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Results for “spatial sequencing”

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At least 145 records · Page 8Linked to original sources
PubMed1988

A pattern formation mechanism to control spatial organization in the embryo of Drosophila melanogaster.

It is known that cells are already committed to a particular segment at the cellular blastoderm stage during embryogenesis of Drosophila melanogaster. Recently, several segmentation genes have been observed to be expressed in a sequence of banded spatial patterns in the syncytial blastoderm, prior to the formation of the cellular blastoderm. It is demonstrated in this paper that a two component reaction-diffusion (RD) system with net production functions which are antisymmetric with respect to the uniform steady-state values, is capable of producing a sequence of seven spatial patterns in the syncytial blastoderm. The sequence of patterns obtained exhibit a strong preference for banded or striped patterns. The first pattern is a simple anteroposterior gradient while the second is a gradient in the dorsoventral direction. The next five patterns are a sequence of banded patterns which exhibit frequency doubling, i.e. the number of bands in each pattern tend to be double the number in the previous pattern. The predicted pattern sequence is comparable to that observed in the expression of some segmentation genes. It is suggested that a pattern formation mechanism based on such an RD system may exist in the embryo where it produces a sequence of prepatterns to regulate the expression of various segmentation genes leading ultimately to a segmented embryo. There is sufficient spatial information in the sequence of banded prepatterns for the segments to be unique.

Animals↗
PubMed1992

Perceptual and academic patterns of learning-disabled/gifted students.

This research explored ways gifted children with learning disabilities perceive and recall auditory and visual input and apply this information to reading, mathematics, and spelling. 24 learning-disabled/gifted children and a matched control group of normally achieving gifted students were tested for oral reading, word recognition and analysis, listening comprehension, and spelling. In mathematics, they were tested for numeration, mental and written computation, word problems, and numerical reasoning. To explore perception and memory skills, students were administered formal tests of visual and auditory memory as well as auditory discrimination of sounds. Their responses to reading and to mathematical computations were further considered for evidence of problems in visual discrimination, visual sequencing, and visual spatial areas. Analyses indicated that these learning-disabled/gifted students were significantly weaker than controls in their decoding skills, in spelling, and in most areas of mathematics. They were also significantly weaker in auditory discrimination and memory, and in visual discrimination, sequencing, and spatial abilities. Conclusions are that these underlying perceptual and memory deficits may be related to students' academic problems.

Achievement↗
PubMed1994

[Functional imaging of the human brain with conventional MRI].

It was shown in 1991 by Belliveau and co-workers that the activation of the human brain can be visualized in a completely noninvasive way by MRI. First publications coming from the US claimed that very high magnetic field strength or echo planar imaging, both available only at a few research sites, would be necessary to do this job. Recently, it was demonstrated that functional imaging of the human brain can be done with high spatial resolution MRI using conventional FLASH-sequences with the commercial widely available 1,5 Tesla systems. First results have been reported for visual as well as primary motor cortex activation in healthy volunteers. The key to a successful application of the conventional technique lies in the design of extremely low bandwidth, long echo-time FLASH-sequences with high spatial resolution.

Adult↗
PubMed1995

SD filtering for enhancement of a nuclear medicine image sequence.

This paper explores the use of an image sequence processing algorithm, called the simultaneous diagonalization (SD) filter, which can be effectively applied to long noisy image sequences. This filter was developed to filter a spatially invariant image sequence to form one new image in which a desired feature is enhanced and one or more undesired features (and noise) are suppressed in the filtered image. This filtering technique, applied to a long noisy image sequence, can be used to achieve significant data compression for image storage and provide surprisingly good enhanced image reconstructions. For this investigation, SD filtering is applied to a temporal image sequence, a renogram, with compression of a very noisy 180-image sequence to a 4-image set. The renogram, a nuclear medicine technique, was chosen due to its low signal-to-noise ratio over a long image sequence. Before the application of the SD filter, classical image processing techniques, median and averaging filtering, are used as a preliminary method to reduce the image sequence noise content. Compared to any of the images in the original image sequence, the reconstructed images are remarkably good. The SD filter with prefiltering, thus, can collect information distributed over a 180-image temporal sequence with low signal-to-noise ratio.

Algorithms↗
PubMed1980

Localization of SV40 genes within supercoiled loop domains.

Recent studies indicate that eukaryotic DNA is organized into supercoiled loop domains. These loops appear to be anchored at their bases to an insoluble nuclear skeleton or matrix. Most of the DNA in the loops can be released from the matrix by nuclease digestion; the residual DNA remaining with the nuclear matrix represents sequences at the base of the loops, and possibly other sequences which are intimately associated with the nuclear matrix for other reasons. Using a quantitative application of the Southern blotting technique, we have found this residual DNA from SV40 infected 3T3 cells to be enriched in SV40 sequences, indicating that they reside near matrix-DNA attachment points. An enrichment of 3-7 fold relative to total cellular DNA, was found in each of three different lines of SV40 infected 3T3 cells. Control experiments with globin genes showed no such enrichment in this residual matrix DNA. This sequence specificity suggests that the spatial organization of DNA sequences within loops may be related to the functionality of these sequences within the cell.

Animals↗
PubMed2025

Stereo-cell: Spatial enhanced-resolution single-cell sequencing with high-density DNA nanoball-patterned arrays.

Single-cell sequencing technologies have advanced our understanding of cellular heterogeneity and biological complexity. However, existing methods face limitations in throughput, capture uniformity, cell size flexibility, and technical extensibility. We present Stereo-cell, a spatial enhanced-resolution single-cell sequencing platform based on high-density DNA nanoball (DNB)-patterned arrays, which enables scalable and unbiased cell capture at a wide input range and supports high-fidelity transcriptome profiling. Stereo-cell further allows integration with imaging-based modalities and multiomics strategies, including immunofluorescence and epitope profiling. This platform is also compatible with profiling extracellular vesicles, microstructures, and large cells, whereas its spatial resolution facilitates in situ analysis of cell-cell interactions, cellular microenvironments, and subcellular transcript localization. Together, Stereo-cell provides a flexible framework for expanding single-cell research applications.

Animals↗
PubMed1986

Transcription initiation of the Saccharomyces cerevisiae iso-1-cytochrome c gene. Multiple, independent T-A-T-A sequences.

The expression of the Saccharomyces cerevisiae CYC1 gene, which encodes iso-1-cytochrome c, produces a family of messenger RNAs whose 5' ends map in the region from position +7 to -93 relative to the first nucleotide at position +1 of the protein-coding DNA sequence. The mechanism of transcription initiation of the CYC1 gene has been examined by using linker-scanning deletions and gene fusions. The various CYC1 derivatives with mutations in the 5' non-coding region were constructed, reintroduced into yeast using a multicopy plasmid, and the mRNA starts mapped by primer extension. The results indicate that four, and possibly five T-A-T-A sequences are located within the 5' non-coding region of the CYC1 gene, and that each T-A-T-A is required for a specific subset of mRNA starts. This conclusion has been confirmed by oligonucleotide mutagenesis of a chromosomal CYC1 T-A-T-A sequence. A loose spatial relationship also exists between the T-A-T-A sequences and the mRNA start sites, and this distance relationship varies from 100 to 60 base-pairs (+/- 15 base-pairs).

Base Sequence↗
PubMed1990

Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression.

Molecular probes have now provided an unprecedented wealth of detail revealing the changing spatial patterns of gene products in early Drosophila development. This is examined for dynamic properties which might provide insights into the underlying behaviour of the patterning process. What emerges is that transcripts and protein products of members of the major categories of zygotically active genes involved in segmentation pass through transient spatial patterns that are suggestive of harmonic sequences arising from spatial frequency-doubling bifurcations. That is to say, these patterns are typically periodic in space and show a doubling in the number of domains of spatial expression as development proceeds. One of these patterns reflects the primary functional role of the gene in the establishment of the spatial pattern. The different categories of segmentation gene pass through these transients at different rates, those with the longest functional wavelength progressing most slowly. Each gene in a category has its own unique phase relationship to other members, as well as particular variations on the harmonic sequence theme. The result is that the developing embryo experiences a spatial hierarchy of phase-shifted patterning influences that span the range from the whole embryo to single segments, providing progressively more spatial resolution in the patterning process. The characteristic transients and the dynamic relationships between genes of the different categories suggest that gene products expressed in longer-wavelength patterns act as bifurcation parameters on the dynamic system generating the next shorter wavelength category. Such parametric influences are known to result in frequency-doubling bifurcations in Turing reaction-diffusion systems. A general model is proposed of a hierarchically-nested set of quasi-autonomous dynamic systems involving gene activities that can generate the progressively finer spatial order that emerges during embryogenesis. This model has implications for the general stability properties of evolving epigenetic systems.

Animals↗
PubMed1995

Adapted techniques for clinical MR imaging of tendons.

To determine whether the echo time of magnetic resonance gradient-echo and spin-echo imaging sequences may be important for the occurrence of high signal strength from tendon with pathological alterations, imaging sequences with sufficient spatial resolution and very short echo times were developed for whole-body imagers with standard gradient system. The sequences were applied on the Achilles tendons of five healthy volunteers and seven patients with achillodynia. Some affected regions inside tendon, probably corresponding with tissue with subtle edema in the collagen bundles were only revealed in images recorded with very short echo times TE < 5 ms, whereas stronger affections and protons in liquids between the fiber bundles were also shown in images with longer echo times TE > 10 ms. Gradient-echo methods allow shorter echo times than spin-echo techniques for a given gradient system of the imager and given spatial resolution. So minimum echo time gradient-echo sequences should be used for sensitive imaging of tendon alterations, because no considerable signal dephasing due to susceptibility effects were found in tendon.

Achilles Tendon↗
PubMed1984

The effects of visual and spatial interference on spatial working memory.

Baddeley and Lieberman (1980) have shown that processing within spatial working memory is disrupted by a spatial secondary task, but not significantly by a visual processing secondary task. In the present study their experiment was replicated under broadly similar circumstances. The spatial and verbal primary tasks involved remembering descriptions of spatially arranged or nonsense sequences of digits, respectively. The secondary visual and spatial tasks involved either judging the level of brightness or pressing an unseen matrix of buttons in a predetermined sequence. In contrast to the finding of Baddeley and Lieberman, both the visual and spatial secondary tasks significantly impaired spatial working memory. Neither of these secondary tasks significantly interfered with concurrent verbal processing. The present findings suggest that spatial working memory draws from resources from both visual and spatial quarters.

Adult↗
PubMed2025

scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.

MOTIVATION: Emerging spatial omics technologies empower comprehensive exploration of biological systems from multi-omics perspectives in their native tissue location in 2D and 3D space. However, the limited sequencing depth, increasing spatial resolution, and growing spatial spots in spatial omics technologies present significant computational challenges in identifying biologically meaningful molecules with variable spatial distributions across various omics modalities. RESULTS: We introduce scBSP, an open-source, versatile, and user-friendly package for identifying spatially variable features in large-scale spatial omics data. scBSP demonstrates significantly enhanced computational efficiency, processing high-resolution spatial omics data within seconds, and exhibits robust cross-platform performance by consistently identifying spatially variable features with high reproducibility across various sequencing platforms. AVAILABILITY AND IMPLEMENTATION: scBSP is available for download from R CRAN at https://cran.r-project.org/web/packages/scBSP/index.html and PyPI at https://pypi.org/project/scbsp/.

Software↗
PubMed1994

Automatic detection of spatial and dynamic heterogeneity of repolarization.

Heterogeneity of ventricular repolarization is associated with the development of life-threatening ventricular arrhythmias. Temporal heterogeneity of repolarization may be manifest in an individual beat (spatial heterogeneity) or in a sequence of beats (dynamic heterogeneity). Spatial inhomogeneity of repolarization throughout the myocardium may be expressed electrocardiographically as dispersion of repolarization durations computed in simultaneously recorded leads. The beat-to-beat changes in the repolarization pattern (duration and/or amplitude) may account for a dynamic (time-dependent) dimension of heterogeneity, occasionally seen as T-wave alternans. A visual detection of heterogeneous repolarization is a time-consuming, observer-dependent, and frequently inaccurate process. Therefore, we developed computer algorithms designed to detect automatically (1) dispersion of repolarization and (2) nonvisible T-wave alternans from digitally recorded (1,000 Hz) X, Y, and Z electrocardiogram leads. This automatic approach was subsequently tested in 10 patients with idiopathic long QT syndrome and in 10 age-matched normal subjects. Long QT syndrome patients presented with significantly higher indices of heterogeneity in comparison with the control subjects; the dispersion of repolarization was 44 +/- 11 and 13 +/- 6 ms, respectively (P < .01), and T-wave alternans index was 0.40 +/- 0.37 and 0.03 +/- 0.06, respectively (P < .01). Simultaneous evaluation of spatial (dispersion of repolarization) and dynamic (T-wave alternans) aspects of repolarization provides new insight into heterogeneity of electrical recovery after myocardial depolarization. The automatic detection of repolarization dispersion and T-wave alternans in digital electrocardiogram recordings provides a practical method to evaluate heterogeneity of repolarization and may be useful for stratifying patients at risk of ventricular arrhythmias.

Arrhythmias, Cardiac↗
PubMed1973

Development of auditory neuronal responses in avian embryos.

Neurons in the cochlear nuclei of duck embryos become responsive to tonal stimuli in an orderly spatial and temporal sequence. Cells responding to lower frequencies are recorded before those responding to higher frequencies. Auditory neurons are spatially arranged according to their characteristic frequencies, indicating a point-by-point projection of the basilar membrane. Areas of the nuclei where the apical segment of the basilar membrane projects become responsive to sound before regions representing more basal segments. These progressive changes with age are accompanied by a gradual rise both in neuronal sensitivity and in frequency range of maximum sensitivity. The development of auditory neural responses is timed to prepare the embryo for the onset of prenatal mother-young communication.

Action Potentials↗
PubMed1987

Sequences required for transcriptional initiation of the Saccharomyces cerevisiae CYC7 genes.

A series of BAL 31 deletions were constructed in the upstream region of the Saccharomyces cerevisiae CYC7 gene to determine sequences required for transcriptional initiation. These deletions identified the TATA box as an alternating A-T sequence at -160 and the initiation sequences as well as the spatial relationship between them. The TATA box was necessary for wild-type levels of expression of the CYC7 gene. Decreasing the distance between the TATA sequence and the initiation site did not alter gene expression, but the site of transcription was shifted 3'-ward. In most cases, transcription initiated at a number of sites, the 5'-most of which was the first suitable site greater than 45 base pairs 3' of the TATA sequence, suggesting a spatial relationship between these sequences. Consensus sequences previously proposed for initiation sites were evaluated with respect to the start sites identified in this study as well as the start sites of other yeast genes.

Base Sequence↗
PubMed1990

Hydrogen ultrathin phase-encoded spectroscopy (HUPSPEC).

This paper describes a new clinical spectroscopy pulse program, hydrogen ultrathin phase-encoded spectroscopy. This sequence combines high spatial resolution with magnitude hydrogen spectroscopy. A linear volume is spatially frequency encoded with a conventional readout gradient and phase encoded spectrally by incrementing the timing of acquisition. The pulse sequence is implemented on a whole-body MRI scanner and supports several standard scanner options, including autoprescanning, offset of the center of field of view in the frequency-encoding direction, and oblique imaging. Some preliminary experimental experience is reported, demonstrating the possibility of observing the spectral linewidths of fat and water in marrow, and of observing the spectral linewidths of fat and water in marrow, and of observing multiline spectra. Combination of the technique with water suppression methods in a sequence called WASHUP is also discussed.

Adult↗
PubMed1988

[Digitalized angiography in coronary disease].

In cardiology, digital subtraction angiography after intravenous injection of contrast medium allows only the visualization of relative large structures as the ventricles and the great vessels. Subselective intra-arterial injections are attractive, but do not provide an appreciable reduction of the injected amount of contrast medium. A reduction is possible with selective injections, but good subtraction is only possible for non-moving arteries or for arteries with truly periodic movement (ECG gated subtraction). With the improvement of spatial and temporal resolution, digital angiography (without image subtraction) could replace conventional angiography, provided that the main problem of prohibitive costs associated to the stockage of image sequences with high spatial (1024 x 1024) and temporal (25 images/s) resolution is solved. At the present, however, the cinefilm 35 mm is still unbeaten in density of information, handling and costs. In interventional cardiology, the visualization of small coronary branches and of fine, fast moving guide-wires is improved by the digitalization of the images at the source, pulsed fluoroscopy, progressive scanning of the TV camera with temporary stockage of image sequences and the selective reinforcement of the image contrast in real time. Digital angiography is also more attractive than the cinefilm in view of a better exploitation of the information contained in angiographic sequences by sophisticated, computer assisted methods. For instance, parametric imaging for analysis of the contraction and relaxation of the left ventricle, or for the visualization of the progression of contrast medium to investigate the coronary circulation, condensing in one single image the information looked for, are fields where digital angiography has given new impulses to cardiologic research.

Coronary Angiography↗
PubMed1992

Molecular analysis of cis-regulatory sequences at the alpha-amylase locus in Drosophila melanogaster.

The Amylase locus in Drosophila melanogaster contains duplicate, divergently transcribed structural genes for alpha-amylase, AmyA and AmyB. A sensitive and reliable transient expression assay was developed for testing amylase activities produced by exogenous Amy genes in somatically transformed larvae of an amylase-null strain of flies. Alleles tested, AmyA and AmyB, came from recombinant clone lambda Dm65, which contains genomic DNA from a Canton-S strain. The transient assay was used in a deletion analysis aimed at locating cis-regulatory sequences within the 5' region of AmyB. Results suggest that upstream regulatory sequences for correct spatial expression of AmyA and AmyB in third-instar larvae are located within 446 and 430 bp of their respective starts for transcription. A sequence required for high levels of AmyB expression was located within its 5' upstream region between the base pairs at -332 and -219. AmyA does not appear to have a comparable regulatory element in its 5'-flanking sequence. Barely detectable expression of AmyB was observed when it was flanked by only 92 bp of upstream sequence. A model is proposed for incomplete coordinate control of the duplicate Amy genes.

Amino Acid Sequence↗