Characterization of oligodeoxyribonucleotide synthesis on glass plates

Achieving high fidelity chemical synthesis on glass plates has become increasingly important, since glass plates are substrates widely used for miniaturized chemical and biochemical reactions and analyses. DNA chips can be directly prepared by synthesizing oligonucleotides on glass plates, but the characterization of these micro-syntheses has been limited by the sub-picomolar amount of material available. Most DNA chip syntheses have been assayed using in situ coupling of fluorescent molecules to the 5′-OH of the synthesized oligonucleotides. We herein report a systematic investigation of oligonucleotide synthesis on glass plates with the reactions carried out in an automated DNA synthesizer using standard phosphoramidite chemistry. The analyses were performed using ³²P gel electrophoresis of the oligonucleotides cleaved from glass plates to provide product distribution profiles according to chain length of oligonucleotides. 5′-Methoxythymidine was used as the chain terminator, which permits assay of coupling reaction yields as a function of chain length growth. The results of this work reveal that a major cause of lower fidelity synthesis on glass plates is particularly inefficient reactions of the various reagents with functional groups close to glass plate surfaces. These problems cannot be detected by previous in situ fluorescence assays. The identification of this origin of low fidelity synthesis on glass plates should help to achieve improved synthesis for high quality oligonucleotide microarrays.     

西藏唐北地区湖泊动态及空间格局预测

本研究评估了西藏唐古拉山以北地区(唐北地区)湖泊动态并预测了湖泊空间格局变化.使用面向对象分类和光谱角向量变化检测方法生成了2000-2015年西藏唐北地区每5年一期的生态系统分布数据.以此为基础,分析了湖泊与其他生态系统之间的转换和空间格局特征,评估了湖泊空间格局的动态及其与相关自然地理因素的关系.通过增强回归树识别了不同因素对湖泊动态的贡献,使用GEOMOD模型预测了湖泊到2030年的空间变化.结果表明:唐北地区在2000-2015年间湖泊增加了14.2%,是唐北地区生态系统变化的主要形式之一.区域内15个面积大于10 km2的湖泊有10个增加,另有5个减少,且缩减量较低.通过空间格局分析发现,唐北地区湖泊斑块表现为面积和数量同时增加,大斑块面积比重略有上升.扩张幅度高的湖泊多分布于海拔高、坡度大、温度低、降水少、距离冰川近的区域.位于现有湖泊周边、温度低、降水少、坡度小的区域转变为湖泊的几率较高.根据过去15年的趋势,到2030年,唐北地区湖泊将继续增加119 km2,主要变化形式从大湖扩张转变为小型水面扩张.     

降水量和温度对植被覆盖指数影响的空间非平稳性特征——以新疆伊犁河谷地区为例

多变量空间相关分析多基于时间序列数据,对数据时长与统计要求严格,空间非平稳性特征分析可以利用单期数据分析多变量之间的相关性。通过空间变系数回归模型分析了2006年和2011年的新疆伊犁地区降水量和温度对植被覆盖度指数影响的空间变化特征,利用局部线性地理加权回归(GWR)方法估计得到了回归系数曲面,揭示出变量间相互影响的空间异质性,同时利用线性回归最小二乘估计进行了对比。结果表明:(1)空间变系数回归模型可以用于变量间的空间相关分析;(2)局部线性GWR估计方法明显优于线性回归最小二乘估计;(3)拟合结果表明,伊犁地区降水量和温度对植被覆盖指数的影响具有显著的空间非平稳性特征;(4)模型估计误差是降水、气温之外的地形、地貌及人类活动等多种因素造成的,需进一步研究。方法可为具有空间非平稳性特征变量间空间相关性分析以及植被覆盖指数的空间模拟分布提供思路和方法。     

1998—2017年祁连山南坡不同海拔、坡度和坡向生长季NDVI变化及其与气象因子的关系

祁连山是我国西北地区重要的水源涵养保护区,是我国地形第一、二阶梯分界线,对气候变化极其敏感。基于气温、降水量和归一化植被指数(NDVI)数据,使用趋势分析、小波分析和相关分析方法,结合数字高程模型(DEM)数据,从海拔、坡度和坡向的角度探讨祁连山南坡NDVI变化及其与气温和降水的关系。结果表明: 1998—2017年,祁连山南坡生长季NDVI整体呈增长趋势,增长趋势为0.023·10 a^-1。NDVI值在不同海拔、坡度和坡向上的变化存在差异性,NDVI值随海拔的升高呈先增后降趋势,海拔2700～3700 m区域的植被覆盖状况较好,＞4700 m区域的植被出现退化现象;NDVI值随坡度增加呈降低态势;NDVI值在坡向上的差异较小,但阳坡的植被覆盖状况好于阴坡。生长季NDVI与气温、降水的关系密切,生长季NDVI、气温、降水均具有14年的变化周期,而不同海拔、坡度、坡向的植被受到气温和降水的影响不同,海拔＜3700 m、＞4700 m区域、坡度＜25°区域和各坡向区域的植被均易受降水影响。     

A simple method for extraction of fungal genomic DNA

We have developed a new, simple and effective method for extraction of fungal genomic DNA. The initial steps involved suspension of freeze-dried mycelium in buffer containing sodium dodecyl sulphate, detachment of DNA from polysaccharides by mild shearing, NaCl precipitation of polysaccharides and protein, chloroform extraction and ethanol precipitation. The ethanol precipitate was then subjected to a second round of mild shearing, NaCl precipitation, chloroform extraction and ethanol precipitation. The procedure required approximately 1 h to perform. The method yielded 8-32 microg of high molecular weight DNA per 30 mg of freeze-dried mycelium when tested on six fungal species: Aspergillus niger, A. flavus, Fusarium graminarum, Neotyphodium lolii, Penicillium citrinum and Rhizopus nigricanes. The DNA was digestible with EcoRI, HindIII, SalI and BamHI. For the slow-growing N. lolii, a modification of the method was developed that removed the agar residue from colonies grown on agar plates by centrifugation at 13 000 rev min(-1) in the presence of CsCl. The modified method yielded 1.5-2 microg of high molecular weight DNA per colony.     

Data-adaptive longitudinal model selection in causal inference with collaborative targeted minimum loss-based estimation

Causal inference methods have been developed for longitudinal observational study designs where confounding is thought to occur over time. In particular, one may estimate and contrast the population mean counterfactual outcome under specific exposure patterns. In such contexts, confounders of the longitudinal treatment-outcome association are generally identified using domain-specific knowledge. However, this may leave an analyst with a large set of potential confounders that may hinder estimation. Previous approaches to data-adaptive model selection for this type of causal parameter were limited to the single time-point setting. We develop a longitudinal extension of a collaborative targeted minimum loss-based estimation (C-TMLE) algorithm that can be applied to perform variable selection in the models for the probability of treatment with the goal of improving the estimation of the population mean counterfactual outcome under a fixed exposure pattern. We investigate the properties of this method through a simulation study, comparing it to G-Computation and inverse probability of treatment weighting. We then apply the method in a real-data example to evaluate the safety of trimester-specific exposure to inhaled corticosteroids during pregnancy in women with mild asthma. The data for this study were obtained from the linkage of electronic health databases in the province of Quebec, Canada. The C-TMLE covariate selection approach allowed for a reduction of the set of potential confounders, which included baseline and longitudinal variables.     

次降雨条件下坡度对坡面产流产沙的影响

以野外径流小区的次降雨产流产沙数据为基础,对不同次降雨条件下坡面产流产沙随坡度的变化规律进行研究.结果表明:降雨性质的差异对坡面产流随坡度而变化的影响较小,在研究区的6场次降雨中,坡面产流量随坡度的变化规律基本一致,坡面径流量均随坡度增大而增大,但坡面径流量随坡度增加而增加的趋势较弱,这主要由降雨量与入渗量之间的转化程度所决定;次降雨性质对不同坡度的坡面产沙规律有重要影响,一般情况下存在临界侵蚀坡度,但临界坡度不是唯一值,而是随着降雨特性的不同而不同,临界侵蚀坡度随径流量的增大而增大,临界坡度较大时,坡面产沙量随坡度变化而变化的趋势也往往较大.     

基于移动窗口法的中国东北地区景观格局

基于GIS技术,利用移动窗口法,对2006年中国东北地区景观格局特征及其与水分梯度、热量梯度、海拔因子和人为干扰因子的相关关系进行了研究.结果表明：2006年,中国东北地区林地景观所占比例最大,为61.69%,耕地次之,占25.11%;中国东北地区的景观多样性具有圈层结构的特点,为破碎化程度较高的敏感区域提供了缓冲区间,使不良的生态后果可以控制在一定区域内;研究区景观格局指数与水分梯度、热量梯度的相关系数均在0.4以下,与海拔因子的相关系数在0.07以下,相关性不高说明研究区景观格局的异质性不是由单一的自然因素所决定.     

The standardization of infectivity titrations of poliovaccines--a WHO collaborative study

The reproducibility of a method for infectivity titrations of live poliovaccines using microtitre plates was investigated in a WHO collaborative study involving eight laboratories. The large variation (up to 100-fold) in estimates of infectivity observed between laboratories using their local methods of assay was reduced to no more than fourfold when a common method was used. However, expressing infectivities relative to those of the monovalent reference viruses improved the agreement between the laboratories irrespective of the titration method employed. On the basis of these results, WHO adopted the common method used in the study as its recommended method for poliovirus titrations and established the preparations studied as international reference materials for the infectivity titrations of live poliovaccines.     

Ecological correlates and determinants in the geographical variation of deer morphology

Previous studies on patterns in ungulate size variations have emphasized the effect of a particular environmental factor such as Bergmann's rule and the island rule. However, although multiple environmental factors may influence the body size, these studies focused on a single factor, and various measurements that may be influenced by different environmental factors (at least partly) were used as indices of body size. In this study, we used several skull and limb measurements to examine size variations among island populations of sika deer (Cervus nippon) in southern Japan considering the effects of multiple environmental factors. We found that all measurements differed markedly between populations. We focused on the skull and limb condylobasal length (CBL) and metacarpal length because they had the most important variations among the populations and the largest sample sizes. The common environmental factors influencing CBL and metacarpal length were island area and precipitation. Since these environmental factors reflect the availability of food resources, the causal factor of body size variation may be food resources. Interpopulation variation in metacarpal length was greater than that of CBL, indicating that metacarpal length may be affected by additional factors besides the common factors shared with CBL. Specific environmental factors influencing relative (CBL adjusted) metacarpal length were precipitation and slope. A common direct cause of those environmental factors was discussed in relation to topography. Analyses of phenotypic variation using multiple measurements with multiple environmental factors are useful to gain insight into underlying causes and can lead to identification of a measurement-specific variation with a specific driving force.     

Evaluation of Plastic Multi-Well Plates for Serological Screening of Salmonella Cultures with Spicer-Edwards Pooled Antisera

We compared the relative advantages of using glass test tubes and plastic multi-well plates in the serological identification of Salmonella cultures by the Spicer-Edwards method, and we conclude that the advantages of multi-well plates outweigh those of test tubes.     

天童常绿阔叶林林窗的地形分布格局

为探究多维地形因素对林窗分布的影响,以天童20 hm²常绿阔叶林动态监测样地内的林窗为对象,结合地理信息系统软件,分析了林窗空隙率、林窗密度以及林窗面积在海拔、坡度、坡向、坡形、坡位5种地形因子下的分布格局.结果表明: 该样地林窗空隙率为13.1%,林窗密度为9.5个·hm^-2,林窗平均面积为137.82 m²;因高海拔台风干扰的强度较大,高海拔段(≥500 m)林窗的空隙率和密度显著大于中低海拔段(<500 m);台风带来的强降雨极易引起小范围滑坡,使得沟谷的林窗空隙率和密度显著大于侧坡,林窗平均面积显著大于侧坡和山脊.台风及其带来的强降雨是造成林窗在海拔及坡位梯度上具有显著性差异的主要原因.     

天童常绿阔叶林林窗的地形分布格局

为探究多维地形因素对林窗分布的影响,以天童20 hm²常绿阔叶林动态监测样地内的林窗为对象,结合地理信息系统软件,分析了林窗空隙率、林窗密度以及林窗面积在海拔、坡度、坡向、坡形、坡位5种地形因子下的分布格局.结果表明: 该样地林窗空隙率为13.1%,林窗密度为9.5个·hm^-2,林窗平均面积为137.82 m²;因高海拔台风干扰的强度较大,高海拔段(≥500 m)林窗的空隙率和密度显著大于中低海拔段(<500 m);台风带来的强降雨极易引起小范围滑坡,使得沟谷的林窗空隙率和密度显著大于侧坡,林窗平均面积显著大于侧坡和山脊.台风及其带来的强降雨是造成林窗在海拔及坡位梯度上具有显著性差异的主要原因.     

六盘山叠叠沟小流域典型坡面土壤水分的植被承载力

确定土壤水分的植被承载力是我国北方半干旱地区合理调控土壤水分和植被生长关系、科学恢复林草植被的核心问题。我国北方半干旱地区的土壤水分主要来自大气降水, 作为土壤水分限制型生态系统的坡面植被, 植物种类和植被密度等结构特征与降水量紧密相关。根据六盘山石质山区的特点, 基于水量平衡原理, 建立了阴坡华北落叶松(Larix principis-rupprechti)和阳坡草地的土壤水分植被承载力数学模型, 即由4~10月的生长季降雨量(P)计算得到可承载的叶面积指数(Leaf area index, LAI)公式: LAI_tree= exp((0.773 1×P-186.12)/146.46)和LAI_grass= exp((0.511 2×P-345.93)/227.89), 并提出了考虑坡面水分再分配影响的不同坡位的土壤水分植被承载力计算方法。阴坡华北落叶松的植被承载力(用LAI表示)从坡顶的1.45升高到坡中的4.83, 然后稳定在3.0~3.3。对于阳坡草地, 土壤水分可承载的LAI从坡顶的0.37上升到坡中的0.46, 然后在0.41~0.47之间变动, LAI的计算值与实测值较为接近, 计算结果比较合理。     

Adhesion forces measured at the level of a terminal plate of the fly's seta

The attachment pads of fly legs are covered with setae, each ending in small terminal plates coated with secretory fluid. A cluster of these terminal plates contacting a substrate surface generates strong attractive forces that hold the insect on smooth surfaces. Previous research assumed that cohesive forces and molecular adhesion were involved in the fly attachment mechanism. The main elements that contribute to the overall attachment force, however, remained unknown. Multiple local force-volume measurements were performed on individual terminal plates by using atomic force microscopy. It was shown that the geometry of a single terminal plate had a higher border and considerably lower centre. Local adhesion was approximately twice as strong in the centre of the plate as on its border. Adhesion of fly footprints on a glass surface, recorded within 20 min after preparation, was similar to adhesion in the centre of a single attachment pad. Adhesion strongly decreased with decreasing volume of footprint fluid, indicating that the layer of pad secretion covering the terminal plates is crucial for the generation of a strong attractive force. Our data provide the first direct evidence that, in addition to Van der Waals and Coulomb forces, attractive capillary forces, mediated by pad secretion, are a critical factor in the fly's attachment mechanism.     

Computational models evaluating the impact of sieve plates and radial water exchange on phloem pressure gradients

The sugar conducting phloem in angiosperms is a high resistance pathway made up of sieve elements bounded by sieve plates. The high resistance generated by sieve plates may be a trade‐off for promoting quick sealing in the event of injury. However, previous modeling efforts have demonstrated a wide variation in the contribution of sieve plates towards total sieve tube resistance. In the current study, we generated high resolution scanning electron microscope images of sieve plates from balsam poplar and integrated them into a mathematical model using Comsol Multiphysics software. We found that sieve plates contribute upwards of 85% towards total sieve tube resistance. Utilizing the Navier–Stokes equations, we found that oblong pores may create over 50% more resistance in comparison with round pores of the same area. Although radial water flows in phloem sieve tubes have been previously considered, their impact on alleviating pressure gradients has not been fully studied. Our novel simulations find that radial water flow can reduce pressure requirements by half in comparison with modeled sieve tubes with no radial permeability. We discuss the implication that sieve tubes may alleviate pressure requirements to overcome high resistances by regulating their membrane permeability along the entire transport pathway.     

祁连山高寒草地甘肃臭草叶性状与坡向间的关系北大核心CSCD

植物功能性状可反映植物对环境的适应。在祁连山高寒退化草地,利用Arc GIS建立研究区域的数字高程模型,提取坡向数据,采用标准化主轴估计方法(standardized major axis estimation,SMA),研究了不同坡向甘肃臭草(Melica przewalskyi)叶性状间的关系。结果表明:1)甘肃臭草叶面积和叶体积在北坡最大,东坡、西坡、南坡逐渐减小,叶干质量无显著变化;2)叶面积与叶干质量在北坡、东坡和西坡呈等速生长关系,在南坡呈异速生长关系,且叶干质量的增长速度大于叶面积的增长速度;3)叶体积与叶干质量在4个坡向上呈异速生长关系,且叶干质量的增长速度均小于叶体积的增长速度。甘肃臭草叶性状关系随坡向的变化反映了该物种在异质生境中具有较强的叶片形态可塑性,从而有利于其适应和占据高寒退化生境。     

An adhesion-based method for plasma membrane isolation: Evaluating cholesterol extraction from cells and their membranes

A method to isolate large quantities of directly accessible plasma membrane from attached cells is presented. The method is based on the adhesion of cells to an adsorbed layer of polylysine on glass plates, followed by hypotonic lysis with ice-cold distilled water and subsequent washing steps. Optimal conditions for coating glass plates and time for cell attachment were established. No additional chemical or mechanical treatments were used. Contamination of the isolated plasma membrane by cell organelles was less than 5%. The method uses inexpensive, commercially available polylysine and reusable glass plates. Plasma membrane preparations can be made in 15 min. Using this method, we determined that methyl-β-cyclodextrin differentially extracts cholesterol from fibroblast cells and their plasma membranes and that these differences are temperature dependent. Determination of the cholesterol/phospholipid ratio from intact cells does not reflect methyl-β-cyclodextrin plasma membrane extraction properties.     

Slope-related variations in twig and leaf traits of Robinia pseudoacacia in the northern mountains of Lanzhou

 枝叶生长关系是植物在环境胁迫条件下提高空间资源利用能力的一种策略, 弄清枝叶生长关系对理解植物应对环境异质性的表型可塑性具有重要意义。该文利用ArcGIS建立研究区域的数字高程模型, 研究了兰州市北山不同坡向人工林刺槐(Robinia pseudoacacia)小枝茎截面积-总叶面积和出叶强度-单叶面积的生长关系。结果表明: 随着坡向由北坡向东坡、南坡和西坡转变, 刺槐林群落的郁闭度、高度和土壤含水量呈现先减小后增大的趋势, 刺槐小枝茎截面积、总叶面积和单叶面积呈现先减小后增大的趋势, 出叶强度呈现先增大后减小的趋势; 北坡、东坡、南坡和西坡4个坡向的刺槐小枝的茎截面积和总叶面积均呈显著的正相关关系(p < 0.05), 并存在显著大于1的共同斜率, 刺槐的出叶强度与单叶面积均呈显著的负相关关系(p < 0.05), 并存在接近于–1的共同斜率; 随着坡向由北坡向东坡、南坡和西坡转变, 茎截面积-总叶面积和出叶强度-单叶面积两组关系的回归方程截距呈现先减小后增大的趋势。刺槐枝叶在不同坡向上的异速生长关系反映了植物功能性状对生长环境的响应和适应, 以及植物构型构建的投资权衡机制。     

Microimmunofluorescence using Terasaki plates and direct plate freezing method--rapid and reliable screening system of hybridomas

Microimmunofluorescence using Terasaki plates and a direct plate freezing method were combined for effective screening of hybridoma supernatants. The microplates, in which the fused cells (myeloma and spleen cells) were cultured and hybridoma colonies were growing, were frozen after harvest of supernatants and saved at -80 C for several weeks without affecting antibody production ability of hybridomas. Microimmunofluorescence was performed in Terasaki plates on which target cells were attached by poly-L-lysine and glutaraldehyde or by short time culture of the cells in Terasaki plates. The direct plate freezing method prevented initial hybridoma cells from changes or disappearance of antibody productions during screening of hybridoma supernatants; the microimmunofluorescence staining method permits fast and detailed estimation of specificity of antibodies of hybridomas by saving time and minimal consumption of supernatant for checking. The combination of these two methods is a powerful tool for obtaining desired monoclonal antibodies.