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At least 811 records · Page 45Linked to original sources

PubMed2001

Ghost imaging in MRI.

Needle biopsies and other interventions done under MR Fluoroscopy sometimes do not show the target well, either because the rapid sequence does not have adequate contrast or because a contrast agent may have washed out of the target. In these cases, an image that shows the target can be saved and scaled to match the spatial parameters of the fluoroscopic sequence, and used as a virtual or ghost field upon which the fluoroscopic images are superimposed, thus providing a view of the target, useful for needle pre-localization and for monitoring its progress as it is inserted.

Biopsy, Needle↗

PubMed2000

Targeting the Hprt locus in mice reveals differential regulation of Tie2 gene expression in the endothelium.

To study the in vivo expression of the murine Tie2 gene, we have targeted the hypoxanthine phosphoribosyltransferase (Hprt) gene locus to generate two single-copy transgenic mice: T1, containing the 2,100-bp Tie2 promoter upstream from the beta-galactosidase (LacZ) gene, and T5, which also included an enhancing element originating from the first intron of the Tie2 gene. Comparing T1 and T5 embryos at day E10.5 revealed differential endothelial cell-specific expression of LacZ, whereas colocalization analyses showed that the expression was confined to endothelial cells. Moderate reporter gene activity was observed in the brain and kidney of T1 adults, whereas extensive LacZ gene expression was seen in the vasculature of most organs of the T5 adults. This study demonstrates the feasibility of targeting the Hprt locus with endothelial cell-specific sequences to analyze the spatial-temporal expression of transgenes. Of particular importance is the observation that the analysis of a single transgene copy in a defined locus allows for an accurate and rapid comparison of transcriptional activity among regulatory DNA sequences.

Animals↗

PubMed1995

Expression, purification and kinetic behaviour of fission yeast low M(r) protein-tyrosine phosphatase.

A gene named stp1+, coding for a 17.5-kDa protein, that rescues cdc25-22 when overexpressed, has been previously isolated from fission yeast. Here we describe the expression and purification of Stp1 protein as a fusion with the glutathione S-transferase in E. coli and its kinetic characterisation. Stp1 deduced protein sequence shows an high homology to members of a class of cytosolic low M(r) protein phosphatase previously known to exist only in mammalian species. Stp1 has a kinetic behaviour that appears to be intermediate with respect to the two isoenzymatic forms of low M(r) protein tyrosine phosphatases present in mammalian tissues. These differing kinetic characteristics are mainly due to the sequence 45-56 that is spatially close to the active site pocket.

Amino Acid Sequence↗

PubMed1996

Geographic homogeneity and non-equilibrium patterns of mtDNA sequences in Tuscany, Italy.

The geographical distribution of 49 mtDNA sequences from 22 localities in Southern Tuscany, Italy, was studied by molecular analysis of variance, by a new spatial autocorrelation statistic specifically designed for sequence data and by reconstructing genealogies of haplotypes. All these methods indicated a high homogeneity of populations. Nevertheless, genetic variability showed significant departure from equilibrium expectations, in agreement with the predicted effects of a population expansion. We suggest that a past population expansion that was probably associated with a migrational wave and with local gene flow between localities prevented spatial structuring in Southern Tuscany.

Analysis of Variance↗

PubMed2005

Sequence evolution and sex-specific expression patterns of the C class floral identity gene, SpAGAMOUS, in dioecious Spinacia oleracea L.

Development in dioecious cultivated spinach, Spinacia oleracea, is distinguished by the absence of alternative reproductive organ primordia in male and female flowers. Given the highly derived floral developmental program in spinach, we wished to characterize a spinach C class floral identity gene and to determine the patterns of sequence evolution as well as compare the spatial and temporal expression patterns with those of AGAMOUS. The isolated cDNA sequence clusters phylogenetically within the AGAMOUS/FARINELLI C class clade. In comparison with the SLM1 sequence from the related Silene latifolia, amino acid replacements are highly conservative and non-randomly distributed, being predominantly found in hinge regions or on exposed surfaces of helices. The spinach gene (SpAGAMOUS) appears to be exclusively expressed in reproductive tissues and not in vegetative organs. Initial expression of SpAGAMOUS is similar in male and female floral primordia. However, upon initiation of the first whorl organs, SpAGAMOUS becomes restricted to meristemic regions from which the reproductive primordia will develop. This results in an early gender-specific pattern. Thus, the spinach C class gene is differentially expressed prior to reproductive organ development and is, at least, correlated with, if not directly involved in, the sexual dimorphism in spinach.

Amino Acid Sequence↗

PubMed1999

Structural and evolutionary inference from molecular variation in Neisseria porins.

The porin proteins of the pathogenic Neisseria species, Neisseria gonorrhoeae and Neisseria meningitidis, are important as serotyping antigens, putative vaccine components, and for their proposed role in the intracellular colonization of humans. A three-dimensional structural homology model for Neisseria porins was generated from Escherichia coli porin structures and N. meningitidis PorA and PorB sequences. The Neisseria sequences were readily assembled into the 16-strand beta-barrel fold characteristic of porins, despite relatively low sequence identity with the Escherichia proteins. The model provided information on the spatial relationships of variable regions of peptide sequences in the PorA and PorB trimers and insights relevant to the use of these proteins in vaccines. The nucleotide sequences of the porin genes from a number of other Neisseria species were obtained by PCR direct sequencing and from GenBank. Alignment and analysis of all available Neisseria porin sequences by use of the structurally conserved regions derived from the PorA and PorB structural models resulted in the recovery of an improved phylogenetic signal. Phylogenetic analyses were consistent with an important role for horizontal genetic exchange in the emergence of different porin classes and confirmed the close evolutionary relationships of the porins from N. meningitidis, N. gonorrhoeae, Neisseria lactamica, and Neisseria polysaccharea. Only members of this group contained three conserved lysine residues which form a potential GTP binding site implicated in pathogenesis. The model placed these residues on the inside of the pore, in close proximity, consistent with their role in regulating pore function when inserted into host cells.

Amino Acid Sequence↗

PubMed1990

Spin echo 31P spectroscopic imaging in the human brain.

Spectroscopic imaging of phosphorus metabolites in the human brain has been carried out with two data acquisition methods: by observation of the free induction decay (FID) signal and by a short spin echo sequence. The resultant spectral images and spatially resolved spectra are compared. Spin echo observation is found to provide spectra of superior quality, and by suitably selecting the sequence timing, no significant increase in T2 losses, as compared with the FID method, is encountered. 31P images with approximately 3.5 cm spatial resolution are obtained within times of 37 min at 2.0 T field strength.

Brain↗

PubMed1996

Fourier phase mapping of the human heart. The use of spatial modulation of magnetization cine magnetic resonance imaging.

RATIONALE AND OBJECTIVES: Fourier phase mapping of cine cardiac magnetic resonance (MR) imaging offers noninvasive analysis of temporal cardiac activation patterns. The aim of our investigation was to extend this analysis to intramyocardial dynamics. METHODS: A fast-imaging with steady-state precision (FISP) two-dimensional gradient echo spatial modulation of magnetization (SPAMM) sequence and a segmented two-dimensional FISP-SPAMM sequence were applied to acquire cine MR images of the complete cardiac cycle on a 1.5-tesla imager. Signal intensity data were submitted to pixel-wise Fourier phase analysis. Color-encoded amplitude and phase maps were displayed for visual analysis. RESULTS: Using the unsegmented SPAMM two-dimensional FISP sequence, a more consistent tag-to-myocardium contrast and a higher number of cardiac phases was achieved than by using the segmented version of this sequence. The typical tag displacement reflected complex intramyocardial dynamics, including rotation. Phase mapping displayed a pattern of contraction consistent with electrophysiologic concepts of cardiac activation. In contrast, the segmented sequence did not reflect any differences in the onset of cardiac contraction, although tag displacement was apparent with this sequence as well. CONCLUSIONS. Fourier phase mapping of cardiac MR imaging tagging studies allows for noninvasive analysis of intramyocardial activation patterns. A temporal resolution of 50 mseconds per image at a heart rate of 75 beats per minute allows for an assessment of spatial differences in the onset of myocardial activation.

Adult↗

PubMed2004

Combination of low and high resolution sequences in two orientations for dynamic contrast-enhanced MRI of the breast: more than a compromise.

The purpose was to combine T1-weighted 3D gradient echo sequences at low and high spatial resolution (and short and longer acquisition time, respectively) in two orientations without compromising signal/time curve analysis and to evaluate the incremental value of assessing architectural features in high resolution images in dynamic contrast-enhanced MR mammography. T1-weighted 3D-FLASH sequences in a 1.5-T scanner (512 x 256 pixel matrix at high resolution; 256 x 128 pixels at low resolution sequences, 72 slices, 1.7-mm slice thickness, TR 8.8 ms, TE 4.5 ms, flip angle 25 degrees) were acquired in a special order during a single investigation. Three observers evaluated architectural features of 36 histopathologically proven lesions using high or low resolution images independently. Architectural features of each lesion were assessed by rating on two three-point scales. Kappa statistics verified the decrease of inter-observer variability. All observers improved assessment of architectural features regarding high resolution images in transversal and coronal orientation (observer A: eight positive, three negative corrections; B: 12/5; C: 16/4). Most positive corrections resulted from improved detection of morphologic criteria of malignancy. Mean inter-observer agreement significantly (P<0.05) increased from "slight" to "moderate" (mean weighted kappa increased from 0.185 to 0.422). This protocol at the charge of slightly enlarged time for measurement offers an elegant way to improve analysis of architectural features in MRM.

Adolescent↗

PubMed1989

Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues.

We have identified the regulatory sequences required for the periodic expression of the Drosophila pair rule gene even skipped (eve). We find that the gradually changing pattern of periodic eve expression during early embryogenesis is directed by two distinct regulatory programs. Initially, eve expression in individual stripes is established by different regulatory elements, each of which responds to nonperiodic spatial cues provided, at least in part, by the gap genes. Later, coordinate expression of eve in all seven stripes is directed by a single regulatory region that responds to periodic cues provided by primary pair rule genes, including eve itself. As a consequence of this two-step regulatory program, eve functions both in the establishment of the periodic pattern of gene expression and in the subsequent specification of parasegmental boundaries.

Animals↗

PubMed1998

Characterization of Toscana virus-defective interfering particles generated in vivo.

Toscana (TOS) virus stocks strongly interfering with standard virus replication were obtained by sequential passages of virus in suckling mouse brain. Characterization of viral RNAs in these stocks showed the presence of a heterogeneous population of defective RNA molecules derived from the L genomic segment, in both nucleocapsid (NC) and messenger RNAs, suggesting that these molecules could be replicated, assembled, and transcribed. Subgenomic RNAs from the L segment but not from the S or M segments were found in cells infected with these stocks. Defective RNA molecules interfered with virus replication and retained 5' and 3' genomic termini. Nucleotide sequence analysis of some cloned defective interfering (DI) RNAs revealed they contained one or more internal deletions reducing their length to 7-13% of the full-length L segment. An identical sequence motif, of variable length, was found at both terminal sites of the RNA junction on standard L sequences. This motif was retained only in one copy in the subgenomic RNA. These results are consistent with the generation of TOS virus DI particles in vivo and suggest that the defective genomic RNAs could be generated by polymerase jumping from a sequence to an identical one spatially closed because of the RNA structure.

Animals↗

PubMed1997

Disruption of short-term recognition memory for tones: streaming or interference?

A sequence of auditory stimuli interpolated between the initial presentation of a tone and a comparison tone impairs recognition performance. Notably, the impairment is much less with interpolated speech than with tones. Six experiments converge on the conclusion that this pattern of impairment is due more to the organization of the interpolated sequence than to its similarity to the to-be-remembered standard. Factors that contribute to the coherence of the interpolated sequence into a stream distinct from the initial tone are primary determinants of the level of impairment. This is demonstrated by manipulating factors that contribute to the coherence of the interpolated sequence by the action of temporal, spatial, timbral, and tonal attributes. However, the relative immunity of recognition performance to the interpolation of unprocessed digit sequences is not explained wholly by such coherence.

Auditory Perception↗

PubMed1999

New mode of DNA binding of multi-zinc finger transcription factors: deltaEF1 family members bind with two hands to two target sites.

SIP1, a Smad-interacting protein, and deltaEF1, a transcriptional repressor involved in skeletal and T-cell development, belong to the same family of DNA binding proteins. SIP1 and deltaEF1 contain two separated clusters of zinc fingers, one N-terminal and one C-terminal. These clusters show high sequence homology and are highly conserved between SIP1 and deltaEF1. Each zinc finger cluster binds independently to a 5'-CACCT sequence. However, high-affinity binding sites for full-length SIP1 and deltaEF1 in the promoter regions of candidate target genes like Xenopus Xbra2, and human alpha4-integrin and E-cadherin, are bipartite elements composed of one CACCT and one CACCTG sequence, the orientation and spacing of which can vary. Using transgenic Xenopus embryos, we demonstrate that the integrity of these two sequences is necessary for correct spatial expression of a Xbra2 promoter-driven reporter gene. Both zinc finger clusters must be intact for the high-affinity binding of SIP1 to DNA and for its optimal repressor activity. Our results show that SIP1 binds as monomer and contacts one target sequence with the first zinc finger cluster, and the other with the second cluster. Our work redefines the optimal binding site and, consequently, candidate target genes for vertebrate members of the deltaEF1 family.

Animals↗

PubMed1976

The evolution of plants and animals under domestication: the contribution of studies at the molecular level.

Protein molecules are essential catalysts in life processes and also form much of the substance of living material. Their three dimensional structures determine their biological function. Their biosynthesis is primarily determined by arrays of nucleic acid macromolecules (DNA and RNA), and the amino acid sequences that constitute their long spatially organized peptide-chain molecules reflect at one remove this DNA coding system, and thus record a step-by-step history of some of the viable genetic events (natural or man-controlled) that have created the organism and the breed. Amino acid sequences can be used to trace the progress of controlled breeding in two ways: by extrapolation back from living breeds, and by analysis of ancient protein material. Of the latter, bone or tendon or skin collagens and hair keratins are the most perfectly preserved as molecular structures through 20,000 years and indeed much longer. Amino acid sequences are expensive to determine (collagen has 1052 amino acid residues), and the potential of this palaeobiological information has been as yet little exploited. The first approach has, however, been more explored, in both plants and animals. Several protein systems must be studied in conjunction to reveal the phylogenetic threads in any one breed. As the three dimensional quaternary structure of protein molecules becomes more appreciated in relation to biological function, and as new techniques and procedures are developed, amino acid sequence data can become more informative in our ultimate understanding of early selective breeding.

Amino Acid Sequence↗

PubMed1987

Nucleotide sequence analysis of alpha-amylase and thiol protease genes that are hormonally regulated in barley aleurone cells.

We have determined the nucleotide sequences of Amy32b, a type A alpha-amylase gene, and of the gene for aleurain, a thiol protease closely related to mammalian cathepsin H. Both are expressed in barley aleurone cells under control of the plant hormones gibberellic acid and abscisic acid, but only aleurain is expressed at high levels in other barley tissues. Sequence analysis indicates that the 5' end of the aleurain gene, comprising 3 exons and 2 introns, may have become associated with the remainder of the gene, encoding the protease domain of the protein, by some sort of recombination event. This 5' domain of the gene is very G + C-rich and is flanked by inverted repetitive sequences. We found two different groups of homologous sequence elements. The first group consists of four blocks of sequences conserved in the same spatial arrangement in both genes; these are arranged at similar intervals upstream from the Amy32b TATA box and from a TATA box present in intron 3 of aleurain, outside of the 5' domain and upstream from the protease domain. A part of two of these conserved sequences is similar to the core sequence of certain enhancer elements characterized from mammalian cells. The second group of homologous elements is present in the upstream region of both genes. We speculate that these conserved sets of sequences may have some role in either the tissue specificity of expression of the genes or in some part of the hormonal regulation imposed on them.

Abscisic Acid↗

PubMed2005

Visual spatial attention tracking using high-density SSVEP data for independent brain-computer communication.

The steady-state visual evoked potential (SSVEP) has been employed successfully in brain-computer interface (BCI) research, but its use in a design entirely independent of eye movement has until recently not been reported. This paper presents strong evidence suggesting that the SSVEP can be used as an electrophysiological correlate of visual spatial attention that may be harnessed on its own or in conjunction with other correlates to achieve control in an independent BCI. In this study, 64-channel electroencephalography data were recorded from subjects who covertly attended to one of two bilateral flicker stimuli with superimposed letter sequences. Offline classification of left/right spatial attention was attempted by extracting SSVEPs at optimal channels selected for each subject on the basis of the scalp distribution of SSVEP magnitudes. This yielded an average accuracy of approximately 71% across ten subjects (highest 86%) comparable across two separate cases in which flicker frequencies were set within and outside the alpha range respectively. Further, combining SSVEP features with attention-dependent parieto-occipital alpha band modulations resulted in an average accuracy of 79% (highest 87%).

Adult↗

PubMed2006

Temporal encoding of place sequences by hippocampal cell assemblies.

Both episodic memory and spatial navigation require temporal encoding of the relationships between events or locations. In a linear maze, ordered spatial distances between sequential locations were represented by the temporal relations of hippocampal place cell pairs within cycles of theta oscillation in a compressed manner. Such correlations could arise due to spike "phase precession" of independent neurons driven by common theta pacemaker or as a result of temporal coordination among specific hippocampal cell assemblies. We found that temporal correlation between place cell pairs was stronger than predicted by a pacemaker drive of independent neurons, indicating a critical role for synaptic interactions and precise timing within and across cell assemblies in place sequence representation. CA1 and CA3 ensembles, identifying spatial locations, were active preferentially on opposite phases of theta cycles. These observations suggest that interleaving CA3 neuronal sequences bind CA1 assemblies representing overlapping past, present, and future locations into single episodes.

Action Potentials↗

PubMedDate not supplied

[Conformation of dinucleoside phosphates: the conformation encoding hypothesis].

The temperature dependence of the spin-lattice relaxation rate of nucleic bases protones and HI' of ApA, ApC, CpA and CpC (D2O, pH 7) were measured. The possible closed conformers of these dinucleoside phosphates (DNP) were computed by atom-atom potential method. On the basis of conformational calculation and experimental data the composition of closed state was determined. Besides the right-handed "canonic" conformers, the "non-canonic" right- and left-handed conformers were shown to be present in the solution of all DNP studied. It is important to note that, "canonic" conformers of DNP studied being equally probable, the possibility of the realization of "non-canonic" conformers is determined by the nucleotide sequence. It may be expected that different nucleotide sequences have unique "non-canonic" conformations. That type of dependence of the spatial organization of polynucleotides on its nucleotide sequence we call "the conformational encoding".

Adenosine↗