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At least 793 records · Page 44Linked to original sources

An autonomously replicating sequence from HeLa DNA shows a similar organization to the yeast ARS1 element.

A HeLa DNA fragment, which may function as an anchorage point to the nuclear matrix for human chromosomes 1 and 2, also functions as an autonomously replicating sequence (ARS) in the yeast Saccharomyces cerevisiae. In the present report we show that this DNA fragment contains both bent DNA and an A-T rich region which appear to be associated with the ARS function. More interestingly, DNA sequence analysis shows that the spatial distribution of these features is strikingly similar to that found in the yeast ARS1 element.

Base Sequence↗

Hemispheric specialization of human inferior temporal cortex during coarse-to-fine and fine-to-coarse analysis of natural visual scenes.

Recent models of visual recognition have suggested that perceptual analysis may start with a parallel extraction of different spatial frequencies (SF), using a preferential coarse-to-fine (low-to-high SF) sequence of processing. A rapid extraction of low spatial frequency (LSF) information may thus provide an initial and crude parsing of the visual scene, subsequently refined by slow but more detailed high spatial frequency (HSF) information. However, the sequence of SF analysis could be flexible, a high-to-low (HtL) being sometimes preferred to a low-to-high (LtH) SF sequence depending on task demands. Furthermore, it has also been suggested that the right vs. left hemisphere might be differentially specialized in LSF vs. HSF analysis, respectively. By manipulating the temporal succession of LSF and HSF stimuli, the present fMRI study investigated whether such hemispheric specialization may underlie the flexible use of different time-course in SF analysis. Participants performed a matching task between two successive images of natural scenes (LSF or HSF) that were displayed either in an LtH (LSF scene presented first and HSF scene second) or in a reverse HtL sequence. A direct inter-hemispheric comparison of the neural responses evoked by each SF sequence revealed greater activations within the right occipito-temporal cortex for the LtH sequence and within the left occipito-temporal cortex for the HtL sequence. These fMRI results suggest that the hemisphere preferentially engaged during the sequential processing of different SF might be determined by the initial SF-band appearing in this sequence, and that both a coarse-to-fine and fine-to-coarse analysis might independently take place in the two hemispheres.

Adult↗

First tryptophan-containing weak neurotoxin from cobra venom.

With the purpose of studying structure-function relationships among weak neurotoxins (called so because of their low toxicity), we have isolated a toxin (WTX) from the venom of cobra Naja kaouthia using a combination of gel-filtration and ion-exchange chromatography. The amino acid sequence of the isolated toxin was determined by means of Edman degradation and MALDI mass spectrometry, the primary structure obtained being confirmed by 1H-NMR in the course of spatial structure analysis. The WTX sequence differs slightly from that of the toxin CM-9a isolated earlier from the same venom (Joubert and Taljaard, Hoppe-Seyler's Z. Physiol. Chem., 361 (1980) 425). The differences include an extra residue (Trp36) between Ser35 and Arg37 as well as interchanging of two residues (Tyr52 and Lys50) in the C-terminal part of the toxin molecule. These changes improve the alignment that can be made with other weak neurotoxin sequences. An extended sequence comparison reveals that WTX is the first case of a tryptophan-containing weak neurotoxin isolated from cobra venom. WTX was found to compete with radioiodinated alpha-bungarotoxin for binding to the membrane-bound nicotinic acetylcholine receptor from Torpedo californica.

Amino Acid Sequence↗

The role of the nucleus in organogenesis: Part 2.

In a previous paper, it was proposed that the spatial orientation of stem cells was dependent on nucleus/nucleus contact. This proposition is discussed in more detail here. The correct spatial orientation of the cells making up the organs of the adult demands a molecular plan of some type to be encoded in the DNA, and it is suggested that the plan is encoded in the nontranscribed DNA. This DNA is present in the form of loops and folds, giving rise to a spatial array of enormous complexity, and the general belief is that the spatial array is dependent on sequence-specific proteins which firmly bind to the DNA. It is proposed that the binding proteins can also join the DNA of two adjacent stem-cell nuclei once nucleus/nucleus contact has been made, and in this way determine the spatial orientation of the future specialized cells. There is enough information encoded in the spatial arrays to correctly position the myriad of cells that make up the adult organism. If cell alignment is carried out by nuclear union, then the development of the neuron can be better understood. It is suggested that malignancy may be due to a fault in either the nontranscribed DNA responsible for spatial orientation or in the sequence-specific binding proteins.

Adult↗

Phylogenetic study of the spatial distribution of protein-coding and control segments in DNA chains.

We examine the size and spatial distributions of the protein-coding and control segments of genes in DNA nucleotide sequences from GenBank. Phylogenetic analysis of these data suggests the presence of spatial order in sequences of higher organisms, irrespective of the nature of nucleotide base content. This is characterized by defined two-point correlation functions and measured by fractal dimensions and singularity spectrum.

Algorithms↗

Vitelline envelope genes of the yellow fever mosquito, Aedes aegypti.

Vitelline envelope genes from the mosquito Aedes aegypti were analyzed with respect to their DNA sequences, genomic representation, temporal and spatial expression profiles and response to 20-hydroxyecdysone. Genomic clones of three vitelline envelope genes, 15a-1, 15a-2 and 15a-3 were isolated. Southern analysis indicates that all three genes are represented by a single copy in the genome. The deduced amino acid sequences of all three vitelline envelope genes contain a conserved region of 46 residues that overlaps with a region that is conserved in four Drosophila melanogaster vitelline envelope genes. DNA was sequenced flanking the 15a-1, 15a-2 and 15a-3 coding regions. A 360 bp sequence 5' of the 15a-2 coding region was identified with 72% identity to a sequence upstream of the Ae. aegypti VgA1 vitellogenin gene. The temporal patterns of 15a-1, 15a-2 and 15a-3 expression, as determined by Northern analysis, were similar. The spatial patterns of expression, as determined by whole-mount in situ hybridization, differed between the three genes. 15a-1 and 15a-3 were only expressed in the middle and posterior regions of the follicle, while 15a-2 was also expressed at the anterior region. Vitelline envelope gene expression was higher in ovaries that were dissected at 0, 2 and 10 h following a blood meal and then incubated in vitro for 10 h in medium containing 10(-5) M 20-hydroxyecdysone, compared to ovaries that were incubated without hormone.

Aedes↗

"Chess-board pattern" spatial modulation of magnetization. Assessment of myocardial function.

Heart motion is a complex combination of translation, rotation, and concentric contraction. Evaluation of these complex motions has been difficult using conventional slice-selective methods. Noninvasive tagging of the heart has been obtained by the use of slice-selective radiofrequency pulses. Through spatial modulation of the magnetization the entire image can be labeled in different patterns. Two new pulse sequences are presented, giving a chess-board like spatial modulation. These pulse sequences have several advantages compared with the previously published methods, as the modulation time is half that required to obtain a 2-dimensional grid, the area in the image with high signal intensity was significantly larger, and the radiofrequency power deposition was substantially decreased. By labeling the heart at diastole the chess-board pattern tagging of the heart wall could be followed through systole. Using this method the complex motions of the heart can be mapped.

Computer Simulation↗

Crystal structure of Aplysia ADP ribosyl cyclase, a homologue of the bifunctional ectozyme CD38.

ADP ribosyl cyclase synthesizes the novel secondary messenger cyclic ADP ribose (cADPR) utilizing NAD as a substrate. The enzyme shares extensive sequence similarity with two lymphocyte antigens, CD38 and BST-1, which hydrolyse as well as synthesize cADPR. The crystal structure provides a model for these cell surface enzymes. Cyclase contains two spatially separated pockets composed of sequence conserved residues, suggesting that the cyclization reaction may entail use of distinct sites. The enzyme dimer encloses a cavity which may entrap the intermediate, ADP ribose.

ADP-ribosyl Cyclase↗

Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin gamma of plasmid R6K.

The plasmid R6K possesses three distinct origins of replication: alpha, beta, and gamma. The replication origin gamma of plasmid R6K performs a dual function: (i) as an origin itself and (ii) as an enhancer element required in cis for the activation at a distance of the other two replication origins alpha and beta. We have dissected the gamma origin/enhancer by site-directed mutagenesis and have reached the following conclusions. The origin function can be specifically inactivated without impairing the enhancer function by insertion and/or deletion mutations near the opposite ends of the origin gamma sequence. One such mutation deleted sequences that included the left DnaA site I. The second mutation involved insertion of linker sequences that resulted in a spatial alteration between the right DnaA site II and the VIIth pi binding iteron (tandemly repeated binding sites). Other mutations that either partly or completely deleted the A+T-rich sequence adjacent to, but not including, the pi binding iterons also abrogated enhancer and origin function and suggested that pi binding sites were necessary but not sufficient for enhancer activity. Finally, the functional analysis of a set of mutants of the gamma origin/enhancer suggested that a continuous stretch of 300 base pairs is necessary for origin gamma function and that the sequences that included the binding sites for pi, DnaA, and integration host factor proteins are required in the correct stereochemical alignment to impart origin activity.

Bacterial Proteins↗

Black-blood MR angiography. Techniques, and clinical applications.

As there are limitations in WB-MR angiography, so there are limitations in BB-MR angiography. Vessel morphology is visualized by means of the innermost nonattenuated layer of tissue, which, under ideal conditions, coincides with the luminal surface of the vessel wall. Vessel morphology may be depicted inaccurately whenever a portion of the vessel wall is undetectable with the MR imaging technique used. In such cases, vessel segments with exaggerated lumen diameter may result at locations where tissues with either a very short T2 or a low proton density are present. Another phenomenon that could potentially degrade the accuracy of vessel depiction with BB techniques is the effect of slowly flowing blood near the vessel walls. Residual blood signal would result in apparent vessel narrowing. Preliminary clinical experience in the brain, however, suggests that this adverse effect is less prominent with a turbo-SE-based BB technique than with a TOF WB technique. BB-MR angiography data sets may also present image postprocessing difficulties arising from the isointensity between the vessels and other dark structures such as bones and air-filled cavities. A limitation that is more specific to hybrid-SE-based BB-MR pulse sequences, particularly for very high spatial resolution applications, stems from the comparatively high RF specific absorption rates that result from the intensive use of 180 degrees refocusing pulses. GRASE-based BB-MR techniques that generate a fraction of the RF energy constitute a promising alternative for very high spatial resolution applications. In summary, to be effective, a BB technique must produce strong signal attenuation from flowing spins, ideally to the level of the baseline noise. Simultaneously it should produce good depiction of tissues with the comparatively short T2s characteristic of vessel walls and muscle, hence the need to operate with the shortest possible TE. Finally, high spatial resolution combined with fast data acquisition are requisites for imaging small vessels in the presence of motion, such as the carotid arteries. The flow properties of BB-MR angiographic sequences that meet these criteria were reviewed for different anatomic locations.

Humans↗

1H NMR spectroscopic imaging of the monkey brain using binomial water suppression in a stimulated-echo sequence.

A new proton, two-dimensional pulse sequence for 1H NMR spectroscopic imaging (chemical shift imaging) was tested in phantoms and in the monkey brain. The pulse sequence consisted of one binomial chemically selective pulse and two spatially selective pulses in the stimulated-echo sequence. The point-spread function (which is influenced by k-space filtering and the number of phase-encoded steps) of a 1 mm source phantom was measured using a 16 x 16 spatial matrix and was found to have a FWHM of 10 mm (100 mm field of view) with very little rippling outside the main lobe. The binomial excitation profile was measured in order to correct the NMR intensity for the variable flip angles. Spectroscopic images were measured in the monkey brain with a 15 mm slice thickness and a 16 x 16 spatial matrix. Proton spectra derived from the brain contained sharp resonances of choline, creatine and N-acetyl aspartate with minimal lipid contamination. Proton spectra derived from the subcutaneous fat and adipose tissue behind the eyes contained large lipid resonances.

Animals↗

Sequential pointing in children and adults.

The development of visuomotor control in sequential pointing was investigated in 6- to 10-year-old children and in adults. In 3 experiments we manipulated task difficulty by changing the number, the size, and the spacing of the targets in the sequences. In Experiment 4, only 1 movement was required; we varied independently the distance between targets and the distance of the starting point from the participant's body. Children's temporal and spatial parameters of the motor sequences showed large age-dependent trends, but did not reach the adult values. Comparison of performance across levels of difficulty and ages suggests that motor development is not a uniform fine-tuning of stable strategies. Instead, we argue that each stage of development is best characterized by the set of strategic components potentially available at that stage, and by the (age-dependent) rules for the selection of components in a given context.

Adult↗

Entropy of protein sequences: an integral approach.

Several classifications of protein spatial structures and their structural elements are known. This makes revealing of the relation between these structural elements and sequence fragments rather topical. The most important move in this direction would be the determination of positional sensitivity levels and ranges between the residues in protein sequences. In this work the Shannon-Weaver informational entropy was used as a disorder criterion for solving this problem. This entropy was computed as function of the distance between the amino acid residues in different sets of unhomological protein sequences. Similarity of this function for different sets of protein sequences was shown. Analysis of informational entropy allows detecting a long-range positional correlation (> or =30) between the amino acid residues and oscillations with periods of 3.6 and 2.9. These oscillation periods correspond to periodicity of alpha- and 3(10)-helices.

Computational Biology↗

A segment-interleaved motion-compensated acquisition in the steady state (SIMCAST) technique for high resolution imaging of the inner ear.

MRI, with ever-increasing spatial resolution, recently has depicted progressively more anatomic details of the inner ear and is playing an important role in the diagnostic evaluation of patients with sensorineural hearing loss. We present a three-dimensional (3D) segment-interleaved, motion-compensated acquisition in steady state (SIMCAST) sequence that allows further increase in spatial resolution in reasonable scan times minimizing artifacts due to susceptibility and motion. The sequence uses gradient moment nulling over TR and segmented interleaved acquisition of multiple data sets with different radiofrequency (RF) phase-cycling schemes. Combination of data from multiple acquisitions by averaging and maximum intensity projection were compared. Images of phantoms and in vivo inner ears were obtained with both full and fractional echoes and compared with other high resolution techniques such as three-dimensional gradient-echo and two-dimensional (2D) and three-dimensional fast spin-echo (FSE) sequences. The new sequence achieves improved signal-to-noise ratio (SNR) and spatial resolution resulting in improved depiction of inner ear structures.

Adult↗

Regulatory elements involved in the tissue-specific expression of the yellow gene of Drosophila.

We have assessed the DNA sequence requirements for the correct spatial pattern and phenotypic expression of y in the late embryo/larvae. The wild-type larval phenotype requires both the regions between -294 bp and -92 bp and a portion of the intron; the sequence element(s) located within the intron can act in a position independent manner to effect the wild-type larval phenotype. The larval expression pattern was examined by tissue experiments in situ and by staining germline transformants derived from various y/lacZ fusion constructs. The larval expression of y is restricted to the mouthparts, microsetae and anal plates. While the -495 bp to +194 bp region alone cannot effect a wild-type larval expression pattern, this region in conjunction with the intron appears to be sufficient to drive beta-gal expression in an essentially wild-type pattern. Our data further suggest that the -294 bp to -92 bp region contains elements which specify the larval pattern and that the element(s) in the intron normally act to enhance the level of expression necessary for the wild-type larval phenotype. We also present a phenotypic analysis of the adult cuticle structures of germline transformants derived from a variety of deletion and rearrangement constructs of the y gene. This analysis has revealed several new features associated with the regulation of y expression.

Animals↗

DNA mapping using microfluidic stretching and single-molecule detection of fluorescent site-specific tags.

We have developed a rapid molecular mapping technology--Direct Linear Analysis (DLA)--on the basis of the analysis of individual DNA molecules bound with sequence-specific fluorescent tags. The apparatus includes a microfluidic device for stretching DNA molecules in elongational flow that is coupled to a multicolor detection system capable of single-fluorophore sensitivity. Double-stranded DNA molecules were tagged at sequence-specific motif sites with fluorescent bisPNA (Peptide Nucleic Acid) tags. The DNA molecules were then stretched in the microfluidic device and driven in a flow stream past confocal fluorescence detectors. DLA provided the spatial locations of multiple specific sequence motifs along individual DNA molecules, and thousands of individual molecules could be analyzed per minute. We validated this technology using the 48.5 kb lambda phage genome with different 8-base and 7-base sequence motif tags. The distance between the sequence motifs was determined with an accuracy of +/-0.8 kb, and these tags could be localized on the DNA with an accuracy of +/-2 kb. Thus, DLA is a rapid mapping technology, suitable for analysis of long DNA molecules.

Bacteriophage lambda↗

A localized double-quantum filter for in vivo detection of taurine.

Noninvasive detection of taurine, an important amino acid involved in numerous physiological processes, by in vivo (1)H magnetic resonance (MR) spectroscopy is complicated by severe overlap of the taurine resonances with those of a number of other metabolites. Unambiguous differentiation of the taurine resonances requires spectral editing. In this study, the development of a localized spectral editing technique based on double-quantum filtering optimized for in vivo detection of taurine is described. The sequence recovers the taurine signal while substantially eliminating overlapping resonances and provides excellent three-dimensional spatial localization. The performance of the sequence is demonstrated both in phantoms and in rat brain in vivo. Magn Reson Med 42:454-460, 1999.

Animals↗

Microscopic displacement imaging with pulsed field gradient turbo spin-echo NMR.

We present a pulse sequence that enables the accurate and spatially resolved measurements of the displacements of spins in a variety of (biological) systems. The pulse sequence combines pulsed field gradient (PFG) NMR with turbo spin-echo (TSE) imaging. It is shown here that by ensuring that the phase of the echoes within a normal spin-echo train is constant, displacement propagators can be generated on a pixel-by-pixel basis. These propagators accurately describe the distribution of displacements, while imaging time is decreased by using separate phase encoding for every echo in a TSE train. Measurements at 0.47 T on two phantoms and the stem of an intact tomato plant demonstrate the capability of the sequence to measure complete and accurate propagators, encoded with 16 PFG steps, for each pixel in a 128 x 128 image (resolution 117 x 117 x 3,000 microm) within 17 min. Dynamic displacement studies on a physiologically relevant time resolution for plants are now within reach.

Solanum lycopersicum↗