Persistence of Common Alleles in Two Related Populations or Species

Mathematical studies are conducted on three problems that arise in molecular population genetics. (1) The time required for a particular allele to become extinct in a population under the effects of mutation, selection, and random genetic drift is studied. In the absence of selection, the mean extinction time of an allele with an initial frequency close to 1 is of the order of the reciprocal of the mutation rate when 4Nv << 1, where N is the effective population size and v is the mutation rate per generation. Advantageous mutations reduce the extinction time considerably, whereas deleterious mutations increase it tremendously even if the effect on fitness is very slight. (2) Mathematical formulae are derived for the distribution and the moments of extinction time of a particular allele from one or both of two related populations or species under the assumption of no selection. When 4Nv << 1, the mean extinction time is about half that for a single population, if the two populations are descended from a common original stock. (3) The expected number as well as the proportion of common neutral alleles shared by two related species at the tth generation after their separation are studied. It is shown that if 4Nv is small, the two species are expected to share a high proportion of common alleles even 4N generations after separation. In addition to the above mathematical studies, the implications of our results for the common alleles at protein loci in related Drosophila species and for the degeneration of unused characters in cave animals are discussed.     

The Problem of Nucleolar Number in Cell Nuclei and in Sections of Cell Nuclei

In this paper the mean number N of nucleoli of cell nuclei and the relative frequency PN of cell nuclei with N nucleoli are investigated. To solve the first problem, the stereological model of convex shaped nuclei and nucleoli and the assumption of randomly-isotropically distributed objects in space are used. The model is developed for non-vanishing thickness T of tissue sections. The relationship between the unknown number N of nucleoli in cell nuclei and the mean number n of nucleoli in nuclear sections determined by counting is N = n (D+T)/(d + T). Here D and d are the mean values of caliper diameter for nuclei and for nucleoli, resp. The second problem is illustrated by means of some biomedical examples: The relative frequency PN of cell nuclei with N nucleoli can be approximated by a generalized Poisson distribution in all investigated cases. Therefore the mean nucleolar number N is the essential parameter to describe the frequencies of cell nuclei with different numbers of nucleoli.     

Linkage between loci of quantitative traits and marker loci: multi-trait analysis with a single marker

An efficient approach to increase the resolution power of linkage analysis between a quantitative trait locus (QTL) and a marker is described in this paper. It is based on a counting of the correlations between the QTs of interest. Such correlations may be caused by the segregation of other genes, environmental effects and physiological limitations. Let a QT locus A/a affect two correlated traits, x and y. Then, within the framework of mixture models, the accuracy of the parameter estimates may be seriously increased, if bivariate densities f _aa(x, y), f _Aa(x, y) and f _AA(x, y) rather than the marginals are considered as the basis for mixture decomposition. The efficiency of the proposed method was demonstrated employing Monte-Carlo simulations. Several types of progeny were considered, including backcross, F₂ and recombinant inbred lines. It was shown that provided the correlation between the traits involved was high enough, a good resolution to the problem is possible even if the QTL groups are strongly overlapping for their marginal densities.     

Electronic sizing and counting of bacteria

An electronic apparatus is described that permits rapid determination of the concentration and size distribution of bacteria in electrolyte suspensions by a resistance method. The resulting size-concentration distribution may be displayed on an oscilloscope and recorded with an X–Y plotter and an electric typewriter-tape punch unit. The paper tape is analyzed with a computer program. Comparisons are made between electronic measurements of bacterial cell concentration and size distribution and values obtained by other methods. Effects of heat-killing and disruption of the cell membrane on the electrical counting characteristics of the organisms are discussed.     

The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting

Summary Various methods for the estimation of populations of algae and other small freshwater organisms are described. A method of counting is described in detail. It is basically that of Utermöhl and uses an inverted microscope.If the organisms are randomly distributed, a single count is sufficient to obtain an estimate of their abundance and confidence limits for this estimate, even if pipetting, dilution or concentration are involved.The errors in the actual counting and in converting colony counts to cell numbers are considered and found to be small relative to the random sampling error.Data are also given for a variant of Utermöhl's method using a normal microscope and for a method of using a haemocytometer for the larger plankton algae.     

A convenient, efficient, and inexpensive method for scintillation counting of polyacrylamide gel slices after electrophoresis

A method is described for analyzing the radioactivity of ³H-labeled RNA after separation by gel electrophoresis. The gels were soaked in 10% acetic acid and were sliced. The gel slices were dehydrated in alcohol, then saturated with toluene, and finally permeated with a toluene-based scintillation fluid containing butyl-PBD. The radioactivity of RNA was then analyzed in situ in the gel slices using a liquid scintillator. The counting efficiency of this technique is high, about 58%. This is even slightly better than the counting efficiency attained after solubilization of the RNA in Soluene 350 (about 55%). With the same fluor, Permablend III, the counting efficiencies of the two techniques are alike.     

Application of immunohistochemistry in stereology for quantitative assessment of neural cell populations illustrated in the göttingen minipig

Background

Stereology is the study of estimating geometric quantities. When successfully applied, the combination of immunohistochemistry (IHC) and stereology eliminates intra- and interobserver variability for cell type identification.

Methodology/Principal Findings

We propose a method to validate existing antibody based cell type markers for stereological application. Comparison was made on the 100-days-old Göttingen minipig (G-mini) neocortex between estimates of total neuron number derived from Giemsa staining using morphological criteria and immunohistochemistry-based cell counting with NeuN. The mean total neuron numbers estimated by the two staining methods were not significantly different. Estimated quantities, including glial cell number, neocortical volume, cell densities and glial-to-neuron ratio were also presented. Additionally, we assessed other commonly used glial markers and discussed how to evaluate the advantages and disadvantages of these markers for stereological estimation of cell number.

Conclusion/Significance

The concordance in quantitative estimates of total neuron number derived from NeuN- and Giemsa-stained sections provides evidence for the sensitivity and specificity of NeuN as a neuronal marker in the G-mini. Although time-consuming, quantitative validation of IHC should always be considered in stereological studies if there is doubt of the sensitivity, specificity, or reproducibility of cell type markers. Inaccurate staining may cause both over- and underestimation of the total cell number and inflict considerable limitation when analyzing the results.     

An improved method for assaying pyrophosphate exchange measuring Cerenkov radiation

The determination of the amount of radioactivity in ³²P-labeled nucleotides absorbed to charcoal is greatly simplified when the same medium is used for extraction and for counting the secondary Cerenkov radiation. Addition of 4-methylumbelliferone increases the efficiency and decreases quenching caused by charcoal particles. With regard to reproducibility and amount of background the method is comparable to other published methods. Its application in a pyrophosphate exchange assay is described.     

A STOCHASTIC SIMULATION STUDY ON SPECIATION BY SEXUAL SELECTION

A two-locus multi-allele sexual isolation model incorporating mutation and genetic drift which was first proposed by Nei et al. (1983) is studied here. One locus controls the male mating character, and the other controls female receptivity. All females are assumed to have equal mating success. Therefore, the frequencies of female receptivity alleles are changed by mutation, drift, and hitchhiking with male character alleles. Without hitchhiking, development of sexual isolation between allopatric populations proceeds faster in smaller populations, as expected. The hitchhiking effect, by triggering the mutual reinforcement of mating behavior of both sexes (or the runaway process, Fisher [1958]), speeds up the evolution of sexual isolation significantly. For populations with 2Nv ≤ 0.2 (N = population size, ν = mutation rate), the rates of divergence all approach the maximum possible rate. Sympatric sexual isolation develops quite frequently if two favorable conditions are met: 1) There is no selection on female phenotype (except in some limited cases), and 2) The population size is large enough to carry several female receptivity alleles. Because of stochastic factors, these alleles may lead to the formation of two discrete groups of females, each group receptive to males of different mating characters. The formation of sympatric sexually-isolated groups is also aided significantly, at the incipient stage, by the runaway process.     

A stereological method for estimating fish fecundity

This paper describes the application and evaluation of a stereological method for counting fish oocytes. The method has been applied to herring, Clupea harengus L., Dover sole, Solea solea L., and mackerel, Scomber scombrus L., and compared with existing volumetric and/or automated particle counter methods. The stereological method has been shown to given similar results and to have a number of distinct advantages over the other methods.     

Comparison of airborne spore concentrations and fungal allergen content

The exposure to spores causing health effects is usually assessed by determining the concentration of viable spores per cubic meter of air (CFU/m³).Since allergens might also be present in dead spores or smaller particles, the objective of this study was to investigate the correlation between the viable spores of Alternaria and Cladosporium at different indoor and outdoor sites and the corresponding allergen concentration detected with a specially developed ELISA (Enzyme Linked Immunosorbent Assay). In outdoor air, the results show a strong correlation between the different sampling techniques applied for viable spores (Slit-Sampler and Multistage Liquid Impinger) and between the viable spores and the allergen concentrations detected in the liquid samples of the impingers. Indoors, the number of viable spores and the allergen concentration do not correlate and the allergen load is underestimated if colony counting methods are used. This revised version was published online in June 2006 with corrections to the Cover Date.     

Performance of the Coriolis air sampler,a high-volume aerosol-collection system for quantification of airborne spores and pollen grains

The Coriolis δ air sampler manufactured by Bertin Technologies (France) is a continuous air sampler, dedicated to outdoor monitoring of airborne spores and pollen grains. This high-volume sampler is based on patented Coriolis technology delivering a liquid sample. The air is drawn into a conical vial in a whirling type motion using suction; particles are pulled against the wall by centrifugal force. Airborne particles are separated from the air and collected in a liquid medium. This innovative solution allows rapid analysis by several techniques including PCR assay and serological assay in order to measure the antigenicity/allergenicity of pollen grains and fungal spores. Also, traditional counting of pollen grains or taxa identification by optical microscopy can be done. A study has been carried out by the Health Protection Agency (HPA), Porton Down, UK, to measure the physical efficiency of the Coriolis air sampler. The physical efficiency of the sampler for collection of micro-organism-laden particles of various sizes has been compared with that of membrane filter samplers using the techniques described by ISO 14698-1. The Coriolis was operated simultaneously with membrane filter samplers in a controlled room where they were challenged with uniform-sized particles of different diameters containing bacterial spores. For the larger particle sizes, it was found that the physical efficiency of the Coriolis was 92% for 10-μm particles. The biological performance of the Coriolis in the collection of airborne fungal spores and pollen grains was evaluated in comparison with a Hirst spore trap (one-week tape-on-drum type sampler) which is one of the most frequently used traps in the measurement of outdoor pollen grain concentrations. The advantages and limitations of both technologies are discussed. The Coriolis was operated simultaneously with a Hirst spore trap in the sampling station of Réseau National de Surveillance Aérobiologique, France (RNSA); the pollen grain and fungal spore counts were analysed by optical microscopy. The pollen grain count m⁻³ collected was compared for both devices. The dispersion values were obtained and statistical analysis was carried out. This study shows that the Coriolis air sampler provided equivalent recovery of pollen grain and fungal spores compared with the volumetric trap standard method (not significantly different, W test, α = 0.05). Nowadays, the French-led project, acronym MONALISA, with financial support from the European Commission––Life-Environment (LIFE05 ENV/F/000068), is testing this innovative air sampler in order to measure the antigenicity/allergenicity of the main aeroallergen particles, i.e. Betula (birch), Poaceae (grasses), Parietaria (pellitory), Olea spp (olive tree), and Artemisia (mugwort) pollen grains, and Alternaria (fungal spores) to validate a new approach of monitoring instead of quantifying pollen grains by their morphology. The robustness and efficiency of the MONALISA system is being demonstrated at a national level throughout Europe in eight different countries with different bio-climatic and topography characteristics: France, UK, Finland, Poland, Spain, Portugal, Switzerland, and Italy.     

Assessment of Three Methods for Detection and Quantification of Nitrite-Oxidizing Bacteria and Nitrobacter in Freshwater Sediments (MPN-PCR, MPN-Griess, Immunofluorescence)

Abstract Nitrification in freshwater, a key process in the nitrogen cycle, is now well known to take place predominantly on suspended particles and in sediment. Nitrobacter is the most commonly isolated nitrite oxidizing bacteria from water environments. Three methods for counting nitrite oxidizing communities (especially Nitrobacter) in sediment were investigated: MPN-Griess, fluorescent antibodies (immunofluorescence), and a more recent molecular method coupling specific DNA amplification by PCR and statistical MPN quantification. After preliminary adjustments of the MPN-PCR technique, the detection level and the yield of each method were determined by inoculating a sediment with a pure Nitrobacter culture. The best recovery yield was obtained with the immunofluorescence technique (21.3%) and the lowest detection level was reached with the MPN-Griess method (10³ Nitrobacter/g dry weight sediment). The MPN-PCR method resulted in the lowest recovery yields and needs further adaptation to become a reliable and precise tool for investigations of nitrifying bacteria in sediment. Received: 6 July 1998; Accepted: 17 December 1998     

New,sensitive, radioactive-free bioluminescence-enhanced detection system in protein blotting and nucleic acid hybridization

A relatively simple, very sensitive bioluminescence-enhanced detection system for protein blotting and nucleic acid hybridization is described. The method utilizes antibodies conjugated with alkaline phosphatase or nucleotide probes complexed with alkaline phosphatase. Then the alkaline phosphatase takes part in a reaction by releasing D -luciferin (Photinus pyralis) from D -luciferin-O-phosphate. Liberated D -luciferin reacts with luciferase, ATP and oxygen under light emission. Light is measured using the Argus-100 a photon counting camera system or photographic films. Bound alkaline phosphatase conjugated antibodies or hybridized nucleotide probes can be visualized. The limit of detection is at present 5 to 50 fg of protein (IgG), corresponding, for example to 30 to 300 × 10^?21 mol. This means a much higher sensitivity of the detection system in comparison to systems used at present. Experiments concerning nucleic acid hybridization and visualization of the emitted light by a photon counting camera (Argus-100) are under investigation.     

A simple technique for the measurement of swimming speed of Chlamydomonas

A simple technique for the measurement of swimming speed of Chlamydomonas reinhardi is described. The technique is based on a rapid statistical counting method which treats the swimming cells as a dilute, kinetic gas and its accuracy has been confirmed by direct photomicrographic measurements. In principle, this technique can be applied to any suspension of organisms satisfying certain statistical criteria.     

Stereological Determination of Orientations,Second-Order Quantities and Correlations for Random Spatial Fibre Systems

This paper presents methods for the stereological analysis of spatial fibre systems on the base of planar or thin sections. Under the assumption that the cross-section figures of the tubular fibres can be measured, the orientation distribution of the fibre system and its line density L_v can be determined from one section only and without distributional assumptions. A simple way to study the degree of randomness of fibre systems consists in the statistical analysis of the point pattern of centres of intersection figures. More sophisticated methods are of stereological nature and yield the spatial reduced second moment measure. Similarly also correlations between two fibre systems can be quantified. The methods are demonstrated by two examples concerning samples of human brain.     

The ultrastructure of dormant,germinating, and photo-inhibited uredospores of the rust fungusPuccinia graminis f. sp.tritici

Summary A comparison was made of fixed and non-fixed uredospores of the wheat stem rust fungusPuccinia graminis f. sp.tritici, using thin sectioning and freeze-etching. The latter technique yielded new information on the ultrastructure of dormant, germinating, and photo-inhibited uredospores, although the distribution of intramembranous particles (IMPs) was similar in each case. A stereological analysis of thin sectioned specimens provided quantitative data on organelle volumetric densities complementing the qualitative information. Evidence suggests that light acts by preventing the dissolution of wall material in the germ pore regions. Methylcis-ferulate, the uredospore self-inhibitor, is also believed to act at this stage in the germination process, and possible links between photo-inhibition and self-inhibition are discussed.     

Flavin-linked mitochondrial α-glycerophosphate dehydrogenase of Candida utilis

The 150-fold purification of the l-α-glycerophosphate dehydrogenase of Candida utilis electron-transport particles by very mild procedures is described. The active enzyme contains FAD, iron and copper. The function of the metals, if any, is not clear. Its molecular weight is about 5·10⁵. The subunit composition is complex and remains unresolved because the enzyme is contaminated with protease(s). The activity of this enzyme is very low in Saccharomyces cerevisiae unless the cells are grown in glycerol. The NAD-dependent cytoplasmic α-glycerophosphate dehydrogenase is present in C. utilis but could not be demonstrated in glucose-grown S. cerevisiae.     

Assessment of counting efficiencies for labeled protein and other macromolecules in filter disk assays

A several-fold greater counting efficiency is observed for protein labeled with [³H]leucine than for free [³H]leucine using a conventional filter disk assay. A similar, though less marked, effect is noted for ¹⁴C-labeled molecules. These results are comparable to those reported by others for counting efficiencies of labeled DNA and deoxynucleotides and illustrate the generality of this effect with regard to macromolecules and their low-molecular weight precursors. This phenomenon, presumably due to differences in the distribution of large and small molecules within filters, gives rise to errors in the quantitation of macromolecule synthesis if a counting efficiency identical to that of the precursor is assumed to apply. A convenient method for determining counting efficiencies of various molecules bound to filters is presented which eliminates this problem.