Dual-Axis Tomography: An Approach with Alignment Methods That Preserve Resolution

Tomographic reconstructions of biological specimens are now routinely being generated in our high voltage electron microscope by tilting the specimen around two orthogonal axes. Separate tomograms are computed from each tilt series. The two tomograms are aligned to each other with general 3-D linear transformations that can correct for distortions between the two tomograms, thus preserving the inherent resolution of the reconstruction throughout its volume. The 3-D Fourier transforms of the two tomograms are then selectively combined to achieve a single tomogram. Unlike a single-axis tomogram, a dual-axis tomogram shows good resolution for extended features at any orientation in the plane of the specimen; it also has improved resolution in the depth of the specimen. Calculations indicate that the improvements available from double tilting and from tilting to higher angles are largely additive. Actual and model data were used to assess whether varying the increment between tilted views in proportion to the cosine of the tilt angle would allow a reduction in the number of pictures required to achieve a given resolution of reconstruction. Analysis by Fourier sector correlation indicated that the variable tilt increment improved the reconstruction in some respects but degraded it in others. A varying tilt increment thus does not give an unqualified improvement, at least when using back-projection algorithms for the reconstruction.     

ABUNDANCE OF IRRAWADDY DOLPHINS (ORCAELLA BREVIROSTRIS) AND GANGES RIVER DOLPHINS (PLATANISTA GANGETICA GANGETICA) ESTIMATED USING CONCURRENT COUNTS MADE BY INDEPENDENT TEAMS IN WATERWAYS OF THE SUNDARBANS MANGROVE FOREST IN BANGLADESH

Independent observer teams made concurrent counts of Irrawaddy dolphins Orcaella brevirostris and Ganges River dolphins Platanista gangetica gangetica in mangrove channels of the Sundarbans Delta in Bangladesh. These counts were corrected for missed groups using mark-recapture models. For Irrawaddy dolphins, a stratified Lincoln-Petersen model, which incorporated group size and sighting conditions as covariates, and a Huggins conditional likelihood model, which averaged models that individually incorporated group size, sighting conditions, and channel width as covariates, generated abundance estimates of 397 individuals (CV = 10.2%) and 451 individuals (CV = 9.6%), respectively. For Ganges River dolphins, a stratified Lincoln-Petersen model, which incorporated group size as a covariate, and a Huggins conditional likelihood model, which averaged the same models described above, generated abundance estimates of 196 individuals (CV = 12.7%) and 225 individuals (CV = 12.6%), respectively. Although the estimates for both models were relatively close, the analytical advantages of the Huggins models probably outweigh those of the Lincoln-Petersen models. However, the latter should be considered appropriate when simplicity is a priority. This study found that waterways of the Sundarbans support significant numbers of Irrawaddy and Ganges River dolphins, especially compared to other areas where the species have been surveyed.     

Effects of endophyte fungal species and host plant genotype on the leaf shape and leaf area of endophyte-grass symbionts

Epichloë内生真菌感染能够影响宿主植物的生长发育, 但关于内生真菌感染对宿主植物叶形状和叶面积的研究很少。该研究以羽茅(Achnatherum sibiricum)为实验材料, 采用长宽系数计算和扫描测定叶面积相结合的方法探究内生真菌种类和羽茅母本基因型对羽茅-内生真菌共生体叶形状和叶面积的影响。结果表明: 内生真菌感染与否、内生真菌种类和宿主母本基因型对反映叶形状的叶校正系数、叶片长度、宽度和长宽比均无显著影响, 经计算与验证, 确定了羽茅叶片的校正系数为0.594 9。采用该校正系数及叶长宽计算的叶面积与实测叶面积无显著差异, 且二者均未受到内生真菌感染与否、内生真菌种类或宿主植物母本基因型的显著影响。     

Matrix effects in PIXE analysis of aerosols and ashes

A comparison of instrumental neutron activation analysis (INAA) and proton-induced X-ray emission (PIXE) results for sizefractionated atmospheric aerosols (“coarse” and “fine” fractions with an equivalent aerodynamic diameter of 2–10 Μm and < 2 Μm, respectively, or the PM10 fraction) showed that PIXE yielded significantly lower results for the PM10 and coarse fractions, especially for elements with a low Z resulting from a particle size effect. Somewhat lower PIXE results were also obtained for the fine fraction of atmospheric aerosols. A correction is also needed for irregularly shaped deposits of combustion aerosols collected by a cascade impactor in 11 size fractions ranging from 0.016 to 14.3 Μm, as well as for thick samples of fly and bottom ashes. An equivalent layer thickness (ELT) model is proposed to correct the matrix effects in PIXE. The approaches for the calculation of ELT using a comparison of PIXE and INAA results or by comparing PIXE results obtained using two different incident proton beam energies (1.31 and 2.35 MeV) are described. The correction for the ash pellets and irregular deposits are also discussed.     

Wald Tests of Location for Symmetric Nonnormal Data

For nonnormal data we suggest a test of location based on a broader family of distributions than normality. Such a test will in a sense fall between the standard parametric and non parametric tests. We see that the Wald tests based on this family of distributions have some advantages over the score tests and that they perform well in comparison to standard parametric and nonparametric tests in a variety of situations. We also consider when and how to apply such tests in practice.     

Applying polynomial standard curve method to correct bias encountered in estimating allele frequencies using DNA pooling strategy

DNA pooling approach is a cost-saving strategy which is crucial for multiple-SNP association study and particularly for laboratories with limited budget. However, the biased allele frequency estimates cannot be completely abolished by κ correction. Using the SNaPshot™, we systematically examined the relations between actual minor allele frequencies (AMiAFs) levels and estimates obtained from the pooling process for all six types of SNPs. We applied principle of polynomial standard curves method (PSCM) to produce allele frequency estimates in pooled DNA samples and compared it with the κ method. The results showed that estimates derived from the PSCM were in general closer to AMiAFs than those from the κ method, particularly for C/G and G/T polymorphisms at the range of AMiAF between 20–40%. We demonstrated that applying PSCM in the SNaPshot™ platform is suitable for multiple-SNP association study using pooling strategy, due to its cost effectiveness and estimation accuracy.     

维甲酸核受体RARα真核表达载体的构建、突变纠正及表达

目的构建维甲酸核受体RARα真核表达载体,并检测其在人肺腺癌细胞A549中表达。方法从小鼠巨噬细胞RAW264.7中提取总RNA,以RT-PCR法扩增RARαcDNA,克隆至真核表达载体pDsRed1-C1中,测序结果显示RARα第1040位A→G,导致其编码蛋白的氨基酸发生改变。通过二次PCR将其纠正,重组载体RedC1-RARα转化大肠埃希菌Top10,筛选阳性克隆做酶切及测序鉴定。脂质体瞬时转染A549细胞,在荧光显微镜下观察RARα的表达。RT-PCR法检测RARα的mRNA水平表达。结果通过RT-PCR及二次PCR得到RARαcDNA,构建其真核表达载体,脂质体瞬时转染A549细胞得到了成功表达,RARα基因产物定位于细胞核内。结论成功构建维甲酸核受体RARα真核表达载体,且证实RARα编码蛋白定位于细胞核内,本研究结果为进一步探讨结核分枝杆菌固有免疫机制奠定了基础。     

A possible mechanism for the dynamics of transition between polymerase and exonuclease sites in a high-fidelity DNA polymerase

The fidelity of DNA synthesis by DNA polymerase is significantly increased by a mechanism of proofreading that is performed at the exonuclease active site separate from the polymerase active site. Thus, the transition of DNA between the two active sites is an important activity of DNA polymerase. Here, based on our proposed model, the rates of DNA transition between the two active sites are theoretically studied. With the relevant parameters, which are determined from the available crystal structure and other experimental data, the calculated transfer rate of correctly base-paired DNA from the polymerase to exonuclease sites and the transfer rate after incorporation of a mismatched base are in good agreement with the available experimental data. The transfer rates in the presence of two and three mismatched bases are also consistent with the previous experimental data. In addition, the calculated transfer rate from the exonuclease to polymerase sites has a large value even with the high binding affinity of 3′-5′ ssDNA for the exonuclease site, which is also consistent with the available experimental value. Moreover, we also give some predictive results for the transfer rate of DNA containing only A:T base pairs and that of DNA containing only G:C base pairs.     

不同大气校正方法对森林叶面积指数遥感估算影响的比较

利用TM原始图像以及经过6S模型和基于影像自身的Gilabert模型大气校正后的地面绝对反射率图像,分别计算了褒河流域阔叶林和针阔混交林2种林型的5类光谱植被指数(SR、NDVI、MNDVI、ARVI和RSR),并建立各林型森林叶面积指数与同时相的各个植被指数的相关关系。结果表明,2种大气校正模型均显著提高了各植被指数与森林叶面积指数的相关关系,除了对森林叶面积指数与植被指数SR和NDVI的相关关系影响不显著外,对森林叶面积指数与植被指数MNDVI、ARVI和RSR相关关系的影响均非常显著。说明不同大气校正模型对叶面积指数的遥感估算结果有较大影响。因此,在利用遥感数据进行定量分析、信息提取和生态遥感应用时,不仅要进行大气校正,而且还要慎重选择大气校正模型和植被指数。