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Results for “spatial sequencing”

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PubMed1992

[Methods of NMR signal spatial localization for in vivo spectroscopy. A metabolic approach to diseases].

State-of-the-art methods for in vivo localized NMR spectroscopy are described. The methods are presented according to the type of pulse sequences implemented and the number of spatial dimensions which are obtained. The advantages and limitations of methods based either on (i) surface coil, (ii) complex radiofrequency pulse sequences with or without gradients, or (iii) double phase encoding (spectroscopic imaging) are discussed. The specific features of 31P and 1H localized spectroscopy are presented with a description of potential clinical applications of this approach which affords precise biochemical and metabolic information on a variety of organs and tissues in a strictly non-invasive manner.

Humans↗

PubMed1993

Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos.

We have analysed the replication of the chromosomal ribosomal DNA (rDNA) cluster in Xenopus embryos before the midblastula transition. Two-dimensional gel analysis showed that replication forks are associated with the nuclear matrix, as in differentiated cells, and gave no evidence for single-stranded replication intermediates (RIs). Bubbles, simple forks and double Ys were found in each restriction fragment analysed, showing that replication initiates and terminates without detectable sequence specificity. Quantification of the results and mathematical analysis showed that the average rDNA replicon replicates in 7.5 min and is 9-12 kbp in length. This time is close to the total S phase duration, and this replicon size is close to the maximum length of DNA which can be replicated from a single origin within this short S phase. We therefore infer that (i) most rDNA origins must be synchronously activated soon in S phase and (ii) origins must be evenly spaced, in order that no stretch of chromosomal DNA is left unreplicated at the end of S phase. Since origins are not specific sequences, it is suggested that this spatially and temporally concerted pattern of initiation matches some periodic chromatin folding, which itself need not rely on DNA sequence.

Animals↗

PubMed2004

Synfire chains and cortical songs: temporal modules of cortical activity.

How can neural activity propagate through cortical networks built with weak, stochastic synapses? We find precise repetitions of spontaneous patterns of synaptic inputs in neocortical neurons in vivo and in vitro. These patterns repeat after minutes, maintaining millisecond accuracy. Calcium imaging of slices reveals reactivation of sequences of cells during the occurrence of repeated intracellular synaptic patterns. The spontaneous activity drifts with time, engaging different cells. Sequences of active neurons have distinct spatial structures and are repeated in the same order over tens of seconds, revealing modular temporal dynamics. Higher order sequences are replayed with compressed timing.

2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-ben↗

PubMed2002

Magnetic resonance imaging with lateralized arterial spin labeling.

We report the development of a new MRI technique which allows spins from right-sided arteries to be labeled separately from spins from left-sided arteries. This method uses two spatially-selective adiabatic inversion pulses to alternate the labeling of the right carotid and vertebral artery separate from the left carotid and vertebral artery. Normal volunteers were scanned on a clinical 1.5 T system and the resultant brain images correlated with the T2 anatomic images. Arterial anatomy was depicted using the new sequence and corresponded to the labeling scheme employed by the sequence. It was demonstrated that spatially selective inversion pulses permit the encoding of the spins within specific vascular origins and the observation of their run-off territory.

Brain↗

PubMed2004

Comparison of MR imaging sequences for liver and head and neck interventions: is there a single optimal sequence for all purposes?

RATIONALE AND OBJECTIVES: To compare the appropriate pulse sequences for interventional device guidance during magnetic resonance (MR) imaging at 0.2 T and to evaluate the dependence of sequence selection on the anatomic region of the procedure. MATERIALS AND METHODS: Using a C-arm 0.2 T system, four interventional MR sequences were applied in 23 liver cases and during MR-guided neck interventions in 13 patients. The imaging protocol consisted of: multislice turbo spin echo (TSE) T2w, sequential-slice fast imaging with steady precession (FISP), a time-reversed version of FISP (PSIF), and FISP with balanced gradients in all spatial directions (True-FISP) sequences. Vessel conspicuity was rated and contrast-to-noise ratio (CNR) was calculated for each sequence and a differential receiver operating characteristic was performed. RESULTS: Liver findings were detected in 96% using the TSE sequence. PSIF, FISP, and True-FISP imaging showed lesions in 91%, 61%, and 65%, respectively. The TSE sequence offered the best CNR, followed by PSIF imaging. Differential receiver operating characteristic analysis also rated TSE and PSIF to be the superior sequences. Lesions in the head and neck were detected in all cases by TSE and FISP, in 92% using True-FISP, and in 84% using PSIF. True-FISP offered the best CNR, followed by TSE imaging. Vessels appeared bright on FISP and True-FISP imaging and dark on the other sequences. CONCLUSION: In interventional MR imaging, no single sequence fits all purposes. Image guidance for interventional MR during liver procedures is best achieved by PSIF or TSE, whereas biopsies in the head and neck are best performed using FISP or True-FISP sequences.

Adult↗

PubMed2004

Making your next move: dorsolateral prefrontal cortex and planning a sequence of actions in freely moving monkeys.

Prefrontal damage disrupts planning, as measured by disorders of the activities of daily living (Humphreys & Forde, 1998; Shallice & Burgess, 1991). In a monkey model of this form of planning, a variant of the delayed alternation task was performed by freely moving monkeys. In a 16 x 16-ft. testing room, four feeders were located in the middle of each wall. In the north task, monkeys alternated between feeders: west-north-east-north-west, and so forth. In the south task, the alternation sequence was east-south-west-south-east, and so forth. Neuronal activity was recorded during walking along the eight paths, constituting the north and south tasks. To succeed, monkeys had to memorize the alternation rule and monitor both their place in the sequence and the previously made spatially directed action before deciding to walk to a new location to the left or right of the current location. Responsive dorsolateral prefrontal neurons are strikingly selective. Sustained neuronal activity reflects the spatial direction of an ongoing or upcoming response. It is important that such selective responses occur in one but not both tasks, even though the movements are exactly the same in both tasks and at each location. We suggest that selective neuronal activity is tuned through learning and reflects the fundamental units of a planning mechanism: Individual neurons encode specific components of a sequence of behavioral actions and their temporal order. Populations of such neurons represent all the steps necessary to perform the north and south tasks. The sustained activity of these neurons suggests that planning and working memory mechanisms are integrated.

Animals↗

PubMed1993

The effect of visual similarity on short-term memory for spatial location: implications for the capacity of visual short-term memory.

Evidence from the recency effect suggests that visual short-term memory is limited to preserving information about a single pattern. Three experiments explored the capacity of visual short-term memory using a task which involved presenting a series of patterns in a random spatio-temporal sequence and probing memory for the spatial location of one of them. Experiment 1 used sequences of quasi-random block patterns which were either visually similar or dissimilar. Serial position curves showed a single-item recency effect. However, there was also a deleterious effect of visual similarity for the earlier patterns, indicating that visual short-term memory was supporting their retention. Experiment 2 showed that performance was unaffected by articulatory suppression, confirming that phonological coding is not an important factor in the localisation task. Experiment 3 switched to letter stimuli and, because of the known tendency for this type of stimulus to be phonologically recoded, required articulatory suppression. Letters were shown in a customised form in sequences which were either visually similar or visually dissimilar. The results replicated experiment 1 in showing restricted recency combined with an effect of visual similarity extending across earlier list items. When the same letters were shown in standard form, the recency effect remained but the similarity effect disappeared, ruling out possible interpretations in terms of semantic as well as phonological coding. It is concluded that the recency effect gives a misleading indication of the capacity of visual short-term memory. The visual similarity effect suggests that it is capable of supporting the retention of several patterns.

Adult↗

PubMed1999

Detection of transient in vivo interactions between substrate and transporter during protein translocation into the endoplasmic reticulum.

The split-ubiquitin technique was used to detect transient protein interactions in living cells. Nub, the N-terminal half of ubiquitin (Ub), was fused to Sec62p, a component of the protein translocation machinery in the endoplasmic reticulum of Saccharomyces cerevisiae. Cub, the C-terminal half of Ub, was fused to the C terminus of a signal sequence. The reconstitution of a quasi-native Ub structure from the two halves of Ub, and the resulting cleavage by Ub-specific proteases at the C terminus of Cub, serve as a gauge of proximity between the two test proteins linked to Nub and Cub. Using this assay, we show that Sec62p is spatially close to the signal sequence of the prepro-alpha-factor in vivo. This proximity is confined to the nascent polypeptide chain immediately following the signal sequence. In addition, the extent of proximity depends on the nature of the signal sequence. Cub fusions that bore the signal sequence of invertase resulted in a much lower Ub reconstitution with Nub-Sec62p than otherwise identical test proteins bearing the signal sequence of prepro-alpha-factor. An inactive derivative of Sec62p failed to interact with signal sequences in this assay. These in vivo findings are consistent with Sec62p being part of a signal sequence-binding complex.

Base Sequence↗

PubMed2003

Differential temporal and spatial expression of immediate early genes in retinal neurons after ischemia-reperfusion injury.

PURPOSE: To investigate genes that are up- and downregulated in rat retinal ischemia-reperfusion injury systematically by using an oligonucleotide microarray system and to determine temporal and spatial expression changes of some genes that showed upregulation in the analysis. METHODS: Retinal ischemia was induced in rats by increasing intraocular pressure to 110 mm Hg for 1 hour. Gene expression at 12 hours after reperfusion was compared with that in the control retina by using oligonucleotide microarrays that display a total of 8800 genes and expressed sequence tags (ESTs). Temporal and spatial expression changes of immediate early genes and cell-cycle-related genes were studied by using real-time polymerase chain reaction (PCR) and immunohistochemical methods. RESULTS: At 12 hours after reperfusion, 135 genes and ESTs were found to be up- or downregulated. The upregulated genes were classified into seven groups: (1) immediate early genes; (2) cell-cycle-related genes; (3) stress-responsive protein genes; (4) cell-signaling protein genes; (5) cell-adhesion and cell surface protein genes; (6) genes for translation and protein turnover; and (7) genes for metabolism. Real-time PCR analyses showed peaks of Fra-1 expression at 6 hours after reperfusion, whereas those for c-Jun, Jun B, and cyclin D1 were at 24 hours. Fra-1 and Jun B immunoreactivities were found in Müller cells, whereas c-Jun and cyclin D1 immunoreactivities were found in apoptotic retinal neurons. CONCLUSIONS: Gene expression changes after a retinal ischemia-reperfusion injury were profiled by using an oligonucleotide microarray system. Seven groups of genes were found to be upregulated by the injury. Among the immediate early genes, Fra-1 and Jun B immunoreactivities were found in Müller cells whereas c-Jun and cyclin D1 immunoreactivities were found in apoptotic retinal neurons.

Animals↗

PubMedDate not supplied

[Conformational aspects of biological activity of functional fragments of the p21ras oncoproteins. 3. Fragment 34-46 of the native oncoprotein and the decapeptide corresponding to its 35-44 sequence].

Theoretical conformational analysis was used to study the spatial structure of a putative binding site responsible for binding of p21 oncoproteins to other oncoproteins. Conformational properties of the isolated address sequence localized in fragment 34-46 of native p21 and of the decapeptide molecule corresponding to the 35-44 sequence in the primary structure of oncoproteins of this family were revealed. Our calculations demonstrated a similarity between the spatial structures of the peptides, which confirms the hypothesis on the identity of their biological functions.

Models, Molecular↗

PubMed1989

Regulation of cytomegalovirus late-gene expression: differential use of three start sites in the transcriptional activation of ICP36 gene expression.

We have investigated the transcriptional regulation of the human cytomegalovirus gamma gene encoding the ICP36 family (p52, the major late DNA-binding protein). The ICP36 transcription unit initiates at three distinct sites which are separated by approximately 50 nucleotides and are differentially regulated during infection. At early times (8 h postinfection), only two of these start sites, the most proximal and distal site, were active whereas at late times (36 h postinfection), the middle start site was activated. Expression from this late start site was dependent upon DNA replication. Consensus TATA elements were located upstream of all three start sites, although the element upstream of the late start site was unusual in both sequence and position when compared with conventional TATA elements. Deletion analysis was used in conjunction with transient assays to define independent promoters in this region. The two early start sites and associated TATA elements functioned as separable independently regulated promoters. The region containing the late start site and TATA element but excluding either of the flanking TATA elements was inactive in transient assays. Our work establishes that the ICP36 gene is under complex early and late transcriptional regulation and that the sequences regulating transcriptional activation are temporally and spatially distinct.

Base Sequence↗

PubMed1985

Plant peroxidases. Their primary, secondary and tertiary structures, and relation to cytochrome c peroxidase.

The amino acid sequences of the 51% different horseradish peroxidase HRP C and turnip peroxidase TP 7 have previously been completed by us, but the three-dimensional structures are unknown. Recently the amino acid sequence and the crystal structure of yeast cytochrome c peroxidase have appeared. The three known apoperoxidases consist of 300 +/- 8 amino acid residues. The sequences have now been aligned and show 18% and 16% identity only, between the yeast peroxidase and plant peroxidase HRP C and TP 7, respectively. We show that different structural tests all support similar protein folds in plant peroxidases and yeast peroxidase and, therefore, a common evolutionary origin. The following tests support this thesis: (a) predicted helices in the plant peroxidases follow the complex pattern observed in the crystal structure of cytochrome c peroxidase; (b) their hydropathic profiles are similar and agree with observed buried and exposed peptide chain in cytochrome c peroxidase; (c) half-cystines which are distant in the amino acid sequence of plant peroxidases become spatial neighbours when fitted into the cytochrome c peroxidase model; (d) the two-domain structure proposed from limited proteolysis of apoperoxidase HRP C is observed in the crystal structure of cytochrome c peroxidase. The similarities and differences of the plant and yeast peroxidases and the reactive side chains of a plant peroxidase active site are described. The characteristics of Ca2+-binding sequences, derived from several superfamilies, are applied to predict the Ca2+-binding sequences in plant peroxidases.

Amino Acid Sequence↗

PubMed2006

What makes faces special?

What may be special about faces, compared to non-face objects, is that their neural representation may be fundamentally spatial, e.g., Gabor-like. Subjects matched a sequence of two filtered images, each containing every other combination of spatial frequency and orientation, of faces or non-face 3D blobs, judging whether the person or blob was the same or different. On a match trial, the images were either identical or complementary (containing the remaining spatial frequency and orientation content). Relative to an identical pair of images, a complementary pair of faces, but not blobs, reduced matching accuracy and released fMRI adaptation in the fusiform face area.

Adult↗

PubMed1992

Endogenous peptides of a soluble major histocompatibility complex class I molecule, H-2Lds: sequence motif, quantitative binding, and molecular modeling of the complex.

To gain insight into the rules that govern the binding of endogenous and viral peptides to a given major histocompatibility complex (MHC) class I molecule, we characterized the amino acid sequences of a set of self peptides bound by a soluble analogue of murine H-2Ld, H-2Lds. We tested corresponding synthetic peptides quantitatively for binding in several different assays, and built three-dimensional computer models of eight peptide/H-2Lds complexes, based on the crystallographic structure of the human HLA-B27/peptide complex. Comparison of primary and tertiary structures of bound self and antigenic peptides revealed that residues 2 and 9 were not only restricted in sequence and tolerant of conservative substitutions, but were spatially constrained in the three-dimensional models. The degree of sequence variability of specific residues in MHC-restricted peptides reflected the lack of structural constraint on those amino acids. Thus, amino acid residues that define a peptide motif represent side chains required or preferred for a close fit with the MHC class I heavy chain.

Amino Acid Sequence↗

PubMedDate not supplied

[From determination of amino acid residue conformation to reconstruction of the spatial structure of proteins (from the data of nuclear Overhauser enhancement spectroscopy].

A new approach to the calculation of the spatial protein structure based on the joint utilization of the theoretical conformational analysis method and nuclear Overhauser enhancement (NOE) spectroscopy data is proposed and verified. The quality in determining various molecule structural parameters is estimated in terms of the expected NOE spectral parameters derived from the X-ray analysis data of the avian pancreatic polypeptide. The proposed approach is shown to correctly determine such structural parameters of protein molecules as local amino acid residue conformations, reciprocal spatial orientation of the C alpha atoms neighbouring along amino acid sequence and reapproached segments of the polypeptide chain. Spatially remote molecule fragments are mainly responsible for the error in determining structural parameters.

Amino Acids↗

PubMed1989

Codon preference and primary sequence structure in protein-coding regions.

The stochastic complexity of a data base of 365 protein-coding regions is analysed. When the primary sequence is modeled as a spatially homogeneous Markov source, the fit to observed codon preference is very poor. The situation improves substantially when a non-homogeneous model is used. Some implications for the estimation of species phylogeny and substitution rates are discussed.

Amino Acids↗

PubMed1984

Testing a theory of brain function by computer methods. III. Detecting cerebral asymmetry in normal adults.

Pursuing a plan for overall testing of the timing and sequencing of brain processes, testing techniques are introduced for probing a normal adult's short-term central processes, especially those which are employed in reading a digit span of 6 numbers or less. The tests are administered by means of a personal computer and can provide information on the individual subject's characteristic sequencing and timing of particular central processes. In a subject whose first language is read from left to right, the presented tests reported in this paper reveal an asymmetry in normal adults wherein digits presented in the left visual field are processed more efficiently than those presented in the right visual field. It is suggested that the right hemisphere 'holds the image' while the left hemisphere 'transforms' the spatial image into a temporal sequence for use in speech. The 'right-positioned' or 'later' components must be held at least until a successful spoken response is completed.

Brain↗

PubMed2003

Using a neural network and spatial clustering to predict the location of active sites in enzymes.

Structural genomics projects aim to provide a sharp increase in the number of structures of functionally unannotated, and largely unstudied, proteins. Algorithms and tools capable of deriving information about the nature, and location, of functional sites within a structure are increasingly useful therefore. Here, a neural network is trained to identify the catalytic residues found in enzymes, based on an analysis of the structure and sequence. The neural network output, and spatial clustering of the highly scoring residues are then used to predict the location of the active site.A comparison of the performance of differently trained neural networks is presented that shows how information from sequence and structure come together to improve the prediction accuracy of the network. Spatial clustering of the network results provides a reliable way of finding likely active sites. In over 69% of the test cases the active site is correctly predicted, and a further 25% are partially correctly predicted. The failures are generally due to the poor quality of the automatically generated sequence alignments. We also present predictions identifying the active site, and potential functional residues in five recently solved enzyme structures, not used in developing the method. The method correctly identifies the putative active site in each case. In most cases the likely functional residues are identified correctly, as well as some potentially novel functional groups.

Algorithms↗