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PubMed1995

Development and mapping of ten porcine microsatellite markers.

Thirty (TG)n microsatellite clones were isolated from a pig genomic library, sequenced, and tested for their suitability to detect polymorphism on a panel of animals by means of the polymerase chain reaction. Ten of these clones were developed into suitable markers and subsequently segregation of these markers was determined in the five PiGMaP reference pedigrees. A linkage analysis was performed on these 10 microsatellites together with 365 other loci that have been typed on these reference families. Eight of the microsatellites have been mapped to eight different linkage groups that have been previously assigned to different chromosomes (chromosomes 1, 6, 7, 9, 14, 15, 17 and 18). Of the remaining two markers, one is X-linked and the other shows no linkage. The number of alleles detected by these microsatellites, in the reference pedigrees, varied from six to sixteen and the heterozygosity varied from 42 to 85% in the 26 unrelated founder animals of these reference pedigrees.

Animals↗

PubMedDate not supplied

Development of comparative anchor tagged sequences (CATS) for canine genome mapping.

The development of a useful genetic map of the domestic dog would benefit by the inclusion of type I markers; coding genes that can connect the canine map to the homologous gene maps of other mammalian species. A group of 280 comparative anchor tagged sequences (CATS), and universal mammalian sequence tagged sites (UM-STS), were optimized for canine assessment. One hundred and five were screened for genetic polymorphism among nine canine breeds and three wild species of Canis in an attempt to promote gene mapping of comparative type I markers. Three categories of variation--size, restriction fragment length polymorphism (RFLP), and single-strand conformation polymorphism (SSCP)--were assessed. The data showed that 50% of the type I markers discriminate between species and 40% showed genetic variation among dog breeds. Although polymorphism incidence between nominated breeds for gene mapping is more limited than found for established reference pedigrees in other species, the concept and application of these CATS and UM-STS markers is useful in capturing the comparative information required for the full application and efficacy of the dog gene map.

Animals↗

PubMed1989

Recombination events suggest potential sites for the Huntington's disease gene.

The Huntington's disease gene (HD) maps distal to the D4S10 marker in the terminal 4p16.3 subband of chromosome 4. Directed cloning has provided several DNA segments that have been grouped into three clusters on a physical map of approximately 5 X 10(6) bp in 4p16.3. We have typed RFLPs in both reference and HD pedigrees to produce a fine-structure genetic map that establishes the relative order of the clusters and further narrows the target area containing the HD gene. Despite the large number of meiotic events examined, the HD gene cannot be positioned relative to the most distal cluster. One recombination event with HD suggests that the terminal-most markers flank the disease gene; two others favor a telomeric location for the defect. Efforts to isolate the HD gene must be divided between these two distinct intervals until additional genetic data resolve the apparent contradiction in localization.

Cell Line↗

PubMed1989

Functional topography during sensorimotor activation studied with event-related desynchronization mapping.

Event-related desynchronization (ERD) of alpha components was studied in four subjects during self-paced voluntary movements and somatosensory stimulation. EEG was recorded from 29 electrodes with a common right ear reference; local average reference derivations were calculated and used for computing ERD maps at 250-ms intervals. It was found that upper alpha components were desynchronized close to electrodes C3 and C4 overlying the primary sensorimotor cortex during voluntary movements and somatosensory stimulation. ERD started contralaterally more than 2 s before the movement and some hundreds of milliseconds before the stimulation. During the performance of unilateral movement and unilateral stimulation, ERD was bilaterally symmetric. Desynchronization of lower alpha components was found over the superior parietal cortex, clearly starting some hundreds of milliseconds after the desynchronization of upper frequency components. Therefore, the desynchronization of lower and upper alpha components reflects activation of different neuronal structures.

Arousal↗

PubMed2001

Short tandem repeat (STR) haplotypes in HLA: an integrated 50-kb STR/linkage disequilibrium/gene map between the RING3 and HLA-B genes and identification of STR haplotype diversification in the class III region.

We present a dense STR/linkage disequilibrium(LD)/gene map between the RING3 and HLA-B loci, reference allelic sizes on the most prevalent HLA haplotypes and their allelic frequencies in pedigree founders. This resource will facilitate LD, evolution and gene mapping studies, including comparisons of HLA and STR haplotypes and identification of HLA recombinants. The map was constructed by testing novel and previously reported STRs using a panel of 885 individuals in 211 families and 60 DNA samples from cell lines and bone marrow donors homozygous in the HLA-A, -B and -DR loci selected from over 15 000 entries into the registry of Swedish bone marrow donors. We have also analysed the variability of STR alleles/haplotypes on the most prevalent HLA haplotypes to identify STRs useful for fine mapping of disease genes in the region previously implicated in susceptibility to many disorders. The analysis of 40 HLA-A*01, B*0801, DRB1*03011, DQB1*0201 haplotypes in homozygous donors showed a surprising stability in 23 STRs between the class II recombination hot spot and HLA-B, with the average of 1.9% (16/838) variant alleles. However, 40% variant alleles were found at the D6S2670 locus in intron 19 of the tenascin-X gene both in the families and homozygous donors. The nucleotide sequence analysis of this STR showed a complex polymorphism consisting of tetra- (CTTT)(8-18) and penta-nucleotide (CTTTT)(1-2) repeats, separated by an intervening non-polymorphic sequence of 42 bp. The HLA-A1, B*0801, DRB1*03011, DQB1*0201 haplotypes had five (CTTT)(14-18)/(CTTTT)(2) variants with a predominant (CTTT)(16) allele, implicating the tetranucleotide component as the source of this ancestral haplotype diversification, which may be due to the location of D6S2670 in the region of the highest GC content in the human MHC.

Centromere↗

PubMed2000

Functional MR imaging activation after finger tapping has a shorter duration in the basal ganglia than in the sensorimotor cortex.

BACKGROUND AND PURPOSE: Repetitive motor tasks that produce sustained neuronal activity in the sensorimotor cortex produce transient neuronal activity in subcortical regions. We tested the hypothesis that a reference function modeling a transient hemodynamic response would more reliably detect activation in the basal ganglia than would a conventional reference function, which models a sustained hemodynamic response. METHODS: Functional MR imaging data were acquired in eight subjects performing an alternating-hand finger-tapping task. Postprocessing was performed by cross-correlation to two types of reference functions: one that models a sustained hemodynamic response to finger tapping and one that models an initial transient hemodynamic response. Activation in the sensorimotor cortex, supplementary motor area, cerebellum, thalamus, and corpus striatum was tabulated for each reference function. RESULTS: With the conventional boxcar reference function, activation was detected in the sensorimotor cortex, supplementary motor area, and cerebellum, but intermittently in the corpus striatum in all subjects. With the reference function for a transient response, activation in the corpus striatum was not detected in all subjects. CONCLUSION: In the corpus striatum, activation is detected more frequently with a reference function that models a transient response. Activated cortical and subcortical regions can be mapped with an alternating-hand finger-tapping paradigm and a combination of reference functions.

Adult↗

PubMedDate not supplied

A reassessment of the lower visual field map in striate-recipient lateral suprasylvian cortex.

Lateral suprasylvian visual cortex in the cat has been studied extensively, but its retinotopic organization remains controversial. Although some investigators have divided this region into many distinct areas, others have argued for a simpler organization. A clear understanding of the region's retinotopic organization is important in order to define distinct areas that are likely to subserve unique visual functions. We therefore reexamined the map of the lower visual field in the striate-recipient region of lateral suprasylvian cortex, a region we refer to as the lateral suprasylvian area, LS. A dual mapping approach was used. First, receptive fields were plotted at numerous locations along closely spaced electrode penetrations; second, different anterograde tracers were injected at retinotopically identified sites in area 17, yielding patches of label in LS. To visualize the resulting data, suprasylvian cortex was flattened with the aid of a computer. Global features of the map reported in many earlier studies were confirmed. Central visual field was represented posteriorly, and elevations generally shifted downward as one moved anteriorly. Often (though not always) there was a progression from peripheral locations towards the vertical meridian as the electrode moved down the medial suprasylvian bank. The map had some remarkable characteristics not previously reported in any map in the cat. The vertical meridian's representation was split into two pieces, separated by a gap, and both pieces were partially internalized within the map. Horizontal meridian occupied the gap. The area centralis usually had a dual representation along the posterior boundary of the lower field representation, and other fragments of visual field were duplicated as well. Finally, magnification appeared to change abruptly and unexpectedly, so that compressed regions of representation adjoined expanded regions. Despite its complexity, we found the map to be more orderly than previously thought. There was no clearcut retinotopic basis on which to subdivide LS's lower field representation into distinct areas.

Animals↗

PubMed1986

Effects of prenatal X-irradiation on open-field behavior in rats: application of randomized fostering technique and mapping results.

Sprague-Dawley (SD) rats were given X-irradiation (150 R) on Day 17 of gestation. After birth, all male pups were pooled once and then assigned randomly to irradiated mothers and control mothers. Offspring were administered an open-field test at about 7 weeks of age. The analysis was performed on the basis of two approaches: In the per subject approach, individual subject data (aggregation across Day 2 through Day 4) were treated as the basic unit of statistical analysis. In the per litter approach, double aggregation (aggregation across Day 2 through Day 4 for each subject and aggregation across subjects within each litter) was used. The per subject approach was slightly more sensitive as to the treatment effect, but it induced a reduction in the magnitude of eta squared. A principal component analysis was performed using eta squared together with those of several reference groups. Results were plotted on a map constructed from component scores. The characteristics of behavior in X-irradiated rats were very similar to those of the earlier stage of trials in terms of the location on the map. The postnatal maternal effect on open-field behavior was not serious and was adequately negligible in practice. A new fostering procedure was proposed and its advantages discussed.

Animals↗

PubMed1986

Restriction enzyme map of cryptic plasmid accompanying pR711b and pR409; identity of pR409 and pR388.

A reference strain containing the IncW plasmid, pR409, was found to contain also a cryptic, conjugative plasmid, here named pJR15. After the separation of the two plasmids into different strains of bacteria, pR409 was found to have an identical restriction enzyme map to the IncW plasmid, pR388. Both pR409 and pR388 were isolated from the same hospital in London and confer sulphonamide and trimethoprim resistance. Originally pR409 was reported to confer resistance to tetracycline, but this was not confirmed by the Plasmid Reference Center. pR409 appears to represent another isolate of pR388 in a different host background. The restriction enzyme map of the cryptic plasmid, pJR15 (39 kb), has been determined. pJR15 was found compatible with plasmids from 15 different incompatibility groups and has been found also in the reference strain of the IncD plasmid, pR711b. The HindIII and BglII digests of pR711b are shown. The possible presence of the conjugative plasmid, pJR15, should be examined for studies on the sex pili or chromosomal mobilization properties of pR711b.

DNA Restriction Enzymes↗

PubMed2001

A high-resolution 6.0-megabase transcript map of the type 2 diabetes susceptibility region on human chromosome 20.

Recent linkage studies and association analyses indicate the presence of at least one type 2 diabetes susceptibility gene in human chromosome region 20q12-q13.1. We have constructed a high-resolution 6.0-megabase (Mb) transcript map of this interval using two parallel, complementary strategies to construct the map. We assembled a series of bacterial artificial chromosome (BAC) contigs from 56 overlapping BAC clones, using STS/marker screening of 42 genes, 43 ESTs, 38 STSs, 22 polymorphic, and 3 BAC end sequence markers. We performed map assembly with GraphMap, a software program that uses a greedy path searching algorithm, supplemented with local heuristics. We anchored the resulting BAC contigs and oriented them within a yeast artificial chromosome (YAC) scaffold by observing the retention patterns of shared markers in a panel of 21 YAC clones. Concurrently, we assembled a sequence-based map from genomic sequence data released by the Human Genome Project, using a seed-and-walk approach. The map currently provides near-continuous coverage between SGC32867 and WI-17676 ( approximately 6.0 Mb). EST database searches and genomic sequence alignments of ESTs, mRNAs, and UniGene clusters enabled the annotation of the sequence interval with experimentally confirmed and putative transcripts. We have begun to systematically evaluate candidate genes and novel ESTs within the transcript map framework. So far, however, we have found no statistically significant evidence of functional allelic variants associated with type 2 diabetes. The combination of the BAC transcript map, YAC-to-BAC scaffold, and reference Human Genome Project sequence provides a powerful integrated resource for future genomic analysis of this region.

Base Composition↗

PubMedDate not supplied

Mapping the SF-12 to the EuroQol EQ-5D Index in a national US sample.

BACKGROUND: Preference scores for the Medical Outcomes Study (MOS) SF-12 would enable its use in cost-effectiveness analyses. Previous mapping studies of MOS instruments top reference-based instruments have not examined performance in national samples. PARTICIPANTS: 15,000 adults in the 2000 Medical Expenditure Panel Survey annual survey including the SF-12 and EQ-5D Index. METHODS: Regression of the EQ-5D Index scores onto the physical and mental component summary scores of the SF-12, testing 2nd-4th degree polynomial and spline models, including and excluding sociodemographics. RESULTS: A 2nd degree polynomial model explained 63% of the variance in EQ-5D scores, with robust internal and external validation. More complex mod-els explained minimally additional variance. Compared with EQ-5D valuations, prediction models overestimated the lowest health states (6% of the population). CONCLUSIONS: The mapped SF-12 yields usable preference-scaled scores, with some caution for the lowest health states.

Adult↗

PubMed2003

Use of radar remote sensing (RADARSAT) to map winter wetland habitat for shorebirds in an agricultural landscape.

Many of today's agricultural landscapes once held vast amounts of wetland habitat for waterbirds and other wildlife. Successful restoration of these landscapes relies on access to accurate maps of the wetlands that remain. We used C-band (5.6-cm-wavelength), HH-polarized radar remote sensing (RADARSAT) at a 38 degree incidence angle (8-m resolution) to map the distribution of winter shorebird (Charadriiformes) habitat on agricultural lands in the Willamette Valley of western Oregon. We acquired imagery on three dates (10 December 1999, 27 January 2000, and 15 March 2000) and simultaneously collected ground reference data to classify radar signatures and evaluate map accuracy of four habitat classes: (1) wet with < or = 50% vegetation (considered optimal shorebird habitat), (2) wet with > 50% vegetation, (3) dry with < or = 50% vegetation, and (4) dry with > 50% vegetation. Overall accuracy varied from 45 to 60% among the three images, but the accuracy of focal class 1 was greater, ranging from 72 to 80%. Class 4 coverage was stable and dominated maps (40% of mapped study area) for all three dates, while class 3 coverage decreased slightly throughout the study period. Among wet classes, class 1 was most abundant (30% coverage) in December and January, decreasing in March by 15%. Conversely, class 2 increased dramatically from January to March, likely due to transition from class 1 as vegetation grew. This approach was successful in detecting optimal habitat for shorebirds on agricultural lands. For modest classification schemes, radar remote sensing is a valuable option for wetland mapping in areas where cloud cover is persistent.

Agriculture↗

PubMed2004

Use of radar remote sensing (RADARSAT) to map winter wetland habitat for shorebirds in an agricultural landscape.

Many of today's agricultural landscapes once held vast amounts of wetland habitat for waterbirds and other wildlife. Successful restoration of these landscapes relies on access to accurate maps of the wetlands that remain. We used C-band (5.6-cm-wavelength), HH-polarized radar remote sensing (RADARSAT) at a 38 degrees incidence angle (8-m resolution) to map the distribution of winter shorebird (Charadriiformes) habitat on agricultural lands in the Willamette Valley of western Oregon. We acquired imagery on three dates (10 December 1999, 27 January 2000, and 15 March 2000) and simultaneously collected ground reference data to classify radar signatures and evaluate map accuracy of four habitat classes: (1) wet with < or = 50% vegetation (considered optimal shorebird habitat), (2) wet with > 50% vegetation, (3) dry with < or = 50% vegetation, and (4) dry with > 50% vegetation. Overall accuracy varied from 45 to 60% among the three images, but the accuracy of focal class 1 was greater, ranging from 72 to 80%. Class 4 coverage was stable and dominated maps (40% of mapped study area) for all three dates, while coverage of class 3 decreased slightly throughout the study period. Among wet classes, class 1 was most abundant (about 30% coverage) in December and January, decreasing in March to approximately 15%. Conversely, class 2 increased dramatically from January to March, likely due to transition from class 1 as vegetation grew. This approach was successful in detecting optimal habitat for shorebirds on agricultural lands. For modest classification schemes, radar remote sensing is a valuable option for wetland mapping in areas where cloud cover is persistent.

Agriculture↗

PubMed1998

Preparation of a candidate primary reference material for the international standardisation of HbA1c determinations.

We prepared a candidate primary reference material for the forthcoming international standardisation of beta-N-terminal glycated hemoglobin A measurements. It consists of well-defined mixtures of purified beta-N-terminal glycated hemoglobin A and non-glycated hemoglobin A. First, beta-N-terminal glycated hemoglobin A and non-glycated hemoglobin A were isolated, purified to homogeneity, and characterised. The techniques used were cation exchange and affinity chromatography for the purification, and high performance liquid chromatography, capillary isoelectric focusing, electrospray ionisation mass spectrometry, and peptide mapping for the characterisation. Hemoglobins from blood of healthy, non-diabetic volunteers were obtained with a purity of > 99.5% for non-glycated hemoglobin A and of > 98.5% for beta-N-terminal glycated hemoglobin A. However, results from peptide mapping indicate that the beta-N-terminal glycated hemoglobin A preparations still contain some non-beta-N-terminal glycated hemoglobins, co-eluting with beta-N-terminal glycated hemoglobin A. The exact content of beta-N-terminal glycated hemoglobin A in these preparations could be determined by a procedure consisting of standard addition, enzymatic cleavage and quantification of the resulting beta-N-terminal peptides to be in the range from 95-97.5%. Since the beta-N-terminal glycated hemoglobin A and non-glycated hemoglobin A content could be exactly determined in the materials prepared, mixtures of both components could be successfully used to calibrate the candidate reference methods.

Chromatography, Affinity↗

PubMed1996

Development and mapping of polymorphic microsatellite markers derived from a chicken brain cDNA library.

Until now the genetic linkage map in chicken has ben based mainly on random genomic markers. The addition of expressed sequence tags (ESTs) to the genetic linkage maps is becoming more important because ESTs can form the basis for comparative mapping studies. This may be helpful for the detection of candidate genes for quantitative trait loci (QTLs). In our study we used a (TG)13 repeat as probe for the detection of microsatellites in a chicken brain cDNA library. After hybridization 0.15% of the cDNA clones gave a positive signal. The cDNA complexity of the library was high; of the 90 cDNA clones that were sequenced 60 occurred only once. For 29 clones primer sets for the polymerase chain reaction could be developed. Twenty-one microsatellites were polymorphic on one or more of the test panels and 15 markers could be mapped on either or both of the international reference families. Because sequence homology between chicken and mammalian cDNAs is sometimes low it was difficult to assess the level of sequence homology that indicated a true homologous transcript. In our study seven cDNA cones, of which three could be mapped, showed a relatively high percentage of sequence homology with sequences found in other species. Because sequencing and mapping of expressed sequence tags in human and mouse is progressing very rapidly, it is predicted that further information will soon be readily available. Therefore, increasing the number of expressed sequences on the chicken genetic linkage map will be of value for comparative mapping studies in the near future.

Animals↗

PubMed1996

Assignment of the human tryptophanyl-tRNA synthetase gene (WARS) to chromosome 14q32.2 --> q32.32.

Tryptophanyl-tRNA synthetase catalyzes the aminoacylation of tRNAtrp with tryptophan, an essential function in the cell's protein synthesis machinery. It has been shown that tryptophanyl-tRNA synthetase is induced by interferon, and this has led to hypotheses about other possible functions of tryptophanyl-tRNA synthetase. We have mapped a cDNA probe of the tryptophanyl-tRNA synthetase gene (WARS) by a combination of somatic cell hybrid analysis, fluorescence in situ hybridization (FISH), and linkage analysis. Both FISH and linkage analysis independently supported a more distal position of WARS than had been previously reported. FISH mapping indicated a most likely location at 14q32.31. Linkage analysis was based on the 40 reference families from the CEPH collaboration and resulted in a 13-point map, placing WARS, with odds of more than 1,000:1, within an area of approximately 10 cM and, with odds of 198:1, in an approximately 6 cM interval between pCMM101 and D14S27. The study provides additional integration of the physical and genetic maps of the distal part of 14q, as well as genetic tools enabling a more complete understanding of the function of tryptophanyl-tRNA synthetase, especially with regard to the cryptic inducibility of interferon.

Chromosome Mapping↗

PubMed1984

Sequential hemodynamic and oxygen transport abnormalities in patients with acute pancreatitis.

Physiologic abnormalities were evaluated by sequential hemodynamic and oxygen transport measurements in 33 patients with acute pancreatitis. The hypotensive crisis, which was defined as the lowest mean arterial pressure (MAP), was used as the common temporal reference point to align the data in a coherent fashion. The data of the 48-hour periods before and after the hypotensive crisis then were evaluated. The patients were divided into normotensive and hypotensive groups and the latter were divided into survivors and nonsurvivors to evaluate the severity of the disorder and to identify the patterns representative of survival and death. The physiologic abnormalities of the hypotensive patients include decreased systemic vascular resistance index (SVRI) and compromised cardiac function. The latter was demonstrated during the hypotensive episode by significantly reduced left ventricular stroke work index (LSWI), despite increases in heart rate (HR), central venous pressure (CVP), pulmonary capillary wedge pressure (WP), and cardiac index (CI). The normotensive group had increased oxygen consumption (Vo2), oxygen delivery (Do2), pulmonary shunt (Qsp/Qt), LSWI, normal SVRI, and high CI. The hypotensive nonsurvivors had lower MAP, LSWI, SVRI, Do, and hematocrit as well as higher pulmonary vascular resistance index (PVRI) and Qsp/Qt than did the survivors. These findings do not support myocardial depression as the primary cardiovascular abnormality in acute pancreatitis, but rather suggest the decreased vascular tone from flow maldistribution in the peripheral microcirculation limits tissue oxygenation in the face of increased metabolic requirements of the hypercatabolic state.

Acute Disease↗

PubMed1967

Aromatic amino acid biosynthesis: gene-enzyme relationships in Bacillus subtilis.

Single step mutants of Bacillus subtilis which required either one or all of the aromatic amino acids for growth were isolated. The relevant gene defect was determined for each mutant by enzyme assays in vitro. A mutant deficient in each enzyme step of aromatic amino acid biosynthesis was found with the exceptions of the shikimate kinase and the phenylalanine and tyrosine transaminases. Representative mutants carrying the defective genes were mapped by deoxyribonucleic acid mediated transformation by reference to the aromatic amino acid gene (aro) cluster and, alternately, to any of the other unlinked aro genes. The genes coding for dehydroquinate synthetase, 3-enol pyruvylshikimate 5-phosphate synthetase, one form of chorismate mutase, and prephenate dehydrogenase are linked to the aro cluster. Except for the previously identified linkage between the genes of 3-deoxy-d-arabino heptulosonic acid 7-phosphate synthetase and one species of chorismate mutase, the other genes involved in this pathway are neither linked to the aro cluster nor to each other.

Amino Acids↗