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PubMedDate not supplied

Right or left ear reference changes the voltage of frontal and parietal somatosensory evoked potentials.

Short-latency cortical somatosensory evoked potentials (SEPs) to left median nerve stimulation were recorded with either the left or right earlobe as reference. With a right earlobe reference the voltage of the parietal N20 and P27 was reduced while the voltage of the frontal P20 and N30 was enhanced. The effects were consistent, but their size varied with the SEP component considered and also among the subjects. Analysis of SEPs at different scalp sites and at either earlobe suggested that the ear contralateral to the side stimulated picked up transient potential differences, depending a.o. on side asymmetry and geometry of the neural generators as disclosed in topographic mapping. For example, the right ear potential can be shifted negatively by the right N20 field evoked by left median nerve stimulation. The changes involve the absolute potential values, but not the time features or the gradients of potential fields. Scalp current density (SCD) maps are not affected. The results are pertinent for current discussions about which reference to use and document the practical recommendation of recording short-latency cortical SEPs with a reference at the ear ipsilateral (not contralateral) to the side of stimulation.

Adult↗

PubMed1989

Precise localization of NF1 to 17q11.2 by balanced translocation.

A female patient is described with von Recklinghausen neurofibromatosis (NF1) in association with a balanced translocation between chromosome 17 and 22 [46,XX,t(17;22)(q11.2;q11.2)]. The breakpoint in chromosome 17 is cytogenetically identical to a previously reported case of NF1 associated with a 1;17 balanced translocation and suggests that the translocation events disrupt the NF1 gene. This precisely maps the NF1 gene to 17q11.2 and provides a physical reference point for strategies to clone the breakpoint and therefore the NF1 gene. A human-mouse somatic cell hybrid was constructed from patient lymphoblasts which retained the derivative chromosome 22 (22pter----22q11.2::17q11.2----17qter) but not the derivative 17q or normal 17. Southern blot analysis with genes and anonymous probes known to be in proximal 17q showed ErbA1, ErbB2, and granulocyte colony-stimulating factor (CSF3) to be present in the hybrid and therefore distal to the breakpoint, while pHHH202 (D17S33) and beta crystallin (CRYB1) were absent in the hybrid and therefore proximal to the breakpoint. The gene cluster including ErbA1 is known to be flanked by the constitutional 15;17 translocation breakpoint in hybrid SP3 and by the acute promyelocytic leukemia (APL) breakpoint, which provides the following gene and breakpoint order: cen-SP3-(D17S33,CRYB1)-NF1-(CSF3,ERBA1, ERBB2)-APL-tel. The flanking breakpoints of SP3 and API are therefore useful for rapidly localizing new markers to the neurofibromatosis critical region, while the breakpoints of the two translocation patients provide unique opportunities for reverse genetic strategies to clone the NF1 gene.

Adult↗

PubMed2000

A consensus linkage map of the chicken genome.

A consensus linkage map has been developed in the chicken that combines all of the genotyping data from the three available chicken mapping populations. Genotyping data were contributed by the laboratories that have been using the East Lansing and Compton reference populations and from the Animal Breeding and Genetics Group of the Wageningen University using the Wageningen/Euribrid population. The resulting linkage map of the chicken genome contains 1889 loci. A framework map is presented that contains 480 loci ordered on 50 linkage groups. Framework loci are defined as loci whose order relative to one another is supported by odds greater then 3. The possible positions of the remaining 1409 loci are indicated relative to these framework loci. The total map spans 3800 cM, which is considerably larger than previous estimates for the chicken genome. Furthermore, although the physical size of the chicken genome is threefold smaller then that of mammals, its genetic map is comparable in size to that of most mammals. The map contains 350 markers within expressed sequences, 235 of which represent identified genes or sequences that have significant sequence identity to known genes. This improves the contribution of the chicken linkage map to comparative gene mapping considerably and clearly shows the conservation of large syntenic regions between the human and chicken genomes. The compact physical size of the chicken genome, combined with the large size of its genetic map and the observed degree of conserved synteny, makes the chicken a valuable model organism in the genomics as well as the postgenomics era. The linkage maps, the two-point lod scores, and additional information about the loci are available at web sites in Wageningen (http://www.zod.wau.nl/vf/ research/chicken/frame_chicken.html) and East Lansing (http://poultry.mph.msu.edu/).

Animals↗

PubMed2001

Directed isolation and mapping of microsatellites from swine Chromosome 1q telomeric region through microdissection and RH mapping.

Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD <6). Out of the 15 microsatellite markers, 9 were polymorphic in NIAI reference population based on the Meishan and Göttingen miniature pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs.

Animals↗

PubMed1985

Chromosomal map of Pseudomonas putida PPN, and a comparison of gene order with the Pseudomonas aeruginosa PAO chromosomal map.

The generalized transducing phage Pf16h2 has been used to confirm linkage relationships of chromosomal markers of Pseudomonas putida previously determined from their time-of-entry in Hfr crosses, and to map new auxotrophic mutations. By means of spot matings using Hfr donors of known origin of transfer, catabolic markers forming part of a closely linked group of operons referred to as a superoperonic cluster have been shown to be chromosomally located and their map positions determined. R-prime-mediated interspecific complementation has been used to equate functionally 21 auxotrophic loci in P. putida and P. aeruginosa, and the distribution of these loci on the two genetic maps has been compared. While both maps reveal that auxotrophic markers are largely restricted to about 40% of the chromosome and that auxotrophic markers of similar phenotype are not clustered, there is evidence of at least seven chromosomal rearrangements since divergence from a presumed common ancestor.

Chromosome Mapping↗

PubMed1992

Topography of excitatory bandwidth in cat primary auditory cortex: single-neuron versus multiple-neuron recordings.

1. The spatial distribution of the sharpness of tuning of single neurons along the dorsoventral extent of primary auditory cortex (AI) was studied. A sharpness of tuning gradient was initially obtained with multiple-unit recordings, and in combination with the cochleotopic organization, served as a frame of reference for the locations of single neurons. The frequency selectivity or "integrated excitatory bandwidth" of multiple units varied systematically along the dorsoventral extent of AI. The most sharply tuned unit clusters were found at the approximate center of the dorsoventral extent. A gradual broadening of the integrated excitatory bandwidth in both dorsal and ventral directions was consistently seen. 2. The multiple-unit measures of the bandwidth 10 (BW10) and 40 dB (BW40) above minimum threshold, pooled across several animals and expressed in octaves, were similar to those described within individual cases in cats. As in the individual animals, the bandwidth maps were V shaped with minima located at the approximate center of the dorsal-ventral extent of AI. The location of the minimum in the multiple-unit bandwidth map (i.e., the most sharply tuned area) was used as a reference point to pool single-neuron data across animals. 3. For single neurons, the dorsal half of the BW40 distribution showed a gradient paralleling that found for multiple units. For both single and multiple units, the average excitatory bandwidth increased at a rate of approximately 0.27 octaves/mm from the center of AI toward the dorsal fringe. Differing from the dorsal half of AI, the ventral half of AI showed no clear BW40 gradient for single units along its dorsoventral extent. At 40 dB above minimum threshold, most ventral neurons encountered were sharply tuned. By contrast, the multiple-unit BW40 showed a gradient similar to the dorsal half with 0.23 octaves/mm increasing from the center toward the ventral border of AI. 4. For single neurons, BW10 showed no clear systematic spatial distribution in AI. Neither the dorsal nor the ventral gradient was significantly different from zero slope, although the dorsal half showed a trend toward increasing BW10s. Contrasting single neurons, both dorsal and ventral halves of AI showed BW10 slopes for multiple units confirming a V-shaped map of the integrated excitatory bandwidth within the dorsoventral extent of AI. 5. On the basis of the distribution of the integrated (multiple-unit) excitatory bandwidth, AI was parceled into three regions: the dorsal gradient, the ventral gradient, and the central, narrowly tuned area.(ABSTRACT TRUNCATED AT 400 WORDS)

Acoustic Stimulation↗

PubMed1985

Neurotransmitter receptor alterations in Huntington's disease: autoradiographic and homogenate studies with special reference to benzodiazepine receptor complexes.

In vitro receptor autoradiography was used to construct semiquantitative maps of subtypes of muscarinic cholinergic (labeled with [3H]N-methylscopolamine), benzodiazepine ([3H]flunitrazepam), gamma-aminobutyric acid ([3H]muscimol), dopamine, and serotonin ([3H]spiperone) receptors in frontal cortex, parietal cortex, caudate, putamen, and globus pallidus in tissue sections from 5 patients with clinically well-evaluated Huntington's disease and 5 controls matched with respect to age, sex, and postmortem delay. Homogenates were prepared from the remaining cortical and striatal tissue and used to characterize pharmacologically these same receptors, as well as histamine, adenosine, and nitrendipine receptors. Neuronal loss and gliosis were assessed in the contralateral formalin-fixed caudate and putamen. All binding sites measured (except serotonin) were reduced relative to control values in striatum primarily because of changes in the number of receptors rather than in affinity. Autoradiographic studies generally revealed that these changes were greater in the caudate than the putamen, paralleling the more severe neuropathological changes present in the caudate. In addition, autoradiographic studies demonstrated an increase in gamma-aminobutyric acid-related receptors in the globus pallidus. In the cortex, receptor alterations were limited to an increase in the number of benzodiazepine receptors in the frontal cortex which was most prominent in superficial cortical layers.

Autoradiography↗

PubMed2001

An overview of the genetic analysis of complex diseases, with reference to type 1 diabetes.

Despite extensive efforts by many groups, progress in the mapping of complex diseases has been exceedingly slow, only a few genes and some genetic regions having been identified. The general picture is one of difficulty in locating disease genes and in the replication of linkages. This results from the role in disease of a large number of genes, many with a relatively minor effect and many involving common genetic variation. A multi-strategy approach to the mapping of complex diseases is required: no single method is sufficient or optimal. The role of human leukocyte antigens in type 1 diabetes has been known for nearly 30 years, and the associations, linkage and genetic contribution to disease are all strong, but all the human leukocyte antigen region genes involved in the disease process have not yet been identified. The methods used in study of this component to type 1 diabetes are a model for all complex diseases.

Chromosome Mapping↗

PubMed1989

32P-postlabeling analysis of DNA adducts in liver of wild English sole (Parophrys vetulus) and winter flounder (Pseudopleuronectes americanus).

The 1-butanol adduct enhancement version of the 32P-postlabeling assay was used to measure the levels of hepatic DNA adducts in the marine flatfish, English sole (Parophrys vetulus), sampled from the Duwamish Waterway and Eagle Harbor, Puget Sound, WA, where they are exposed to high concentrations of sediment-associated chemical contaminants and exhibit an elevated prevalence of hepatic neoplasms. Hepatic DNA was also analyzed from English sole from a reference area (Useless Bay, WA) and from reference English sole treated with organic-solvent extracts of sediments from the two contaminated sites. Autoradiograms of thin-layer chromatograms of 32P-labeled hepatic DNA digests from English sole from the contaminated sites exhibited up to three diagonal radioactive zones, which were not present in autoradiograms of thin-layer chromatogram maps of 32P-labeled DNA digests from English sole from the reference site. These diagonal radioactive zones contained several distinct spots as well as what appeared to be multiple overlapping adduct spots. The levels (nmol of adducts/mol of nucleotides) of total DNA adducts for English sole from Duwamish Waterway and Eagle Harbor were 26 +/- 28 (DS) and 17 +/- 9.6, respectively. All autoradiograms of DNA from fish from the contaminated sites exhibited a diagonal radioactive zone where DNA adducts of chrysene, benzo(a)pyrene, and dibenz(a,h)anthracene, formed in vitro using English sole hepatic microsomes, were shown to chromatograph. English sole treated with extracts of the contaminated sediments had adduct profiles generally similar to those for English sole from the respective contaminated sites. The chromatographic characteristics of the adducts and the similarities in adduct profiles between field-sampled English sole and those treated with contaminated sediment extracts suggested that hydrophobic aromatic compounds of anthropogenic origin were adducted to hepatic DNA of sole from contaminated sites, but not in sole from the reference site. Moreover, an initial study with winter flounder (Pseudopleuronectes americanus) from Boston Harbor, MA, an area where high concentrations of sediment-associated chemicals are present, revealed a pattern of hepatic DNA-adducts (9.0 +/- 7.8 nmol of adducts/mol of nucleotides) similar to that observed for English sole from Eagle Harbor.

Animals↗

PubMed2005

New Arabidopsis recombinant inbred line populations genotyped using SNPWave and their use for mapping flowering-time quantitative trait loci.

The SNPWave marker system, based on SNPs between the reference accessions Colombia-0 and Landsberg erecta (Ler), was used to distinguish a set of 92 Arabidopsis accessions from various parts of the world. In addition, we used these markers to genotype three new recombinant inbred line populations for Arabidopsis, having Ler as a common parent that was crossed with the accessions Antwerp-1, Kashmir-2, and Kondara. The benefit of using multiple populations that contain many similar markers and the fact that all markers are linked to the physical map of Arabidopsis facilitates the quantitative comparison of maps. Flowering-time variation was analyzed in the three recombinant inbred line populations. Per population, four to eight quantitative trait loci (QTL) were detected. The comparison of the QTL positions related to the physical map allowed the estimate of 12 different QTL segregating for flowering time for which Ler has an allele different from one, two, or three of the other accessions.

Arabidopsis↗

PubMed2004

Genetic linkage mapping of an annual x perennial ryegrass population.

Annual (Lolium multiflorum Lam.) and perennial ( L. perenne L.) ryegrass are two common forage and turfgrass species grown throughout the world. Perennial ryegrass is most commonly used for turfgrass purposes, and contamination by annual ryegrass, through physical seed mixing or gene flow, can result in a significant reduction in turfgrass quality. Seed certifying agencies in the United States currently use a test called seedling root fluorescence (SRF) to detect contamination between these species. The SRF test, however, can be inaccurate and therefore, the development of additional markers for species separation is needed. Male and female molecular-marker linkage maps of an interspecific annual x perennial ryegrass mapping population were developed to determine the map location of the SRF character and to identify additional genomic regions useful for species separation. A total of 235 AFLP markers, 81 RAPD markers, 16 comparative grass RFLPs, 106 SSR markers, 2 isozyme loci and 2 morphological characteristics, 8-h flowering, and SRF were used to construct the maps. RFLP markers from oat and barley and SSR markers from tall fescue and other grasses allowed the linkage groups to be numbered, relative to the Triticeae and the International Lolium Genome Initative reference population P150/112. The three-generation population structure allowed both male and female maps to be constructed. The male and female maps each have seven linkage groups, but differ in map length with the male map being 537 cm long and the female map 712 cm long. Regions of skewed segregation were identified in both maps with linkage groups 1, 3, and 6 of the male map showing the highest percentage of skewed markers. The (SRF) character mapped to linkage group 1 in both the male and female maps, and the 8-h flowering character was also localized to this linkage group on the female map. In addition, the Sod-1 isozyme marker, which can separate annual and perennial ryegrasses, mapped to linkage group 7. These results indicate that Lolium linkage groups 1 and 7 may provide additional markers and candidate genes for use in ryegrass species separation.

Chromosome Mapping↗

PubMed1996

Mapping quantitative trait loci for complex binary diseases using line crosses.

A composite interval gene mapping procedure for complex binary disease traits is proposed in this paper. The binary trait of interest is assumed to be controlled by an underlying liability that is normally distributed. The liability is treated as a typical quantitative character and thus described by the usual quantitative genetics model. Translation from the liability into a binary (disease) phenotype is through the physiological threshold model. Logistic regression analysis is employed to estimate the effects and locations of putative quantitative trait loci (our terminology for a single quantitative trait locus is QTL while multiple loci are referred to as QTLs). Simulation studies show that properties of this mapping procedure mimic those of the composite interval mapping for normally distributed data. Potential utilization of the QTL mapping procedure for resolving alternative genetic models (e.g., single- or two-trait-locus model) is discussed.

Chromosome Mapping↗

PubMed2001

Bioinformatics beyond sequence: mapping gene function in the embryo.

The spatio-temporal expression pattern of a gene during development is a valuable piece of information. But there is no way to compare precisely the patterns of expression of different genes, or the way the patterns are changed in a mutant. One way to solve this problem is to construct digital reference images of development (a bioinformatics framework), to which expression patterns can be mapped and stored, then compared. Such frameworks are under active development in several model systems. They will form the basis of powerful and integrated gene expression databases, which facilitate comparisons between genes, tissues and species.

Animals↗

PubMed2002

Diffusion tensor imaging using single-shot SENSE-EPI.

SENSitivity Encoding (SENSE) greatly enhances the quality of diffusion-weighted echo-planar imaging (EPI) by reducing blurring and off-resonance artifacts. Such improvement would also be desirable for diffusion tensor imaging (DTI), but measures derived from the diffusion tensor can be extremely sensitive to any kind of image distortion. Whether DTI is feasible in combination with SENSE has not yet been explored, and is the focus of this study. Using a SENSE-reduction factor of 2, DTI scans in eight healthy volunteers were carried out with regular- and high-resolution acquisition matrices. To further improve the stability of the SENSE reconstruction, a new coil-sensitivity estimation technique based on variational calculus and the principles of matrix regularization was applied. With SENSE, maps of the trace of the diffusion tensor and of fractional anisotropy (FA) had improved spatial resolution and less geometric distortion. Overall, the geometric distortions were substantially removed and a significant resolution enhancement was achieved with almost the same scan time as regular EPI. DTI was even possible without the use of quadrature body coil (QBC) reference scans. Geometry-factor-related noise enhancement was only discernible in maps generated with higher-resolution matrices. Error boundaries for residual fluctuations in SENSE reconstructions are discussed. Our results suggest that SENSE can be combined with DTI and may present an important adjunct for future neuroimaging applications of this technique.

Brain↗

PubMed1996

Evaluation of reference systems for quantitative wall motion analysis from three-dimensional endocardial surface reconstruction: an echocardiographic study in subjects with and without myocardial infarction.

Six relevant computer-implemented reference systems for three-dimensional quantitative assessment of left ventricular wall motion abnormalities were compared with visual wall motion analysis of two-dimensional images. Endocardial borders were traced in three apical echocardiographic views at end-diastole and end-systole in 10 patients with myocardial infarction and 5 healthy subjects, and three-dimensional reconstruction of endocardial surfaces was performed. End-diastolic and end-systolic surfaces were aligned in a common axis system depending on the reference system, and systolic wall motion was assessed at 1,024 points on the endocardial surface. The localization of abnormal wall motion was displayed in bull's-eye maps, and the area was determined as a percentage of total endocardial area. For each reference system, the segmental concordance between three-dimensional computerized and visual assessment was determined. The best agreement between computerized and visual analysis was obtained with a reference system based on wall motion towards the major ventricular axis, whereas the poorest result was obtained using the center of left ventricular cavity as reference. Correlation between the estimated area of wall motion abnormality and visually determined wall motion score index was best using the aligned center of mitral valve plane as reference (r = .92).

Adult↗

PubMed2006

Method for mapping population-based case-control studies: an application using generalized additive models.

BACKGROUND: Mapping spatial distributions of disease occurrence and risk can serve as a useful tool for identifying exposures of public health concern. Disease registry data are often mapped by town or county of diagnosis and contain limited data on covariates. These maps often possess poor spatial resolution, the potential for spatial confounding, and the inability to consider latency. Population-based case-control studies can provide detailed information on residential history and covariates. RESULTS: Generalized additive models (GAMs) provide a useful framework for mapping point-based epidemiologic data. Smoothing on location while controlling for covariates produces adjusted maps. We generate maps of odds ratios using the entire study area as a reference. We smooth using a locally weighted regression smoother (loess), a method that combines the advantages of nearest neighbor and kernel methods. We choose an optimal degree of smoothing by minimizing Akaike's Information Criterion. We use a deviance-based test to assess the overall importance of location in the model and pointwise permutation tests to locate regions of significantly increased or decreased risk. The method is illustrated with synthetic data and data from a population-based case-control study, using S-Plus and ArcView software. CONCLUSION: Our goal is to develop practical methods for mapping population-based case-control and cohort studies. The method described here performs well for our synthetic data, reproducing important features of the data and adequately controlling the covariate. When applied to the population-based case-control data set, the method suggests spatial confounding and identifies statistically significant areas of increased and decreased odds ratios.

Case-Control Studies↗

PubMed2003

Comparison of GenFlex Tag array and Pyrosequencing in SNP genotyping.

With the completion of the Human Genome Project, over 2 million sequence-verified single nucleotide polymorphisms (SNPs) have been deposited in public databases. The challenge has shifted from SNP identification to high-throughput SNP genotyping. Although this has had little impact on molecular diagnostics, it provides the potential for future molecular diagnostics of complex traits to include SNP profiling. Accordingly, efficient, accurate, and flexible SNP genotyping are needed. In addition, the drive for low cost has pushed genotyping reactions toward multiplexing capability. We compared two SNP genotyping techniques: Affymetrix GenFlex Tag array and Pyrosequencing. The reference method was a well-established, solid-phase, single nucleotide extension reaction technique based on tritium detection. Fourteen SNPs were selected from the fine mapping project of a multiple sclerosis locus on chromosome 17q. Using all three techniques and the reference method, the SNPs were analyzed in 96 related individuals. Without extensive optimization, we successfully genotyped 11 of 14 SNPs with both GenFlex and Pyrosequencing. Our study suggests that the Pyrosequencing technique provides higher accuracy between the two systems which is most likely due to the single-stranded template in the extension reaction. Thus, Pyrosequencing has potential for diagnostic applications. Pyrosequencing, however, is not optimal for large SNP profiling analyses wherein multiplexing potential is an advantage.

Alleles↗

PubMed1992

A preliminary analysis of consortium data for markers tightly linked to multiple endocrine neoplasia type 2A.

We have analyzed DNA marker typing data contributed by six independent groups to estimate the pairwise genetic distances between these markers and the locus for multiple endocrine neoplasia type 2A (MEN 2A). We used LIPED to calculate these distances for female, male, and sex-average linkage maps and to determine the corresponding LOD scores. The preliminary analyses of this large data set (89 MEN 2A families and five non-MEN 2A references families, with 1,934 total individuals) are reported here. These refined estimates of the genetic map in this region will aid in the assignment of presymptomatic diagnoses. This study clearly points out the limitation of pairwise linkage analysis in further refining the position of MEN2A in this small region of chromosome 10. Further refinement of the genetic map position of MEN2A will be best accomplished by finding, verifying, and accurately mapping crossovers in specific families.

Chromosome Mapping↗