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PubMed1998

Sequence assembly validation by multiple restriction digest fragment coverage analysis.

DNA sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. This report examines the possibility of analyzing multiple, independent restriction digests as a method for testing the fidelity of sequence assembly. A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genomic sequencing projects. The method is shown to reliably detect errors in sequence fragment assembly without the necessity of making reference to an overlying physical map. An html form-based interface is available at http:/(/)www.ibc.wustl.edu/services/validate. html.

Algorithms↗

PubMed1993

Autoradiographic mapping of 5-HT1 receptors in the guinea-pig brain with particular reference to the 5-HT1D receptor sites.

The anatomical distribution of 5-HT1 receptors in the guinea-pig brain was studied by means of in vitro quantitative autoradiography using [3H]-5-HT as ligand. The relative presence of the subtypes of the 5-HT1 binding site was investigated by adding selective concentrations of 8-OH-DPAT, (-)21,009, mesulergine and 5-CT. In addition, differentiation of 5-HT1D receptors was achieved by incubation of the tissues with [3H]-5-HT in the presence of 100 nmol/l 8-OH-DPAT together with 100 nmol/l mesulergine. Areas presenting high densities of 5-HT1A receptors included the neocortex (internal layers), hippocampal formation (dentate gyrus, CA1 field), septum and raphe nuclei, while 5-HT1C sites accounted for most of the [3H]-5-HT binding to the choroid plexus. Non 5-HT1A-non 5-HT1C sites (mainly 5-HT1D and, also probably, 5-HT1E receptors) were clearly predominant in the guinea-pig brain. These sites were mainly present in the neocortex (external layers), basal ganglia, hypothalamus and midbrain (substantia nigra, superior colliculus). As previously described, sites with the properties of 5-HT1B receptors could not be clearly identified in the guinea-pig brain. The present results, in addition to providing a detailed map of the 5-HT1 receptors in the guinea-pig brain, indicate that the guinea-pig is a useful laboratory animal for the study of 5-HT1D receptors.

Animals↗

PubMed2001

On-line correction and visualization of motion during MRI-controlled hyperthermia.

Displacement of tissue during MRI-controlled hyperthermia therapy can cause significant problems. Errors in calculated temperature may result from motion-related image artifacts and inter-image object displacement, leading to incorrect spatial temperature reference. Here, cyclic navigator echoes were incorporated in rapid gradient-echo MRI sequences, used for temperature mapping based on the proton resonance frequency. On-line evaluation of navigator information was used in three ways. First, motion artifacts were minimized in echo-shifted (TE > TR) gradient-echo images using the phase information of the navigator echo. Second, navigator profiles were matched for a quantitative evaluation of displacement. Together with a novel processing method, this information was employed to correct the reference temperature maps, thereby avoiding persistence of motion-related temperature errors throughout the hyperthermic period. Third, on-line visualization of displacement, together with temperature maps and thermal dose images, was developed, allowing physician intervention at all times. Examples are given of on-line corrections during hyperthermia procedures with focused ultrasound and radiofrequency heat sources. Magn Reson Med 45:128-137, 2001.

Animals↗

PubMed1990

A genetic map of chromosome 1: comparison of different data sets and linkage programs.

We have used 22 chromosome 1 loci to construct a genetic linkage map of this autosome using the Venezuelan Reference Pedigree. These markers formed two linkage groups separated by an interval of more than 30 cM. Linkage maps were constructed separately using the computer programs LINKAGE and MAPMAKER to determine their relative speed, efficiency, and accuracy. We found that both programs generated maps with the same order and distances, although the LINKAGE program derived more information from the data, allowing placement of one additional marker. Many of the probes have previously been mapped using the CEPH pedigrees. However, the current map is generated from a different data set and so can be used to increase the certainty of locus order and map position. Ultimately, the generation and confirmation of a 1-cM map of this chromosome will require such multiple data sets.

Alleles↗

PubMed2005

Dynamic cerebral autoregulation in acute lacunar and middle cerebral artery territory ischemic stroke.

BACKGROUND AND PURPOSE: We addressed whether dynamic cerebral autoregulation (dCA) is affected in middle cerebral artery (MCA) territory (MCAS) and lacunar ischemic stroke (LS). METHODS: Blood pressure (MAP) and MCA velocity (V) were measured in 10 patients with large MCAS (National Institutes of Health Stroke score, 17+/-2; mean+/-SEM), in 10 with LS (score, 9+/-1), and in 10 reference subjects. dCA was evaluated in time (delay of the MCA Vmean counter-regulation during changes in MAP) and frequency domains (cross-spectral MCA Vmean-to-MAP phase lead). RESULTS: In reference subjects, latencies for MAP increments (5.3+/-0.5 seconds) and decrements (5.6+/-0.5 seconds) were comparable, and low frequency MCA Vmean-to-MAP phase lead was 56+/-5 and 59+/-5 degrees (left and right hemisphere). In MCAS, these latencies were 4.6+/-0.7 and 5.6+/-0.5 seconds in the nonischemic hemisphere and not detectable in the ischemic hemisphere. In the unaffected hemisphere, phase lead was 61+/-6 degrees versus 26+/-6 degrees on the ischemic side (P<0.05). In LS, no latency and smaller phase lead bilaterally (32+/-6 and 33+/-5 degrees) conformed to globally impaired dCA. CONCLUSIONS: In large MCAS infarcts, dynamic cerebral autoregulation was impaired in the affected hemisphere. In LS, dynamic cerebral autoregulation was impaired bilaterally, a finding consistent with the hypothesis of bilateral small vessel disease in patients with lacunar infarcts.

Blood Flow Velocity↗

PubMed1992

Closure of a genetic linkage map of human chromosome 7q with centromere and telomere polymorphisms.

We have constructed a 2.4-cM resolution genetic linkage map for chromosome 7q that is bounded by centromere and telomere polymorphisms and contains 66 loci (88 polymorphic systems), 38 of which are uniquely placed with odds for order of at least 1000:1. Ten genes are included in the map and 11 markers have heterozygosities of at least 70%. This map is the first to incorporate several highly informative markers derived from a telomere YAC clone HTY146 (locus D7S427), including HTY146c3 (HET 92%). The telomere locus markers span at least 200 kb of the 7q terminus and no crossovers within the physical confines of the locus were observed in approximately 240 jointly informative meioses. The sex-equal map length is 158 cM and the largest genetic interval between uniquely localized markers in this map is 11 cM. The female and male map lengths are 181 and 133 cM, respectively. The map is based on the CEPH reference pedigrees and includes over 4000 new genotypes, our previously reported data plus 29 allele systems from the published CEPH version 5 database, and was constructed using the program package CRI-MAP. This genetic linkage map can be considered a baseline map for 7q, and will be useful for defining the extent of chromosome deletions previously reported for breast and prostate cancers, for developing additional genetic maps such as index marker and 1-cM maps, and ultimately for developing a fully integrated genetic and physical map for this chromosome.

Centromere↗

PubMed1992

Autosomal dominant retinitis pigmentosa (adRP; RP6): cosegregation of RP6 and the peripherin-RDS locus in a late-onset family of Irish origin.

We recently reported the localization of a gene for late-onset autosomal dominant retinitis pigmentosa (adRP; RP6), on the short arm of chromosome 6, by linkage analysis in a large family of Irish origin. It is notable that the gene encoding peripherin-RDS, a photoreceptor-specific protein, recently has been physically mapped on 6p. In our own analysis, an intrageneic marker derived from this gene cosegregated with the adRP disease locus with zero recombination (lod score 5.46 at q = .00). Using the CEPH reference panel, we now report the mapping of the peripherin-RDS gene relative to other 6p markers in the CEPH data base. Incorporation of these data into a multipoint analysis produced a lod score for adRP of 8.21, maximizing at the peripherin-RDS locus. This study provides strong evidence suggesting a role for peripherin-RDS in the etiology of one form of adRP.

Base Sequence↗

PubMed1998

[Polymorphism of the gene of heat shock protein hsp70 in lines of rats with normal and hypertensive status].

RFLP in the hsp70 gene encoding a major heat shock protein was analyzed in rat strains with high and normal arterial blood pressure. Dimorphism in the sets of DNA fragments was revealed after hybridization of the hsp gene leader sequence with rat DNA digested with BamHI restriction endonuclease. Type I RFLP was represented by the fragments of 12,200, 6500, 41,000 and 1600 bp in size. Type II RFLP corresponded to the set that included the fragments of 12,200, 6500, 2900, 1600, and 1200 bp in size. Interstrain polymorphism was demonstrated for the fragments of 4100, 2900 and 1200 bp. Furthermore, analysis of different rat strains showed that the 2900- and 1200-bp fragments were linked and formed by cleavage of the 4100-bp fragment with restriction endonuclease. This polymorphism was probably caused by the point A-->T mutation occurring in the BamHI recognition site located in the leader sequence of the hsp70 gene at a distance of +35 bp from the coding sequence. Examination of interstrain RFLP in the hsp70 gene indicated that the presence of 2900-bp fragment was not associated with hypertensive status in all experimental models of inherited arterial hypertension. This confirms the assumption on genetic heterogeneity of this common disease.

Animals↗

PubMed2000

Mixing location-relevant and location-irrelevant choice-reaction tasks: influences of location mapping on the Simon effect.

The Simon effect refers to the finding that reaction times are faster when stimulus and response locations correspond than when they do not in tasks where stimulus location is defined as irrelevant. The authors examined the Simon effect for situations in which location-irrelevant trials were intermixed with trials for which stimulus location was relevant. Compatible mapping of the location-relevant trials enhanced the Simon effect relative to an unmixed condition, whereas incompatible mapping reversed the Simon effect. The reversal with incompatible mapping remained evident when task uncertainty was removed by use of a precue and was larger than the reversed effect produced by making incongruent trials more frequent than congruent trials. This result suggests that both attentional biases and task-defined associations contribute to the reversal of the Simon effect.

Choice Behavior↗

PubMed1988

[Effect of preoperative continuous nifedipine maintenance medication on hemodynamics and myocardial lactate extraction in coronary surgery patients].

The cardioprotective efficacy of preoperatively maintained long-term oral nifedipine application to 21 patients undergoing coronary artery bypass grafting (CABG) was investigated during fentanyl-N2O-anaesthesia. Two groups were defined at random; one group of patients receiving their normal morning doses together with the premedication, the other, who received the last nifedipine medication in the evening before surgery. Measurements where performed: 1. before induction of anaesthesia (reference value), 2. after induction, 3. at skin incision, 4. during sternotomy. There were no significant differences of hemodynamic parameters between the two groups. The hemodynamic parameters heart rate (HR), mean arterial pressure (MAP), cardiac index (CI), and coronary perfusion pressure (CPP) decreased after induction in accordance with the plasma-concentrations of epinephrine and norepinephrine in both groups and increased again during sternotomy with HR and CI remaining below and MAP and CPP rising above the reference value. The nifedipine-plasma-concentrations were significantly higher in the group with the morning dose and just within the minimal therapeutic range before and after induction of anaesthesia. But during skin incision and sternotomy the plasma levels fell below 10 ng/ml, i.e. below the therapeutic level. The incidence of myocardial lactate extraction values greater than 10% was highest immediately after induction of anaesthesia and lowest during sternotomy with one patient in both groups exhibiting negative lactate extraction as a symptom of myocardial ischemia. The results suggest that the preoperatively maintained oral nifedipine medication of 10-20 mg p.o. was not able to provide sufficiently high nifedipine-plasma-levels during sternotomy nor to improve the hemodynamic state in patients with CABG.(ABSTRACT TRUNCATED AT 250 WORDS)

Anesthesia, General↗

PubMed1995

High resolution microscopic mapping of DNA using multi-color fluorescent hybridization.

We describe a procedure for microscopically mapping the relative positions of DNA probes along extended strands of DNA. The procedure referred to as direct visual hybridization (DIRVISH) DNA mapping involves the simultaneous hybridization of multiple probes and the fluorescent colors, red green and blue to produce images that convey high-resolution mapping information. The images appear as long strings of fluorescent signals positioned as they are in the genome. A visual multi-color map is generated within 2 days. Cosmid probes span a distance of 10 microms or more and have been observed to contain patterns within the strings of signals. We have developed computer imaging programs to scan through the strings of signals and plot the intensities. Scans through multiple signal strings for one cosmid probe revealed consistent patterns. We have interpreted the patterns as the result of suppression of repetitive DNA sequence hybridization. These patterns may prove useful as fingerprints for regions of DNA.

Animals↗

PubMed1995

A 37-marker PCR-based genetic linkage map of human chromosome 9: observations on mutations and positive interference.

Refinement of an "index" marker genetic linkage map of human chromosome 9 using the CEPH reference pedigrees has been achieved through the addition of 11 markers to the previous map of 26 markers. Five of the 11 markers added to the map are new markers of the GATA repeat type, 1 is a complex repeat, and the remaining 5 as well as the original 26 markers are all GT/CA repeats. Twelve definite and five probable mutations were detected in this analysis and were more common for the GATA repeats than the GT/CA repeats. Strong evidence for positive interference was seen over the length of the chromosome, but there were significantly more double recombination events in the pericentromeric region than elsewhere, suggesting that interference is less strong in that region.

Base Sequence↗

PubMed1991

Molecular basis of spectrin and ankyrin deficiencies in severe hereditary spherocytosis: evidence implicating a primary defect of ankyrin.

While varying degrees of spectrin deficiency have been found in the majority of patients with hereditary spherocytosis (HS), a combined severe deficiency of both spectrin and the spectrin-binding protein, ankyrin, has been reported only in two patients with severe HS. To elucidate the molecular basis of these protein deficiencies, we have studied the synthesis, assembly, and the mRNA levels of spectrin and ankyrin in peripheral blood reticulocytes in one of the previously reported probands. Pulse-labeling studies showed that in HS reticulocytes, the synthesis of alpha-spectrin was comparable with control reticulocytes while that of beta-spectrin was increased about fourfold, presumably reflecting increased erythropoietic drive. On the HS reticulocyte membrane, the amount of newly assembled spectrin was reduced to about half of the control values, presumably reflecting a decrease in the synthesis of the spectrin binding protein, ankyrin: the ankyrin synthesis was nearly absent in the cytosol and the amounts of membrane-associated ankyrin were reduced to about half of the normal values. The changes in the amounts of spectrin and ankyrin mRNAs quantitated by slot blot and Northern blot analyses were comparable with changes in the synthesis of these proteins: The alpha spectrin mRNA was within a control range and the beta-spectrin mRNA was slightly increased, while the amounts of ankyrin mRNA were reduced to about 50% of control values. We conclude that the primary defect underlying the combined spectrin and ankyrin deficiency is a deficiency of ankyrin mRNA leading to a reduced synthesis of ankyrin which, in turn, underlies the decreased assembly of spectrin on the membrane.

Adult↗

PubMed1998

Mapping chicken genes using preferential amplification of specific alleles.

To map the chicken genome, an international reference population was developed at our laboratory (East Lansing, MI) using an F2 backcross between inbred jungle fowl (JF) and inbred white leghorns (WL). To augment the number of type I genes on the East Lansing (E) map, segregation of the JF-specific allele was followed using preferential amplification of specific alleles (PASA) in polymerase chain reactions (PCR). Among 15 functional genes that were added to the E map, agrin and mannose-6-phosphate receptor genes were found to occur in conserved syntenic groups. Using this PCR-based approach, six conserved groups spanning more than 243 centimorgans (cM) in the chicken were syntenic with human and mouse.

Alleles↗

PubMed2004

[Comparison between the female- and male-linkage maps in pigs].

The difference between the length of female- and male-linkage map, which was created with a reference pedigree based on a commercial porcine population and using 163 microsatellite markers as well as 3 type-I markers (RYR1, PRKAG3, PIT1), was statistic analyzed. The results showed that the total length of female linkage map of autosomes is 2625.9 cm and the total length of the male linkage map is 2259.7 cm; the ratio between the total length of the female- and male-linkage maps is 1.16 : 1; except for the chromosomes 1 and 14, the female linkage maps of the other chromosomes are longer than the male linkage maps. The difference between the length of female- and male-linkage maps of chromosomes 1, 3, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17 and 18 is very significant (P<0.01) and the difference of chromosome 9 is significant (P<0.05); but there is no significance on chromosomes 2, 4, 12 and 15.

Animals↗

PubMed1992

Assessment of valvular regurgitation using cine magnetic resonance imaging coupled with phase compensation technique: comparison with Doppler color flow mapping.

To elucidate whether or not a newly developed technique in cinematic-displayed (cine) magnetic resonance imaging (MRI) can improve the semiquantitative evaluation of valvular regurgitant flow, 20 patients with valvular lesions were studied. Three pulse sequences of cine MRI, ie, standard, short echo time (TE), and rephasing scans, were compared with reference obtained by Doppler color flow mapping. Short TE technique and rephasing scan technique improved image quality remarkably as compared with standard technique. Each of the three cine MRI techniques showed good correlation with the Doppler method (p < 0.001). However, short TE and rephasing scan techniques gave a faithful estimation of the extent as compared with the Doppler method, whereas standard technique overestimated the regurgitation. Thus, cine magnetic resonance imaging with phase compensation technique can be utilized for the semiquantitative assessment of valvular regurgitation in a manner similar to that of Doppler color flow mapping.

Aged↗

PubMed1990

A deletion linked to a poly(ADP-ribose) polymerase gene on chromosome 13q33-qter occurs frequently in the normal black population as well as in multiple tumor DNA.

The nuclear enzyme poly(ADP-ribose) polymerase (PADPRP) is thought to play a role in DNA recombination, replication, and repair. In view of the implication of these processes in tumorigenesis, and based on preliminary evidence which indicated the presence of an extraneous polymorphic restriction fragment for murine PADPRP loci in strains of mice susceptible to plasmacytomas, we investigated correlations between the restriction fragment length polymorphism of the PADPRP gene(s) and human Burkitt lymphoma. No increase in the frequency of polymorphisms on chromosome 1 (containing the active gene) or on chromosome 14 (a pseudogene) was observed. However, restriction fragment length polymorphism analysis of PADPRP sequences on chromosome 13 (either a processed pseudogene or a gene with extensive identity to PADPRP) revealed that of 19 DNA samples derived from endemic Burkitt lymphoma all contained at least one copy of a rare allele (B). Simple two-allele (A/B) polymorphisms in this PADPRP-like locus were identified by digestion with a number of restriction enzymes including HindIII, PstI, KpnI, and MspI. These restriction fragment length polymorphisms always segregated together, suggesting that they identify a deletion within or close to the PADPRP sequences on chromosome 13, which we mapped precisely to 13q33-qter. Based upon family studies the A and B alleles were shown to be transferred in a Mendelian codominant fashion. Subsequently, this probe was used as a linkage marker to study the frequency of this deletion in various tumors including B-cell follicular lymphomas, small cell lung carcinomas, breast carcinomas, and colorectal carcinomas. In noncancer control populations, the frequency of this deletion was 3-fold higher among Blacks as compared to Caucasians. When DNA from various tumors was compared to normal DNA from racially appropriate noncancer controls, the frequency of this deletion was still 2- to 3-fold higher in the tumor DNA. Matched samples provided instances of tumor-specific loss of heterozygosity but also revealed that the predominant source of this deletion is the germ line, suggesting that the chromosome 13 region neighboring the PADPRP locus may harbor a gene whose loss may predispose individuals to malignancy.

Alleles↗

PubMed2002

Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations.

Linkage analysis and allelic association (also referred to as linkage disequilibrium) studies are two major approaches for mapping genes that control simple or complex traits in plants, animals, and humans. But these two approaches have limited utility when used alone, because they use only part of the information that is available for a mapping population. More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations. The new strategy makes use of a random sample from a panmictic population and the open-pollinated progeny of the sample. In this article, we extend the new strategy to map quantitative trait loci (QTL), using molecular markers within the EM-implemented maximum-likelihood framework. The most significant advantage of this extension is that both linkage and linkage disequilibrium between a marker and QTL can be estimated simultaneously, thus increasing the efficiency and effectiveness of genome mapping for recalcitrant outcrossing species. Simulation studies are performed to test the statistical properties of the MLEs of genetic and genomic parameters including QTL allele frequency, QTL effects, QTL position, and the linkage disequilibrium of the QTL and a marker. The potential utility of our mapping strategy is discussed.

Algorithms↗