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PubMed1997

Multiple-complete-digest restriction fragment mapping: generating sequence-ready maps for large-scale DNA sequencing.

Multiple-complete-digest mapping is a DNA mapping technique based on complete-restriction-digest fingerprints of a set of clones that provides highly redundant coverage of the mapping target. The maps assembled from these fingerprints order both the clones and the restriction fragments. Maps are coordinated across three enzymes in the examples presented. Starting with yeast artificial chromosome contigs from the 7q31.3 and 7p14 regions of the human genome, we have produced cosmid-based maps spanning more than one million base pairs. Each yeast artificial chromosome is first subcloned into cosmids at a redundancy of x15-30. Complete-digest fragments are electrophoresed on agarose gels, poststained, and imaged on a fluorescent scanner. Aberrant clones that are not representative of the underlying genome are rejected in the map construction process. Almost every restriction fragment is ordered, allowing selection of minimal tiling paths with clone-to-clone overlaps of only a few thousand base pairs. These maps demonstrate the practicality of applying the experimental and software-based steps in multiple-complete-digest mapping to a target of significant size and complexity. We present evidence that the maps are sufficiently accurate to validate both the clones selected for sequencing and the sequence assemblies obtained once these clones have been sequenced by a "shotgun" method.

Base Composition↗

PubMed1988

Vesikin, a vesicle associated ATPase from squid axoplasm and optic lobe, has characteristics in common with vertebrate brain MAP 1 and MAP 2.

Vesikin, a protein that can associate with squid axoplasmic vesicles or optic lobe microtubules, has been implicated as a force-generating molecule involved in microtubule-dependent vesicle transport [Gilbert and Sloboda, 1986, 1988]. Because vesikin crossreacts with an antibody to porcine brain microtubule associated protein 2 (MAP 2), studies were conducted to compare squid vesikin and brain MAPs. When taxol stabilized microtubules containing vesikin as a microtubule associated protein were incubated in the presence of ATP, vesikin dissociated from the microtubule subunit lattice. This behavior would be expected for an ATP-dependent, force generating molecule that serves as a crossbridge between vesicles and microtubules. When chick brain microtubules were treated under the same conditions, MAP 2 remained bound to the microtubules while MAP 1 dissociated in a manner similar to vesikin. One dimensional peptide mapping procedures revealed that, although digestion of vesikin and MAP 2 generated several peptides common to both proteins, vesikin and MAP 2 are clearly not identical. Furthermore, the addition of vesikin or MAPS 1 and 2 to purified tubulin stimulated microtubule assembly in a manner dependent on the concentration of added protein. These findings demonstrate that brain MAPs share characteristics common to squid vesikin and support the suggestion that brain MAPs 1 and 2 might act as a force generating complex for vesicle transport in higher organisms.

Adenosine Triphosphate↗

PubMed1995

Rapid construction of integrated maps using inner product mapping: YAC coverage of human chromosome 11.

Inner product mapping (IPM) has been proposed as a hybridization-based method for achieving low-cost, high-throughput, high-resolution radiation hybrid (RH) mapping of clones. Using Alu-PCR products of chromosome 11-specific clones, we serially hybridized a set of RHs against gridded filters of YACs having an average size of 350 kb. We then combined these hybridization data with preexisting RH map data to build an inner product map. This binning of 865 YACs provides the first high-resolution large-scale (> twofold redundancy) clonal coverage of human chromosome 11 and is the first inner product map ever constructed. We verified the accuracy and precision of this chromosome 11 map by performing a novel likelihood analysis on independent YAC hybridization data. These results establish that IPM is a highly rapid, inexpensive, accurate, and precise large-scale long-range mapping method, particularly when preexisting RH maps are available, and that IPM can replace or complement more conventional short-range mapping methods. IPM may enable the rapid construction of sequence-ready maps and the binning of expressed sequences.

Chromosome Mapping↗

PubMed1999

Integrated mapping package--a physical mapping software tool kit.

We have developed an integrated physical mapping computer software package (IMP), originally designed to support the physical mapping of human chromosome 13 and expanded to support several gene-identification projects based on the positional candidate approach. IMP displays map data in a form that provides useful guidelines to the end users. An integrated map with high resolution and confidence is constructed from different types of mapping data, including hybridization experiments, STS-based PCR assays, genetic linkage mapping, cDNA localization, and FISH data. The map is also designed to provide suggestions for specific experiments that are required to obtain maps with even higher resolution and confidence. To this end, the optimization employs multiple constraints that take into account already established STS "scaffold" maps. This software thus serves as an important general tool kit for physical mapping, sequencing, and gene-hunting projects.

Algorithms↗

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↗

PubMed2002

Assignment of 280 swine genomic inserts including 31 microsatellites from BAC clones to the swine RH map (IMpRH map).

A precise genetic map containing anonymous markers and genes is indispensable for the efficient selection of candidate gene(s) responsible for quantitative trait loci (QTL) traits. For this purpose, a first version of a radiation hybrid cell (RH) map has been constructed by using the INRA-University of Minnesota RH panel for 757 markers (IMpRH) (Hawken et al. 1999, Mamm. Genome 10: 824--830). In this study, 280 swine genomic fragments in BAC clones were assigned to the IMpRH map; 255 BAC clones were successfully linked to first-generation linkage groups (LOD > 4.8). The remaining 25 clones could not be mapped, because their lod-scores to the closest markers in the first generation map were less than 4.8. In addition, 16 BAC clones, mapped to swine Chromosome (Chr) 1 by IMpRH mapping, were subjected to isolation of microsatellites (MSs). Thirty-one MSs were isolated from 15 BAC clones, and 24 of 31 (77%) MSs derived from 14 clones were found to be polymorphic. We also mapped both termini of 12 BAC clones to the IMpRH map, in order to measure resolution of the IMpRH map; the resolution was found to range from 8 kb/centiRay to more than 126 kb/centiRay depending on the region.

Animals↗

PubMed2004

MAP-O-MAT: internet-based linkage mapping.

UNLABELLED: MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. MAP-O-MAT facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps (exclusive to the deCODE genotyping data). The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly. AVAILABILITY: MAP-O-MAT is located at http://compgen.rutgers.edu/mapomat/ CONTACT: matise@biology.rutgers.edu.

Chromosome Mapping↗

PubMed1999

A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits.

Chromosome Mapping↗

PubMed1981

Alignment of a restriction map with the genetic map of bacteriophage T4.

A restriction map of the bacteriophage T4 genome was aligned with the T4 genetic map. Included were the cleavage sites for BamHI, BglII, KpnI, PvuI, SalI, and XbaI. The alignment utilized the fact that the T4 genetic map had been oriented previously with respect to a T2/T4 heteroduplex map. DNA fragments from a BglII digestion of cytosine-containing DNA from a T4 dCTPase- denA denB(rIIH23B) alc mutant were hybridized with full-length chromosomal strands of bacteriophage T2, and the heteroduplexes were examined by electron microscopy. From their lengths and patterns of substitution and deletion loops, the heteroduplexes formed with 6 of the 13 BglII fragments could be unambiguously identified and positioned on the T2/T4 heteroduplex map. The ends of the T4 DNA strands in the heteroduplexes directly identified the location of 10 BglII cleavage sites. The remaining three BglII cleavage sites could be assigned to the T2/T4 heteroduplex map based on their relative locations on the restriction map. It was also possible to identify the source of the DNA strands (i.e., T2 or T4) in four previously unassigned deletion loops on the T2/T4 heteroduplex. Among the BglII fragments identified in heteroduplexes was the fragment containing the rIIH23B deletion; this deletion was used as the primary point of reference for alignment of the T4 restriction map with the T2/T4 heteroduplex map and, hence, with the T4 genetic map.

Chromosome Mapping↗

PubMed2002

Linkage mapping of genes controlling resistance to white rust (Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana.

Genes for resistance to white rust (Albugo candida) in oilseed Brassica rapa were mapped using a recombinant inbred (RI) population and a genetic linkage map consisting of 144 restriction fragment length polymorphism (RFLP) markers and 3 phenotypic markers. Young seedlings were evaluated by inoculating cotyledons with A. candida race 2 (AC2) and race 7 (AC7) and scoring the interaction phenotype (IP) on a 0-9 scale. The IP of each line was nearly identical for the two races and the population showed bimodal distributions, suggesting that a single major gene (or tightly linked genes) controlled resistance to the two races. The IP scores were converted to categorical resistant and susceptible scores, and these data were used to map a single Mendelian gene controlling resistance to both races on linkage group 4 where resistance to race 2 had been mapped previously. A quantitative trait loci (QTL) mapping approach using the IP scores detected the same major resistance locus for both races, plus a second minor QTL effect for AC2 on linkage group 2. These results indicate that either a dominant allele at a single locus (Acal) or two tightly linked loci control seedling resistance to both races of white rust in the biennial turnip rape cultivar Per. The map positions of white rust resistance genes in B. rapa and Brassica napus were compared and the results indicate where additional loci that have not been mapped may be located. Alignment of these maps to the physical map of the Arabidopsis genome identified regions to target for comparative fine mapping using this model organism.

Arabidopsis↗

PubMed2002

Map error reduction: using genetic and sequence-based physical maps to order closely linked markers.

The Marshfield comprehensive genetic maps are frequently used for linkage and association studies, however, for some regions of these maps the marker order has low level of likelihood ratio support. In order to investigate the level of statistical support and the accuracy of the genetic maps compared to sequence-based physical maps, two approximately 30 cM autosomal regions were selected. The first region was selected from chromosome 3 and consisted predominately of draft sequence. The second region was selected from chromosome 21 and consisted of finished sequence data. The physical order of these markers was based upon their position on Celera (CEL) and Human Genome Project-Santa Cruz (HGP-sc) sequence-based physical maps. The chromosome 3 and 21 regions contained 100 and 61 markers, respectively, on the Marshfield genetic map. The genetic and physical map order was consistent for 88.9 and 89.2% of the markers in the region on chromosome 3 and 21, respectively. Using a novel scoring criterion to assess inconsistent marker order between genetic and physical maps, it was determined that the physical order was likely the correct order for 3.3 and 7.1% of the markers in the chromosome 3 and 21 regions, respectively. To increase the accuracy of the order of markers selected for fine mapping a method is presented which combines information from genetic and sequence-based physical maps.

Genetic Linkage↗

PubMed2000

Catalytic activation of mitogen-activated protein (MAP) kinase phosphatase-1 by binding to p38 MAP kinase: critical role of the p38 C-terminal domain in its negative regulation.

Mitogen-activated protein (MAP) kinase phosphatase-1 (MKP-1) is the archetypal member of the dual-specificity protein phosphatase family, the expression of which can be rapidly induced by a variety of growth factors and cellular stress. Since MKP-1 protein localizes in the nucleus, it has been suggested to play an important role in the feedback control of MAP kinase-regulated gene transcription. Recently it has been demonstrated that the interaction of several cytosolic MAP kinase phosphatases with MAP kinases can trigger the catalytic activation of the phosphatases. It is unclear whether such a regulatory mechanism can apply to nuclear MAP kinase phosphatases and serve as an additional apparatus for the feedback control of MAP kinase-mediated gene expression. Here we have shown that MKP-1 associates directly with p38 MAP kinase both in vivo and in vitro, and that this interaction enhances the catalytic activity of MKP-1. The point mutation Asp-316-->Asn in the C-terminus of p38, analogous to the ERK2 (extracellular-signal-regulated kinase 2) sevenmaker mutation, dramatically decreases its binding to MKP-1 and substantially compromises its stimulatory effect on the catalytic activity of this phosphatase. Consistent with its defective interaction with MKP-1, this p38 mutant also displays greater resistance to dephosphorylation by the phosphatase. Our studies provide the first example of catalytic activation of a nuclear MAP kinase phosphatase through direct binding to a MAP kinase, suggesting that such a regulatory mechanism may play an important role in the feedback control of MAP kinase signalling in the nuclear compartment.

Asparagine↗

PubMed2001

A high-resolution consensus linkage map of the rat, integrating radiation hybrid and genetic maps.

We have constructed a high-resolution consensus genetic map of the rat in a single large intercross, which integrates 747 framework markers and 687 positions of our whole-genome radiation hybrid (RH) map of the rat. We selected 136 new gene markers from the GenBank database and assigned them either genetically or physically to rat chromosomes to evaluate the accuracy of the integrated linkage-RH maps in the localization of new markers and to enrich existing comparative mapping data. These markers and 631 D-Got- markers, which are physically mapped but still uncharacterized for evidence of polymorphism, were tested for allele variations in a panel of 16 rat strains commonly used in genetic studies. The consensus linkage map constructed in the GK x BN cross now comprises 1620 markers of various origins, defining 840 resolved genetic positions with an average spacing of 2.2 cM between adjacent loci, and includes 407 gene markers. This whole-genome genetic map will contribute to the advancement of genetic studies in the rat by incorporating gene/EST maps, physical mapping information, and sequence data generated in rat and other mammalian species into genetic intervals harboring disease susceptibility loci identified in rat models of human genetic disorders.

Animals↗

PubMed1987

Fine detail in body surface potential maps: accuracy of maps using a limited lead array and spatial and temporal data representation.

In order to evaluate the accuracy with which a limited lead array can be used to estimate fine details of the thoracic distribution of cardiac potentials, we compared 192-lead body surface maps and those constructed using a subset of 32 leads. We also evaluated preservation of detail in body surface maps reconstructed following spatial and temporal data representation, a method proposed for quantitative comparison of maps. Maps were analyzed with respect to four previously reported normal map features recorded with extensive lead arrays. The maps constructed from 32 leads accurately reproduced all map features with 92% or greater accuracy. Maps constructed after spatial and temporal data representation had a reproduction accuracy of 93% and 98% respectively for two map features more than 100 microV in amplitude but accuracy with respect to the two map features less than 100 microV in amplitude was 86% and 59% respectively. The study demonstrates that a selected limited lead array permits accurate estimation of the body surface distribution of cardiac potentials even when potentials are low level or occur in regions not directly sampled by a recording electrode. To represent potentials of less than 100 microV, more coefficients would be required to permit accurate spatial and temporal representation.

Electrocardiography↗

PubMed1988

Experimental study on significance of QRS area map--comparison with VAT map.

The QRS area map, which is obtained by time integration of the QRS potential, is assumed to correlate with the ventricular activation time (VAT) map. Using 16 mongrel dogs, the QRS area map and VAT map from cardiac and body surface were compared during sinus rhythm and left and right ventricular endocardial pacing. The cardiac surface QRS area map resembled the cardiac surface VAT map, and it was considered useful to estimate the excitation sequence. The body surface QRS area map localized the stimulus site more easily during pacing than the body surface VAT map. Therefore, it was considered useful to determine the site at which a ventricular extrasystole occurs. The QRS area map proved to be more reproducible than the VAT map.

Animals↗

PubMed2001

p38 mitogen-activated protein (MAP) kinase but not p44/p42 MAP kinase is involved in prostaglandin E1-induced vascular endothelial growth factor synthesis in osteoblasts.

We investigated the mechanism underlying vascular endothelial growth factor (VEGF) synthesis stimulated by prostaglandin E1 (PGE1) in osteoblast-like MC3T3-E1 cells. PGE1 induced the phosphorylation of both p44/p42 mitogen-activated protein (MAP) kinase and p38 MAP kinase. SB203580, a specific inhibitor of p38 MAP kinase, inhibited the PGE1-stimulated VEGF synthesis as well as PGE1-induced phosphorylation of p38 MAP kinase. PD98059, an inhibitor of the upstream kinase that activates p44/p42 MAP kinase, which reduced the PGE1-induced phosphorylation of p44/p42 MAP kinase, had little effect on the VEGF synthesis stimulated by PGE1. AH-6809, an antagonist of the subtypes of the PGE receptor, EP1 and EP2, or SC-19220, an antagonist of EP1 receptor, did not inhibit the PGE1-induced VEGF synthesis. H-89, an inhibitor of cAMP-dependent protein kinase, and SQ22536, an inhibitor of adenylate cyclase, reduced the VEGF synthesis induced by PGE1. Cholera toxin, an activator of G(s), and forskolin, an activator of adenylate cyclase, induced VEGF synthesis. SB203580 and PD169316, another specific inhibitor of p38 MAP kinase, reduced the cholera toxin-, forskolin- or 8bromo-cAMP-stimulated VEGF synthesis. However, PD98059 failed to affect the VEGF synthesis stimulated by cholera toxin, forskolin or 8-bromoadenosine-3',5'-cyclic monophosphate (8bromo-cAMP). SB203580 reduced the phosphorylation of p38 MAP kinase induced by forskolin or 8bromo-cAMP. These results strongly suggest that p44/p42 MAP kinase activation is not involved in the PGE1-stimulated VEGF synthesis in osteoblasts but that p38 MAP kinase activation is involved.

Alprostadil↗

PubMed1992

Activation of mitogen-activated protein (MAP) kinase by a MAP kinase-kinase.

Previously it has been shown that acute 12-O-tetradecanoylphorbol-13-acetate treatment of intact U937 cells results in activation of mitogen-activated protein (MAP) kinase and a MAP kinase activator. MAP kinase activator induces phosphorylation of MAP kinase on tyrosine and threonine residues, thereby activating MAP kinase. Here, experiments with the irreversible kinase inhibitor, 5'-p-fluorosulfonylbenzoyladenosine (FSBA), show that MAP kinase activator is in fact a MAP kinase-kinase. Treatment of MAP kinase activator with FSBA results in complete inactivation. This inactivation is prevented by a 10-fold excess of ATP. Inactivation of MAP kinase by FSBA does not affect the extent of threonine/tyrosine phosphorylation induced by MAP kinase-kinase.

Adenosine↗

PubMed2005

[Comparison between three-dimensional electro-anatomical mapping and conventional mapping in the ablation of atrial tachycardias].

In atrial tachycardias, catheter ablation using conventional mapping system is associated with high immediate success and low recurrence. Three-dimensional electroanatomical mapping system combined to catheter ablation of atrial tachycardias has reached, in small uncontroled series, success rates of 100%. However, limited data are available about rates of recurrence or complication using this approach. In order to compare both mapping systems, we have conducted a study of 65 consecutive patients (36 women and 29 men) that underwent both electrophysiologic study and catheter ablation for suspected atrial tachycardias. Pre-existing heart disease was noted in 43%, hypertension in 32% and a history of atrial fibrillation of flutter in 52%. Catheter ablation guided by conventional mapping was undertaken in 44 patients and by three-dimensional electroanatomical mapping in 21. Successful ablation was performed in 68% of patients with conventional mapping and in 90% with three-dimensional electroanatomical mapping. No complication and recurrence were observed with the latter approach, while 5 patients had a recurrence and 2 had immediate complication with conventional mapping. Catheter ablation of atrial tachycardias combined with three-dimensional electroanatomical mapping appeared to be effective and safe, however, conventional mapping system still remains a reliable approach that must be considered as the first choice for atrial tachycardias ablation.

Adult↗