Gene pool and gene geography of the USSR population]

Gene pool and gene geography are discussed from the point of view of their conceptual history beginning from the original concept of A.S. Serebrovski? (1928). Difference between the present-day gene geography and gene geography of gene pool is accentuated: the former only represents a portion of the latter. Historical and territorial integrity of the USSR population gene pool, in conjunction with its huge diversity, is the main problem being analysed by various means of computerized genetic cartography. Coupled with the gene frequency mapping, following methods were also used: mapping of average heterozygosity, of interpopulation differentiation, of principal component scores and mapping of geographical trend for each mapped genetic parameter. The work is based on 100 allelic genes and haplotypes from 30 independent loci studied on the average in 225 local populations. Statistical analysis of gene geographical maps is based on 3975 nodes of regular cartographic net for the USSR territory. The wind rose of systematic changes in the USSR gene pool has three main geographic orientations: W-E, SW-NE and S-N. At the same time, there are only two main systematic forces of gene pool evolution: the force of social history with predominant W-E orientation and the force of natural history with predominant S-N orientation of their actions. The heterozygosity level of gene pool declines strictly in accordance with the resultant in the SW-NE direction.     

Gene geography of South America: testing models of population displacement based on archeological evidence.

Gene frequencies for 13 marker systems are used to construct synthetic gene frequency maps of South America. The surfaces generated using the first three principal components exhibit clines which validate models of population displacement based on archeological data and a previous analysis of craniometrical variation.     

An atlas of human kinase regulation

The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision‐making has been limited by the small number of simultaneously monitored phospho‐regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs. Co‐regulation along the conditions predicts kinase–complex and kinase–substrate associations. Additionally, the kinase regulation profile acts as a molecular fingerprint to identify related and opposing signaling states. Using this atlas, we identified essential mediators of stem cell differentiation, modulators of Salmonella infection, and new targets of AKT1. This provides a global view of human phosphorylation‐based signaling and the necessary context to better understand kinase‐driven decision‐making.     

Beta-thalassemia in the Po Delta: selection, geography, and population structure

The allele frequencies for beta-thalassemia for 51 localities in the province of Rovigo, and in 25 localities in the province of Ferrara, were studied. It was observed that in the province of Ferrara there is a significant cline of frequencies; these decrease from the coast of the Adriatic Sea toward the west. No such gradient was visible in Rovigo. It was advanced, also on the basis of geography documented by ancient maps, that in the province of Rovigo there were multiple foci of selection for the thalassemia gene, and that in the province of Ferrara selection was stronger in the Oriental part of the area. Examination of the isolation by distance model with these data showed that the Malécot-Morton model fits for the Ferrara data and geography, whereas it does not for Rovigo.     

Medico-genetic study of the population of Turkmenia. IV. The population geography of hemoglobinopathies

Large-scale screening for hereditary haemoglobinopathies in five districts and among main Turkmen tribes was carried out. The frequencies of ABO and HP pheno- and genotypes were determined in the same populations. The different kinds of haemoglobinopathies genes were discovered (beta +, beta 0-thalassemia, alpha beta-thalassemia, alpha-thalassemia, HPFH, haemoglobins D and E). The geographic and ethnic differentiation of Turkmen population for beta-thalassemia géne was discovered. The FST values were found to be the same for ABO, Hp and beta-thal gene systems. The role of genetic drift in differentiation of Turkmen population is discussed.     

Spatial interaction models: from human geography to plant-herhivore interactions

The spatial pattern of defoliation by mammalian herbivores across vegetation mosaics bas been frequently discussed, but rarely spatially quantified. Here we considered the role of plant-herbivore interactions in determining the spatial distribution of shrub defoliation by a large mammalian herbivore across a grass-shrub mosaic.
We investigated the spatial pattern of heather defoliation by sheep in heather-grass mosaics. Heather-grass mosaics are two-phased vegetation mosaics, in which a spatially localized plant community (grass) fulfils nutritional needs, whilst a spatially extensive plant community (heather) meets energy requirements but is nutritionally marginal.
We used a spatial analysis method, originating from human geography, to show that heather defoliation was not spread across the mosaic homogeneously, but that the spatial pattern was determined by geometric characteristics of the mosaic, grazing intensity, and the contrast between preferred and less preferred communities.
The spatial analysis method proved to be a powerful tool to describe the spatial pattern of shrub defoliation. Applications of the method are explored and the implications of the spatial distribution of shrub defoliation are discussed.     

Osteometry by computer-aided image analysis: application to the human atlas

Computer-assisted image-analysis having almost not been applied to macroscopical anatomy, particularly to osteometry, we used it for the automatic measurement of 8 osteological parameters on a series of 150 human atlases. From these measured parameters, 5 parameters have been directly calculated. The values obtained by image analysis and by measurement with vernier calliper are identical and similar to the data of the literature. The accuracy, the sources of error, and the great advantages of the image analysis method are then discussed.     

Genetic variation within two linguistic Amerindian groups: relationship to geography and population size

Nine Carib and eight Tupi groups were studied for a minimum of eight common polymorphic systems and compared in terms of genetic distances using the methods of Nei and Edwards. Two levels of genetic information were distinguished, one with a maximum of 20 loci and another with a maximum of 12 loci considered. The dendrograms produced consistent, reproducible results, independent of the method used, when a minimum of ten polymorphic systems were included in the analysis. Irrespective of the number of systems or the method used, the Tupi showed two to three times higher average interpopulation genetic distances than the Carib groups, which may be due to their lower average population sizes, allowing for the action of genetic drift and/or founder effects, as these two sets of populations do not differ significantly in geographic range, years of contact with non-Indians, or degree of acculturation.     

The human secretome atlas initiative: Implications in health and disease conditions

Proteomic analysis of human body fluids is highly challenging, therefore many researchers are redirecting efforts toward secretome profiling. The goal is to define potential biomarkers and therapeutic targets in the secretome that can be traced back in accessible human body fluids. However, currently there is a lack of secretome profiles of normal human primary cells making it difficult to assess the biological meaning of current findings. In this study we sought to establish secretome profiles of human primary cells obtained from healthy donors with the goal of building a human secretome atlas. Such an atlas can be used as a reference for discovery of potential disease associated biomarkers and eventually novel therapeutic targets. As a preliminary study, secretome profiles were established for six different types of human primary cell cultures and checked for overlaps with the three major human body fluids including plasma, cerebrospinal fluid and urine. About 67% of the 1054 identified proteins in the secretome of these primary cells occurred in at least one body fluid. Furthermore, comparison of the secretome profiles of two human glioblastoma cell lines to this new human secretome atlas enabled unambiguous identification of potential brain tumor biomarkers. These biomarkers can be easily monitored in different body fluids using stable isotope labeled standard proteins. The long term goal of this study is to establish a comprehensive online human secretome atlas for future use as a reference for any disease related secretome study. This article is part of a Special Issue entitled: An Updated Secretome.     

Estimation of the population density and its significance in gene geography]

A factor of the association between gene geographical data and populations of the mapped region was analyzed. This allowed for correction of the equations for the major statistical parameters of gene geographical maps (mean, variance, etc.) and gene geographical methods of estimating the spatial nonstationarity of data within a mapped region. The proposed approach is based on the use of the population density in a mapped region as a factor reflecting the anisotropy of the geographical space. The population density of the North Eurasian indigenous populations was mapped, and the application of the resulting map was illustrated with an example.     

Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling

A great need exists for the systematic generation of specific antibodies to explore the human proteome. Here, we show that antibodies specific to human proteins can be generated in a high-throughput manner involving stringent affinity purification using recombinant protein epitope signature tags (PrESTs) as immunogens and affinity-ligands. The specificity of the generated affinity reagents, here called mono-specific antibodies (msAb), were validated with a novel protein microarray assay. The success rate for 464 antibodies generated towards human proteins was more than 90% as judged by the protein array assay. The antibodies were used for parallel profiling of patient biopsies using tissue microarrays generated from 48 human tissues. Comparative analysis with well-characterized monoclonal antibodies showed identical or similar specificity and expression patterns. The results suggest that a comprehensive atlas containing extensive protein expression and subcellular localization data of the human proteome can be generated in an efficient manner with mono-specific antibodies.