SEARCH · PubMed Health

Results for “reference mapping”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources

PubMed2006

An enhanced microsatellite map of diploid Fragaria.

A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. x ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F2 mapping population (FVxFN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes of known function, for comparative mapping purposes within Rosaceae.

Chromosome Mapping↗

PubMed1998

A YAC contig map of Arabidopsis thaliana chromosome 3.

We have constructed a YAC contig map of Arabidopsis thaliana chromosome 3. From an estimated total size of 25 Mb, about 21 Mb were covered by 148 clones arranged into nine YAC contigs, which represented most of the low-copy regions of the chromosome. YAC clones were anchored with 259 molecular markers, including 111 for which linkage information was previously available. Most of the genetic map was included in the YAC coverage, and more than 60% of the genetic markers from the reference recombinant inbred line map were anchored, giving a high level of integration between the genetic and physical maps. The submetacentric structure of the chromosome was confirmed by physical data; 3R (the top arm of the linkage map) was about 12 Mb, and 3L (the bottom arm of the linkage map) was about 9 Mb. This YAC physical map will aid in chromosome walking experiments and provide a framework for large-scale DNA sequencing of chromosome 3.

Arabidopsis↗

PubMed2001

Comparison of reproductive parameters in male yellow-blotched map turtles (Graptemys flavimaculata) from a historically contaminated site and a reference site.

From May to September of 1998, we collected monthly plasma samples from male yellow-blotched map turtles captured at two sites in the Pascagoula River drainage, Mississippi. One site (Vancleave) has a documented history of pollution from industrial sources (principally 2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD). Fish consumption advisories at the Vancleave site were lifted in 1996 and current impacts appear minimal. However, the yellow-blotched map turtle, a federally protected species, continues to decline in numbers. To determine if endocrine disruption could be a factor in the low reproductive rates observed in Vancleave turtles, we examined levels of plasma testosterone (T) and estradiol-17beta (E(2)) from males at this site and a second site (Leaksville), which has no known source of industrial pollution. Plasma was also tested for vitellogenin (VTG), which, in males, can be a biomarker of exposure to estrogenic contaminants. No males had detectable plasma VTG nor did mean monthly E(2) levels differ between sites. However, 10% of males from the historically polluted site were found to have high levels of E(2) (equivalent to levels found in females) and T was significantly lower for males captured at this site for 3 of 5 months. Our data suggest that the current impact of contaminants on reproduction in this population is limited. However, a portion of the population may have been affected developmentally, as represented by differences in reproductive parameters detected between sites.

Animals↗

PubMed1997

Reporting levels of spinal blockade.

With spinal anesthesia the level of surgical analgesia is mostly reported without reference to the neuroanatomic map of spinal nerves. The classical maps are variably and inconsistently reported in many textbooks. Because of the differences between the classical maps of Keegan and Garrett and of Foerster, and also because of the variability in their interpretation, we applied them to the same clinical data. This resulted in a theoretically clinically significant difference of two segments. It is concluded that clear reference should be made to the implemented segmental map in expressing the level of spinal blockade.

Anesthesia, Obstetrical↗

PubMed1995

Index, comprehensive microsatellite, and unified linkage maps of human chromosome 14 with cytogenetic tie points and a telomere microsatellite marker.

Three sets of linkage maps (index, comprehensive microsatellite, and unified) have been constructed for human chromosome 14 based on genotypes from the CEPH reference pedigrees. The index maps consist of 18 microsatellite markers, with heterozygosities of at least 68% and intermarker spacing no greater than 11 cM. The sex-average comprehensive microsatellite map is 125 cM in length and includes 115 markers with 54 loci uniquely placed with odds for marker order of at least 1000:1. The sex-average index map length is 121 cM, and the female- and male-specific maps are 143 and 101 cM, respectively. A unified map was also constructed from 147 loci (162 marker systems), which includes 32 RFLP markers in addition to the 115 microsatellites. The sex-average length of the unified map is 128 cM with 69 loci uniquely placed. Our maps are anchored by a microsatellite telomere marker sCAW1 (D14S826), developed from a telomere YAC clone TYAC196, which extends the linkage map to the physical terminus of the long arm of chromosome 14. Furthermore, we have also physically mapped seven of the loci by fluorescence in situ hybridization of cosmid clones or Alu-PCR products amplified from YACs containing the marker sequences. Together with previously established cytogenetic map designations for other loci, our maps display links between genetic markers for 10 of 13 cytogenetic bands of chromosome 14 at the 550 genome band resolution.

Base Sequence↗

PubMed1999

Mapping of histologically identified long fiber tracts in human cerebral hemispheres to the MRI volume of a reference brain: position and spatial variability of the optic radiation.

The interpretation of the anatomical basis of functional deficits after subcortical infarcts could be considerably improved, if the precise topography and interindividual variability in size and course of long fiber tracts in adult human cerebral hemispheres were available in a spatial reference system. We therefore developed a method enabling the mapping of long fiber tracts to the volume of a standard reference brain. The examined fiber tracts were identified in myelin-stained histological serial sections of 10 human brains. The reference brain is a 3-D reconstruction of in vivo obtained magnetic resonance images (MRIs). The warping of histological volumes with the labeled fiber tracts to the reference brain by means of linear and nonlinear transformation procedures results in population maps that demonstrate the interindividual variability in position, size, and course of fiber tracts. In this paper, we present population maps of the optic radiation and the lateral geniculate body as a first example of this mapping strategy. Both structures present a considerable interindividual variability. Furthermore, voxel-based morphometry shows significant side differences with larger volumes of both structures in the left hemisphere than in the right hemisphere. A more than twofold variability of size in the interhemispheric extension of the optic radiation and the lateral geniculate body is found even after normalization of absolute brain size. Our observations demonstrate that the present approach based on population maps of fiber tracts and nuclei can improve the anatomical localization and interpretation of brain lesions visible in MRIs at the level of microstructurally identified architectonical units.

Adult↗

PubMed2001

A two-dimensional map and database of soluble nuclear proteins from HepG2 cells as reference for identification of nutrient-regulated transcription factors.

BACKGROUND: Eukaryotic cells of higher organisms are able to regulate gene transcription in response to changes in the supply of nutrients. In hepatocytes, extracellular glucose levels affect transcription of genes that encode enzymes engaged in glycolysis, gluconeogenesis and lipogenesis. While glucose response elements have been located within a few model gene promoters, the identity of glucose-sensing transcription factors and the mechanisms of their activation remain to be elucidated. AIM OF THE STUDY: We intended to establish a two-dimensional map of nuclear proteins as a reference for identification of nutrient-regulated transcription factors. METHODS: Human hepatoma HepG2 cells were used for the preparation of nuclear extracts. 150-200 microg of the protein mixture were analyzed by 2-dimensional gel electrophoresis (2-DE) and silver-stained protein spots were identified by MALDI-TOF mass spectrometry. RESULTS: Nuclear extracts capable of transcriptional initiation and elongation and containing low amounts of cytoplasmic contaminations were prepared. 543 spots between 17 and 100 kDa and pI 3.7 and 8.8 have been resolved. From these, 65 spots were analyzed by MALDI-TOF mass spectrometry and 53 spots were identified as known proteins of which six represented transcription factors. Regulation by glucose was shown for the activator protein-1 component cJun. Since cJun was not visible on the silver stained 2-DE gel, western blotting of 1-DE gels and immunological detection had to be used in this case. The data were used to construct an online database. CONCLUSIONS: A 2-DE map and database of soluble nuclear proteins is presented. The identification of several transcription factors was possible on the silver-stained gels. However, further fractionation of the nuclear extracts will facilitate the detection of larger numbers of transcriptional regulators. The database and 2-DE map shown here may provide a useful reference for the identification of transcription factors from liver nuclei that are activated by different stimuli, e. g., nutrients.

Carcinoma, Hepatocellular↗

PubMed2003

The effect of 'missing' information on children's retention of fast-mapped labels.

This paper explores 'fast mapping', one of several processes that have been proposed to be involved in the rapid vocabulary expansion observed in the preschool years. An adaptation of a receptive word matching task examined how well children retained a just-mapped relation between word and referent when some information was later missing. Thirty-nine children between the ages of 3;0 and 5;6 (mean age 4;3) were taught to select a black square if the correct match for a spoken label was not visible in an array of pictures presented on a computer screen. This procedure allowed children to respond even when they perceived that the correct referent was absent. In experimental sessions, children experienced a single exposure to a word-referent relation. Then, under one condition they heard the just-learned label but were not presented with the matching referent; instead, a completely novel referent was visible along with the black square. Under another condition, they were presented with a just-learned referent (and the balck square) but heard a completely new label. The question of interest was whether the children appreciated that an earlier-learned map precluded re-assigning a label to a new referent or re-assigning a referent with a second new label. If so, they should select the black square under both conditions. The majority of children (69%) resisted re-assigning a just-mapped label to a completely novel referent and selected the black square, even when the original referent was not in sight. However, fewer of these children resisted accepting a second label for a just-named referent (46%). Older children were significantly more likely to adhere to original maps than were younger children.

Child Language↗

PubMed2006

Mapping VIPS concepts for nursing interventions to the ISO reference terminology model for nursing actions: A collaborative Scandinavian analysis.

The aims of this study were to analyze the coherence between the concepts for nursing interventions in the Swedish VIPS model for nursing recording and the ISO Reference Terminology Model for Nursing Actions and to identify areas in the two models for further development. Seven Scandinavian experts analyzed the VIPS model's concepts for nursing interventions using prototypical examples of nursing actions, involving 233 units of analyses, and collaborated in mapping the two models. All nursing interventions in the VIPS model comprise actions and targets, but a few lack explicit expressions of means. In most cases, the recipient of care is implicit. Expressions for the aim of an action are absent from the ISO model. By this mapping we identified areas for future development of the VIPS model and the experience from nursing terminology work in Scandinavia can contribute to the international standardization efforts.

Cooperative Behavior↗

PubMed2002

Comparative mapping of Homo sapiens chromosome 4 (HSA4) and Sus scrofa chromosome 8 (SSC8) using orthologous genes representing different cytogenetic bands as landmarks.

The recently published draft sequence of the human genome will provide a basic reference for the comparative mapping of genomes among mammals. In this study, we selected 214 genes with complete coding sequences on Homo sapiens chromosome 4 (HSA4) to search for orthologs and expressed sequence tag (EST) sequences in eight other mammalian species (cattle, pig, sheep, goat, horse, dog, cat, and rabbit). In particular, 46 of these genes were used as landmarks for comparative mapping of HSA4 and Sus scrofa chromosome 8 (SSC8); most of HSA4 is homologous to SSC8, which is of particular interest because of its association with genes affecting the reproductive performance of pigs. As a reference framework, the 46 genes were selected to represent different cytogenetic bands on HSA4. Polymerase chain reaction (PCR) products amplified from pig DNA were directly sequenced and their orthologous status was confirmed by a BLAST search. These 46 genes, plus 11 microsatellite markers for SSC8, were typed against DNA from a pig-mouse radiation hybrid (RH) panel with 110 lines. RHMAP analysis assigned these 57 markers to 3 linkage groups in the porcine genome, 52 to SSC8, 4 to SSC15, and 1 to SSC17. By comparing the order and orientation of orthologous landmark genes on the porcine RH maps with those on the human sequence map, HSA4 was recognized as being split into nine conserved segments with respect to the porcine genome, seven with SSC8, one with SSC15, and one with SSC17. With 41 orthologous gene loci mapped, this report provides the largest functional gene map of SSC8, with 30 of these loci representing new single-gene assignments to SSC8.

Animals↗

PubMedDate not supplied

Left adrenal vein localization by 3D real-time volume-rendering CTA before laparoscopic nephrectomy in living renal donors.

BACKGROUND: We investigated whether the left adrenal vein could be consistently localized on three-dimensional (3D) real-time volume-rendering computed tomographic angiographic (CTA) mapping in a group of living renal donors before laparoscopic nephrectomy. METHODS: Sixty-six consecutive potential renal donors were referred for CTA vascular mapping before laparoscopic donor nephrectomy. Thirty-three patients were examined on a single-detector helical CT scanner and the other 33 were examined on a multidetector unit. In each patient, arterial phase and venous phase volumetric data sets were acquired after the intravenous injection of 150 cc of non-ionic contrast material. Three radiologists reviewed the data sets at a free-standing workstation after the application of 3D volume-rendering software and reached a consensus on whether the left adrenal vein was visualized and, when seen, its position relative to the abdominal aorta. RESULTS: The left adrenal vein was found in 92.5% of the 66 donors (91% in the single-detector group and 94% in the multidetector group). The junction of the left adrenal vein and left renal vein averaged 5.2 mm (range = 0-13 mm) from the left lateral wall of the abdominal aorta. CONCLUSION: Three-dimensional real-time volume-rendering CTA with single-detector and multidetector scanners permits consistent localization of the left adrenal vein in more than 90 % of prospective living renal donors.

Adrenal Glands↗

PubMed1990

A genetic map of human chromosome 17p.

A genetic linkage map was constructed with 18 loci from the short arm and pericentric region of chromosome 17 typed on the CEPH reference families. The genetic map includes three markers extracted from the CEPH public database. Nine loci could be ordered using a threshold of odds of at least 1000:1 against alternative orders during the map construction process. With a reduced tolerance of 100:1, a total of 13 loci could be placed on the map spanning a distance of approximately 60 cM in females and 46 cM in males. There were statistically significant differences between the male and the female genetic maps. The order inferred from the genetic data was consistent with the physical localizations of these probes obtained from somatic cell hybrids and tumor deletion studies. This map should be useful for genetic fine mapping of 17p loci.

Alleles↗

PubMed1990

Toward a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellite sites.

The genomes of all eukaryotes appear to contain a special class of loci, termed microsatellites, which can serve, if sequenced and taken as the substrate for the polymerase chain reaction, as highly informative, locus-specific markers. By analogy to the "sequence tagged sites" recently proposed by Olsen et al. for standardizing the human physical gene map, these microsatellite markers are termed "sequence tagged microsatellite sites" (STMS). Genetic maps based on STMS will share with the Olsen physical maps the advantage that mapping vocabularies will be standardized to the DNA sequence base and that access to any particular locus will not require shipping or storing cloned probes. The species map will consist simply of a listing of nucleotide sequences. Reference populations for developing STMS maps can be chosen on the basis of biological or economic interest. It will not be necessary to maximize for genetic divergence.

Animals↗

PubMed2006

Mapped Ds/T-DNA launch pads for functional genomics in barley.

A system for targeted gene tagging and local saturation mutagenesis based on maize transposable elements (Ac/Ds) was developed in barley (Hordeum vulgare L.). We generated large numbers of transgenic barley lines carrying a single copy of the non-autonomous maize Ds element at defined positions in the genome. Independent Ds lines were either generated by activating Ds elements in existing single-copy lines after crossing with AcTPase-expressing plants or by Agrobacterium-mediated transformation. Genomic DNA flanking Ds and T-DNA insertion sites from over 200 independent lines was isolated and sequenced, and was used for a sequence based mapping strategy in a barley reference population. More than 100 independent Ds insertion sites were mapped and can be used as launch pads for future targeted tagging of genes in the vicinity of the insertion sites. Sequence analysis of Ds and T-DNA flanking regions revealed a sevenfold preference of both mutagens for insertion into non-redundant, gene-containing regions of the barley genome. However, whilst transposed Ds elements preferentially inserted adjacent to regions with a high number of predicted and experimentally validated matrix attachment regions (nuclear MARs), this was not the case for T-DNA integration sites. These findings and an observed high transposition frequency from mapped launch pads demonstrate the future potential of gene tagging for functional genomics and gene discovery in barley.

Base Composition↗

PubMed1994

Microsatellite markers for genetic mapping in the chicken.

Microsatellite markers have been found to be abundant, evenly distributed, and highly polymorphic in a number of eukaryotic genomes. The objective of this study was to determine the utility of (TG)n microsatellites in the chicken. A chicken library enriched for (TG)n repeats was generated and 42 unique clones containing (TG)n microsatellites were identified and sequenced. The number of uninterrupted TG repeats ranged from 4 to 14 with an average of 7.8, which was considerably less than the number of repeats found in mammalian species. When primers designed to amplify across the (TG)n microsatellites were used in polymerase chain reactions (PCR) containing genomic chicken DNA, 19 of the 33 primer sets examined yielded polymorphisms in at least one of the three sets of chicken families: 15, 11, and 11 primer sets detected polymorphisms in the East Lansing (EL) reference population, the Compton (C) reference family, and between Line 63 and Line 72 chickens, respectively. The polymorphic microsatellite markers in the EL and C reference families were genetically mapped. Nine and seven mapped markers in the EL and C reference families, respectively, are polymorphic between Line 63 and Line 72, indicating that microsatellite markers will greatly enhance the ability to genotype specific loci of any chicken population.

Animals↗

PubMed1994

Subregional mapping of the human lymphocyte-specific protein tyrosine kinase gene (LCK) to 1p35-->p34.3 and its position relative to the 1p marker D1S57.

The LCK gene encodes a lymphocyte-specific member of the Src family of protein tyrosine kinases. This gene was previously assigned to human chromosome region 1p35-->p32 by isotopic in situ hybridization. We report here its more refined localization to bands 1p35-->p34.3 by fluorescence in situ hybridization on R-banded metaphase chromosomes and its mapping relative to the reference marker pYNZ2 (D1S57).

Base Sequence↗

PubMed2003

Mapping from a clinical data warehouse to the HL7 Reference Information Model.

Large-scale data integration efforts to support clinical and biologic research are greatly facilitated by the adoption of standards for the representation and exchange of data. As part of a larger project to design the necessary architecture for multi-institutional sharing of disparate biomedical data, we explored the potential of the HL7 Reference Information Model (RIM) for representing the data stored in a local academic clinical data warehouse. A necessary first step in information exchange with such a warehouse is the development and utilization of tools for transforming between local data schemas and standards-based conceptual data models. We describe our initial efforts at mapping clinical concepts from a relational data warehouse to the HL7 RIM.

Computer Communication Networks↗

PubMed1996

Polymerase chain reaction-based polymorphisms in the porcine cholecystokinin (CCK) gene and assignment to chromosome 13.

Polymorphisms were identified in the porcine cholecystokinin (CCK) gene by digestion of products from polymerase chain reaction (PCR) with the restriction enzyme DpnII. Individuals from the European pig gene mapping project (PiGMaP) consortium reference families (eight full-sib families, 91 total progeny) were genotype to determine linkage relationships between the CCK gene and previously mapped loci. Linkage analysis revealed that the CCK gene is located on porcine chromosome 13.

Animals↗