Integral evaluation of phenotypic and genotypic variability of morphologic and psychophysiologic human traits

The paper demonstrates the expedience of the developed populational-genetic approach to studying the genetic bases of a complex of quantitative characters pertaining to different levels of human organization: anthropometry, neurodynamics and psychodynamics. The studies were carried out in eight human populations of different degree of isolation and ethnical background. It is shown that correlation phenotypic variability is higher for these characters, as compared to genotypic variability, the number of general genes responsible for this variability being decreased, respectively.     

Comparisons of the variability of three markers of the human circadian pacemaker

A circadian pacemaker within the central nervous system regulates the approximately 24-h physiologic rhythms in sleep cycles, hormone secretion, and other physiologic functions. Because the pacemaker cannot be examined directly in humans, markers of pacemaker function must be used to study the pacemaker and its response to environmental stimuli. Core body temperature (CBT), plasma cortisol, and plasma melatonin are three marker variables frequently used to estimate the phase of the human pacemaker. Measurements of circadian phase using markers can contain variability due to the circadian pacemaker itself, the intrinsic variability of the marker relative to the pacemaker, the method of analysis of the marker, and the marker assay. For this report, we compared the mathematical variability of a number of methods of identifying circadian phase from CBT, plasma cortisol, and plasma melatonin data collected in a protocol in which pacemaker variability was minimized using low light levels and regular timing of both the light pattern and the rest/activity schedule. We hoped to assess the relative variabilities of the different physiological markers and the analysis methods. Methods were based on the crossing of an absolute threshold, on the crossing of a relative threshold, or on fitting a curve to all data points. All methods of calculating circadian phase from plasma melatonin data were less variable than those calculated using CBT or cortisol data. The standard deviation for the phase estimates using CBT data was 0.78 h, using cortisol data was 0.65 h, and for the eight analysis methods using melatonin data was 0.23 to 0.35 h. While the variability for these markers might be different for other subject populations and/or less stringent study conditions, assessment of the intrinsic variability of the different calculations of circadian phase can be applied to allow inference of the statistical significance of phase and phase shift calculations, as well as estimation of sample size or statistical power for the number of subjects within an experimental protocol.     

Comparative population analysis of the variability of human neurodynamics and psychodynamics

A number of characteristics of morphological, neurodynamical, and psychodynamical levels of organization of individual personality was studied in five isolated different ethnical populations and two panmixic ones. The degree of heritability was found to decrease and that of variability to increase with the rise of organization level. Significant interpopulational differences were shown in the mean values of characteristics under study and their dispersions. The results obtained were discussed in connection with peculiarities of genetical and social structures of investigated human populations.     

Quantitative variability of 342 plasma proteins in a human twin population

The degree and the origins of quantitative variability of most human plasma proteins are largely unknown. Because the twin study design provides a natural opportunity to estimate the relative contribution of heritability and environment to different traits in human population, we applied here the highly accurate and reproducible SWATH mass spectrometry technique to quantify 1,904 peptides defining 342 unique plasma proteins in 232 plasma samples collected longitudinally from pairs of monozygotic and dizygotic twins at intervals of 2–7 years, and proportioned the observed total quantitative variability to its root causes, genes, and environmental and longitudinal factors. The data indicate that different proteins show vastly different patterns of abundance variability among humans and that genetic control and longitudinal variation affect protein levels and biological processes to different degrees. The data further strongly suggest that the plasma concentrations of clinical biomarkers need to be calibrated against genetic and temporal factors. Moreover, we identified 13 cis‐SNPs significantly influencing the level of specific plasma proteins. These results therefore have immediate implications for the effective design of blood‐based biomarker studies.     

Increased brain signal variability accompanies lower behavioral variability in development

As the brain matures, its responses become optimized. Behavioral measures show this through improved accuracy and decreased trial-to-trial variability. The question remains whether the supporting brain dynamics show a similar decrease in variability. We examined the relation between variability in single trial evoked electrical activity of the brain (measured with EEG) and performance of a face memory task in children (8–15 y) and young adults (20–33 y). Behaviorally, children showed slower, more variable response times (RT), and less accurate recognition than adults. However, brain signal variability increased with age, and showed strong negative correlations with intrasubject RT variability and positive correlations with accuracy. Thus, maturation appears to lead to a brain with greater functional variability, which is indicative of enhanced neural complexity. This variability may reflect a broader repertoire of metastable brain states and more fluid transitions among them that enable optimum responses. Our results suggest that the moment-to-moment variability in brain activity may be a critical index of the cognitive capacity of the brain.     

Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers

Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary.     

Deciphering allelic variability and population structure in buckwheat: An analogy between the efficiency of ISSR and SSR markers

Food and nutritional security continue to be the issues of concern in developing countries like ours. Exploring the reservoir of high potential unexplored genetic resources could address the world’s food and nutritional insecurity. The availability of diverse data and the population structure of any crop germplasm is a valuable genetic resource for discovering genes that can help achieve food and nutritional stability. We used seven ISSR and seven SSR markers to investigate diversity among 63 buckwheat genotypes, including landraces from India''s northwestern Himalayas. Various parameters such as percent polymorphism, PIC, resolving power, and marker index was used to evaluate the inequitable efficacy of these markers. We foundthat both marker systems are effective in detecting polymorphism in buckwheat germplasm. Seven ISSRs produced 55 polymorphic bands, while seven SSRs produced 32bands. When compared to ISSRs, SSRs had a greater average PIC value (0.43) than that of (0.36). ISSRs, on the other hand, had a resolving power of (4.38) compared to (1.42) for SSRs. The hierarchical cluster analysis dendrogram divided genotypes into three major clusters. We found that both marker systems were equally accurate in grouping buckwheat genotypes according to their geographical origins. Using 7 ISSR and 7 SSR markers, the model-based STRUCTURE analysis established a population with two sub-populations that correspond to species-based groupings. Within the population, there was a high level of genetic diversity. These results have consequences for both buckwheat breeding and conservation efforts.Keyword: Buckwheat, SSR, ISSR, Genetic diversity, Population structure     

Genetic variability at neutral markers,quantitative trait land trait in a subdivided population under selection

Genetic variability in a subdivided population under stabilizing and diversifying selection was investigated at three levels: neutral markers, QTL coding for a trait, and the trait itself. A quantitative model with additive effects was used to link genotypes to phenotypes. No physical linkage was introduced. Using an analytical approach, we compared the diversity within deme (H(S)) and the differentiation (F(ST)) at the QTL with the genetic variance within deme (V(W)) and the differentiation (Q(ST)) for the trait. The difference between F(ST) and Q(ST) was shown to depend on the relative amounts of covariance between QTL within and between demes. Simulations were used to study the effect of selection intensity, variance of optima among demes, and migration rate for an allogamous and predominantly selfing species. Contrasting dynamics of the genetic variability at markers, QTL, and trait were observed as a function of the level of gene flow and diversifying selection. The highest discrepancy among the three levels occurred under highly diversifying selection and high gene flow. Furthermore, diversifying selection might cause substantial heterogeneity among QTL, only a few of them showing allelic differentiation, while the others behave as neutral markers.     

Analysis of population genetic structure and variability using RAPD markers in the endemic and endangered Limonium dufourii (Plumbaginaceae)

Limonium dufourii (Plumbaginaceae) is a triploid species, with apomictic reproduction, endemic to the east mediterranean coast of Spain, where it is present in only six populations with a few individuals in most of them. L. dufourii is included in the Red List of Endangered Species by the IUCN. Genetic variation and population structure in this species has been studied using RAPDs. Twelve different primers provided 124 reliable bands of which 33 were polymorphic among the 165 individuals analysed. Those polymorphic bands were able to define 44 different patterns, of which all but six were present in only one population. Several methods for statistical evaluation have been used for intra- and interpopulation analysis of genetic variability. Relationships among patterns have led to the identification of four main clusters. Two of them show a perfect correspondence to the population of origin of those individuals that present them (Cullera and Torreblanca), and the other two (Groups A and B) include patterns found in individuals coexisting in the same populations (Marjal del Moro populations) and in El Saler. Most of the variation found in this species is due to differences among populations as shown by the analysis of molecular variance. This agrees with the expectation for an apomictic species such as L. dufourii . The analysis of homogeneity of variance shows that substantial differences in the amount of genetic variability present in the six populations exist. These results have been used to understand the evolutionary and demographic history of L. dufourii , which is a requisite in order to establish efficient conservation measures for this species.     

The variability of orchid population size

Orchid population size has long been believed to be highly variable in time and space. Here we present the first quantitative assessment of the variability of orchid population sizes and compare them with plant and animal population data from the literature. Three measures of temporal variation were used (standard deviation of log₁₀ (population size), Hurst exponent and variance in the intrinsic rate of increase). Eight unfertilized plots of Orchis morio in a factorial fertilizer experiment were assessed for variability in population size over a 26 year period. The Hurst exponent across the eight plots gave measures consistent with pink noise well into black noise (0.86 to 1.87). The variation in the intrinsic rate of increase suggested that the expected time to extinction in the plots differed by an order of magnitude. Standard deviation of log₁₀ (population size) across plots was greater than the corresponding temporal variation within plots. Standard deviation of log₁₀ (population size) reached an asymptote between 10 and 20 years. The range of temporal variation between plots in this and other orchid populations was as great as the mean values reported for birds, insects and mammals. These results have highlighted the importance of spatial variation: until we know the relative importance of spatial and temporal variation for more plant species we will be unable to assess whether orchid populations are more variable in size than other species.     

Ultrasound versus biological markers in the evaluation of periportal fibrosis in human Schistosoma mansoni

In this paper, the authors review the literature and share their experience of the principal biological markers of fibrosis for the evaluation of periportal fibrosis (PPF) caused by mansoni schistosomiasis. These biological markers are compared to diagnostic ultrasound (US) scans as means of grading PPF. We also review procollagen type I and III, collagen type IV, laminin, hyaluronic acid (HA), immunoglobulin G, platelets, aspartate aminotransferase to platelet ratio index (APRI) and gamma-glutamyl transpeptidase as markers of the disease. Although there are several good markers for evaluating PPF and portal hypertension, such as HA, platelets or APRI, none can yet replace US. These markers may, however, be used to identify patients at greater risk of developing advanced disease in endemic areas and determine who will need further care and US studies.     

Patterns and variability in electrophoretic polypeptide profiles of human saliva in a healthy population

Electrophoretic polypeptide profiles of normal human saliva differ markedly between different reports. Since both methodological variations and polymorphism may explain these differences, in this study we aimed to establish whether or not the salivary electrophoretic polypeptide profiles of subjects from a healthy population share discrete molecular features. To this end, parotid, submandibular/sublingual and whole salivas were collected separately from each of 40 young and 34 elderly clinically healthy adults and processed for SDS-polyacrylamide gel electrophoresis and Coomassie blue staining. Each type of glandular saliva displayed a different group of invariant (i.e. present in every subject) electrophoretic polypeptide bands while whole saliva showed a profile that reflected mostly the combined contribution of the major salivary glands. Some minor variant (i.e. absent in some subjects) bands were identified in each type of saliva. Regarding those interindividual variations, no age- or sex-dependence was appreciated. Altogether, these results demonstrate the occurrence of distinctive electrophoretic polypeptide patterns, in addition to some minor variations, for each type of normal saliva, thus providing a background for further populational studies on salivary polypeptide profiles.     

Genetic variability and population structure of Bergenia ciliata (Saxifragaceae) in the Western Himalaya inferred from DAMD and ISSR markers

Genetic variability and population structure of Bergenia ciliata (Haw.) Sternb., commonly known as “Pashanbheda” (Stone-breaker), collected from the Western Himalayan region of India were estimated using two DNA fingerprinting methods viz., directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR). The cumulative data analysis of DAMD and ISSR markers for 74 accessions from eight populations showed 86.1% polymorphism. Analysis of molecular variance (AMOVA) showed highest percentage of variation within individuals of populations (73.6%) and 21.7% among populations. STRUCTURE and PCoA analyses on the hierarchical partitioning of genetic diversity showed strong admixture of individuals among the eight assumed geographical populations of B. ciliata. The data suggests that high genetic flow is one of the major factors responsible for low genetic differentiation. Preservation of genetic diversity of B. ciliata is important, both to promote adaptability of the populations to changing environment as well as to preserve a large gene pool for future prospection. The present study using DAMD and ISSR markers, therefore, provide the means of rapid characterization of accessions within the populations, and thus enable the selection of appropriate accessions for further utilization in conservation and prospection programmes.     

PRP gene variability in the us cattle population

Abstract

The primary amino acid sequence of the prion protein (PrP) has previously been correlated with changes in the incubation period of subacute spongiform encephalopathies. We have analyzed the PrP gene from 65 different cattle representing 14 breeds by polymerase chain reaction and restriction enzyme analysis. Two distinct PrP alleles differing in the number of octapeptide repeats are present. The predominant genotype is homozygous for 6 octapeptide repeats. Few individuals (8) were found to be heterozygous for these repeats and only 1 animal was homozygous for the 5 octapeptide repeat allele.     

Genetic variability and population structure of Mexican chickpea (Cicer arietinum L.) germplasm accessions revealed by microsatellite markers

Journal of Plant Biochemistry and Biotechnology - Globally, the chickpea is the second most important dried grain legume after bean. Mexico occupies eighth place as producer and fourth as exporter...     

Quantifying temporal variability in population abundances

Understanding variability of population abundances is of central concern to theoretical and applied evolutionary ecology, yet quantifying the conceptually simple idea has been substantially problematic. Standard statistical measures of variability are particularly biassed by rare events, zero counts and other 'non-Gaussian' behaviour, which are often inappropriately weighted or excluded from analysis. I conjecture that these problems are primarily a function of calculating variation as deviation from an average abundance, while the average may not be static, nor actually reflect abundance at any point in the time series. Here I describe a simple metric (population variability PV) that quantifies variability as the average percent difference between all combinations of observed abundances. Zero counts can be included if desired. Similar to standard metrics, variability is measured on a proportional scale, facilitating comparative applications. Standard metrics are based on Gaussian distributions, are over-sensitive to rare events and heavy tailed behaviour, and can inappropriately indicate 'more time-more variation' effects (reddened spectrum). Here I demonstrate that, while PV behaves similarly for 'normal' time series, it is independent of deviation from mean abundance for heavy tailed distributions, its robustness to non-Gaussian behaviour resolves artificial reddened spectrum issues, and variability calculated using PV from short time series is substantially more accurate at estimating known long term variability than standard metrics. PV therefore provides common ground for evaluating the variability of populations undergoing different dynamics, and with different statistical distributions of abundance, and can be easily generalized to a variety of contexts and disciplines.