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Gene polymorphism identified by PvuII in familial lipoprotein lipase deficiency.

We previously demonstrated that the PvuII polymorphism is a useful marker to analyze the genetic defects in familial lipoprotein lipase (LPL) deficiency. In this study, we have mapped this polymorphic site and cloned the gene fragments containing this site from a patient and a normal subject. Comparative sequence analysis revealed that a C-T transition occurred in the gene of the patient at the PvuII site in the intron 6. Interestingly, the sequence near the PvuII site showed a significant homology to the consensus sequence of the 3' splice site. In addition, the insertional event into the human LPL gene, which was recently reported for a population of Caucasian patients, was not observed for eight unrelated Japanese patients, suggesting that genetic defects underlying familial LPL deficiency should be heterogeneous among races.

Base Sequence↗

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

Database Management Systems↗

Cognitive dysfunction in cortical cerebellar atrophy correlates with impairment of the inhibitory system.

The aim of the present study was to evaluate the profile of cognitive impairment in patients with cortical cerebellar atrophy (CCA) by measurement of event-related potentials (ERP) and neuropsychological tests. We studied 13 CCA patients and 13 age-, sex- and education-matched normal controls. For ERP recording, we used the conventional auditory oddball task as well as the continuous performance task, which evaluates the attentional performance and ability to control a motor response, i.e., to execute ("Go") or inhibit a motor reaction ("No Go"). Brain electric activity was recorded using 20 scalp electrodes and computed into series of potential distribution maps. For components of ERP, reference-independent measures [global field power (GFP)] were determined, and low-resolution brain electromagnetic tomography (LORETA) was used to compute the three-dimensional intracerebral distribution of electric activity of the P3 component of Go and No Go responses. A comprehensive neuropsychological test battery was also assessed. GFP peak latency was prolonged and GFP peak was attenuated under the No Go condition in patients with CCA, although there were no differences in the auditory oddball task and in the Go condition between the two groups. LORETA showed low activation of frontal source in CCA patients in No Go P3 compared with the controls. However, neuropsychological tests revealed no differences between the two groups. Our results indicate that degeneration of the cerebellum contributes to frontal dysfunction, and suggest this dysfunction is characterized by an impairment of the inhibitory system.

Aged↗

Multishot partial-k-space EPI for high-resolution fMRI demonstrated in a rat whisker barrel stimulation model at 3T.

A multishot partial-k-space EPI technique is presented and validated by fMRI at high spatial resolution. High-resolution phase maps corrected by phase-encoded reference scans have less off-resonance effects. Phantom studies demonstrate that this method can substantially improve partial-k-space EPI image formation. BOLD fMRI at submillimeter spatial resolution (156 x 156 x 2000 microm(3), 0.049 microl) was achieved in a rat whisker barrel stimulation model using this technique. The study included eight rats, five of which were administered an intravascular contrast agent (monocrystalline iron oxide nanocolloid (MION)) after the BOLD experiments. In two rats the highest BOLD responses were in the deep layers (IV-VI), and in six rats the highest responses were on the surface and in the deep cortical layers. Most of the pixels that exhibited high BOLD responses had high blood volume weightings. The benefits of this technique are expected to increase for high-resolution fMRI at higher magnetic fields, where T(2) (*) is shorter.

Animals↗

Reference and target region modeling of [11C]-(R)-PK11195 brain studies.

UNLABELLED: PET with [(11)C]-(R)-PK11195 is currently the modality of choice for the in vivo imaging of microglial activation in the human brain. In this work we devised a supervised clustering procedure and a new quantification methodology capable of producing binding potential (BP) estimates quantitatively comparable with those derived from plasma input with robust quantitative implementation at the pixel level. METHODS: The new methodology uses predefined kinetic classes to extract a gray matter reference tissue without specific tracer binding and devoid of spurious signals (in particular, blood pool and muscle). Kinetic classes were derived from an historical database of 12 healthy control subjects and from 3 patients with Huntington's disease. BP estimates were obtained using rank-shaping exponential spectral analysis (RS-ESA) (both plasma and reference input) and the simplified reference tissue model (SRTM). Comparison between plasma- derived BPs and those produced with the new reference methodology was performed using 6 additional healthy control subjects. Reliability of the new methodology was performed on 4 test-retest studies of patients with Alzheimer's disease. RESULTS: The new algorithm selected reference voxels in gray matter tissue avoiding regions with specific binding located, in particular, in the venous and arterial circulation. Using the new reference, BP values obtained using a plasma input and a reference input were in excellent agreement and highly correlated (r = 0.811, P < 10(-5)) when calculated with RS-ESA and less so (r = 0.507, P < 0.005) when SRTM was used. In the production of parametric maps, SRTM was used with the new reference extraction, resulting in test-retest variability (10.6%; mean ICC = 0.878) that was superior to that obtained using the previous unsupervised clustering approach (mean ICC = 0.596). CONCLUSION: Reference region modeling combined with supervised reference tissue extraction produces a robust and reproducible quantitative assessment of [(11)C]-(R)-PK11195 studies in the human brain.

Algorithms↗

Epitope mapping of human thyroid peroxidase defined seven epitopes recognized by sera from patients with thyroid pathologies.

Human thyroid peroxidase (hTPO) is the major component of the microsomal antigen. In almost cases, antibodies against this protein are found in sera from patients with autoimmune thyroid diseases. Overlapping cDNAs which correspond to the complete hTPO mRNA obtained from a thyroid library or by polymerase chain reaction were cloned and expressed as fusion proteins in a prokaryotic vector. Seven antigenic determinants between 21 and 49 amino acids were defined by cloning, subcloning of the immunoreactive regions and screenings with the two rabbit polyclonal anti hTPO antibodies. This study confirms the antigenic nature of the sequences 70-160 and 590-675 but above all refines the localization of three shorter distinct antigenic peptides corresponding to the sequences 68-105, 106-126 and 574-621. Moreover, four other determinants were characterized on the sequences 233-277, 467-515, 641-685 and 701-730. Analysis of sera from patients with autoimmune thyroid diseases (AITD) against the seven immunoreactive peptides confirms the heterogeneous nature of autoantibodies to hTPO.

Autoantibodies↗

Presence of cell lineage-specific hypomethylated sites in the major breakpoint cluster region.

To examine the role of DNA methylation in breakpoint location of chromosomal translocation, HpaII sites in and flanking the M-bcr on chromosome 22 were mapped in DNA from blood granulocytes and lymphocytes, bone marrow cells, thymic tissue, and spermatozoa from normal individuals. Allelic HpaII sites were identified clustered in a 600-base pair genomic area of the M-bcr. Bone marrow cells and blood granulocyte DNA showed identical allelic patterns. Thymic tissue and blood lymphocytes showed identical allelic patterns distinct from bone marrow cells and blood granulocytes. Spermatozoa showed a third methylation pattern. In all individuals, the HpaII sites were present within the BamHI/BglII fragment of the M-bcr, the same area associated with high breakpoint frequency in chronic myelogenous leukemia (CML). Three of 15 patients with chronic phase CML showed fully methylated rearranged BglII/BglII M-bcr restriction fragments not seen in normal bone marrow cells. These methylation patterns of the M-bcr may be important in CML breakpoint location and may be a marker for tissue differentiation.

Blotting, Southern↗

Analysis of a recycling-impaired mutant of low density lipoprotein receptor in familial hypercholesterolemia.

A mutant low density lipoprotein (LDL) receptor with abnormal ligand binding and recycling abilities was found in a patient with familial hypercholesterolemia. The molecular weights of the precursor and the mature form of the receptor were 72,000 and 115,000, respectively, which were about 45,000 smaller than those of the normal receptor. The mutant receptor was concluded to be present on the cell surface because the mature form was susceptible to Pronase digestion, and specific monoclonal antibody against the LDL receptor (IgG-C7) could bind to the cell surface. This mutant receptor could not bind LDL, but could bind other ligands for the LDL receptor, beta-migrating very low density lipoprotein, and the apolipoprotein E-lipid complex. After the receptor bound to the ligand, it disappeared from the cell surface of the mutant cells faster than that of normal cells, showing that, in the mutant cells, the receptor was not efficiently recycled back to the cell surface. Southern blotting of the genomic DNA from the patient showed a large deletion of about 12 kilobases around the epidermal growth factor precursor homology domain. For further characterization of the mutant, we cloned a 9.4-kilobase EcoRI/XbaI fragment, which was expected to contain the deletion joint. Mapping and sequencing analyses of the receptor gene showed that exons 7-14 were deleted. The nucleotide sequence suggested that this mutation may have occurred by recombination between repetitive Alu sequences in introns 6 and 14 of the receptor gene. The recombination brought about a complete deletion of the gene coding the epidermal growth factor precursor homology domain. The characteristics of the receptor protein produced by this mutation were similar to those of an artificial mutation constructed by Davis et al. (Davis, C. G., Goldstein, J. L., Südhof, T. C., Anderson, R. G. W., Russell, D. W., and Brown, M. S. (1987) Nature 326, 760-765) in which the whole gene coding this domain was deleted. The clinical phenotype of the patient having this mutation was similar to that of so-called "receptor-defective" type familial hypercholesterolemia, in which cells show detectable, but markedly reduced activity of the LDL receptor.

Base Sequence↗

Identification of a single nucleotide C-to-T transition and five different deletions in patients with severe hemophilia B.

DNA of 70 unrelated hemophilia B patients, including three inhibitor patients, was analyzed by using various restriction enzymes and was hybridized with both a factor IX cDNA and 3'- and 5'-flanking probes. When the gene was mapped this way, six patients all afflicted with severe hemophilia B were shown to have a deviating hybridization pattern. One inhibitor patient showed a partial deletion of about 9 kb that removes exons a-c. A partial deletion of at least 11 kb that removed exon a and that had a maximum size of 35 kb in the 5'-flanking region could be identified in a patient of unknown status. In another three noninhibitor patients a complete deletion of the factor IX gene and two partial deletions could be observed. The partial deletions are of approximately 8 kb and approximately 1.5 kb, removing exons d and e and exon g, respectively. As detected by oligonucleotide probing, a C-to-T transition at amino acid 338 gave rise to an altered TaqI restriction pattern that could be observed in a sixth patient. The other 64 hemophilia B patients, including two inhibitor patients, showed a hybridization pattern indistinguishable from a normal one.

Chromosome Deletion↗

Statistical aspects of genetic mapping in autopolyploids.

Many plant species of agriculture importance are polyploid, having more than two copies of each chromosome per cell. In this paper, we describe statistical methods for genetic map construction in autopolyploid species with particular reference to the use of molecular markers. The first step is to determine the dosage of each DNA fragment (electrophoretic band) from its segregation ratio. Fragments present in a single dose can be used to construct framework maps for individual chromosomes. Fragments present in multiple doses can often be used to link the single chromosome maps into homologous groups and provide additional ordering information. Marker phenotype probabilities were calculated for pairs of markers arranged in different configurations among the homologous chromosomes. These probabilities were used to compute a maximum likelihood estimator of the recombination fraction between pairs of markers. A likelihood ratio test for linkage of multidose markers was derived. The information provided by each configuration and power and sample size considerations are also discussed. A set of 294 RFLP markers scored on 90 plants of the species Saccharum spontaneum L. was used to illustrate the construction of an autopolyploid map. Previous studies conducted on the same data revealed that this species of sugar cane is an autooctaploid with 64 chromosomes arranged into eight homologous groups. The methodology described permitted consolidation of 54 linkage groups into ten homologous groups.

Chromosomes↗

Ambulatory pulse pressure is a relatively sleep-independent variable.

OBJECTIVES: Characterization of sleep-induced pulse and mean arterial pressure (MAP) dip. DESIGN: Prospective study of consecutive referred patients. SETTING: Hypertension unit of community university hospital. PARTICIPANTS: A total of 500 consecutive subjects referred to our unit for ambulatory blood pressure (BP) monitoring. There were 200 men and 300 women, the majority of which were treated hypertensives. Mean age was 59.7 +/- 16.6 years. MAIN OUTCOME MEASURES: Effect of sleep on MAP and pulse pressure (PP). RESULTS: Twenty-four hour MAP was 98 +/- 10 mmHg. Awake and asleep MAPs were 101 +/- 11 and 87 +/- 11 mmHg, respectively. Twenty-four hour, awake and asleep pulse pressures were 60 +/- 13, 61 +/- 13 and 58 +/- 13 mmHg, respectively. MAP dip was 14%, 95% confidence interval (CI) 13.4-14.6, whereas PP dip was 5%, 95% CI 4.1-5.8. Thus, the MAP dip was almost three times the PP dip (P < 0.0001). This held true for normotensives, hypertensives (treated and untreated), men, women and diabetic subjects. CONCLUSIONS: Although pulse pressure is derived from BP, it is more stable during a 24-h period, with a lesser effect of sleep compared with MAP. This more rigid nature of the PP could explain its better prognostic value, compared to that of MAP.

Adult↗

Linkage mapping bovine EST-based SNP.

BACKGROUND: Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. RESULTS: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM. Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. CONCLUSION: Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.

Alleles↗

A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes.

Genomic analysis of bacteriophages frequently reveals a mosaic structure made up from modules that come from disparate sources. This fact has led to the general acceptance of the notion that rampant and promiscuous lateral gene transfer (LGT) plays a critical role in phage evolution. However, recent sequencing of a series of the T4-type phages has revealed that these large and complex genomes all share 2 substantial syntenous blocks of genes encoding the replication and virion structural genes. To analyze the pattern of inheritance of this core T4 genome, we compared the complete genome sequences of 16 T4-type phages. We identified a set of 24 genes present in all these T4-type genomes. Somewhat surprisingly, only one of these genes, that encodes for ribonucleotide reductase (NrdA), displayed evidence of LGT with the bacterial host. We test the congruence of the inheritance of the other 23 markers using heat map analyses and comparison of a reference topology with the 23 individual gene phylogenies. The vast majority of these core genes share a common evolutionary history. In contrast, analyses of all the noncore genes present in the same 16 genomes, located in the hyperplastic regions of the genome, show considerable evidence of frequent LGT. The similar evolution of the core replication and virion structural genes in the T4-type phage genomes suggests that, unlike the situation in many other phage groups, such portions of T4-type genome have been inherited as a block, without significant LGT, from a distant common ancestor. The preservation of the synteny of the core T4 genome could result from several factors acting in synergy, such as the constraints imposed by the sophisticated regulation of the transcription. Moreover, numerous and complex protein-protein interactions during virion morphogenesis could also impose a supplementary barrier against LGT. Finally, there may be some real evolutionary advantage to maintaining large regions of conserved sequence. Such segments could be a sort of genetic glue that maintains the genetic cohesion of the T4-type phages via recombination within the most conserved sequences. This could mediate the swapping of nonconserved sequences that they flank.

Bacteriophage T4↗

Immunocytochemical mapping of NPY and VIP neuronal elements in the cat subcortical visual nuclei, with special reference to the pretectum and accessory optic system.

The aim of this study was to describe the distribution patterns of neuropeptide Y (NPY) and vasoactive intestinal polypeptide (VIP)-immunoreactive (ir) neuronal elements in subcortical visual centers of the cat. Numerous NPY-ir neurons were present in the feline nucleus of the optic tract and in the anterior pretectal nucleus. Only a few NPY-ir neurons were found in the posterior, medial and olivary pretectal nuclei and in the accessory optic nuclei. Diffuse and heavily beaded NPY-ir fiber plexuses were observed throughout the superior colliculus, pretectum, and accessory optic system. Extensively arborising NPY-ir fibers were present in the mesencephalon and ventral lateral geniculate nucleus, while the dorsal visual thalamic nuclei contained only a few NPY-ir fibers. VIP-ir cells were present mainly in the accessory optic nuclei, and they were absent in the dorsal visual thalamus. Both NPY- and VIP-ir neurons were multipolar and fusiform in shape in the regions studied. Enucleation did not alter the appearance of NPY- and VIP-containing neuronal elements in the superior colliculus and pretectum while in the thalamus a subset of NPY-ir fiber population disappeared, indicating their retinal origin. Although there is a partial overlap in the topographical localization of the NPY- and VIP-ergic neurons in the pretectum, the colocalization of the two peptides could not be demonstrated. The present observations demonstrate the existence of two different and separate peptidergic (NPY and VIP) neuronal populations in the pretectum.

Animals↗

Proopiomelanocortin gene expression in normal and tumoral human lung.

Proopiomelanocortin (POMC) gene expression is not restricted to the pituitary corticotroph cell, but also takes place in many normal and tumoral nonpituitary tissues. In contrast, the ectopic ACTH syndrome is a rare event. Because it is most often associated with lung tumors, we specifically studied this tissue, analyzing the different forms of POMC RNAs in normal specimens as well as in various types of tumors. The endocrine nature of the tumors was assessed by both histological examination and measurements of secretogranin-I fragments in the tissue extracts. POMC RNA was first detected by Northern blot analysis; its absolute amounts and its various molecular forms were more precisely quantified and discriminated by S1 mapping studies using a single stranded DNA probe located at the 5' end of exon 3. In five bronchial carcinoid tumors associated with the ectopic ACTH syndrome, a highly predominant, if not single, POMC RNA identical to the 1200-nucleotide (nt) pituitary message was present, the high amounts of which were correlated with those of POMC peptides in the same tissues. In five bronchial carcinoid tumors not associated with the ectopic ACTH syndrome, the same message was detected (four of five), with a second, often predominant, short RNA of about 800 nt (five of five), and the overall amounts of POMC RNAs were low. Similar patterns of POMC RNAs were observed in squamous cell tumors, adenocarcinomas, and normal lung, where the short 800-nt RNA tended to be predominant. These results show that POMC gene expression can be demonstrated in normal lung tissue and in all types of lung tumors. The ectopic ACTH syndrome only occurs with tumors capable of generating high amounts of the pituitary-like message, a phenomenon that seems to be restricted to an occasional tumor with features of neuroendocrine differentiation.

Carcinoid Tumor↗

Dual displays.

The study examined whether the simultaneous presentation of different map displays can aid situational awareness in spatial tasks relying on ego-centred and world-centred reference frames. Two commonly used aircraft displays, track-up and north-up maps, were compared with a dual aircraft display consisting of both track-up and north-up maps. Participants took part in two tasks: one relied on an ego-centred reference frame (ERF) and the other on a world-centred reference frame (WRF). The ERF task involved left/right judgements with respect to the aircraft's current heading while in the WRF task participants were asked to identify the compass heading associated with a landmark. A moderate amount of training resulted in a significant improvement with the dual maps in both the WRF task (relative to track-up maps) and the ERF task (relative to north-up maps). The findings are discussed with reference to how attention is allocated to visual displays.

Adolescent↗

A genetic analysis of the Werner syndrome region on human chromosome 8p.

Werner syndrome (WRN) is an inherited disorder that produces symptoms of premature aging. This disease is caused by a recessive mutation that has previously been mapped to chromosome 8p. We have now used genetic linkage analysis to map the WRN gene relative to chromosome 8 reference loci, to screen candidate genes, and to identify a novel dinucleotide repeat polymorphic marker closely linked to WRN. The WRN locus was mapped relative to the marker loci, PLAT, ANK1, D8S135, and D8S87 of the comprehensive chromosome 8 linkage map. The heregulin (HRG) and the fibroblast growth factor receptor 1 genes (FGFR1) have been mapped to chromosome 8p and are involved in cellular growth. Recombination events were detected between WRN and the HRG and FGFR1 genes, excluding them as candidates for the WRN gene. A polymorphic marker generated in this study, WT251, is linked to WRN at a recombination fraction of 0.006, with a lod score of 16.5.

Base Sequence↗

Comparison of ephedrine and etilefrine for the treatment of arterial hypotension during spinal anaesthesia in elderly patients.

Thirty ASA II-III patients (greater than 65 years) undergoing hip surgery under bupivacaine spinal anaesthesia, and presenting a 25% reduction in mean arterial pressure (MAP), were included in the study. The patients were randomly allocated to receive, under double-blind conditions, either ephedrine 0.07 mg kg-1 or etilefrine 0.03 mg kg-1 boluses i.v. when MAP decreased by 25% from the preanaesthetic reference value. There were no significant differences (mean +/- s.d.) in the time interval between the sympathomimetics administered (ephedrine 20.2 +/- 17.1 min, etilefrine 16.6 +/- 7.0 min) or the number of sympathomimetics needed (ephedrine 3.8 +/- 1.9, etilefrine 3.6 +/- 2.2). In regard to MAP and diastolic arterial pressure (DAP), ephedrine was slightly more potent in restoring arterial blood pressure compared with etilefrine. The increases in systolic arterial pressure (SAP) and heart rate were similar in both groups. The administration of repeated doses of either sympathomimetic showed the same tendency to increase SAP, DAP, and MAP values as the first dose.

Aged↗