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Results for “spatial sequencing”

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At least 1,009 records · Page 56Linked to original sources

PubMed2000

Matching tire tracks on the head using forensic photogrammetry.

In the field of the documentation of forensics-relevant injuries, from the reconstructive point of view, the forensic, CAD-supported photogrammetry plays an important role; particularly so when a detailed 3-D reconstruction is vital. This is demonstrated with a soft-tissue injury to the face caused by being run over by a car tire. Since the objects (injury and surface of the tire) to be investigated will be evaluated in virtual space, they must be series photographed. These photo sequences are then evaluated with the RolleiMetric multi-image evaluation system. This system measures and calculates the spatial location of points shown in the photo sequences, and creates 3-D data models of the objects. In a 3-D CAD program, the model of the injury is then compared against the model of the possible injury-causing instrument. The validation of the forensic, CAD-supported photogrammetry, as shown by the perfect 3-D match between the tire tread and the facial injury, demonstrates how greatly this 3-D method surpasses the classic 2-D overlay method (one-to-one photography).

Accidents, Traffic↗

PubMed2000

Anatomic MR images obtained with silent sequences.

The authors evaluated silent magnetic resonance (MR) imaging sequences for their suitability in providing high-spatial-resolution anatomic images that are of sufficient quality to be useful in a clinical setting. The authors compared the images obtained with a silent rapid acquisition with relaxation enhancement (RARE) sequence to its standard counterpart with respect to signal-to-noise ratio, distribution of gray level, and spatial resolution. No real differences were observed between the standard and the silent RARE MR images. Anatomic images were also acquired with a silent spin-echo sequence. Acoustic noise levels with the silent sequences were at least 22 dB (A-weighted scale) lower than those with standard sequences, without loss of image quality.

Adult↗

PubMed2005

Does new magnetic resonance imaging technology provide better geometrical accuracy during stereotactic imaging?

OBJECT: The authors sought to compare the accuracy of stereotactic target imaging using the Siemens 1T EXPERT and 1.5T SYMPHONY magnetic resonance (MR) units. METHODS: A water-filled cylindrical Perspex phantom with axial and coronal inserts containing grids of glass rods was fixed in the Leksell stereotactic frame and subjected to MR imaging in Siemens 1T EXPERT and Siemens 1.5T SYMPHONY units. Identical sequences were used for each unit. The images were transferred to the GammaPlan treatment planning system. Deviations between stereotactic coordinates based on MR images and estimated real geometrical positions given by the construction of the phantom insert were evaluated for each study. The deviations were further investigated as a function of the MR unit used, MR sequence, the image orientation, and the spatial position of measured points in the investigated volume. CONCLUSIONS: Larger distortions were observed when using the SYMPHONY 1.5T unit than those with the EXPERT 1T unit. Typical average distortion in EXPERT 1T was not more than 0.6 mm and 0.9 mm for axial and coronal images, respectively. Typical mean distortion for SYMPHONY 1.5T was not more than 1 mm and 1.3 mm for axial and coronal images, respectively. The image sequence affected the distortions in both units. Coronal T2-weighted spin-echo images performed in subthalamic imaging produced the largest distortions of 2.6 mm and 3 mm in the EXPERT 1T and SYMPHONY 1.5T, respectively. Larger distortions were observed in coronal slices than in axial slices in both units, and this effect was more pronounced in SYMPHONY 1.5T. Noncentrally located slice positions in the investigated volume of the phantom were associated with larger distortions.

Equipment Design↗

PubMed1999

Instruction differentiates the processing of temporal and spatial sequential patterns: evidence from slow wave activity in humans.

Event-related potentials (ERPs) were recorded while subjects monitored a visually presented sequence of stimuli that provided information about both a temporal pattern (rhythm) and a spatial pattern, and responded to rhythmical or spatial deviants. A third task, which required the monitoring of the same sequence for screen flickers served as a perceptual baseline condition and controlled for response preparation effects. The monitoring of temporal and spatial sequential information elicited negative slow potentials (SPs) over distinct topographical areas. Thus, attention to the temporal and to the spatial domain of one and the same stimulus sequence are reflected by distinct ERP components, providing evidence for distinct cortical sources.

Adult↗

PubMed1996

Molecular organization and alternative splicing in zipper, the gene that encodes the Drosophila non-muscle myosin II heavy chain.

Genomic sequence of the entire zipper gene, that encodes non-muscle myosin II heavy chain (MHC) in Drosophila melanogaster, reveals a new, differentially spliced exon in this essential locus and identifies a molecular lesion that is responsible for a severe embryonic lethal zipper allele. There are two alternative splices in the head domain. The first is present in the 5' untranslated sequence which, when employed, produces an N-terminal extension of 45 amino acids (aa). This splicoform produces a protein that is stable in flies but less prevalent than the isoform that lacks the extension. The second alternative exon (40 aa) is close to the nucleotide binding pocket. The position, size and sequence of this exon is conserved in D. simulans and putative alternative exons of different size (7 to 16 aa) but identical position have been reported for other myosins throughout phylogeny. The functional significance of neither alternative splice is clear. Sequence analysis of genomic DNA identifies the lesion responsible for zipIIF107, one of the original severe embryonic lethal zipper alleles. Our primary structural data confirm and correct our previous sequence of the cDNA, establish the spatial relationship between zipper and unzipped (the gene originally thought to have been disrupted in zipper mutations), and provide a high resolution template for the precise mapping of mutations.

Alleles↗

PubMed2002

Spatial patterns of soil moisture as affected by shrubs, in different climatic conditions.

Abstract. At three study sites, representing Mediterranean, semi-arid and mildly-arid climatic conditions, the effect of shrubs on the spatial patterns of soil moisture was studied. At each site soil moisture was measured, on hillslopes, at the vicinity of 8 shrubs. For each shrub the measurements have been taken at 3 microenvironments, i.e. under the shrub (US), at the margins of shrub (MS) and between shrubs (BS). At the microenvironments US and MS the measurements were taken at 3 directions: upslope, downslope and sideslope of the shrubs. At all sampling points soil samples were taken from 3 depths: 0-2, 2-5 and 5-10 cm. In addition, rock fragments cover percentage near the shrubs was determined. A soil moisture pattern was found, around each shrub, which is composed of a radial gradient and a downslope gradient. The radial gradient is expressed by soil moisture decreasing from the US microenvironment, in all directions, through the MS towards the BS microenvironment. The US microenvironment has a 'spatial advantage' of higher soil moisture content due to (1) relatively higher infiltration rate, (2) capture overland flow from the BS area upslope that shrub and (3) low evaporation rate because of the shading effect. The downslope gradient is expressed by decreasing soil moisture from the upslope direction of each shrub (MS and US microenvironments) towards the downslope direction of that shrub (MS and US microenvironments, respectively). This gradient is controlled by the relatively high content of rock fragments near the shrubs at their upslope direction. Such rock fragments spatial distribution is attributed to (1) the detachment and transport of rock fragments by sheep and goats trampling and (2) the effect of shrub on the continuity of overland flow and sediment transport. The effect of rock fragments is similar to that of shrubs regarding increasing infiltration and decreasing evaporation rate. The relatively high soil moisture at the upslope direction of each shrub enhances annuals growth producing a positive feedback loop: soil moisture--annuals growth--trampling. This sequence maintains the typical rock fragments spatial organization and contributes to the sustainability of the grazing system. At all the study sites at the US microenvironment there is a trend of decreasing soil moisture with increasing soil depth. At microenvironments MS and BS soil moisture increases with soil depth. The results are of great relevance for rehabilitation strategies as they suggest that in order to combat desertification in degraded semi-arid and mildly-arid areas, where the main land use is grazing, both shrubs and rock fragment should be kept at their present spatial distribution.

Agriculture↗

PubMed2001

Nutrient-induced spatial patterning of human duodenal motor function.

The spatiotemporal patterning of duodenal motor function has been evaluated comprehensively for the first time in humans, with a novel 21-lumen manometric assembly. In nine young, healthy volunteers (6 male, 3 female), duodenal motility was recorded during fasting and three 45-min intraduodenal (ID) nutrient infusion periods (Intralipid at 0.25, 0.5, and 1.5 kcal/min). Pressures were recorded along the length of the duodenum with an array of 18 sideholes at 1.5-cm intervals. Pressure patterns were compared for the final 20 min of each of the four periods. Compared with fasting, ID lipid was associated with regional variation in pressure wave (PW) sequences, with fewer proximally and more distally; this was not observed during fasting (P < 0.001). During fasting and all rates of lipid infusion, most (87-90%) PW sequences were short (1.5-4.5 cm), with a small number (2-4%) of 10.5 cm or longer. At all times, antegrade PW sequences occurred more frequently than retrograde sequences over all distances examined (3, 4.5, and >6 cm), and the proportion of antegrade sequences increased with greater PW sequence length (P = 0.0001). Increasing ID lipid rates appeared to produce dose-related suppression of PW sequences (P < 0.001). The frequency and spatial patterning of human duodenal motor function show substantial variability in response to different nutrient delivery rates. These complex patterns are likely to be involved in duodenal modulation of flow and gastric emptying rate.

Adult↗

PubMed2006

Fourier decompositions and pulse sequence design algorithms for nuclear magnetic resonance in inhomogeneous fields.

In this paper, we introduce algorithms based on Fourier synthesis for designing phase compensating rf pulse sequences for high-resolution nuclear magnetic resonance (NMR) spectroscopy in an inhomogeneous B0 field. We show that using radio frequency pulses and time varying linear gradients in three dimensions, it is possible to impart the transverse magnetization of spins phase, which is a desired function of the spatial (x,y,z) location. Such a sequence can be used to precompensate the phase that will be acquired by spins at different spatial locations due to inhomogeneous magnetic fields. With this precompensation, the chemical shift information of the spins can be reliably extracted and high resolution NMR spectrum can be obtained.

Journal Article↗

PubMed1996

Transposition of DNase hypersensitive chromatin to the nuclear periphery coincides temporally with nerve growth factor-induced up-regulation of gene expression in PC12 cells.

To test the hypothesis that the nonrandom organization of the contents of interphase nuclei represents a compartmentalization of function, we examined the relative, spatial relationship of small nuclear ribonucleoproteins (snRNPs) and of DNase I hypersensitive chromatin (DHC) in rat pheochromocytoma cells. In controls, DHC and snRNPs colocalized as pan-nuclear speckles. During nerve growth factor-induced differentiation, both snRNPs and DHC migrated to the nuclear periphery with the migration of DHC preceding that of snRNPs, resulting in their transient separation. The formation of DHC shells temporally coincided with an up-regulation of neurofilament light chain mRNA. This indicates that the expression of this sequence may be associated with its spatial transposition to the nuclear periphery.

Animals↗

PubMed2000

Epitope mapping of rat cytochrome P450 2B1 using glutathione S-transferase-2B1 fusion constructs.

We have previously produced 12 monoclonal antibodies (MAbs) against rat cytochrome P450(CYP)2B1, and 8 of these inhibit CYP2B1 catalytic activity to varying extents. Using competitive binding studies we showed that this collection of 12 MAbs recognize at least 6 spatially distinct epitopes. The complete coding sequence of CYP2B1 DNA in plasmid pSR-P450 was inserted into a glutathione S-transferase (GST) expression vector pGEX-1lambdaT so that it was in frame with the GST gene. Expression of GST-CYP2B1 was detected with most of the MAbs in Western blots except those which were conformation-specific. Fourteen different constructs were then made using PCR with oligonucleotide primers having EcoRI sites at their ends and were introduced into the GST expression vector at the EcoRI site. Each fusion construct was expressed in Escherichia coli, subjected to SDS-PAGE, blotted, and probed individually with each MAb. MAbs, which inhibited catalytic activity and were mutually competitive in binding to CYP2B1 (viz. BEA33, BE44, BE45, and BE28), recognized several fusion constructs and by deduction recognized amino acids 250-261 in CYP2B1. Other antibodies inhibiting catalytic activity recognized amino acids 262-272 (BEF29) and 306-491 (BE46, B50, and BE49) on CYP2B1. Non-inhibitory MAbs BE26 and BE32 were mapped to region 380-398 in CYP2B1. It was interesting to note that MAbs BEA33 and BE26, which also recognize spatially distinct epitopes on human CYP2E1 but not rat CYP2E1, had corresponding regions of high homology in human CYP2E1 but not rat CYP2E1. Identifying the epitopes recognized by this collection of MAbs will add to our understanding the sequences that may be important for producing inhibitory and specific antibodies to closely related antigens.

Amino Acid Sequence↗

PubMed2007

Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry.

A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain.

Amino Acid Sequence↗

PubMed1995

Modeling of the spatial structure of eukaryotic ornithine decarboxylases.

We used sequence and structural comparisons to determine the fold for eukaryotic ornithine decarboxylase, which we found is related to alanine racemase. These enzymes have no detectable sequence identity with any protein of known structure, including three pyridoxal phosphate-utilizing enzymes. Our studies suggest that the N-terminal domain of ornithine decarboxylase folds into a beta/alpha-barrel. Through the analysis of known barrel structures we developed a topographic model of the pyridoxal phosphate-binding domain of ornithine decarboxylase, which predicts that the Schiff base lysine and a conserved glycine-rich sequence both map to the C-termini of the beta-strands. Other residues in this domain that are likely to have essential roles in catalysis, substrate, and cofactor binding were also identified, suggesting that this model will be a suitable guide to mutagenic analysis of the enzyme mechanism.

Amino Acid Sequence↗

PubMed1982

Hemispheric specialization for the processing of tactual stimuli in congenitally deaf and hearing children.

A group of congenitally deaf and a group of normal hearing children were given two dichhaptically presented tests of hemispheric specialization. Left hemisphere specialization for language was assessed by a letter sequences task and right hemisphere specialization for spatial stimuli was measured by the nonsense shapes test of Witelson (1974). The results showed a significant right tactual field superiority for the processing of tactually presented letter sequences. There were no significant differences between the tactual fields for the processing of tactually presented nonsense shapes. The pattern of lateralization demonstrated on the letter sequences task was consistent across both groups. However, groups differed significantly on the overall performance of the verbal task, with deaf subjects demonstrating lower accuracy scores compared to hearing subjects. Age and I.Q. factors produced significant differences between sub-groups on the nonsense shapes task.

Adolescent↗

PubMed1995

Comparative protein modeling by satisfaction of spatial restraints.

Approximately one third of known protein sequences are related to at least one known protein structure. As a result, an order of magnitude more sequences can be modeled by comparative modeling than there are experimentally determined protein structures. A large fraction of these models has an accuracy approaching that of a low resolution X-ray structure or a medium resolution nuclear magnetic resonance structure. The number of applications where homology modeling has been proven useful is growing rapidly.

Amino Acid Sequence↗

PubMed1985

[Study of the spatial structure of a cyclic analog of bradykinin in solution by two-dimensional NMR spectroscopy].

H NMR resonances of [cyclo (9----18) Lys1, Gly6]bradykinin (CBK) in (CD3)2SO and H2O solution have been assigned by combined analysis of two-dimensional COSY and NOESY spectra. The presence of two slowly interchangeable conformers of CBK in (CD3)2SO is established, the minor conformer not exceeding 15% in the population. The minor conformer is absent from the aqueous solution, chemical shifts of the CBK and bradykinin NH and C alpha H protons differ insignificantly. The major CBK conformer contains at least two X-Pro trans-peptide groups and three amide protons NH Phe5, NH Arg9 and N zeta H Lys1 protected from solvent. A system of cross-peaks from the NOESY spectra of CBK in (CD3)2SO has been analysed and the maximum distance between backbone protons and neighbouring amino acid residues evaluated. The experimental data agree well with the assumed type II beta-bend in the sequence Pro2-Pro3-Gly4-Phe5. Spatial structure models for the backbone fragment 6-9 of CBK containing two intramolecular hydrogen bonds that involve the NH Arg9 and N zeta H Lys1 protons and the carbonyl groups of Phe5 and Gly4 are proposed.

Amino Acid Sequence↗

PubMedDate not supplied

[Structure of leghemoglobin].

The structure of the high spin complex of lupin leghemoglobin with acetate is refined at 2.0 A resolution using Diamond and Jack-Levitt technique (R=19%). The 0.05 A displacement of the iron atom from porphyrin plane to the distal side and the weakening of iron-nitrogen bond to the proximal histidine (2.37 A) give an explanation of the high affinity of the leghemoglobin for molecular oxygen. The ruffling of the porphyrin core may also favour it. Binding of nicotinate is accompanied by small conformational movements. Swinging out of the distal histidine from the heme pocket is the most prominent feature of this complex. The known amino acid sequences of leghemoglobin are analysed in view of the spatial structure of lupin hemoglobin.

Amino Acid Sequence↗

PubMedDate not supplied

Temporospatial organization of membrane-synaptic modifications and topograms of slow oscillations in cortical potentials during learning.

This report concerns the important question of the specificity of the organization of the different stages of formation of a conditioned reflex, considered at the level of membrane-synaptic modifications, which are compared with changes in the spatial organization of slow cortical potentials. A defined sequence of involvement of cellular mechanisms is demonstrated during learning, which may be responsible for various features of the spatial organization of slow cortical potentials. Changes in cellular excitability in cortical neurons are probably connected with oscillations in the overall level of instantaneous topograms and, thus, with the general level of spatial synchronization; the involvement of excitatory and inhibitory synaptic connections (with efficiencies corresponding to different stages in the reflex) may determine the formation of the relief seen in topograms. Parameters at both levels depend on the effects of the hypothalamus on the cortex.

Animals↗

PubMed2003

Evolutionary relationship between Old World West Nile virus strains. Evidence for viral gene flow between Africa, the Middle East, and Europe.

Little is known about the genetic relationships between European and other Old-World strains of West Nile virus (WNV) and persistence of WNV North of Mediterranean. We characterized the complete genomes of three WNV strains from France (horse-2000), Tunisia (human-1997) and Kenya (mosquito-1998), and the envelope, NS3 and NS5 genes of the Koutango virus. Phylogenetic analyses including all available full-length sequences showed that: (1) Koutango virus is a distant variant of WNV; (2) the three characterized strains belong to lineage 1, clade 1a; (3) the Tunisian strain roots the lineage of viruses introduced in North America. We established that currently available partial envelope sequences do not generate reliable phylogenies. Accordingly, establishing a large WNV sequence database is pivotal for the understanding of spatial and temporal epidemiology of this virus. For rapid completion of that purpose, colinearized E-NS3-NS5 gene sequences were shown to constitute a valuable surrogate for complete sequences.

Africa↗