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PubMedDate not supplied

Soybean genetic map of RAPD markers assigned to an existing scaffold RFLP map.

A 356-marker linkage map of Glycine max (L.) Merr. (2n = 20) was established by anchoring 106 RAPD markers to an existing RFLP map built with a large recombinant inbred line population (330 RILs). This map comprises 24 major and 11 minor linkage groups for this genome which is estimated to be approximately 3,275 cM. The RAPD markers show similar distribution throughout the genome and identified similar levels of polymorphism as the RFLP markers used in the framework. By using a subset population to anchor the RAPD markers, it was possible to enhance the throughput of selecting and adding reliable marker loci to the existing map. The procedures to generate a dependable genetic linkage map are also described in this report.

Chromosome Mapping↗
PubMed1991

The impact of two-dimensional pulsed-field gel electrophoresis techniques for the consistent and complete mapping of bacterial genomes: refined physical map of Pseudomonas aeruginosa PAO.

The SpeI/DpnI map of the 5.9 Mb Pseudomonas aeruginosa PAO (DSM 1707) genome was refined by two-dimensional (2D) pulsed-field gel electrophoresis techniques (PFGE) which allow the complete and consistent physical mapping of any bacterial genome of interest. Single restriction digests were repetitively separated by PFGE employing different pulse times and ramps in order to detect all bands with optimum resolution. Fragment order was evaluated from the pattern of 2D PFGE gels: 1. Partial-complete digestion. A partial restriction digest was separated in the first dimension, redigested to completion, and subsequently perpendicularly resolved in the second dimension. 2D-gel comparisons of the ethidium bromide stain of all fragments and of the autoradiogram of end-labeled partial digestion fragments was nearly sufficient for the construction of the macrorestriction map. 2. Reciprocal gels. A complete restriction digest with enzyme A was run in the first dimension, redigested with enzyme B, and separated in the second orthogonal direction. The order of restriction digests was reverse on the second gel. In case of two rare-cutters, fragments were visualized by ethidium bromide staining or hybridization with genomic DNA. If a frequent and a rare cutter were employed, linking fragments were identified by end-labeling of the first digest. 3. A few small fragments were isolated by preparative PFGE and used as a probe for Southern analysis.--38 SpeI and 15 DpnI fragments were positioned on the map. The zero point was relocated to the 'origin of replication'. The anonymous mapping techniques described herein are unbiased by repetitive DNA, unclonable genomic regions, unfavourable location of restriction sites, or cloning artifacts as frequently encountered in other top-down or bottom-up approaches.

Blotting, Southern↗
PubMed1993

Happy mapping: linkage mapping using a physical analogue of meiosis.

We have devised a simple method for ordering markers on a chromosome and determining the distances between them. It uses haploid equivalents of DNA and the polymerase chain reaction, hence 'happy mapping'. Our approach is analogous to classical linkage mapping; we replace its two essential elements, chromosome breakage and segregation, by in vitro analogues. DNA from any source is broken randomly by gamma-irradiation or shearing. Markers are then segregated by diluting the resulting fragments to give aliquots containing approximately 1 haploid genome equivalent. Linked markers tend to be found together in an aliquot. After detecting markers using the polymerase chain reaction, map order and distance can be deduced from the frequency with which markers 'co-segregate'. We have mapped 7 markers scattered over 1.24 Mbp using only 140 aliquots. Using the 'whole-genome' chain reaction, we also show how the approach might be used to map thousands of markers scattered throughout the genome. The method is powerful because the frequency of chromosome breakage can be optimized to suit the resolution required.

Base Sequence↗
PubMed2000

Congenic mapping of the type 1 diabetes locus, Idd3, to a 780-kb region of mouse chromosome 3: identification of a candidate segment of ancestral DNA by haplotype mapping.

Type 1 diabetes in the nonobese diabetic (NOD) mouse arises as a consequence of T cell-mediated destruction of the insulin-producing beta cells of the pancreas. Although little is known of the events that initiate and subsequently drive beta-cell destruction it is clear that the entire process is under complex genetic control. At present 19 loci have been mapped that influence the development of diabetes either at the level of initiation of insulitis or at the level of progression from insulitis to overt diabetes, or both. Previously, we have mapped one of these loci, Idd3, to a 0.35-cM interval on proximal mouse chromosome 3. In the present study we have narrowed the map position of this locus to an interval of 0.15 cM by a combination of novel congenic strains and an ancestral haplotype analysis approach. We have constructed a physical contig in bacterial artificial chromosome (BAC) clones across the minimal interval. Restriction mapping of the BAC contig placed the maximum size of the Idd3 interval at 780 kb between the markers D3Nds36 and D3Nds76. To refine further the Idd3 interval we developed a series of novel single nucleotide polymorphisms (SNPs) and carried out haplotype analysis on DNA from mouse strains known to carry either Idd3 susceptibility or protective alleles. This haplotype analysis identified a 145-kb segment of ancestral DNA between the microsatellite marker D3Nds6 and the SNP 81.3. One haplotype of this ancestral segment of DNA is found in mouse strains carrying an Idd3 susceptibility allele and another is found in mouse strains carrying an Idd3 protective allelle. Within the 780-kb congenically defined interval this 145-kb segment represents the most likely location for Idd3. The Il2 gene, which encodes the cytokine interleukin 2 (IL2), maps to this interval and is a strong candidate for Idd3. To investigate whether sequence variation exists in the promoter region of the Il2 gene, which might alter its expression, we sequenced the promoter region of the Il2 gene from mouse strains carrying either an Idd3 susceptibility or resistance allele. Two sequence variants were identified, neither of which fell in known regulatory elements within the Il2 promoter. In agreement with this observation steady-state Il2 mRNA levels showed no variation between susceptible and resistant mouse strains. These data suggest that the profound protection from diabetes seen in congenic mice carrying an Idd3 protective allele is unlikely to be due to differences in the level of expression of the Il2 gene. Instead, all of the current data support our hypothesis that Idd3 corresponds to amino acid variation at the amino terminus of Il2.

Alleles↗
PubMed2004

Genus zero surface conformal mapping and its application to brain surface mapping.

We developed a general method for global conformal parameterizations based on the structure of the cohomology group of holomorphic one-forms for surfaces with or without boundaries (Gu and Yau, 2002), (Gu and Yau, 2003). For genus zero surfaces, our algorithm can find a unique mapping between any two genus zero manifolds by minimizing the harmonic energy of the map. In this paper, we apply the algorithm to the cortical surface matching problem. We use a mesh structure to represent the brain surface. Further constraints are added to ensure that the conformal map is unique. Empirical tests on magnetic resonance imaging (MRI) data show that the mappings preserve angular relationships, are stable in MRIs acquired at different times, and are robust to differences in data triangulation, and resolution. Compared with other brain surface conformal mapping algorithms, our algorithm is more stable and has good extensibility.

Algorithms↗
PubMed2004

Radiation hybrid map assignments of 11 ESTs obtained from a 28-day-old swine embryo cDNA library to the IMpRH map.

In order to improve the map resolution and to locate more genes on the porcine radiation hybrid map, expressed sequence tags (ESTs) were isolated from a 28-day-old normal pig embryo cDNA library. The ESTs were sequenced from the 5'-end and similarities were checked with sequences registered in the NCBI DNA database (http://www.ncbi.nlm.nih.gov/blast/). The ESTs sequences which have high identity scores (>80%) against human genes or ESTs were further sequenced from the 3' untranslated region. The ESTs which were sequenced successfully were used to design primers for PCR analysis of the radiation hybrid panel. Eleven ESTs were physically mapped to porcine chromosomes 2, 4, 8, 10, 13, 14 and X. The localizations are in agreement with the comparative mapping data between human and pig. The results will provide unique information to the comparative map of human and pig.

Animals↗
PubMed1993

Phosphorylation and activation of human tyrosine hydroxylase in vitro by mitogen-activated protein (MAP) kinase and MAP-kinase-activated kinases 1 and 2.

Mitogen-activated protein-kinase (MAP) kinase-activated protein kinases 1 and 2 (MAPKAP kinase-1, MAPKAP kinase-2), were found to phosphorylate bacterially expressed human tyrosine hydroxylase in vitro at comparable rates to other proteins thought to be physiological substrates of these protein kinases. The phosphorylation of all four alternatively spliced forms of human tyrosine hydroxylase by MAPKAP kinases-1 and -2 reached plateau values at 1 mol/mol subunit and 2 mol/mol subunit, respectively; the sites of phosphorylation were identified as Ser40 (MAPKAP kinase-1) and Ser19 and Ser40 (MAPKAP kinase-2). In contrast to calmodulin-dependent protein kinase-II, which phosphorylates Ser19 faster than Ser40, MAPKAP kinase-2 phosphorylated Ser40 about twice as fast as Ser19. The maximal activation of tyrosine hydroxylase by MAPKAP kinase-1 or-2 was about 3-fold, and activation by MAPKAP kinases-1 and -2 or calmodulin-dependent protein kinase-II correlated with the extent of phosphorylation of Ser40. The four alternatively spliced forms of human tyrosine hydroxylase were phosphorylated at Ser31 by MAP kinase, but at markedly different rates (3 = 4 > 1 >> 2). Forms 3 and 4 were phosphorylated rapidly and stoichiometrically by MAP kinase doubling the activity, while phosphorylation of form 1 by MAP kinase to 0.4 mol/mol subunit increased activity by 40%. The effect on activity of phosphorylating both Ser31 and Ser40 was not additive. The possible roles of MAPKAP kinase-1, MAPKAP kinase-2 and MAP kinase in the regulation of tyrosine hydroxylase in vivo are discussed.

Alternative Splicing↗
PubMed2004

Preoperative mapping for patients with supplementary motor area epilepsy: multimodality brain mapping.

Surgical management and strategies for the supplementary motor area (SMA) epilepsy are described. The following is our preoperative evaluations. The steps include functional magnetic resonance imaging (fMRI), interictal dipole tracing (DT), subdural electrodes mapping, measurements of movement-related cortical potential (MRCP), and the use of the intraoperative open MRI under conscious craniotomy. Six patients with SMA epilepsy underwent surgery after the mapping procedures and are now seizure-free. Combinations of preoperative (fMRI, subdural electrodes mapping) and intraoperative mapping allow exact localization and identification of the critical functional areas. Early postoperative deficits in motor and speech function were profound but patients recovered rapidly. It is concluded that the step of mapping procedures plays an important role in the management of SMA epilepsy surgery.

Adolescent↗
PubMed1987

Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children.

An efficient strategy for mapping human genes that cause recessive traits has been devised that uses mapped restriction fragment length polymorphisms (RFLPs) and the DNA of affected children from consanguineous marriages. The method involves detection of the disease locus by virtue of the fact that the adjacent region will preferentially be homozygous by descent in such inbred children. A single affected child of a first-cousin marriage is shown to contain the same total information about linkage as a nuclear family with three affected children. Calculations show that it should be practical to map a recessive disease gene by studying DNA from fewer than a dozen unrelated, affected inbred children, given a complete RFLP linkage map. The method should make it possible to map many recessive diseases for which it is impractical or impossible to collect adequate numbers of families with multiple affected offspring.

Chromosome Mapping↗
PubMed1998

Linkage map of Escherichia coli K-12, edition 10: the traditional map.

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Chromosome Mapping↗
PubMed1999

Mapping and ablation of ventricular tachycardia with the aid of a non-contact mapping system.

OBJECTIVE: Treatment of ventricular tachycardia (VT) in coronary heart disease has to date been limited to palliative treatment with drugs or implantable defibrillators. The results of curative treatment with catheter ablation have proved disappointing because the complexity of the VT mechanism makes identification of the substrate using conventional mapping techniques difficult. The use of a mapping technology that may address some of these issues, and thus make possible a cure for VT with catheter ablation, is reported. PATIENTS AND INTERVENTION: The non-contact system, consisting of a multielectrode array catheter (MEA) and a computer mapping system, was used to map VT in 24 patients. Twenty two patients had structural heart disease, the remainder having "normal" left ventricles with either fasicular tachycardia or left ventricular ectopic tachycardia. RESULTS: Exit sites were demonstrated in 80 of 81 VT morphologies by the non-contact system, and complete VT circuits were traced in 17. In another 37 morphologies of VT 36 (30)% (mean (SD)) of the diastolic interval was identified. Thirty eight VT morphologies were ablated using 154 radiofrequency energy applications. Successful ablation was achieved by 77% of radiofrequency within diastolic activation identified by the non-contact system and was significantly more likely to ablate VT than radiofrequency at the VT exit, or remote from diastolic activation. Over a mean follow up of 1.5 years, 14 patients have had no recurrence of VT and only two target VTs have recurred. Five patients have had recurrence of either slower non-sustained, undocumented or fast non-target VT. Five patients have died, one from tamponade from a pre-existing temporary pacing wire, and four from causes unrelated to the procedure. CONCLUSION: The non-contact system can safely be used to map and ablate haemodynamically stable VT with low VT recurrence rates. It is yet to be established whether this system may be applied with equal success to patients with haemodynamically unstable VT.

Adult↗
PubMed1994

Sensory motor cortex: correlation of presurgical mapping with functional MR imaging and invasive cortical mapping.

PURPOSE: To describe a clinically useful application of functional magnetic resonance (MR) imaging--presurgical mapping of the sensory motor cortex--and to validate the results with established physiologic techniques. MATERIALS AND METHODS: Functional MR mapping of the sensory motor cortex was performed in two women, aged 24 and 38 years. Both had intractable, simple partial motor seizures due to tumors located in or near the sensory motor cortex. They subsequently underwent invasive cortical mapping--direct cortical stimulation and/or sensory-evoked-potential recording--to localize the affected sensory motor area prior to tumor resection. RESULTS: In both patients, the functional MR study demonstrated task activation of the sensory motor cortex. In both cases, results of cortical functional mapping with invasive techniques matched those obtained with functional MR imaging. CONCLUSION: Presurgical mapping of the sensory motor cortex is a potentially useful clinical application of functional MR imaging.

Adult↗
PubMed2006

Assignment of 101 genes localized in HSA10 to a swine RH (IMpRH) map to generate a dense human-swine comparative map.

Economically important traits such as growth and backfat in pigs have been shown to be influenced by genes in swine chromosome (SSC) 10q12-->qter corresponding to human chromosome (HSA) 10p. However, since gene information in the swine chromosomal region was limited, we attempted to generate a dense comparative map between SSC10 and HSA10 by mapping the 115 genes of HSA10 to a swine RH map (IMpRH map). In the mapping ten genes were assigned to SSC10, 88 to SSC14, and one to SSC3. One gene was suggested to link to SSC3, and another to SSC9. The correspondences between HSA10 and SSC10 and between HSA10 and SSC14 were essentially consistent with the observations obtained from bi/uni-directional chromosome painting or other results. This study further indicated that a large number of intrachromosomal rearrangements occurred in the synteny-conserved regions following species separation.

Animals↗
PubMed1997

A cytogenetically anchored genetic map of bovine chromosome 1 obtained by integrating flow-sorted chromosome-derived microsatellite markers into the international bovine map.

A genomic library was constructed from a peak of flow-sorted bovine chromosomes 1 + X after PCR amplification. Forty-three bovine chromosome 1 microsatellites were isolated, genetically mapped and integrated in the international genetic map. In addition, BAC clones from a goat BAC library were identified for five markers (DVEPC119, INRA011, BM4307, KAP8 and MAF64). These goat BACs could be mapped by FISH onto bovine chromosome 1 to bands 1q44-->q45, 1q25, 1q21, 1q12 and 1q14-->q21, respectively. This map reduces the average interval between consecutive markers on the international bovine genetic map from 5.5 cM to 2.5 cM, and provides a good starting point for positional cloning projects in cattle, sheep or goats.

Animals↗
PubMed2001

A hierarchical dynamical map as a basic frame for cortical mapping and its application to priming.

A hierarchical dynamical map is proposed as the basic framework for sensory cortical mapping. To show how the hierarchical dynamical map works in cognitive processes, we applied it to a typical cognitive task known as priming, in which cognitive performance is facilitated as a consequence of prior experience. Prior to the priming task, the network memorizes a sensory scene containing multiple objects presented simultaneously using a hierarchical dynamical map. Each object is composed of different sensory features. The hierarchical dynamical map presented here is formed by random itinerancy among limit-cycle attractors into which these objects are encoded. Each limit-cycle attractor contains multiple point attractors into which elemental features belonging to the same object are encoded. When a feature stimulus is presented as a priming cue, the network state is changed from the itinerant state to a limit-cycle attractor relevant to the priming cue. After a short priming period, the network state reverts to the itinerant state. Under application of the test cue, consisting of some feature belonging to the object relevant to the priming cue and fragments of features belonging to others, the network state is changed to a limit-cycle attractor and finally to a point attractor relevant to the target feature. This process is considered as the identification of the target. The model consistently reproduces various observed results for priming processes such as the difference in identification time between cross-modality and within-modality priming tasks, the effect of interval between priming cue and test cue on identification time, the effect of priming duration on the time, and the effect of repetition of the same priming task on neural activity.

Brain Mapping↗
PubMed2006

Quantitative DNA fiber mapping in genome research and construction of physical maps.

Efforts to prepare a first draft of the human DNA genomic sequence forced multidisciplinary teams of researchers to face unique challenges. At the same time, these unprecedented obstacles stimulated the development of many highly innovative approaches to biomedical problem solving, robotics, and bioinformatics. High-resolution physical maps are required for ordering individual segments of information for the construction of a comprehensive map of the entire genome. This chapter describes a novel way to identify, delineate, and characterize selected, often small DNA sequences along a larger piece of the human genome. The technology is based on immobilization of high molecular weight DNA molecules on a solid substrate (such as a glass slide) followed by uniform stretching of the DNA molecule by the force of a receding meniscus. The hydrodynamic force stretches the DNA molecules homogeneously to approximately 2.3 kb/microm, so that distances measured after probe binding in microm can be converted directly into kb distances. Out of a large number of applications, this article focuses on mapping of genomic sequences relative to one another, the assembly of physical maps with near kb resolution, and, finally, quality control during physical map assembly and sequencing.

Chromosomes, Artificial↗
PubMed2001

[Construction of genetic map in sorghum and fine mapping of the germination stimulant production gene response to Striga asiatica].

Sorghum is the fifth important crop in the world. It is also the major food resource in African countries. Striga asiatica is a parasitism weed on sorghum and some other important crops. In this report, two sorghum lines with the difference in response to Striga asiatica, SRN39 (lower Germination Stimulant-GermStim production) and Shanguihong (high GermStim production), were selected as the parents for the construction of a recombinant inbred (RI) population. Ninety-four RI lines were collected for the molecular analysis and GermStim production evaluation. A genetic map was constructed with 251 molecular markers that distributed on 10 different linkage groups. The map covers sorghum genome of 1,779 cm with an average map distance of 7.1 cm between linked markers. It is one of the complete sorghum molecular map in the world. Co-segregation analysis indicated that the germination stimulant gene (GermStim) was located on linkage group J, which was at a distance of 13 cm from the closed marker. Further RAPD analysis between two parents and two DNA pools different in the amount of germination stimulant production, several polymorphic DNA fragments were identified and cloned. Mapping results showed two of them flanked with the GermStim gene at a distance of 1.6 cm and 2.1 cm respectively.

Chromosome Mapping↗
PubMed2004

Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality.

Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.

Arabidopsis↗