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At least 1,747 records · Page 97Linked to original sources
PubMed2005

Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome.

Velo-cardio-facial syndrome/DiGeorge syndrome results from unequal crossing-over events between two 240-kb low-copy repeats termed LCR22 (LCR22-2 and LCR22-4) on Chromosome 22q11.2, comprised of modules, each of which are >99% identical in sequence. To delineate regions in the LCR22s that might contain hotspots for 22q11.2 rearrangements, we scanned the interval for increased rates of recombination with the hypothesis that these regions might be more prone to breakage. We generated an algorithm to detect sites of altered recombination by searching for single nucleotide polymorphic positions in BAC clones from different libraries mapped to LCR22-2 and LCR22-4. This method distinguishes single nucleotide polymorphisms from paralogous sequence variants and complex polymorphic positions. Sites of shared polymorphism are considered potential sites of gene conversion or double cross-over between the two LCR22s. We found an inverse correlation between regions of paralogous sequence variants that are unique to a given position within one LCR22 and clusters of shared polymorphic sites, suggesting that these clusters depict altered recombination and not remnants of ancestral single nucleotide polymorphisms. We postulate that most shared polymorphic sites are products of past transfers of DNA information between the LCR22s, suggesting that frequent traffic of genetic material may induce genomic instability in the two LCR22s. We also found that gaps up to 1.5 kb long can be transferred between LCR22s.

Algorithms↗
PubMed1999

Prospective comparison of MR lung perfusion and lung scintigraphy.

This study attempted to assess the accuracy and potential of lung magnetic resonance (MR) perfusion imaging compared with perfusion scintigraphy in the evaluation of patients with suspected lung perfusion defects. The technique, which uses an inversion recovery turbo-FLASH sequence with ultra-short TE (1.4 msec), was tested in 24 patients suspected clinically of having acute pulmonary embolism (n = 19) and in patients with severe pulmonary emphysema (n = 5). Perfusion lung scintigraphy was performed within 48 hours prior to the MRI examination in both groups of patients. The dynamic study was acquired in the coronal plane and consisted of 10 images of 6 slices (a total of 60 images per series). Gadopentetate dimeglumine (0.1 mmol/kg) was manually injected as a compact bolus during the acquisition of the first image. Three senior radiologists reviewed all unprocessed two-dimensional coronal sections. They were blinded to clinical data and other imaging modalities. For the three observers, the average sensitivity and specificity of MR were 69% and 91%, respectively. The overall agreement between MR and scintigraphy appears to be good, with a good correlation between the two modalities (kappa = 0.63). However, the data showed variability depending on the location of the perfusion defect, with higher accuracy in the upper lobes. The agreement between MR perfusion and scintigraphy appears to be moderate in the left inferior lobe (kappa = 0.48). The data showed an overall good interobserver agreement (kappa = 0.66). MR perfusion of the lung is a promising technique in detecting lung perfusion defects.

Adult↗
PubMed2000

An analytical SMASH procedure (ASP) for sensitivity-encoded MRI.

The simultaneous acquisition of spatial harmonics (SMASH) method of imaging with detector arrays can reduce the number of phase-encoding steps, and MRI scan time several-fold. The original approach utilized numerical gradient-descent fitting with the coil sensitivity profiles to create a set of composite spatial harmonics to replace the phase-encoding steps. Here, an analytical approach for generating the harmonics is presented. A transform is derived to project the harmonics onto a set of sensitivity profiles. A sequence of Fourier, Hilbert, and inverse Fourier transform is then applied to analytically eliminate spatially dependent phase errors from the different coils while fully preserving the spatial-encoding. By combining the transform and phase correction, the original numerical image reconstruction method can be replaced by an analytical SMASH procedure (ASP). The approach also allows simulation of SMASH imaging, revealing a criterion for the ratio of the detector sensitivity profile width to the detector spacing that produces optimal harmonic generation. When detector geometry is suboptimal, a group of quasi-harmonics arises, which can be corrected and restored to pure harmonics. The simulation also reveals high-order harmonic modulation effects, and a demodulation procedure is presented that enables application of ASP to a large numbers of detectors. The method is demonstrated on a phantom and humans using a standard 4-channel phased-array MRI system.

Fourier Analysis↗
PubMed2002

Rapid method for correction of CSF partial volume in quantitative proton MR spectroscopic imaging.

Partial volume effects with cerebrospinal fluid (CSF), if uncorrected, can lead to underestimation of metabolite concentrations in quantitative proton magnetic resonance spectroscopic imaging (MRSI) of the brain. A rapid method for the correction of CSF partial volume effects is described based on selective CSF imaging using long echo time (TE) fast spin echo (FSE) magnetic resonance imaging (MRI). In order to achieve maximum suppression of signal from brain parenchyma, the FSE sequence is coupled with an inversion recovery (IR) pulse. Scan time is minimized using single shot (SS) IR-FSE. The method is validated against a current "gold standard" for the determination of CSF volumes, namely, segmented 3D spoiled gradient-echo (SPGR) scans. Excellent agreement in CSF percentage determined by the two methods was found (linear regression analysis: slope = 0.99 +/- 0.02, intercept = 2.08 +/- 0.45; mean +/- standard errors, R = 0.93) in pooled data from four healthy subjects. An example of the use of SS-IR-FSE for partial volume correction in a leukodystrophy patient with T(2) hyperintense lesions is demonstrated. SS-IR-FSE is a simple and rapid method for applying partial volume corrections in quantitative proton MRSI, which may be of particular value in the clinical environment when time constraints do not allow longer, perhaps more accurate segmentation methods to be used.

Adult↗
PubMed1987

1H NMR relaxation measurements of human tissues in situ by spatially resolved spectroscopy.

Spatially resolved spectroscopy (SPARS) is a method for obtaining high-resolution NMR spectra of well-defined volumes of human tissues in situ. This method was combined with the Carr-Purcell-Meiboom-Gill multiple-echo sequence for T2, and with inversion recovery for T1 relaxation measurements. Relaxation times obtained by SPARS were compared with standard CPMG and IR relaxation measurements and with imaging methods, using a number of relaxation phantoms. Spectroscopically resolved relaxation data of human bone marrow, muscle, and adipose tissue in situ were obtained. T2 measurements of human adipose tissue gave different results when using single-echo measurements rather than the CPMG method. This difference was interpreted as a J modulation effect, which shows up in fatty acid proton resonances. This J modulation effect influences the intensity of adipose tissue in routine 1H NMR images.

Adipose Tissue↗
PubMed1993

Contrast-enhanced first pass myocardial perfusion imaging: correlation between myocardial blood flow in dogs at rest and during hyperemia.

The sensitivity of contrast-enhanced MR first pass perfusion imaging in detection and quantification of hypoperfused myocardium was evaluated using an instrumented, closed-chest dog model where graded regional hypoperfusion was induced by applying predetermined levels of stenosis to the left anterior descending artery (LAD). All measurements were performed at rest and under stress induced by dipyridamole (DIP). Myocardial perfusion was assessed both with MR and radiolabeled microspheres injected immediately before the administration of the MR contrast agent. Ultrafast MR imaging was performed using a Turbo FLASH sequence with a 180 degrees inversion prepulse. A Gd-DTPA bolus was injected into the left atrium and T1-weighted images were acquired with every heart beat. Signal intensity measured from the images in regions of the LAD and left circumflex (LCx) perfusion beds was plotted against time to generate signal intensity versus time curves (SI time curve). Various flow indices were derived according to the indicator dilution theory, and compared with and without volume correction due to vasodilation to the myocardial blood flow (MBF) calculated from radiolabeled microspheres. Correlation of the MR and MBF data demonstrated that different transmural and regional myocardial perfusion levels can be easily visualized in the perfusion images and accurately monitored by the SI time curves. Detection of the impairment of myocardial perfusion improved significantly after administration of DIP. The inverse mean transit time calculated from the SI time curve was found to yield a linear correlation to absolute MBF derived from the microsphere data. These results suggest that with intracardiac injections of exogenous contrast agent, myocardial perfusion can be assessed parametrically with first pass contrast enhanced ultrafast MRI.

Animals↗
PubMed1997

MRI quantitative myocardial perfusion with compartmental analysis: a rest and stress study.

K1 (first-order transfer constant from arterial plasma to myocardium for Gd-DTPA) and Vd (distribution volume of Gd-DTPA in myocardium) were measured in vivo in a canine model (n = 5) using MRI-derived myocardial perfusion curves and a compartmental model. Perfusion curves were obtained after a bolus injection of Gd-DTPA (0.04 mM/kg) with an inversion-prepared fast gradient echo sequence. Myocardium and blood signal intensity were converted to a concentration of Gd-DTPA, according to a model appropriate for short (<1 s) interimage intervals characteristic of cardiac-triggered acquisitions. Before dipyridamole-induced stress, K1 and Vd, obtained from the fit of the MRI-derived perfusion curves, were 6.2 +/- 1.4 (mHz) and 17.5 +/- 4.2%, respectively. After dipyridamole infusion, a K1 increase of a factor of 2.82 +/- 0.72 was measured (P = 0.003). No change was observed in Vd (P = 0.98). These results suggest that the K1 increase after dipyridamole reflects a flow-related effect that can be useful to quantify the MRI-derived perfusion curves.

Animals↗
PubMed2006

MRI to detect atherosclerosis with gadolinium-containing immunomicelles targeting the macrophage scavenger receptor.

The ability to specifically image macrophages may enable improved detection and characterization of atherosclerosis. In this study we evaluated the in vitro uptake of gadolinium (Gd)-containing immunomicelles (micelles linked to macrophage-specific antibody), micelles, and standard contrast agents by murine macrophages, and sought to determine whether immunomicelles and micelles improve ex vivo imaging of apolipoprotein E knockout (ApoE KO) murine atherosclerosis. Murine RAW 264.7 macrophages were incubated with Gd-DTPA, micelles, and immunomicelles. Cell pellets were prepared and imaged using a 1.5 T MR system with an inversion recovery spin-echo sequence to determine the in vitro T1 values. Ex vivo analysis of mouse aortas was performed using a 9.4T MR system with a high-spatial-resolution sequence (78x39x78 microm3). The T1 value was significantly decreased in cells treated with micelles compared to Gd-DTPA (P<0.0001), and in cells incubated at 4 degrees C with immunomicelles compared to micelles (P<0.05). Ex vivo MRI signal intensity (SI) was significantly increased by 81% and 20% in aortas incubated with immunomicelles and micelles, respectively. Confocal microscopy demonstrated in vitro and ex vivo uptake of fluorescent immunomicelles by macrophages. Immunomicelles and micelles improve in vitro and ex vivo MR detection of macrophages, and may prove useful in the detection of macrophage-rich plaques.

Animals↗
PubMed1999

Nucleocytoplasmic export of type D simian retrovirus genomic RNA: identification of important genetic subregions and interacting cellular proteins.

The simian retrovirus (SRV) genome contains a constitutive transport element (CTE) within its 3' intergenic region (IR) that mediates the nuclear export of unspliced SRV RNA. The serogroup 2 SRV CTE is predicted to form a stable stem-loop structure containing two major internal loops exhibiting 180 degrees inverse symmetry, with loop face sequences A, A', B, and B' and additional minor internal and terminal loops. To begin the identification of potential CTE-interacting proteins and to assess structural requirements for protein interaction, we conducted RNA mobility shift assays using IR fragments that obliterated this region's known stable stem-loop structure. Using immunoblotting assays, we have determined that RNA helicase A, implicated in the nuclear export of unspliced SRV genomic RNA, does not appear to interact directly with either the complete serogroup 2 SRV 3' IR or the subregion RNAs and that formation of RNA-protein complexes is conferred by interaction with other novel proteins. UV crosslinking of RNA-protein complexes, coupled with RNase T1/A digestion, indicates that a novel protein of 120 kDa molecular weight interacts with the complete CTE or with individual subregion RNAs. Transfection analyses indicate that SRV recombinants containing A, A', B, or B' sequences forming the faces for two open loops undergo RNA export; only the complete sense CTE recombinant or a second recombinant containing two subregions in sense orientation that reconstitute the 3' two-thirds of the 3' IR, and contain only A' and B that form the faces for two terminal loops, are capable of SRV RNA export. These experiments indicate that secondary structural determinants of the 3' IR and multiple protein interactions may be important factors in the nuclear export of unspliced SRV RNA.

Animals↗
PubMed1982

Pleiotropic effects associated with the deletion of heterochromatin surrounding rDNA on the X chromosome of Drosophila.

In Drosophila melanogaster X chromosome heterochromatin (Xh) constitutes the proximal 40% of the X chromosome DNA and contains a number of genetic elements with homologous sites on the Y chromosome, one of which is well defined, namely, the bobbed locus, the repetitive structural locus for the 18S and 28S rRNAs. This report presents the localisation of specific repeated DNA sequences within Xh and the employment of this sequence map in constructing new chromosomes to analyse the nature of the heterochromatin surrounding the rDNA region. Repeated sequences were located relative to inversion breakpoints which differentiate Xh cytogenetically. When the rDNA region was manipulated to be in a position in the chromosome so that it was without the Xh which normally surrounds it, the following observations were made. (i) The rDNA region of Xh is intrinsically heterochromatic, remaining genetically active and yet possessing major heterochromatic properties even in the absence of the flanking heterochromatin regions. (ii) The size of the deletion removing the portion of Xh normally located distal to the rDNA region affected the dominance relationship between the X and Y nucleolar organizers (activity/endoreduplication assayed in male salivary glands). The X rDNA without any flanking heterochromatin was dominant over Y rDNA while the presence of some Xh allowed both the X and Y rDNA to be utilized. (iii) Enhancement of the position effect variegation on the white locus was demonstrated to occur as a result of the Xh deletions generated. EMS mutagenesis studies argue that the regions of Xh flanking the rDNA region contain no vital loci despite the fact that they strongly effect gene expression in some genotypes. This is consistent with early studies using X-ray mutagenesis (Lindsley et al., 1960). The pleiotropic effects of deleting specific regions of Xh is discussed in relation to the possible influence of heterochromatin on the organisation of the functional interphase nucleus.

Animals↗
PubMed1985

Vocal cues to deception: a comparative channel approach.

The study investigated the leakage potential of different voice and speech cues using a cue isolation and masking design. Speech samples taken from an earlier experiment were used in which 15 female students of nursing dissimulated negative affect produced by an unpleasant movie or told the truth about positive affect following a pleasant movie. Several groups of judges rated these speech samples in five conditions: (1) forward or clear, (2) electronic filtering, (3) random splicing, (4) backwards, (5) pitch inversion, (6) tone-silence sequences. The results show that vocal cues do indeed carry leakage information and that, as reflected in the differences among the conditions masking different types of cues respectively, voice quality cues may be centrally implicated. In addition, gender differences in decoding ability are discussed.

Affect↗
PubMed2001

Comparison between patient characteristics and cranial MR findings in chronic thinner intoxication.

Chronic thinner intoxication is one of the most serious social problems among teenagers and young adults in Japan. The purpose of this study was to evaluate clinical characteristics of patients with thinner intoxication who had positive MR findings. During the past 4 years, cranial MR imaging of 85 patients (51 males and 34 females) with chronic thinner intoxication was done at a national psychiatric hospital. The MR imaging was performed on a 1.0-T scanner with use of standard pulse sequences including fluid-attenuated inversion recovery (FLAIR). The established characteristic MR findings of chronic thinner intoxication were observed in 8 of the 85 patients: 4 males and 4 females. The female patients tended toward emaciation and were approximately 5 years younger than the male patients. Six of the 8 patients had severe neurological symptoms such as cerebellar ataxia and decreased visual acuity. In contrast, only 3 of 77 (4%) patients with normal MR findings had mild neurological abnormalities such as tremor. If patients with chronic thinner intoxication have significant neurological symptoms, MR imaging should be performed for evaluation of brain abnormalities. Emaciated female patients may be particularly vulnerable to neurological damage caused by thinner intoxication.

Adolescent↗
PubMed1998

Quantification of emotion by nonlinear analysis of the chaotic dynamics of electroencephalograms during perception of 1/f music.

The goal of this study is to quantify and determine the way in which the emotional response to music is reflected in the electrical activities of the brain. When the power spectrum of sequences of musical notes is inversely proportional to the frequency on a log-log plot, we call it 1/f music. According to previous research, most listeners agree that 1/f music is much more pleasing than white (1/f0) or brown (1/f2) music. Based on these studies, we used nonlinear methods to investigate the chaotic dynamics of electroencephalograms (EEGs) elicited by computer-generated 1/f music, white music, and brown music. In this analysis, we used the correlation dimension and the largest Lyapunov exponent as measures of complexity and chaos. We developed a new method that is strikingly faster and more accurate than other algorithms for calculating the nonlinear invariant measures from limited noisy data. At the right temporal lobe, 1/f music elicited lower values of both the correlation dimension and the largest Lyapunov exponent than white or brown music. We observed that brains which feel more pleased show decreased chaotic electrophysiological behavior. By observing that the nonlinear invariant measures for the 1/f distribution of the rhythm with the melody kept constant are lower than those for the 1/f distribution of melody with the rhythm kept constant, we could conclude that the rhythm variations contribute much more to a pleasing response to music than the melody variations do. These results support the assumption that chaos plays an important role in brain function, especially emotion.

Auditory Perception↗
PubMed1999

Genomic studies of the Lucké tumor herpesvirus (RaHV-1).

Ranid herpesvirus 1 (RaHV-1) is the etiological agent of the Lucké renal adenocarcinoma of the North American leopard frog Rana pipiens. Construction of cosmid libraries containing RaHV-1 DNA inserts allowed the derivation of a BamHI map for the viral genome. Summation of fragment sizes indicates that the genome is 217 kbp in size, a value in accordance with the most recent published estimate (220 kbp) obtained by field-inversion gel electrophoresis. The DNA sequence of the 39,757-bp insert in 1 cosmid (cos54) was determined and was predicted to contain 21 complete and 3 partial genes. In all, 12 genes have distant counterparts in a fish herpesvirus (ictalurid herpesvirus 1) and are present in 2 blocks, 1 of which is relatively inverted. This indicates that RaHV-1 belongs to the fish virus lineage of the herpesvirus family rather than to the lineage populated by mammalian and avian viruses. The remaining 12 genes in cos54 lack counterparts in any other herpesvirus. One of these encodes a putative DNA (cytosine-5) methyltransferase. This raises the possibility that biological processes induced in the host by RaHV-1 might involve methylation of cellular DNA by the viral enzyme.

Adenocarcinoma↗
PubMed2002

Molecular characterization of fervidolysin, a subtilisin-like serine protease from the thermophilic bacterium Fervidobacterium pennivorans.

The fls gene encoding fervidolysin, a keratin-degrading proteolytic enzyme from the thermophilic bacterium Fervidobacterium pennivorans, was isolated using degenerate primers combined with Southern hybridization and inverse polymerase chain reaction. Further sequence characterization demonstrated that the 2.1-kb fls gene encoded a 699-amino-acid preproenzyme showing high homology with the subtilisin family of the serine proteases. It was cloned into a pET9d vector, without its signal sequence, and expressed in Escherichia coli. The heterologously produced fervidolysin was purified by heat incubation followed by ion exchange chromatography and emerged in the soluble fraction as three distinct protein bands, as judged from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Amino-terminal-sequence analysis of these bands and their comparison with that determined from biochemically purified keratinase and its predicted protein sequence, identified them as a 73-kDa fervidolysin precursor, a 58-kDa mature fervidolysin, and a 14-kDa fervidolysin propeptide. Using site-directed mutagenesis, the active-site histidine residue at position 79 was replaced by an alanine residue. The resulting fervidolysin showed a single protein band corresponding in size to the 73-kDa fervidolysin precursor, indicating that its proteolytic cleavage resulted from an autoproteolytic process. Knowledge-based modeling experiments showed a distinctive binding region for subtilases, in which binding of the propeptide could take place prior to autoproteolysis. Assays using keratin and other proteinaceous substrates did not display fervidolysin activity, perhaps because of the tight binding of the propeptide in the substrate-binding site, where it could then function as an inhibitor.

Amino Acid Sequence↗
PubMed2006

Targeted Ds-tagging strategy generates high allelic diversity at the Arabidopsis HY2 locus.

The targeted (or directed) tagging is a strategy aimed to mobilize a tranposon into a specific gene (target). Only a very few Arabidopsis genes have been tagged by this way, thus the efficiency of the strategy, as well as the diversity of the alleles obtained are not well documented. We have used a maize Ds element in a directed tagging of HY2. The starting Ds element, located 22 kb proximal to HY2, has been remobilized in a cross with an Ac transposase source line. From the F2 progeny of 4800 F1 we phenotypically isolated seven hy2 mutants. Molecular analysis of these alleles revealed that two contained a Ds element in HY2 and were instable, three have a large deletion that partially or completely removed HY2, one has a footprint in a HY2 exon and one leaky allele consisted of a 22 kb inversion upstream the HY2 coding sequence. Thus, the transposon-based directed tagging strategy generates a wide diversity of tagged and non-tagged alleles that can be used to generate allelic series or deletion of clustered genes.

Alleles↗
PubMed1983

Molecular cloning and restriction endonuclease mapping of the murine cytomegalovirus genome (Smith Strain).

We have cloned EcoRI and HindIII fragments of the Smith strain of murine cytomegalovirus (MCMV) in the plasmid vector pACYC184. These cloned fragments were used to establish a restriction endonuclease map of the genome with respect to the EcoRI and HindIII sites. The map was constructed on the basis of data derived from cross-hybridizations of EcoRI and HindIII cloned fragments, double-digestions of the cloned fragments with EcoRI and HindIII, and hybridization of cloned HindIII fragments to Southern blots of MCMV DNA cleaved with EcoRI. From our mapping data, we have determined that the length of the MCMV genome is approximately 240 kbp. The genome does not appear to undergo inversions and lacks detectable repeated sequences. One HindIII cloned fragment was obtained which contained both HindIII termini. The existence of this fragment may be related to the mode of replication of the MCMV genome.

Animals↗
PubMed2005

High-resolution black-blood MRI of the carotid vessel wall using phased-array coils at 1.5 and 3 Tesla.

RATIONALE AND OBJECTIVES: The aim of this report is to investigate the magnetic field dependence of the signal-to-noise ratio (SNR) for carotid vessel wall magnetic resonance imaging using phased-array (PA) surface coils by comparing images obtained at 1.5 and 3 Tesla (T) and determine the extent to which the improved SNR at the higher field can be traded for improved spatial resolution. MATERIALS AND METHODS: Two pairs of dual-element PA coils were constructed for operation at the two field strengths. The individual elements of each PA were matched to 50 Omega impedance on the neck and tuned at the respective frequencies. The coils were evaluated on a cylindrical phantom positioned with its axis parallel to the main field and the coils placed on either side of the phantom parallel to the sagittal plane. In vivo magnetic resonance images of the carotid arteries were obtained in five subjects at both field strengths with a fast spin-echo double-inversion black-blood pulse sequence with fat saturation. SNR was measured at both field strengths by using standard techniques. RESULTS: At a depth corresponding to the average location of the carotid arteries in the study subjects, mean phantom SNR for the two coils was higher at 3 T by a factor of 2.5. The greater than linear increase is caused by only partial coil loading of these relatively small coils. The practically achievable average SNR gain in vivo was 2.1. The lower in vivo SNR gain is attributed to a reduction in T2 and prolongation of T1 at the higher field strength and, to a lesser extent, the requirement for a decreased refocusing pulse flip angle to operate within specific absorption rate limits. The superior SNR at 3 T appears to provide considerably improved vessel-wall delineation. CONCLUSIONS: Carotid artery vessel-wall magnetic resonance imaging using PA surface coils provides a considerable increase in SNR when field strength is increased from 1.5 to 3 T. This increase can be traded for enhanced in-plane resolution.

Adult↗