A rapid,inexpensive, quantitative technique for the analysis of two-dimensional electrophoretograms

We describe a rapid, reproducible, and relatively inexpensive method for quantitative analysis of two-dimensional gel radiofluorograms. The equipment required includes a mediumresolution black and white video camera for data acquisition, a video digitizing circuit for data translation, and a microcomputer for data analysis. The system described can also be used to quantitate protein- or DNA-stained one- or two-dimensional gels or chromatograms.     

Estimating analytical variability in two-dimensional data

Throughout the course of drug development there are many instances in which a variability assessment within a set of analytical data is required, which may be challenging for techniques that produce two-dimensional data. This note describes an interval-based approach to variability assessment and demonstrates its applicability for analysis of near-UV circular dichroism (CD) spectra. The approach is generalizable and could be applied to two-dimensional data from other analytical techniques as well.     

Ultraviolet imaging densitometry of unstained gels for two-dimensional electrophoresis

A system suitable for ultraviolet imaging densitometry of two-dimensional electrophoretic gels that are unstained is described, together with its applications. A flying-spot densitometer linked with a personal computer was used for data acquisition, generation of mapping data, and image processing. Randomly distributed zones of proteins on two-dimensional gels were detected at 280 nm without being stained by two-dimensional scanning, and the densitometric value of each pixel (0.2 x 0.2 mm) was memorized by the computer, which generated a mapping pattern with density contours. The amount and densitometric value of cytochrome c had a linear relationship in the range of 2-200 micrograms. Zone locations of bovine liver proteins separated on two-dimensional gels were indicated on a map expressed in X-Y coordinates, and the pIs and molecular weights could be calculated from the map by use of pI and molecular weight markers on the same gel.     

Importance of observation interval in two-dimensional video analysis of individual diatom cells

The effect of the observation interval on two-dimensional trajectory analysis of motility of individual diatom cells of Navicula sp. was studied by comparing thinned-out observation data. The trajectory of cell movement was visualized accurately even after thinning the data interval. However, the analysis of velocity fluctuations of individual cells was found to be significantly affected by the data interval. Reproducibility of the results was guaranteed by analyzing many independent cells. In addition, comparison between automatic and manual determination of cell positions proved that automatic determination was a reliable process. Our data indicated that two-dimensional trajectory analysis using a computer can be a powerful technique to study diatom locomotion.     

细胞支架研究进展

目前细胞培养通常采用二维平面培养技术,但由于在培养板和培养瓶二维细胞培养并不能完全模拟体内细胞的三维生长环境,因此所得的试验数据与在体情况有偏差。然而细胞支架材料却能为细胞提供一个良好的三维生长环境,更利于细胞粘附、生长和增殖。目前可用于细胞支架材料的来源有天然和人工两大类,现将细胞支架研究进展综述如下。     

Computer aided evaluation of two-dimensional NMR spectra of proteins

A computer program for the automatic evaluation of two-dimensional NMR spectra of peptides and proteins has been developed. The used strategy is described, the advantages and limits of this approach are discussed. The program was successfully tested on a COSY-spectrum of the neuropeptide Glp-Pro-Pro-Gly-Gly-Ser-Lys-Val-Ile-Leu-Phe from hydra, resulting in a drastic reduction of the time needed for the evaluation of two-dimensional NMR data.     

Sequence-specific recognition of DNA: assignment of nonexchangeable proton resonances in the consensus Pribnow promoter DNA sequence by two-dimensional NMR

The resonances of most of the nonexchangeable protons of both + and - strands of the consensus Pribnow dodecamer d( CGTTATAATGCG ) have been assigned by two-dimensional nuclear magnetic resonance methods. Application of the two-dimensional nuclear Overhauser effect ( NOESY ) sequential connectivity method, combined with two-dimensional autocorrelated ( COSY ) spectra to reveal scalar-coupled protons, results in assignment of virtually all of the base and sugar protons, except the sugar C5 protons which are inadequately resolved. Analysis of the nuclear Overhauser data indicates that the helix assumes a fairly uniform B form conformation.     

Lung cancer rate predictions using generalized additive models

Predictions of lung cancer incidence and mortality are necessary for planning public health programs and clinical services. It is proposed that generalized additive models (GAMs) are practical for cancer rate prediction. Smooth equivalents for classical age-period, age-cohort, and age-period-cohort models are available using one-dimensional smoothing splines. We also propose using two-dimensional smoothing splines for age and period. Variance estimation can be based on the bootstrap. To assess predictive performance, we compared the models with a Bayesian age-period-cohort model. Model comparison used cross-validation and measures of predictive performance for recent predictions. The models were applied to data from the World Health Organization Mortality Database for females in five countries. Model choice between the age-period-cohort models and the two-dimensional models was equivocal with respect to cross-validation, while the two-dimensional GAMs had very good predictive performance. The Bayesian model performed poorly due to imprecise predictions and the assumption of linearity outside of observed data. In summary, the two-dimensional GAM performed well. The GAMs make the important prediction that female lung cancer rates in these countries will be stable or begin to decline in the future.     

Two-dimensional map of membrane proteins from human erythrocytes

Human erythrocyte membrane proteins were analyzed by a modified two-dimensional electrophoresis performed according to O'Farrell. This method was used to construct a two-dimensional map of human erythrocyte membrane proteins. The map plotted in the coordinates "relative molecular mass versus relative electrophoretic mobility during IEF" was used for the characterization of 189 proteins. The position of major membrane proteins in the map was determined on the basis of their Mr, pI as well as literature data. Carboanhydrase was positioned by coelectrophoresis. A comparative analysis of erythrocyte membrane and cytosol preparations by two-dimensional protein mapping revealed that some of erythrocyte proteins have dual localization.     

Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics

Two-dimensional linear ion trap mass spectrometers are rapidly becoming the new workhorse instruments for shotgun proteomic analysis of complex peptide mixtures. The objective of this study was to compare the potential for false positive peptide sequence matches between a two-dimensional ion trap instrument and a traditional, three-dimensional ion trap instrument. Through the comparative analysis of a complex protein sample, we found that in order to minimize false positive sequence matches, sequence match scoring criteria must be more stringent for data from the two-dimensional ion trap compared to the three-dimensional ion trap data. Given this increased potential for false positives, we also investigated two potential filtering strategies to reduce the false positive matches for data derived from the two-dimensional ion trap, including trypsin enzyme cleavage filtering, and the addition of peptide physicochemical information as a constraint, specifically peptide isoelectric point. The results described here provide a cautionary tale to researchers, demonstrating the need for careful analysis of MS/MS data from this new class of ion trap instruments, as well as the effectiveness of trypsin enzyme cleavage filtering and peptide pI information in maximizing high confidence protein identifications from this powerful proteomic instrumentation.     

Biosynthesis of methanofuran in Methanobacterium thermoautotrophicum.

The 13C NMR signals of methanofuran were assigned by two-dimensional 1H and 13C NMR experiments. On this basis, the incorporation of 13C-labeled acetate and pyruvate into methanofuran by growing cells of Methanobacterium thermoautotrophicum was analyzed by one- and two-dimensional 13C NMR experiments. The data were analyzed by a retrobiosynthetic approach based on a comparison of labeling patterns in a variety of metabolites. The data show that the furan ring is formed by condensation of two molecules from the pyruvate/triose pool. The tetracarbocylic acid moiety is assembled from ketoglutarate, two molecules of acetyl CoA, and one molecule of carbon dioxide.     

细胞支架研究进展

目前细胞培养通常采用二维平面培养技术,但由于在培养板和培养瓶二维细胞培养并不能完全模拟体内细胞的三维生长环境,因此所得的试验数据与在体情况有偏差。然而细胞支架材料却能为细胞提供一个良好的三维生长环境,更利于细胞粘附、生长和增殖。目前可用于细胞支架材料的来源有天然和人工两大类,现将细胞支架研究进展综述如下。     

Estimation of Genetic Variability in Natural Populations of DROSOPHILA SIMULANS by Two-Dimensional and Starch Gel Electrophoresis

Genic variation in natural populations of Drosophila simulans was surveyed using allozymic and two-dimensional electrophoretic techniques. Consistent with some previous reports, allozymic heterozygosity appeared lower than in the sibling species D. melanogaster (0.07 vs. 0.16). No variation was detected by two-dimensional electrophoresis of 19 lines scored for 70 abundant proteins. This is consistent with reported reductions in estimates of genic heterozygosity by two-dimensional electrophoresis in D. melanogaster, Mus musculus, and man. Although the amount of intraspecific variation detected in abundant proteins was lower than that detected for allozymes in D. simulans and D. melanogaster, the genetic distances between the sibling species calculated from the two data sets are not significantly different (0.35 and 0.20). The allozyme and two-dimensional electrophoresis data confirmed the impression from other measures of genetic variation (mitochondrial DNA restriction maps and inversion polymorphisms) that D. simulans is substantially less variable than D. melanogaster.     

Chronobiological analysis of superimposed period data sets using bivariate cosine series models

The non-linear cosine fit (so-called cosinor method) of chronobiological sets is suited to one-dimensional effect versus time data. Extending the method to multiple components allows one to look for subharmonics or superimposed underlying periods. In more complex two-dimensional chronobiological time series, alternative models may be advantageous to visualise the time structure. Bivariate cosine series and the corresponding numerical surface discussion including first and second partial derivatives may be a suited method to characterise individual maxima or minima. Moreover, the method permits one to define a mean over two periods (bivariate MESOR) of a two-dimensional data set.     

Fluorescence2D: Software for Accelerated Acquisition and Analysis of Two-Dimensional Fluorescence Spectra

The Fluorescence2D is free software that allows analysis of two-dimensional fluorescence spectra obtained using the accelerated “triangular” acquisition schemes. The software is a combination of Python and MATLAB-based programs that perform conversion of the triangular data, display of the two-dimensional spectra, extraction of 1D slices at different wavelengths, and output in various graphic formats.     

染色体三维结构重建方法研究

染色体三维结构重构问题是近年生物领域中基因组学的热点研究问题,是以二维交互频率数据为基础来预测其三维空间结构。最新相关实验表明染色质的三维空间结构对于基因表达、调控等方面都具有重要意义。而Hi-c数据能利用染色质交互信息形成二维接触矩阵重构出染色体三维结构。本综述以染色体三维结构重建方法为研究对象,通过对染色体三维结构重建方法进行比较分析,综述了目前基于Hi-c数据在染色体三维结构重建中的经典方法,系统介绍了染色体三维结构重建技术的发展脉络,以促进染色体三维结构重建的进一步研究。     

Averaging data derived from images of helical structures with different symmetries.

There are many examples of macromolecules that form helical tubes or crystals, which are useful for structure determination by electron microscopy and image processing. Helical crystals can be thought of as two-dimensional crystals that have been rolled into a cylinder such that two lattice points are superimposed. In many real cases, helical crystals of a particular macromolecule derive from an identical two-dimensional lattice but have different lattice points superimposed, thus producing different helical symmetries which cannot be simply averaged in Fourier-space. When confronted with this situation, one can select images corresponding to one of the observed symmetries at the expense of reducing the number of images that can be used for data collection and averaging, or one can calculate separate density maps from each symmetry, then align and average them together in real-space. Here, we present a third alternative, which is based on averaging of the Fourier-Bessel coefficients, gn,l(r), and which allows the inclusion of data from all symmetry groups derived from a common two-dimensional lattice. The method is straightforward and simple in practice and is shown, through a specific example with real data, to give results comparable to real-space averaging.     

基于二维与三维信息的南京市主城区生态网络格局对比分析

生境破碎化导致生物多样性锐减,影响生境的生态系统服务,合理而有效的生态网络建设可以恢复城市内破碎生境斑块之间的连接。现有城市生态网络的构建与模拟多基于二维数据信息,未能很好地考虑植被三维结构信息所表征的多元生态位对生境质量的影响,致使生态网络的功能有效性有待验证。选取南京市主城区为研究区,基于高分辨率遥感影像与机载激光雷达数据,对研究区三维绿地植被结构进行了量化,在二维、三维两种情景下分别进行生态源地的提取与景观阻力面的设定,基于最小费用路径识别出两种情景下的生态廊道,并依据电路理论方法识别出廊道中需要重点保护的生态关键节点,进而分析使用二维、三维生态空间信息对生态网络构建结果产生的影响。研究结果表明:1)研究区不同情景下提取的生态源地共有11处不同,与传统二维情景下仅使用绿地面积指标作为斑块属性相比,使用三维植被参数可以更准确地识别具有丰富植被结构的生态源地;2)二维与三维情景下构建的生态廊道分别有137条与129条,平均每条廊道的单位距离阻力值分别为18.2与24.0,运用传统二维信息的模拟结果会在一定程度上高估研究区的景观连通性;3)不同情境下生态关键节点的空间分布基本一致,主要集中于研究区的西北侧、中部以及东南侧,并较多出现在距离较近的源地斑块之间。基于以上分析结果,有针对性地提出了南京市主城区生态网络格局优化的相关策略。     

The synthesis and storage of histones during the oogenesis of Xenopus laevis

Further data, including two-dimensional gel electrophoresis and peptide mapping of newly synthesized proteins, confirms the view that oocytes make several types of histone. The newly synthesized histone is present in both nucleus and cytoplasm, but at a higher concentration in the oocyte nucleus and in great excess over the DNA binding sites. The unfertilized egg seems to contain a pool of histones detectable on two-dimensional electrophoretograms. The peptide maps of these proteins are consistent with their identification as histones. The egg contains enough histone to support nuclear replication through most of cleavage.