百山祖常绿阔叶林灌草层物种组成和 分布的10年动态

森林群落的动态受多方面因素的影响。林下的草本植物和木本植物幼苗幼树对于森林的更新及动态具有重要作用。为了解百山祖常绿阔叶林群落下层植物物种组成和分布的动态变化, 我们分析了2003-2013年间百山祖5 ha森林动态样地灌草层物种(包括DBH < 1 cm的木本植物和所有草本植物)在物种重要值、α多样性以及物种分布等方面的变化。结果表明: (1) 10年间, 群落灌草层植物个体数减少了28.7%, 其中草质藤本植物个体数下降比例最大(76.9%), 而乔木的幼苗和幼树下降比例最小(14.4%); (2)整个灌草层的物种数明显下降, 同时乔木的幼苗和幼树及直立灌木的均匀度均下降, 而草本植物均匀度有所上升; (3)除短尾柯(Lithocarpus brevicaudatus)、叶萼山矾(Symplocos phyllocalyx)、显脉野木瓜(Stauntonia conspicua)和福建悬钩子(Rubus fujianensis)等植物重要值逆势上扬外, 直立灌木物种重要值10年间的变化值与其在2003年时的重要值呈显著正相关, 而其余各类生活型植物都显示, 初始重要值越高的物种在10年后下降幅度越大; (4)物种分布与生境类型的相关性变化复杂, 除与山谷生境正相关的物种数量增加外, 研究期间与生境存在显著相关性的物种数都有所减少; (5) 10年来仅陡坡处物种多样性指数没有显著下降。总体来说, 百山祖常绿阔叶林灌草层群落仍未达到顶极状态, 2003-2013年间正缓慢向顶极群落演替。群落内部的种间和种内竞争应是当前群落动态的主导因素。     

基于抗性恢复的高效克隆超短片段重组质粒的构建

分子克隆作为一种常规技术被广泛应用于DNA及蛋白质的研究。在传统的分子克隆中,主要通过限制性内切酶先分别消化目的 DNA片段及载体,再纯化回收,然后用DNA连接酶将二者连接。而对一些超短基因片段(300 bp),通过酶切及切胶纯化后,回收率极低,导致插入表达载体比较困难。文中介绍了一种新的利用质粒抗性恢复进行克隆的方法,大大提高了克隆效率,为短基因片段的分子克隆提供了一种高效的方法。     

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

The solution structure of d(CGCGAATTCGCG)₂ has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear ¹³C-¹H and ¹⁵N-¹H and qualitative homonuclear ¹H-¹H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative ¹H-¹H and 22 ³¹P-¹H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 ³¹P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of ¹³C-¹H and ¹⁵N-¹H dipolar couplings. In the newly calculated structures, ³¹P-¹H dipolar and ³Jsub H3 P sub couplings and ³¹P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of 10°, which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2-endo and C3-endo deoxyribose puckers (sugar switching). The C2-H2/H2 dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR J_HH couplings, with a population of the minor C3-endo form higher for pyrimidines than for purines.     

Genetic immunization by jet injection of targeted pDNA-coated nanoparticles

Genetic immunization strategies have largely focused on the use of "naked" plasmid DNA or the gene gun. However, there remains a clear need to further improve the efficiency and/or cost of potential DNA vaccines. The theoretical basis of our research is to rationally design genetic immunization methodologies for nanoparticle-based delivery systems of plasmid DNA, perhaps in combination with already commercially available needle-free devices, such as the Biojector 2000. These methodologies may both reduce the dose of pDNA required and enhance the breadth and depth of protective immune responses (i.e., humoral and cellular). The purpose of this article is to provide detailed experimental methods to (1) engineer and characterize pDNA-coated cationic nanoparticles (<100nm) directly from oil-in-water microemulsion precursors and (2) enhance both the breadth and depth of immune responses after immunization of mice with pDNA-coated nanoparticles by different routes of administration, including intradermal, using a needle-free jet injection device.     

浙江九龙山香果树群落乔木层物种的多样性格局

为了解香果树(Emmenopterys henryi)群落的物种多样性及其驱动因素,在浙江九龙山自然保护区建立了35个以香果树为中心15 m半径的样圆,调查样圆内胸径2.5 cm以上的乔木层树木的物种和胸径。通过线性混合效应模型分析α多样性与海拔、坡向、香果树胸高断面积的关系,通过Mantel检验和方差分解分析样地间距离、海拔、坡向和香果树胸高断面积差异对β多样性的影响。结果表明,九龙山香果树群落乔木层物种丰富(50科96属145种),且以落叶或半常绿树种占优势;样地乔木层Shannon-Wiener指数为2.37～3.40,Simpson指数为0.86～0.94;群落乔木层α多样性随海拔升高呈先升高后下降的变化趋势,但与样地坡向和香果树胸高断面积无关;群落乔木层Sorenson指数为0.15～0.95,物种周转组分对群落β多样性的贡献达74.88%;样地间地理距离与乔木层β多样性及其组分呈显著正相关,样地间海拔差异与其乔木层β多样性及其物种丰富度差异组分呈显著正相关,而样地间香果树胸高断面积差异仅与物种周转组分显著正相关;样地地理距离对于乔木层β多样性及其组分具有最高的解释度(23%...     

An improved procedure for isolating adult mouse cardiomyocytes for epicardial activation mapping

Cardiovascular disease is a leading cause of death and disability worldwide. Although genetically modified mouse models offer great potential for robust research in vivo, in vitro studies using isolated cardiomyocytes also provide an important approach for investigating the mechanisms underlying cardiovascular disease pathogenesis and drug actions. Currently, isolation of mouse adult cardiomyocytes often relies on aortic retrograde intubation under a stereoscopic microscope, which poses considerable technical barriers and requires extensive training. Although a simplified, Langendorff-free method has been used to isolate viable cardiomyocytes from the adult mouse heart, the system requires enzymatic digestions and continuous manual technical operation. This study established an optimized approach that allows isolation of adult mouse cardiomyocytes and epicardial activation mapping of mouse hearts using a Langendorff device. We used retrograde puncture through the abdominal aorta in vivo and enzymatic digestion on the Langendorff perfusion device to isolate adult mouse cardiomyocytes without using a microscope. The yields of isolated cardiomyocytes were amenable to patch clamp techniques. Furthermore, this approach allowed epicardial activation mapping. We used a novel, simplified method to isolate viable cardiomyocytes from adult mouse hearts and to map epicardial activation. This novel approach could be beneficial in more extensive research in the cardiac field.     

Solution structure of (gamma)S-crystallin by molecular fragment replacement NMR

The solution structure of murine gammaS-crystallin (gammaS) has been determined by multidimensional triple resonance NMR spectroscopy, using restraints derived from two sets of dipolar couplings, recorded in different alignment media, and supplemented by a small number of NOE distance restraints. gammaS consists of two topologically similar domains, arranged with an approximate twofold symmetry, and each domain shows close structural homology to closely related (approximately 50% sequence identity) domains found in other members of the gamma-crystallin family. Each domain consists of two four-strand "Greek key" beta-sheets. Although the domains are tightly anchored to one another by the hydrophobic surfaces of the two inner Greek key motifs, the N-arm, the interdomain linker and several turn regions show unexpected flexibility and disorder in solution. This may contribute entropic stabilization to the protein in solution, but may also indicate nucleation sites for unfolding or other structural transitions. The method used for solving the gammaS structure relies on the recently introduced molecular fragment replacement method, which capitalizes on the large database of protein structures previously solved by X-ray crystallography and NMR.     

Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs)

Virtual screening was employed to identify new drug-like inhibitors of NAD synthetase (NADs) as antibacterial agents. Four databases of commercially available compounds were docked against three subsites of the NADs active site using FlexX in conjunction with CScore. Over 200 commercial compounds were purchased and evaluated in enzyme inhibition and antibacterial assays. 18 compounds inhibited NADs at or below 100 μM (7.6% hit rate), and two were selected for future SAR studies.     

An Efficient Augmented Lagrangian Method for Statistical X-Ray CT Image Reconstruction

Statistical iterative reconstruction (SIR) for X-ray computed tomography (CT) under the penalized weighted least-squares criteria can yield significant gains over conventional analytical reconstruction from the noisy measurement. However, due to the nonlinear expression of the objective function, most exiting algorithms related to the SIR unavoidably suffer from heavy computation load and slow convergence rate, especially when an edge-preserving or sparsity-based penalty or regularization is incorporated. In this work, to address abovementioned issues of the general algorithms related to the SIR, we propose an adaptive nonmonotone alternating direction algorithm in the framework of augmented Lagrangian multiplier method, which is termed as “ALM-ANAD”. The algorithm effectively combines an alternating direction technique with an adaptive nonmonotone line search to minimize the augmented Lagrangian function at each iteration. To evaluate the present ALM-ANAD algorithm, both qualitative and quantitative studies were conducted by using digital and physical phantoms. Experimental results show that the present ALM-ANAD algorithm can achieve noticeable gains over the classical nonlinear conjugate gradient algorithm and state-of-the-art split Bregman algorithm in terms of noise reduction, contrast-to-noise ratio, convergence rate, and universal quality index metrics.