Natural,modified DNA bases

The four canonical bases that make up genomic DNA are subject to a variety of chemical modifications in living systems. Recent years have witnessed the discovery of various new modified bases and of the enzymes responsible for their processing. Here, we review the range of DNA base modifications currently known and recent advances in chemical methodology that have driven progress in this field, in particular regarding their detection and sequencing. Elucidating the cellular functions of modifications remains an ongoing challenge; we discuss recent contributions to this area before exploring their relevance in medicine.     

基于地面LiDAR数据的塔里木河下游胡杨林结构参数反演

以塔里木河下游天然胡杨林为研究对象,利用Riegl VZ-1000型地面激光扫描仪(Terrestrial Laser Scanning, TLS)获取离河道不同距离的8个样方内513棵胡杨的三维点云数据,通过建立冠层高度模型、Hough变换等方法获取单木株数和结构参数,并与传统的每木检尺实测数据和无人机(Unmanned Aerial Vehicle, UAV)低空影像进行对比,验证激光雷达方法的测树精度;对TLS获取的胡杨树形参数进行相关性分析,并建立关系模型;探讨不同水胁迫条件(不同离河道距离,不同地下水埋深)对胡杨单木结构参数的影响;最后按不同径级划分胡杨的年龄,得出各龄级胡杨所占比例。结果表明:(1)TLS能够高精度获取不同密度和长势的胡杨单木株数和结构参数,单株准确分割比率为94%—100%,相对于UAV低空影像更为准确;(2)TLS获取的胡杨树高(Tree height,TH)、胸径(Diameter at breast height, DBH)、冠幅直径(Crown diameter,CD)和冠幅面积(Crown area,CA)与传统实测值拟合度R~2较高,分别为0.95、0.97、0.77和0.84,表明实测数据和TLS获取数据无明显差异;(3)胡杨CD、CA分别与TH呈显著正相关,其相关性系数为0.73、0.67;基于此构建了胡杨TH与CD的关系模型,即TH=2.6274×CD~(0.706),R~2为0.64;(4)根据径级划分胡杨年龄段可知,DBH为15—30 cm的近熟林比例最大,占8个样方内监测胡杨总株数的47%,表明胡杨种群年龄结构相对稳定并总体态势良好,呈现了生态输水对塔河下游胡杨种群恢复有明显的促进作用。总之,激光雷达技术能够客观反映胡杨树形结构参数,可替代耗力、耗费、耗时的传统实测方法,为时时掌握胡杨林生长发育、长势动态以及多尺度、多时相生态耗水研究提供高精度信息,为干旱区荒漠河岸林的有效保护与可持续管理提供科学依据。     

老年慢性阻塞性肺疾病患者和坠积性肺炎患者肺内病原菌比较及感染影响因素分析

目的对比老年慢性阻塞性肺疾病(chronic obstructive pulmonary disease,COPD)患者和坠积性肺炎患者肺内一般病原菌和多重耐药菌的分布,同时分析COPD患者和坠积性肺炎患者多重耐药菌感染的影响因素。方法对入选COPD患者和坠积性肺炎患者下呼吸道痰标本进行培养和鉴定,对比两组患者病原菌以及多重耐药菌的检出率,同时比较两组患者性别、年龄、住院时间、糖尿病病史、有创机械通气治疗和留置尿管等因素对多重耐药菌感染的影响。结果 COPD患者革兰阴性菌的检出率(48.39%)显著低于坠积性肺炎患者(66.13%),COPD患者真菌的检出率(11.06%)显著高于坠积性肺炎患者(2.42%)。两组患者检出的多重耐药菌均以产超广谱β-内酰胺酶肠杆菌科细菌、耐甲氧西林金黄色葡萄球菌和多重耐药/泛耐药铜绿假单胞菌为主。COPD患者中感染多重耐药菌患者的年龄和住院时间显著高于非感染患者;坠积性肺炎患者中感染多重耐药菌患者的住院时间、机械通气治疗率和留置尿管使用率显著高于非感染患者。结论影响老年COPD患者和坠积性肺炎患者多重耐药菌感染的因素有区别,应有针对性地应用抗生素以减少多重耐药菌的感染。     

环介导恒温扩增法检测肺炎链球菌的研究

目的 建立环介导恒温扩增(LAMP)检测肺炎链球菌的方法.方法 用LAMP技术扩增肺炎链球菌菌株,并应用50例临床标本采用传统培养法、PCR法、LAMP法进行检测,比较3种方法的检出率,同时检测方法特异性和灵敏度.结果 所测肺炎链球菌均获扩增产物,对其他非肺炎链球菌无交叉反应.LAMP检测灵敏度可达102 CFU/mL.50例临床标本使用LAMP法检出9例肺炎链球菌阳性(18.0％),使用传统培养法检出阳性4例(8.0％).结论 LAMP法较传统培养检测方法特异性强、灵敏度高、操作方便、快速,适合临床标本的肺炎链球菌检测.     

埃博拉病毒检测与防治技术在中国的专利申请状况分析

近年来,埃博拉病毒(EBOV)因其在非洲造成的严峻疫情而引起了广泛关注。本文对涉及埃博拉病毒检测与防治技术方面的在中国申请的国内外专利申请数量、年代分布、技术发展状况等信息进行分析,对国内埃博拉病毒检测、免疫、治疗相关专利技术进行简要总结,并对目前热点关注药物(jk-05,ZMapp,VSV-EBOV)专利申请信息进行比较概括,结果表明,我国申请人在提出的相关专利申请数量以及技术多样性上与国外申请人存在差距,为国内科研人员提供了相关技术领域参考。     

Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish

The effectiveness and accuracy of detection using environmental DNA (eDNA) is dependent on understanding the influence laboratory methods such as DNA extraction and PCR strategies have on detection probability. Ideally choice of sampling and extraction method will maximize eDNA yield and detection probability. Determining the survey effort required to reach a satisfactory detection probability (via increased PCR replicates or more sampling) could compensate for a lower eDNA yield if the sampling and extraction method has other advantages for a study, species or system. I analysed the effect of three different sampling and extraction methods on eDNA yield, detection probability and PCR replication for detecting the endangered freshwater fish Macquaria australasica from water samples. The impact of eDNA concentration, PCR strategy, target amplicon size and two marker regions: 12S (a mitochondrial gene) and 18S (a nuclear gene) was also assessed. The choice of sampling and extraction method and PCR strategy, rather than amplicon size and marker region, had the biggest effect on detection probability and PCR replication. The PCR replication effort required to achieve a detection probability of 0.95, ranged from 2 to 6 PCR replicates depending on the laboratory method used. As all methods yielded eDNA from which M. australasica was detected using the three target amplicons, differences in eDNA yield and detection probability between the three methods could be mitigated by determining the appropriate PCR replication effort. Evaluating the effect sampling and extraction methods will have on the detection probability and determining the laboratory protocols and PCR replication required to maximize detection and minimize false positives and negatives is a useful first step for eDNA occupancy studies.