Mixture-model classification in DNA content analysis.

DNA abundance provides important information about cell physiology and proliferation activity. In a typical in vitro cellular assay, the distribution of the DNA content within a sample is comprised of cell debris, G0/G1-, S-, and G2/M-phase cells. In some circumstances, there may be a collection of cells that contain more than two copies of DNA. The primary focus of DNA content analysis is to deconvolute the overlapping mixtures of the cellular components, and subsequently to investigate whether a given treatment has perturbed the mixing proportions of the sample components. We propose a restricted mixture model that is parameterized to incorporate the available biological information. A likelihood ratio (LR) test is developed to test for changes in the mixing proportions between two cell populations. The proposed mixture model is applied to both simulated and real experimental data. The model fitting is compared with unrestricted models; the statistical inference on proportion change is compared between the proposed LR test and the Kolmogorov-Smirnov test, which is frequently used to test for differences in DNA content distribution. The proposed mixture model outperforms the existing approaches in the estimation of the mixing proportions and gives biologically interpretable results; the proposed LR test demonstrates improved sensitivity and specificity for detecting changes in the mixing proportions.     

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study

Simple cells in primary visual cortex were famously found to respond to low-level image components such as edges. Sparse coding and independent component analysis (ICA) emerged as the standard computational models for simple cell coding because they linked their receptive fields to the statistics of visual stimuli. However, a salient feature of image statistics, occlusions of image components, is not considered by these models. Here we ask if occlusions have an effect on the predicted shapes of simple cell receptive fields. We use a comparative approach to answer this question and investigate two models for simple cells: a standard linear model and an occlusive model. For both models we simultaneously estimate optimal receptive fields, sparsity and stimulus noise. The two models are identical except for their component superposition assumption. We find the image encoding and receptive fields predicted by the models to differ significantly. While both models predict many Gabor-like fields, the occlusive model predicts a much sparser encoding and high percentages of ‘globular’ receptive fields. This relatively new center-surround type of simple cell response is observed since reverse correlation is used in experimental studies. While high percentages of ‘globular’ fields can be obtained using specific choices of sparsity and overcompleteness in linear sparse coding, no or only low proportions are reported in the vast majority of studies on linear models (including all ICA models). Likewise, for the here investigated linear model and optimal sparsity, only low proportions of ‘globular’ fields are observed. In comparison, the occlusive model robustly infers high proportions and can match the experimentally observed high proportions of ‘globular’ fields well. Our computational study, therefore, suggests that ‘globular’ fields may be evidence for an optimal encoding of visual occlusions in primary visual cortex.     

Abnormal blood group galactosyltransferase in blood type A1B-subjects whose sera contain anti-B agglutinin

Summary A blood type A₁B female, whose plasma agglutinates B red blood cells from other subjects but not her own, was found. Her sister with blood type A₁B (sister-1) exhibited the same peculiarity. The agglutination titer of red cells from these two subjects is lower than that of normal B. Her father is blood type B, and his plasma did not agglutinate B red cells from other subjects and his own. Her mother and another sister (sister-2) were usual blood type A₁. Blood group galactosyltransferase (B-enzyme) activity of plasma from the propositus, sister-1, and their father was very low. Km for 2-fucosyllactose of B-enzyme of these subjects was 1.3 mM, which was more than two times higher than that of the normal value. Km for UDP-Gal was similar, but the pH-activity profile differed for the two enzymes.Red cell membranes from her father contained about 70% ungalactosylated H-sites, whereas, virtually all H-sites are galactosylated in the usual B red cell membranes. The blood group ABH components are known to be heterogeneous. Because of the abnormal B-enzyme with low activity and low substrate affinity, some H components might not be galactosylated, particularly in A₁B cases (i.e., the propositus and her sister-1), due to competition by A₁ enzyme. The lack of certain B components is likely to be the cause of the existence of the anti-B agglutinin in their sera.     

Different forms of quinoprotein aldose-(glucose-) dehydrogenase in Acinetobacter calcoaceticus

The ratios of the oxidation rates of aldose sugars, determined in cell-free extracts of Acinetobacter calcoaceticus, vary with the strain and growth conditions used. Three distinct forms of glucose dehydrogenase with different substrate specificities, occurring in variable proportions in these extracts, are responsible for this effect. One form is the already known soluble glucose dehydrogenase, the other two forms are complexes containing enzyme and components of the respiratory chain. The proportions in which the enzyme forms are found in the cell-free extract correlate with the oxidative behaviour of whole cells with respect to aldose sugars. It is concluded, therefore, that the enzyme forms are not an artefact of the isolation procedure but that they exist as such in vivo. Since the two complexes can be converted into the soluble enzyme form, aldose dehydrogenase can, probably, be integrated in three different ways into the respiratory chain.The presence of glucose during growth does not stimulate aldose dehydrogenase production. This is not surprising since the enzyme has no function in carbon metabolism, except perhaps in strains growing on pentoses at high pH. Therefore, the physiological role of quinoprotein aldose dehydrogenase in this organism may be primarily in energy generation.Non-standard abbreviations quinoproteins enzymes containing 2,7,9-tricarboxy-1 H-pyrrolo [2,3f] quinoline-4,5-dione (pyrrolo-quinoline quinone) as the coenzyme     

A hybridisation barrier between two evolutionary lineages of <Emphasis Type="Italic">Barbarea vulgaris</Emphasis> (Brassicaceae) that differ in biotic resistances

Hybridisation barriers are likely to evolve during allopatric separation of populations, in parallel with divergent adaptation to different conditions in the two ranges. If the populations secondarily come into contact, limited interbreeding between them may affect the subsequent spread of the two lineages and their adaptations in the region of sympatry. Barbarea vulgaris include two genetically divergent lineages that differ in secondary metabolites and resistances to insects and a pathogen. The two plant types grow in different Eurasian ranges but co-occur in Denmark and neighbouring countries, posing the question why they have not merged and the resistances spread from one type into the range of the other. Here, we tested whether a hybridisation barrier contribute to this. Different proportions of plants of the two types were placed in net tents and pollinated by flies, and paternity of the resulting seeds determined with genetic markers. Lower proportions of fruits and seeds developed successfully in mixtures with higher proportions of heterotypic plants (i.e. of the other plant type). When combined with results on offspring paternity in a statistical analysis, we found that heterotypic pollen was much less successful in fertilizing embryos and that heterotypic seeds survived less frequently than the contypic. Mature F₁ hybrids in addition produced lower proportions of mature pollen. The two B. vulgaris plant types are thus separated by substantial prezygotic and postzygotic barriers, as strong as reported for crosses between closely related but taxonomically recognised plant species. This may explain why the two B. vulgaris types have not merged in sympatry and why genes for insect-resistance have not introgressed to any extent from one to the other.     

Modulation of the reaction rate of regulating protein induces large morphological and motional change of amoebic cell

Morphologies of moving amoebae are categorized into two types. One is the "neutrophil" type in which the long axis of cell roughly coincides with its moving direction. This type of cell extends a leading edge at the front and retracts a narrow tail at the rear, whose shape has been often drawn as a typical amoeba in textbooks. The other one is the "keratocyte" type with widespread lamellipodia along the front side arc. Short axis of cell in this type roughly coincides with its moving direction. In order to understand what kind of molecular feature causes conversion between two types of morphologies, and how two typical morphologies are maintained, a mathematical model of amoebic cells is developed. This model describes movement of cell and intracellular reactions of activator, inhibitor and actin filaments in a unified way. It is found that the producing rate of activator is a key factor of conversion between two types. This model also explains the observed data that the keratocyte type cells tend to rapidly move along a straight line. The neutrophil type cells move along a straight line when the moving velocity is small, but they show fluctuated motions deviating from a line when they move as fast as the keratocyte type cells. Efficient energy consumption in the neutrophil type cells is predicted.     

Contribution of genetic effects to genetic variance components with epistasis and linkage disequilibrium

Background

Cockerham genetic models are commonly used in quantitative trait loci (QTL) analysis with a special feature of partitioning genotypic variances into various genetic variance components, while the F_∞ genetic models are widely used in genetic association studies. Over years, there have been some confusion about the relationship between these two type of models. A link between the additive, dominance and epistatic effects in an F_∞ model and the additive, dominance and epistatic variance components in a Cockerham model has not been well established, especially when there are multiple QTL in presence of epistasis and linkage disequilibrium (LD).

Results

In this paper, we further explore the differences and links between the F_∞ and Cockerham models. First, we show that the Cockerham type models are allelic based models with a special modification to correct a confounding problem. Several important moment functions, which are useful for partition of variance components in Cockerham models, are also derived. Next, we discuss properties of the F_∞ models in partition of genotypic variances. Its difference from that of the Cockerham models is addressed. Finally, for a two-locus biallelic QTL model with epistasis and LD between the loci, we present detailed formulas for calculation of the genetic variance components in terms of the additive, dominant and epistatic effects in an F_∞ model. A new way of linking the Cockerham and F_∞ model parameters through their coding variables of genotypes is also proposed, which is especially useful when reduced F_∞ models are applied.

Conclusion

The Cockerham type models are allele-based models with a focus on partition of genotypic variances into various genetic variance components, which are contributed by allelic effects and their interactions. By contrast, the F_∞ regression models are genotype-based models focusing on modeling and testing of within-locus genotypic effects and locus-by-locus genotypic interactions. When there is no need to distinguish the paternal and maternal allelic effects, these two types of models are transferable. Transformation between an F_∞ model's parameters and its corresponding Cockerham model's parameters can be established through a relationship between their coding variables of genotypes. Genetic variance components in terms of the additive, dominance and epistatic genetic effects in an F_∞ model can then be calculated by translating formulas derived for the Cockerham models.

     

Proteins of the hard keratins of echidna, hedgehog, rabbit, ox and man

In the accompanying paper it has been shown that two major groups of proteins (low-sulphur and high-sulphur) of ovine wool, horn, and hoof contain similar components although the overall proportions of the groups of proteins and the relative proportions of components within the groups may show significant differences. In the present paper it has been shown for five other species (echidna, hedgehog, rabbit, ox and man) that the hard keratins produced by one animal contain the same groups of protein components but in different relative proportions. The wide apparent differences in the type and relative proportions of the the low-sulphur components which comprise the major constituent proteins of the microfibrils suggest that microfibrils can tolerate a considerable variation in the constituent proteins and still produce functional structures. The low-sulphur protein components are sufficiently well resolved by sodium dodecyl sulphate-polyacrylamide gel electrophoresis to make this procedure potentially useful for animal identification and classification.     

Susceptibility of cell populations to transduction by retroviral vectors

Retroviral transduction efficiency is related to the multiplicity of infection and the physiological state of the target cells. It is generally not known what proportion of a cell population is susceptible to transduction. We used coinfection with two retroviral vectors containing the marker genes for green fluorescent protein and the truncated human nerve growth factor receptor. In the CD34+ cell line TF-1 or human primary CD34+ hematopoietic progenitor cells, it was found that cells transduced with one vector had a better than random chance of transduction by the other vector. A probability model was developed to estimate target cell susceptibility; susceptibility was calculated as the product of the proportions of transgene-positive cells divided by the proportion of double-positive cells. By using this relationship, it was found that susceptibility was related to the target cell type and culture conditions but not the retroviral titer or the retroviral packaging envelope protein used in this study. Cotransduction with two vectors is a relatively simple procedure that provides a means to assess the maximum transduction level possible in a given cell population.     

Comparative ultrastructure of a filamentous mutant and the wild type ofAgmenellum quadruplicatum

Summary A filamentous variant of the marine coccoid cyanophycean alga,Agmenellum quadruplicatum has been produced after treatment of cells with the chemical mutagen, N-methyl-N-nitro-N-nitrosoguanidine (NTG). The mutation to the filamentous condition is stable and has been compared ultrastructurally with the unicellular wild type. The structural basis for the maintenance of the filamentous state is due to a failure of the homogeneously-structured transverse wall to differentiate into the stratified longitudinal wall. A manifestation of this condition is the continued synthesis of the investment membrane resulting in proliferations at each constriction. The wild type cells are nearly spherical while the filamentous mutant cells are smaller and elongate. An analysis of the structure and morphology of the nucleoplasmic regions is presented for both strains and a correlation between the morphology of these regions and the unicellular and filamentous conditions is made.     

THE POWER OF THE " A" -" NOT A" METHOD

The " A" - " Not A" method is a rating method with two categories. It is often treated as a discrimination method. Unlike forced choice procedures, the Thurstonian model for this method involves a choice criterion. In statistical tests, it is treated as a comparison of two proportions. In this paper, the power for hypothesis tests involving the monadic and replicated monadic " A" - " Not A" method is discussed. The power functions and the sample sizes needed for 80% power are given based on Thurstone's δ. Designs with equal and unequal allocations for A and A (Not A) samples are considered. The power of the method is also compared with that of four forced choice methods under the assumption that the perceptual variance is identical among methods. The comparison shows that, in general, the power for the five methods ranks from high to low: the 3-AFC, 2-AFC, " A" - " Not A", triangular and duo-trio. The comparison also shows that, based on the same number of panelists and/or the same sample size for the A and A⁻ samples for the methods, if the panelists are not too discrepant and the choice criterion in the " A" - " Not A" method is not too strict or too lax, the power of the " A" - " Not A" method is very close to that of the 2-AFC method.     

Counterion diffusion in heparin solutions

The physiological importance of heparin is due to its strong interaction with bivalent counterions, especially Ca2+. A diffusional approach of this property is presented in this article: the observable is the self-diffusion coefficient of the counterions, as a function of the ratio of the polyelectrolyte over the added salt concentrations. All the results are in agreement with a simple "quasi-chemical model" in which two different states are assumed for the counterions: "free" or "bound." The proportions of these two types of ions are calculated according to the distribution function of the counterions around the polyion. We assume that those of counterions located at a distance closer than a, the characteristic distance, are bound; the others are free. The ionic distribution function is evaluated by a numerical integration of a cell model Poisson-Boltzmann equation. Finally, this model leads to a very good agreement with the experimental results, if the radius of heparin polyion is assumed to be 6 and 10 A.     

Asymmetry and directionality in production of new cell types during clonal growth: the switching pattern of homothallic yeast.

Homothallic Saccharomyces yeasts efficiently interconvert between two cell types, the mating types a and alpha. These interconversions have been proposed to occur by genetic rearrangement ("cassette" insertion) at the locus controlling cell type (the mating type locus). The pattern of switching from one cell type to the other during growth of a clone of homothallic cells has been followed by direct microscopic observation, and the results have been summarized as "rules" of switching. First, when a cell divides, it produces either two cells with the same mating type as the original cell or two cells that have switched to the other mating type. This observation suggests that the mating type locus is changed early in the cell cycle, in late Gl or during S. Second, the ability to produce cells that have switched mating type is restricted to cells that have previously divided ("experienced cells"). Spores and buds ("inexperienced cells") rarely if ever give rise to cells with changed mating type. A homothallic yeast cell thus exhibits asymmetric segregation of the potential for mating type interconversion--at each cell division, the mother, but not the daughter, is capable of switching cell types in its next division. Homothallic cells also exhibit directionality in switching: experienced cells switch to the opposite cell type in more than 50% of cell divisions. These results show that the process of mating type interconversion is itself controlled during growth of a clone of homothallic cells. By analogy and extension of these results, we propose that multiple cell types can be produced in a specific pattern during development of a higher eucaryote in a model involving sequential cassette insertion.     

Differentiation-dependent expression of lectin binding sites on normal and neoplastic keratinocytes in vivo and in vitro.

We used lectins as probes to demonstrate the composition of membrane carbohydrates of canine keratinocytes in various functional stages and various degrees of differentiation. Keratinocytes during normal epidermal turnover were compared by lectin immunohistochemistry to cells of hyperplastic epidermis and neoplastic keratinocytes. Three types of epidermal tumors and oral squamous cell carcinomas were examined. In addition, two in vitro tissue culture systems for keratinocytes were studied and compared with in vivo epithelium. In normal skin, PNA reacted only weakly with basal cells, whereas in hyperplastic skin basal cells bound this lectin strongly, demonstrating increasing expression of PNA binding sites with increasing thickness of the stratified squamous epithelium. ConA bound to basal cell tumors only. In oral squamous cell carcinomas, the expression of distinct lectin binding sites correlated with certain histological growth patterns, e.g., UEA-I reacted with highly invasive tumors but not with tumors showing a solid growth pattern. Using cell surface iodination and polyacrylamide gel electrophoresis, distinct differences in cell membrane protein expression were demonstrated between normal and neoplastic keratinocytes. SDS-polyacrylamide gel electrophoresis of cultured normal and neoplastic keratinocytes revealed several cell surface proteins that are specific for either cell type. Neoplastic cells specifically express a 140 KD lectin binding cell surface glycoprotein. The results of this study show that lectin binding patterns of keratinocytes are dependent on the functional state and the degree of differentiation of the cells and demonstrate correlation of some histological growth patterns with distinct lectin binding phenotypes, suggesting association of expression of cell membrane carbohydrate moieties with growth patterns. In addition, close similarities between "lifted cultures" grown at the air-liquid interface and native tissue demonstrate the value of this culture system as a model for differentiated stratified squamous epithelium.     

A comparative study of the main components of the nucleolus in different populations of rat trophoblast cells during differentiation. II. The nucleoli of the trophospongium cells, the glycogen cells and the secondary giant cells

A comparative study was performed of the arrangement of different nucleolar components during differentiation of trophoblast cell populations in the junctional zone of placenta (glycogen cells and trophospongium) and in the secondary giant cells. Each cell type is characterized by specific interrelation of nucleolar components. Some glycogen cells show signs of segregation of nucleolar components: strands of nucleolar components with fibrillar centers (FCs) are displaced to the periphery of the nucleolus and contact with the perinucleolar chromatin. Large reticular nucleoli in trophospongium cells contain many FCs which are gathered into several "chains" by strands of dense fibrillar component. Such a "chain" has also been found in nucleoli of secondary giant cells, with greater number of FCs in each "chain". Relationship between the arrangement of nucleolar components and the level of cell differentiation is discussed.     

Non-inferiority of new procedure to standard procedure in stratified matched-pair design

We consider the statistical testing for non-inferiority of a new treatment compared with the standard one under matched-pair setting in a stratified study or in several trials. A non-inferiority test based on the efficient scores and a Mantel-Haenszel (M-H) like procedure with restricted maximum likelihood estimators (RMLEs) of nuisance parameters and their corresponding sample size formulae are presented. We evaluate the above tests and the M-H type Wald test in level and power. The stratified score test is conservative and provides the best power. The M-H like procedure with RMLEs gives an accurate level. However, the Wald test is anti-conservative and we suggest caution when it is used. The unstratified score test is not biased but it is less powerful than the stratified score test when base-line probabilities related to strata are not the same. This investigation shows that the stratified score test possesses optimum statistical properties in testing non-inferiority. A common difference between two proportions across strata is the basic assumption of the stratified tests, we present appropriate tests to validate the assumption and related remarks.     

Fitting mixture distributions to phenylthiocarbamide (PTC) sensitivity.

A technique for fitting mixture distributions to phenylthiocarbamide (PTC) sensitivity is described. Under the assumptions of Hardy-Weinberg equilibrium, a mixture of three normal components is postulated for the observed distribution, with the mixing parameters corresponding to the proportions of the three genotypes associated with two alleles A and a acting at a single locus. The corresponding genotypes AA, Aa, and aa are then considered to have separate means and variances. This paper is concerned with estimating the parameters of the model, and their standard errors, by using an application of the EM algorithm. This technique also caters for the fact that the sensitivity measurements are only known to lie between the endpoints of certain intervals and that the exact measurement of the attribute is not possible.     

Characterization of biotinylated proteins in mammalian cells using 125I-streptavidin

The presence of biotinylated proteins in detergent extracts of cells is demonstrated using 125I-streptavidin. Four components with apparent molecular masses (Mr) ranging from 70 to 220 kDa have been detected. These probably represent the biotinylated subunits of the carboxylase enzymes. The proportions of the four components were found to vary from cell type to cell type and also the Mr varied from species to species.     

Altered CD161bright CD8+ Mucosal Associated Invariant T (MAIT)-Like Cell Dynamics and Increased Differentiation States among Juvenile Type 1 Diabetics

Type 1A diabetes (T1D) is believed to be caused by immune-mediated destruction of β-cells, but the immunological basis for T1D remains controversial. Microbial diversity promotes the maturation and activation of certain immune subsets, including CD161^bright CD8⁺ mucosal associated invariant T (MAIT) cells, and alterations in gut mucosal responses have been reported in type 1 diabetics (T1Ds). We analyzed T cell populations in peripheral blood leukocytes from juvenile T1Ds and healthy controls. We found that proportion and absolute number of MAIT cells were similar between T1Ds and controls. Furthermore, while MAIT cell proportions increased with age among healthy controls, this trend was not observed among long-standing T1Ds. Additionally, the CD27- MAIT cell subset is significantly increased in T1Ds and positively correlated with HbA1c levels. However, after T1Ds are stratified by age, the younger group has significantly increased proportions of CD27- MAIT cells compared to age-matched controls, and this proportional increase appears to be independent of HbA1c levels. Finally, we analyzed function of the CD27- MAIT cells and observed that IL-17A production is increased in CD27- compared to CD27⁺ MAIT cells. Overall, our data reveal disparate MAIT cell dynamics between T1Ds and controls, as well as signs of increased MAIT cell activation in T1Ds. These changes may be linked to hyperglycemia and increased mucosal challenge among T1Ds.