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PubMed1991

Analysis of the structural relationships between the DNA-binding phosphoproteins pp42, pp43 and pp44 by in situ peptide mapping.

A structural homology is established between three DNA-binding phosphoproteins located in the 42 to 44 kDa range, referred to as pp42, pp43 and pp44, from Chironomus tentans salivary gland cells by in situ peptide mapping. The staining patterns of pp42, pp43 and pp44 which resulted from digestion with Staphylococcus aureus V8, trypsin or papain proteases show the presence of 8 to 15 spots majority of which have identical mobility. In the patterns of the digests generated by treatments with trypsin about 10 spots appear in common between any pair of the protein substrates. In addition, each pattern includes two to three peptides of mobility not present in the other. Thus the peptide mapping of pp42, pp43 and pp44 based on the staining patterns of proteolytic digests suggest the existence of structural homology between the three unlabelled substrates. The proteolytic peptides carrying the rapidly turning over phosphate groups form markedly different electrophoretic patterns than the unlabelled peptides visualized by staining. Treatment of 32P-labelled pp42, pp43 and pp44 with V8 generates only one labelled fragment in the 30 kD range. The cleavage patterns of pp44 produced by chymotrypsin or papain contain seven to ten labelled fragments while those of pp42 and pp43 contain only two. The 32P-labelled tryptic peptides of pp42, pp43 and pp44 exhibit a ladder pattern for each substrate which probably arise by a consecutive removal of 25 to 35 amino acid residues from the primary digestion products pp29, pp29.5 and pp30 by cleavage of four to five putative interdomain regions. The possibility that these three structurally related phosphoproteins belong to the category of transcription factors is discussed.

Animals↗

PubMedDate not supplied

Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus).

We report construction of second-generation integrated genetic linkage and radiation hybrid (RH) maps in the domestic cat (Felis catus) that exhibit a high level of marker concordance and provide near-full genome coverage. A total of 864 markers, including 585 coding loci (type I markers) and 279 polymorphic microsatellite loci (type II markers), are now mapped in the cat genome. We generated the genetic linkage map utilizing a multigeneration interspecies backcross pedigree between the domestic cat and the Asian leopard cat (Prionailurus bengalensis). Eighty-one type I markers were integrated with 247 type II markers from a first-generation map to generate a map of 328 loci (320 autosomal and 8 X-linked) distributed in 47 linkage groups, with an average intermarker spacing of 8 cM. Genome coverage spans approximately 2,650 cM, allowing an estimate for the genetic length of the sex-averaged map as 3,300 cM. The 834-locus second-generation domestic cat RH map was generated from the incorporation of 579 type I and 255 type II loci. Type I markers were added using targeted selection to cover either genomic regions underrepresented in the first-generation map or to refine breakpoints in human/feline synteny. The integrated linkage and RH maps reveal approximately 110 conserved segments ordered between the human and feline genomes, and provide extensive anchored reference marker homologues that connect to the more gene dense human and mouse sequence maps, suitable for positional cloning applications.

Animals↗

PubMed2005

A statistical approach for array CGH data analysis.

BACKGROUND: Microarray-CGH experiments are used to detect and map chromosomal imbalances, by hybridizing targets of genomic DNA from a test and a reference sample to sequences immobilized on a slide. These probes are genomic DNA sequences (BACs) that are mapped on the genome. The signal has a spatial coherence that can be handled by specific statistical tools. Segmentation methods seem to be a natural framework for this purpose. A CGH profile can be viewed as a succession of segments that represent homogeneous regions in the genome whose BACs share the same relative copy number on average. We model a CGH profile by a random Gaussian process whose distribution parameters are affected by abrupt changes at unknown coordinates. Two major problems arise: to determine which parameters are affected by the abrupt changes (the mean and the variance, or the mean only), and the selection of the number of segments in the profile. RESULTS: We demonstrate that existing methods for estimating the number of segments are not well adapted in the case of array CGH data, and we propose an adaptive criterion that detects previously mapped chromosomal aberrations. The performances of this method are discussed based on simulations and publicly available data sets. Then we discuss the choice of modeling for array CGH data and show that the model with a homogeneous variance is adapted to this context. CONCLUSIONS: Array CGH data analysis is an emerging field that needs appropriate statistical tools. Process segmentation and model selection provide a theoretical framework that allows precise biological interpretations. Adaptive methods for model selection give promising results concerning the estimation of the number of altered regions on the genome.

Algorithms↗

PubMed1993

Four-year-olds' disambiguation of action and object word reference.

Preschool-age children show a very strong tendency to map a novel noun onto an unfamiliar rather than a familiar object. This so-called disambiguation effect has been interpreted as evidence that youngers expect object labels to be mutually exclusive. In Experiment 1, 4-year-olds were observed to map a novel verb onto an unfamiliar action about twice as often as they mapped it onto a familiar one. When the unfamiliar action had been preexposed, but the familiar one had not, the mapping preference was eliminated. In Experiment 2, 4-year-olds mapped a novel noun onto an unfamiliar object about five times as often as they mapped it onto a familiar object, and this tendency was not affected by preexposure. Even when action embedding and question complexity were controlled, the disambiguation effect was stronger for object than for action words. An account is presented in which two lexical principles, Mutual Exclusivity and Feeling of Novelty, are hypothesized to apply differently to action than to object words.

Child Language↗

PubMedDate not supplied

Crossing over in chicken oogenesis: cytological and chiasma-based genetic maps of the chicken lampbrush chromosome 1.

Chiasmata in diplotene bivalents are located at the points of physical exchange (crossing-over) between homologous chromosomes. We have studied chiasma distribution within chicken lampbrush chromosome 1 to estimate the crossing-over frequency between chromosome landmarks. The position of the centromere and chromosome region 1q3.3-1q3.6 on lampbrush chromosome 1 were determined by comparative physical mapping of the TTAGGG repeats in the chicken mitotic and lampbrush chromosomes. The comparison of the chiasma (=crossing over)-based genetic distances on chicken chromosome 1 with the genetic linkage map obtained in genetic experiments showed that current genetic distances estimated by the high-resolution genetic mapping of the East Lansing, Compton, and Wageningen chicken reference populations are 1.2-1.9 times longer than those based on chiasma counts. Conceivable reasons for this discrepancy are discussed.

Animals↗

PubMed1995

Coronary artery mapping: a method for three-dimensional reconstruction of epicardial anatomy.

Evaluation of coronary anatomy with conventional coronary angiography requires visual integration of multiple images from different viewing orientations to generate a mental interpretation of three-dimensional (3D) structure. The epicardial surface is, in many ways, analogous to the earth's surface topography and may be effectively depicted using cartographic methods. To show coronary anatomy visualized as topographic maps, we used cartographic projection methods to analyze the coronary vessels of a canine heart after immediate postmortem injection with a radio-opaque gelatinous solution. A volumetric image data set was obtained with x-ray spiral computed tomography. The principal axis of the image volume was calculated and the image volume reformatted to a reference coordinate system defined by the principal axis as the ordinate. A cylindrical projection map of the epicardial surface was created using a maximum-intensity projection volume-rendering technique. After converting the Cartesian reference coordinate system to a polar coordinate system, additional mapping projections from user-defined orientations were generated. The results show that interpretative difficulties of coronary angiography may be diminished by generating 3D maps of coronary anatomy using volumetric datasets acquired noninvasively and displayed with cartographic methods.

Algorithms↗

PubMed2004

Using prime-and-switch phasing to reduce model bias in molecular replacement.

Atomic models are commonly used to calculate phases in macromolecular crystallography. When combined with measured amplitudes, model-based phases yield electron-density maps with features of the correct structure but with a significant bias towards features of the model. The present contribution shows applications of the technique of prime-and-switch phasing to reduce this bias. An atomic model is used to generate phases that are close to the correct set but that may be biased. An unbiased source of phase information, an estimate of the probability that the electron-density map corresponds to a macromolecule, is then used to select a set of phases that are near the biased set, without further reference to the biased phases. The probability that the electron-density map corresponds to a macromolecule is based on agreement of the map with expectations such as a flat solvent region. Prime-and-switch phasing can be useful even for crystals with low solvent content and may reduce errors in interpretation of electron density in a wide range of applications of macromolecular crystallography, including molecular replacement, model building, ligand-binding and conformation-change studies, refinement and structure validation.

Bias↗

PubMed1999

The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades: MSK1 as a potential histone H3/HMG-14 kinase.

The nucleosomal response refers to the rapid phosphorylation of histone H3 on serine 10 and HMG-14 on serine 6 that occurs concomitantly with immediate-early (IE) gene induction in response to a wide variety of stimuli. Using antibodies against the phosphorylated residues, we show that H3 and HMG-14 phosphorylation is mediated via different MAP kinase (MAPK) cascades, depending on the stimulus. The nucleosomal response elicited by TPA is ERK-dependent, whereas that elicited by anisomycin is p38 MAPK-dependent. In intact cells, the nucleosomal response can be selectively inhibited using the protein kinase inhibitor H89. MAPK activation and phosphorylation of transcription factors are largely unaffected by H89, whereas induction of IE genes is inhibited and its characteristics markedly altered. MSK1 is considered the most likely kinase to mediate this response because (i) it is activated by both ERK and p38 MAPKs; (ii) it is an extremely efficient kinase for HMG-14 and H3, utilizing the physiologically relevant sites; and (iii) its activity towards H3/HMG-14 is uniquely sensitive to H89 inhibition. Thus, the nucleosomal response is an invariable consequence of ERK and p38 but not JNK/SAPK activation, and MSK1 potentially provides a link to complete the circuit between cell surface and nucleosome.

Animals↗

PubMed1992

Construction of a GT polymorphism map of human 9q.

To construct a framework map of human chromosome 9 consisting of highly informative markers, we identified 36 cosmid clones from chromosome 9 that contained long GT repeat sequences. The cosmids were found to cluster on the long arm of the chromosome, particularly in the q32-34 region. Thirteen highly informative polymorphisms from 9q were identified, with median observed heterozygosity 0.75 and median calculated heterozygosity based upon allele frequencies of 0.75. These new GT repeat polymorphisms (D9S56, D9S58-67), as well as anchor GT polymorphisms for D9S15 (MCT112, 9q13), and ABL and ASS (both 9q34.1) were utilized to construct a linkage map of human 9q by the typing of the Venezuelan Reference Pedigree. Care was taken to avoid errors, including analysis of the data with CHROMLOOK and verification of all double crossover events detected within a 30 cM interval by repetition of the marker analysis. The map was generated using the MAPMAKER program. All positions in the resulting map are favored by odds of greater than 10(4):1. The map has a sex-averaged length of 90 cM (Kosambi function) with a single maximum intermarker recombination fraction of 26%. All other intermarker recombination fractions are less than 15%. As D9S15 is known to be closely linked to markers on proximal 9p, and ASS/ABL are in band 34.1, this set of GT polymorphisms spans the length of 9q and provides a useful panel for linkage analysis of disease genes to this region. The marker order was confirmed by in situ hybridization of the cosmid clones to metaphase spreads of normal human chromosomes, which indicated an excess of recombination in the telomeric region in comparison to centromeric 9q, in agreement with previous chiasmata distribution observations. Two spontaneous new mutations for these GT repeat markers were identified, giving an overall observed spontaneous mutation rate of 0.00045 per locus per gamete. Direct observation of new mutations has not been previously reported for dinucleotide polymorphisms, but the observed rate is consistent with frequencies observed for other VNTR polymorphisms.

Base Sequence↗

PubMed2004

Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels.

Image registration describes the process of manipulating a distorted version of an image such that its pixels overlay the equivalent pixels in a clean, master or reference image. The need for it has assumed particular prominence in the analysis of images of electrophoretic gels used in the analysis of protein expression levels in living cells, but also has fundamental applications in most other areas of image analysis. Much of the positional information of a data feature is carried in the phase of a complex transform, so a complex transform allows explicit specification of the phase, and hence of the position of features in the image. Registration of a test gel to a reference gel is achieved by using a multiresolution movement map derived from the phase of a complex wavelet transform (the Q-shift wavelet transform) to dictate the warping directly via movement of the nodes of a Delaunay-triangulated mesh of points. This warping map is then applied to the original untransformed image such that the absolute magnitude of the spots remains unchanged. The technique is general to any type of image. Results are presented for a simple computer simulated gel, a simple real gel registration between similar "clean" gels with local warping vectors distributed about one main direction, a hard problem between a reference gel and a "dirty" test gel with multi-directional warping vectors and many artifacts, and some typical gels of present interest in post-genomic biology. The method compares favourably with others, since it is computationally rapid, effective and entirely automatic.

Animals↗

PubMed1996

MAD Phasing Strategies Explored with a Brominated Oligonucleotide Crystal at 1.65A Resolution.

The crystal structure of a brominated oligonucleotide d(CGCG(Br)CG), chemical formula C(114)N(48)O(68)P(10)Br(2), has been analysed by multiwavelength anomalous dispersion (MAD) methods. The oligonucleotide crystallizes in space group P2(1)2(1)2(1) with a = 17.97, b = 30.98, c = 44.85 A, alpha = beta = gamma 90 degrees . Data to a resolution of 1.65 A were collected at four wavelengths about the K-absorption edge of the bromine atom (lambda(1) = 0.9323 A, a reference wavelength at the long-wavelength side of the edge; lambda(2) = 0.9192 A, at the absorption-edge inflection point; lambda(3) = 0.9185 A, at the ;white line' absorption maximum; lambda(4) = 0.8983 A, a reference wavelength at the short-wavelength side) using synchrotron radiation at Station PX9.5, SRS, Daresbury. Multiwavelength data could be collected on a single-crystal as the sample was radiation stable. Anomalous and dispersive Patterson maps were readily interpretable to give the bromine anomalous scatterer positions. Phase calculations to 1.65 A, resolution, using all four wavelengths, gave a figure of merit of 0.825 for 2454 reflections. The electron-density map was readily interpretable showing excellent connectivity for the sugar/phosphate backbone and each base was easily characterized. The two nucleotide strands paired up as expected in an antiparallel Watson-Crick-type manner. The structure was refined to 1.65 A using all the data (R-factor = 17.0% based on 3151 reflections, with a data-to-parameter ratio of 2.6). In addition to the four-wavelength analysis, a variety of other phasing strategies, and the associated quality of the resulting electron-density maps, were compared. These included use of either of the reference wavelength data sets in the two possible three-wavelength phasing combinations to assess their relative effectiveness. Moreover, the time dependence upon measuring the Bijvoet differences and its effect upon phasing was also investigated. Finally, the use of only two wavelengths, including Friedel pairs, is demonstrated (the theoretical minimum case); this is of particular interest when considering overall beam time needs and is clearly a feasible experimental strategy, as shown here.

Journal Article↗

PubMed2001

Description of the test area and reference sampling at Dornach.

The selected test area for the comparative evaluation of European methods on sampling and sample preparation of soils (CEEM Soil) at Dornach near Basel (Switzerland) is located at approximately 400 m a.S.l. on the north-west rolling footslope of the Jura mountain chain that has a temperate climate. The area is known to be airborne polluted by emissions of a non-ferrous metal recycling plant. The geology is dominated by Jurassic limestone and (decarbonated) loess loam. The land use is deciduous forest (beech, oak) in the upper part and traditional cherry orchards with permanent grassland which have mostly been converted into arable land. The detailed soil survey distinguishes four different soil mapping units in the test area of 0.61 ha. The reference sampling was performed in a 190-m-long and 20-40 m large transect area following four devices: (1) composite samples (0-10 cm and 0-20 cm), each from 25 stratified single samples of 61 squares of 10 x 10 m; (2) hypotheses and soil horizon-based composite samples at nine locations; (3) horizon-related samples from the four described soil profiles representing the mapping units; and (4) three soil cores with 5-cm interval samples taken in the major land use units. Altogether 301 reference soil samples were taken.

Environmental Monitoring↗

PubMed1997

Otolithic and tonic neck receptors control of limb blood flow in humans.

The aim of this study was to evaluate the role of otolithic receptors and neck mechanoreceptors on the control of the cardiovascular system. We measured calf (CBF) and forearm blood flow (FBF) by strain-gauge plethysmography, mean arterial pressure (MAP), and heart rate (HR) in 12 healthy subjects in two body positions (lying prone and on the left side) and three head positions (reference, flexion, and extension). When the subjects were lying prone, CBF and FBF were lower in head flexion (5.2 +/- 0.6 and 3.2 +/- 0.4 ml.min-1.100 ml-1, respectively) than in reference position (5.8 +/- 0.4 and 3.8 +/- 0.3 ml.min-1.100 ml-1; P < 0.05), with no significant difference in MAP and HR. When the subjects were lying on the side, changing the head position from reference to flexion significantly increased FBF (from 3.7 +/- 0.2 to 4.2 +/- 0.4 ml.min-1. 100 ml-1), MAP (from 97.2 +/- 3.3 to 102.4 +/- 5.8 mmHg), and HR (from 63.7 +/- 1.4 to 65.9 +/- 2.5 beats/min; P < 0.05). Because otolithic receptors and neck mechanoreceptors are involved when the subjects are lying prone, and otolithic receptors are not involved when the subjects are lying on the side, the results suggest that otolithic and neck mechanoreceptors exert significant influences over the cardiovascular system.

Adult↗

PubMed1998

Efficacy of radiofrequency catheter ablation for ventricular tachycardia in healed myocardial infarction.

Radiofrequency catheter ablation has been useful in the treatment of ventricular tachycardia (VT) in selected patients with healed myocardial infarction. Previous studies have demonstrated success rates of 60% to 96% for targeted VT morphologies; however, these studies included patients only after they have had successful mapping procedures and have received radiofrequency lesions. All patients referred for VT ablation from July 1992 to November 1996 were included in this analysis on an intention-to-treat basis. Ninety-five procedures were performed in 66 patients for 77 distinct presentations with tolerated, sustained VT. Fifty-five procedures were successful (58%) and 40 procedures failed. Reasons for procedural failure included failed radiofrequency application despite adequate VT mapping (21 procedures), no tolerated VT induced (12), and aborted procedures due to complications or technical difficulties (7). Fifty-five patients (71%) eventually had a successful VT ablation, although 10 required > 1 procedure. This analysis revealed factors that contribute to failure of VT ablation procedures in addition to inadequate mapping and lesion formation. Procedural difficulties, particularly the inability to induce tolerated VT, frequently prevent successful catheter ablation in patients who present with tolerated, sustained VT.

Aged↗

PubMed1989

A deletion map of the WAGR region on chromosome 11.

The WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) region has been assigned to chromosome 11p13 on the basis of overlapping constitutional deletions found in affected individuals. We have utilized 31 DNA probes which map to the WAGR deletion region, together with six reference loci and 13 WAGR-related deletions, to subdivide this area into 16 intervals. Specific intervals have been correlated with phenotypic features, leading to the identification of individual subregions for the aniridia and Wilms tumor loci. Delineation, by specific probes, of multiple intervals above and below the critical region and of five intervals within the overlap area provides a framework map for molecular characterization of WAGR gene loci and of deletion boundary regions.

Abnormalities, Multiple↗

PubMed1999

The polar average reference effect: a bias in estimating the head surface integral in EEG recording.

A reference-independent measure of potential is helpful for studying the multichannel EEG. The potentials integrated over the surface of the body is a constant, i.e. inactive across time, regardless of the activity and distribution of brain electric sources. Therefore, the average reference, the mean of all recording channels at each time point, may be used to approximate an inactive reference. However, this approximation is valid only with accurate spatial sampling of the scalp fields. Accurate sampling requires a sufficient electrode density and full coverage of the head's surface. If electrodes are concentrated in one region of the surface, such as just on the scalp, then the average is biased toward that region. Differences from the average will then be smaller in the center of the region, e.g. the vertex, than at the periphery. In this paper, we illustrate how this polar average reference effect (PARE) may be created by both the inadequate density and the uneven distribution of EEG electrodes. The greater the coverage of the surface of the volume conductor, the more the average reference approaches the ideal inactive reference.

Brain↗

PubMed1999

The utility of quantitative body surface isoarea mapping for predicting ventricular tachyarrhythmias.

Noninvasive techniques, such as the signal averaged ECG, have been used to assess risk of ventricular tachyarrhythmias (VT). However, these methods produce false positive and negative results. The purpose of this study was to develop body surface map algorithms which would enhance prediction of susceptibility to VT. Fifty-three patients referred for programmed electrical stimulation were enrolled in this study. All patients underwent signal averaged ECG, body surface map, programmed electrical stimulation. Group I patients had no sustained inducible VT and group II patients had either inducible sustained VT at electrophysiology study or previously documented spontaneous, sustained VT. For body surface map analysis, the difference between extrema on isoarea maps was calculated and defined as the gradient range. An abnormal body surface map was defined as a QRST gradient range < or = 109 mv.ms. The mean QRST gradient range in group II was significantly < that in group I (P < 0.05). By logistic regression analysis, the presence of coronary artery disease, a QRST gradient range < or = 109 mv.ms, an EF < 40% and a signal averaged ECG QRS duration > 114 ms predicted VT. The sensitivity, specificity, positive and negative predictive values for predicting VT susceptibility of an algorithm which combines the signal averaged ECG QRS duration and the QRST gradients were 0.93, 0.76, 0.79, and 0.91, respectively, while those for the signal averaged ECG alone were 0.52, 0.69, 0.63, and 0.59 for VT susceptibility. A combined body surface map-signal averaged ECG algorithm was more sensitive in detecting susceptibility to VT than the signal averaged ECG alone.

Adolescent↗

PubMedDate not supplied

FDG-PET findings in the Wernicke-Korsakoff syndrome.

This study reports FDG-PET findings in Wernicke-Korsakoff patients. Twelve patients suffering amnesia arising from the Korsakoff syndrome were compared with 10 control subjects without alcohol-related disability. Subjects received [18F]-fluorodeoxyglucose (FDG-PET) imaging as well as neuropsychological assessment and high-resolution MR imaging with volumetric analysis. Volumetric MRI analysis had revealed thalamic and mamillary body atrophy in the patient group as well as frontal lobe atrophy with relative sparing of medial temporal lobe structures. Differences in regional metabolism were identified using complementary region of interest (ROI) and statistical parametric mapping (SPM) approaches employing either absolute methods or a reference region approach to increase statistical power. In general, we found relative hypermetabolism in white matter and hypometabolism in subcortical grey matter in Korsakoff patients. When FDG uptake ratios were examined with occipital lobe metabolism as covariate reference region, Korsakoff patients showed widespread bilateral white matter hypermetabolism on both SPM and ROI analysis. When white matter metabolism was the reference covariate; Korsakoff patients showed relative hypometabolism in the diencephalic grey matter, consistent with their known underlying neuropathology, and medial temporal and retrosplenial hypometabolism, interpreted as secondary metabolic effects within the diencephalic-limbic memory circuits. There was also evidence of a variable degree of more general frontotemporal neocortical hypometabolism on some, but not all, analyses.

Adult↗