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Results for “spatial sequencing”

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PubMed1993

Functional conservation of vertebrate seven-up related genes in neurogenesis and eye development.

Several members of the steroid receptor superfamily, including the transcription factor COUP, are closely related to the Drosophila gene seven-up (svp) which is required for the development of the embryonic central nervous system (CNS) and specific photoreceptor cells of the eye. We have identified and characterized two zebrafish (Brachydanio rerio) members of this subfamily of orphan nuclear receptors. While one of them (svp[44]) is the zebrafish cognate of COUP, the second (svp[46]) seems to be a novel member of the COUP/svp group. The proteins encoded by both genes contain highly conserved DNA-binding and putative ligand-binding domains, indicating close similarities in target sequence recognition and ligand binding. Analysis of the spatial distribution of their transcripts in whole-mount embryos revealed that the CNS is a major site of expression for both genes. At early embryonic stages, both genes are expressed in domains corresponding to specific rhombomere primordia in the hindbrain. This suggests an involvement in hindbrain segmentation and/or rhombomere specification. Moreover, transcripts derived from both genes are detected within distinct areas of the eye rudiments, suggesting roles in eye patterning and/or cell differentiation. In the case of the svp[44] gene, expression is also observed within specific parts of the midbrain, diencephalon and telencephalon. These results represent the first evidence that at least some of the nervous system and eye-specific functions of Drosophila svp are conserved in vertebrates.

Amino Acid Sequence↗

PubMed1983

Auditory spatial alternation transforms auditory time.

Recent research has shown that a sequence of auditory events that is alternated between the ears is stretched out in auditory memory, as compared with nonalternating sequences. Although the stimulus-onset asynchronies (SOAs) of the interaural and monaural sequences were the same, the perceptual-onset asynchronies (POAs) differed by 24 msec. Because this result was only established for a restricted range of SOAs (125-250 msec), the present study tested a much larger range (40-2,130 msec). It turned out that the POA difference of 25 msec remained invariant over this whole range. Furthermore it was investigated how the angle of alternation affected the POA difference. It was found that (a) this difference increased linearly with increasing angular separation, and (b) the effects of SOA and angular separation on the POA difference were additive. The merits of six different attention-switching models were inspected to explain these results, but none of the models could describe the effects satisfactorily. We offer a new model, the space-time network, that copes not only with the present results but also explains several other studies reported in the literature.

Attention↗

PubMed2005

Spatial diversity in mitochondrial cytochrome c oxidase in house flies.

DNA sequence analysis at mitochondrial gene COI was surveyed in 293 house flies, Musca domestica Linneaus (Diptera: Muscidae), in 29 populations from North, Central and South America, Europe, Asia, Africa, and the Western Pacific. Nei's gene diversity index (H(S)) was 0.47, the chance that two randomly chosen flies have different COI haplotypes. Haplotype diversity was greater in the Old World (H(S) = 0.58) than the New World (H(S) = 0.31). The hierarchical partition of the total diversity indicated substantial differentiation at all levels (G(ST) = 0.30), and highly structured populations. All pairwise estimates of gene flow between zoogeographical regions were less than 0.70 reproducing females per generation. The results are compared to those of a similar study based on the single-strand conformation polymorphism method. Probable colonization scenarios for house flies into the New World are discussed and it is concluded that house flies are a recent addition to the fauna of the Western Hemisphere.

Animals↗

PubMed2001

Sex-biased gene flow in spectacled eiders (Anatidae): inferences from molecular markers with contrasting modes of inheritance.

Genetic markers that differ in mode of inheritance and rate of evolution (a sex-linked Z-specific microsatellite locus, five biparentally inherited microsatellite loci, and maternally inherited mitochondrial [mtDNA] sequences) were used to evaluate the degree of spatial genetic structuring at macro- and microgeographic scales, among breeding regions and local nesting populations within each region, respectively, for a migratory sea duck species, the spectacled eider (Somateria fisheri). Disjunct and declining breeding populations coupled with sex-specific differences in seasonal migratory patterns and life history provide a series of hypotheses regarding rates and directionality of gene flow among breeding populations from the Indigirka River Delta, Russia, and the North Slope and Yukon-Kuskokwim Delta, Alaska. The degree of differentiation in mtDNA haplotype frequency among breeding regions and populations within regions was high (phiCT = 0.189, P < 0.01; phiSC = 0.059, P < 0.01, respectively). Eleven of 17 mtDNA haplotypes were restricted to a single breeding region. Genetic differences among regions were considerably lower for nuclear DNA loci (sex-linked: phiST = 0.001, P > 0.05; biparentally inherited microsatellites: mean theta = 0.001, P > 0.05) than was observed for mtDNA. Using models explicitly designed for uniparental and biparentally inherited genes, estimates of spatial divergence based on nuclear and mtDNA data together with elements of the species' breeding ecology were used to estimate effective population size and degree of male and female gene flow. Differences in the magnitude and spatial patterns of gene correlations for maternally inherited and nuclear genes revealed that females exhibit greater natal philopatry than do males. Estimates of generational female and male rates of gene flow among breeding regions differed markedly (3.67 x 10(-4) and 1.28 x 10(-2), respectively). Effective population size for mtDNA was estimated to be at least three times lower than that for biparental genes (30,671 and 101,528, respectively). Large disparities in population sizes among breeding areas greatly reduces the proportion of total genetic variance captured by dispersal, which may accelerate rates of inbreeding (i.e., promote higher coancestries) within populations due to nonrandom pairing of males with females from the same breeding population.

Animals↗

PubMed1994

Enzyme-linked fluorescent detection for automated multiplex DNA sequencing.

Initiatives to sequence DNA on a large scale have created a need for increased throughput and decreased costs. One scheme for increasing throughput, multiplex sequencing, involves the processing of a mixture of sequencing templates followed by sequential hybridization to reveal the individual sequence ladders on a membrane. Because multiplex sequencing has not been fully automated, and has not seemed automatable, few sequencing efforts have attempted to exploit it. We describe here a scheme for the automation of multiplex sequencing. Probe hybridized to target DNA is detected via spatially localized enzyme-linked fluorescence. Light output is high enough that imaging is possible with simple instrumentation. Direct imaging within an automated hybridization apparatus is made feasible so that the entire process will be automatic once a multiplex membrane is produced. The technique has the potential to increase severalfold the throughput of automated sequencing instruments required for sequencing the human genome.

Base Sequence↗

PubMed1992

The eukaryotic CCAAT and TATA boxes, DNA spacer flexibility and looping.

Regulation of RNA transcription in eukaryotic polymerase II promoters involves a complex assembly of protein factors. Some of the factors bind to their cognate DNA-sequence elements while others mediate between the DNA bound ones. In order to enable protein-protein interaction, their spatial positioning with respect to each other is critical. Here two DNA-sequence-elements are investigated, the CCAAT and the TATA boxes and their spacers. Whereas the position of the TATA is fixed at about -30, that of the CCAAT can vary substantially from -50 to -200. Despite the variable loop sizes, the CTF (CCAAT-binding) protein interacts--either directly or indirectly via a co-activator--with the general basal TATA-binding transcription factors. Sequence analysis of the spacers, as a function of their sizes, reveals that in the upstream regions of the spacers RR and YY are abundant. In the downstream, 3' region of the spacers RY and YR are very frequent. The DNA sequence elements and their intervening spacers are analyzed in terms of their geometry, anisotropic flexibility and local superhelical density. Our results indicate that the CCAAT and its vicinity is rigid, whereas the TATA and its surroundings is flexible. It is the large flexibility of this region in twist and in roll which allows DNA looping. General mechanistic implications for pol II promoters are discussed.

Animals↗

PubMed2026

Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.

Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.

Bacillus↗

PubMed2003

Spatiotemporal anisotropic diffusion filtering to improve signal-to-noise ratios and object restoration in fluorescence microscopic image sequences.

We present an approach for significantly improving the quantitative analysis of motion in noisy fluorescence microscopic image sequences. The new partial differential equation based method is a general extension of a 2-D nonlinear anisotropic diffusion filtering scheme to a specially adapted 3-D nonlinear anisotropic diffusion filtering scheme, with two spatial image dimensions and the time t in the image sequence as the third dimension. Motion in image sequences is considered as oriented, line-like structures in the spatiotemporal x,y,t domain, which are determined by the structure tensor method. Image enhancement is achieved by a structure adopted smoothing kernel in three dimensions, thereby using the full 3-D information inherent in spatiotemporal image sequences. As an example for low signal-to-noise ratio (SNR) microscopic image sequences we have applied this method to noisy in vitro motility assay data, where fluorescently labeled actin filaments move over a surface of immobilized myosin. With the 3-D anisotropic diffusion filtering the SNR is significantly improved (by a factor of 3.8) and closed object structures are reliably restored, which were originally degraded by noise. Generally, this approach is very valuable for all applications where motion has to be measured quantitatively in low light level fluorescence microscopic image sequences of cellular, subcellular, and molecular processes.

Actins↗

PubMed2002

A rotational approach to localized SPAMM 1-1 tagging.

Magnetic resonance tagging usually relies on controlling the phase dispersion of the transverse magnetization component. Phase dispersion is, however, affected by the inherent phase of selective excitation pulses, thus limiting their combination with tagging sequences to the application of refocusable pulses, as in the localized spatial modulation of magnetization (L-SPAMM) technique. In this study, we examine the effect of selective excitation pulses on a L-SPAMM 1-1 sequence, showing that in the case of two identical pulses the phase component is canceled out, and thus preemphasis and refocus gradients are not needed, allowing us to take advantage of a constant gradient throughout the tagging sequence, and also that one might choose nonrefocusable maximum and minimum phase pulses.

Journal Article↗

PubMed1989

Visual demonstration and movement production: effects of timing variations in a model's action.

The purpose of this study was to determine whether movement production during modelling would register timing changes communicated by a model during video-demonstration of a throwing action. 60 boys, 12 yr. of age, were placed in three groups and observed a computer-simulated, point-light demonstration of a darts-style movement used by a model to project a lightweight ball about 2.5 m in a forward direction. Only the relative motion of model's wrist, elbow, and shoulder were displayed. First, subjects were required to identify the action. Immediate response was 88% for the fastest demonstration (model's natural cadence with a wrist velocity of 3.5 rad./sec.), 81% (1.45 rad./sec.), and 65% (0.92 rad./sec.). Second, 3 subjects (1 from each of the original groups) modelled the action when the directional change of the model's arm and its spatial arrangement were held constant but the timing of traverse of the arm was randomly varied (3 levels). Analysis showed that all subjects produced the correct sequence of movement. There were no differences in production of the spatial parameters of the demonstrations but significant differences in the modelling of the timing parameters. These findings are related to the use of visual demonstrations during motor skill instruction and, particularly, the communication of specific aspects of an action.

Attention↗

PubMed1997

VET imaging: magnetic resonance imaging with variable encoding time.

A methodology of MRI data acquisition is introduced which involves lengthening the duration of signal readout period with complementary shortening of the phase encode pulses, and vice versa, in sequences where gradient encoding time is limited by RF pulse spacing. This variable encoding time (VET) methodology can be used to increase spatial resolution or reduce data acquisition time in 2D and 3D FT MRI based on CPMG and gradient echo sequences. Advantages of higher image SNR and different spatial frequency distributions in k-space are discussed and evaluated in preliminary experiments.

Aged↗

PubMed2003

Developing mechanisms of temperamental effortful control.

Studies of temperament from early childhood to adulthood have demonstrated inverse relationships between negative affectivity and effortful control. Effortful control is also positively related to the development of conscience and appears as a protective factor in the development of behavior disorders. In this study, the development of attentional mechanisms underlying effortful control was investigated in 2- to 3-year-old children, as indexed by their performance in a) making anticipatory eye movements to ambiguous locations and b) resolving conflict between location and identity in a spatial conflict task. The ability to make anticipatory eye movements to ambiguous locations within a sequence was clearly present at 24 months. By 30 months, children could also successfully perform a spatial conflict task that introduced conflict between identity and location, and at that age, children's success on ambiguous anticipatory eye movements was related to lower interference from conflict in the spatial conflict task. Children's performance on the eye-movement task was correlated with performance and reaction time on spatial tasks, and both were related to aspects of effortful control and negative affect as measured in children's parent-reported temperament.

Child, Preschool↗

PubMed1988

A regulatory domain that directs lineage-specific expression of a skeletal matrix protein gene in the sea urchin embryo.

DNA sequences derived from the 5' region of a gene coding for the 50-kD skeletal matrix protein (SM50) of sea urchin embryo spicules were linked to the CAT reporter gene and injected into unfertilized eggs. CAT mRNA and enzyme were synthesized from these fusion constructs in embryos derived from these eggs, and in situ hybridization with a CAT antisense RNA probe demonstrated that expression is confined to skeletogenic mesenchyme cells. A mean of 5.5 of the 32-blastula-stage skeletogenic mesenchyme cells displayed CAT mRNA (range 1-15), a result consistent with earlier measurements indicating that incorporation of the exogenous injected DNA probably occurs in a single blastomere during early cleavage. In vitro mutagenesis and deletion experiments showed that CAT enzyme activity in the transgenic embryos is enhanced 34-fold by decreasing the number of SM50 amino acids at the amino-terminus of the fusion protein from 43 to 4. cis-regulatory sequences that are sufficient to promote lineage-specific spatial expression in the embryo are located between -440 and +120 with respect to the transcriptional initiation site.

Amino Acid Sequence↗

PubMed2005

Myocardial first pass perfusion: steady-state free precession versus spoiled gradient echo and segmented echo planar imaging.

The imaging sequences used in first pass (FP) perfusion to date have important limitations in contrast-to-noise ratio (CNR), temporal and spatial resolution, and myocardial coverage. As a result, controversy exists about optimal imaging strategies for FP myocardial perfusion. Since imaging performance varies from subject to subject, it is difficult to form conclusions without direct comparison of different sequences in the same subject. The purpose of this study was to directly compare the saturation recovery SSFP technique to other more commonly used myocardial first pass perfusion techniques, namely spoiled GRE and segmented EPI. Differences in signal-to-noise ratio (SNR), CNR, relative maximal upslope (RMU) of signal amplitude, and artifacts at comparable temporal and spatial resolution among the three sequences were investigated in computer simulation, contrast agent doped phantoms, and 16 volunteers. The results demonstrate that SSFP perfusion images exhibit an improvement of approximately 77% in SNR and 23% in CNR over spoiled GRE and 85% SNR and 50% CNR over segmented EPI. Mean RMU was similar between SSFP and spoiled GRE, but there was a 58% increase in RMU with SSFP versus segmented EPI.

Adult↗

PubMed2001

Two types of pea leghemoglobin genes showing different O2-binding affinities and distinct patterns of spatial expression in nodules.

Five distinct cDNA clones for leghemoglobin (Lb) were isolated from pea (Pisum sativum) nodules. They were classified into two groups designated PsLbA and PsLbB according to sequence homology, O(2)-binding affinities of the recombinant proteins, and in situ localization of the mRNAs. The PsLbB group was comprised of four cDNA clones: PsLb120-1, -8, -29, and -34. They showed a high similarity of deduced amino acid sequences and O(2)-binding affinities of their recombinant proteins. Among them, the spatial expression pattern of PsLb120-1 was investigated in great detail, indicating that its transcripts were localized in the region from infection zone II to the distal part of nitrogen fixation zone III in effective nodules. PsLb5-10, which is the only cDNA clone of the PsLbA type, differed considerably from the PsLbB type in amino acid sequence, and the recombinant protein had a higher O(2)-binding affinity than those of the PsLbB type. The transcripts of PsLb5-10 were detected throughout the central tissue of effective nodules. However, in ineffective nodules on the pea mutant E135 (sym13), transcripts of PsLb5-10 were restricted to the distal portion of the central tissue as well as those of PsLb120-1. These findings indicate that the pea genome contains two types of Lb genes and suggest that they have different roles in the development of nitrogen-fixing symbiosis in pea nodules.

Amino Acid Sequence↗

PubMed1997

Perception of biological motion.

Boundary conditions for perception of biological motion were explored with the use of computer-generated point-light animation sequences. Perception of this unique form of structure from motion is immune to variations in dot contrast polarity, dot disparity, and spatial-frequency filtering. Biological motion is perceived in texture-defined animation sequences that presumably stimulate only second-order motion pathways, and it is undisturbed by dichoptic presentation of portions of the animation tokens separately to the two eyes.

Computer Graphics↗

PubMed2001

The Isolation of differentially expressed mRNA sequences by selective amplification via biotin and restriction-mediated enrichment.

Molecular analysis of development frequently implies the isolation and characterization of genes with specific spatial and temporal expression patterns. Several methods have been developed to identify such DNA sequences. The most comprehensive technique involves the genomewide probing of DNA sequence microarrays with mRNA sequences. However, at present this technology is limited to the few organisms for which the entire genome has been sequenced. Here, we describe a subtractive hybridization technique, called selective amplification via biotin and restriction-mediated enrichment (SABRE), which allows the selective amplification of cDNA fragments representing differentially expressed mRNA species. The method involves the competitive hybridization of an excess of driver cDNA fragments (D) to a trace of tester cDNA fragments (T), and the subsequent purification of tester homohybrids (in which both strands are contributed by the tester cDNA). After competitive hybridization, cDNA fragments that are more abundant in the tester than in the driver are enriched in the tester homohybrids. However, as the fraction of tester homohybrids is very small [T(2)/(D + T)(2)], their purification requires highly efficient procedures. In SABRE, the isolation of tester homohybrids is afforded by a combination of three successive steps: removal of biotinylated terminal sequences from most of the heterohybrids by S1 nuclease digestion, capture of biotinylated hybrids with streptavidin-coated paramagnetic beads, and specific release of homohybrids from the beads by restriction nuclease digestion. If several rounds of SABRE selection are performed in series, even relatively rare differentially expressed mRNA sequences may result in the production of predominant cDNA fragments in the final tester homohybrid population.

Animals↗

PubMed2002

MR Imaging of the heart with cine true fast imaging with steady-state precession: influence of spatial and temporal resolutions on left ventricular functional parameters.

The influence of changes in spatial and temporal resolutions on functional parameters in the left ventricle (LV) were investigated with magnetic resonance (MR) imaging with a modified true fast imaging with steady-state precession, or FISP, two-dimensional sequence that provided temporal resolution of 21-90 msec and spatial resolution of 1-3 mm. MR imaging in the heart was performed in 15 healthy volunteers. A decrease in LV functional parameters was observed with reduced spatial and temporal resolutions. The influence of temporal resolution was more relevant.

Adult↗