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PubMed1995

First international workshop on porcine chromosome 6. Report and abstracts.

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

Animals↗

PubMed1992

Three-dimensional whole-brain mapping.

The implementation and use of a computerized whole-brain mapping system which can be used in conjunction with MRI, CT, angiographic and other brain imaging techniques is described. Three mapping systems based upon common reference structures about the third and fourth ventricular core of the brain are used in conjunction with internationally recognized nomenclature to create a normalized whole-brain mapping system according to the Talairach/Tournoux proportional grid technique.

Brain↗

PubMed1995

Genetic and physical mapping of the natural resistance-associated macrophage protein 1 (NRAMP1) in chicken.

The chicken natural resistance-associated macrophage protein 1 (NRAMP1) gene has been mapped by linkage analysis by use of a reference panel to develop the chicken molecular genetic linkage map and by fluorescence in situ hybridization. The chicken homolog of the murine Nramp 1 gene was mapped to a linkage group located on Chromosome (Chr) 7q13, which includes three genes (CD28, NDUSF1, and EF1B) that have previously been mapped either to mouse Chr 1 or to human Chr 2q. Physical mapping by pulsed-field gel electrophoresis revealed that NRAMP1 is tightly linked to the villin gene and that the genomic organization (gene order and presence of CpG islands) of the chromosomal region carrying NRAMP1 is well conserved between the chicken and mammalian genomes. The regions on mouse Chr 1, human Chr 2q, and chicken Chr 7q that encompass NRAMP1 represent large conserved chromosomal segments between the mammalian and avian genomes. The chromosome mapping of the chicken NRAMP1 gene is a first step in determining its possible role in differential susceptibility to salmonellosis in this species.

Animals↗

PubMed2005

Localization of repetitive DNA sequences on in vitro Xenopus laevis chromosomes by primed in situ labeling (PRINS).

Xenopus laevis is an important reference model organism used in many vertebrate studies. Gene mapping in X. laevis, in comparison to other reference organisms, is in its early stages. Few studies have been conducted to localize DNA sequences on X. laevis chromosomes. Primed in situ labeling (PRINS) is a recently developed innovative tool that has been used to locate specific DNA sequences in various organisms. PRINS has been reported to have increased sensitivity compared to other in situ hybridization techniques. In the present study, PRINS was first used to label the location of telomeres at the ends of in vitro X. laevis chromosomes. The terminal location was as expected from in vivo reports, however, the overall amount seemed to decrease in the in vitro chromosomes. Once the PRINS technique was optimized, this technique was used to determine the chromosomal location of the satellite 1 repetitive sequence, which is an important sequence in X. laevis development. The sequence was observed on the interstitial regions of the majority of the chromosomes similar to the in vivo locations reported. In contrast to the telomeric sequence, the amount of sequence appeared to increase in the satellite 1 sequence. PRINS was found to be useful in the localization of repetitive DNA sequences in the X. laevis genome.

Animals↗

PubMed1990

A genetic linkage map of chromosome 17.

We have developed a genetic linkage map of 19 markers (including nine genes) on human chromosome 17, providing 13 reference points along virtually the entire length of this chromosome. The map covers an estimated 149 cM in length (sex-averaged), with a total length of 214 cM in females and 95 cM in males. This sex difference appears to be significant along virtually the entire length of the map. This map will be useful both for providing reference points for fine structure genetic and physical mapping and for genetic linkage studies of diseases, including von Recklinghausen neurofibromatosis and Charcot-Marie-Tooth disease.

Chi-Square Distribution↗

PubMed1989

Perceptual and conceptual factors in distortions in memory for graphs and maps.

We propose that representations of visual stimuli are a consequence of both perceptual and conceptual factors that may be revealed in systematic errors in memory. Three experiments demonstrated increased (horizontal or vertical) symmetry in perception and memory of nearly symmetric curves in graphs and rivers in maps. Next, a conceptual factor, an accompanying description biasing toward symmetry or asymmetry, also distorted memory in the expected direction for the symmetric descriptions. In the two final experiments, we investigated conceptual factors in selection of a frame of reference. Subjects remembered lines in graphs, but not in maps, as closer to the imaginary 45 degrees line. Combined with earlier research, this suggests that the reference frame for map lines is the canonical axes and for graph lines, the imaginary 45 degrees line.

Adult↗

PubMed2002

Wavelet-aided parametric mapping of cerebral dopamine D2 receptors using the high affinity PET radioligand [11C]FLB 457.

The study of human neuroreceptor systems by means of positron emission tomography (PET) and suitable radioligands has proven to be of great importance in research on normal brain functions and the pathophysiology and treatment of neuropsychiatric disorders. A for long identified goal is to produce detailed parametric maps of showing neuroreceptor binding parameters for the entire human brain in vivo. The application of wavelet filters has recently been proposed as a solution to handle the inherently low signal-to-noise ratio of PET images. In the present study we applied the wavelet approach to data obtained from 10 healthy subjects who were examined with [11C]FLB 457. This high affinity dopamine D2-receptor antagonist provides a signal from a range of regions with a hundredfold difference in receptor density and should thus be suitable for evaluation of the wavelet approach. For cross-validation purposes the data were analysed with four methods: a traditional region-of-interest (ROI) based analysis, a pixel-based analysis and two variants of wavelet-aided analyses. In both variants the wavelet filter was spatially applied, but a two-dimensional filter was used in one case and a three-dimensional one in the other. The same linear-graphical binding potential (BP) estimation step was used for all methods and the results of the three parametric mapping techniques were compared to the reference ROI-based method by calculating the average BP of representative ROIs. The pixel-based and the two-dimensional-wavelet-based methods yielded highly correlated but systematically lower values when compared to the reference ROI-based method. The approach utilising three-dimensional wavelet filters yielded BP maps with regional averages closely matching the values of the ROI-based method. The results show that the combination of three-dimensional spatial wavelet filtering with established parameter estimation procedures provides detailed, accurate maps of radioligand binding parameters. Such maps can be used for in inter-individual or multi-condition comparisons of binding parameters at subregional levels.

Adult↗

PubMed1994

Genetic mapping of 14 short tandem repeat polymorphisms on human chromosome 22.

We have constructed a linkage map of 14 short tandem repeat polymorphisms (11 with heterozygosity > 70%) on the long arm of human chromosome 22 using 23 non-CEPH pedigrees. Twelve of the markers could be positioned uniquely with a likelihood of at least 1,000:1, and distributed at an average distance of 6.62 cM (range 1.5-16.1 cM). The sex-combined map covers a total of 79.6 cM, the female map 93.2 cM and the male map 64.6 cM. Based on comparisons between physical maps and other genetic maps, we estimate that our map covers 70%-80% of the chromosome. The map integrates markers from previous genetic maps and uniquely positions one marker (D22S307). Data from physical mapping on the location of four genetic markers correlates well with our linkage map, and provides information on an additional marker (D22S315). This map will facilitate high resolution mapping of additional polymorphic loci and disease genes on chromosome 22, and act as a reference for building and verifying physical maps.

Chromosome Mapping↗

PubMed2006

Transthoracic percutaneous access for electroanatomic mapping and catheter ablation of atrial tachycardia in patients with a lateral tunnel Fontan.

BACKGROUND: The incidence of atrial tachycardia following Fontan surgery is high, but access to the pulmonary venous atrium, a frequent site of arrhythmia origin, is limited. OBJECTIVES: The purpose of this study is to report our results with a novel transthoracic percutaneous technique that provides direct access to the pulmonary venous atrium for electrophysiologic procedures. METHODS: Six transthoracic ablation procedures were performed in five patients (age 1.2-17 years, weight 9.2-68.4 kg) with a lateral tunnel Fontan. Under biplane fluoroscopy, a percutaneous needle was advanced at the selected intercostal space toward the pulmonary venous atrium. Once access was confirmed, a sheath was placed over a wire and a Navistar CARTO catheter advanced for mapping and ablation. Additional catheters were placed in the baffle and esophagus for pacing and reference. Atrial tachycardia was induced, electroanatomic mapping performed, and candidate areas tested with entrainment techniques. Radiofrequency ablation was performed and success defined as the inability to reinduce tachycardia using the initiating protocol. RESULTS: All tachycardias were ablated. Procedure time ranged from 3.7 to 4.9 hours, and fluoroscopy time ranged from 31 to 70 minutes. Hospital stay was 2 days. One patient had a pneumothorax and two had a hemothorax that was drained. Tachycardia recurred in one patient at 3 months. Ablation was repeated successfully. Four patients are free of tachycardia at follow-up ranging from 6 to 29 months. Follow-up is not available for one child. CONCLUSION: Transthoracic percutaneous access provided a direct route to the pulmonary venous atrium for successful mapping and radiofrequency ablation in Fontan patients.

Adolescent↗

PubMed1977

Human papillomavirus DNA: physical mapping of the cleavage sites of Bacillus amyloliquefaciens (BamI) and Haemophilus parainfluenzae (HpaII) endonucleases and evidence for partial heterogeneity.

The DNA of human papillomavirus (HPV) obtained from a pool of plantar warts is cleaved by bacillus amyloliquefaciens (BamI) and Haemophilus parainfluenzae (HpaII) restriction endonucleases at one and four specific sites, respectively. These sites were localized on the previously established cleavage map of HPV DNA, using the Hind, HindIII, HpaI, and EcoRI endonuclease restriction sites as reference. The four HpaII sites were mapped, clockwise, at 1.4, 41.1, 44.3, and 52.8% of the genome length from the unique BamI cleavage site taken as point zero. The HpaII site mapped at 1.4% of the genome length was absent in 40 to 50% of the molecules, thus showing a genetic heterogeneity of HPV DNA.

Bacillus↗

PubMed2006

An fMRI task battery for assessing hemispheric language dominance in children.

Hemispheric dominance for language is an important issue in functional neuroimaging, particularly driven by efforts to overcome the need for the invasive Wada test, which is all the more pressing in children. Here, we aimed at developing new paradigms for functional magnetic resonance imaging (fMRI) for assessment of language dominance that can be used in younger children and allow for performance monitoring. Two new tasks (letter and animal task) were developed and compared to two reference tasks (synonyms and verb generation task) from the literature. Overall, 23 healthy children participated (13 boys, 10 girls, 10.2 +/- 2.5 years, range 6.1-15.3 years). Analysis was done using statistical nonparametrical mapping (SnPM2) on SPM2. Both reference tasks show activation in a number of left-frontal brain regions. The letter task induced a very localized activation in the left hemisphere's Broca's region, while not activating other frontal brain regions. Lateralization (as assessed in different anatomically and functionally defined regions) was consistent and strong. The animal task failed to activate frontal brain regions and was not suitable for assessing language dominance in children in this form. We conclude that while both reference tasks are useful for determining language dominance, they coactivate a number of task-related frontal areas not directly involved in language processing. Additionally, one task is not applicable in young children while the other does not allow performance monitoring. The letter task allows to selectively activate language areas in the dominant hemisphere and is applicable even in the very lowest age group amenable to fMRI investigations while still allowing performance monitoring. It may thus be a useful tool in assessing normal and pathological language organization.

Animals↗

PubMed1994

Chromosomal assignment of HepG2 3'-directed partial cDNA sequences by Southern blot hybridization using monochromosomal hybrid cell panels.

Large-scale sequencing of a 3'-directed cDNA library from the human liver cell line HepG2 has generated several hundred species of cDNA gene signatures, about 85% of which identify novel genes. They are useful molecular landmarks for human genome mapping. We used 160 of these novel signatures as probes for Southern hybridization to human DNA. We then identified the copy number of the corresponding genes and assigned them to chromosomes, with reference to monochromosomal hybrid cell mapping panels. The distribution profile of the expressing genes among chromosomes suggested that the expressing gene density is not uniform.

Animals↗

PubMed2006

Obesity-specific circuits in the human brain: exploration by dynamic Brain Self-Reference (dynBSR).

In the last decade many efforts have been made in order to identify brain regions that may be abnormal in obese subjects. Most of the lines of research have examined links between brain circuits, behavioral processing, and overweight. We introduce here a novel analysis to the brain mapping, 'dynamic Brain Self-Reference' (dynBSR), based on the electrical response evoked during passively viewing a simple stimulus. Hypothetically, it should be possible to monitor both task-related networks and task-irrelevant networks during a mental state with low cognitive demand, as shown previously by others using fMRI and establishing the latter as the neural correlates of an 'inherent' brain activation pattern. However, this fact has been usually ignored. Our results showed that a distinct set of interconnected brain regions including, frontal areas (middle, inferior, orbitofrontal, and dorsolateral), dorsal/ventral striatum, thalamus, superior temporal region, insula cortex, post-central gyrus, left supramarginal gyrus, and parietal regions, whose activities seem to be tonically maintained, displays cohesive functional state in obesity during passively viewing a simple stimulus. This organized network is maintained in a dynamic equilibrium with the transient activation of the right supramarginal gyrus. These brain areas have been previously implicated in the regulation of taste, reward, and behavioral processing and most of them have also structural abnormalities regarding normal-weight subjects. Although exploratory, the most important result here is that the evaluation of the visual-evoked responses with dynBSR provides a foundation for investigating the brain circuits in obesity, and becomes the first attempt, to our knowledge, to imply task-irrelevant networks in these individuals.

Adult↗

PubMed2005

Salivary polytene chromosome mapping of Anopheles (Cellia) subpictus Grassi (Culicidae: Diptera).

With the introduction of molecular taxonomy of mosquitoes, polytene chromosome maps have become indispensable as standard references for locating genes, puffs, and inversion breakpoints of unique DNA sequences. We present a line map and a photomap of the salivary polytene chromosomes of Anopheles (Cellia) subpictus Grassi, an important emerging vector of malaria in India. In addition, we discuss the nature of this species complex consisting of sibling species A, B, C, and D. The comparative study is in relevance to the X chromosome heterozygous inversion differences between 2 allopatric populations of the species and the recognition of 4 X-chromosome inversion genotypes viz: species A-X(+a+b), B-X(ab), C-X(a+b) and D-X(+ab).

Animals↗

PubMed1990

An intron mutation in the human alpha 1(I) collagen gene alters the efficiency of pre-mRNA splicing and is associated with osteogenesis imperfecta type II.

This study describes a homozygous, G----A transition at the moderately conserved +5 position within the splice donor site of intron 14 in the human alpha 1(I) collagen gene. The mutation reduced the efficiency of normal splice-site selection since the exon upstream of the mutation was spliced alternatively. Moreover, the extent of alternative splicing was sensitive to the temperature at which the mutant cells were grown, suggesting that the mutation directly affected spliceosome assembly. To achieve exon skipping, this effect must be propagated so as to disrupt the selection of a second splice site in the adjacent intron.

Adenine↗

PubMed2002

Development and mapping of microsatellite markers derived from chicken chromosome-specific libraries.

Chromosome-specific painting probes and libraries were developed for chicken Macrochromosomes 1, 2, 3, and 4 by chromosome microisolation and microcloning. Fluorescent in situ hybridization results using the painting probes on normal chicken metaphase chromosomes indicated the purity and specificity of each probe. Chromosome-specific libraries for chicken Macrochromosomes 1, 2, 3, and 4 were prepared in a phage vector. Fifty-two additional unique microsatellite markers of the (AC)n type were developed from these chromosome-specific libraries. These markers were mapped on the East Lansing reference population to increase the marker density on the four macrochromosomes. Results of the current study suggest that development of markers from chromosome-specific libraries is very useful for constructing high-density linkage maps for chicken macrochromosomes.

Animals↗

PubMed2005

Methodological aspects of the genetic dissection of gene expression.

MOTIVATION: Dissection of the genetics underlying gene expression utilizes techniques from microarray analyses as well as quantitative trait loci (QTL) mapping. Available QLT mapping methods are not tailored for the highly automated analyses required to deal with the thousand of gene transcripts encountered in the mapping of QTL affecting gene expression (sometimes referred to as eQTL). This report focuses on the adaptation of QTL mapping methodology to perform automated mapping of QTL affecting gene expression. RESULTS: The analyses of expression data on > 12,000 gene transcripts in BXD recombinant inbred mice found, on average, 629 QTL exceeding the genome-wide 5% threshold. Using additional information on trait repeatabilities and QTL location, 168 of these were classified as 'high confidence' QTL. Current sample sizes of genetical genomics studies make it possible to detect a reasonable number of QTL using simple genetic models, but considerably larger studies are needed to evaluate more complex genetic models. After extensive analyses of real data and additional simulated data (altogether > 300,000 genome scans) we make the following recommendations for detection of QTL for gene expression: (1) For populations with an unbalanced number of replicates on each genotype, weighted least squares should be preferred above ordinary least squares. Weights can be based on repeatability of the trait and the number of replicates. (2) A genome scan based on multiple marker information but analysing only at marker locations is a good approximation to a full interval mapping procedure. (3) Significance testing should be based on empirical genome-wide significance thresholds that are derived for each trait separately. (4) The significant QTL can be separated into high and low confidence QTL using a false discovery rate that incorporates prior information such as transcript repeatabilities and co-localization of gene-transcripts and QTL. (5) Including observations on the founder lines in the QTL analysis should be avoided as it inflates the test statistic and increases the Type I error. (6) To increase the computational efficiency of the study, use of parallel computing is advised. These recommendations are summarized in a possible strategy for mapping of QTL in a least squares framework. AVAILABILITY: The software used for this study is available on request from the authors.

Algorithms↗

PubMed2004

Receptor-binding residues lie in central regions of Duffy-binding-like domains involved in red cell invasion and cytoadherence by malaria parasites.

Erythrocyte invasion by malaria parasites and cytoadherence of Plasmodium falciparum-infected erythrocytes to host capillaries are 2 key pathogenic mechanisms in malaria. The receptor-binding domains of erythrocyte-binding proteins (EBPs) such as Plasmodium falciparum EBA-175, which mediate invasion, and P falciparum erythrocyte membrane protein 1 (PfEMP-1) family members, which are encoded by var genes and mediate cytoadherence, have been mapped to conserved cysteine-rich domains referred to as Duffy-binding-like (DBL) domains. Here, we have mapped regions within DBL domains from EBPs and PfEMP-1 that contain receptor-binding residues. Using biochemical and molecular methods we demonstrate that the receptor-binding residues of parasite ligands that bind sialic acid on glycophorin A for invasion as well as complement receptor-1 and chondroitin sulfate A for cytoadherence map to central regions of DBL domains. In contrast, binding to intercellular adhesion molecule 1 (ICAM-1) requires both the central and terminal regions of DBLbetaC2 domains. Determination of functional regions within DBL domains is the first step toward understanding the structure-function bases for their interaction with diverse host receptors.

Animals↗