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Results for “spatial sequencing”

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At least 1,063 records · Page 59Linked to original sources

PubMed1989

Coordinate action of a proximal homeoprotein binding site and a distal sequence confers the Ultrabithorax expression pattern in the visceral mesoderm.

Spatially regulated expression of the homeotic gene Ultrabithorax (Ubx) in the visceral mesoderm can be mimicked in transformed Drosophila embryos by expression of a Ubx--beta-galactosidase fusion gene. Here we show that a proximal homeoprotien binding sequence downstream of the Ubx transcription start site, the B element, is required for this pattern. A distal upstream Ubx sequence, but not the B element, is sufficient to confer the pattern if linked to an hsp70 TATA box in a heterologous construct. The pattern in this case requires Ubx function, like endogenous Ubx expression in the visceral mesoderm, suggesting that the distal upstream sequence contains an important target sequence for autoregulation. We propose that the B element, in the context of the Ubx promoter, functions to mediate enhancer function of the distal sequence. Thus, the visceral mesoderm pattern requires coordinate action of a proximal and a distal regulatory element.

Animals↗

PubMed2005

Velocity imaging by ex situ NMR.

A pulsed field gradient stimulated spin-echo NMR sequence is combined with imaging methods to spatially resolve velocity distributions and to measure 2D velocity maps ex situ. The implementation of these techniques in open sensors provides a powerful non-invasive tool to measure molecular displacement in a large number of applications inaccessible to conventional closed magnets. The method is implemented on an open tomograph that provides 3D spatial localization by combining slice selection in the presence of a uniform static magnetic field gradient along the depth direction with pulsed field gradients along the two lateral directions. Different pipe geometries are used to demonstrate that the sequence performs well even in the extremely inhomogeneous B0 and B1 fields of these sensors.

Journal Article↗

PubMed1993

Suspected pulmonary embolism: prospective evaluation with pulmonary MR angiography.

PURPOSE: To prospectively evaluate three magnetic resonance (MR) imaging techniques for detection of pulmonary embolism. MATERIALS AND METHODS: Eighteen patients in whom the presence of acute or chronic pulmonary emboli was suspected underwent examination with the following pulse sequences: cardiac-gated spin echo, cine spatial modulation of magnetization, and two-dimensional time-of-flight pulmonary breath-hold (PBH) MR angiography. Three radiologists independently and blindly reviewed each case and graded a total of 518 arterial segments for each pulse sequence with a continuous scale of 0%-100% for likelihood of pulmonary embolism. RESULTS: The overall sensitivity of PBH MR angiography for detection of acute pulmonary emboli was 0.85; for chronic emboli, which were smaller in anteroposterior (AP) diameter, the overall sensitivity was 0.42. Emboli larger than 1 cm in AP diameter were typically identified with > 75% confidence with all pulse sequences. CONCLUSION: Acute pulmonary emboli greater than 1 cm in AP diameter were as accurately identified on PBH MR angiograms obtained in 15 seconds as they were on MR images obtained with longer pulse sequences not dependent on breath holding.

Acute Disease↗

PubMed2006

Cerebral activation related to implicit sequence learning in a Double Serial Reaction Time task.

Using functional magnetic resonance imaging (fMRI), we examined the distribution of cerebral activations related to implicitly learning a series of fixed stimulus-response combinations. In a novel - bimanual - variant of the Serial Reaction Time task (SRT), simultaneous finger movements of the two hands were made in response to pairs of visual stimuli that were presented in a fixed order (Double SRT). Paired stimulus presentation prevented explicit sequence knowledge occurring during task practice, which implied that a dual task paradigm could be avoided. Extensive prescanning training on randomly ordered stimulus pairs allowed us to focus on the acquisition of implicit sequence knowledge. Activation specifically related to the acquisition of fixed sequence knowledge was highly significant in the right ventrolateral prefrontal cortex. The medial prefrontal and right ventral premotor cortex were more indirectly related with such procedural learning. We conclude that this set of activations reflects a stage of implicit sequence learning constituted by components of (i) spatial working memory (right ventral prefrontal cortex), (ii) response monitoring and selection (medial prefrontal cortex), and (iii) facilitated linkage of visuospatial cues to compatible responses (right ventral premotor). Comparing the random-order stimulus-response actions with fixed sequences showed activations in dorsal premotor and posterior parietal cortices, consistent with a dorsal pathway dominance in real-time visuomotor control. The relative long time during which performance improves in the DoSRT provides an opportunity for future study of various stages in both general skill and fixed sequence learning.

Adult↗

PubMed1999

Combined reduced 4D 13C exchange and 1H spin diffusion experiment for determining the length scale of dynamic heterogeneities.

A multidimensional static solid-state NMR experiment is described that combines 13C exchange sequences with 1H spin diffusion. It realizes a spatial correlation of different reorientation rates. By means of this experiment the length scale of dynamic heterogeneities can be measured directly. The pulse sequence and phase cycle as well as the experimental setup procedure and data analysis are described in detail. It complements the previous letter on this subject where a brief report of the main results were presented (U. Tracht et al., 1998, Phys. Rev. Lett. 81, 2727). Application of this experiment to an amorphous polymer in the supercooled state yields a length scale of immobile regions of about 3 nm.

Magnetic Resonance Spectroscopy↗

PubMed2005

The reproducibility of left ventricular volume and mass measurements: a comparison between dual-inversion-recovery black-blood sequence and SSFP.

The aim of this study was to compare a dual-inversion-recovery black-blood (BB) magnetic resonance imaging (MRI) sequence with steady-state free precession (SSFP) for the assessment of left ventricular parameters. The improved endocardial border definition seen with SSFP was not observed at the epicardial border. Improvements in segmentation at the left ventricular epicardial border have been observed with this black-blood sequence. Left ventricular (LV) mass and LV end-diastolic volume (EDV) measurements as well as inter-observer and intra-observer variability were compared between images acquired with a dual inversion BB and SSFP sequence. The mean+/-1 standard deviation (SD) for LV EDV was 178.3+/-52.7 ml measured with SSFP and 158.8+/-62.2 ml with BB. This difference was not statistically significant (p=0.22). For SSFP, the mean value of LV mass was 124.0+/-27.0 g and 147.5+/-37.4 g for BB, a statistically significant difference (p<0.0001). The dual-inversion-recovery BB imaging showed improved reproducibility for LV mass measurements compared with SSFP and improved spatial resolution. For studies requiring LV mass measurements, the dual-inversion-recovery BB sequence offers improved spatial resolution and improved reproducibility to SSFP.

Adult↗

PubMed1986

Pathways of regenerated retinotectal axons in goldfish. I. Optic nerve, tract and tectal fascicle layer.

This study investigates the order of regenerating retinal axons in the goldfish. The spatiotemporal pattern of axon regrowth was assessed by applying horseradish peroxidase (HRP) to regenerating axons in the optic tract at various times after optic nerve section and by analysing the distribution of retrogradely labelled ganglion cells in retina. At all regeneration stages labelled ganglion cells were widely distributed over the retina. There was no hint that axons from central (older) ganglion cells might regrow earlier, and peripheral (younger) ganglion cells later, as occurs in normal development. The absence of an age-related ordering in the regenerated optic nerve was demonstrated by labelling a few axon bundles intraorbitally with HRP (Easter, Rusoff & Kish, 1981) caudal to the previous cut. The retrogradely labelled cells in retina were randomly distributed in regenerates and not clustered in annuli as in normals. Tracing regenerating axons which were stained anterogradely from intraretinal HRP applications or retrogradely from single labelled tectal fascicles illustrated the fact that the regenerating axons coursed in abnormal routes in the optic nerve and tract. On the surface of the tectum regenerated fibres re-established a fascicle fan. The retinal origin of tectal fascicles was assessed by labelling individual peripheral, intermediate and rostral fascicles with HRP. The retrogradely labelled ganglion cells in the retina were often more widely distributed than in normals, but were mostly found in peripheral, intermediate and central retina, respectively. The order of fibre departure from each tectal fascicle was revealed by placing HRP either on the fascicle's proximal or on its distal half. With proximal labelling sites labelled ganglion cells were found in the temporal and nasal retina, and with distal labelling sites labelled ganglion cells were confined to nasal retina only. Further, the axonal trajectories of anterogradely labelled dorsotemporal retinal ganglion cells were compared to those of dorsonasal retinal ganglion cells in tectal whole mounts. Dorsotemporal axons were confined to the rostral tectal half, whereas dorsonasal axons followed fascicular routes into the fascicle's distal end and reached into caudal tectum. This suggests that the fibres exited along their fascicle's course in a temporonasal sequence. Thus in the tectum, fibres in fascicles restore a gross spatial and age-related order and tend to follow their normal temporonasal sequence of exit.

Animals↗

PubMed2026

Optics-free spatial genomics for mapping mammalian brain aging by IRISeq.

Spatial transcriptomics has emerged as a transformative approach for in situ mapping of cellular heterogeneity and interactions, yet existing methods often compromise throughput, cost and tissue coverage. Here we introduce Imaging Reconstruction using Indexed Sequencing (IRISeq): an optics-free, cost-effective platform that leverages spatial interaction mapping by indexed sequencing to profile tissues at adjustable sizes and resolutions (5-50 µm). We applied IRISeq to map gene expression across more than 70 coronal sections from both adult and aged mouse brains, including wild-type and two lymphocyte-deficient models (Rag1 and Prkdc mutants) and generated more than 460,000 spatial transcriptome profiles. Our integrated analysis with 783,264 single-cell transcriptomes revealed region-specific aging signatures that are lymphocyte dependent, notably a downregulation of interferon signaling and inflammation in ventricular regions upon lymphocyte depletion, alongside mutant-specific upregulation of senescence pathways. Furthermore, lymphocyte deficiency was linked to preserved abundance of ependymal cells that line the brain's ventricles and to distinct microglial state dynamics, highlighting a key role for lymphocytes in driving inflammatory processes during brain aging. Overall, IRISeq provides a high-throughput and cost-effective solution for spatially resolved transcriptomic profiling, opening new avenues for elucidating region-specific cellular mechanisms underlying aging and identifying potential therapeutic targets to preserve brain homeostasis.

Animals↗

PubMed2004

A population survey of members of the phylum Bacteroidetes isolated from salt marsh sediments along the east coast of the United States.

The population diversity of cultured isolates of the phylum Bacteroidetes was investigated from salt-marsh sediments. A total of 44 isolates that belonged to this phylum were isolated either from high-dilution plates or from end-dilution most-probable-number (MPN) tubes. The majority of the isolates came from Virginia, with others isolated from salt marshes in Delaware and North Carolina. All the isolates were aerobic Gram-negative, catalase positive small rods that formed uniform colonies; most had either yellow or orange pigmentation. Riboprinting of 40 isolates revealed they were genotypically diverse, consisting of 33 different riboprint patterns; there were four riboprint groups with two or more members. The isolates could be divided into 23 different fatty acid methyl ester (FAME) profiles at the species level with 14 of the profiles being unique to single isolates. One group of 10 isolates was closely related, suggesting this group may be well adapted for life in salt marshes. Thirteen of the isolates were selected for sequencing of the small-subunit ribosomal RNA gene representing a diverse group of isolates that fell within the classes Sphingobacteria and Flavobacteria. Only one of the isolates was >97% similar at the 16S rDNA to a described species of Cytophaga marinoflava; the other isolates were 94 to 96.5% related to undescribed isolates mostly within the class Flavobacteria. There was good concordance between the FAME dendrogram and a phylogenetic tree based on comparison of 16S sequences. There were no obvious temporal or spatial distribution patterns to the isolates, suggesting that this group of bacteria is inherently diverse.

Bacteroidetes↗

PubMed1998

Large-scale screening for developmental genes in embryonic stem cells and embryoid bodies using retroviral entrapment vectors.

Mammalian development is orchestrated by a variety of cellular proteins with expression that is regulated precisely. Although some of the genes encoding these factors have been identified, largely by homology to those of simpler organisms, the majority of them presumably remain unknown. We report here on the results of a large-scale genetic screen that can potentially lead to the identification of many of these unidentified genes in mice. The method we developed takes advantage of the fact that many of the factors that regulate early development are expressed at highly specific stages of early embryogenesis. We therefore established a method for tagging candidate developmental genes by virtue of their expression in a stage-specific manner during formation of embryoid bodies without a bias for their expression in undifferentiated embryonic stem (ES) cells. Of 2,400 ES cell clones with random insertions of retroviral vectors carrying a human placental alkaline phosphatase reporter gene (AP), 41 clones exhibited stage-specific reporter gene expression during embryoid body formation. The majority of these insertions were in genes that are not expressed in undifferentiated ES cells. Eleven ES cell clones with characteristic patterns of AP reporter gene expression in vitro were chosen for further examination in vivo for AP expression in developing embryos. Ten ES cell clones exhibited AP expression between day 7.5 and day 10.5 of development. Clones that showed restricted reporter gene expression in vitro also exhibited similar temporally and spatially restricted AP expression in vivo. Sequence analysis of genomic DNA flanking several vector insertions and corresponding cDNAs suggested that several of the insertions identified a previously unidentified gene. Thus, screening for reporter gene expression during embryoid body formation provides an efficient means of enriching clones that contain vector insertions into potentially novel genes that are important for regulating different stages of early postimplantation development.

Alkaline Phosphatase↗

PubMed1983

The value of WISC-R profile analysis for the differential diagnosis of learning disabled children.

Examined the research on WISC-R profile analysis germane to the differential diagnosis of learning disabled children in relation to several methodological problems that concern score use and interpretation. The evidence based on Bannatyne's (1974) recategorization of the subtests indicates a Spatial greater than Conceptual greater than Sequencing pattern of performance for learning disabled children. The application of this evidence of group characteristics to the individual child is problematic. The trend is not consistent. In addition, the interpretation of the individual profile is complicated by the unreliability of a few of the subtests, the unreliability of subtest difference scores, the unreliability of Bannatyne category difference scores, and the invalidity of the difference scores for discriminating between learning disabled and other children. It was recommended that clinicians not use the WISC-R profile to diagnose specific learning disabilities. Instead, the analysis may have greater utility in the prevention and remediation of learning problems, especially at the preschool level.

Affective Symptoms↗

PubMed2000

Monitoring of high-intensity focused ultrasound-induced temperature changes in vitro using an interleaved spiral acquisition.

An interleaved, spoiled gradient-echo spiral acquisition technique was implemented to monitor high-intensity focused ultrasound heating of porcine kidney ex vivo by measuring temperature induced phase shifts in the detected MR signal. Echo time, flip angle, repetition time, number of interleaves, and readout time were varied to observes effects on temperature sensitivity and phase-difference noise. The temperature response of the interleaved spiral acquisition was found to be comparable to a spoiled fast gradient-echo sequence of comparable in-plane spatial resolution. However, when imaging with an optimal echo time, spiral acquisition offers dramatically increased temporal resolution for comparable spatial resolution. Magn Reson Med 43:909-912, 2000.

Animals↗

PubMed1990

Timing and topography of cerebral blood flow, aura, and headache during migraine attacks.

Ten years of study has resulted in considerable but fragmented knowledge about regional cerebral blood flow in migraine with aura (classic migraine). In the present study, the number of repeatedly studied patients (n = 63) was large enough to determine statistically significant sequences of events and statistically significant spatial relations. The first observable event was a decrease of regional cerebral blood flow posteriorly in one cerebral hemisphere. Further development of this pathological process was accompanied by the aura symptoms. Thereafter headache occurred while regional cerebral blood flow remained decreased. During the headache phase, regional cerebral blood flow gradually changed from abnormally low to abnormally high without apparent change in headache. In some patients headache disappeared while regional cerebral blood flow remained increased. Although regional cerebral blood flow reduction and aura symptoms in the great majority of patients were unilateral, one-third had bilateral headache. Unilateral headache usually localized to the side on which regional cerebral blood flow was reduced and from which the aura symptoms originated (i.e., aura symptoms were perceived to occur contralaterally but presumably originated in the hypoperfused hemisphere). Our results suggest a simple model for migraine attacks: A pathological disturbance in one cerebral hemisphere causes the aura symptoms and after a time delay, it also causes the headache by stimulating local vascular nociceptors. Bilateral headache caused by a unilateral cerebral disturbance may be explained by recent neuroanatomical and neurophysiological findings.

Adolescent↗

PubMed1986

Hormonal and developmental specificities of transcription lie within a 1.5 kb region 5' to the ecdysone inducible Drosophila P1 gene.

P-element-mediated transformation was used to investigate 5' cis-acting regulatory sequences flanking the P1 gene of Drosophila melanogaster, which is selectively expressed in the fat body of late third instar larvae under the positive control of ecdysone. A hybrid gene was constructed by fusing a 1.5 kb DNA fragment directly adjacent to and including the first 25 transcribed bases of the P1 gene to the Escherichia coli xanthine guanine phosphoribosyltransferase (Ecogpt) gene itself linked at its 3' end to the SV40 t antigen splicing and polyadenylation sequences. Five transformed lines of D. melanogaster containing only one copy of the hybrid gene were established. In each of these lines the gpt sequence is transcribed with the same spatial, temporal and hormonal specificities as those of the P1 gene. This provides evidence that control elements essential for the ecdysone and developmentally regulated expression of P1 are located within a 1.5 kb region 5' to this gene.

Journal Article↗

PubMed2026

High-Content CRISPR Screening: Methods and Applications.

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 screening has become a central technology in functional genomics, enabling genome-scale interrogation via pooled perturbations. Early CRISPR screens employed survival or simple phenotypic readouts to identify essential genes and drug resistance mechanisms. However, as biological questions have shifted toward understanding regulatory networks, cellular heterogeneity, and context-dependent gene functions, there has been increasing demand for screening strategies capable of capturing complex cellular phenotypes beyond cell fitness. Recent advances in single-cell sequencing, high-content imaging, and spatial transcriptomics have expanded the resolution of CRISPR screening by enabling multidimensional phenotypic characterization following genetic perturbation. By integrating pooled perturbations with diverse readouts, these approaches systematically map targeted gene edits to transcriptional states, cellular phenotypes, and microenvironmental contexts. Meanwhile, innovations in library design, delivery, and computational pipelines have further improved the robustness and interpretability of high-content screening platforms. This review synthesizes the methodological evolution of CRISPR screening, emphasizing advances in perturbation strategies, delivery systems, and multimodal readouts. Representative applications spanning oncology, immunotherapy, developmental biology, neurobiology, and infectious diseases are delineated to demonstrate refined gene network annotations. Additionally, existing technical bottlenecks, such as scalability, cost constraints, and in vivo limitations, are critically assessed. Finally, future directions are proposed to facilitate the development of precise medicine.

CRISPR screening↗

PubMed2003

Real-time imaging of two-dimensional cardiac strain using a harmonic phase magnetic resonance imaging (HARP-MRI) pulse sequence.

The harmonic phase (HARP) method provides automatic and rapid analysis of tagged magnetic resonance (MR) images for quantification and visualization of myocardial strain. In this article, the development and implementation of a pulse sequence that acquires HARP images in real time are described. In this pulse sequence, a CINE sequence of images with 1-1 spatial modulation of magnetization (SPAMM) tags are acquired during each cardiac cycle, alternating between vertical and horizontal tags in successive heartbeats. An incrementing train of imaging RF flip angles is used to compensate for the decay of the harmonic peaks due to both T(1) relaxation and the applied imaging pulses. The magnitude images displaying coarse anatomy are automatically reconstructed and displayed in real time after each heartbeat. HARP strain images are generated offline at a rate of four images per second; real-time processing should be possible with faster algorithms or computers. A comparison of myocardial contractility in non-breath-hold and breath-hold experiments in normal humans is presented.

Adult↗

PubMed1995

NMR microscopy of single neurons using spin echo and line narrowed 2DFT imaging.

NMR microimages of single neural cells were acquired at 500 MHz using a conventional spin echo pulse sequence and a line-narrowing sequence that eliminates susceptibility effects. The data show that any contribution to the measured T2 relaxation rate arising from diffusion in local field inhomogeneities using spin echo sequences at high fields and high spatial resolution is relatively small. We conclude that the measured T2 difference between the nucleus and cytoplasm in these cells represents primarily a true T2 relaxation effect arising from the interactions of water with macromolecules in the two compartments and does not result from microsusceptibility differences. These observations have implications regarding water compartmentation in single cells and the interpretation of the MR characteristics of tissues in vivo.

Animals↗

PubMed1997

Quantitative measurements of regional cerebral blood volume using MRI in rats: effects of arterial carbon dioxide tension and mannitol.

A three-dimensional (3D) T1-weighted sequence was used to acquire high spatial resolution whole brain images in rats before and after the injection of an intravascular contrast agent. These T1-weighted images were used to estimate regional cerebral blood volume (rCBV) as a percentage of blood volume in each voxel. Ventilation was manipulated to investigate the effects of altered arterial carbon dioxide tension (PaCO2) on rCBV. In addition, different doses of a hypertonic mannitol solution were used to investigate the sensitivity of the proposed method in a serial monitoring paradigm. An rCBV of 2.40% +/- 0.34% was obtained before any physiological manipulation, in good agreement with literature values using alternative techniques. Using this method, it was found that there exists a linear relationship between PaCO2 and rCBV (R2 = 0.77) and that rCBV increased in a dose and time dependent fashion in mannitol-treated rats. High signal-to-noise was available due to the substantial increase in blood signal from the intravascular contrast agent.

Animals↗