A simple method for estimating cytoplasmic diffusion coefficients

The diffusion coefficients of radioactively labelled substances in cytoplasm or other fluids are determined in vitro. The fluid containing the labelled substance is filled into a cylinder with one open end, through which the labelled substance diffuses out into a stirred outer medium. The diffusion coefficient is calculated by a one-dimensional diffusion equation from the rate of loss from the cylinder, and the length of the cylinder. The diffusion coefficients of tritiated water in several fluids have been determined. The results are in good agreement with those obtained by other methods.     

A simple method for estimating intactness of spinach leaf protoplasts by glycolate oxidase assay

A method was developed for the quantitative analysis of intactness of spinach leaf protoplasts using glycolate oxidase activity as an index. Since glycolate does not penetrate into protoplasts at neutral pH, the increase of O₂ consumption by the addition of glycolate to protoplast suspension was due to the glycolate oxidase activity released from damaged protoplasts. The proportion of damaged protoplasts in the whole preparation was calculated from the ratio of released and total glycolate oxidase activity. Freshly prepared spinach leaf protoplasts were found to be 80 to 90% intact as estimated by the method. The effect of osmolarity on the respiratory activities of spinach leaf protoplasts was also examined by applying the same principle.     

A simple method for estimating homotoneity of sets of phytosociological relevés

The homogeneity of sets of phytosociological relevés or syntaxa—the homotoneity—is tested by means of a homotoneity-coefficient. This coefficient consists of the basic homotoneity-coefficient expressing the proportion of highly constant species (61–100%) in the species composition of the average relevé and the correcting factor which is proportional to the difference of species number between the richest and poorest relevé. Successive analysis of heterotoneity of sets of relevés for detecting sources of heterotoneity is proposed.     

A simple method for estimating the parameter of substitution rate variation among sites

When the rate variation among sites is described by a gamma distribution, an important problem is how to estimate the shape parameter alpha, which is an index of the degree of among-site rate variation. The parsimony-based methods for estimating alpha are simple but biased, i.e., alpha tends to be overestimated. On the other hand, the likelihood-based methods are asymptotically unbiased but take a huge amount of computational time. In this paper, we have developed a new method to solve this problem: we first estimate the expected number of substitutions at each site, which is corrected for multiple hits, and then estimate the parameter alpha. Our method is computationally as fast as the parsimony method, and the estimation accuracy is much higher than that of parsimony and similar to that of the likelihood method.      

A simple in situ method for estimating fungal population size in the rumen

Sediment and the overlying water samples were collected from 67 fresh and 38 salt water sites in the UK. Only 13% (five) of the samples taken from salt water sites were negative for magnetotactic bacteria compared with 47·7% (32) of the fresh water ones. Of the seven types of salt water habitats examined, saltmarsh ponds were found to be most suited to magnetotactic bacteria, 96% (25/26) of sites being positive.     

A simple method for detecting steroid aggregation and estimating solubility in aqueous solutions

Steroids are generally sparingly soluble in water. Thus, for in vitro studies of steroid metabolism or enzymology it is common practice to solubilize steroids by the addition of a small amount (2–10%, v/v) of an organic cosolvent. Methanol, ethanol, and 1,2-propanediol, singly or in combination, have been widely used (1). Effects of organic solvents on the kinetic parameters, K_m and V_max, of steroid-metabolizing enzymes with various substrates have been demonstrated (2,3), and the results are consistent with the conclusion that organic solvent influences on catalytic activity reflect, in part, effects on the aggregation state and solubility of steroid substrates.Light-scattering measurements have been applied extensively in studies of macromolecular structure (4) and micelle formation by a large variety of amphiphilic substances [reviewed in Ref. (5)]. Jones and Gordon (6) used a commercial instrument, designed specifically for light-scattering measurements, to characterize micelle formation in aqueous solutions by Δ5-3-ketosteroids containing various substituents at the 17β position. They showed that turbidity versus concentration plots were of the form seen in studies of micelle formation (5) and that steroids can exist in solution in monomeric or micellar forms, their aggregation state being a function of the polarity of the steroid solute and the composition of the solvent.To estimate solubility quantitatively ³H- or ¹⁴C-labeled steroids have been used in conjunction with centrifugation (3), dialysis (7), or filtration (8). These techniques allow for accurate estimates of solubility, but one may encounter problems due to nonspecific absorption on membranes or the unavailability of the labeled steroid of interest.We have observed that steroid aggregation and solubility can be estimated easily and with high sensitivity with a commercially available fluorometer. In this report the method is described and examples demonstrating the reproducibility and sensitivity of the technique are presented.     

A simple method for estimating the intensity of purifying selection in protein-coding genes.

We propose a method by which the intensity of purifying selection on a functional protein-coding gene is estimated by using three aligned homologous sequences: a processed pseudogene (psi), a functional paralog from the same species (g), and a functional ortholog from a different species (o). For each such trio, we calculate the numbers of nucleotide substitutions along the branches leading to psi and g, i.e., K psi and K(g). If we assume that the mutation rates are the same in the genes and the pseudogenes and that mutations occurring in a pseudogene do not affect the fitness of the organism, we can show that the fraction of mutations that are selectively neutral, fg, is equal to the ratio K(g)/K psi. Since advantageous mutations occur only very rarely, such that they do not contribute significantly to the rate of molecular evolution, the fraction of deleterious mutations that are subject to purifying selection is 1-fg. Therefore, the K(g)/K psi ratio can be used directly to estimate the intensity of purifying selection, thereby isolating its effects on the rate of evolution from those of mutation. We compared the selection intensities of 12 orthologous protein-coding pairs from humans and murids. As expected, the fraction of mutations that are subject to purifying selection is strongest in the second codon position and weakest in the third. Interestingly, the mean fractions of effectively neutral mutations in the third codon position were only 41% and 42% for murids and humans, respectively, indicating that many synonymous mutations are subject to selective constraint. In several orthologous genes, we found that the intensity of purifying selection is very different between murid and human orthologous genes. There was no statistically significant difference in overall intensity of purifying selection between humans and murids. Thus, purifying selection does not seem to be an important factor contributing to the observed differences in the rates of evolution between these two taxa.     

A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides

Volume, 63, no. 4, p. 1627-1630. After publication of this article, it was brought to the attention of the authors that an earlier paper, similar in both methodology and salient findings to ours, was published by Y. P. Hsieh and C. H. Yang. Both papers describe a diffusion method for the extraction and recovery of reduced inorganic sulfides from sediment samples placed in sealed reaction vessels. Our paper describes the application of the method to the measurement of sulfate reduction rates. The earlier work contains important information, but unfortunately, the existence of the work was realized only after publication of our paper. We regret this omission, and the following reference should have been cited in our article. 13a.Hsieh, Y. P., and C. H. Yang. 1989. Diffusion methods for the determination of reduced inorganic sulfur species in sediments. Limnol. Oceanogr. 34: 1126-1130. [This corrects the article on p. 1627 in vol. 63.].     

A simple method of estimating the stress acting on a bilaterally symmetric abdominal aortic aneurysm

We extended a method of estimating the stress acting on an axisymmetric abdominal aortic aneurysm (AAA) under a load in vivo (Elger, D. F., Blackketter, D. M., Budwig, R. S., Johansen, K. H. (1996) The influence of shape on the stresses in model abdominal aortic aneurysms, Journal of Biomechanical Engineering, 118, pp. 326-32.) to bilaterally-symmetric AAAs, which are symmetric about the sagittal plane. Stresses were calculated along the anterior and posterior median lines of the AAA wall. Of the two force equilibrium equations, the Laplace equation held in this study. The longitudinal equilibrium was extended to hold by approximating the meridional tension and the directional cosine of the wall surface as constants along the circumference. The estimated stresses were compared with the results of a finite element analysis. Comparisons showed that the maximal principal stress, usually the circumferential stress or sometimes the meridional stress depending on location, sufficiently represented the wall stress. The proposed method provides a reasonable index for evaluating the rupture risk using the peak value of the maximal principal stress and its location without using the stress-free geometry and constitutive equation.     

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2′deoxycytidine (DAC), where we found a 1–16% decrease in Alu element and 18–60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.     

A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences

Predicting functional amino acid residues in silico is important for comparative genomics. In this paper, we focus on the issue of how to statistically identify cluster-specific amino acid residues that are related to the functional divergence after gene duplication. We approach this problem using a framework based on site-specific shift of amino acid property (type-II functional divergence), as opposed to site-specific shift of evolutionary rate (type-I functional divergence). An efficient statistical procedure is implemented to facilitate the development of phylogenomic database for cluster-specific residues of large-scale protein families. Our method has the following features: 1) statistical testing of the type-II functional divergence and 2) the site-specific Bayesian profile to measure how amino acid residues contribute to type-II (cluster-specific) functional divergence. Consequently, one may obtain the posterior probability for "functional" cluster-specific residues. Case studies are presented and indicate that radical cluster-specific residues are responsible for most of inferred type-II functional divergence, whereas conserved cluster-specific residues appear less than even those imperfect radical cluster-specific residues to this type of functional divergence.