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PubMed1996

Resolving ambiguities in the karyotype of domestic sheep (Ovis aries). II. G-, Q-, and R-banded idiograms, and chromosome-specific molecular markers.

Internally consistent G-, Q- and R-banded karyotypes and idiograms for sheep chromosomes at the 422-band level of resolution are presented. These were derived by sequential Q- to G-staining, and sequential Q- to R-staining of prometaphase spreads prepared from sheep with normal and Robertsonian chromosomes. The fused chromosomes served as stable morphological markers. To minimise confusion due to chromosomal nomenclature, we have listed chromosome-specific (reference) molecular markers that have been mapped by in situ hybridization to sheep chromosomes. The use of molecular markers in conjunction with the sequential Q- to G- and sequential Q- to R-banded karyotypes and iodiograms provided here will elimiate ambiguities in identifying and numbering sheep chromosomes and will facilitate their comparison with cattle chromosomes.

Animals↗

PubMed1997

Use of allele specificity of comigrating AFLP markers to align genetic maps from different potato genotypes.

The allele specificity of AFLP markers was assessed in five relatively unrelated potato genotypes. To this end, two diploid mapping populations of potato, F1SH x RH and F1AM x RH, were analysed using four and six AFLP primer combinations, respectively, recently applied to the analysis of the genetically well characterized backcross population BC_C x E. The AFLP profiles of the five parents revealed 733 AFLP markers and, when identical primer combinations were used, 131 comigrating AFLP markers were identified. After construction of five parental maps, the genomic positions of these comigrating AFLP markers were compared and 117 markers (89%) which targeted the same genomic region were assumed to be homologous. Of these putative homologues, 20 markers, each cloned from at least two genotypes, were sequenced and 19 sets of amplification products were shown to be nearly identical. The number of AFLP markers previously mapped in population BC_C x E ranged from three to eleven per chromosome, which allowed a reliable assessment of chromosome numbers from individual linkage groups obtained in populations F1SH x RH and F1AM x RH. The high incidence of corresponding AFLP alleles was confirmed by using an additional set of five primer combinations. The 733 AFLP markers localized provide a valuable reference collection for future mapping studies in potato. As a consequence AFLP analysis may replace more laborious locus-specific marker techniques.

Alleles↗

PubMed1997

DNA marker technology: a revolution in animal genetics.

The development of DNA-based markers has had a revolutionary impact on gene mapping and, more generally, on all of animal and plant genetics. With DNA-based markers, it is theoretically possible to exploit the entire diversity in DNA sequence that exists in any cross. For this reason, high resolution genetic maps are being developed at an unprecedented speed. The most commonly used DNA-based markers include those based on a cloned and (usually) sequenced DNA fragment and other, more random, assays for genetic polymorphism that can be grouped under the heading of fingerprint markers. The advantages and disadvantages of the various marker types are discussed, along with their application to the reference chicken genetic linkage maps and to the search for quantitative trait loci (QTL). The prospects for the use of DNA-based markers in marker-assisted selection are considered, along with likely future trends in poultry gene mapping. Further development of both physical and linkage genome maps of the chicken will allow animal scientists to more efficiently detect and characterize QTL and will provide them access to the wealth of genetic information that is being generated about the human genome and the genomes of model species, such as the mouse and Drosophila.

Animals↗

PubMed2005

White matter fiber tracts of the human brain: three-dimensional mapping at microscopic resolution, topography and intersubject variability.

The position and extent of individual fiber tracts within the white matter of human brains can be identified in vivo using diffusion tensor imaging (DTI) and fiber tracking methods. Previous to this study, however, the lack of three-dimensional (3-D) probability maps precluded comparing the anatomical precision of MRI studies with microscopically defined fiber tracts in human postmortem brains. The present study provides 3-D registered maps of the topography, course and intersubject variability of major fiber tracts, which were identified at microscopic resolution. The analyzed tracts include the corticospinal tract, optic and acoustic radiations, fornix, cingulum, corpus callosum, superior longitudinal, superior and inferior occipito-frontal and uncinate fascicles; sources and targets of fiber tracts include the lateral and medial geniculate nuclei and mamillary bodies. Tracts and nuclei were identified in serial myelin-stained histological sections of ten postmortem brains. The sections were 3-D reconstructed and registered to a standardized stereotaxic space of an in vivo MR reference brain by means of linear and non-linear, elastic transformations. The individual fiber tracts and nuclei were superimposed in the reference space, and probability maps were generated as a quantitative measure of intersubject variability for each voxel of the stereotaxic space. This study presents the first stereotaxic atlas of the course, location and extent of fiber tracts and related nuclei based on microscopically defined localization and topographic data taken at multiple levels on each of the three orthogonal planes. The maps are useful for evaluating and identifying fiber bundles in DTI, for localizing subcortical lesions visible in anatomical MR images and for studying neuronal connectivity.

Adult↗

PubMed2006

Short-term reorganization of input-deprived motor vibrissae representation following motor disconnection in adult rats.

It has been proposed that abnormal vibrissae input to the motor cortex (M1) mediates short-term cortical reorganization after facial nerve lesion. To test this hypothesis, we cut first the infraorbital nerve (ION cut) and then the facial nerve (VII cut) in order to evaluate M1 reorganization without any aberrant, facial-nerve-lesion-induced sensory feedback. In each animal, M1 output was assessed in both hemispheres by mapping movements induced by intracortical microstimulation. M1 output was compared in different types of peripheral manipulations: (i) contralateral intact vibrissal pad (intact hemispheres), (ii) contralateral VII cut (VII hemispheres), (iii) contralateral ION cut (ION hemispheres), (iv) contralateral VII cut after contralateral ION cut (ION + VII hemispheres), (v) contralateral pad botulinum-toxin-injected after ION cut (ION + BTX hemispheres). Right and left hemispheres in untouched animals were the reference for normal M1 map (control hemispheres). Findings demonstrated that: (1) in ION hemispheres, the mean size of the vibrissae representation was not significantly different from those in intact and control hemispheres; (2) reorganization of the vibrissae movement representation clearly emerged only in hemispheres where the contralateral vibrissae pad had undergone motor output disconnection (VII cut hemispheres); (3) the persistent loss of vibrissae input did not change the M1 reorganization pattern during the first 48 h after motor paralysis (ION + VII cut and ION + BTX hemispheres). Thus, after motor paralysis, vibrissa input does not provide the gating signal necessary to trigger M1 reorganization.

Animals↗

PubMed2006

Cytoarchitectonic analysis of the human extrastriate cortex in the region of V5/MT+: a probabilistic, stereotaxic map of area hOc5.

Functional imaging studies identified a motion-sensitive area (V5/MT+) in the vicinity of the posterior branch of the inferior temporal sulcus that has no correlate in any classical cytoarchitectonic map. The aim of the present study was to identify a cytoarchitectonic correlate of this region in 10 human postmortem brains and to provide a probability map of this area. Observer-independent mapping revealed an area, hOc5 (h for human, Oc for occipital lobe), that has a broad layer III, a high cell density in layer II/III, and a low one in layer V. Most of area hOc5 is found in the depths of the anterior occipital sulcus and the anterior parts of either the inferior lateral occipital or the inferior occipital sulcus. After 3-dimensional reconstruction and registration to a standard reference space, a probability map of the area measured the individual variability of its size and location. The mean spatial locations of area hOc5 are -43, -73, 10 (left) and 49, -70, 11 (right). The locations and their relationships to sulci strongly suggest that hOc5 is the cytoarchitectonic correlate of human V5/MT+. This hypothesis was supported by comparing the cytoarchitectonic probabilistic map with results from a functional imaging study.

Adult↗

PubMed1992

The gene map of the pig (Sus scrofa domestica L.): a review.

A review of the present status of the porcine gene map is given with references. A total of 84 loci have now been studied, and genes have been assigned to 17 chromosomes. Among them, six chromosomes are defined by only one marker. No loci have been attributed yet to three chromosomes.

Animals↗

PubMed1999

Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21.

The temperate Streptococcus thermophilus bacteriophage Sfi21 possesses 15-nucleotide-long cohesive ends with a 3' overhang that reconstitutes a cos-site with twofold hyphenated rotational symmetry. Over the DNA packaging, head and tail morphogenesis modules, the Sfi21 sequence predicts a gene map that is strikingly similar to that of lambdoid coliphages in the absence of any sequence similarity. A nearly one to one gene correlation was found with the phage lambda genes Nu1 to H, except for gene B-to-E complex, where the Sfi21 map resembled that of coliphage HK97. The similarity between Sfi21 and HK97 was striking: both major head proteins showed an N-terminal coiled-coil structure, the mature major head proteins started at amino acid positions 105 and 104, respectively, and both major head genes were preceded by genes encoding a possible protease and portal protein. The purported Sfi21 protease is the first viral member of the ClpP protease family. The prediction of Sfi21 gene functions by reference to the gene map of intensively investigated coliphages was experimentally confirmed for the major head and tail gene. Phage Sfi21 shows nucleotide sequence similarity with Lactococcus phage BK5-T and a lactococcal prophage and amino acid sequence similarity with the Lactobacillus phage A2 and the Staphylococcus phage PVL. PVL is a missing link that connects the portal proteins from Sfi21 and HK97 with respect to sequence similarity. These observations and database searches, which demonstrate sequence similarity between proteins of phage from gram-positive bacteria, proteobacteria, and Archaea, constrain models of phage evolution.

Amino Acid Sequence↗

PubMed2004

Comparative genome assembly.

One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With the rapid growth in the number of sequenced genomes has come an increase in the number of organisms for which two or more closely related species have been sequenced. This has created the possibility of building a comparative genome assembly algorithm, which can assemble a newly sequenced genome by mapping it onto a reference genome. We describe here a novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer. The software is available as part of the open-source AMOS project.

Algorithms↗

PubMedDate not supplied

[Physical mapping of the human genome: on the way to developing an optimal strategy].

Physical mapping of the human genome appears to be a complicated problem for the molecular genetics of higher organisms. The difficulties are not only due to the great amount of work to be done, but mostly due to the peculiarities of genome organization (repeated nucleotide sequences, non-clonable, methylated and toxic fragments, etc.). Mapping procedures based on molecular hybridization do not allow to obtain the unambiguous results due to the occurrence of the repeats of different types common for the genome as a whole. Giant DNA fragments (e.g. YAC--Yeast Artificial Chromosomes) undergo deletions, transformations and chimerism and cannot be the main approach for genome mapping. The new strategy for genome mapping is described with reference to the human chromosome 3--one of the largest human chromosomes. The main steps of this new strategy are the following: 1) sequencing of STS (Sequence Tagged Sites) flanking DNA rare-cutting restriction sites; 2) alignment of the STS along the chromosomal DNA (generation of the contigs) based on the comparative computer analysis of STS from the same and from the neighboring restriction sites, 3) determination of the distance between STS by hybridization of large DNA fragments with STS. In order to apply this strategy called "shot-gun sequencing strategy for long range genome mapping" a new family of vectors (SK series) specially designed for the genome cloning was constructed and the simplified inexpensive technology for preparing the jumping/linking libraries was developed. Chromosome 3 fragments were sequenced around NotI sites, and the contigs covering about 50 Mbp of genomic DNA were constructed. The perspectives for the whole human genome mapping are discussed.

Bacteriophages↗

PubMed1991

Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8.

Linkage mapping in a large, seven-generation family with type 2 autosomal dominant retinitis pigmentosa (ADRP) demonstrates linkage between the disease locus (RP1) and DNA markers on the short arm of human chromosome 8. Five markers were most informative for mapping ADRP in this family using two-point linkage analysis. The markers, their maximum lod scores, and recombination distances were ANK1 (ankyrin)--2.0 at 16%; D8S5 (TL11)--5.3 at 17%; D8S87 [a(CA)n repeat]--7.2 at 14%; LPL (lipoprotein lipase)--1.5 at 26%; and PLAT (plasminigen activator, tissue)--10.6 at 7%. Multipoint linkage analysis, using a simplified pedigree structure for the family (which contains 192 individuals and two inbreeding loops), gave a maximum lod score of 12.2 for RP1 at a distance 8.1 cM proximal to PLAT in the pericentric region of the chromosome. Based on linkage data from the CEPH (Paris) reference families and physical mapping information from a somatic cell hybrid panel of chromosome 8 fragments, the most likely order for four of these five loci and the diseases locus is 8pter-LPL-D8S5-D8S87-PLAT-RP1. (The precise location of ANK1 relative to PLAT in this map is not established). The most likely location for RP1 is in the pericentric region of the chromosome. Recently, several families with ADRP with tight linkage to the rhodopsin locus at 3q21-q24 were reported and a number of specific rhodopsin mutations in families with ADRP have since been reported. In other ADRP families, including the one in this study, linkage to rhodopsin has been excluded. Thus mutations at two different loci, at least, have been shown to cause ADRP. There is no remarkable clinical disparity in the expression of disease caused by these different loci.

Base Sequence↗

PubMed1999

Noninvasive localization of accessory pathways in patients with Wolff-Parkinson-White syndrome with the use of myocardial Doppler imaging.

This study sought to examine the diagnostic accuracy of noninvasive prediction of accessory pathway localization in patients with manifest Wolff-Parkinson-White syndrome with the use of myocardial Doppler imaging as a new noninvasive mapping procedure. Myocardial Doppler imaging measures myocardial velocities and therefore can determine the site of earliest ventricular activation in patients with accessory bypass tracts. Twenty-five patients with manifest preexcitation were studied with the use of pulsed wave and M-mode myocardial Doppler imaging for the evaluation of the shortest electromechanical time interval in 9 basal myocardial segments. The new diagnostic test was compared with 3 electrocardiographic algorithms. An invasive mapping procedure served as reference standard. Abnormally short electromechanical time intervals were found in preexcited segments (27 +/- 12 ms vs 64 +/- 27 ms). Myocardial Doppler imaging correctly localized 84% of the accessory pathways and electrocardiographic algorithms only 48% to 60% of cases. Noninvasive prediction of accessory pathway localization by myocardial Doppler imaging is accurate and proved to be superior to prediction based on electrocardiographic algorithms.

Adult↗

PubMed1995

Genetic linkage mapping of HSD3B1 and HSD3B2 encoding human types I and II 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4-isomerase close to D1S514 and the centromeric D1Z5 locus.

The enzyme 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4-isomerase (3 beta-HSD) catalyses an essential step in the biosynthesis of all steroid hormones. Consequently, classical 3 beta-HSD deficiency is responsible for a severe form of congenital adrenal hyperplasia. The HSD3B1 and HSD3B2 genes encoding the types I and II 3 beta-HSD isoenzymes, respectively, have been previously assigned by in situ hybridization to the chromosome 1p13.1 region. To determine the physical distance between these two genes, NotI and SacII digests of genomic DNA were resolved by pulse-field gel electrophoresis and hybridized with type I and type II 3 beta-HSD cDNAs used as probes. The detection of a single band under low stringency conditions indicates that HSD3B1 and HSD3B2 are located within an approximately 0.29 megabase SacII DNA fragment. We constructed a high resolution genetic map of the region flanking the polymorphic HSD3B1 and HSD3B2 genes including ten Généthon markers and the two NIH/CEPH markers AMY2B and D1Z5. The HSD3B1A and HSD3B2A markers were mapped relative to other reference markers through eight CEPH reference families. The order of polymorphic genes and markers is: pter-[AMY2B-D1S239]-D1S457-D1S502-D1S250-+ ++D1S252-[HSD3B1A -HSD3B2A-D1S514]-[D1Z5-D1S442]-D1S305-D 1S303-D1S484-qter. The D1S514 marker was thus closely linked to HSD3B1A (theta < 0.001; lod = 14.13) and HSD3B2 (theta = 0.008; lod = 35.36). The HSD3B loci are located 1-2 cM of the centromeric marker D1Z5.

Animals↗

PubMed1996

Mapping functional chicken genes: an alternative approach.

Functional genes were selected for linkage analysis mapping using the East Lansing (EL) reference population ¿[Jungle Fowl (JF) x White Leghorn (WL)] x WL¿. The approach used was based on the identification of DNA sequence polymorphisms in the introns of those genes found in JF and WL. Deoxyribonucleic acid sequence analysis revealed single base substitutions in introns of six Type I marker genes: adenylate kinase 1 (AK1), aldolase B (ALDOB), a lysosomal membrane protein gene (LAMP1), vitellogenin 2 (VTG2), apolipoprotein A1 (APOA1), and creatine kinase B (CKB). Transitions or transversions were found in introns of AK1, ALDOB, LAMP1, VTG2, APOA1, and CKB. A transversion in the intron of the JF allele of AK1 generated a unique BspHI cleavage site. The design of polymerase chain reaction (PCR) primers based on the site of base substitution led to the specific amplification of the JF allele in the remaining five genes. A size polymorphism in the PCR production derived from iron response element binding protein (IREBP) distinguished the JF from the WL allele. Linkage analysis of the EL reference population revealed that these candidate genes were located in the following EL linkage groups (E) or chromosomes (Chrom) of the chicken genome: AK1 (E41), VTG2 (E43), APOA1 (E49), CKB (E07), LAMP1 (E01), ALDOB (Chrom Z), and IREBP (Chrom Z). Provided that a base substitution can be found in the parents of the reference population, this PCR-based approach can be used to map any cloned candidate gene. This approach will lead to further information on synteny of the chicken genome with cognate genes of mammalian species.

Adenylate Kinase↗

PubMed1985

Demonstration of the colinearity of human cytomegalovirus genomes and construction of restriction maps of unknown isolates using cloned subgenomic fragments.

In this study, we have established the colinearity of human cytomegalovirus (HCMV) genomes using stringent conditions of DNA-DNA filter hybridization of HCMV HindIII fragments and cosmid-cloned AD169 strain HCMV DNA fragments. Large cosmid-cloned fragments of AD169 DNA were used for the preparation of radioactive probes by nick translation. These probes were hybridized to HindIII digests of DNA from three fresh isolates of HCMV and to that of the Davis strain. Using published HindIII restriction maps for the AD169 strain as a reference, the results obtained by hybridization allowed us to construct HindIII restriction maps for the genomes of the three fresh isolates. Confirmation of our methodology was found in the correspondence between the HindIII map we constructed for the Davis strain and that published previously. Furthermore, it is shown that variation in the restriction profiles of the unique regions of the genome are due to the absence or gain of restriction sites, and not to a rearrangement of fragments. This technique allows rapid construction of physical maps of the DNA of any fresh isolate for a given restriction enzyme provided the corresponding restriction map of a strain to be used as reference is available.

Base Sequence↗

PubMed1987

Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals.

The 14 kb human Duchenne muscular dystrophy (DMD) cDNA corresponding to a complete representation of the fetal skeletal muscle transcript has been cloned. The DMD transcript is formed by at least 60 exons which have been mapped relative to various reference points within Xp21. The first half of the DMD transcript is formed by a minimum of 33 exons spanning nearly 1000 kb, and the remaining portion has at least 27 exons that may spread over a similar distance. The DNA isolated from 104 DMD boys was tested with the cDNA for detection of deletions and 53 patients exhibit deletion mutations. The majority of deletions are concentrated in a single genomic segment corresponding to only 2 kb of the transcript.

Amino Acid Sequence↗

PubMed1994

Clinical and linkage study of a large family with simple ectopia lentis linked to FBN1.

Simple ectopia lentis (EL) was studied in a large family, by clinical examination and analysis of linkage to markers in the region of FBN1, the gene for fibrillin which causes Marfan syndrome on chromosome 15. No patient had clinical or echocardiographic evidence of Marfan syndrome, although there was a trend towards relatively longer measurements of height; lower segment; arm span; middle finger, hand, and foot length in the affected members of the family, compared with unaffected sibs of the same sex. Analysis of linkage to intragenic FBN1 markers was inconclusive because they were relatively uniformative. Construction of a multipoint background map from the CEPH reference families identified microsatellite markers linked closely to FBN1 which could demonstrate linkage of EL in this family to the FBN1 region. LINKMAP analysis detected a multipoint lod score of 5.68 at D15S119, a marker approximately 6 cM distal to FBN1, and a multipoint lod score of 5.04 at FBN1. The EL gene in this family is likely to be allelic to Marfan syndrome, and molecular characterization of the FBN1 mutation should now be possible.

Adolescent↗

PubMed2003

Attenuation compensation in cerebral 3D PET: effect of the attenuation map on absolute and relative quantitation.

It is generally well accepted that transmission (TX)-based non-uniform attenuation correction can supply more accurate absolute quantification; however, whether it provides additional benefits in routine clinical diagnosis based on qualitative interpretation of 3D brain positron emission tomography (PET) images is still the subject of debate. The aim of this study was to compare the effect of the two major classes of method for determining the attenuation map, i.e. uniform versus non-uniform, using clinical studies based on qualitative assessment as well as absolute and relative quantitative volume of interest-based analysis. We investigated the effect of six different methods for determining the patient-specific attenuation map. The first method, referred to as the uniform fit-ellipse method (UFEM), approximates the outline of the head by an ellipse assuming a constant linear attenuation factor (mu=0.096 cm(-1)) for soft tissue. The second, referred to as the automated contour detection method (ACDM), estimates the outline of the head from the emission sinogram. Attenuation of the skull is accounted for by assuming a constant uniform skull thickness (0.45 cm) within the estimated shape and the correct micro value (0.151 cm(-1)) is used. The usual measured transmission method using caesium-137 single-photon sources was used without (MTM) and with segmentation of the TX data (STM). These techniques were finally compared with the segmented magnetic resonance imaging method (SMM) and an implementation of the inferring attenuation distributions method (IADM) based on the digital Zubal head atlas. Several image quality parameters were compared, including absolute and relative quantification indexes, and the correlation between them was checked. The qualitative evaluation showed no significant differences between the different attenuation correction techniques as assessed by expert physicians, with the exception of ACDM, which generated artefacts in the upper edges of the head. The mean squared error between the different attenuation maps was also larger when using this latter method owing to the fact that the current implementation of the method significantly overestimated the head contours on the external slices. Correlation between the mean regional cerebral glucose metabolism (rCGM) values obtained with the various attenuation correction methods and those obtained with the gold standard (MTM) was good, except in the case of ACDM (R(2)=0.54). The STM and SMM methods showed the best correlation (R(2)=0.90) and the regression lines agreed well with the line of identity. Relative differences in mean rCGM values were in general less than 8%. Nevertheless, ANOVA results showed statistically significant differences between the different methods for some regions of the brain. It is concluded that the attenuation map influences both absolute and relative quantitation in cerebral 3D PET. Transmission-less attenuation correction results in a reduced radiation dose and makes a dramatic difference in acquisition time, allowing increased patient throughput.

Algorithms↗