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Results for “Sequence Inversion”

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At least 325 records · Page 18Linked to original sources
PubMed1997

Can running cause the appearance of marrow edema on MR images of the foot and ankle?

PURPOSE: To determine if runners have an increased prevalence of marrow edema in the foot and ankle compared with nonrunners at magnetic resonance (MR) imaging. MATERIALS AND METHODS: Ankles and feet were imaged in 20 runners and 12 nonrunners with a fast short inversion time inversion-recovery sequence at 1.5 T. Edema within each bone was graded from 0 (no edema) to 3 (severe edema). Total scores for each subject equaled the sum of the grades. RESULTS: Reader 1 found edema in 16 of 20 runners and four of 12 nonrunners (P < .04); runners had a mean score of 4.7 and nonrunners had a mean score of 0.9 (P < .006). The average number of bones with edema was 3.4 for runners and 0.7 for nonrunners (P < .005). Reader 2 found edema in 16 of 20 runners and two of 12 nonrunners (P < .002); runners had a mean score of 4.5 and nonrunners had a mean score of 0.3 (P < .001). The average number of bones with edema was 3.6 for runners and 0.3 for nonrunners (P < .001). CONCLUSION: When the fast short inversion time inversion-recovery sequence is performed, edema seen within the marrow of runners on MR images may be due to exercise alone.

Adult↗
PubMed1986

Optimal pulse sequence for imaging hepatic metastases.

For magnetic resonance (MR) imaging studies in which the diagnosis is dependent on image contrast, it is essential that an optimized imaging technique be used. Using detection of hepatic metastases as an example, the authors describe a rational strategy for optimizing MR imaging technique. First, for a single patient with proved hepatic metastases, a variety of imaging sequences is discussed and evaluated, leading to characterization of the patient's hepatic tissues. Then the characteristics of the tissues of a representative patient population are presented. These are used to determine two optimal pulse sequences that maximize the achievable signal difference-to-noise ratio achievable in a fixed imaging time. The recommended imaging sequence for detection of hepatic metastases at 0.15 T is either a three-dimensional volume spin-echo (SE) sequence with echo time (TE) = 12 msec and repetition time (TR) = 184 msec or a multisection inversion recovery sequence with TE = 22 msec, inversion time = 250 msec, and TR = 1,375 msec. The variation of this optimum pulse sequence with field strength is also presented.

Humans↗
PubMed2006

Asymmetry of shufflon-specific recombination sites in plasmid R64 inhibits recombination between direct sfx sequences.

The shufflon of plasmid R64 consists of four DNA segments separated and flanked by seven sfx recombination sites. Rci-mediated recombination between any inverted sfx sequences causes inversion of the DNA segments independently or in groups. The R64 shufflon selects one of seven pilV genes encoding type IV pilus adhesins, in which the N-terminal region is constant, while the C-terminal regions are variable. The R64 sfx sequences are asymmetric. The sfx central region and right arm sequences are conserved, but left arm sequences are not. Here we constructed a symmetric sfx sequence, in which the sfx left arm sequence was changed to the inverted repeat of the right arm sequence and made artificial shufflon segments carrying symmetric sfx sequences in inverted or direct orientations. The symmetric sfx sequence exhibited the highest inversion frequency in a shufflon segment flanked by two inverted sfx sequences. Rci-dependent deletion of a shufflon segment flanked by two direct symmetric sfx sequences was observed, suggesting that asymmetry of R64 sfx sequences inhibits recombination between direct sfx sequences. In addition, intermolecular recombination between symmetric sfx sequences was also observed. The extra C-terminal domain of Rci was shown to be essential for inversion of the R64 shufflon using asymmetric sfx sequences but not essential for recombination using symmetric sfx sequences, suggesting that the Rci C-terminal segment helps the binding of Rci to asymmetric sfx sequences. Rci protein lacking the C-terminal domain bound to both arms of symmetric sfx sequence but only to the right arm of asymmetric sfx sequence.

Base Sequence↗
PubMed2006

IR-SE and IR-MEMRI allow in vivo visualization of oscine neuroarchitecture including the main forebrain regions of the song control system.

Songbirds share with humans the capacity to produce learned vocalizations (song). Recently, two major regions within the songbird's neural substrate for song learning and production; nucleus robustus arcopallii (RA) and area X (X) are visualized in vivo using Manganese Enhanced MRI (MEMRI). The aim of this study is to extend this to all main interconnected forebrain Song Control Nuclei. The ipsilateral feedback circuits allow Mn2+ to reach all main Song Control Nuclei after stereotaxic injection of very small doses of MnCl2 (10 nl of 10 mM) into HVC of one and MAN (nucleus magnocellularis nidopallii anterioris) of the other hemisphere. Application of a high resolution (80 micron) Spin Echo Inversion Recovery sequence instead of conventional T1-weighted Spin Echo images improves the image contrast dramatically such that some Song Control Nuclei, ventricles, several laminae, fibre tracts and other specific brain regions can be discerned. The combination of this contrast-rich IR-SE sequence with the transsynaptic transport property of Manganese (Inversion Recovery based MEMRI (IR-MEMRI)) enables the visualization of all main interconnected components of the Song Control System in telencephalon and thalamus.

Animal Communication↗
PubMed2001

On the impact of calcified deposits within the rotator cuff tendons in shoulders of patients with shoulder pain and dysfunction.

We wanted to prove the hypothesis that calcified deposits within the rotator cuff tendons are merely an epiphenomenon of complex morphological alterations in the shoulders of patients with shoulder pain and dysfunction. The shoulders of 92 patients with calcified deposits within the rotator cuff tendons as noted on plain radiographs were investigated by means of magnetic resonance imaging (MRI; mean age of patient 51.1 years), as well as the shoulders of 28 age- and sex-matched patients with similar clinical symptoms but without any signs of such calcified deposits on plain radiographs. The MRI protocol comprised a coronal, oblique, T1-weighted, spin-echo sequence, a T2-weighted, turbo spin-echo sequence, a sagittal, oblique, T2-weighted, turbo spin-echo sequence, and an axial, T1-weighted, spin-echo sequence. Furthermore, a coronal, oblique, short tau-inversion recovery sequence and a gradient echo sequence were used. The results were compared with data from healthy, asymptomatic volunteers as reported in the literature. The MRI investigations showed no substantial differences between patients with or without calcified deposits within the rotator cuff tendons, but distinct differences between such patients and healthy, asymptomatic volunteers. For patients with shoulder pain, shoulder dysfunction, and calcified deposits within the rotator cuff tendons, these calcified deposits are most probably not the main cause of the clinical symptoms. Rather, it seems to be useful to consider the results of MRI investigations whenever planning therapeutic procedures for patients with shoulder pain and dysfunction, irrespective of whether or not there are signs of calcified deposits within the rotator cuff tendons on plain radiographs.

Adult↗
PubMed1993

Fat suppression techniques in MR imaging of mature ovarian teratomas: comparison with CT.

OBJECTIVE: The aim of this study is to analyze the ability of MR fat suppression techniques to characterize fat components of ovarian mature cystic teratomas (MCT) shown by CT. SUBJECTS AND METHODS: MR images of eight MCTs of the ovary were obtained using standard sequences followed by a SPIR (spectral presaturation with inversion recovery) sequence in six cases and by Dixon sequences in two cases. In all cases correlation with CT and pathologic findings was achieved. RESULTS: MR fat suppression sequences showed to be as accurate as CT in detecting fat inside the cystic part of the teratomas (8/8). CONCLUSION: MR fat suppression sequences should be performed when presence of fat is suspected on images of ovarian tumors produced by standard MR sequences.

Adult↗
PubMed1995

Magnetic resonance imaging: spinal cord imaging with the turbo-fluid attenuated inversion recovery (FLAIR) pulse sequence.

Twelve patients with suspected or proven spinal cord disease were studied with a fluid attenuated repeated echo sequence employing a fast spin-echo data acquisition (Turbo-FLAIR) and the results were compared with those obtained with conventional T1- and T2-weighted spin-echo sequences. The Turbo-FLAIR sequence utilized an unselected 180 degrees pulse to reduce the signal from CSF followed by a spin-echo sequence based on the Rapid Acquisition with Relaxation Enhancement (RARE) pulse sequence for data acquisition. Three and four echo versions were used. Four low signal intensity lesions (cysts or syrinxes) were seen of which three were better seen with the Turbo-FLAIR sequence than with the other sequences. The remaining lesion was equally well seen. Of the seven high signal lesions found, six were better seen with the Turbo-FLAIR sequence and one was equally well seen. The Turbo-FLAIR sequence is more rapid than the T2-weighted spin-echo sequence and compares favourably with the combined results of both the T1- and T2-weighted spin-echo sequences for lesion conspicuity.

Cysts↗
PubMed1984

An inverse control by phytochrome of the expression of two nuclear genes in barley (Hordeum vulgare L.).

During the light-dependent transformation of etioplasts to chloroplasts a rapid decrease of the NADPH-protochlorophyllide oxidoreductase is induced. At the same time the mRNA activity coding for this enzyme protein also declines rapidly under the influence of phytochrome (Pfr). On the other hand the apoprotein of the light-harvesting chlorophyll a/b protein and its mRNA activity are inversely affected by the same photoreceptor. Cloned cDNA sequences which are complementary to these mRNAs have been used to assess the effect of phytochrome (Pfr) on the concentration of the two transcripts. The phytochrome-induced changes of the two translatable mRNAs are paralleled by corresponding changes in the steady-state concentration of the mRNA sequences. This inverse relationship between the light-dependent regulation of the NADPH-protochlorophyllide oxidoreductase and the light-harvesting chlorophyll a/b protein suggests that a single reversible triggering event can increase the transcription of certain genes and decrease the transcription of others.

Chlorophyll↗
PubMed1997

Staging of symptomatic primary breast cancer with MR imaging.

OBJECTIVE: This study was designed to investigate the accuracy of contrast-enhanced MR imaging in the locoregional staging of symptomatic primary breast cancer and to determine the impact of contrast-enhanced MR imaging in planning surgical management. MATERIALS AND METHODS: Ninety patients with primary breast cancer (including two bilateral cancers) diagnosed and treated on the basis of conventional triple assessment (clinical, cytologic, and mammographic examination) underwent MR imaging at 1.0 T using a three-dimensional fast low-angle shot T1-weighted pulse sequence before and after contrast enhancement. A short inversion time inversion recovery sequence was also obtained to evaluate the axilla of each patient. After resection, tumors were histopathologically mapped in detail and correlated with the extent of contrast enhancement on MR imaging. RESULTS: On the basis of triple assessment, 53 cancers were treated by wide local excision, of which 17 (32%) had positive margins at excision. Residual disease at reexcision was detected in eight of these 17 patients, a finding that correlated accurately with the extent of contrast enhancement on MR imaging. MR imaging was more accurate than mammography in determining invasive tumor size (r2 = .93 versus r2 = .59), in depicting multifocality and extensive intraductal component (sensitivity, 81% versus 62%), and in assessing nipple-retroareolar complex. MR imaging-histopathologic correlation was possible in 75 axillae. Sensitivity and specificity for axillary node metastases were 90% and 82%, respectively. CONCLUSION: MR imaging of the breast has value in the preoperative locoregional staging of symptomatic primary breast cancer and is useful in planning a single definitive surgical resection in patients with breast cancer.

Adult↗
PubMed1998

[Recent developments and applications of MRI sequence technique. I: turbo spin echo, HASTE, turbo inversion recovery, turbo gradient echo, turbo gradient spin sequences].

Goal of this two-part report is to provide clinical MRI radiologists with a guide to the world of new and clinically available MRI pulse sequences. Discussed are the principles of rapid scan techniques like multiple spin-echo imaging, multiple gradient echo imaging, echo planar imaging, diffusion and perfusion imaging, and future perspectives (review article).

Echo-Planar Imaging↗
PubMed1980

Methylation of integrated adenovirus type 12 DNA sequences in transformed cells is inversely correlated with viral gene expression.

The adenovirus type 12 (Ad12) DNA sequences integrated into the DNA of four lines of Ad12-transformed hamster cells are extensively methylated. Methylation in mammalian cell DNA is believed to occur predominantly at 5'-C-G-3' sequences. The majority, although not all, of the 5'-C-C-G-G-3' sequences present in integrated Ad12 DNA are methylated. Ad12 DNA isolated from purified virions, on the other hand, is not methylated to any significant extent. The segments of the integrated viral DNA comprising early genes, which are expressed as mRNA in two lines of Ad2-transformed hamster cells, are undermethylated in comparison to late viral segments, which are not expressed and are extensively methylated. In contrast, in two lines of Ad12-induced rat brain tumor cells, some of the late viral genes have been shown to be expressed as mRNA. The segment of the integrated Ad12 DNA that comprises these late genes, the EcoRI B fragment, is undermethylated in comparison to the extensive methylation of the same fragment in Ad12-transformed hamster cells. Thus, there appears to exist a striking inverse correlation between the levels of methylation of specific DNA segments and the extent to which these segments are expressed as mRNA. The functional significance of this correlation remains to be determined. It may provide a clue to understanding the regulation of gene expression in transformed cells and perhaps in eukaryotic cells in general.

Adenoviruses, Human↗
PubMed2002

Use of inverse PCR to amplify and sequence breakpoints of HPRT deletion and translocation mutations.

Deletion and translocation mutations have been shown to play a significant role in the genesis of many cancers. The hprt gene located at Xq26 is a frequently used marker gene in human mutational studies. In an attempt to better understand potential mutational mechanisms involved in deletions and translocations, inverse PCR (IPCR) methods to amplify and sequence the breakpoints of hprt mutants classified as translocations and large deletions were developed. IPCR involves the digestion of DNA with a restriction enzyme, circularization of the fragments produced, and PCR amplification around the circle with primers oriented in a direction opposite to that of conventional PCR. The use of this technique allows amplification into an unknown region, in this case through the hprt breakpoint into the unknown joined sequence. Through the use of this procedure, two translocation, one inversion, and two external deletion hprt breakpoint sequences were isolated and sequenced. The isolated IPCR products range in size from 0.4 to 1.8 kb, and were amplified from circles ranging in size from 0.6 to 7.7 kb. We have shown that inverse PCR is useful to sequence translocation and large deletion mutant breakpoints in the hprt gene.

Base Sequence↗
PubMed1993

Synchronized inversion recovery-spin echo sequences for precise in vivo T1 measurement of human myocardium: a pilot study on 22 healthy subjects.

An ECG-triggered, two-sequence MRI technique is proposed for the precise measurement of proton T1 relaxation times of the human myocardium at a field strength of 0.5 T. The combination of an inversion recovery (IR) sequence and a spin echo (SE) sequence is not new. It is, however, rarely used in quantitative in vivo cardiac studies. Our approach employs a synchronization of the 90 degrees read pulse to the systolic period. In a study of 22 healthy volunteers, the globally measured T1 value was estimated to be 714 +/- 23 ms. Four of the volunteers also underwent additional imaging scans for the purposes of reproducibility assessment. The T1 precision was found to be 3.9 +/- 1.1% for the IR/SE combination and 16.9 +/- 5.3% for a combination of SE sequences. Total imaging time for the IR and SE sequences was 19.2 +/- 3.0 mins. The relative rapidity of this classic technique and the T1 precision obtained give this technique an obvious application in the discrimination of normal and diseased myocardium. In the same study, valuable supplementary tissue characterization is provided by T2, calculated from the SE sequence. T2 was evaluated to be 50 +/- 3 ms.

Adult↗
PubMed1979

Physical mapping of Staphylococcus aureus penicillinase plasmid pI524: characterization of an invertible region.

The staphylococcal penicillinase plasmid pI524 and a series of derivatives have been extensively mapped by restriction endonuclease digestion and by heteroduplex analysis. We report here the identification of a 2.2 kb region that undergoes a reversible, rec-independent inversion. This sequence is bounded by a pair of inverted repeats 650 base pairs in length, and has asymmetrically located recognition sites for at least three restriction endonucleases. A series of deleted derivatives and one naturally occurring, closely related plasmid, were studied. Two of these retain the inversion; the remainder are incapable of inverting and were all found to be locked in the same orientation of the inversion. The invertible sequence is adjacent to the region of the plasmid encoding beta-lactamase (bla); this entire region appears to be transposable and the inversion may be involved in the regulation of beta-lactamase expression or in translocation.

DNA Restriction Enzymes↗
PubMed1995

Cin-mediated recombination at secondary crossover sites on the Escherichia coli chromosome.

The Cin recombinase is known to mediate DNA inversion between two wild-type cix sites flanking genetic determinants for the host range of bacteriophage P1. Cin can also act with low frequency at secondary (or quasi) sites (designated cixQ) that have lower homology to either wild-type site. An inversion tester sequence able to reveal novel operon fusions was integrated into the Escherichia coli chromosome, and the Cin recombinase was provided in trans. Among a total of 13 Cin-mediated inversions studied, three different cixQ sites had been used. In two rearranged chromosomes, the breakpoints of the inversions were mapped to cixQ sites in supB and ompA, representing inversions of 109 and 210 kb, respectively. In the third case, a 2.1-kb inversion was identified at a cixQ site within the integrated sequences. This derivative itself was a substrate for a second inversion of 1.5 kb between the remaining wild-type cix and still another cixQ site, thus resembling a reversion. In analogy to that which is known from DNA inversion on plasmids, homology of secondary cix sites to wild-type recombination sites is not a strict requirement for inversion to occur on the chromosome. The chromosomal rearrangements which resulted from these Cin-mediated inversions were quite stable and suffered no growth disadvantage compared with the noninverted parental strain. The mechanistic implications and evolutionary relevance of these findings are discussed.

Bacterial Outer Membrane Proteins↗
PubMed2006

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure-function relationships in sequence families and superfamilies.

Base Sequence↗