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Results for “spatial sequencing”

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At least 1,621 records · Page 90Linked to original sources

PubMed2001

Noncontrast MR imaging and MR arthrography of the ulnar collateral ligament of the elbow: prospective evaluation of two-dimensional pulse sequences for detection of complete tears.

OBJECTIVE: To compare MR imaging techniques with differing contrast and spatial resolution for evaluation of complete disruption of the ulnar collateral ligament (UCL) anterior bundle in a cadaveric elbow model. DESIGN: Complete UCL tears were surgically created at the typical location for clinical tears in eight of 28 fresh frozen cadaveric elbow specimens. All specimens underwent 1.5 T MR imaging in the oblique coronal plane, using an extremity coil. The sequences employed were: T1-weighted spin echo (T1 SE), proton density-weighted (PD) fast spin echo (FSE), fat-suppressed T2-weighted FSE (T2 FSE), gradient recalled echo (GRE) with a high matrix, PD FSE with a high matrix (HRPD), and fat suppressed T1-weighted SE with intra-articular gadolinium (MRAr). Two radiologists independently graded the UCL with separate and side-by-side assessments. RESULTS: Sensitivity/specificity pairs were as follows for reader A and reader B, respectively: T1 SE: 0.25/0.95, 0.50/0.95; PD FSE: 0.38/1.00, 0.25/1.00; T2 FSE: 0.50/0.95, 0.63/0.95; GRE: 0.63/0.85, 0.63/0.60; MRAr: 0.88/1.00, 1.00/0.80; HRPD: 0.50/1.00, 0.88/0.80. Kappa statistics for measuring interobserver reliability for each sequence were poor under T1 SE (-0.13) and GRE (0.19), moderate under HRPD (0.41) and T2 FSE (0.44) and good under MRAr (0.62) and PD FSE (0.78). For both readers, the rating for overall image quality was highest for HRPD, and the rating for UCL lesion conspicuity was the highest for MRAr. CONCLUSIONS: Of the MR imaging pulse sequences tested, MRAr showed the greatest ability to identify complete ligamentous injuries with good agreement between readers and had the highest subjective preference for lesion conspicuity. However, HRPD had the least interobserver variability and the highest subjective preference for overall image quality.

Aged↗

PubMed1982

Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs.

We determined the nucleotide sequence of DNA segments containing functional centromeres (CEN3 and CEN11) isolated from yeast chromosomes III and XI. The two centromere regions differ in primary nucleotide sequence, but contain structural features in common. Both centromere regions contain an extremely A + T-rich core segment 87-88 bp in length, flanked by two short sequences (14 bp and 11 bp) that are identical in both DNAs. These elements plus one additional 10 bp region of perfect homology are positioned in an almost identical spatial arrangement within the two centromere regions. Significant homologies are also observed among the sequences flanking the high A + T region and various satellite DNA sequences from higher eucaryotes, although no repeated sequences occur near the yeast centromeres. Centromere activity in vivo is maintained on relatively small DNA fragments (627 bp for CEN3 and 858 bp for CEN11), as assayed by mitotic stabilization of autonomously replicating ars plasmids in yeast.

Base Sequence↗

PubMed1981

Molecuar model of the DNA interaction site for the cyclic AMP receptor protein.

A topological model of the DNA binding site for the cyclic AMP receptor protein (CRP) is presented. A consensus sequence drawn from the known CRP binding sites has several symmetrical subregions that are spatially resolved onto different faces of the DNA helix. Consideration of available biochemical and genetic data suggest one particular choice among the possible symmetrical arrangements. In this case, the sequence of its helical form presents nearly the same pattern of exposed base pairs on two faces of the helix. These two faces are separated by a helix angle of 72 degrees; the similar sequences that are exposed in the grooves occur in opposite orientations on the two faces. We propose that this inverted symmetry arrangement provides each of the identical subunits of the CRP with a similar recognition region within the overall site. In gal and ara, the site appears to accommodate a single molecule of the CRP; in lac, the site repeats the symmetrical arrangement and should accommodate two molecules of the CRP.

Arabinose↗

PubMedDate not supplied

[The role of nontranscribable chromatin in the cellular mechanisms of morphogenesis].

The current ideas about realization of all the genetic information via stage-specific transcription and translation do not account for morphogenetic processes in space. The physical continuity of some cellular structures is only one of the mechanisms underlying the inheritance of morphofunctional properties. A suggestion was put forward that morphogenetic information is contained in nontranscribed DNA sequences. Specific interaction of these sequences with each other and with the nuclear membrane determine the spatial organization of the nucleus and program the functional properties of the endoplasmic reticulum membranes. Interaction between the nucleus and other cell structures, its localization and orientation determine the cell's polar properties and, consequently, morphogenesis of tissues and organs.

Animals↗

PubMed2004

3D imaging with a single-sided sensor: an open tomograph.

An open tomograph to image volume regions near the surface of large objects is described. The central achievement in getting such a tomograph to work is the design of a fast two-dimensional pure phase encoding imaging method to produce a cross-sectional image in the presence of highly inhomogeneous fields. The method takes advantage of the multi-echo acquisition in a Carr-Purcell-Meiboom-Gill (CPMG)-like sequence to significantly reduce the experimental time to obtain a 2D image or to spatially resolve relaxation times across the sensitive volume in a single imaging experiment. Depending on T(2) the imaging time can be reduced by a factor of up to two orders of magnitude compared to the one needed by the single-echo imaging technique. The complete echo train decay has been also used to produce T(2) contrast in the images and to spatially resolve the T(2) distribution of an inhomogeneous object, showing that variations of structural properties like the cross-link density of rubber samples can be distinguished by this method. The sequence has been implemented on a single-sided sensor equipped with an optimized magnet geometry and a suitable gradient coil system that provides two perpendicular pulsed gradient fields. The static magnetic field defines flat planes of constant frequency parallel to the surface of the scanner that can be selected by retuning the probe frequency to achieve slice selection into the object. Combining the slice selection obtained under the presence of the static gradient of the open magnet with the two perpendicular pulsed gradient fields, 3D spatial resolution is obtained.

Equipment Design↗

PubMed2004

Hypercapnic normalization of BOLD fMRI: comparison across field strengths and pulse sequences.

The blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signal response to neural stimulation is influenced by many factors that are unrelated to the stimulus. These factors are physiological, such as the resting venous cerebral blood volume (CBV(v)) and vessel size, as well as experimental, such as pulse sequence and static magnetic field strength (B(0)). Thus, it is difficult to compare task-induced fMRI signals across subjects, field strengths, and pulse sequences. This problem can be overcome by normalizing the neural activity-induced BOLD fMRI response by a global hypercapnia-induced BOLD signal. To demonstrate the effectiveness of the BOLD normalization approach, gradient-echo BOLD fMRI at 1.5, 4, and 7 T and spin-echo BOLD fMRI at 4 T were performed in human subjects. For neural stimulation, subjects performed sequential finger movements at 2 Hz, while for global stimulation, subjects breathed a 5% CO(2) gas mixture. Under all conditions, voxels containing primarily large veins and those containing primarily active tissue (i.e., capillaries and small veins) showed distinguishable behavior after hypercapnic normalization. This allowed functional activity to be more accurately localized and quantified based on changes in venous blood oxygenation alone. The normalized BOLD signal induced by the motor task was consistent across different magnetic fields and pulse sequences, and corresponded well with cerebral blood flow measurements. Our data suggest that the hypercapnic normalization approach can improve the spatial specificity and interpretation of BOLD signals, allowing comparison of BOLD signals across subjects, field strengths, and pulse sequences. A theoretical framework for this method is provided.

Adult↗

PubMed2005

Visuo-spatial working memory deficits in current and former users of MDMA ('ecstasy').

Verbal working memory and executive deficits have been observed in ecstasy users. The present study sought to establish whether these also extended to visuo-spatial working memory. Thirty-six current ecstasy users, 12 former users (abstinent for at least 6 months) and 31 individuals that had never used ecstasy were tested on a maintenance plus type visuo-spatial working memory task. The task required participants to recall a sequence of specially marked cells in a four-by-four matrix display while at the same time performing a concurrent visual judgement task. Both the current and former user groups registered impairments relative to nonusers. These remained significant following statistical controls for a range of potentially confounding variables including the use of various other drugs during the 3 months prior to testing. Users were unimpaired on a simple spatial span measure suggesting that the deficits observed reflected the executive aspects of the spatial working memory task. Also consistent with executive involvement, statistical controls for measures of verbal working memory performance (computation span) removed half of the ecstasy-related variance in spatial working memory. The possibility that the pattern of results obtained might reflect some general impairment in information processing efficiency is discussed.

Adult↗

PubMed1997

Spatially distinct domains of cell behavior in the zebrafish organizer region.

To determine the sequence of cell behaviors that is involved in the morphogenesis of the zebrafish organizer region, we have examined the dorsal marginal zone of vitally stained zebrafish embryos using time-lapse confocal microscopy. During the late-blastula stage, the zebrafish dorsal marginal zone segregates into several cellular domains, including a group of noninvoluting, highly endocytic marginal (NEM) cells. The NEM cell cluster, which lies in a superficial location of the dorsal marginal zone, is composed of both enveloping layer cells and one or two layers of underlying deep cells. The longitudinal position of this cellular domain accurately predicts the site of embryonic shield formation and occupies a homologous location to the organizer epithelium in Xenopus laevis. At the onset of gastrulation, deep cells underneath the superficial NEM cell domain undergo involution to form the nascent hypoblast of the embryonic shield. Deep cells within the NEM cell cluster, however, do not involute during early shield formation, but instead move in front of the blastoderm margin to form a loose mass of cells called forerunner cells. Forerunner cells coalesce into a wedge-shaped mass during late gastrulation and eventually become overlapped by the converging lateral lips of the germ ring. During early zebrafish tail elongation, most forerunner cells are incorporated into the epithelial lining of Kupffer's vesicle, a transient teleostean organ rudiment long thought to be an evolutionary vestige of the neurenteric canal. Owing to the location of NEM cells at the dorsal margin of blastula-stage embryos, as well as their early segregation from other deep cells, we hypothesized that NEM cells are specified by an early-acting dorsalizing signal. To test this possibility, we briefly treated early-blastula stage embryos with LiCl, an agent known to produce hyperdorsalized zebrafish embryos with varying degrees of expanded organizer tissue. In Li(+)-treated embryos, NEM cells appear either within expanded spatial domains or in ectopic locations, primarily within the marginal zone of the blastoderm. These results suggest that NEM cells represent a specific cell type that is specified by an early dorsal patterning pathway.

Animals↗

PubMed2002

High-spatial-resolution MR cisternography of the cerebellopontine angle in 90 seconds with a zero-fill interpolated fast recovery 3D fast asymmetric spin-echo sequence.

BACKGROUND AND PURPOSE: Although the 12-minute 3D fast asymmetric spin-echo (FASE) protocol for imaging the inner ear has been satisfactory, reducing imaging time to minimize patient discomfort and maximize system throughput is desirable. We therefore evaluated the performance of a zero-fill interpolated (ZIP) fast recovery 3D FASE sequence in screening for cerebellopontine (CP) angle lesions in 90 seconds. METHODS: Thirty consecutive patients known or suspected to have CP angle lesions underwent MR imaging at 1.5 T with use of bilateral quadrature phased-array coils designed for examination of the CP angle. Conventional 3D FASE images (4000/240/1 [TR/TE/NEX]) were obtained in 11 minutes 48 seconds with a field of view (FOV) of 16 cm, matrix of 512 x 512 x 40, section thickness of 0.8 mm, and echo train length of 80. Then, ZIP fast recovery 3D FASE images (2000/240/1) were obtained in 90 seconds by using the same FOV. Contrast-enhanced T1-weighted 3D spoiled gradient-echo (SPGR) images were obtained as the reference standard. Three radiologists evaluated the images independently. Conventional 3D FASE and ZIP fast recovery 3D FASE images were reviewed at separate sessions. RESULTS: On 3D SPGR images, 10 tumors were detected in 10 of the 30 patients. All lesions were depicted with both 3D FASE protocols. There were no false-positive results with either 3D FASE protocol. Both protocols showed 100% sensitivity and 100% specificity for all three reviewers. CONCLUSION: High-spatial-resolution MR cisternography with the ZIP fast recovery 3D FASE protocol in 90 seconds results in a substantial reduction (by a factor of about eight) in the time required for screening for CP angle lesions compared with the previously reported conventional 3D FASE protocol, while maintaining high sensitivity and specificity.

Adolescent↗

PubMed2001

Sensitive nonradioactive detection of mRNA in tissue sections: novel application of the whole-mount in situ hybridization protocol.

The relative insensitivity of nonradioactive mRNA detection in tissue sections compared to the sensitive nonradioactive detection of single-copy DNA sequences in chromosome spreads, or of mRNA sequences in whole-mount samples, has remained a puzzling issue. Because of the biological significance of sensitive in situ mRNA detection in conjunction with high spatial resolution, we developed a nonradioactive in situ hybridization (ISH) protocol for detection of mRNA sequences in sections. The procedure is essentially based on the whole-mount ISH procedure and is at least equally sensitive. Increase of the hybridization temperature to 70C while maintaining stringency of hybridization by adaptation of the salt concentration significantly improved the sensitivity and made the procedure more sensitive than the conventional radioactive procedure. Thicker sections, which were no improvement using conventional radioactive ISH protocols, further enhanced signal. Higher hybridization temperatures apparently permit better tissue penetration of the probe. Application of this highly reliable protocol permitted the identification and localization of the cells in the developing heart that express low-abundance mRNAs of different members of the Iroquois homeobox gene family that are supposedly involved in cardiac patterning. The radioactive ISH procedure scarcely permitted detection of these sequences, underscoring the value of this novel method.

Animals↗

PubMed1998

Use of nonbreakpoint DNA probes to detect the t(X;18) in interphase cells from synovial sarcoma: implications for detection of diagnostic tumor translocations.

Fluorescence in situ hybridization studies using non-breakpoint DNA probes were performed to detect the X;18 translocation on 4-microm sections of synovial sarcoma from paraffin blocks. This was done by using commercially available, large target unique sequence DNA probes for regions of the X chromosome short-arm and the 18 chromosome long-arm together with centromere probes for the alternate chromosomes. We determined that such probe combinations could detect the presence of the diagnostic X;18 translocation in interphase cells. Spatial association of dual color signals from the X centromere and the 18 unique sequence probe, as well as between an 18 centromere and the X unique sequence probe, was seen in a significantly higher percentage of synovial sarcoma cells (81.1% +/- 7.7%, confidence interval 95%) than in control nonsynovial soft tissue sarcomas (14.7% +/- 8.3%) and control peripheral blood lymphocytes (5.6% +/- 0.6%). The observed spatial association supports the use of this strategy to detect the X;18 translocation in synovial sarcoma and suggests that this technique could be applied in the diagnosis of other types of tumors with characteristic translocations when histopathological findings are inconclusive. This study is the first report describing the use of nonbreakpoint unique sequence probes for detecting translocations in tumors on paraffin-embedded slides.

Chromosomes, Human, Pair 18↗

PubMed2004

Methods for generating high-resolution structural models from electron microscope tomography data.

Reconstructed volumes generated by tilt-image electron-microscope tomography offer the best spatial resolution currently available for studying cell structures in situ. Analysis is often accomplished by creating surface models that delineate grayscale contrast boundaries. Here, we introduce a specialized and convenient sequence of segmentation operations for making such models that greatly improves their reliability and spatial resolution as compared to current approaches, providing a basis for making accurate measurements. To assess the reliability of the surface models, we introduce a spatial uncertainty measurement based on grayscale gradient scale length. The model generation and measurement methods are validated by applying them to synthetic data, and their utility is demonstrated by using them to characterize macromolecular architecture of active zone material at the frog's neuromuscular junction.

Computer Simulation↗

PubMed2002

Representation and processing of complex DNA spatial architecture and its annotated genomic content.

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.

DNA↗

PubMed2003

Parallel allocation of attention prior to the execution of saccade sequences.

In a series of 5 experiments, the allocation of attention prior to the execution of saccade sequences was examined by using a dual-task paradigm. In the primary task, participants were required to execute a sequence of 2 endogenous saccades. The secondary task was a forced-choice letter identification task. During the programming of the saccade sequences, letters were briefly presented at the saccade goals and at no-saccade locations. The results showed that performance was better for letters presented at any of the saccade goals than for letters presented at any of the no-saccade locations. The results support a spatial model that assumes that prior to the execution of a saccade sequence, attention is allocated in parallel to all saccade goals. ((c) 2003 APA, all rights reserved)

Adult↗

PubMedDate not supplied

On 3-D graphical representation of DNA primary sequences and their numerical characterization.

In this article we (1) outline the construction of a 3-D "graphical" representation of DNA primary sequences, illustrated on a portion of the human beta globin gene; (2) describe a particular scheme that transforms the above 3-D spatial representation of DNA into a numerical matrix representation; (3) illustrate construction of matrix invariants for DNA sequences; and (4) suggest a data reduction based on statistical analysis of matrix invariants generated for DNA. Each of the four contributions represents a novel development that we hope will facilitate comparative studies of DNA and open new directions for representation and characterization of DNA primary sequences.

Base Sequence↗

PubMed2002

Limbic hyperreactivity in bipolar II disorder.

OBJECTIVE: The authors' goal was to determine whether patients with bipolar II disorder had altered regional brain responses to novel motor sequences. METHOD: Regional cerebral blood flow was measured with positron emission tomography in 13 patients with bipolar II disorder and 14 healthy comparison subjects. Participants performed a serial reaction time task in which they were visually cued to press one of four buttons at a time. The order of button presses was determined by a complex sequence that was changed in the latter half of the study. RESULTS: In the comparison subjects a spatial attention circuit in the superior parietal lobe and supplementary motor area was activated in response to the introduction of the new sequence. Patients did not display this activation pattern; instead, a widespread limbic network was activated in response to the new sequence. CONCLUSIONS: The attentional resources of patients with bipolar II disorder are not reallocated when they are confronted with a nonemotional motor task; rather, their performance is altered through activation of limbic circuitry.

Adult↗

PubMed2002

Temporal and spatial expression of biologically active human factor VIII in the milk of transgenic mice driven by mammary-specific bovine alpha-lactalbumin regulation sequences.

Hemophilia A is one of the major inherited bleeding disorders caused by a deficiency or abnormality in coagulation factor VIII (FVIII). Hemophiliacs have been treated with whole plasma or purified FVIII concentrates. The risk of transmitting blood-borne viruses and the cost of highly purified FVIII are the major factors that restrict prophylaxis in hemophilia therapy. One of the challenges created by the biotechnology revolution is the development of methods for the economical production of highly purified proteins in large scales. Recent developments indicate that manipulating milk composition using transgenesis has focused mainly on the mammary gland as a bioreactor to produce pharmaceuticals. In the present study, a hybrid gene containing bovine alpha-lactalbumin and human FVIII cDNA was constructed for microinjection into the pronuclei of newly fertilized mouse eggs. The alphaLA-hFVIII hybrid gene was confirmed to be successfully integrated and stably germ-line transmitted in 12 (seven females/five males) lines. Western-blot analysis of milk samples obtained from eight of the transgenic founders and F1 offspring indicated that the recombinant hFVIII was secreted into the milk of the transgenic mice. The concentrations of rFVIII ranged from 7.0 to 50.2 microg/ml, over 35-200-fold higher than that in normal human plasma. Up to 13.4 U/ml of rFVIII was detected in an assay in which rFVIII restored normal clotting activity to FVIII-deficient human plasma.

Animals↗

PubMed2002

Identification and utilization of arbitrary correlations in models of recombination signal sequences.

BACKGROUND: A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes perform poorly when positions in the site do not independently affect protein binding. We developed a statistical technique for modeling the correlation structure in variable DNA sequence sites. The method places no restrictions on the number of correlated positions or on their spatial relationship within the site. No prior empirical evidence for the correlation structure is necessary. RESULTS: We applied our method to the recombination signal sequences (RSS) that direct assembly of B-cell and T-cell antigen-receptor genes via V(D)J recombination. The technique is based on model selection by cross-validation and produces models that allow computation of an information score for any signal-length sequence. We also modeled RSS using order zero and order one Markov chains. The scores from all models are highly correlated with measured recombination efficiencies, but the models arising from our technique are better than the Markov models at discriminating RSS from non-RSS. CONCLUSIONS: Our model-development procedure produces models that estimate well the recombinogenic potential of RSS and are better at RSS recognition than the order zero and order one Markov models. Our models are, therefore, valuable for studying the regulation of both physiologic and aberrant V(D)J recombination. The approach could be equally powerful for the study of promoter and enhancer elements, splice sites, and other DNA regulatory sites that are highly variable at the level of individual nucleotide positions.

Animals↗