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PubMed1994

[The superior and inferior venae cavae: angiography by TOF 2D magnetic resonance versus spin-echo sequences].

This work was aimed at assessing the usefulness of magnetic resonance angiography (MRA) in the investigation and diagnosis of vena cava conditions. Forty-five subjects that is 20 volunteers and 25 patients, were examined with MRA using a 1.5 T superconductive system (SE and angiography pulse sequences). In the 25 patients, 8 cases of thrombosis were diagnosed, together with 4 cases of suspected tumor spread into either the superior or the inferior vena cava, 2 cases of inferior vena cava agenesis, 5 cases of retroaortic left renal vein and 5 cases of abdominal aortic aneurysm. MRA was performed with the 2D time-of-flight (TOF) technique (FA 18 degrees, TR 30-40 ms, TE 10 ms); the images were acquired on the coronal, sagittal and axial planes with and without presaturation pulse and rotated in the post-processing according to the maximum intensity projection. In all volunteers MRA identified jugular veins, subclavian veins, anonymous veins, superior vena cava, inferior vena cava and common iliac veins. The main limitation of MRA was its spatial resolution. MRA proved to be less accurate than SE sequences in the assessment of tumor spread. As for thrombotic conditions, MRA provided useful additional information and is therefore considered a complementary technique to SE MRI. As for venous anomalies (double inferior vena cava, vena cava agenesis and retroaortic left renal vein) and in the study of the relationships with abdominal aortic aneurysms, MRA proved to be the more accurate of the two techniques.

Adult↗

PubMed2000

Nuclear magnetic resonance in inhomogeneous magnetic fields

The response of the spin system has been investigated by numerical simulations in the case of a nuclear magnetic resonance (NMR) experiment performed in inhomogeneous static and radiofrequency fields. The particular case of the NMR-MOUSE was considered. The static field and the component of the radiofrequency field perpendicular to the static field were evaluated as well as the spatial distribution of the maximum NMR signal detected by the surface coil. The NMR response to various pulse sequences was evaluated numerically for the case of an ensemble of isolated spins (1/2). The behavior of the echo train in Carr-Purcell-like pulse sequences used for measurements of transverse relaxation and self-diffusion was simulated and compared with the experiment. The echo train is shown to behave qualitatively differently depending on the particular phase schemes used in these pulse sequences. Different echo trains are obtained, because of the different superposition of Hahn and stimulated echoes forming mixed echoes as a result of the spatial distribution of pulse flip angles. The superposition of Hahn and stimulated echoes originating from different spatial regions leads to distortions of the mixed echoes in intensity, shape, and phase. The volume selection produced by Carr-Purcell-like pulse sequences is also investigated for the NMR-MOUSE. The developed numerical simulation procedure is useful for understanding a variety of experiments performed with the NMR-MOUSE and for improving its performance. Copyright 2000 Academic Press.

Journal Article↗

PubMed1995

Interaction of normal and mutant SRY proteins with DNA.

In mammals, sex determination is caused by the Y-chromosome gene SRY. The DNA-binding domain of human SRY protein is similar to those of the chromatin protein HMG1. Like HMG1, SRY binds to kinked DNA structures, and bends linear DNA sharply upon binding. We analysed the biochemical properties of mutant SRY proteins from five patients with complete gonadal dysgenesis: two bind and bend DNA almost normally, two bind inefficiently but bend DNA normally, and one binds DNA with almost normal affinity but produces a different angle. The mutations with moderate effect on complex formation can be transmitted to progeny, the ones with severe effects on either binding or bending are de novo. The angle induced by SRY depends on the exact DNA sequence, thus discriminating different target sites. We suggest that the exact spatial arrangement of the nucleoprotein complex organized by SRY in chromatin is essential for the expression of genes involved in testis differentiation.

Base Sequence↗

PubMed1993

Positive and negative regulatory regions control the spatial distribution of polygalacturonase transcription in tomato fruit pericarp.

The tomato fruit consists of a thick, fleshy pericarp composed predominantly of highly vacuolated parenchymatous cells, which surrounds the seeds. During ripening, the activation of gene expression results in dramatic biochemical and physiological changes in the pericarp. The polygalacturonase (PG) gene, unlike many fruit ripening-induced genes, is not activated by the increase in ethylene hormone concentration associated with the onset of ripening. To investigate ethylene concentration-independent gene transcription in ripe tomato fruit, we analyzed the expression of chimeric PG promoter-beta-glucuronidase (GUS) reporter gene fusions in transgenic tomato plants. We determined that a 1.4-kb PG promoter directs ripening-regulated transcription in outer pericarp but not in inner pericarp cells, with a sharp boundary of PG promoter activity located midway through the pericarp. Promoter deletion analysis indicated that a minimum of three promoter regions influence the spatial regulation of PG transcription. A positive regulatory region from -231 to -134 promotes gene transcription in the outer pericarp of ripe fruit. A second positive regulatory region from -806 to -443 extends gene activity to the inner pericarp. However, a negative regulatory region from -1411 to -1150 inhibits gene transcription in the inner pericarp. DNase I footprint analysis showed that nuclear proteins in unripe and ripe fruit interact with DNA sequences within each of these three regulatory regions. Thus, temporal and spatial control of PG transcription is mediated by the interaction of negative and positive regulatory promoter elements, resulting in gene activity in the outer pericarp but not the inner pericarp of ripe tomato fruit. The expression pattern of PG suggests that, although they are morphologically similar, there is a fundamental difference between the parenchymatous cells within the inner and outer pericarp.

Base Sequence↗

PubMed2000

Molecular characterization of a bacteriophage (Chp2) from Chlamydia psittaci.

Comparisons of the proteome of abortifacient Chlamydia psittaci isolates from sheep by two-dimensional gel electrophoresis identified a novel abundant protein with a molecular mass of 61.4 kDa and an isoelectric point of 6.41. C-terminal sequence analysis of this protein yielded a short peptide sequence that had an identical match to the viral coat protein (VP1) of the avian chlamydiaphage Chp1. Electron microscope studies revealed the presence of a 25-nm-diameter bacteriophage (Chp2) with no apparent spike structures. Thin sections of chlamydia-infected cells showed that Chp2 particles were located to membranous structures surrounding reticulate bodies (RBs), suggesting that Chp2 is cytopathic for ovine C. psittaci RBs. Chp2 double-stranded circular replicative-form DNA was purified and used as a template for DNA sequence analysis. The Chp2 genome is 4,567 bp and encodes up to eight open reading frames (ORFs); it is similar in overall organization to the Chp1 genome. Seven of the ORFs (1 to 5, 7, and 8) have sequence homologies with Chp1. However, ORF 6 has a different spatial location and no cognate partner within the Chp1 genome. Chlamydiaphages have three viral structural proteins, VP1, VP2, and VP3, encoded by ORFs 1 to 3, respectively. Amino acid residues in the phiX174 procapsid known to mediate interactions between the viral coat protein and internal scaffolding proteins are conserved in the Chp2 VP1 and VP3 proteins. We suggest that VP3 performs a scaffolding-like function but has evolved into a structural protein.

Abortion, Veterinary↗

PubMed1994

Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.

Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.

Animals↗

PubMed2003

Clinical-electroencephalogram patterns at seizure onset in patients with hippocampal sclerosis.

OBJECTIVE: The purpose of this study is to identify specific clinical-electroencephalogram (EEG) patterns at seizure onset in patients with hippocampal sclerosis (HS). METHODS: Sixty-six ictal video-EEG recordings corresponding to 26 patients with HS have been reviewed, focusing on the EEG features found during the first 30 ictal s. The EEG activity has been classified into the following groups: (A) according to spatial distribution: type 1: temporal electrodes on one side; type 2: temporal and adjacent frontal electrodes on one side; and type 3: non-lateralizing electrographic activity; and (B) according to morphology; subtype (a): regular 5-9 Hz rhythmic activity (RA); subtype (b): low-voltage rapid activity, followed by a 5-9 Hz RA; and subtype (c): irregular EEG sharp waves. We analyzed the clinical symptoms sequence and established the relationship with the ictal EEG patterns. RESULTS: Considering spatial distribution and morphology, the most frequent ictal EEG patterns were type 1 (57%), type 2 (37%), and subtype (a): 62%; subtype (b): 27%; and subtype (c): 11%. The sequence of clinical symptoms observed was: aura-->behavioral arrest-->oro-alimentary automatisms-->unilateral hand automatisms. All seizures with aura and including two or more symptoms of the clinical sequence (65%) were associated with a 1a, 1b, 2a or 2b EEG pattern. CONCLUSIONS: The identification of a specific clinical-EEG pattern provides a useful tool for the epileptogenic zone localization in non-invasive pre-surgical assessment of patients with hippocampal sclerosis. SIGNIFICANCE: The identification of a specific clinical-EEG pattern associated to neuroimaging findings and neuropsychological testing allows indicating surgery for the treatment of epilepsy in patients with hippocampal sclerosis, without performing any further complementary studies.

Adult↗

PubMed1985

Simple and B-cells in cat striate cortex. Complementarity of responses to moving light and dark bars.

This report is based on the quantitatively recorded responses of 72 striate cells in the simple (S and SH) and B-cell (B and BH) families to narrow (0.14 degrees) moving light and dark bars. Cells were regarded as hypercomplex (SH and BH) if the end-zone inhibition reduced the response to 50% of its peak value. The contrast of the bars was relatively low and matched to be equal but opposite for the two kinds of bar. Average response histograms to the two kinds of bar were recorded separately and only subsequently combined. The response histogram from a given S- or SH-cell shows separate response peaks to the light and dark bars. The number of peaks varies from two to five in different cells. Cells with two response peaks were encountered most commonly (54%), and rather less common were cells with three (31%), four (7.5%), and five (7.5%) peaks. By defining the sequence of the response peaks according to the direction preferred by a moving light bar, the number of distinct spatial patterns of responses to the moving bars increases from four to eight since the first response in the sequence can be either to a light bar or to a dark bar. Examples of all eight responses have been recorded. For cells in the simple family with two response peaks, as well as for B-cells, the width of the light-bar peak was the same as, or closely similar to, that of the dark-bar peak. For S- and SH-cells with more than two response peaks this was also true for the two principal peaks, namely the largest and the next-largest immediately adjacent peak. In the simple family, the mean widths of the two principal response peaks remained closely similar despite the progressive decrease in their respective widths as the number of peaks in the pattern increased from two to five. The mean width of the two principal response peaks from S- and SH-cells (0.6 degrees) was significantly less than the mean width for B-cells (1.4 degrees). For simple-family cells the spatial overlap between the two principal peaks (mean 14%) was always less than 50% of the overall width of the two peaks, whereas for B-cells the overlap (mean 79%) was always greater than 50%. For cells in both the simple and B-cell families the length of the receptive field as given by a moving light bar is the same as that given by a moving dark bar.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1984

Characterization of human chromosomal DNA sequences which replicate autonomously in Saccharomyces cerevisiae.

We have characterised two restriction fragments, isolated from a "shotgun" collection of human DNA, which function as autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae. Functional domains of these fragments have been defined by subcloning and exonuclease (BAL 31) deletion analysis. Both fragments contain two spatially distinct domains. One is essential for high frequency transformation and is termed the Replication Sequence (RS) domain, the other, termed the Replication Enhancer (RE) domain, has no inherent replication competence but is essential for ensuring maximum function of the RS domain. The nucleotide sequence of these domains reveals several conserved sequences one of which is strikingly similar to the yeast ARS consensus sequence.

Base Sequence↗

PubMed1991

Formation of the cochlea in the chicken embryo: sequence of innervation and localization of basal lamina-associated molecules.

The purpose of this study was to determine the temporal and spatial gradients in the innervation of the chicken cochlea, the basilar papilla, as it develops in the early embryo. A series of white Leghorn chick embryos (Hamburger-Hamilton Stage 20-43) were prepared for serial sectioning and stained by Toluidine blue or by antibodies to fibronectin or laminin. Light microscopic observations were made on the first fiber bundles to reach each region of the basilar papilla. There is a distinct temporo-spatial pattern of the ingrowth of fiber bundles to the developing basilar papilla. The primary pattern is not described as any simple linear gradient. Fiber ingrowth begins proximally, shifts to a distal and then to a mid-proximal region. The fiber ingrowth correlates temporally and spatially with disruption of fibronectin and laminin staining of the basal lamina where fiber bundles are penetrating. This pattern may reflect not only the sequence of fiber ingrowth but also the displacement of cells and fibers in the elongating basilar papilla, which grows as a result of a contemporaneous mitotic activity throughout the structure rather than progressing from one end to the other.

Animals↗

PubMed1996

Cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences in transgenic mouse embryos.

Peripherin is a neuron-specific type III intermediate filament protein expressed in well-defined populations of neurons projecting towards peripheral targets. To investigate the molecular mechanisms by which a gene is expressed in a specific subset of neurons, we used a transgenic approach in order to define peripherin gene sequences that are necessary for cell-type specific expression. Transgenic mice carrying different various genomic regions of the mouse peripherin gene fused to the Escherichia coli lacZ reporter gene were generated. We used three different peripherin/lacZ constructs containing either 5.8 kb upstream sequences, or both 5.8 kb upstream and 1.1 kb intragenic sequences, or 1.1 kb intragenic sequences associated with an heterologous promoter. Analysis of lacZ gene expression in transgenic mouse embryos showed that cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences. Analysis of transgenic mouse lines expressing the construct containing both upstream and intragenic sequences showed that this transgene contains all regulatory elements essential for both spatial and temporal expression of the mouse peripherin gene during embryogenesis. Furthermore, lacZ+ positive cells isolated from these transgenic lines by fluorescence-activated cell sorting (FACS) can be stained with a peripherin antibody, demonstrating that the transgene containing both upstream and intragenic sequences is expressed in peripherin neurons. These mouse peripherin upstream and intragenic sequences can now be used to identify cis-acting regulatory elements and transcription factors involved in peripherin gene regulation.

Animals↗

PubMed2026

A structural bridge between dengue virus tandem xrRNAs facilitates coordination of exonuclease resistance.

Orthoflavivirus RNA genomes resist host 5'-3' exoribonucleases to produce subgenomic flaviviral RNAs (sfRNAs). This resistance is conferred by exoribonuclease-resistant RNA (xrRNA) structures within the viral 3' untranslated region that often occur in tandem, and whose function can be coupled. In dengue virus serotype 2 (DENV2), this coupling results in changing patterns of sfRNA identity and abundance associated with the ability of the virus to adapt to host vs. vector infections. The physical basis of this coupling was unknown. Using a combination of virology, biochemistry, bioinformatics, structural biology, and biophysics, we explored the structural and sequence determinants of tandem xrRNA coupling in DENV2. We discovered that the spatial proximity, order, and structural integrity of the tandem xrRNAs are all important for coupling. Furthermore, an unpaired A-rich linker that lies between the two xrRNAs is essential in stabilizing a specific structure that correlates to coupling. This A-rich sequence likely forms tertiary contacts with an adjacent stem-loop structure to form a physical bridge between the two xrRNAs, a finding that is supported by a mid-resolution cryo-electron microscopy (cryo-EM) map of the DENV2 tandem xrRNAs. Disruption of the structure of this bridge by mutation changes the relative orientation or spacing between the tandem xrRNAs, which is correlated to their functional coupling. These findings help provide an explanation for the coupling between tandem xrRNAs, suggesting a new mechanistic hypothesis in which the two tandem xrRNAs can simultaneously encounter Xrn1.IMPORTANCEDengue virus (DENV) generates non-coding subgenomic flaviviral RNAs (sfRNAs) that affect several cellular pathways and are important for successful infection. These sfRNAs are formed by structured RNA elements in the viral genome called exoribonuclease-resistant RNAs (xrRNAs), which fold into a distinct three-dimensional topology to block degradation by host cell exoribonucleases and often occur in tandem. Specific patterns of sfRNAs made during infection are important for host vs. vector fitness, and in DENV2, this pattern depends on functional coupling between tandem xrRNAs. However, the source of this functional coupling was unknown. We determined that an unpaired A-rich linker between the tandem xrRNAs is necessary for creating a structural bridge between the tandem xrRNAs. This bridge appears to favor a specific orientation between the tandem xrRNAs that is correlated to coupling and therefore to the patterns and relative abundance of sfRNAs produced during infection.

Dengue Virus↗

PubMed1997

Interspecies exchange of a Hoxd enhancer in vivo induces premature transcription and anterior shift of the sacrum.

The precise activation, in space and time, of vertebrate Hox genes is an essential requirement for normal morphogenesis. In order to assess for the functional potential of evolutionary conserved Hox regulatory sequences, a phylogenetically conserved bipartite regulatory element necessary for proper spatial and temporal activation of the Hoxd-11 gene was replaced by its fish counterpart in the HoxD complex of mice, using an ES cell-based targeted exchange. Fetuses carrying this replacement activated Hoxd-11 transcription prematurely, which led to a rostral shift of its expression boundary and a consequent anterior transposition of the sacrum. These results demonstrate the high phylogenetic conservation of regulatory mechanisms acting over vertebrate Hox complexes and suggest that minor time difference (heterochronies) in Hox gene activation may have contributed to important morphological variations in the course of evolution.

Animals↗

PubMed1994

The mouse tissue plasminogen activator gene 5' flanking region directs appropriate expression in development and a seizure-enhanced response in the CNS.

Tissue plasminogen activator (t-PA) is a secreted serine protease implicated in multiple aspects of development. In the adult rat brain, transcription of t-PA is an immediate-early response in the hippocampus following treatments that induce neuronal plasticity. To study the sequence elements that govern transcription of this gene, in situ analysis was used to define t-PA's temporal and spatial expression pattern in midgestation embryos. Transgenic mice were then generated carrying t-PA 5' flanking sequences linked to the E. coli lacZ gene. Constructs containing 4 kb of the flanking sequences (4.0TAMGAL) confer beta-galactosidase activity mostly to the same tissues that exhibit high levels of t-PA mRNA by in situ analysis. In 4.0TAMGAL embryos from embryonic day 8.5 (E8.5) to 13.5 (E13.5), the majority of expression observed is localized to neural ectoderm-derived tissues. beta-galactosidase activity is first detected in restricted neuromeres in the midbrain and diencephalon, at E8.5 and E9.5 respectively. At E10.5, transgene expression is observed in neural crest-derived cranial nerves and dorsal root ganglia, but not placode-derived cranial nerves. From E10.5 to E13.5, beta-galactosidase activity is observed in postmitotic neurons of the midbrain, spinal cord, neural retina and the developing olfactory system. beta-galactosidase activity is also detected in areas undergoing tissue remodeling such as the pinna of the ear, whisker follicles and the limbs. In adult mice, lacZ is expressed in the hippocampus and this expression was found to be enhanced upon seizure in the giant pyramidal neurons of CA3. These results reinforce the concept that t-PA plays a role in neurogenesis and morphogenesis, and identifies the promoter region that directs its transcriptional regulation both in development and in the CNS.

Animals↗

PubMed1975

Structure and specificity of antibody molecules.

The structure of the Fab' fragment of a human myeloma protein (IgG1 (lambda) New) has been determined by X-ray crystallographic analysis to a nominal resolution of 0.2 nm. Each of the structure subunits corresponding to the variable and to the constant homology regions of the light and heavy polypeptide chains contains two irregular beta-sheets which are roughly parallel to each other and surround a tighly packed interior of hydrophobic side chains. The regions of the hypervariable sequences in the light and heavy chains occur in close spatial proximity at one end of the molecule, defining the active site of IgG New. The role of these hypervariable regions in defining the size and shape of the active site of different immunoglobulins is discussed on the basis of the three-dimensional model of Fab' New. Several ligands that bind to the active centre of IgG New have been used to obtain crystalline ligand-Fab' New complexes which were investigated by difference Fourier maps. These studies are analysed in terms of the biological function and specificity of antibodies.

Amino Acid Sequence↗

PubMed1995

Contrast response of a movement-encoding system.

The ability to identify the direction of apparent motion in a sequence of two short light pulses of different amplitudes at separate spatial locations was studied. The product of pulse amplitudes is a very poor predictor of such performance when one of the two signals is much higher in amplitude than the other: above a certain amplitude the probability of correct identification becomes virtually independent of the amplitude of the larger pulse. There was no noticeable difference in performance between low-high and high-low contrast sequences. Both the direction identification and the simple contrast-detection probabilities can be represented by the same psychometric function of the luminance increment delta L, provided that delta L is normalized by the nth power of the background luminance level, Lb. These results suggest that the general Reichardt-type scheme of movement encoding should be modified in the manner proposed for the fly's visual system [J. Opt. Soc. Am. A 6, 116 (1989)]: (1) the mean luminance is subtracted from the input signal before the signal is subjected to a nonlinear compression and (2) saturation characteristics are inserted into both branches of the two mirror-symmetric motion-detection subunits before multiplication of the input signals. The identical metric of the contrast response suggests that movement discrimination and luminance detection are two different special-purpose computations performed on the output of the same encoding network.

Contrast Sensitivity↗

PubMedDate not supplied

[Tunneling of autowaves through unexcitable parts of active media].

The mechanisms of propagation of autowaves through local heterogeneities in active media were studied by computer simulation. The model proposed by Zel'dovich and Frank-Kamenetsky and that of FitzHugh-Nagumo were used for studying autowave tunneling. It was shown that the underbarrier passage of an autowave through a nonexcitable area is limited by threshold values. It was shown that, for every fixed parameter value corresponding to the degree of nonexcitability of a local area, there exists a critical value for nonexcitable zone latitude. An autowave overcomes the barrier and continues to propagate when the value of zone latitude is less than the critical. Critical conditions for the origination of sources of secondary periodical sequences of impulses in excitable medium were found. It was shown that the properties of sources of secondary autowaves can be modified by regulating the size of the nonexcitable zone and the zone of increased excitability. In particular, the conditions were explored under which spatial irregularity behaves as a source of a unidirectional and/or an asynchronous sequence of impulses.

Biophysical Phenomena↗

PubMed2006

Pointing to places and spaces in a patient with visual form agnosia.

Previous investigations of visuospatial abilities in the visual form agnosic patient D.F. suggest that her egocentric sensorimotor processing is intact while her 'allocentric' judgments of spatial position are impaired. The current investigation extends these previous observations by comparing D.F.'s performance at pointing to a set of spatially distributed stimuli, either directly or by 'pantomiming' the responses in an adjacent homologous workspace. The results showed accurate sensorimotor localization when D.F. pointed directly to single targets or to sequences of targets, presumably as she could use egocentric visual coding. In spite of making relatively spared spatial judgments about the arrays, however, D.F. performed quite poorly when copying them and on the pantomimed pointing task. In this latter task good performance presumably depends on an ability to represent both the categorical and coordinate properties of the array (as does copying them), and to translate these into the effector-based coordinates required for accurate action. D.F.'s pantomimed pointing was similar to her copies of target arrays, as in both tasks there was evidence of spared (although somewhat degraded) appreciation of the relative spatial positions of the stimuli. Remarkably, her accuracy in this allocentric task was not worsened by longer pointing sequences. It is possible that D.F.'s degraded performance reflects a relative (though not complete) preservation of categorical coding within the ventral stream, despite a loss of coordinate coding there.

Adult↗