On the concept of the effective population size

The concept of the effective population size is discussed. It is shown that the “eigenvalue” and the “inbreeding” effective population sizes are in principle different, even though they have been sometimes identified in the literature. On the other hand the “eigenvalue” and “variance” effective sizes are usually both close when the latter exists. Since, however, there are many models for which a variance effective size cannot in principle exist, it seems useful to introduce the eigenvalue effective size and to examine some of its properties.     

Gene genealogies when the sample size exceeds the effective size of the population

We study the properties of gene genealogies for large samples using a continuous approximation introduced by R. A. Fisher. We show that the major effect of large sample size, relative to the effective size of the population, is to increase the proportion of polymorphisms at which the mutant type is found in a single copy in the sample. We derive analytical expressions for the expected number of these singleton polymorphisms and for the total number of polymorphic, or segregating, sites that are valid even when the sample size is much greater than the effective size of the population. We use simulations to assess the accuracy of these predictions and to investigate other aspects of large-sample genealogies. Lastly, we apply our results to some data from Pacific oysters sampled from British Columbia. This illustrates that, when large samples are available, it is possible to estimate the mutation rate and the effective population size separately, in contrast to the case of small samples in which only the product of the mutation rate and the effective population size can be estimated.     

On the concept of effective number.

A generalized conceptual basis for Wright's notion of effective size is presented. The concept is applied to the calculation of effective numbers based on the rate of change of genetic variability. With particular reference to the inbreeding, the eigen value, and the newly introduced "diversity" effective size, the use of the concept as a means for discrimination between and identification of various effective sizes is demonstrated.     

Determination of the plasma effective charge from the soft X-ray spectrum and plasma conductivity at the L-2M stellarator after boronization of the vacuum chamber

Boronization of the vacuum chamber wall results in a considerable change in the composition of the plasma generated in working pulses of the L-2M stellarator and, accordingly, in the plasma effective charge. The paper presents results of measurements of the plasma effective charge carried out by two methods in the ohmic heating mode: from the data on the plasma conductivity and from the soft X-ray spectrum of plasma emission. Comparison of the values of the plasma effective charge obtained by these two methods makes it possible to determine the conditions in which the two values are in good agreement. Under these conditions, the plasma effective charge can be correctly estimated from spectral measurements.     

On the Potential for Estimating the Effective Number of Breeders from Heterozygote-Excess in Progeny

The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn from an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need to be explored.     

Plasmid delivery in the rat brain

Neurodegenerative diseases as a class do not have effective pharmacotherapies. This is due in part to a poor understanding of the pathologies of the disease processes, and the lack of effective medications. Gene delivery is an attractive possibility for treating these diseases. For the paradigm to be effective, efficient, safe and versatile vectors are required. In this study we evaluated three plasmid delivery systems for transgene expression in the rat hippocampus. Two of these systems were designed to have enhanced intracellular biodegradability. It was hypothesized that this system would be less toxic and could increase the free (non-vector) associated plasmids within the cell, leading to increased transgene activity. Polyethylenimine (PEI) and r-AAV-2 (recombinant adeno associated virus-2) were used as positive, non-viral and viral controls respectively, in the in vivo experiments. The results from the studies indicate there is a distinct difference between the various vectors in terms of total cells transfected, type of cell transfected, and toxicity. Non-viral systems were effective at transfecting both neurons and glia cells within the hippocampus, while the r-AAV-2 transfected mainly neurons. In summary, plasmid-mediated systems are effective for transgene expression within the brain and deserve further study.     

Analysis of the structure of the components of the convulsive action of corazole following administration of sulazepam and its metabolites to mice]

A study was made of the interrelationship between the minimal effective doses of pseudoclonic and clonico-tonic convulsions, and also tonic extension caused by the intravenous injection of corazol to mice and the effect of anticonvulsive action of sulazepam and its metabolites (diazepam, desmethyldiazepam and oxadiazepam) on this process. It was shown that all the compounds under study increased the values of the minimal effective doses by the recorded indices of the convulsive seizure, whereas the maximum of the anticonvulsive activity was reached 15 minutes after the sulazepam and oxazepam, and 5 to 30 min after diazepam administration. There proved to be a distinct correlation between the minimal effective doses values of the recorded indices of the confulsive seizure in the control animals which also persisted after the administration of the agents under study. It is supposed that sulazepam and its metabolites increased the minimal effective doses of corazol for the recorded effects, but failed to alter the general picture of the convulsive attack and did not influence the dispersion corazol dose-effect dependence.     

Relation between the electron and information factors and the radioprotective effectiveness of sulfur-containing compounds

There is a simple relationship between the radioprotective effectiveness of sulfur-containing preparations and chemical structure of the compounds. It is established that the administration of the protector to the organism is just as effective as introduction of certain portion of information which should exceed some threshold for the effective radioprotectors.     

棉铃虫羽化高峰期有效积温预测法的校正

为减小年际间气温变化对昆虫有效积温预测误差的影响,以新疆石河子垦区121团棉铃虫Helicoverpa armigera(Hübner)羽化高峰期为例,利用single sine模型分别计算12年2种有效积温范围(10～30℃和10～35℃)的累计有效积温值,并获得其多年平均值,依此进行棉铃虫羽化高峰期预测;通过当年与12年(有效积温>0日期至羽化高峰日期)平均气温之差,对预测误差进行校正。结果表明:当年平均气温与12年平均值差值越大,预测误差也越大;各代直线回归校正模型均达到显著水平(P<0.05);2种有效积温范围下,校正后各代平均预测误差天数均有所减少,对越冬代误差校正效果最优,校正后各代历史符合率分别为83.33%、100%、100%和100%、100%、93.33%。该校正方法能够显著提高预测准确度,尤其适用于年际间棉铃虫发育期间平均气温变化较大的代别和地区,同时可为多种害虫预测误差校正提供了依据。     

Characterization of the solubilization of lipid bilayers by surfactants

This communication addresses the state of aggregation of lipid-detergent mixed dispersions. Analysis of recently published data suggest that for any given detergent-lipid mixture the most important factor in determining the type of aggregates (mixed vesicles or mixed micelles) and the size of the aggregate is the detergent to lipid molar ratio in these aggregates, herein denoted the effective ratio, Re. For mixed bilayers this effective ratio has been previously shown to be a function of the lipid and detergent concentrations and of an equilibrium partition coefficient, K, which describes the distribution of the detergent between the bilayers and the aqueous phase. We show that, similar to mixed bilayers, the size of mixed micelles is also a function of the effective ratio, but for these dispersions the distribution of detergent between the mixed micelles and the aqueous medium obeys a much higher partition coefficient. In practical terms, the detergent concentration in the mixed micelles is equal to the difference between the total detergent concentration and the critical micelle concentration (cmc). Thus, the effective ratio is equal to this difference divided by the lipid concentration. Transformation of mixed bilayers to mixed micelles, commonly denoted solubilization, occurs when the surfactant to lipid effective ratio reaches a critical value. Experimental evaluation of this critical ratio can be based on the linear dependence of detergent concentration, required for solubilization, on the lipid concentration. According to the 'equilibrium partition model', the dependence of the 'solubilizing detergent concentration' on the lipid concentration intersects with the lipid axis at -1/K, while the slope of this dependence is the critical effective ratio. On the other hand, assuming that when solubilization occurs the detergent concentration in the aqueous phase is approximately equal to the critical micelle concentration, implies that the above dependence intersects with the detergent axis at the critical micelle concentration, while its slope, again, is equal to the critical effective ratio. Analysis of existing data suggests that within experimental error both these distinctively different approaches are valid, indicating that the critical effective ratio at which solubilization occurs is approximately equal to the product of the critical micelle concentration and the distribution coefficient K. Since the nature of detergent affects K and the critical micelle concentration in opposite directions, the critical ('solubilizing') effective ratio depends upon the nature of detergent less than any of these two factors.     

The Effect of Spatial Inhomogeneity of the Cornea on the Deformation Properties of the Eyeball and the Results of Maklakoff Applanation Tonometry

A two-component model of the eyeball that represents the cornea as a momentless, linearly elastic deformable surface and the scleral region, as an elastic element that responds to intraocular pressure changes by volume changes, has been used to analyze the effect of spatial inhomogeneity in the distribution of effective corneal stiffness on the mechanical properties of the eye. The effective stiffness of the cornea characterized both the elastic properties and the thickness of the cornea within the framework of the model. Various axisymmetric forms of the effective stiffness distribution characterized by monotonic increase along the arc between a point on the corneal surface and the apex of the cornea were studied. The considered distributions simulated both natural inhomogeneity and apical region weakening due to surgical interventions. Numerical simulation yielded the dependences of deformation parameters on intraocular pressure changes. These parameters characterized the deformation properties of both the cornea (apex displacement) and the eyeball as a whole (intraocular volume change). In the case of moderate inhomogeneity, the dependences were only slightly different from those for a homogeneous cornea with an effective stiffness equal to the mean value for the corresponding inhomogeneous distribution. A noticeable increase in the integral response of the cornea and the eyeball as a whole to changes in pressure was observed if the effective stiffness amplitude was very high (two or more times higher than the mean value). The effect of inhomogeneity on the results of tonometric measurements with a Maklakoff tonometer (flat stamp) was studied. The tonometric difference, that is, the difference between the tonometric pressure (in the loaded eye) and the true pressure (before loading), mainly depended on the average stiffness of the cornea in this case as well, with a substantial increase observed at very high stiffness amplitudes only. Apical weakening of the cornea led to an increase (although not very pronounced) of the tonometric difference.     

Experiments on the effects of hyperbaric oxygen on flap survival in the pig

The use of hyperbaric oxygen has been advocated as a method of improving survival of ischemic flaps. Experiments were done in the pig using modern flap designs and hyperbaric oxygen protocols that have been reported to be effective in rodents. The results of these experiments indicate that hyperbaric oxygen is not effective in improving flap survival in the pig.     

DNA replication in the malaria parasite

Malaria is increasing as a global problem. Many of the drugs that were effective earlier in this century are now becoming obsolete as the parasite develops resistance to them and, despite earlier hopes, an affordable and effective vaccine remains elusive. It is hoped that a deeper understanding of the parasite's cell and molecular biology will give us a resource for the future and help us to achieve effective control. One aspect of parasite metabolism that has been the subject of recent studies is DNA replication: its timing during parasite development, the enzymes involved and the genes encoding them. In this review John White and Brian Kilbey report on the present status of these studies.     

Estimating effective paternity number in social insects and the effective number of alleles in a population

Estimating paternity and genetic relatedness is central to many empirical and theoretical studies of social insects. The two important measures of a queen's mating number are her actual number of mates and her effective number of mates. Estimating the effective number of mates is mathematically identical to the problem of estimating the effective number of alleles in population genetics, a common measure of genetic variability introduced by Kimura & Crow (1964). We derive a new bias-corrected estimator of effective number of types (mates or alleles) and compare this new method to previous methods for estimating true and effective numbers of types using Monte Carlo simulations. Our simulation results suggest that the examined estimators of the true number of types have very similar statistical properties, whereas the estimators of effective number of types have quite different statistical properties. Moreover, our new proposed estimator of effective number of types is approximately unbiased, and has considerably lower variance than the original estimator. Our new method will help researchers more accurately estimate intracolony genetic relatedness of social insects, which is an important measure in understanding their ecology and social behaviour. It should also be of use in population genetic studies in which the effective number of alleles is of interest.     

Effective competition determines the global stability of model ecosystems

We investigate the stability of Lotka-Volterra (LV) models constituted by two groups of species such as plants and animals in terms of the intragroup effective competition matrix, which allows separating the equilibrium equations of the two groups. In matrix analysis, the effective competition matrix represents the Schur complement of the species interaction matrix. It has been previously shown that the main eigenvalue of this effective competition matrix strongly influences the structural stability of the model ecosystem. Here, we show that the spectral properties of the effective competition matrix also strongly influence the dynamical stability of the model ecosystem. In particular, a necessary condition for diagonal stability of the full system, which guarantees global stability, is that the effective competition matrix is diagonally stable, which means that intergroup interactions must be weaker than intra-group competition in appropriate units. For mutualistic or competitive interactions, diagonal stability of the effective competition is a sufficient condition for global stability if the inter-group interactions are suitably correlated, in the sense that the biomass that each species provides to (removes from) the other group must be proportional to the biomass that it receives from (is removed by) it. For a non-LV mutualistic system with saturating interactions, we show that the diagonal stability of the corresponding LV system close to the fixed point is a sufficient condition for global stability.     

Transfer entropy—a model-free measure of effective connectivity for the neurosciences

Understanding causal relationships, or effective connectivity, between parts of the brain is of utmost importance because a large part of the brain’s activity is thought to be internally generated and, hence, quantifying stimulus response relationships alone does not fully describe brain dynamics. Past efforts to determine effective connectivity mostly relied on model based approaches such as Granger causality or dynamic causal modeling. Transfer entropy (TE) is an alternative measure of effective connectivity based on information theory. TE does not require a model of the interaction and is inherently non-linear. We investigated the applicability of TE as a metric in a test for effective connectivity to electrophysiological data based on simulations and magnetoencephalography (MEG) recordings in a simple motor task. In particular, we demonstrate that TE improved the detectability of effective connectivity for non-linear interactions, and for sensor level MEG signals where linear methods are hampered by signal-cross-talk due to volume conduction.     

Effects of harvesting method and growth stage on the flocculation of the green alga Botryococcus braunii

Flocculating activity was determined to evaluate the effective harvesting method and an optimal growth stage for the recovery of the green alga Botryococcus braunii growing in batch cultures. Flocculating activity was highest at 2 weeks of incubation, regardless of harvesting methods. The degree of flocculation was different with harvesting methods and growth stages. A high pH value (pH 11) was more effective for flocculation than treatment with aluminium sulphate or a microbial flocculant, Pestan, until the third week of incubation. The lipid content of the algae on a dry weight basis was unaffected by harvesting methods. These results indicate that the most effective harvesting method is to adjust pH to 11 after 2 weeks of incubation.     

In vitro evaluation of the effects of some plant essential oils on Ascosphaera apis,the causative agent of Chalkbrood disease

Ascosphaera apis is one of the major fungal pathogens of honey bee broods and the causative agent of Chalkbrood disease. The factors responsible for the pathogenesis of Chalkbrood disease are still not fully understood, and the increasing resistance of A. apis to commonly used antifungal agents necessitates a search for new agents to control this disease. The in vitro antifungal activities of 27 plant essential oils against two isolates of A. apis (Aksu-4 and Aksu-9) were evaluated. Out of the 27 plant essential oils tested, 21 were found to be effective in killing both isolates of A. apis. Based on their minimum fungicidal concentration (MFC) values, the effective oils were grouped into three categories: highly effective, moderately effective and minimally effective. Mountain pepper oil, Kala Bhangra oil, spearmint oil, babuna oil, betel leaf oil, carrot seed oil, cumin seed oil and clove bud oil were highly effective, with MBC values between 50.0 μg/mL and 600.0 μg/mL. Mountain pepper was the most effective essential oil, with an MBC value of 50.0 μg/mL. Citral and caryophyllene containing oils were the most effective with MIC 50 ppm. The essential oils tested exhibited significant antimicrobial activities against both strains of A. apis, and they may contain compounds that could play an important role in the treatment or prevention of Chalkbrood disease of honeybee.     

Field experiments on the control of sheep maggots

Field experiments on about 4700 sheep at about forty different farms in North Wales are discussed. Crutching is the most effective control measure for lambs. Regular dipping with commercial arsenic-sulphur dips gives reasonable control except during adverse weather conditions. Dipping with zinc arsenite or with calomel proved, on the whole, less effective than dipping with commercial dip. Addition of calomel to commercial dip proved to be more effective than commercial dip alone. Preliminary observations are presented on the variation of the surface tension and viscosity of the dipping fluid as the number of sheep passing through the dip increased.     

Quantifying the slightly deleterious mutation model of molecular evolution

We have attempted to quantify the frequency and effects of slightly deleterious mutations (SDMs), those that have selective effects close to the reciprocal of the effective population size of a species, by comparing the level of selective constraint in protein-coding genes of related species that have different present-day effective population sizes. In our two comparisons, the species with the smaller effective population size showed lower constraint, implying that SDMs had become fixed. The fixation of SDMs was supported by the observation of a higher fraction of radical to conservative amino acid substitutions in species with smaller effective population sizes. The fraction of strongly deleterious mutations (which rarely become fixed) is >70% in most species. Only approximately 10% or fewer of mutations seem to behave as SDMs, but SDMs could comprise a substantial fraction of mutations in protein-coding genes that have a chance of becoming fixed between species.