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At least 181 records · Page 10Linked to original sources
PubMed2003

The comprehensive mouse radiation hybrid map densely cross-referenced to the recombination map: a tool to support the sequence assemblies.

We have developed a unique comprehensive mouse radiation hybrid (RH) map of nearly 23,000 markers integrating data from three international genome centers and over 400 independent laboratories. We have cross-referenced this map to the 0.5-cM resolution recombination-based Jackson Laboratory (TJL) backcross panel map, building a complete set of RH framework chromosome maps based on a high density of known-ordered anchor markers. We have systematically typed markers to improve coverage and resolve discrepancies, and have reanalyzed data sets as needed. The cross-linking of the RH and recombination maps has resulted in a highly accurate genome-wide map with consistent marker order. We have compared these linked framework maps to the Ensemble mouse genome sequence assembly, and show that they are a useful medium resolution tool for both validating sequence assembly and elucidating chromosome biology.

Animals↗
PubMed2000

Rat somatosensory cerebropontocerebellar pathways: spatial relationships of the somatotopic map of the primary somatosensory cortex are preserved in a three-dimensional clustered pontine map.

In the primary somatosensory cortex (SI), the body surface is mapped in a relatively continuous fashion, with adjacent body regions represented in adjacent cortical domains. In contrast, somatosensory maps found in regions of the cerebellar hemispheres, which are influenced by the SI through a monosynaptic link in the pontine nuclei, are discontinuous ("fractured") in organization. To elucidate this map transformation, the authors studied the organization of the first link in the SI-cerebellar pathway, the SI-pontine projection. After injecting anterograde axonal tracers into electrophysiologically defined parts of the SI, three-dimensional reconstruction and computer-graphic visualization techniques were used to analyze the spatial distribution of labeled fibers. Several target regions in the pontine nuclei were identified for each major body representation. The labeled axons formed sharply delineated clusters that were distributed in an inside-out, shell-like fashion. Upper lip and other perioral representations were located in a central core, whereas extremity and trunk representations were found more externally. The multiple clusters suggest that the pontine nuclei contain several representations of the SI map. Within each representation, the spatial relationships of the SI map are largely preserved. This corticopontine projection pattern is compatible with recently proposed principles for the establishment of subcortical topographic patterns during development. The largely preserved spatial relationships in the pontine somatotopic map also suggest that the transformation from an organized topography in SI to a fractured map in the cerebellum takes place primarily in the mossy fiber pontocerebellar projection.

Animals↗
PubMed2002

A protein molecular weight map of ES2 clear cell ovarian carcinoma cells using a two-dimensional liquid separations/mass mapping technique.

A molecular weight map of the protein content of ES2 human clear cell ovarian carcinoma cells has been produced using a two-dimensional (2-D) liquid separations/mass mapping technique. This method uses a 2-D liquid separation of proteins from whole cell lysates coupled on-line to an electrospray ionization-time of flight (ESI-TOF) mass spectrometer to map the accurate intact molecular weight (M(r)) of the protein content of the cells. The two separation dimensions involve the use of liquid isoelectric focusing as the first phase and nonporous silica reversed-phase high-performance liquid chromatography (HPLC) as the second phase of separation. The detection by ESI-TOF-MS provides an image of pI versus M(r) analogous to 2-D gel electrophoresis. Each protein is then identified based upon matrix-assisted laser desorption/ionization (MALDI)-TOF-MS peptide mapping and intact M(r) so that a standard map is produced against which other ovarian carcinoma cell lines can be compared. The accurate intact M(r) together with the pI fraction, and peptide map serve to tag the protein for future interlysate comparisons. An internal standard is also used to provide a means for quantitation for future interlysate studies. In the ES2 cell line under study it is shown that nearly 900 M(r) bands are detected over 17 pI fractions from pH 4 to 12 and a M(r) range up to 85 kDa and that around 290 of these bands can be identified using mass spectrometric based techniques. The protein M(r) is detected within an accuracy of 150 ppm and it is shown that many of the proteins in this human cancer sample are modified compared to the database. The protein M(r) map may serve as a highly reproducible standard Web-based method for comparing proteins from related human cell lines.

Chromatography, High Pressure Liquid↗
PubMed2003

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

It is well known that any genus zero surface can be mapped conformally onto the sphere and any local portion thereof onto a disk. However, it is not trivial to find a general method which finds a conformal mapping between two general genus zero surfaces. We propose a new variational method which can find a unique mapping between any two genus zero manifolds by minimizing the harmonic energy of the map. We demonstrate the feasibility of our algorithm by applying it 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 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

Hippocampal lesions do not disrupt navigational map retention in homing pigeons under conditions when map acquisition is hippocampal dependent.

In contrast to map-like navigation by familiar landmarks, understanding the relationship between the avian hippocampal formation (HF) and the homing pigeon navigational map has remained a challenge. With the goal of filling an empirical gap, we performed an experiment in which young homing pigeons learned a navigational map while being held in an outdoor aviary, and then half the birds were subjected to HF ablation. The question was whether HF lesion would impair retention of a navigational map learned under conditions known to require participation of HF. The pigeons, which had never flown from the aviary before, together with an additional control group that learned a navigational map with free-flight experience, were then released from two distant release sites. Contrary to expectation, the HF-lesioned birds oriented in a homeward direction in manner indistinguishable from the intact control pigeons raised in the same outdoor aviary. HF lesion did not result in a navigational map retention deficit. Together with previous results, it is now clear that regardless of the learning environment present during acquisition, HF plays no necessary role in the subsequent retention or operation of the homing pigeon navigational map.

Animals↗
PubMed1995

A 2D crossover-based map of the human X chromosome as a model for map integration.

We have constructed a two-dimensional map of 243 markers on the X chromosome. The average distance between markers ordered by two recombinants is 5.4 centiMorgans (cM), which is reduced to 3.2 cM using a less stringent criterion of one recombinant. Map resolution is enhanced by replacing the usual reference marker format with a 2D format, and the two-recombinant rule is more conservative than the lod 3.0 criterion for order. Taken together, crossover mapping and the 2D format produces maps with greater reliability and higher resolution than maps constructed using currently accepted standards. This first high-density crossover-based map of an entire human chromosome provides a model for integrating physical and genetic maps.

Chromosome Mapping↗
PubMed2002

Molecular-feature domains with posterodorsal-anteroventral polarity in the symmetrical sensory maps of the mouse olfactory bulb: mapping of odourant-induced Zif268 expression.

Individual glomeruli in the mammalian olfactory bulb presumably represent a single type of odourant receptor. Thus, the glomerular sheet provides odourant receptor maps at the surface of the olfactory bulb. To understand the basic spatial organization of the olfactory sensory maps, we first compared the spatial distribution of odourant-induced responses measured by the optical imaging of intrinsic signals with that detected immunohistochemically by expressions of Zif268, one of the immediate early gene products in juxtaglomerular cells. In the dorsal surface of the bulb, we detected a clear correlation in the spatial pattern between these responses. In addition, the molecular-feature domains and their polarities (spatial shifts of responses with an increase in carbon chain length) that were defined by the optical imaging method could be also detected by the Zif268 mapping method. We then mapped the Zif268 signals over the entire olfactory bulb using a homologous series of fatty acids and aliphatic alcohols as stimulus odourants. We superimposed the Zif268 signals onto the standard unrolled map with the help of cell adhesion molecule compartments. Each odourant typically elicited two pairs of clusters of dense Zif268 signals. The results showed that molecular-feature domains and their polarities were arranged symmetrically at stereotypical positions in a mirror-image fashion between the lateral and the medial sensory maps. The polarity of each domain was roughly in parallel with the posterodorsal-anteroventral axis that was defined by the cell adhesion molecule compartments. These results suggest that the molecular-feature domain with its fixed polarity is one of the basic structural units in the spatial organization of the odourant receptor maps in the olfactory bulb.

Animals↗
PubMed2002

Global and local dispersion of ventricular repolarization: endocardial monophasic action potential mapping in swine and humans by using an electro-anatomical mapping system.

This article evaluates whether the global dispersion of ventricular repolarization (DVR) can be estimated from measurements between a few adjacent or remote sites. Monophasic action potentials (MAP) were recorded from 61 +/- 18 left (LV) or right ventricular (RV) sites in 10 pigs and 44 +/- 16 LV, or RV sites in 8 patients by using the CARTO mapping system. MAP duration (MAPd) and end-of-repolarization time were calculated at each site and 13 repolarization maps from pigs and 10 from patients were reconstructed. Global dispersions in MAPd and EOR over the LV or RV were compared with the adjacent DVR among 3 - 7 MAPs in areas > or = 0.7 and < or = 1 cm(2) and with the remote DVRs between 2 MAPs with the greatest activation time difference (remote DVR1) and between the apical and laterobasal LV or RV (remote DVR2). The adjacent dispersions in end-of-repolarization and MAPd were significantly smaller than the global ones, 13 +/- 3 and 12 +/- 3 ms vs. 44 +/- 9 and 42 +/- 12 ms in pigs and 13 +/- 7 and 14 +/- 8 ms vs. 72 +/- 24 and 66 +/- 22 ms in patients. The remote DVR1 (30 +/- 8 and 17 +/- 10 ms in pigs and 40 +/- 28 and 28 +/- 17 ms in patients) and remote DVR2 (16 +/- 7 and 11 +/- 10 ms in pigs and 35 +/- 24 and 21 +/- 21 ms in patients) were also significantly smaller than the global DVRs. In conclusion, global DVR is poorly estimated from MAP recordings from a few adjacent or remote sites, suggesting the importance of obtaining global information in evaluating DVR.

Action Potentials↗
PubMed1999

The p38 MAP kinase pathway signals for cytokine-induced mRNA stabilization via MAP kinase-activated protein kinase 2 and an AU-rich region-targeted mechanism.

Stabilization of mRNAs contributes to the strong and rapid induction of genes in the inflammatory response. The signaling mechanisms involved were investigated using a tetracycline-controlled expression system to determine the half-lives of interleukin (IL)-6 and IL-8 mRNAs. Transcript stability was low in untreated HeLa cells, but increased in cells expressing a constitutively active form of the MAP kinase kinase kinase MEKK1. Destabilization and signal-induced stabilization was transferred to the stable beta-globin mRNA by a 161-nucleotide fragment of IL-8 mRNA which contains an AU-rich region, as well as by defined AU-rich elements (AREs) of the c-fos and GM-CSF mRNAs. Of the different MEKK1-activated signaling pathways, no significant effects on mRNA degradation were observed for the SAPK/JNK, extracellular regulated kinase and NF-kappaB pathways. Selective activation of the p38 MAP kinase (=SAPK2) pathway by MAP kinase kinase 6 induced mRNA stabilization. A dominant-negative mutant of p38 MAP kinase interfered with MEKK1 and also IL-1-induced stabilization. Furthermore, an active form of the p38 MAP kinase-activated protein kinase (MAPKAP K2 or MK2) induced mRNA stabilization, whereas a negative interfering MK2 mutant interfered with MAP kinase kinase 6-induced stabilization. These findings indicate that the p38 MAP kinase pathway contributes to cytokine/stress-induced gene expression by stabilizing mRNAs through an MK2-dependent, ARE-targeted mechanism.

3' Untranslated Regions↗
PubMed1993

Mapping chromosome rearrangement breakpoints to the physical map of Caenorhabditis elegans by fluorescent in situ hybridization.

A scheme for rapidly mapping chromosome rearrangements relative to the physical map of Caenorhabditis elegans is described that is based on hybridization patterns of cloned DNA on meiotic nuclei, as visualized by fluorescent in situ hybridization. From the nearly complete physical map, DNA clones, in yeast artificial chromosomes (YACs), spanning the rearrangement breakpoint were selected. The purified YAC DNAs were first amplified by degenerate oligonucleotide-primed polymerase chain reaction, then reamplified to incorporate fluorescein dUTP or rhodamine dUTP. The site of hybridization was visualized directly (without the use of antibodies) on meiotic bivalents. This allows chromosome rearrangements to be mapped readily if the duplicated, deficient or translocated regions do not pair with a normal homologous region, because the site or sites of hybridization of the probe on meiotic prophase nuclei will be spatially distinct. The pattern, or number, of hybridization signals from probes from within, or adjacent to, the rearranged region of the genome can be predicted from the genetic constitution of the strain. Characterization of the physical extent of the genetically mapped rearrangements places genetic landmarks on the physical map, and so provides linkage between the two types of map.

Animals↗
PubMed1990

Towards a physical map of the Drosophila melanogaster genome: mapping of cosmid clones within defined genomic divisions.

A physical map of the D. melanogaster genome is being constructed, in the form of overlapping cosmid clones that are assigned to specific polytene chromosome sites. A master library of ca. 20,000 cosmids is screened with probes that correspond to numbered chromosomal divisions (ca. 1% of the genome); these probes are prepared by microdissection and PCR-amplification of individual chromosomes. The 120 to 250 cosmids selected by each probe are fingerprinted by Hinfl digestion and gel electrophoresis, and overlaps are detected by computer analysis of the fingerprints, permitting us to assemble sets of contiguous clones (contigs). Selected cosmids, both from contigs and unattached, are then localized by in situ hybridization to polytene chromosomes. Crosshybridization analysis using end probes links some contigs, and hybridization to previously cloned genes relates the physical to the genetic map. This approach has been used to construct a physical map of the 3.8 megabase DNA in the three distal divisions of the x chromosome. The map is represented by 181 canonical cosmids, of which 108 clones in contigs and 32 unattached clones have been mapped individually by in situ hybridization to chromosomes. Our current database of in situ hybridization results also includes the beginning of a physical map for the rest of the genome: 162 cosmids have been assigned by in situ hybridization to 129 chromosomal subdivisions elsewhere in the genome, representing 5 to 6 megabases of additional mapped DNA.

Animals↗
PubMed2003

Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map.

An international effort is underway to generate a comprehensive haplotype map (HapMap) of the human genome represented by an estimated 300,000 to 1 million 'tag' single nucleotide polymorphisms (SNPs). Our analysis indicates that the current human SNP map is not sufficiently dense to support the HapMap project. For example, 24.6% of the genome currently lacks SNPs at the minimal density and spacing that would be required to construct even a conservative tag SNP map containing 300,000 SNPs. In an effort to improve the human SNP map, we identified 140,696 additional SNP candidates using a new bioinformatics pipeline. Over 51,000 of these SNPs mapped to the largest gaps in the human SNP map, leading to significant improvements in these regions. Our SNPs will be immediately useful for the HapMap project, and will allow for the inclusion of many additional genomic intervals in the final HapMap. Nevertheless, our results also indicate that additional SNP discovery projects will be required both to define the haplotype architecture of the human genome and to construct comprehensive tag SNP maps that will be useful for genetic linkage studies in humans.

Base Sequence↗
PubMed2002

Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes.

Three populations composed of a total of 215 doubled haploid lines and 151 F2 individuals were used to design an intraspecific consensus map of pepper (Capsicum annuum L.). The individual maps varied from 685 to 1668 cM with 16 to 20 linkage groups (LGs). The alignment of the three individual maps permitted the arrangement of 12 consensus major linkage groups corresponding to the basic chromosome number of pepper and displaying a complex correspondence with the tomato map. The consensus map contained 100 known-function gene markers and 5 loci of agronomic interest (the disease-resistance loci L, pvr2, and Pvr4; the C locus, which determines capsaicin content; and the up locus, controlling the erect habit of the fruits). The locations of three other disease-resistance loci (Tsw, Me3, and Bs3) and the y locus, which determines the yellow fruit colour, were also found on this consensus map thanks to linked markers. Here we report on the first functional detailed map in pepper. The use of candidate gene sequences as genetic markers allowed us to localize four clusters of disease-resistance gene analogues and to establish syntenic relationships with other species.

Capsicum↗
PubMed2005

A comparison of genetic maps constructed from haploid and BC1 mapping populations from the same crossing between Gossypium hirsutum L. and Gossypium barbadense L.

Simple sequence repeat (SSR) genetic maps have been separately constructed based on doubled haploid (DH) and (or) haploid and BC1 populations from the same cross between Gossypium hirsutum L. 'TM-1' and Gossypium barbadense L. 'Hai7124'. The BC1 population was produced by pollinating individual plants of the 'TM-1' x 'Hai7124' F1 with 'TM-1', whereas the DH and (or) haploid population developed from the offspring of Vsg x ('TM-1' x 'Hai7124'). Vsg is a virescently marked semigamy line of Gossypium barbadense L. Pima. The BC1 map included 34 linkage groups with an average distance between markers of 9.80 cM (Kosambi, K) and covered 4331.2 cM (K) or approximately 78.7% of the tetraploid cotton genome constructed using 440 SSR and 2 morphological marker genes. Among them, 26 were assigned to 20 chromosomes, 7 to A or D subgenomes, and 1 was unassigned. The haploid map comprised 444 SSR markers mapped to 40 linkage groups with an average distance of 7.35 cM (K) between markers, covering 3262.9 cM (K) or approximately 60.0% of the tetraploid genome. Twenty-nine linkage groups were assigned to all 19 identified chromosomes, 10 to A or D subgenomes, and 1 was unassigned. Fairly good collinearity of marker order was observed along most of the chromosomes or linkage groups. Significant differences in recombination between maps was observed at the chromosomal and genomic level and possible reasons were discussed. Map comparison and combined data provided an essential basis for further mapping of interested genes and QTLs and for studies of diversity, population structure, and phylogeny in Gossypium species.

Chromosome Mapping↗
PubMed1997

Construction of two near-kilobase resolution restriction maps of the 5' regulatory region of the human apolipoprotein B gene by quantitative DNA fiber mapping (QDFM).

Quantitative DNA fiber mapping (QDFM) is a high-resolution technique for physical mapping of DNA. The method is based on hybridization of fluorescently labeled DNA probes to individual DNA molecules stretched on a chemically modified glass surface. We now demonstrate and validate a rapid QDFM-based approach for the mapping of multiple restriction sites and precise localization of restriction fragments in large genomic clones. Restriction fragments of a 70-kb P1 clone (P1-70) containing the 5' region of the human apolipo-protein B gene (APOB) were subcloned and mapped along straightened P1-70 DNA molecules. Multicolor fluorescence in situ hybridization (FISH) and digital image analysis allowed us to rapidly position 29 restriction fragments, ranging in size from 0.5 kb to 8 kb, and to map 43 restriction sites. The restriction map obtained by QDFM was in excellent agreement with information obtained by RecA-assisted restriction endonuclease (RARE) cleavage, long-range PCR, and DNA sequence analyses of the P1-70 clone. These data demonstrate that QDFM is a rapid, reliable method for detailed restriction site-mapping of large DNA clones.

Apolipoproteins B↗
PubMed2001

DNA fiber mapping techniques for the assembly of high-resolution physical maps.

High-resolution physical maps are indispensable for directed sequencing projects or the finishing stages of shotgun sequencing projects. These maps are also critical for the positional cloning of disease genes and genetic elements that regulate gene expression. Typically, physical maps are based on ordered sets of large insert DNA clones from cosmid, P1/PAC/BAC, or yeast artificial chromosome (YAC) libraries. Recent technical developments provide detailed information about overlaps or gaps between clones and precisely locate the position of sequence tagged sites or expressed sequences, and thus support efforts to determine the complete sequence of the human genome and model organisms. Assembly of physical maps is greatly facilitated by hybridization of non-isotopically labeled DNA probes onto DNA molecules that were released from interphase cell nuclei or recombinant DNA clones, stretched to some extent and then immobilized on a solid support. The bound DNA, collectively called "DNA fibers," may consist of single DNA molecules in some experiments or bundles of chromatin fibers in others. Once released from the interphase nuclei, the DNA fibers become more accessible to probes and detection reagents. Hybridization efficiency is therefore increased, allowing the detection of DNA targets as small as a few hundred base pairs. This review summarizes different approaches to DNA fiber mapping and discusses the detection sensitivity and mapping accuracy as well as recent achievements in mapping expressed sequence tags and DNA replication sites.

Animals↗
PubMed2006

Mapping of panda plumage color locus on the microsatellite linkage map of the Japanese quail.

BACKGROUND: Panda (s) is an autosomal recessive mutation, which displays overall white plumage color with spots of wild-type plumage in the Japanese quail (Coturnix japonica). In a previous study, the s locus was included in the same linkage group as serum albumin (Alb) and vitamin-D binding protein (GC) which are mapped on chicken (Gallus gallus) chromosome 4 (GGA4). In this study, we mapped the s locus on the microsatellite linkage map of the Japanese quail by linkage analysis. RESULTS: Segregation data on the s locus were obtained from three-generation families (n = 106). Two microsatellite markers derived from the Japanese quail chromosome 4 (CJA04) and three microsatellite markers derived from GGA4 were genotyped in the three-generation families. We mapped the s locus between GUJ0026 and ABR0544 on CJA04. By comparative mapping with chicken, this locus was mapped between 10.0 Mb and 14.5 Mb region on GGA4. In this region, the endothelin receptor B subtype 2 gene (EDNRB2), an avian-specific paralog of the mammalian endothelin receptor B gene (EDNRB), is located. Because EDNRB is responsible for aganglionic megacolon and spot coat color in mouse, rat and equine, EDNRB2 is suggested to be a candidate gene for the s locus. CONCLUSION: The s locus and the five microsatellite markers were mapped on CJA04 of the Japanese quail. EDNRB2 was suggested to be a candidate gene for the s locus.

Animals↗
PubMed2004

[Linkage map construction and mapping of a dominant genic male sterility gene (Ms) in Brassica napus].

A backcross population derived from a cross between the dominant genic male sterile line Rs1046A and the double-low cultivar 'Samourai' was used for linkage map construction in Brassica napus. A linkage map with a total length of 2 646 cM was developed using 138 AFLP markers, 83 SSR markers and one morphology trait, which were distributed over 18 major linkage groups, two triplets and one linkage pair. 11.7% of the mapped markers distorted from the expected 1:1 ratio. The dominant genic male sterility gene (Ms) was mapped in LG10 and surrounded by five closely linked AFLP markers. Meanwhile,two evident marker segregation distortion regions were observed in both LG8 and LG16. The map constructed in the present study and the mapping of Ms gene are highly valuable in designing marker-assisted breeding program for the genic male sterile two-type line in Brassica napus. They are also important to map-based cloning of the Ms gene and to better understanding of the mechanism of genic male sterility at molecular level.

Brassica napus↗