A reliable method for assessing topographical arrangement of proteins in the chromaffin granule membrane

An efficient and reliable method for preparing chromaffin granules and membranes for topographical analysis has been designed to meet the following criteria. Only labeling of truly intact organelles is analyzed for cytoplasmic surface probes. No. resealing of open membranes occurs under specified reaction conditions. Saturation of available sites must be demonstrated. Problems in meeting these conditions are discussed, in particular the interference of granule lysate with labeling reactions.This work was supported by a grant from the National Institutes of Health, NS-13201.     

A method for quantifying rotational symmetry

Here, a new approach for quantifying rotational symmetry based on vector analysis was described and compared with information obtained from a geometric morphometric analysis and a technique based on distance alone. A new method was developed that generates a polygon from the length and angle data of a structure and then quantifies the minimum change necessary to convert that polygon into a regular polygon. This technique yielded an asymmetry score (s) that can range from 0 (perfect symmetry) to 1 (complete asymmetry). Using digital images of Geranium robertianum flowers, this new method was compared with a technique based on lengths alone and with established geometric morphometric methods used to quantify shape variation. Asymmetry scores (s) more clearly described variation in symmetry and were more consistent with a visual assessment of the images than either comparative technique. This procedure is the first to quantify the asymmetry of radial structures accurately, uses easily obtainable measures to calculate the asymmetry score and allows comparisons among individuals and species, even when the comparisons involve structures with different patterns of symmetry. This technique enables the rigorous analysis of polysymmetric structures and provides a foundation for a better understanding of symmetry in nature.     

A reliable method for storage of tailed phages

A universal and effective method for long-term storage of bacteriophages has not yet been described. We show that randomly selected tailed phages could be stored inside the infected cells at −80 °C without a major loss of phage and host viability. Our results suggest the suitability of this method as a standard for phage preservation.     

A simple and reliable multi-gene transformation method for switchgrass

Key Message

A simple and reliable Agrobacterium -mediated transformation method was developed for switchgrass. Using this method, many transgenic plants carrying multiple genes-of-interest could be produced without untransformed escape.

Abstract

Switchgrass (Panicum virgatum L.) is a promising biomass crop for bioenergy. To obtain transgenic switchgrass plants carrying a multi-gene trait in a simple manner, an Agrobacterium-mediated transformation method was established by constructing a Gateway-based binary vector, optimizing transformation conditions and developing a novel selection method. A MultiRound Gateway-compatible destination binary vector carrying the bar selectable marker gene, pHKGB110, was constructed to introduce multiple genes of interest in a single transformation. Two reporter gene expression cassettes, GUSPlus and gfp, were constructed independently on two entry vectors and then introduced into a single T-DNA region of pHKGB110 via sequential LR reactions. Agrobacterium tumefaciens EHA101 carrying the resultant binary vector pHKGB112 and caryopsis-derived compact embryogenic calli were used for transformation experiments. Prolonged cocultivation for 7 days followed by cultivation on media containing meropenem improved transformation efficiency without overgrowth of Agrobacterium, which was, however, not inhibited by cefotaxime or Timentin. In addition, untransformed escape shoots were completely eliminated during the rooting stage by direct dipping the putatively transformed shoots into the herbicide Basta solution for a few seconds, designated as the ‘herbicide dipping method’. It was also demonstrated that more than 90 % of the bar-positive transformants carried both reporters delivered from pHKGB112. This simple and reliable transformation method, which incorporates a new selection technique and the use of a MultiRound Gateway-based binary vector, would be suitable for producing a large number of transgenic lines carrying multiple genes.     

湖泊生态系统健康定量评价方法

提出了湖泊生态系统健康定量评价的一种新方法生态系统健康指数法。该方法首先设计了一个0～100的生态系统健康指数作为定量尺度,然后通过评价指标选择、各指标生态系统健康分指数计算、各指标权重计算、生态系统健康综合指数计算等基本步骤,评价湖泊生态系统健康状态。以实用实例对意大利西西里湖泊群及单个湖泊进行了生态系统健康评价。结果表明,该方法原理简单,计算简便,结果可靠、直观,既可用于同一湖泊又可用于不同湖泊生态系统健康状态的定量评价与比较,是一种值得推广的定量评价方法。     

A reliable method for demonstrating axonal degeneration shortly after axotomy

A method has been elaborated by which degenerating axons can be selectively impregnated with silver. Based on reconsideration of the physicochemical mechanisms of the degeneration methods it takes advantage of physical developers over the chemical ones. The staining procedure is applied to frozen sections of brains fixed with formol. It consists of 6 steps: (1) pretreatment with alkaline hydroxylamine, (2) washing in acetic acid, (3) impregnation in silver nitrate in the presence of ferric ions, (4) washing in citric acid, (5) physical development, and (6) washing in acetic acid. By electron microscopy silver precipitates by this method are almost entirely restricted to the cytoplasm of dense, degenerating axons, sparing mitochondria and myelin sheaths. No special expertise is required to achieve reproducible results. Large numbers of sections treated simultaneously, and large sections, can be stained uniformly. Light microscopic criteria are described which help diagnose the source of possible failures. Low background staining allows dark field illumination and television image analysis to be applied. The method works at survival times of only 3 to 5 days after axotomy. Hence, degenerating axons and axon terminals can be stained in alternating sections from the same brain using this method and another being described separately, which, using different conditions, demonstrates degenerating axon terminals.     

A fast top-down method for constructing reliable radiation hybrid frameworks

MOTIVATION: Radiation Hybrid Mapping (RHM) is a technique used to order a set of markers on a genome and estimating physical distances between them. RHM provides information on marker placement independent from other methods such as sequencing, and can therefore be used for example in genome sequencing to help ordering contigs. A radiation hybrid framework can be constructed by choosing a set of markers so that the chromosome coverage is good and so that the markers can be ordered with high confidence. Automatically constructing RHM frameworks is a computationally challenging problem. RESULTS: We have developed a new method for constructing radiation hybrid frameworks. Given a relatively large set of markers for a chromosome, the algorithm aims to select an ordered subset that makes up a framework, and that contains as many markers as possible. The algorithm has a time complexity that is better than any of the existing methods that we are aware of. Furthermore, we propose a method for comparing if two frameworks are consistent, giving a visual presentation as well as quantitative measures of how well the two frameworks agree. Applying our method on marker sets from 22 human chromosomes and comparing the resulting frameworks with previously published frameworks, we demonstrate that our automatic method efficiently constructs frameworks with good coverage of each chromosome and with high degree of agreement on the marker ordering.     

A reliable method to concentrate circulating DNA

Concentration of circulating DNA probes is required to increase the amount of DNA involved in subsequent study (by polymerase chain reaction, sequencing, and microarray). This work was dedicated to the comparison of five different methods used for concentration of DNA circulating in blood. Precipitation of circulating DNA with acetone in the presence of triethylamine provides minimal DNA loss, high reproducibility, and at least three times higher DNA yield in comparison with the standard ethanol protocol.     

蛋白质二级结构预测方法的评价

目前评价蛋白质二级结构预测方法主要考虑预测准确率,并没有充分考虑方法自身参数对方法的影响。本文提出一种新型评价方法,将内在评价与外在评价相结合评价预测方法的优劣。以基于混合并行遗传算法的蛋白质二级结构预测方法为例,通过内在评价,合理选取内在参数——切片长度和组内类别数,有效提高预测准确率,同时,通过外在评价,与其他基于随机算法的蛋白质二级结构预测算法比较和与CASP所提供的结论比较,说明了方法的有效性与正确性,以此验证内在评价和外在评价的客观性、公正性和全面性。     

A reliable method for extraction of RNA from various conifer tissues

Summary A simple and efficient procedure suitable for extraction of high-quality RNA from cultured conifer tissues, somatic embryos, zygotic embryos, needles, stem and root tissues was developed. It produced from 100 g up to 700 g total RNA per gram tissue dependent on the types of tissues used. RNA quality was estimated by spectrophotometry, agarose gel electrophoresis, in vitro translation of mRNA, cDNA synthesis and Northern blot analysis. The method also worked well with Arabidopsis thaliana and tobacco tissues.Abbreviations CTAB cetyltrimethylammonium bromide - DEPC diethylpyrocarbonate - PVP polyvinylpyrrolidone - SDS-PAGE sodium dodecyl sulphate-polyacrylamide gel electrophoresis     

A fast and reliable computational method for estimating population genetic parameters

The estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination.