Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13–158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.     

DNA水凝胶应用于环境样品快速检测的研究进展

DNA作为生物大分子既可以引导生物发育和生命机能活动,也可以被用作构筑纳米生物材料.DNA水凝胶可以制备成兼具DNA生物功能和水凝胶特质,应用于环境样品的分析检测.依据制备DNA水凝胶长链的方法,对比分析了聚合酶链反应、杂交链式反应、滚环扩增技术的制备,物理水凝胶和化学水凝胶的合成过程和改性方法技术特点;并结合环境样品...     

An examination of the factors involved in determining phosphatase activities in estuarine water. 1: Analytical procedures

The effects of assay pH, magnesium addition, temperature, sodium azide, and of sample storage and filtration on the apparent phosphatase activities in natural water bodies, and in particular estuaries, have been examined. Phosphatase activity was assessed by monitoring the cleavage of p-nitrophenol from p-nitrophenyl phosphate (pNPP). Magnesium concentrations in natural waters were found to be generally in excess of the requirement of the assay procedure. Several pH maxima occurred for phosphatase activities in the estuarine waters examined. These optima were not constant with respect to sampling stations or sampling time. This was considered to be, in part, the result of differences in the biomass composition. Sample storage times and temperatures employed in the present study did not influence the phosphatase activities of these low biomass waters. Phosphatase activities increased with increased incubation temperature. The rate of orthophosphate release from pNPP during incubation was linear over time to 120 h. Sodium azide was found to be an adequate preservative when long incubation times were required. The effects of assay conditions are discussed in relation to the assay procedures and data interpretation.     

Simultaneous analysis of artemisinin and flavonoids of several extracts of Artemisia annua L. obtained from a commercial sample and a selected cultivar

Artemisia annua L. (Qinghao) is a promising and potent antimalarial herbal drug. This activity has been ascribed to its component artemisinin, a sesquiterpene lactone that is very effective against drug-resistant Plasmodium species with a low toxicity. Our studies indicate that several flavonoids of A. annua can promote and enhance the reaction of artemisinin with hemin. These data are in good agreement with previous investigations on the in vitro potentiation of antimalarial activity of artemisinin by such flavonoids. As a consequence, in view of a possible use of the phytocomplex rather than pure artemisinin, an HPLC/DAD/MS method is proposed for the simultaneous detection and quantification of both flavonoids and artemisinin. Different extracts, obtained from two different herbal drugs, a commercial sample and a selected cultivar, were analyzed in order to determine which solvents provide the best yields of both artemisinin and flavonoids. Qualitative and quantitative results obtained using an HPLC method are described, which will be useful for developing highly effective herbal drug preparations.     

近35年官厅水库消落带消涨特征及分区

水库消落带作为重要的生态交错带,是深入分析生态要素内在作用机制的特殊区域。以华北内陆大型水库——官厅水库为研究对象,选择1979—2013年Landsat MSS/TM/ETM+/OLI影像作为数据源,分析35年来官厅水库消落带的消涨特征、时空分布差异及其变化趋势,在此基础上进行消落带淹水时长和淹水频次的分区研究,揭示消落带生态结构的形成过程。研究结论如下:(1)近35年来,官厅水库水位落差较大,达8.19m,水位变化分为3个特征时期:1979—1996年,涨落周期约为4—5a的间歇涨落期;1996—2007年,水位持续下降达7.12m的持续萎缩期;2007—2013年,涨落周期为2 a,且年际变化差稳定在0.75m的频繁涨落期。(2)35年来,官厅水库水位消涨形成118.31km~2的消落带,对应3个特征时期形成消落带的面积依次为80.20km~2,76.81 km~2和19.89km~2。间歇涨落期形成的消落带主要分布在永定河河口及平坦的康西草原一带;持续萎缩期的消落带有明显向西北河岸带扩张的趋势;频繁涨落期的消落带以库心区域水位回升为主,面积仅19.89 km~2。(3)1979—2013年,基于淹水累计时长的分区中,消落带整体上表现为淹水累计时长随边岸向库区中心逐渐递增的趋势,25.85%的消落带淹水时长不足5a,71.77%的消落带淹水时长大于16 a,但随着淹水时长减少,消落带区域植物旱化现象突出,同时植被群落盖度和多样性降低。淹水频次分区中,相同淹水频次的区域在空间上离散分布,一次淹水区面积为32.79km~2,在消落带中所占比例优势明显,但累计淹水时长差异同样显著,分别为2 a和26 a,淹水最为频繁的消落带共经历了9次淹水过程;分区中的土壤有机质含量差异表明,淹水频次越高越有利于土壤有机质的积淀。     

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples

EPA Method 1615 was developed with a goal of providing a standard method for measuring enteroviruses and noroviruses in environmental and drinking waters. The standardized sampling component of the method concentrates viruses that may be present in water by passage of a minimum specified volume of water through an electropositive cartridge filter. The minimum specified volumes for surface and finished/ground water are 300 L and 1,500 L, respectively. A major method limitation is the tendency for the filters to clog before meeting the sample volume requirement. Studies using two different, but equivalent, cartridge filter options showed that filter clogging was a problem with 10% of the samples with one of the filter types compared to 6% with the other filter type. Clogging tends to increase with turbidity, but cannot be predicted based on turbidity measurements only. From a cost standpoint one of the filter options is preferable over the other, but the water quality and experience with the water system to be sampled should be taken into consideration in making filter selections.     

人粪样中雌马酚含量调查及其与菌群结构相关性研究

目的 调查人粪样中大豆素和雌马酚的含量及其与年龄和性别的关系;了解人粪样中雌马酚含量高低与菌群结构的关系.方法 采用高效液相色谱(HPLC)对来自杭州的125份粪样进行大豆素和雌马酚含量检测,并使用生物统计学软件SPSS进行统计学分析;使用PCR-DGGE对粪样中雌马酚含量的高低与菌群结构的关系进行初步研究.结果 HPLC检测结果表明,尽管粪样中雌马酚含量的高低与性别关系不大,但却与年龄大小存在很大的相关性,41 ～50岁年龄组的粪样中雌马酚含量明显高于其他年龄组.PCR-DGGE结果表明,粪样中雌马酚含量的高低与菌群结构无明显相关性.结论 人粪样中雌马酚含量的高低与年龄大小有很强的相关性.     

海南岛热带山地雨林林分生物量估测方法比较分析

本文通过对海南岛热带山地雨林林分生物量估测方法的比较分析,表明材积转换法不适宜估算海南岛热带山地雨林林分生物量,其结果与皆伐法相比较一般偏高20％—40％;而用实测资料建立的生物量回归模型,对原始林林分有较好的估测结果,除树枝和树叶生物量外,树干、树皮及地上部分生物量的回归模型值,与皆伐法的结果比较,相对误差一般在±10％以内,为允许误差范围,而对热带山地雨林的更新林生物量的估测则效果较差,应建立相应的估测模型。平均木法有工作量小的优点,且误差也在16％以下,但要注意取样的树种多样性和取样强度,在实际中应当慎用。另外本文对测定热带山地雨林生物量(原始林)的所需面积大小问题作了研究,提出了生物量-面积曲线的概念,确定其最小调查面积为2500m~2以上。     

海州湾近岸海域的微生物群落结构和抗生素抗性基因时空变化

【背景】近岸海域抗生素抗性基因(antibiotic resistance genes, ARGs)的污染和累积将直接影响海产品质量和安全,海州湾作为江苏省的四大渔场之一,是江苏渔业发展的主要载体,有多条大小河流注入,沿岸为重要农业区,对公众健康产生重大影响。【目的】对海州湾夏秋季的水样及沉积物展开微生物及ARGs检测。【方法】基于宏基因组测序技术开展海州湾夏秋两季近岸6个站点中水体和沉积物中ARGs种类和相对丰度以及微生物群落的组成研究。【结果】变形菌门(Proteobacteria)和放线菌门(Actinobacteria)是夏秋季度两种介质中最优势的门类,水样中优势的科级细菌为红细菌科(Rhodobacteraceae),沉积物样品中为脱硫杆菌科(Desulfobacteraceae);夏季水样中的ARGs相对丰度要明显高于秋季,但沉积物中不同季节的ARGs相对丰度未表现出明显的变化趋势;在水样中主要门级微生物群落的抗性机制主要是抗生素靶位替换和抗生素靶位保护,沉积物样品则以抗生素灭活机制为主,而主要科级微生物群落的抗性机制更加多样;冗余分析(redundancyanalysis...