DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns

Genetic isolation among populations can be effectively investigated by multilocus DNA fingerprinting. If populations have diverged, it is expected that the mean proportion of bands shared by individuals from the same population, Bw, exceeds the corresponding mean, Bb, calculated from pairs of individuals from distinct populations. A problem arises in deciding whether any difference between Bw and Bb is statistically significant. In fact, any two band-sharing data (bij), contributing to Bw or Bb, are not independent if they share a common individual (like bij and bjl). This prevents a correct application of parametric tests, such as the Student's t-test. Recently, a modification of this test has been proposed that should avoid the independence problem. Using a large number of samples of fingerprints, simulated from an appropriate 'genetic' model, under a wide range of conditions, we compared the performances of the Student's t-test, the modified t-test and five new permutation tests, where individuals, rather than bij values, are permuted. We found that: (i) the Student's t-test can be very permissive, rejecting too often the null hypothesis when true, but is correct or conservative in certain cases; (ii) the modified t-test is extremely conservative when the null hypothesis is true and very inefficient otherwise; (iii) all five permutation tests are strictly correct, provided that individuals are ordered randomly on gels; and (iv) in this case, the permutation tests are equally efficient, and are not inferior to the Student's t-test when the latter is approximately correct and provides a fair benchmark.     

Possible Specificity of Cellular Interactions Due to Electrostatic Forces

It is known that the cells from a mixed population in a culture medium will finally segregate. This “social behavior” of the cells is a direct consequence of both physical and chemical interactions between cells. The physical forces involved in cell-cell interactions are considered to be the electrostatic, van der Waals, and very-short-range hydration forces.

It has been believed until now that the electrostatic forces acting between identical cells were always repulsive and nonspecific. In the present work, we try to suggest that even the electrostatic forces could manifest a slightly specific character, so that a completely random Brownian motion of the cells could be influenced, corrected, and transformed into a “docking maneuver,” which could favor the specific interactions between cells suspended in a culture medium. The main point of our approach is that the peculiar patterns of electric charge distribution on the cell surfaces act like specific electrostatic fingerprints that could be responsible for the preferential interactions which precede cellular segregation (1).     

Evaluation of colilert-marine water for detection of total coliforms and Escherichia coli in the marine environment.

A test that allows for early detection of fecally contaminated coastal water would enhance public health protection. Colilert-Marine Water (Colilert-MW; Environetics, Branford, Conn.) is a rapid 24-h test that has recently been developed to detect total coliforms and Escherichia coli in coastal water. We performed a premarketing evaluation of the Colilert-MW product, testing it in parallel with the multiple tube fermentation (MTF) method for 86 coastal water samples in southern California. Statistical analysis was performed by using paired t tests and linear regression. Bacterial isolates were evaluated by biochemical and genetic analysis. The results of this study showed a strong correlation between the traditional MTF and the Colilert-MW method for detection of total coliforms (r = 0.95) and E. coli (r = 0.89) in ocean water samples. Paired t-test results indicated that the Colilert-MW and MTF were equivalent in detecting E. coli and that the Colilert-MW may be more sensitive in the detection of total coliforms. We conclude that Colilert-MW would be a useful tool with which to monitor coastal beach water.     

Can the Red-Green Duochrome Test Be Used Prior to Correcting the Refractive Cylinder Component?

Purpose

A primary task of the eye care professional is determining the refraction, or optical correction, of a patient. The duochrome red-green test is a standard tool for verification of the final refraction. Traditionally, it is recommended for use both prior to and subsequent to determining the cylindrical or astigmatic component of the refraction. In order for it to be effective when used before correcting the cylinder it is necessary that the COLC (Circle of Least Confusion) be on the retina. This study examined whether it is necessarily true that the duochrome response in uncorrected astigmatism will be as trust-worthy as it is with corrected cylinders.

Methods

The red-green examination was performed monocularly under the following three conditions: a. fully corrected refraction for the subgroup of eyes that had spherical refractions and for the subgroup of eyes with sphero-cylindrical refractions. b. best sphere-only correction without cylinder correction in sphero-cylindrical eyes c. an induced cylinder error in spherical eyes. The interval between the last “red” response and the first “green” response for the right eyes as a group and separately for the physiological cylinder and induced cylinder correction sub-groups was calculated and compared using a paired, two-tailed t-test.

Results

The intervals between “red” and “green” responses were not significantly different in the population as a whole and in the uncorrected physiological cylinder and induced cylinder subgroups examined.

Conclusion

Based on the finding that the interval of red-green equality with fully corrected cylinder and without the cylindrical correction are not significantly different, the red-green duochrome test can indeed be used both before and after cylindrical correction.     

Biases and Power for Groups Comparison on Subjective Health Measurements

Subjective health measurements are increasingly used in clinical research, particularly for patient groups comparisons. Two main types of analytical strategies can be used for such data: so-called classical test theory (CTT), relying on observed scores and models coming from Item Response Theory (IRT) relying on a response model relating the items responses to a latent parameter, often called latent trait. Whether IRT or CTT would be the most appropriate method to compare two independent groups of patients on a patient reported outcomes measurement remains unknown and was investigated using simulations. For CTT-based analyses, groups comparison was performed using t-test on the scores. For IRT-based analyses, several methods were compared, according to whether the Rasch model was considered with random effects or with fixed effects, and the group effect was included as a covariate or not. Individual latent traits values were estimated using either a deterministic method or by stochastic approaches. Latent traits were then compared with a t-test. Finally, a two-steps method was performed to compare the latent trait distributions, and a Wald test was performed to test the group effect in the Rasch model including group covariates. The only unbiased IRT-based method was the group covariate Wald’s test, performed on the random effects Rasch model. This model displayed the highest observed power, which was similar to the power using the score t-test. These results need to be extended to the case frequently encountered in practice where data are missing and possibly informative.     

梨小食心虫自然种群与室内继代饲养种群生物学特性比较

【目的】为明确梨小食心虫Grapholita molesta自然种群与室内继代饲养种群生物学特性的差异, 以期为梨小食心虫的人工饲养以及测报与防治提供理论依据。【方法】本研究对室内继代饲养的和从田间采集的梨小食心虫, 在室内同等条件下饲养, 较系统地观察两者的生物学特性并对其主要生命表参数进行了比较。【结果】在本试验条件下, 梨小食心虫室内继代饲养种群的蛹期极显著长于自然种群（t=-10.78, df=4, P=0.0004）; 卵期、 幼虫期以及预蛹期均稍长于自然种群, 但无显著差异。室内继代饲养种群的幼虫存活率、 化蛹率、 羽化率极显著高于自然种群（存活率： t=-7.61, df=4, P=0.0016; 化蛹率： t=-24.32, df=4, P=0.0017; 羽化率： t=-6.96, df=4, P=0.0022）; 两个种群的卵孵化率、 蛹重、 成虫寿命、 产卵前期、 产卵期及单雌产卵量均无显著差异。自然种群蛀果率高于室内继代饲养种群, 但差异不显著。生命表分析表明, 梨小食心虫室内继代饲养种群的种群趋势指数I、 净增殖率R₀、 内禀增长率r_m、 平均世代周期T、 周限增长率λ均极显著高于自然种群（I： t=-12.20, df=4, P=0.0003; R₀： t=-11.72, df=4, P=0.0003; r_m： t=-9.77, df=4, P=0.0006; T： t=-12.05, df=4, P=0.0003; λ： t=-9.79, df=4, P=0.0006）, 种群加倍时间Dt极显著低于自然种群（t=7.17, df=4, P=0.0020）。【结论】室内继代饲养种群在室内连续饲养50多代后, 与自然种群比较, 不仅各生命表参数和钻蛀危害果实的能力没有下降, 反而在与自然种群同等的室内饲养条件下, 表现了更好的适应性, 在本供试条件下, 后代具有更大的种群增长潜力。所以, 利用室内继代饲养种群进行的相关试验研究结果可以作为梨小食心虫预测预报与防治实践的依据。     

A comment on phylogenetic correction

Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifact due to phylogeny and there is an expectation that the corrected regression or correlation coefficients will usually be closer to zero. It is shown here that this is not an accurate way to interpret these methods. The effect of taking phylogeny into account is to reduce the variance of the estimated regression or correlation coefficients. Their means are not because since estimates of regression coefficients are unbiased whether or not the correct phylogeny is taken into account. Estimates of correlations are only slightly biased (and in the opposite direction that many expect).     

Ocular melanoma in a patient successfully treated for diffuse malignant peritoneal mesothelioma: a case report

Myoid hamartomas of the breast are extremely rare breast lesions, with a poorly understood pathogenesis. We describe the case of a 38-year-old premenopausal woman who presenting with a mass in the left breast. Mammography revealed an oval mass that was partly indistinct, and ultrasonography showed a hypoechoic mass with a slightly irregular margin. Bilateral breast dynamic magnetic resonance imaging was performed for a more detailed evaluation. The images showed rapid initial enhancement and a microlobulated margin. Because the suspicion of malignancy was strong at that time, core needle biopsy was performed. Histologically, the tumor was identified as fibroadenoma. A case of myoid hamartoma of the breast that proved difficult to diagnose is reported, and discussed with reference to the literature.     

Distribution of age at menopause in two Danish samples

We analyzed the distribution of reported age at natural menopause in two random samples of Danish women (n = 176 and n = 150) to determine the shape of the distribution and to disclose any possible trends in the distribution parameters. It was necessary to correct the frequencies of the reported ages for the effect of differing ages at reporting. The corrected distribution of age at menopause differs from the normal distribution in the same way in both samples. Both distributions could be described by a mixture of two normal distributions. It appears that most of the parameters of the normal distribution mixtures remain unchanged over a 50-year time lag. The position of the distribution, that is, the mean age at menopause, however, increases slightly but significantly.     

Contribution of protein and lipid components to the salt response of envelopes of an extremely halophilic bacterium

Kushner, D. J. (National Research Council, Ottawa, Ontario, Canada), and H. Onishi. Contribution of protein and lipid components to the salt response of envelopes of an extremely halophilic bacterium. J. Bacteriol. 91:653-660. 1966.-Removal of protein from envelopes of Halobacterium cutirubrum by peptic digestion left residues that required little or no salt for stability. The salt requirement of envelopes was also lowered by incubation in 0.1 m MgCl(2), and could be lowered even further by digestion with trypsin or chymotrypsin in 0.1 m MgCl(2). Dissolution of envelopes in low salt concentrations made their protein more susceptible to attack by these and other proteolytic enzymes. Removal of lipids raised the requirement for divalent cations, particularly for Mg(++); it slightly increased the Na(+) requirement and did not affect the requirement for K(+). It was concluded that the requirement for high salt concentrations in extreme halophiles is due to mutual repulsion between negatively charged groups on proteins rather than to repulsion between negatively charged phosphate groups on the lipids. The latter act primarily as sites on which divalent cations, especially Mg(++) which is required in high concentrations by growing cells, are bound. In this manner, the phosphate groups support envelope structure.     

Sex determination using the femur in an ancient Anatolian population

Determination of sex from the femur measurements has been attempted in several populations. Numerous studies have also demonstrated the importance of creating population specific standards in the metric assessment of sex. The present study attempts to establish metric standards for sex determination by using femur measurements for ancient Anatolian populations. Osteometric data were obtained from skeletal remains of 130 adults (67 males and 63 females) from the Dilkaya medieval collection. Eight femur measurements were taken and the data were analyzed using t-test and discriminant analysis with the help of Statistical Package for the Social Sciences (SPSS). The basic statistics showed that all measurements were sexually dimorphic. For the univariate discriminant function derived, precision of sex determination was 86.5 % with the condyle breadth. Our prediction values showed that sex differentiation can be done by femur measurements with reliability between 76 % and 88.5 %, with values for female slightly higher than for males. It is suggested that discriminant formulas developed by combinations of femur measurements in this study can be used for sex determination accurately on fragmentary skeletal remains in ancient Anatolian populations.     

Simultaneous determination of glucose, ethanol and lactate in alcoholic beverages and serum by amperometric flow injection analysis with immobilized enzyme reactors.

Glucose, ethanol and lactate were determined simultaneously in a flow injection system by using a parallel configuration of immobilized enzyme reactors. Hydrogen peroxide produced was monitored amperometrically at the potential of +0.65 V vs. Ag/AgCl. Linear relations between sensor responses and each species were observed in the ranges of 0.02-10 mM (glucose), 5 x 10(-4)-0.1% (v/v) (ethanol) and 0.005-1 mM (lactate) with correlation coefficients larger than 0.999 for each species. The relative standard deviations for 10 successive injections were 1.4, 0.5 and 1.1% for glucose (1 mM), ethanol (5 x 10(-3)% (v/v] and lactate (0.05 mM), respectively. Analysis of serum samples was performed with urate-eliminating reactors which were set just before each immobilized enzyme reactor. Interference of ascorbate in a serum sample was completely eliminated by using an ascorbate-eliminating reactor which was set before the sample injection valve. Application of the system to alcoholic beverages and control serum was described and the results were compared with those of free enzymatic, spectrophotometric analysis (F-kit or C-test method).     

Theoretical analysis of simultaneous mixed irradiation with multiple types of radiation.

A survival model Eq.1 was presented for cells irradiated simultaneously with multiple types of radiation using the extended Zaider-Rossi model, which is model for mixed irradiation with two types of radiation. [equation : see text] Eq.1. Where q(t)=2t0/t-2(t0/t)2 ?1-exp(-t0/t)? Eq.2. Eq.1 was proved by mathematical induction using the concept that mixed irradiation with n types of radiation is considered as mixed irradiation with two types of radiation regarding n-1 types as one type of radiation. The model is not limited by the dose rate of radiation, because its effect is corrected by reduction factor Eq.2. The problem of the model is that Eq.2 was led assuming repair function to be exponential given by Eq.3. tau(t)=exp(-t/t0) Eq.3. However, the repair function is usually expressed by biphasic Eq.4 rather than monophasic Eq.3. tau(t)=Aexp(-t/01)+(1-A)exp(-t/t02) Eq.4. It is, therefore, important to keep in mind that Eq. 4 should be used instead of Eq.3.     

Effect of inbreeding depression on outcrossing rates among populations of a tropical pine

Inbreeding depression is common among plants and may distort mating system estimates. Mating system studies traditionally ignore this effect, nonetheless an assessment of inbreeding depression that may have occurred before progeny evaluation could be necessary. In the neotropical Pinus chiapensis inbreeding depression was evaluated using regression analysis relating progeny F-values with seed germinability, the mating system was analysed in three populations with contrasting size, using isozymes, obtained a corrected outcrossing rate. Selfing decreased seed viability by 19%, relative to an outcrossed plant. Multilocus outcrossing rates, t(m), varied widely among populations. In the two smallest populations t(m) congruent with 1. Therefore, inbreeding depression did not affect the estimates, but overestimated t(m) by 10% in the third population, which has a true mixed mating system (selfing was the major source of inbreeding), and an unusually low t(m) for pines (t(m) = 0.54, uncorrected, t(m) = 0.49, corrected). Inbreeding depression may be an uneven source of bias for outcrossing estimates even at the infraspecific level. Accuracy [corrected] but not precision [corrected] may be gained by including inbreeding depression in outcrossing estimates. Therefore, caution should be taken when comparing t(m) among species or even populations within the same species.     

Size and shape determination of fixed chylomicrons and emulsions with fluid or solid surfaces by three-dimensional analysis of shadows

Chylomicrons and chylomicron-sized emulsions are spherical particles in suspension but their shape and apparent size may be distorted by electron microscopy processing. To assess adsorption to grids, flattening, and shrinkage, chylomicrons and emulsions were fixed with osmium tetroxide and together with polystyrene beads were shadowed with platinum. Vertical profiles projected from particle shadows indicated that the chylomicrons and emulsions were slightly shrunken, slightly truncated, oblate spheroids while the polystyrene beads were spheres. Particle diameters were corrected by assuming that volumes of oblate spheroids on the grid surface were equal to volumes of spheres in the original lipid suspension. Because of the compensating effects of shrinkage (decreases diameter) and flattening (increases diameter) the differences between the means of measured diameters and corrected diameters were less than or equal to 5%.     

逐级递增负荷踏车试验测定最大耗氧量和无氧阈的重复性

本文目的旨在研究在逐级递增负荷踏车试驻中测定最大耗氧量和无氧阈的重复性。21名运动员各完成三次重复性递增负荷踏车试验。通过与Apple Ⅱ_E计算机辅助联机的Jaeger EOS自动分析系统,根据通气和气体交换参数的变化,对无氧阈及最大耗氧量进行无创性测定。结果表明,采用递增负荷踏车试验测定最大耗氧量时,有必要对不熟悉试验程序的受试者进行重复测定以提高准确性,无创性测定无氧阈具有令人满意的重复性,多次重复测定将可提高无氧阈测定的准确性。     

Recovery of biological materials through ultrafiltration

Experiments were performed on a cellulose acetate ultrafiltration membrane (HF-200, ABCOR Inc., Cambridge, Mass.) to test its efficacy in concentrating and purifying a crude enzyme (trypsin) preparation. Studies were also made to determine the influence of inorganic salts, pressure, and temperature on the rate of ultrafiltration for this membrane. The results showed reductions in the rates will be encountered due to the presence of inorganic salts. However, the reduced rates were still sufficiently high to make this method extremely attractive. Operating at filtration pressures above 75 psi at, 20 to 30°C for this membrane does not show any beneficial effect in terms of ultrafiltration rates. However, at 10°C there were continual increases in the filtration rates up to 100 psi. Concentration and purification studies with trypsin yielded a concentration factor of 8.35 and a purification factor 2.35. It was shown concretely that the purification of the enzyme was due to the passage of low molecular weight proteins (below 20,000) through the membrane. Enzyme activity slightly greater than 90% was obtained: 70% was found in the concentrate and 20% in the filtrate. It is concluded that membrane ultrafiltration is an ideal simple, rapid, and economical method for the recovery of biological active substances.     

Developmental toxicity evaluation of 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) in Wistar rats

3-Chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) is a genotoxic chlorination by-product in drinking water. There is some evidence that it has developmental toxic effects in vitro but its potential to cause developmental effects in vivo is not known. The developmental effects were evaluated in Wistar rats. Rats (22-26 dams per dose group) were administered MX by gavage at the dose levels of 3, 30, or 60 mg/kg in water on gestation days 6-19. Control animals received plain water. Clinical signs, body weight, and food and water consumption were recorded for the dams. On gestation day 20, a cesarean section was performed and the ovaries anduterine contents of the dams were examined and the liver, kidneys, spleen, and thyroid glands weighed. The fetuses of all dose groups were weighed, sexed, and observed for external and skeletal malformations and the fetuses of the two highest dose groups were evaluated for visceral malformations. The highest dose, 60 mg/kg of MX, was slightly toxic to the dams. It decreased the corrected body weight gain of dams by 32% and the water consumption by 16-17%. Kidney and liver weights were slightly increased. MX did not affect the number of implantations nor did it cause any resorptions. The body weights of fetuses were not significantly affected. MX did not cause external malformations or skeletal anomalies. Two fetuses at 60 mg/kg and one fetus at 30 mg/kg had major visceral malformations (persistent truncus arteriosus, diaphragmatic hernia, dilated aorta with a stenosis of pulmonary arteries) and two minor artery abnormalities were observed in those animals. The frequency of unilateral displaced testis was slightly higher (9.2%) in the 60-mg/kg dose group than in controls (1.6%). Since the abnormalities did not form a consistent pattern and occurred most at maternally toxic dose, we conclude that MX can be regarded as non-teratogenic.     

Nitration of annexin II tetramer.

Annexin II tetramer (AII(t)) is a member of the Ca(2+)- and phospholipid-binding protein family and is implicated in membrane fusion during surfactant secretion. It had previously been shown that high concentrations of nitric oxide (NO) inhibit surfactant secretion from lung type II cells. NO reacts with superoxide (O(2)(-)) to form peroxynitrite (ONOO(-)), a tyrosine nitrating agent, which is found in lungs under certain pathological conditions. It is therefore hypothesized that nitration of AII(t) by ONOO(-) may be a mechanism for the NO inhibition of regulated exocytosis. We therefore performed in vitro studies to test effects of ONOO(-) on AII(t). Western blot analysis using anti-nitrotyrosine antibodies showed a dose-dependent nitration of tyrosine residues in AII(t) treated with ONOO(-). Nitration occurred on the core domain of the p36 subunit, as well as on the p11 subunit. ONOO(-) also caused the formation of dimers between p36 and p11 subunits which were stable in the presence of heating, SDS, and beta-mercaptoethanol. AII(t)-mediated liposome aggregation was inhibited by ONOO(-) with an IC(50) of approximately 30 microM. The inhibition was abolished by urate (a scavenger of ONOO(-) and *OH), but not by mannitol (a scavenger of *OH) or superoxide dismutase (a scavenger of O(2)(-)) and appeared to be specific to AII(t), since ONOO(-) only slightly influenced annexin I-mediated liposome aggregation. The conformational change of AII(t) induced by Ca(2+) had no effect on the inhibition. Furthermore, ONOO(-) only partially inhibited the binding of AII(t) to membranes. Nitration of AII(t) also occurred in intact A549 cells, a lung epithelial cell line, treated with ONOO(-). The results of this study suggest that AII(t)-mediated liposome aggregation was inhibited by nitration of the protein.     

Linkage and the Maintenance of Heritable Variation by Mutation-Selection Balance

The role of linkage in influencing heritable variation maintained through a balance between mutation and stabilizing selection is investigated for two different models. In both cases one trait is considered and the interactions within and between loci are assumed to be additive. Contrary to most earlier investigations of this problem no a priori assumptions on the distribution of genotypic values are imposed. For a deterministic two-locus two-allele model with recombination and mutation, related to the symmetric viability model, a complete nonlinear analysis is performed. It is shown that, depending on the recombination rate, multiple stable equilibria may coexist. The equilibrium genetic and genic variances are calculated. For a polygenic trait in a finite population with a possible continuum of allelic effects a simulation study is performed. In both models the equilibrium genetic and genic variances are roughly equal to the house-of-cards prediction or its finite population counterpart as long as the recombination rate is not extremely low. However, negative linkage disequilibrium builds up. If the loci are very closely linked the equilibrium additive genetic variance is slightly lower than the house-of-cards prediction, but the genic variance is much higher. Depending on whether the parameters are in favor of the house-of-cards or the Gaussian approximation, different behavior of the genetic system occurs with respect to linkage.