molecules. Studies of t RFs in plants have been based on conventional small RNA sequencing, and focused on profiling of t RF-5 and t RF-3 species. A more comprehensive and quantitative analysis of the entire t RF population is highly necessary. Here, we employ t RNA-seq and YAMAT-seq, and develop a bioinformatics tool to comprehensively profile the expressions of t RNAs and t RFs in plants. We show that in Arabidopsis,approximately half of t RNA genes are extremely weakly expressed, accounting for only 1% of total t RNA abundance, while～12% of t RNA genes contribute to ～80% of t RNA abundance. Our t RNA sequencings in various plants reveal that t RNA expression profiles exhibit a cross-species conserved pattern. By characterizing the composition of a highly heterogeneous t RF population, we show that t RNA halves and previously unnoticed 10–16-nt tiny t RFs represent substantial portions. The highly accumulated 13-nt and 16-nt tiny t RFs in Arabidopsis indicate that tiny t RFs are not random t RNA degradation products. Finally,we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of t RNAs and t RFs in the model plants Arabidopsis and rice.     

不稳定EGFP细胞模型的构建及其在基因编辑体系评价中的应用*

目的:为了更好地评价基因编辑效率,满足高通量筛选应用中快速、高效的检测要求,在细胞上建立一个原位检测方法具有重要的意义。通过检测荧光蛋白信号强度的变化可以评价CRISPR系统在细胞中的基因编辑情况,然而这一方法的效率受限于荧光蛋白较长的半衰期。方法:将鸟氨酸脱羧酶降解结构域(含PEST序列)与EGFP融合,通过慢病毒系统感染HEK-293T细胞,获得了表达单拷贝、EGFP-PEST报告基因的稳转细胞系。结果:与EGFP相比,EGFP-PEST在细胞内的降解速度明显加快,荧光水平在4 h内显著降低。利用该模型比较了3种商品化脂质体介导的CRISPR/Cas9基因编辑效率,能够在2~4 d实现定性和定量评价。结论:这一模型能够快速、灵敏地指示基因编辑效果,可以用于不同CRISPR系统或新递送工具的高通量筛选和评价。     

Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort

Tumour-derived DNA found in the plasma of cancer patients provides the probability to detect somatic mutations from circulating cell-free DNA (cfDNA) in plasma samples. However, clonal hematopoiesis (CH) mutations affect the accuracy of liquid biopsy for cancer diagnosis and treatment. Here, we integrated landscape of CH mutations in 11,725 pan-cancer patients of Chinese and explored effects of CH on liquid biopsies in real-world. We first identified 5933 CHs based on panel sequencing of matched DNA of white blood cell and cfDNA on 301 genes for 5100 patients, in which CH number of patients had positive correlation with their diagnosis age. We observed that canonical genes related to CH, including DNMT3A, TET2, ASXL1, TP53, ATM, CHEK2 and SF3B1, were dominant in the Chinese cohort and 13.29% of CH mutations only appeared in the Chinese cohort compared with the Western cohort. Analysis of CH gene distribution bias indicated that CH tended to appear in genes with functions of tyrosine kinase regulation, PI3K-Akt signalling and TP53 activity, suggesting unfavourable effects of CH mutations in cancer patients. We further confirmed effect of driver genes carried by CH on somatic mutations in liquid biopsy of cancer patients. Forty-eight actionable somatic mutations in 17 driver genes were considered CH genes in 92 patients (1.80%) of the Chinese cohort, implying potential impacts of CH on clinical decision-making. Taken together, this study exhibits strong evidence that gene mutations from CH interfere accuracy of liquid biopsies using cfDNA in cancer diagnosis and treatment in real-world.     

肝硬化合并结核病患者的临床特征

目的分析肝硬化合并结核病患者的临床特征,为该类患者的治疗提供参考。方法回顾性分析2014年9月至2017年7月于浙江大学医学院附属第一医院住院的肝硬化合并结核病患者的相关资料,总结患者的临床特征。结果共收治68例肝硬化合并结核病患者,其中男性50例(73.5%),女性18例(26.5%),平均年龄(59.9±13.7)岁。在所有患者中,肝硬化最常见的原因是HBV感染(46例,67.7%)和酒精(9例,13.2%)。肺结核(43例)、结核性腹膜炎(13例)、结核性胸膜炎(12例)是最常见的结核类型,此外骨关节结核、结核性脑膜炎、结核性心包炎、泌尿系结核、肠结核、淋巴结结核均可见。该类患者常见临床表现为乏力、腹胀,出现发热的患者不足半数,有盗汗表现的更为罕见。结论肝硬化患者并发结核后可使病情复杂化,增加治疗难度。此外部分患者临床表现不典型,需提高警惕,避免漏诊。     

香茅精油的抑菌和抗氧化活性研究

选用产自福建厦门的香茅(Cymbopogon nardus),测定香茅精油对白色粘性沙雷氏菌、红色粘性沙雷氏菌、大肠杆菌、金黄葡萄球菌、铜绿假单胞菌和紫色杆菌等6种菌的抑菌活性,并利用ABTS^.+自由基清除法以及超氧阴离子清除法研究香茅精油的抗氧化活性。结果表明,新鲜香茅精油的平均提取率为0.29,对6种供试菌种都有较高的抑制作用,其中对紫色杆菌的抑制活性最强,且香茅精油有极高的清除ABTS^.+自由基以及超氧阴离子自由基的能力,证明香茅精油具有广谱抑菌活性及强抗氧化活性。     

The catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation in oil-contaminated soil

Rhizoremediation is a potential technique for polycyclic aromatic hydrocarbon (PAH) remediation; however, the catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation remain unclear. To address these issues, stable-isotope-probing coupled with metagenomics and molecular ecological network analyses were first used to investigate the phenanthrene rhizoremediation by three different prairie grasses in this study. All rhizospheres exhibited a significant increase in phenanthrene removal and markedly modified the diversity of phenanthrene degraders by increasing their populations and interactions with other microbes. Of all the active phenanthrene degraders, Marinobacter and Enterobacteriaceae dominated in the bare and switchgrass rhizosphere respectively; Achromobacter was markedly enriched in ryegrass and tall fescue rhizospheres. Metagenomes of ¹³C-DNA illustrated several complete pathways of phenanthrene degradation for each rhizosphere, which clearly explained their unique rhizoremediation mechanisms. Additionally, propanoate and inositol phosphate of carbohydrates were identified as the dominant factors that drove PAH rhizoremediation by strengthening the ecological networks of soil microbial communities. This was verified by the results of rhizospheric and non-rhizospheric treatments supplemented with these two substances, further confirming their key roles in PAH removal and in situ PAH rhizoremediation. Our study offers novel insights into the mechanisms of in situ rhizoremediation at PAH-contaminated sites.     

入侵植物三裂叶豚草在中国的潜在适生区预测

[目的] 三裂叶豚草是中国重点防控的入侵植物,研究其潜在的适生区分布格局变化对预警防控具有重要意义。[方法] 基于MaxEnt优化模型预测当前及未来（RCP2.6、RCP4.5、RCP8.5）气候情景下三裂叶豚草潜在的地理分布格局。[结果] 当调控倍频（RM）=3.5,FC（特征组合）=LQH（线性、二次型、片段化组合）时为最优模型,MaxEnt模型的预测结果较准确,受试者工作特征曲线下的面积（AUC值）达0.9287;综合8种途径评估出人类活动因子（hfp,贡献率69%）、等温性（bio3,贡献率8.9%）、温度季节变动系数（bio4,贡献率2.9%）、年降水量（bio12,贡献率7.3%）和海拔（ELEV,贡献率3.7%）是制约三裂叶豚草潜在地理分布的主要环境因子;在当前气候情景下,三裂叶豚草的高适生区主要集中在东北平原、江淮地区、京津冀、山东半岛等经济发达地区。[结论] 在未来气候变化情景下,三裂叶豚草在我国的潜在适生区范围总体呈现不同程度的缩减,即丧失率大于增加率;三裂叶豚草将有向南迁移的趋势;最冷月最低温度（bio6）是最不相似变量分析中出现频次最高的因子,表明温度因素对三裂叶豚草潜在地理分布变迁起到重要制约作用。本研究结果可为三裂叶豚草的预防和控制提供理论基础。     

西伯利亚蝗抗菌肽基因的克隆及表达特性研究

[目的]扩增西伯利亚蝗Gomphocerus sibiricus抗菌肽(attacin)基因,并对其进行生物信息学分析,同时分析西伯利亚蝗不同组织中抗菌肽基因的差异表达.[方法]基于RACE技术从西伯利亚蝗中克隆得到抗菌肽,利用生物信息学软件对西伯利亚蝗抗菌肽的一级结构、二级结构、三级结构、系统进化和亚细胞定位进行分析.采用实时荧光定量PCR技术检测了西伯利亚蝗抗菌肽基因在马氏管、中肠、后肠、脂肪体和唾液腺中的相对表达量.[结果]克隆获得的抗菌肽基因的开放阅读框为282 bp,编码93个氨基酸,其编码蛋白预测理论分子量为9.98 ku,等电点为9.26.抗菌肽氨基酸序列中存在信号肽序列.基因定量分析显示,抗菌肽基因在西伯利亚蝗的中肠中表达量最高.[结论]attacin在西伯利亚蝗成虫不同组织中差异表达,提示其消化道在防御病原微生物的入侵中起着重要的作用.     

不同采收期罗布麻和白麻药材化学成分的差异分析

建立高效液相色谱法,分别测定不同采收期的新疆产罗布麻和白麻药材中绿原酸、金丝桃苷、异槲皮苷、三叶豆苷、紫云英苷、芦丁和白麻苷的含量,进而分析2种药材的最佳采收期。发现不同采收期的新疆产罗布麻和白麻药材中绿原酸、金丝桃苷、异槲皮苷、三叶豆苷、紫云英苷、芦丁和白麻苷的含量存在一定差异,并且罗布麻和白麻呈现出不同特点。以《中国药典》中罗布麻含量测定项下的金丝桃苷为指标,罗布麻和白麻的最佳采收期都是6、7月;但是,以7个成分的总含量和6个黄酮的总含量为指标,罗布麻的最佳采收期是8、9月,白麻的最佳采收期仍是6、7月。该结果可为确定罗布麻和白麻药材的采收时间提供一定参考。     

快速STR分型在法医DNA分析中的应用研究进展

STR分型是目前世界通用的DNA指纹分析方法.传统的分型方法包括DNA提取、DNA定量、PCR扩增和对扩增后的STR片段进行检测和分析,耗时较长(8¹0 h).一些情况下很难满足案件的实际需求.法医学家们在加快STR分型的方法研究一直不懈努力.现从快速提取DNA、无提取直接PCR、快速PCR、微流控芯片技术在STR快速分型方面的应用四方面,对近年来出现的可进行快速STR分型的新技术、新方法进行综述.