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 919 records · Page 51Linked to original sources

PubMed1991

Fragile X genotype characterized by an unstable region of DNA.

DNA sequences have been located at the fragile X site by in situ hybridization and by the mapping of breakpoints in two somatic cell hybrids that were constructed to break at the fragile site. These hybrids were found to have breakpoints in a common 5-kilobase Eco RI restriction fragment. When this fragment was used as a probe on the chromosomal DNA of normal and fragile X genotype individuals, alterations in the mobility of the sequences detected by the probe were found only in fragile X genotype DNA. These sequences were of an increased size in all fragile X individuals and varied within families, indicating that the region was unstable. This probe provides a means with which to analyze fragile X pedigrees and is a diagnostic reagent for the fragile X genotype.

Chromosome Mapping↗

PubMed1981

Importance of new catecholamine pathways in control of blood pressure.

The first comprehensive maps of central catecholamine pathways referred to both noradrenaline and dopamine neurons. They described the catecholamine neurons as having their cell bodies in the brainstem with spinal axons descending mainly from two medullary cell groups (A1 and A2) and with ascending axons arising mainly from more rostral groups (A3-A13). More recent work utilising immunohistochemistry has established the presence of adrenaline neurons in the brain, in two medullary cell groups (C1 and C2). While these were originally thought to lie within the rostral part of the A1 and A2 cell groups, work from this laboratory has now established that the adrenaline neurons are topographically distinct from the A1 and A2 cells, do not fluoresce with standard methods, and are collected into three groups, the third group (C3) lying in the midline of the rostral medulla. Work in this laboratory using a combination of histochemical fluorescence and retrograde transport of horseradish peroxidase has demonstrated that existence of a descending dopaminergic projection from the hypothalamus to the spinal cord, indicating that descending pathways can arise well above the medulla. Recent studies on the A1 neurons have established the presence of projections from the A1 cells to the median eminence of the hypothalamus and towards the nucleus tractus solitarius in the medulla. Other experiments have demonstrated that most of the descending catecholamine axons do not arise from the A1 and A2 cell groups in the caudal medulla, but higher up in the brainstem especially from the A5 and A7 cell groups. These new descriptions of central catecholamine neurons will necessarily modify the interpretation of many experiments on the central regulation of arterial pressure.

Animals↗

PubMed1990

A primary map of 24 loci on human chromosome 16.

A primary genetic map of chromosome 16 has been constructed by linkage analysis of 24 polymorphic loci, typed in 59 reference families. These loci form a continuous map that covers the whole chromosome and spans genetic distances of 187 cM in males and 226 cM in females. Most of the sex-specific recombination rate difference comes from a nontelomeric region that covers 10 cM in males and 74 cM in females. Both telomeric regions show the opposite trend, with a significant increase in the male recombination rate.

Chromosome Fragility↗

PubMed2004

[QTL mapping for ear shape based on a commercial pig population].

A commercial pig population, including 19 hybrid boars [Piétrain x (Piétrain x Hampshire), 52 hybrid sows [Leicoma x (Large White x Landrace)] and their 332 offspring, was used to construct a reference pedigree, with which a linkage map of whole genome was created using 172 microsatellite markers and three type-1 markers (RYR1, PRKAG3, PIT1). The average of the notes of ear shape (pricky ear shape noted by 1; middle ear shape noted by 0; floppy ear noted by -1) detected by a trained technician is 0.23 and the variation 0.82. QTL mapping for ear shape was carried out with the least square regression method. The result showed that only one QTL for ear shape was detected at 1% genomewise level at the end (between Sw1881 and Sw322) of the chromosome 6 and no QTL was found on the other chromosomes even at 10% chromosome-wise level.

Animals↗

PubMed2004

The serum proteome of Equus caballus.

We constructed a reference two-dimensional protein map for horse (Equus caballus) serum. The serum proteins were separated by two-dimensional electrophoresis (2-DE); 29 different gene products were identified. Proteins represented by 25 spots/spot groups were identified by tandem nanoelectrospray mass spectrometry (MS), four by matrix-assisted laser desorption ionization time-of-flight (TOF) MS and one was sequenced by TOF-TOF technology. The identities of four proteins were deduced by similarity to the human plasma protein database. In selected cases, i.e. the immunoglobulins, immunoblotting with specific antibodies provided additional information about the respective proteins. Albumin was detected as the full-length protein and as fragments of various sizes. Spots representing products of different mass and charge were also detected for alpha1-antitrypsin, haptoglobin and transthyretin. Thus, despite the fact that the Equus caballus genome is incompletely characterized, we were able to identify almost all moderate to high abundance proteins stained in the serum 2-DE pattern.

Albumins↗

PubMed2006

Protein kinase resource: an integrated environment for phosphorylation research.

The protein kinase superfamily is an important group of enzymes controlling cellular signaling cascades. The increasing amount of available experimental data provides a foundation for deeper understanding of details of signaling systems and the underlying cellular processes. Here, we describe the Protein Kinase Resource, an integrated online service that provides access to information relevant to cell signaling and enables kinase researchers to visualize and analyze the data directly in an online environment. The data set is synchronized with Uniprot and Protein Data Bank (PDB) databases and is regularly updated and verified. Additional annotation includes interactive display of domain composition, cross-references between orthologs and functional mapping to OMIM records. The Protein Kinase Resource provides an integrated view of the protein kinase superfamily by linking data with their visual representation. Thus, human kinases can be mapped onto the human kinome tree via an interactive display. Sequence and structure data can be easily displayed using applications developed for the PKR and integrated with the website and the underlying database. Advanced search mechanisms, such as multiparameter lookup, sequence pattern, and blast search, enable fast access to the desired information, while statistics tools provide the ability to analyze the relationships among the kinases under study. The integration of data presentation and visualization implemented in the Protein Kinase Resource can be adapted by other online providers of scientific data and should become an effective way to access available experimental information.

Amino Acid Sequence↗

PubMed2004

MDMA-evoked changes in [11C]raclopride and [11C]NMSP binding in living pig brain.

Positron emission tomography (PET) studies with radiolabeled dopamine D2-like receptor ligands reveal d-amphetamine-evoked increases in the competition from endogenous dopamine. However, the corresponding effects of methylenedioxymethamphetamine (MDMA, "Ecstasy"), which releases catecholamines and also serotonin, are unknown. Using PET, we measured the binding potentials (pBs) of the benzamide [11C]raclopride and the butyrophenone N-[11C]methylspiperone ([11C]NMSP) in brain of living pigs first in a baseline condition and at 45 and 165 min after infusion of (+/-)-MDMA-HCl (1 mg/kg, i.v.). Concomitant studies of cerebral blood flow did not reveal significant perfusion changes in the cerebellum reference region or in striatum, supporting the present use of reference tissue methods for the mapping of MDMA-evoked pB changes. Relative to the baseline pB of [11C]raclopride for dopamine D(2/3) receptors in striatum (pB = 1.5-2.2), MDMA-treatment reduced pB by 35% in the first posttreatment scan and by 22% in the second posttreatment scan, comparable to changes typically evoked by d-amphetamine at a similar dose. In most previous studies, the in vivo binding of butyrophenones has been nearly insensitive to d-amphetamine-evoked dopamine release. However, we found the baseline pB of [11C]NMSP for dopamine D2-like receptors in striatum (pB = 4-5) was decreased by 30% in the first post-MDMA scan and by 50% in the second post-MDMA scan, irrespective of assumptions about the extent of equilibrium binding attained during the 90-min-long PET recordings. Distinct properties of MDMA such as simultaneous release of dopamine and serotonin in brain may account for the present finding of progressive decline in the availability of [11C]NMSP binding sites in striatum.

Animals↗

PubMed1976

Isolation and characterization of lambdadargECBH transducing phages and heteroduplex analysis of the argECBH cluster.

Transducing lambda bacteriophages have been isolated which carry the divergently transcribed argECBH operon of E. coli K12 and various portions of the adjacent ppc and bfe chromosomal regions. They were recovered from lysates prepared by the procedure of Schrenk and Weisberg using a Ppc+ Arg+ Bfe+ strain carrying a deletion of the usual attachment site of lambda. Heteroduplex DNA mapping of these lumbdadarg and of the phi 80 darg isolated by B. Konrad indicates that the two kinds of phages carry the arg cluster in opposite orientations, a situation favorable for the isolation of argECBH DNA. A physical map of the ppc argECBH bfe region including 2 unusual attachment sites of lambda has been constructed. The localization of the end points of certain arg deletions provides a useful reference framework for the currently pursued mapping of mutations affecting the control of divergent transcription and for the location of restriction enzyme cleavage sites in the arg region.

Arginine↗

PubMed1975

Cryptic mutations: their predicted biochemical basis, frequencies and effects on gene conversion.

Cryptic mutations are undetected base changes in genetic DNA (or hereditary RNA). Some kinds of base change are normally undetected; others may or may not be detected, depending on experimental conditions, procedures and genotypes. Cryptic mutations could affect gene conversion results because when heterozygous they cause mismatched base pairs in hybrid DNA in the same way as known mutations, but the experimenter is unaware of them. Cryptic heterozygosity will usually be much more frequent in heterothallic than homothallic organisms. The effects of cryptic mutation heterozygosity on recombination and conversion of known mutations are predicted with reference to co-conversion, map expansion and polarity. Relevant evidence is considered.

Base Sequence↗

PubMed1996

Evaluation of the non-invasive localization accuracy of cardiac arrhythmias attainable by multichannel magnetocardiography (MCG).

The accuracy of multichannel magnetocardiography (MCG) for the non-invasive localization of cardiac arrhythmias was investigated. A non-magnetic catheter was used in phantom studies and for cardiac pacing of 6 patients. In a clinical setting, 32 patients with WPW-syndrome, 37 patients with premature ventricular complexes and 12 patients with ventricular tachycardia were studied and the MCG results compared to reference methods, including invasive electrophysiological mapping. Phantom and pacing studies demonstrated the spatial localization accuracy to be better than 15 mm for a dipole-to-dewar distance below 15 cm. In all patients with structural cardiac disease, the ectopic focus was localized at the margin of the damaged area, serving as a proof of MCG localization. Invasive mapping confirmed the MCG result whenever performed (42 patients). In 11 patients (9 WPW, 2 VT) the MCG localization result was verified by successful HF catheter ablation as a gold standard. MCG permits the non-invasive localization of cardiac arrhythmias with high spatial accuracy. MCG guided HF catheter ablation constitutes a new concept of non-invasive localization and minimally invasive causal therapy.

Cardiac Pacing, Artificial↗

PubMedDate not supplied

Tumor cytogenetics revisited: comparative genomic hybridization and spectral karyotyping.

Fluorescence in situ hybridization techniques allow the visualization and localization of DNA target sequences on the chromosomal and cellular level and have evolved as exceedingly valuable tools in basic chromosome research and cytogenetic diagnostics. Recent advances in molecular cytogenetic approaches, namely comparative genomic hybridization and spectral karyotyping, now allow tumor genomes to be surveyed for chromosomal aberrations in a single experiment and permit identification of tumor-specific chromosomal aberrations with unprecedented accuracy. Comparative genomic hybridization utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes. Comparative genomic hybridization is an ideal tool for analyzing chromosomal imbalances in archived tumor material and for examining possible correlations between these findings and tumor phenotypes. Spectral karyotyping is based on the simultaneous hybridization of differentially labeled chromosome painting probes (24 in human), followed by spectral imaging that allows the unique display of all human (and other species) chromosomes in different colors. Spectral karyotyping greatly facilitates the characterization of numerical and structural chromosomal aberrations, therefore improving karyotype analysis considerably. We review these new molecular cytogenetic concepts, describe applications of comparative genomic hybridization and spectral karyotyping for the visualization of chromosomal aberrations as they relate to human malignancies and animal models thereof, and provide evidence that fluorescence in situ hybridization has developed as a robust and reliable technique which justifies its translation to cytogenetic diagnostics.

Animals↗

PubMed1993

Magnetic resonance measurement of velocity and flow: technique, validation, and cardiovascular applications.

With a newly developed magnetic resonance (MR) technique for blood flow measurements, qualitative and quantitative information on both flow volume and flow velocity in the great vessels can be obtained. MR flow quantitation is performed with a gradient-echo MR sequence with high temporal resolution enabling measurements at frequent intervals throughout the cardiac cycle. MR flow quantitation uses the phase rather than the amplitude of the MR signal to reconstruct the images. These images, often referred to as MR velocity maps or velocity-encoded cine MR images, are two-dimensional displays of flow velocity. From these velocity maps, velocity and volume flow data can be obtained. Previous validation experiments have demonstrated the accuracy of MR velocity mapping, and this technique is now being applied successfully in several clinical fields. MR velocity mapping may be of considerable value when Doppler echocardiography results are unsatisfactory or equivocal, particularly because MR is suited for the analysis of volumetric flow and complex flow patterns. Among the vastly growing number of clinical cardiovascular applications that have been reported are the great arteries and veins, coronary vessels, valvular disease, and the abdominal and peripheral vessels. These items are reviewed, and some aspects of the technique that need improvement are discussed.

Aorta↗

PubMed2006

A comprehensive proteomic analysis of the accessory sex gland fluid from mature Holstein bulls.

The expression of proteins in accessory sex gland fluid (AGF) of proven, high use mature Holstein bulls was evaluated. Thirty-seven bulls with documented fertility based on their non-return rates were studied. AGF was obtained by artificial vagina after bulls were surgically equipped with cannulae in the vasa deferentia. Samples of AGF were evaluated by two-dimensional SDS-PAGE, gels stained with Coomassie blue and polypeptide maps analyzed by PDQuest software. A master gel generated by the software representing the best pattern of spots in the AGF polypeptide maps was used as a reference for protein identification. Proteins were identified by Western blots and capillary liquid chromatography-nanoelectrospray ionization tandem-mass spectrometry (CapLC-MS/MS). The product ion spectra were processed using Protein Lynx Global Server 2.1 prior to database search with both PLGS and MASCOT (Matrix Science) software. The entire NCBI database was considered for mass fingerprint matching. An average of 52+/-5 spots was detected in the AGF 2D gels, which corresponded to proteins potentially involved in capacitation (bovine seminal plasma protein-BSP-A1/A2 and A3, BSP 30 kDa, albumin); sperm membrane protection, prevention of oxidative stress, complement-mediated sperm destruction and anti-microbial activity (albumin, clusterin, acidic seminal fluid protein--aSFP, 5'-nucleotidase--5'-NT, phospholipase A2--PLA2); acrosome reaction and sperm-oocyte interaction (PLA2, osteopontin); interaction with the extracellular matrix (tissue inhibitor of metalloproteinase 2, clusterin) and sperm motility (aSFP, spermadhesin Z13, 5'-NT). The 20 spots distinguished in all gels were matched to proteins associated with these functions. Proteins identified by tandem mass spectrometry as ecto-ADP-ribosyltransferase 5 and nucleobindin, never described before in the accessory sex gland secretions, were also detected. In summary, we identified a diverse range of components in the accessory sex gland fluid of a select group of Holstein bulls with documented fertility. Known characteristics of these proteins suggest that they play important roles in sperm physiology after ejaculation.

Animals↗

PubMed2026

TNF-NF-κB signaling mediates immune-biomineralization crosstalk during shell repair under ocean acidification in Mytilus edulis.

Ocean acidification (OA) impairs biomineralization in bivalves, but its effects on immune-biomineralization crosstalk during shell repair remain unknown. Here, we exposed adult Mytilus edulis bearing standardized shell perforations to three pH levels (8.1, 7.9, and 7.7) for up to 40 days. OA slowed early repair and caused microstructural disorganization and an approximately 87% reduction of compressive strength at pH 7.7, yet the damaged area appeared largely closed by day 15, suggesting a decoupling between morphological closure and functional recovery. In addition, transcriptomic profiling of hemocytes and mantle tissue, based on an average of 6.5 Gb of clean reads per sample mapped to the M. edulis reference genome (NCBI Assembly GCF_000511035.1), revealed that these shell-level defects were accompanied by coordinated immune and metabolic reprogramming. Hemocytes, the primary immune effector cells of bivalves, exhibited pH- and time-dependent shifts with moderate acidification (pH 7.9) promoting inflammatory transcripts, whereas severe acidification (pH 7.7) suppressed these signals while upregulating stress-associated pathways; both treatments consistently downregulated lysosomal proteases and NF-κB negative regulators. The mantle, a primarily mineralizing organ, paradoxically upregulated immune-related genes while suppressing oxidative phosphorylation and extracellular matrix pathways. This tissue-level imbalance, with hemocytes recruited but functionally constrained and mantle metabolically suppressed yet immunologically activated, points to TNF-NF-κB pathway modulation as a key mediator of shell repair under acidification. Our findings demonstrate that visible shell closure masks underlying structural and mechanical failure, and that immune regulation, rather than simple suppression or activation, critically shapes the repair outcome. These results advocate for multifunctional indicators beyond closure area to assess shell integrity in acidified marine environments.

Animals↗

PubMed2004

Catheter ablation guided by termination of postinfarction ventricular tachycardia by pacing with nonglobal capture.

OBJECTIVES: We prospectively investigated the prevalence and value of this criterion for identifying a target site for ablation in patients with postinfarction ventricular tachycardia (VT). BACKGROUND: Termination of postinfarction VT by pacing with nonglobal capture identifies a critical component of the reentrant circuit. METHODS: In a consecutive series of 34 patients with prior infarction (age 67 +/- 10 years, ejection fraction 0.26 +/- 0.1) referred for radiofrequency catheter ablation, mapping was performed in the left ventricle. At sites with abnormal electrograms, pacing was performed during VT. If VT terminated with nonglobal capture during the pacing train, radiofrequency energy was delivered. RESULTS: Sixty-two VTs (cycle length 450 +/- 84 ms) were mapped and targeted for radiofrequency ablation. Concealed entrainment was present at 101 endocardial sites. Among the 101 sites, VT terminated by pacing with nonglobal capture at 5 sites (5%). At 10 additional sites in 10 patients, VT terminated by pacing with nonglobal capture, and concealed entrainment could not be documented at these sites because of reproducible termination of the VT. An application of radiofrequency energy resulted in VT termination at all 15 sites where nonglobal capture was documented and the targeted VTs were no longer inducible after ablation. CONCLUSIONS: Termination of VT by pacing with nonglobal capture can be demonstrated in approximately one third of patients with postinfarction VT and is a specific criterion for identifying a critical component of the reentrant circuit, whether or not concealed entrainment can be documented at that site.

Aged↗

PubMed2004

Spatial mapping of collagen fibril organisation in primate cornea-an X-ray diffraction investigation.

New insights are presented into the collagenous structure of the primate cornea. Wide-angle X-ray diffraction was used to map the fibrillar arrangement and distribution of collagen over three common marmoset corneas. The maps provide a point of reference to help interpret data from pathological corneas or primate models of refractive surgery. The results herein disclose a circum-corneal annulus of highly aligned collagen, 0.5-1.5 mm wide, where the cornea and sclera fuse at the limbus; a feature similar to that observed in human tissue. As in humans, the annulus is not uniform, varying in width, fibril angular spread, and collagen density around its circumference. However, more centrally the marmoset cornea exhibits a preferred lamella orientation in which proportionally more fibrils are oriented along the superior-inferior corneal meridian. This observation is in striking contrast with the situation in human cornea, where there is an orthogonal arrangement of preferentially aligned fibrils. Investigation of a further 16 corneas confirmed that approximately 33% (+/-1%) (n = 76) of fibrils in the central marmoset cornea lie within a 45 degrees sector of the superior-inferior meridian. Implications for the mechanical and optical properties of the cornea are discussed.

Age Factors↗

PubMed2005

Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex.

We develop a novel Lagrangian reference frame diffeomorphic image and landmark registration method. The algorithm uses the fixed Langrangian reference frame to define the map between coordinate systems, but also generates and stores the inverse map from the Eulerian to the Lagrangian frame. Computing both maps allows facile computation of both Eulerian and Langrangian quantities. We apply this algorithm to estimating a putative evolutionary change of coordinates between a population of chimpanzee and human cortices. Inter-species functional homologues fix the map explicitly, where they are known, while image similarities guide the alignment elsewhere. This map allows detailed study of the volumetric change between chimp and human cortex. Instead of basing the inter-species study on a single species atlas, we diffeomorphically connect the mean shape and intensity templates for each group. The human statistics then map diffeomorphically into the space of the chimpanzee cortex providing a comparison between species. The population statistics show a significant doubling of the relative prefrontal lobe size in humans, as compared to chimpanzees.

Algorithms↗

PubMed2026

Mining of important genetic loci and evaluation of genetic effects for growth traits in Baicheng You Chicken.

The Baicheng You Chicken is a precious indigenous breed in Xinjiang, China, prized for its strong disease and stress resistance and superior meat quality. However, the lack of scientific breeding and conservation has led to poor production performance, particularly in growth traits. In this study, we collected phenotypic and whole-genome resequencing data from 1,535 18-week-old Baicheng You Chickens (180 males and 1,355 females). After stringent quality control (SNP call rate > 95%, minor allele frequency > 1%), we constructed the breed's first comprehensive SNP-based genome-wide variation map, which comprised 2,020,743 high-quality SNPs across the genome. The filtered SNPs had high mapping quality (99.73% mapped to the bGalGal1.mat.broiler.GRCg7b reference genome, Q30 = 93.26%) and a reasonable Ti/Tv ratio (2.596), guaranteeing the reliability of subsequent analyses. We estimated genetic effects (SNP-based heritability and phenotypic variance explained (PVE) by individual loci) via the restricted maximum likelihood (REML) method, and performed a genome-wide association study (GWAS) using a mixed linear model (MLM) - with sex as a fixed effect and principal components to correct for population stratification - to identify significant loci and their effect sizes (Beta). All eight growth traits showed moderate to high heritability: body weight (BW) had the highest heritability (0.86±0.11), while chest width (CW, 0.41±0.08) and body slanting length (BSL, 0.43±0.09) were the lowest; keel length (KL), chest girth (CG), pelvic width (PW), chest depth (CD) and shank length (SL) had heritabilities of 0.50±0.09, 0.46±0.09, 0.54±0.09, 0.67±0.10 and 0.74±0.10, respectively. GWAS identified 145 significant SNPs, with a maximum Beta value of 0.39 and PVE ranging from 1.25% to 6.25%. We annotated 22 candidate genes, with TAPT1, IGF2BP1, ADGRB3, LDB2, NCAPG and LCORL as key candidates. These quantifiable genetic markers and effect estimates provide direct targets for marker-assisted selection (MAS) and valuable resources for future genomic selection (GS) programs, offering a practical approach to improve the breed's slow growth while preserving its unique meat quality.

Baicheng You Chicken↗