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PubMed1998

Maximizing the response of selection with a predefined rate of inbreeding: overlapping generations.

In a breeding scheme, the aim is high rates of genetic gain with limited inbreeding. A dynamic selection rule is developed that maximizes selection response in populations with overlapping generations. The rule maximizes the genetic merit of selected animals while limiting the average relationship of the population after the current round of selection. The latter is shown to limit the contribution of the current population to the future inbreeding. The rule accounts for the selection of some candidates during previous selection rounds and for the expected future contributions of the selection candidates. Inputs for the rule are the BLUP breeding values and ages of selection candidates, the relationship matrix of all animals, and contributions of animals during previous selection rounds. Output is the optimal number of offspring for each candidate. Computer simulations of dairy cattle nucleus schemes showed that predefined rates of inbreeding were actually achieved, without compromising long-term selection response, at least up to 20 yr of selection. At the same rates of inbreeding, the dynamic selection rule obtained up to 44% more genetic gain than direct selection for BLUP breeding values. The advantage of the dynamic rule over BLUP selection decreased with increasing population sizes and with greater predefined rates of inbreeding. Consequently, the dynamic rule should be especially useful in small selection schemes in which relatively low rates of inbreeding are desired.

Age Factors↗
PubMed2003

Exploring the origin of the ion selectivity of the KcsA potassium channel.

The availability of structural information about biological ion channels provides an opportunity to gain a detailed understanding of the control of ion selectivity by biological systems. However, accomplishing this task by computer simulation approaches is very challenging. First, although the activation barriers for ion transport can be evaluated by microscopic simulations, it is hard to obtain accurate results by such approaches. Second, the selectivity is related to the actual ion current and not directly to the individual activation barriers. Thus, it is essential to simulate the ion currents and this cannot be accomplished at present by microscopic MD approaches. In order to address this challenge, we developed and refined an approach capable of evaluating ion current while still reflecting the realistic features of the given channel. Our method involves generation of semimacroscopic free energy surfaces for the channel/ions system and Brownian dynamics (BD) simulations of the corresponding ion current. In contrast to most alternative macroscopic models, our approach is able to reproduce the difference between the free energy surfaces of different ions and thus to address the selectivity problem. Our method is used in a study of the selectivity of the KcsA channel toward the K+ and Na+ ions. The BD simulations with the calculated free energy profiles produce an appreciable selectivity. To the best of our knowledge, this is the first time that the trend in the selectivity in the ion current is produced by a computer simulation approach. Nevertheless, the calculated selectivity is still smaller than its experimental estimate. Recognizing that the calculated profiles are not perfect, we examine how changes in these profiles can account for the observed selectivity. It is found that the origin of the selectivity is more complex than generally assumed. The observed selectivity can be reproduced by increasing the barrier at the exit and the entrance of the selectivity filter, but the necessary changes in the barrier approach the limit of the error in the PDLD/S-LRA calculations. Other options that can increase the selectivity are also considered, including the difference between the Na+...Na+ and K+...K+ interaction. However, this interesting effect does not appear to lead to a major difference in selectivity since the Na+ ions at the limit of strong interaction tend to move in a less concerted way than the K+ ions. Changes in the relative binding energies at the different binding sites are also not so effective in changing the selectivity. Finally, it is pointed out that using the calculated profiles as a starting point and forcing the model to satisfy different experimentally based constraints, should eventually provide more detailed understanding of the different complex factors involved in ion selectivity of biological channels.

Algorithms↗
PubMed1988

Polygenic control of quantitative antibody responsiveness: restrictions of the multispecific effect related to the selection antigen.

Among the differences observed between the various high (H) and low (L) antibody responder lines of mice resulting from distinct bidirectional selective breedings, one of the most puzzling is the variation in the "multispecific effect," i.e., in the modification of antibody responses to antigens unrelated to those used during the selection. The best examples are the H and L lines of selection IV, selected on the basis of responses to somatic antigen of Salmonella which do not differ in their antibody responses to sheep erythrocytes (SE). However, a wide range of variability is observed in the responses of (HIV X LIV)F2 hybrids to this antigen, and it was therefore hypothesized that distinct groups of genes might regulate antibody responses to SE and the somatic antigen. Indeed, a new selection (IV-A) for anti-SE responsiveness started from these (HIV X LIV)F2 successfully produced a high and a low anti-SE responder line. The results of selection IV-A and the variance analysis of (HIV-A X LIV-A)F2 hybrids are reported. They are roughly similar to those in selection I, also carried out for anti-SE responsiveness. In vivo attempts to identify the major regulatory mechanism which contributes to the interline difference indicate that the efficiency of macrophage accessory function has been modified in selection IV-A, as was observed in selection I, whereas this function did not differ in HIV and LIV lines. Probably in relation to the involvement of macrophage function there is a notable increase of the multispecific effect in selection IV-A when compared with selection IV. The results of selection IV-A demonstrate that responsiveness to heterologous erythrocytes and to somatic antigen of Salmonella are under separate polygenic control operating through distinct regulatory mechanisms. The choice of the selection antigen and immunization procedure is of major importance for defining the gene interaction operating in each selective breeding experiment and the extent of its multispecific effect.

Animals↗
PubMed2003

Comparison of selection methods for optimizing genetic gain and gene diversity in a red pine ( Pinus resinosa Ait.) seedling seed orchard.

Four selection methods, individual selection (IS), family selection (FS), family plus within-family selection (FWFS) and combined selection (CS), were used to estimate genetic gain [ E( g)] for stem volume and gene diversity ( GD) for ten theoretical selection intensities in a 108-family, 12-year-old red pine seedling seed orchard. Estimated genetic gain for stem volume ranged from 4.6% to 11.8% across all selection methods and intensities with CS consistently having the highest gains and FS the lowest for any given selection intensity. Genetic diversity ranged from 0.9797 to 0.9954 across all selection methods and intensities. Individual selection was the best selection method for retaining GD, especially at the higher selection intensities, while FWFS was more efficient at the lowest selection intensity. An optimization point, which maximized E( g) and GD relative to each other, was calculated for each selection method. In all cases the optimization point indicated that both E( g) and GD would be favorably high when optimized relative to each other. The implications for volume gain, genetic diversity and potential inbreeding in red pine, a species with inherently low levels of genetic variation, are discussed.

Biological Evolution↗
PubMed2006

Optimizing selection on multiple identified quantitative trait loci in population with overlapping generations.

A method was developed to model and optimize selection on multiple identified quantitative trait loci (QTLs) and polygenic estimated breeding value, in order to maximize a weighted sum of cumulative response to selection over multiple years in a population with overlapping generations. The model allows for a population with multiple sex-age classes, different number of age class between sires and dams, and varied genetic contribution of the age class. The optimization problem was formulated as a multiple-stage optimal control problem and solved by a forward and backward iteration loop. The practical utility of this method was illustrated in an example of pig breeding population with overlapping generations. The selection response of this method was compared with standard QTL selection and conventional best linear unbiased prediction (BLUP) selection. Simulation results show that optimal selection achieved greater selection response than either standard QTL or conventional BLUP selections. The influence of population structure on optimal selection was significant. Optimal QTL selection and standard QTL selection were more favorable in a population with overlapping generations than discrete generations, and obtained more benefits relative to conventional BLUP selection in a population with overlapping generations. Optimal QTL selection relative to conventional BLUP selection is also more favorable following increase of genetic contribution of two-year-old boars and sows in a population with overlapping generations.

Algorithms↗
PubMed1992

Deleterious mutations, apparent stabilizing selection and the maintenance of quantitative variation.

Apparent stabilizing selection on a quantitative trait that is not causally connected to fitness can result from the pleiotropic effects of unconditionally deleterious mutations, because as N. Barton noted, "...individuals with extreme values of the trait will tend to carry more deleterious alleles...." We use a simple model to investigate the dependence of this apparent selection on the genomic deleterious mutation rate, U; the equilibrium distribution of K, the number of deleterious mutations per genome; and the parameters describing directional selection against deleterious mutations. Unlike previous analyses, we allow for epistatic selection against deleterious alleles. For various selection functions and realistic parameter values, the distribution of K, the distribution of breeding values for a pleiotropically affected trait, and the apparent stabilizing selection function are all nearly Gaussian. The additive genetic variance for the quantitative trait is kQa2, where k is the average number of deleterious mutations per genome, Q is the proportion of deleterious mutations that affect the trait, and a2 is the variance of pleiotropic effects for individual mutations that do affect the trait. In contrast, when the trait is measured in units of its additive standard deviation, the apparent fitness function is essentially independent of Q and a2; and beta, the intensity of selection, measured as the ratio of additive genetic variance to the "variance" of the fitness curve, is very close to s = U/k, the selection coefficient against individual deleterious mutations at equilibrium. Therefore, this model predicts appreciable apparent stabilizing selection if s exceeds about 0.03, which is consistent with various data. However, the model also predicts that beta must equal Vm/VG, the ratio of new additive variance for the trait introduced each generation by mutation to the standing additive variance. Most, although not all, estimates of this ratio imply apparent stabilizing selection weaker than generally observed. A qualitative argument suggests that even when direct selection is responsible for most of the selection observed on a character, it may be essentially irrelevant to the maintenance of variation for the character by mutation-selection balance. Simple experiments can indicate the fraction of observed stabilizing selection attributable to the pleiotropic effects of deleterious mutations.

Alleles↗
PubMed1993

Pleiotropic models of polygenic variation, stabilizing selection, and epistasis.

We show that in polymorphic populations many polygenic traits pleiotropically related to fitness are expected to be under apparent "stabilizing selection" independently of the real selection acting on the population. This occurs, for example, if the genetic system is at a stable polymorphic equilibrium determined by selection and the nonadditive contributions of the loci to the trait value either are absent, or are random and independent of those to fitness. Stabilizing selection is also observed if the polygenic system is at an equilibrium determined by a balance between selection and mutation (or migration) when both additive and nonadditive contributions of the loci to the trait value are random and independent of those to fitness. We also compare different viability models that can maintain genetic variability at many loci with respect to their ability to account for the strong stabilizing selection on an additive trait. Let Vm be the genetic variance supplied by mutation (or migration) each generation, Vg be the genotypic variance maintained in the population, and n be the number of the loci influencing fitness. We demonstrate that in mutation (migration)-selection balance models the strength of apparent stabilizing selection is order Vm/Vg. In the overdominant model and in the symmetric viability model the strength of apparent stabilizing selection is approximately 1/(2n) that of total selection on the whole phenotype. We show that a selection system that involves pairwise additive by additive epistasis in maintaining variability can lead to a lower genetic load and genetic variance in fitness (approximately 1/(2n) times) than an equivalent selection system that involves overdominance. We show that, in the epistatic model, the apparent stabilizing selection on an additive trait can be as strong as the total selection on the whole phenotype.

Alleles↗
PubMed2000

The evolution of sexual size dimorphism in the house finch. II. Population divergence in relation to local selection.

Recent colonization of ecologically distinct areas in North America by the house finch (Carpodacus mexicanus) was accompanied by strong population divergence in sexual size dimorphism. Here we examined whether this divergence was produced by population differences in local selection pressures acting on each sex. In a long-term study of recently established populations in Alabama, Michigan, and Montana, we examined three selection episodes for each sex: selection for pairing success, overwinter survival, and within-season fecundity. Populations varied in intensity of these selection episodes, the contribution of each episode to the net selection, and in the targets of selection. Direction and intensity of selection strongly differed between sexes, and different selection episodes often favored opposite changes in morphological traits. In each population, current net selection for sexual dimorphism was highly concordant with observed sexual dimorphism--in each population, selection for dimorphism was the strongest on the most dimorphic traits. Strong directional selection on sexually dimorphic traits, and similar intensities of selection in both sexes, suggest that in each of the recently established populations, both males and females are far from their local fitness optimum, and that sexual dimorphism has arisen from adaptive responses in both sexes. Population differences in patterns of selection on dimorphism, combined with both low levels of ontogenetic integration in heritable sexually dimorphic traits and sexual dimorphism in growth patterns, may account for the close correspondence between dimorphism in selection and observed dimorphism in morphology across house finch populations.

Alabama↗
PubMed2006

Response of fluctuating and directional asymmetry to selection on wing shape in Drosophila melanogaster.

We tested whether directional selection on an index-based wing character in Drosophila melanogaster affected developmental stability and patterns of directional asymmetry. We selected for both an increase (up selection) and a decrease (down selection) of the index value on the left wing and compared patterns of fluctuating and directional asymmetry in the selection index and other wing traits across selection lines. Changes in fluctuating asymmetry across selection lines were predominantly small, but we observed a tendency for fluctuating asymmetry to decrease in the up-selected lines in both replicates. Because changes in fluctuating asymmetry depended on the direction of selection, and were not related to changes in trait size, these results fail to support existing hypotheses linking directional selection and developmental stability. Selection also produced a pattern of directional asymmetry that was similar in all selected lines whatever the direction of selection. This result may be interpreted as a release of genetic variance in directional asymmetry under selection.

Animals↗
PubMed2000

Patient selection for lung volume reduction surgery: An objective model based on prior clinical decisions and quantitative CT analysis.

OBJECTIVES: We used whole-lung quantitative CT analysis (QCT)-an objective method of evaluating emphysema severity and distribution based on measurement of lung density-to determine whether subjective selection criteria for lung volume reduction surgery are applied consistently and to model the patient selection process, and assessed the relationship of the model to postoperative outcome. DESIGN: Logistic regression analysis using QCT indexes of emphysema and preoperative physiologic test results as the independent variables, and the decision to operate as the dependent variable. SETTING: University hospital. PATIENTS: Seventy patients selected for bilateral lung volume reduction surgery and 32 otherwise operable patients excluded from surgery based on subjective assessment of emphysema morphology on chest radiography, CT, and perfusion scintigraphy. INTERVENTION: Bilateral lung volume reduction surgery in the selected group. MEASUREMENTS AND RESULTS: Emphysema in patients selected for surgery was more severe overall and in the upper lungs by multiple QCT indexes (p < 0.01, unpaired two-tailed t test). Physiologic abnormalities were slightly more severe in selected patients (p < 0.05, unpaired two-tailed t test). The range of many QCT and physiologic values overlapped considerably between the selected and excluded groups. The percent severe emphysema (<- 960 Hounsfield units [HU]), upper/lower lung emphysema ratio (- 900 HU threshold), and residual volume were the key variables in the model predicting selection decisions (model r(2) = 0.48; p < 0.0001). The model correctly predicted selection decisions in 87% of all cases, 91% of the selected group, and 78% of the excluded group. Surgical patients with a higher model-derived probability of selection had greater postoperative improvement in FEV(1) and 6-min walk distance. CONCLUSIONS: Radiologic selection criteria are applied consistently to the majority of patients. QCT features are strongly associated with selection decisions, are related to outcome, and may help improve consistency and confidence in patient selection.

Adult↗
PubMed2004

Development of an optimal index to improve lactation yield and persistency with the least selection intensity.

It is important to have improvement in both lactation milk yield and persistency. Modification of the lactation curve requires severe restrictions on selection criteria designed to simultaneously improve both milk yield and persistency. As a result, manipulating the lactation curve for improved persistency requires higher selection intensity than unrestricted selection based on 305-d estimated breeding value (EBV). Our study showed that for a given restriction imposed on both milk EBV and persistency, it is possible to derive different indexes to achieve this selection constraint with different degrees of selection intensity. Of the class of indexes that meets the same restriction, it is preferable to choose the index that requires the least selection intensity because it is easier to achieve the selection goal with the use of an index that requires a lower selection intensity than a higher selection intensity. An optimal index based on random regression (RR) coefficients was developed to achieve the prespecified stage genetic gains with the lowest selection intensity. A conversion equation was derived to convert the selection index based on RR coefficients to the selection index based on stage EBV with the lowest selection intensity. A numerical example is provided to demonstrate the procedures developed compared with conventional selection based on 305-d milk EBV.

Animals↗
PubMed1988

Fat deposition in a broiler sire strain. 5. Comparisons of economic efficiency of direct and indirect selection against fatness.

In a simulation study, selection for weight gain in a broiler sire strain was compared with 1) one and two stage index selection for weight gain and feed conversion and 2) weight gain, slaughter yield, and percentage abdominal fat. Weight gain per day was assigned an economic value of 1.138 Dutch cents (ct)1/g; feed conversion, -138.18 ct/1.0; slaughter yield, 0 or 7.55 ct/%; and percentage abdominal fat, 0 or -10 ct/%. When selection was completely or almost completely (as in two stage selection) based on weight gain, percentage abdominal fat increased; otherwise it decreased. Weight gain, feed conversion, and slaughter yield improved with all selection methods examined. Due to the high positive correlation between feed conversion and percentage abdominal fat, selection for an index of weight gain and feed conversion gave about the same reduction in percentage abdominal fat as selection for an index of weight gain, slaughter yield, and percentage abdominal fat. Selection response of the four traits was dependent more on selection methods than on sets of economic values. Based on economic values, selection for an index of weight gain and feed conversion gave 1.70 to 3.35 times the financial gain of selection for weight gain only, and selection for an index of weight gain, slaughter yield, and percentage abdominal fat gave 1.15 to 3.12 times that attained by selection only for weight gain. The extra financial gains exceeded by far the estimated additional costs of the index selection methods.

Adipose Tissue↗
PubMed1994

Selective salpingography for the diagnosis and treatment of early tubal pregnancy.

OBJECTIVE: To determine whether selective salpingography can accurately diagnose and treat patients with early ectopic pregnancies (EPs). DESIGN: Prospective clinical case study. SETTING: Selective salpingography was performed in an outpatient setting under i.v. sedation. PATIENTS: Selective salpingography was performed in 10 women who had clinical presentation suggestive of EP, two consecutive abnormal hCG measurements < 2,000 mIU/mL, and inconclusive vaginal probe sonogram. INTERVENTION: Selective salpingography was performed under fluoroscopy. A cervical cannula was placed, and the tubal ostium was cannulated with a curved selective salpingography catheter (Bard Gynecology and Radiology, Covington, GA). Methotrexate (MTX) (25 or 50 mg) was injected into the affected tube through the selective salpingography catheter. MAIN OUTCOME MEASURE: The accuracy of selective salpingography in the diagnosis of early EP was determined by the rate of fluoroscopic imaging of an ampullary radiolucency upon injection of contrast material through the selective salpingography catheter. Resolution of the EP after injection of MTX into the tube was detected by serial declining hCG measurements. RESULTS: Selective injection of contrast material into the fallopian tubes detected seven ampullary pregnancies in 10 patients. Two patients demonstrated neither tubal pregnancy nor intrauterine pregnancy. One patient with apparent bilateral proximal cornual occlusions on selective salpingography underwent laparoscopy, followed by salpingostomy of an ampullary pregnancy. All 7 patients who received MTX through the selective salpingography catheter completely resolved the EP. Four patients demonstrated patent fallopian tubes on hysterosalpingograms performed 3 to 6 months later. CONCLUSION: Selective salpingography may diagnose early tubal pregnancies of some patients with equivocal clinical, laboratory, and sonographic findings. These patients can be successfully treated at the same time with a single dose of MTX delivered into the affected tube. Selective salpingography reduced the need for laparoscopy and operative intervention. Selective salpingography is a simple and relatively inexpensive diagnostic and therapeutic alternative in patients with suspected early tubal pregnancy.

Catheterization↗
PubMed2000

Ease of capture in lines of Japanese quail (Coturnix japonica) subjected to contrasting selection for fear or sociability.

Japanese quail (Coturnix japonica) of lines, which have been subjected to contrasting selection for duration of the tonic immobility (TI) reaction or social reinstatement (SR) behaviour over many generations show corresponding differences in underlying fearfulness and sociality. As fearfulness and sociality are particularly influential traits in domesticated species, the finding that such traits respond to artificial selection may have important implications for poultry welfare and performance. However, it is not known if or how such selection has influenced human-animal interactions. The present experiment investigated the influence of fearfulness and SR behaviour on the ease with which birds could be caught and handled. Birds of lines selected for duration of the TI response or SR behaviour were reared in mixed line groups (LTI and STI or HSR and LSR) of 491 and 346 birds, respectively, until 6 weeks of age. When the birds were 2, 4, and 6 weeks of age, they were caught one by one and their individual capture ranks noted. In the group of birds selected for duration of the TI response, birds selected of the line selected for short duration of TI were caught before those selected for long duration of the response. In the group of birds selected for SR motivation, birds of the high line were caught before their low lines counterparts. Coefficients of concordance between capture ranks were significant and capture ranks did not differ significantly across ages. These results imply that selection for low levels of fear or high levels of sociality produces animals that are less disturbed by human interventions than animals selected for the opposite traits. The greater ease of capture of low fear line birds than high fear line birds may be explained by reduced fear of humans. The fact that the birds selected for high levels of SR behaviour are easier to catch than birds selected for low levels of sociality is less readily explicable. One hypothesis is that HSR line chicks tend to be more strongly imprinted on each other and the human caretaker. However, SR behaviour is highly species specific in both lines, existing evidence for line differences in social discrimination is limited and birds of the two lines show similar duration of the TI response. Despite this, whatever their underlying causation, these results demonstrate that genetic selection can be used to reduce negative reactions to human beings and may be of value in the improvement of both animal welfare and productivity.

Journal Article↗
PubMed1997

Quantitative stereological studies of a 'selection' protocol of hepatocarcinogenesis following initiation in neonatal male and female rats.

A modified initiation-selection procedure for neonatal male and female rat hepatocarcinogenesis were examined utilizing the methods of quantitative stereology. In this study, diethylnitrosamine (10 mg DEN/kg) was given a few days after birth. At weaning, the rats were fed 0.02% 2-acetylaminofluorene (AAF) for 2 weeks with a mitotic stimulus [70% partial hepatectomy (PH)] after 1 week on the diet. Quantitative stereological analyses in conjunction with the use of several enzyme markers were used to determine the number and volume of altered hepatic foci (AHF) detected at 1 week, 3 months and 7 months after the selection procedure. This format resulted in an equivalent number of AHF in male and female rats. The AHF were three times larger in males than in females 1 week after discontinuation of AAF administration. Three months after the selection procedure, the number of AHF had decreased by at least a third and their volume percentage was the same in male and female rats. After 7 months, the number and volume fraction of detectable AHF in females were comparable to those which had been observed at 1 week after selection. In the male, the number but not the volume fraction were similar at 7 months compared with 1 week after selection. Both initiation with DEN and selection with AAF/PH contribute independently to the total population of AHF in male and female rats. At least half of the AHF detected 7 months after the selection protocol were due to DEN administration alone. Rats receiving only the AAF/PH selection exhibited one third of the number of AHF observed with the complete protocol. Administration of a non-necrogenic dose of DEN to neonatal rats when coupled with the AAF/PH selection procedure resulted in a significant promotion of the growth of initiated hepatocytes at 1 week, 3 months or 7 months after the selection procedure. These studies demonstrated that (i) the number of AHF detected after a non-necrogenic dose of DEN during the first week of life with subsequent AAF/PH selection after weaning decreases within the first 3 months after the selection procedure, but can re-develop with a promotion stimulus; (ii) the AAF/PH selection procedure itself may initiate hepatocytes in the absence of DEN administration; (iii) the AAF/PH selection procedure is equally effective with respect to the number of AHF observed after phenobarbital promotion in weaning male and female rats initiated near birth.

2-Acetylaminofluorene↗
PubMed1999

Positive selection on the H3 hemagglutinin gene of human influenza virus A.

The hemagglutinin (HA) gene of influenza viruses encodes the major surface antigen against which neutralizing antibodies are produced during infection or vaccination. We examined temporal variation in the HA1 domain of HA genes of human influenza A (H3N2) viruses in order to identify positively selected codons. Positive selection is defined for our purposes as a significant excess of nonsilent over silent nucleotide substitutions. If past mutations at positively selected codons conferred a selective advantage on the virus, then additional changes at these positions may predict which emerging strains will predominate and cause epidemics. We previously reported that a 38% excess of mutations occurred on the tip or terminal branches of the phylogenetic tree of 254 HA genes of influenza A (H3N2) viruses. Possible explanations for this excess include processes other than viral evolution during replication in human hosts. Of particular concern are mutations that occur during adaptation of viruses for growth in embryonated chicken eggs in the laboratory. Because the present study includes 357 HA sequences (a 40% increase), we were able to separately analyze those mutations assigned to internal branches. This allowed us to determine whether mutations on terminal and internal branches exhibit different patterns of selection at the level of individual codons. Additional improvements over our previous analysis include correction for a skew in the distribution of amino acid replacements across codons and analysis of a population of phylogenetic trees rather than a single tree. The latter improvement allowed us to ascertain whether minor variation in tree structure had a significant effect on our estimate of the codons under positive selection. This method also estimates that 75.6% of the nonsilent mutations are deleterious and have been removed by selection prior to sampling. Using the larger data set and the modified methods, we confirmed a large (40%) excess of changes on the terminal branches. We also found an excess of changes on branches leading to egg-grown isolates. Furthermore, 9 of the 18 amino acid codons, identified as being under positive selection to change when we used only mutations assigned to internal branches, were not under positive selection on the terminal branches. Thus, although there is overlap between the selected codons on terminal and internal branches, the codons under positive selection on the terminal branches differ from those on the internal branches. We also observed that there is an excess of positively selected codons associated with the receptor-binding site and with the antibody-combining sites. This association may explain why the positively selected codons are restricted in their distribution along the sequence. Our results suggest that future studies of positive selection should focus on changes assigned to the internal branches, as certain of these changes may have predictive value for identifying future successful epidemic variants.

Amino Acid Substitution↗
PubMed1975

Role of the cell surface in selection during transport of proteins from mother to foetus and newly born.

The transport of immunoglobulins from mother to foetus and newly born mammal involves selective events which are independent of molecular size, related to immunoglobulin class, structure, and species of origin, and involve considerable protein degradation. Such events are briefly described as background information to a discussion of how selection of proteins might take place during transport across the cellular barriers concerned, namely the yolk sac splanchnopleur, chorio-allantoic placenta, and small intesting. Until recently the Brambell hypothesis has been the most favoured explanation. This implies that selection occurs intracellularly, within endodermal cells of the yolk sac splanchnopleur and small intestine, and within the syncytiotrophoblast of the chorio-allantoic placenta, of certain species. It also suggests that specific receptors are present which give attached proteins protection from degradation when the vesicles containing them fuse with lysosomes; such protected proteins are then liberated from the vesicle by exocytosis. This hypothesis is examined in the light of what is now known about the mechanism of uptake and transport of proteins by the endodermal cells and syncytiotrophoblast. It is suggested that rather than being an intracellular event, involving protection from proteolytic degradation, selection takes place at the cell surface. Evidence is presented, some direct and some circumstantial, that proteins may be selectively endocytosed by coated micropinocytotic vesicles, and non-selectively endocytosed through a complex apical canalicular system leading to macropinocytotic vesicle formation. In the small intesting of the suckling rat these two processes appear to be segregated, selective uptake occurring in the proximal half and non-selective uptake occurring in the distal half. In the endodermal cells of the rabbit yolk sac splanchnopleur, and by implication in the syncytiotrophoblast of man and monkey, it is suggested that both selective, and non-selective, uptake of protein occurs. Non-selective uptake into macropinocytotic vesicles is regarded as an event leading to complete degradation of all contained protein and functioning so as to supply the foetus and newly born mammal with essential amino acids. Selective uptake into coated micropinocytotic vesicles is regarded as an event leading to the transport of immunoglobulins across the cell without any contact with lysosomes, and functioning so as to supply the newly born mammal with protection against invasive organism. Specific receptors are still required but only for the initial uptake and segregation of proteins into coated micropinocytotic vesicles. The role which the glycocalyx might have in such selective binding of proteins is considered and possible difficulties in characterization of specific receptors brought to light in view of the likely overwhelming need for non-specific binding to effect non-selective uptake.

Animals↗
PubMed2000

Feature selection and classifier performance in computer-aided diagnosis: the effect of finite sample size.

In computer-aided diagnosis (CAD), a frequently used approach for distinguishing normal and abnormal cases is first to extract potentially useful features for the classification task. Effective features are then selected from this entire pool of available features. Finally, a classifier is designed using the selected features. In this study, we investigated the effect of finite sample size on classification accuracy when classifier design involves stepwise feature selection in linear discriminant analysis, which is the most commonly used feature selection algorithm for linear classifiers. The feature selection and the classifier coefficient estimation steps were considered to be cascading stages in the classifier design process. We compared the performance of the classifier when feature selection was performed on the design samples alone and on the entire set of available samples, which consisted of design and test samples. The area Az under the receiver operating characteristic curve was used as our performance measure. After linear classifier coefficient estimation using the design samples, we studied the hold-out and resubstitution performance estimates. The two classes were assumed to have multidimensional Gaussian distributions, with a large number of features available for feature selection. We investigated the dependence of feature selection performance on the covariance matrices and means for the two classes, and examined the effects of sample size, number of available features, and parameters of stepwise feature selection on classifier bias. Our results indicated that the resubstitution estimate was always optimistically biased, except in cases where the parameters of stepwise feature selection were chosen such that too few features were selected by the stepwise procedure. When feature selection was performed using only the design samples, the hold-out estimate was always pessimistically biased. When feature selection was performed using the entire finite sample space, the hold-out estimates could be pessimistically or optimistically biased, depending on the number of features available for selection, the number of available samples, and their statistical distribution. For our simulation conditions, these estimates were always pessimistically (conservatively) biased if the ratio of the total number of available samples per class to the number of available features was greater than five.

Algorithms↗