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Results for “contingency loci”

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PubMed2025

100+ years of phase variation: the premier bacterial bet-hedging phenomenon.

Stochastic, reversible switches in the expression of Salmonella flagella variants were first described by Andrewes in 1922. Termed phase variation (PV), subsequent research found that this phenomenon was widespread among bacterial species and controlled expression of major determinants of bacterial-host interactions. Underlying mechanisms were not discovered until the 1970s/1980s but were found to encompass intrinsic aspects of DNA processes (i.e. DNA slippage and recombination) and DNA modifications (i.e. DNA methylation). Despite this long history, discoveries are ongoing with expansions of the phase-variable repertoire into new organisms and novel insights into the functions of known loci and switching mechanisms. Some of these discoveries are somewhat controversial as the term 'PV' is being applied without addressing key aspects of the phenomenon such as whether mutations or epigenetic changes are reversible and generated prior to selection. Another 'missing' aspect of PV research is the impact of these adaptive switches in real-world situations. This review provides a perspective on the historical timeline of the discovery of PV, the current state-of-the-art, controversial aspects of classifying phase-variable loci and possible 'missing' real-world effects of this phenomenon.

Gene Expression Regulation, Bacterial↗

PubMedDate not supplied

On the use of the classical tests for detecting linkage.

Some drawbacks of the classical Mather's linkage text XL2 are considered, and the simple contingency analysis is suggested as an alternative method. The former test is conditional on Mendelian segregation at both loci, whereas the simple contingency test is not. Furthermore, the contingency test and the test for Mendelian segregation at each locus are orthogonal when performed using the G statistic. Simulation results show that, when the XL2 is used, the actual type I error probability (alpha a) can be dramatically perturbed. As expected, no alpha a perturbation is observed when the G contingency test is used. On the other hand, when segregation is Mendelian at both loci, the power of the XL2 method is larger than that of the contingency G test when sample size is small and strong marginal distortion is observed. Because strong marginal distortion may suggest that segregation may be non-Mendelian, the XL2 is in general discouraged in favor of the simple contingency analysis.

Computer Simulation↗

PubMed1991

Genetic epidemiology of non-insulin-dependent diabetes mellitus in north India: preliminary analyses of some genetic markers in Punjabis.

Studies on monozygotic (MZ) twins and admixed populations show that the predisposition to non-insulin-dependent diabetes mellitus has a large genetic component. We have examined the distribution of some genetic polymorphisms (ABO, GLO, ESD, AK, ACPA, and GPI) in control and diabetic Punjabis from north India. The distribution of various genetic markers indicate that the differences between the control and diabetic samples are statistically not significant. Moreover, a contingency chi-square analysis over all loci suggests nonsignificant genetic differentiation (p = 0.50) between the Punjabi samples.

Adult↗

PubMed1977

[Genetic structure of an isolated native population group of northern Sibiria, the Nganasani (Tavgi) of the Taimyr. II. An analysis of intrapopulation variability].

Chi-square contingency table analysis of phenotypic (genotypic) and gene frequencies of erythrocyte and blood serum groups and enzymes in a group of reindeer hunter and fishermen revealed heterogeneity within the population studied. Four out of twelve loci which have been compared were found to be involved in the process of differentiation into two local subgroups (subpopulations). No statistical differences have been observed between samples arbitrarily representing three generations. The data obtained support the hypothesis that the whole population still preserves the state of the stability. Traditional migration from adjacent populations close to nganasans by language and culture has made an important contribution into heterogeneity found in nganasans.

Adult↗

PubMed2025

Patterns of Genomic Divergence and Introgression in Two Primulina Hybrid Zones.

Hybrid zones have long been promoted as natural laboratories for understanding the mechanisms of speciation. Multiple or replicated hybrid zones are particularly informative, as they allow for assessing the consistency of genomic divergence and introgression across different environmental contexts and demographic histories, thereby improving our understanding of the factors that drive or hinder speciation on a broader scale. Here, using whole-genome resequencing data, we compare the patterns of genomic divergence and introgression in two Primulina hybrid zones. We found that genomic divergence in both hybrid zones is largely shaped by neutral processes, with only a few genomic regions showing signatures of balancing or lineage-specific selection. Genomic cline analyses identified numerous SNPs that showed significantly steeper clines and biased centres than the genome-wide expectation in both hybrid zones, consistent with the existence of reproductive barriers. Within regions of restricted gene flow, we identified 21 genes shared between the two hybrid zones. Annotation of gene function revealed that several genes are involved in reproductive processes. In addition, many zone-specific outlier loci were linked to genes associated with pollen and flower development, suggesting that these barriers may contribute to reproductive isolation under localised ecological conditions. Overall, these findings suggest that while certain reproductive barriers remain consistent across independent hybrid zones, others may be contingent on local environmental contexts. Our results demonstrate that both general and zone-specific mechanisms contribute to reproductive isolation in Primulina, providing empirical evidence that some genomic barriers recur across independent hybrid zones while others arise through localised adaptation.

Lamiales↗

PubMed1992

CNV evidence for the distinctiveness of frontal and posterior neural processes in a traumatic brain-injured population.

The association between certain behavioral tests of executive functions in humans and the integrity of the prefrontal lobes has rested primarily on studies comparing subjects with frontal versus other loci of damage. Another approach is to compare the within-group variation on a physiological index of frontal functioning with the behavioral tests of interest. In the present study, subjects with traumatic brain injury (TBI) were given four behavioural measures of executive function, two measures of posterior nonexecutive function, and a Contingent Negative Variation (CNV) task, a proposed electrophysiological index of frontal-lobe functioning. We found that three of the four executive function tests were significantly related to the CNV, accounting for 23-52% of the variance, while the CNV did not correlate at all with the posterior tasks.

Adolescent↗

PubMed1975

Modification of auditory and somatosensory system activity during pupillary conditioning in the paralyzed cat.

The role of sensory systems in the development of behavioral conditioned responses was investigated by recording multiple-unit activity in the auditory and somatosensory pathways during Pavlovian conditioning of the pupillary-dilation responses of paralyzed cats. Establishment of conditioned pupillary-dilation responses to a white noise CS+, pupillary discrimination between the CS+ and a tone CS-, and subsequent discrimination reversal provided the behavioral foundation for examining neural changes related to behavioral learning. Multiple-unit responses to the acoustic CS+ were significantly enhanced in the auditory cortex, cochlear nucleus, and somatic cortex, but not in the cuneate nucleus. The possibility that these effects could be due to changes in stimulus intensity at the sensory receptor, to mo-ement artifacts, or to feedback from skeletal responses were ruled out because the animals were immobilized. Nor could these neural changes be attributable to sensitization, as those brain areas which showed conditioned enhancement to the CS+ exhibited significantly larger responses to the CS+ than to the CS-. Furthermore, the changes in neural activity followed the significance of the CS; after reversal of the reinforcement contingencies, the amount of multiple-unit activity evoked by the stimuli gradually reversed too. Although the somatic cortex showed conditioning and discrimination, greater stimulus specificity was found in the auditory system. Only in the somatic cortex was there a significant increase in responses to the CS- as well as the CS4. Furthermore, both somatosensory loci exhibited enhanced responses to those tactile probes presented during the acoustic CS, suggesting a phasic increase in neural excitability to all stimuli. Analysis of the number of trials required to attain an acquisition criterion indicated that the neural changes occurred first in the auditory cortex, then the cochlear nucleus, followed in turn by the somatic cortex, and finally the cuneate nucleus. However, none of these neural changes preceded acquisition of conditioned pupillary dilations. These results suggest that sensory system changes are not essential for the initial associative process. These findings indicate that the study of autonomic conditioned responses may prove beneficial in seeking the critical neural events which underlie the initial association between two stimuli. A hypothetical model, which explains the development of pupillary and sensory system conditioned responses, was also presented.

Acoustic Stimulation↗

PubMed1979

Inferences about linkage disequilibrium.

Existing theory for inferences about linkage disequilibrium is restricted to a measure defined on gametic frequencies. Unless gametic frequencies are directly observable, they are inferred from genotypic frequencies under the assumption of random union of gametes. Primary emphasis in this paper is given to genotypic data, and disequilibrium coefficients are defined for all subsets of two or more of the four genes, two at each of two loci, carried by an individual. Linkage disequilibrium coefficients are defined for genes within and between gametes, and methods of estimating and testing these coefficients are given for gametic data. For genotypic data, when coupling and repulsion double heterozygotes cannot be distinguished. Burrows' composite measure of linkage disequilibrium is discussed. In particular, the estimate for this measure and hypothesis tests based on it are compared to the usual maximum likelihood estimate of gametic linkage disequilibrium, and corresponding likelihood ratio or contingency chi-square tests. General use of the composite measure, whether or not random union of gametes is an appropriate assumption, is recommended. Attention is given to small samples, where the non-normality of gene frequencies will have greatest effect on methods of inference based on normal theory. Even tools such as Fisher's z-transformation for the correlation of gene frequencies are found to perform quite satisfactorily.

Gene Frequency↗

PubMed1976

Hyperthermia and inhibition of feeding produced by self-stimulation in the septum and preoptic area in dogs.

Dogs bearing electrodes implanted in the anterior part of the basal forebrain were tested for their response to food upon electric stimulation of rewarding sites, and for self-stimulation-produced hyperthermia. Self-stimulation and forced (experimenter-induced) stimulation of 12 out of 16 loci evoked a negative reaction to food the strength of which was determined according to occurrence and persistence of three effects: ignoring food (the dog performing self-stimulation in the presence of readily available meat), food rejection (the dog's failure to take meat offered together with passive stimulation of the rewarding site), and food ejection (throwing meat out of the mouth upon passive stimulation). The rise in body temperature during self-stimulation was positively correlated with the rate of responding. Hyperthermia was significantly higher during self-stimulation in sites where stimulation produced a strong negative reaction to food, as compared with those where stimulation failed to stop the animal from eating. The stimulus-contingent negative reaction to food may reflect a short-term satiety which is supposed to play an essential role in the mechanism of reinforcement. Hyperthermia, and particularly stabilization of hypothalamic temperature on an elevated but fairly constant level, argues for a shift of the set-point for temperature regulation. Occurrence of the two effects supports the claim that self-stimulation produces some complex activation of neural processes controlling energy homeostasis.

Animals↗