Computer technology of genogeographic study of the gene pool. IV. Population in the space of principal components

On the basis of maps of principal components ("synthetic maps"), populations were arranged in the space of principal components. In terms of the applied model, nodes of a dense, uniform grid represented human populations. For each node, the frequency of a given gene was interpolated from these values for all original populations. Principal components were estimated and mapped on the basis of maps for all genes. Each population (grid node) was assigned a marker of an ethnic or some other group of populations and was positioned in the space of principal components according to the values from the original maps. The resultant "ethnic clouds" of populations and "ethnic centroids" of principal components provide some new possibilities for explaining the patterns of changes in gene pools. The maps of reliability of principal components allow the researcher to eliminate the information on populations which is unreliable and turn to the "reliable" space of principal components. The method was tested with the use of the maps of principal components for the gene pool of the East European population. Eastern Slavonic (Russians, Ukrainians, and Belarussians) and western and eastern Finno-Ugrian (Estonians and Mordovians, respectively) ethnic groups were mapped to the space of principal components. The relative positions of the populations of these ethnic groups was analyzed in the spaces of the first and the second, the first and the third, and the second and the third principal components of the East European gene pool.     

A high-resolution metric HAPPY map of human chromosome 14

We have mapped 1001 novel sequence-tagged sites on human chromosome 14. The mean spacing between markers is approximately 90 kb, most markers are mapped with a resolution of better than 100 kb, and physical distances are determined. The map was produced using HAPPY mapping, a simple and widely applicable in vitro approach that is analogous to linkage or to radiation hybrid mapping, but that circumvents many of the difficulties and potential artifacts associated with these methods. We show also that the map serves as a robust scaffold for building physical maps using large-insert clones.     

Landmarks in the development of coronary artery bypass surgery

Genetic linkage maps have been produced for a wide range of organisms during the last decade, thanks to the increasing availability of molecular markers. The use of microsatellites (or Simple Sequence Repeats, SSRs) as genetic markers has led to the construction of "second-generation" genetic maps for humans, mouse and other organisms of major importance. We constructed a second-generation single-tree genetic linkage map of Norway spruce (Picea abies K.) using a panel of 72 haploid megagametophytes with a total of 447 segregating bands [366 Amplified Fragment Length Polymorphisms (AFLPs), 20 Selective Amplification of Microsatellite Polymorphic Loci (SAMPLs) and 61 SSRs, each single band being treated initially as a dominant marker]. Four hundred and thirteen markers were mapped in 29 linkage groups (including triplets and doublets) covering a genetic length of 2198.3 cM, which represents 77.4% of the estimated genome length of Picea abies (approximately 2839 cM). The map is still far from coalescing into the expected 12 chromosomal linkage groups of Norway spruce (2n = 2x = 24). A possible explanation for this comes from the observed non-random distribution of markers in the framework map. Thirty-eight SSR marker loci could be mapped onto 19 linkage groups. This set of highly informative Sequence Tagged Sites (STSs) can be used in many aspects of genetic analysis of forest trees, such as marker-assisted selection, QTL mapping, positional cloning, gene flow analysis, mating system analysis and genetic diversity studies.     

Cerebral cartography--a method for visualizing cortical structures

We present a method for visualizing the human cortex on one planar map. The data are taken from a 3D MRI study. Ray tracing with non-parallel rays is used to project the cortical relief onto a non-planar projection surface, which is in turn mapped onto the plane by cartographical projection. Two modifications of the method are proposed: the spherical mapping uses a sphere as the projection surface; the model-based mapping uses an analytically defined model of the scalp to generate the normal vectors. The cerebral cartography can be used for example for producing anatomical reference maps on which EEG measurement data can be superimposed.     

A NotI restriction map of the entire long arm of human chromosome 21

A variety of maps of the human genome have been constructed, including cloned DNA maps. We have isolated 40 of the 42 NotI sites that exist on the long arm of human chromosome 21, as NotI linking clones and constructed a complete NotI restriction map spanning the entire region. This map, which provides the most reliable ordering and distance estimation in the region from a pericentromeric locus to the terminus, demonstrates the usefulness of linking clone mapping for analysing human chromosomes.     

Physical mapping of unique nucleotide sequences on identified rice chromosomes

A physical mapping method for unique nucleotide sequences on specific chromosomal regions was developed combining objective chromosome identification and highly sensitive fluorescence in situ hybridisation (FISH). Four unique nucleotide sequences cloned from rice genomic DNAs, varying in size from 1.3 to 400 kb, were mapped on a rice chromosome map. A yeast artificial chromosome (YAC) clone with a 399 kb insert of rice genomic DNA was localised at the distal end of the long arm of rice chromosome (1q2.1) and a bacterial artificial chromosome (BAC) clone (180 kb) containing the rice leaf blast-resistant gene (Pi-b) was shown to occur at the distal end of the long arm of chromosome 2 (2q2.1). A cosmid (35 kb) with the resistance gene (Xa-21) against bacterial leaf blight was mapped on the interstitial region of the long arm on chromosome 11 (11q1.3). Furthermore a single RFLP marker, 1.29 kb in size, was mapped successfully to the distal region of the long arm of rice chromosome 4 (4q2.1). For precise localisation of the nucleotide sequences within the chromosome region, image analyses were effective. The BAC clone was localised to the specific region, 2q2.1:96.16, by image analysis. The result was compared with the known location of the BAC clone on the genetic map and the consistency was confirmed. The effectiveness and reliability in physically mapping nucleotide sequences on small plant chromosomes achieved by the FISH method using a variety of probes was unequivocally demonstrated.     

Effect of prolonged staining with hematoxylin on detecting Helicobacter pylori in hematoxylin-eosin-stained gastric mucosa

Rab proteins are small GTP-ases localized to distinct membrane compartments in eukaryotic cells and regulating specific steps of intracellular vesicular membrane traffic. The Rab7 protein is localized to the late endosomal compartment and controls late steps of endocytosis. We have isolated, by library screening, the 5' region, including the promoter, of the mouse Rab7 gene and a Rab7 pseudogene. We have mapped, by genetic linkage analysis, the mouse Rab7 gene on Chromosome (Chr) 6 and the Rab7-ps1 pseudogene on Chr 9, where the Rab7 gene has been previously reported to map. By radiation hybrid mapping, we have located the human RAB7 gene on Chr 3, in a region homologous to the mouse Chr 6, where the Rab7 gene maps.     

Porcine linkage and cytogenetic maps integrated by regional mapping of 100 microsatellites on somatic cell hybrid panel

Recently two main genetic maps [Rohrer et al. Genetics 136, 231 (1994); Archibald et al. Mamm. Genome 6, 157 (1995)] and a cytogenetic map [Yerle et al. Mamm. Genome 6, 175 (1995)] for the porcine genome were reported. As only a very few micro-satellites are located on the cytogenetic map, it appears to be important to increase the relationships between the genetic and cytogenetic maps. This document describes the regional mapping of 100 genetic markers with a somatic cell hybrid panel. Among the markers, 91 correspond to new localizations. Our study enabled the localization of 14 new markers found on both maps, of 54 found on the USDA map, and of 23 found on the PiGMaP map. Now 21% and 43% of the markers on the USDA and PiGMaP linkage maps respectively are physically mapped. This new cytogenetic information was then integrated within the framework of each genetic map. The cytogenetic orientation of the USDA linkage maps for Chromosomes (Chrs) 3, 8, 9, and 16 and of PiGMaP for Chr 8 was determined. USDA and PiGMaP linkage maps are now oriented for all chromosomes, except for Chrs 17 and 18. Moreover, the linkage group "R" from the USDA linkage map was assigned to Chr 6.     

Contribution to the physically anchored linkage map of the pig

Thirty-three microsatellites have been mapped on the PiGMaP porcine genetic map. By comparison with the previously published PiGMaP maps, the maps of chromosome 2 (140 cM/70 cM) and chromosome 3 (180 cM/110 cM) were extended and new markers were mapped on the p-arm extremity of chromosome 7 and on the centromeric extremity of chromosome 15. New orders are proposed for markers on chromosomes 3 and 17. Six microsatellites isolated from cosmids were also localized on the cytogenetic map by fluorescent in situ hybridization. We tested the subcloning ligation mixture-polymerase chain reaction (SLiM-PCR) method for isolating microsatellites from cosmids. Subcloning is more effective when the cosmid harbours several microsatellites whereas SLiM-PCR is more straightforward when the cosmid contains a single microsatellite. Fifteen anonymous microsatellites were regionally assigned by using a hybrid cell panel. For map integration, the determination of a regional assignment of anonymous microsatellites by using a hybrid cell panel offers an alternative to microsatellite isolation from cosmids and their localizations by in situ hybridization.     

Unpacking the cognitive map: The parallel map theory of hippocampal function.

In the parallel map theory, the hippocampus encodes space with 2 mapping systems. The bearing map is constructed primarily in the dentate gyrus from directional cues such as stimulus gradients. The sketch map is constructed within the hippocampus proper from positional cues. The integrated map emerges when data from the bearing and sketch maps are combined. Because the component maps work in parallel, the impairment of one can reveal residual learning by the other. Such parallel function may explain paradoxes of spatial learning, such as learning after partial hippocampal lesions, taxonomic and sex differences in spatial learning, and the function of hippocampal neurogenesis. By integrating evidence from physiology to phylogeny, the parallel map theory offers a unified explanation for hippocampal function. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Early Development of Scaling Ability.

The map is a small-scaled version of the space it represents. It has been argued that children have difficulty interpreting maps because they do not understand scale relations. Recent research has shown that even preschoolers can solve problems that involve scaling in one dimension. This study examined whether early scaling ability extends to tasks involving two-dimensional maps and referent spaces of different sizes. Results showed that about 60% of the 4-year-olds and 90% of the 5-year-olds tested used distance information presented on a map to locate an object in a two-dimensional spatial layout. Children had more difficulties in solving mapping tasks with a larger referent space. This decrease in accuracy as a function of space size on the mapping task was greater than would have been expected on the basis of performance on a parallel nonmapping task. The results are discussed in terms of their implications for the mechanisms underlying early scaling ability. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Immunogenetics and the cause of autoimmune disease

Up until recently, neurology was dominated by localisatory thinking. Language and other so-called "centers" were considered to be centers of command controlling the respective functions. Today, there is general agreement that, instead, for every brain function numerous brain regions must act together. For the exploration of these manifold topographic cooperations produced by cognitive tasks, coherence of long-term EEG periods proved to be a proficient parameter for the representation of functionally essential connections. Because of the unequivocal meaningfulness of absolute coherence values, instead, only the signs of significant differences between coherence values during cognitive tasks and periods of EEG at rest before and after the task were considered for all possible electrode pairings and charted on schematic maps of the brain. In addition, the signs of significant changes of amplitude were entered. This procedure was performed for each of 6 frequency bands and for the 19 electrodes of the 10/20 system, thus yielding 171 possible plus or minus values for coherence and 19 for amplitude, respectively. The positions of the electrodes were marked by an MRI contrast medium. After the EEG, MRI examination was performed. The MRI data were segmented and the cortex was mapped onto a plane using a method similar to cartography. The exact electrode positions are registered from a similarly obtained map of the scalp and the electrode position pattern is used as basis for the coherence graphs. A detailed map of the cortex based on the segmented MRI data with the electrode positions marked is provided as a reference enabling allocation of the electrodes to the cortical structures. The usefulness of this procedure is demonstrated with a single subject by means of different cognitive tasks including musical thinking.     

Mapping TNNC1, the gene that encodes cardiac troponin I in the human and the mouse

We have mapped the TNNC1 gene, whose protein product is the cardiac TnI protein. TnI is one of the proteins that makes up the troponin complex, which mediates the response of muscle to calcium ions. The human TNNC1 locus had been assigned to a large region of chromosome 19, and we have refined the mapping position to the distal end of the chromosome by amplification of DNAs from a chromosome 19 mapping panel. We have also mapped the mouse Tnnc1 locus, by following the segregation of an intron sequence through DNAs from the European Interspecific Backcross. Tnnc1 maps close to the centromere on mouse chromosome 7.     

Probability distributions and compartment boundaries in the development of Drosophila

Clone analysis and fate mapping probe several properties of development. Here it is shown that data on fate mapping support a probabilistic model of cell commitment in Drosophila blastoderms. Adult cells have a distribution of possible ancestors, as W. Baker (1978b) inferred from the theory of compartment-boundary development (Garcia-Bellido, Ripoll and Morata 1973). Fate-map data are used here to describe quantitatively the ancestry distributions on the blastoderm fate map. The properties of the distributions are sensitive to, and probes of, developmental events, such as relative time of cellularization and time of commitment. The theory of this analysis shows first how the meaningful interpretation of the stage represented by a fate map depends on the assumptions made in mapping. A general mapping model described below makes it possible to evaluate several interpretations. Interestingly, the data require a 3-dimensional map, and it is argued that this must be due to an effect of the preblastoderm nuclear synctial stage. Second, the theory shows how compartment boundaries affect ancestry distribution and why they have no observable effect on mapping. Third, the variability implied by ancestry variance does not create too much "noise" to make meaningful maps of small areas; rather, oddly enough, it tends to magnify the apparent distances within small areas to make them more resolvable. Empirical results include probabilistic maps of the Drosophila blastoderm. These results argue that time of commitment varies even for cells in the same compartment, demonstrating the need for a more complex model of early development than that proposed in the compartment model. The results also help to evaluate the significance of compartment boundaries in respect to developmental commitment.     

Node-link mapping and the evaluation of drug abuse counseling sessions.

Node-link mapping is a visual representation system that can be used in group and individual counseling sessions to illustrate clients' problems, issues, and plans. One hundred sixty-nine methadone treatment clients and their 10 counselors evaluated each of their individual and group sessions during a 2.5-month period by using the Session Evaluation Questionnaire (W. B. Stiles, 1980) and map rating items. A series of multivariate analyses of variance and correlational analyses indicated that the use of mapping (including the quantity and quality of mapping) was positively related to higher ratings of session depth by both clients and counselors. In addition, mapped group sessions were rated higher on several evaluative dimensions than were mapped individual sessions. (PsycINFO Database Record (c) 2010 APA, all rights reserved)