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At least 397 records · Page 22Linked to original sources
PubMed1999

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

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

Chromosome Mapping↗
PubMed1992

Similarity between average distance maps of structurally homologous proteins.

A similarity between average distance maps (Kikuchi et al., 1988a)--that is, predicted contact maps of two tertiary structurally homologous proteins--is examined. Comparisons of shapes of average distance maps (we refer to this as ADM) are made by superpositions of ADMs for two homologous proteins. Also, we compare shapes of actual contact maps for the pair of proteins. We search a optimal superposition mode of each pair of maps showing that two proteins are most similar. It is concluded that two ADMs are also similar when actual tertiary structures between two proteins show similarity. A criterion for similarity of maps is also proposed. The possibility of application of this method to detect weak homology between protein structures is discussed.

Protein Conformation↗
PubMed1995

A frequency domain analysis of spatial organization of epicardial maps.

Mapping of organized rhythms like sinus rhythm uses activation times from individual electrograms, and often assumes that the map for a single activation is similar to maps for subsequent activations. However, during fibrillation, activation times and electrograms are not easy to define, and maps change from activation to activation. Volume and complexity of data make analysis of more than a few seconds of fibrillation difficult. Magnitude Squared Coherence (MSC), a frequency domain measure of the phase consistency between two signals, can be used to help interpret longer data segments without defining activation times or electrograms. Sinus rhythm, flutter, and fibrillation in humans and swine were mapped with an array of unipolar electrodes (2.5 mm apart) at 240 sites on the atrial or ventricular epicardium. Four-second data segments were analyzed. One site near the center of the array was chosen ad hoc as a reference. MSC maps were made by measuring mean MSC from 0-50 Hz between every point in the array relative to the reference. Isocoherence contours were drawn. The effects of bias in the coherence estimate due to misalignment were investigated. Average MSC versus distance from the reference was measured for all rhythms. Results indicate that in a 4-s segment of fibrillation, there can exist some phase consistency between one site and the reference and little or none between a second site and the reference even when both sites are equidistant from the reference. In fibrillation, isocoherence contours are elongated and irregularly shaped, reflecting long-term, but nonuniform, spatial organization. That is, activation during fibrillation cannot be considered as random over a 4-s interval. Bias in the coherence estimate due to misalignment is significant for sinus rhythm and flutter, but can be corrected by manual realignment. Average MSC drops with distance for all rhythms, being most pronounced for fibrillation, MSC maps may provide insights into long-term spatial organization of rhythms that would otherwise be cumbersome and difficult to interpret with standard time domain analysis.

Animals↗
PubMed1993

Pharmaco-EEG mapping of diazepam effects using different references and absolute and relative power.

The effects of diazepam on the EEG were studied by means of EEG topographic mapping, using recordings with four different references. Subjects were ten healthy, right-handed, male volunteers aged 21-25 years. Double-blind crossover trials with a single oral dose of 10 mg diazepam and placebo controls were conducted in random sequence at intervals of one week. Four referential derivations--ipsilateral earlobe (A1A2), average reference (AV), source derivation (SD), and balanced noncephalic electrode (BNE)--were used. One-minute vigilance-controlled EEGs before drug administration and two hours after drug administration were analyzed using Fourier transformation; absolute power and relative power were calculated for four frequency bands. Diazepam caused a widespread increase of beta-frequency relative power, and a widespread decrease of theta-frequency absolute power when A1A2 and SD were taken as references. From the comparison of different reference electrodes we conclude that the selection of the reference and of spectral parameters (absolute power or relative power) play an important role in pharmaco-EEG studies.

Adult↗
PubMed2004

Physical and linkage mapping of mammary-derived expressed sequence tags in cattle.

This study describes the physical and linkage mapping of 42 gene-associated markers developed from mammary gland-derived expressed sequence tags to the cattle genome. Of the markers, 25 were placed on the USDA reference linkage map and 37 were positioned on the Roslin 3000-rad radiation hybrid (RH) map, with 20 assignments shared between the maps. Although no novel regions of conserved synteny between the cattle and the human genomes were identified, the coverage was extended for bovine chromosomes 3, 7, 15, and 29 compared with previously published comparative maps between human and bovine genomes. Overall, these data improve the resolution of the human-bovine comparative maps and will assist future efforts to integrate bovine RH and linkage map data.

Animals↗
PubMed1997

Restriction mapping of genes by capillary electrophoresis with laser-induced fluorescence detection.

Restriction mapping is one of the essential steps in gene analysis and molecular biology studies. Slab gel electrophoresis is the traditional way to separate DNA fragments for restriction mapping. However, slab gel electrophoresis does not provide sufficient resolution as required in many mapping applications, and the use of radioisotopes in traditional mapping methods creates health hazards. In the present study, capillary electrophoresis coupled with laser-induced fluorescence detection and a modified partial digestion mapping procedure was developed to map DNA fragments. By using capillary electrophoresis, a restriction map of genomic lambda phage clone of human interleukin 5 receptor alpha chain (IL5R alpha) gene was constructed. The IL5R alpha gene was analyzed to have five XbaI enzyme cutting sites at locations 1370, 2290, 2950, 5430, and 9330. The system was further characterized by using pBluescript SK(+) phagemid DNA as a model. Using a sequence-derived map as a reference, the pBluescript SK(+) restriction map constructed by capillary electrophoresis had an accuracy greater than 90%.

DNA↗
PubMed1997

Mapping of growth hormone releasing hormone receptor to swine chromosome 18.

The growth hormone releasing hormone receptor (GHRHR) was mapped in the pig for study as a potential candidate gene in controlling pig quantitative growth and carcass characteristics. Primers were designed from the pig GHRHR sequence to amplify a 1.65-kb intronic fragment between exons 6 and 7. By using a pig-rodent somatic cell hybrid panel, GHRHR was mapped to pig chromosome 18 (SSC18) with 100% concordance, and the regional assignment was SSC18q24 with 89% concordance. The polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) with MseI and TaqI were developed to confirm this assignment with linkage analysis by using the European Pig Gene Mapping Project (PiGMaP) reference families. Pig GHRHR was mapped with strong linkage to SSC18 markers S0062 and S0120 (lod > 8). The GHRHR and IGFBP3 were found to map near to each other on human chromosome 7 (HSA7), and the pig IGFBP3 gene has been mapped to SSC18 by others. Our mapping of pig GHRHR increases the comparative information available on the SSC18 maps and further confirms the synteny conservation between HSA7 and SSC18.

Animals↗
PubMed1989

[Isolation of recombinant vaccine strains of poliovirus from patients with poliomyelitis].

Oligonucleotide maps of some poliovirus type 2 strains isolated from polio cases, while being clearly related to that of the Sabin vaccine type 2 strain, exhibited, nevertheless, marked differences from the reference (vaccine) map. Several large oligonucleotides derived from 4 such strains were subjected to enzymatic sequencing. The results strongly suggest that all of them were intertypic recombinants between the Sabin strains. The 5'-parts of the genomes of these strains were derived from the type 2 vaccine whereas the 3'-parts were of type 1 (in 2 strains) or type 3 (in other 2 strains) origin.

Base Sequence↗
PubMedDate not supplied

Intensity mapping of pain referral areas in sacroiliac joint pain patients.

OBJECTIVE: To identify differences in pain referral areas, using intensity maps, between responders and nonresponders to a double diagnostic sacroiliac joint injection with a short- and long-acting local anesthetic in patients with chronic low back pain. METHODS: From a group of 140 consecutive patients with chronic low back pain, 60 patients who met clinical criteria were included in the study. Twenty-seven demonstrated a positive response to a double diagnostic fluoroscopically guided intra-articular sacroiliac joint block and were compared with 33 patients with a negative response. Each patient's preinjection pain diagram was used to determine areas of pain referral. The summation of these pain referral zones for both groups was used to construct intensity maps. RESULTS: No major differences were observed between responders and nonresponders with regard to mean size and distribution of referral pain areas. Intensity maps, however, showed differences in pain referral at the buttock in the areas overlying the sacroiliac joint (100% of the responders vs 80% of the nonresponders) and the ischial tuberosity (10% of the responders vs 100% of the nonresponders). CONCLUSIONS: Overall referred pain maps appeared not to be useful to discriminate patients with an identified sacroiliac joint pain from chronic low back pain patients with pain from other sources. Differences were only found using intensity maps. By implementing these data, it could be concluded that patients with sacroiliac joint pain are less likely to experience pain in both the 'Fortin' and 'tuber' areas. This knowledge can be used as additional selection criterion for putative sacroiliac joint patients, next to sacroiliac joint pain provocation tests.

Adult↗
PubMed2005

Differentiation of noncancerous tissue and cancer lesions by apparent diffusion coefficient values in transition and peripheral zones of the prostate.

PURPOSE: To compare the apparent diffusion coefficient (ADC) values of prostate cancer in both the peripheral zone (PZ) and the transition zone (TZ) with those of benign tissue in the same zone using echo-planar diffusion weighted imaging with a parallel imaging technique. MATERIALS AND METHODS: A total of 29 consecutive male patients (mean age 61.3 years, age range 53-88 years) with suspected prostate cancer were referred for MR imaging. All patients underwent transrectal ultrasound (TRUS)-guided biopsy of the prostate after MR imaging at 1.5 T, including ADC. For each patient, seven to 10 specimens were obtained from the prostate, and regions of interest (ROIs) were drawn on the ADC map by referring to the urologist's illustration of TRUS-guided biopsy sites. ADC values of cancerous tissue in both the PZ and TZ were compared to those of noncancerous tissue in the same zone. RESULTS: Out of 29 patients, 23 had cancer tissue. In the 23 patients with cancer, the mean ADC value of all cancer ROIs and that of all noncancer ROIs, respectively, were 1.11 +/- 0.41 x 10(-3) and 1.68 +/- 0.40 x 10(-3) mm(2)/second (values are mean +/- SD) (P < 0.01). The mean ADC value of TZ cancer ROIs and that of TZ noncancer ROIs, respectively, were 1.13 +/- 0.42 x 10(-3) and 1.58 +/- 0.37 x 10(-3) mm(2)/second (P < 0.01). CONCLUSIONS: ADC measurement with a parallel imaging technique showed that ADC values of prostate cancer in both the PZ and TZ were significantly lower than those of benign tissue in the PZ and TZ, respectively.

Adenocarcinoma↗
PubMed2006

A first-generation microsatellite-based integrated genetic and cytogenetic map for the European rabbit (Oryctolagus cuniculus) and localization of angora and albino.

Although the European rabbit (Oryctolagus cuniculus) is used both in agronomics and in research, genomic resources for this species are still limited and no microsatellite-based genetic map has been reported. Our aim was to construct a rabbit genetic map with cytogenetically mapped microsatellites so as to build an integrated genetic and cytogenetic map. A reference population of 187 rabbits comprising eight three-generation families with 10-25 offspring per family was produced. One hundred and ninety-four of 305 previously identified microsatellites were included in this study. Of these, 158 were polymorphic with two to seven alleles. The map reported here comprises 111 markers, including 104 INRA microsatellites, five microsatellites from another source and two phenotypic markers (angora and albino). Ninety markers were integrated into 20 linkage groups. The remaining 21 microsatellites mapped to separate linkage groups, 19 with a precise cytogenetic position and two with only a chromosomal assignment. The genetic map spans 2766.6 cM and covers 20 rabbit chromosomes, excluding chromosomes 20, 21 and X. The density of this map is limited, but we used it to verify the location of angora and albino on chromosomes 15q and 1q, respectively, in agreement with previously published data. This first generation genetic/cytogenetic map will help gene identification and quantitative trait loci mapping projects in rabbit.

Alleles↗
PubMed1990

Topographic segmentation of waking EEG in medication-free schizophrenic patients.

Lehmann has demonstrated that EEG topography can be used to segment EEG map series into a sequence of spatially stationary segments characterized by location of potential maxima and minima. We employed topographic segmentation techniques to study 9 channel EEGs recorded from 11 medication-free schizophrenic patients and 10 normal controls during resting and active task conditions, retesting 8 patients after neuroleptic treatment. To define EEG segments, average reference potential maps corresponding to global field power peaks in theta, alpha, and low beta activity were classified according to locations of extreme minimum and maximum values. Normals and schizophrenics did not differ in the number or types of switches between segments, or the frequency of hemisphere crossing of potential extrema. However, EEGs of normal subjects were characterized by significantly more (P less than 0.003) unused theta segment types (of a theoretically possible 36). Moreover, medication significantly (P less than 0.02) increased the number of unused theta segment types in EEGs of schizophrenics. We interpret these findings as evidence of increased spatial variability of brain electrical activity in schizophrenics and discuss their functional implications.

Adult↗
PubMed1998

Physical mapping of the mouse genome.

This review is intended to provide an overview of techniques and a source of reagents for physical mapping of the mouse genome. It focuses on those applications, methods, or resources unique to the mouse and on the generation of comparative physical maps. The reference list is not comprehensive; rather, recent reviews on each topic and selected representative examples are given.

Animals↗
PubMed1997

Mitogen-activated protein kinase activation during IgG-dependent phagocytosis in human neutrophils: inhibition by ceramide.

In FMLP-activated polymorphonuclear leukocytes (PMNs) challenged with IgG-opsonized erythrocytes (EIgG), the termination of phagocytosis correlates with an accumulation of ceramide, a product of sphingolipid metabolism. Furthermore, the exogenous addition of short chain ceramides inhibits EIgG-mediated phagocytosis. In the present study, we identified p42 and p44 mitogen-actived protein (MAP) kinases, referred to as extracellular signal-regulated kinases ERK2 and ERK1, respectively, as intracellular targets of ceramide action during Fc gammaR-mediated phagocytosis. The tyrosine phosphorylation of ERK1 and ERK2 increased within 30 s of addition of EIgG, with maximal phosphorylation by 1 to 5 min. By 30 min, ERK1 and ERK2 were almost completely dephosphorylated. The kinetics of ERK1 and ERK2 tyrosine phosphorylation indicated that MAP kinase activation preceded target ingestion. N-Acetylsphingosine (C2-ceramide) inhibited phagocytosis, reduced ERK1 and ERK2 phosphorylation to basal levels, and reduced ERK1 and ERK2 activity by 85 to 90% and 70 to 80%, respectively. In contrast, N-acetyldihydrosphingosine (dihydro-C2-ceramide) had no effect on either tyrosine phosphorylation or activity of ERK1 and ERK2. In the presence of the MAP kinase kinase (MEK) inhibitor, PD 098059, phagocytosis was reduced by approximately 50%, while ERK1 and ERK2 activity was reduced by 85 to 90%. Thus, engagement of Fc gammaRs led to ERK1 and ERK2 phosphorylation and activation, and the activation of these enzymes was critical for phagocytosis. Furthermore, the inhibition of phagocytosis by C2-ceramide correlated with the inhibition of tyrosine phosphorylation and activation of ERK1 and ERK2. These results suggest that ceramides generated during phagocytosis act on the MAP kinase signaling pathway, ultimately "turning off" the phagocytic response.

Calcium-Calmodulin-Dependent Protein Kinases↗
PubMed2000

Isolation and mapping of microsatellite markers specific for the D genome of bread wheat.

The potential of Aegilops tauschii, the diploid progenitor of the D genome of wheat, as a source of microsatellite markers for hexaploid bread wheat was investigated. By screening lambda phage and plasmid libraries of Ae. tauschii genomic DNA, dinucleotide microsatellites containing GA and GT motifs were isolated and a total of 65 functional microsatellite markers were developed. All primer pairs that were functional in Ae. tauschii amplified well in hexaploid wheat. Fifty-five loci amplified by 48 primer sets were placed onto a genetic framework map of the reference population of the International Triticeae Mapping Initiative (ITMI) 'Opata 85' x 'W7984'. The majority of microsatellite markers could be assigned to the chromosomes of the D genome of wheat. The distribution of the markers along the chromosomes is random. Chromosomal location of 22 loci nonpolymorphic in the reference population was determined using nullitetrasomic lines of Triticum aestivum 'Chinese Spring'. The results of this study demonstrate the value of microsatellite markers isolated from Ae. tauschii for the study of bread wheat. The microsatellite markers developed improve the existing wheat microsatellite map and can be used in a wide range of genetic studies and breeding programs.

Bacteriophage lambda↗
PubMed2002

[Analysis and mapping of homologous sequences of barley disease resistance gene Mlo and maize disease resistance gene Hm1 in rice].

The encoding products of the disease resistance (R) gene of barley, Mlo, and the maize R gene, Hm1, do not contain the recognizable structural domains of most of the known plant R gene products. The two genes do not comply with the gene-for-gene theory in the response to pathogen infection either. Two sequences, OsMlo-1 and DFR-1 which were homologous to the barley Mlo and maize Hm1, respectively, were isolated from rice. The OsMlo-1 was mapped between two molecular markers, RZ667 and RG424, and located at a distance of 20.6 centi-Morgan (cM) from RZ667 and 6.0 cM from RG424 on rice chromosome 6. The DFR-1 was flanked by molecular markers R2635 and RG462 with an estimated genetic distance of 11.3 cM from R2635 and 23.9 cM from RG462 on rice chromosome 1. Using other published rice molecular linkage maps as references, it was found that the chromosomal locations of OsMlo-1 and DFR-1 were correspondence with two previously identified rice blast resistant QTLs (quantitative trait loci), respectively. The results suggest that the genes homologous to barley Mlo and maize Hm1 in rice may be involved in defense responses induced by pathogen infection.

Chromosome Mapping↗
PubMed2006

RBR: library-less repeat detection for ESTs.

MOTIVATION: Repeat sequences in ESTs are a source of problems, in particular for clustering. ESTs are therefore commonly masked against a library of known repeats. High quality repeat libraries are available for the widely studied organisms, but for most other organisms the lack of such libraries is likely to compromise the quality of EST analysis. RESULTS: We present a fast, flexible and library-less method for masking repeats in EST sequences, based on match statistics within the EST collection. The method is not linked to a particular clustering algorithm. Extensive testing on datasets using different clustering methods and a genomic mapping as reference shows that this method gives results that are better than or as good as those obtained using RepeatMasker with a repeat library. AVAILABILITY: The implementation of RBR is available under the terms of the GPL from http://www.ii.uib.no/~ketil/bioinformatics CONTACT: ketil.malde@bccs.uib.no SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗