SEARCH · Search PubMed

Results for “Sequence Inversion”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources

PubMed1995

In search of the ideal protein sequence.

The inverse of a folding problem is to find the ideal sequence that folds into a particular protein structure. This problem has been addressed using the topology fingerprint-based threading algorithm, capable of calculating a score (energy) of an arbitrary sequence-structure pair. At first, the search is conducted by unconstrained minimization of the energy in sequence space. It is shown that using energy as the only design criterion leads to spurious solutions with incorrect amino acid composition. The problem lies in the general features of the protein energy surface as a function of both structure and sequence. The proposed solution is to design the sequence by maximizing the difference between its energy in the desired structure and in other known protein structures. Depending on the size of the database of structures 'to avoid', sequences bearing significant similarity to the native sequence of the target protein are obtained using this procedure.

Algorithms↗

PubMedDate not supplied

Characterization of focal liver lesions with half-fourier acquisition single-shot turbo-spin-echo (HASTE) and inversion recovery (IR)-HASTE sequences.

The half-Fourier acquisition single-shot turbo-spin-echo (HASTE) sequence allows for heavily T2-weighted images, and the inversion recovery (IR)-HASTE sequence represents the T1 value of the tissue in a very short time. This study was undertaken to determine whether characterizing focal liver lesions can be made by combination with these very fast sequences. Seventy-four patients (33 cysts, 28 hemangiomas, and 33 malignant solid liver masses [15 metastatic tumors, 14 hepatocellular carcinomas, and 4 cholangiocarcinomas) underwent dynamic CT and breath-hold abdominal MRI using turbo-spin-echo (TSE), HASTE, and IR-HASTE sequences with variable T1 values on a 1.5-T MR unit. The imaging time for each slice was 2 seconds for HASTE imaging and 2 to 4 seconds for IR-HASTE imaging. Lesion detection and qualitative characterization were evaluated. Quantitative analysis was performed by measuring the contrast-to-noise ratios (CNRs) as well as visual analysis. The inversion time (TI) nulling values were also statistically analyzed. All cystic lesions were detected on both TSE and HASTE imagings. For solid lesions, TSE failed to detect one small solid lesion and HASTE sequence failed to detect three lesions. With HASTE sequences, all cysts and hemangiomas were markedly hyperintense in comparison with malignant solid masses. CNRs of hemangiomas or cysts were significantly higher than those of malignant solid masses (P < .01), and there was no overlap. The TI nulling value was 1,100+/-100 msec for hemangiomas, 1,900+/-110 msec for cysts, and 740+/-140 msec for malignant solid masses. There was no overlap between the TI nulling values of hemangiomas and cysts (P < .01). By combining the CNR from the HASTE sequence and the TI nulling value from the IR-HASTE sequence, complete discrimination among malignant solid masses, hemangiomas, and cysts of the liver could be made. Application of HASTE (representing T2 values) and IR-HASTE (representing T1 values) sequences provided a rapid and reliable imaging method for characterizing focal liver lesions without the use of contrast medium.

Adolescent↗

PubMed1994

[FLAIR images of brain diseases].

FLAIR (fluid-attenuated inversion recovery) images are MR images obtained with an inversion recovery sequence having a long inversion time (TI) and a long echo time (TE). Twenty healthy adults and twenty patients with multiple cerebral infarction, multiple sclerosis, temporal epilepsy, or brain trauma were examined with FLAIR sequences of several types having repetitive times (TR) of 4000-8000 msec, inversion times of 1200-2400 msec and echo times (TE) of 140-200 msec, and the results were compared with spin-echo sequences (TE = 20 msec and TE = 90 msec). With a long repetitive time of 6000 msec and a long inversion time of 1400-1600 msec, the cerebrospinal fluid signals in the lateral ventricles and the cerebral sulci were low-intensity with brain tissue appearing as high signal intensity areas with good T2 contrast. The FLAIR image signal intensities correlated well with T2 relaxation times under 100 msec. Cystic lesions with long T2 relaxation times over 100 msec in multiple sclerosis and cerebral infarction appeared as low-signal areas, and the lesions surrounding the cystic lesions as high-signal areas. In patients with temporal lobe epilepsy, the hippocampus was visualized as a high-signal area. Hippocampal lesions were demonstrated better with FLAIR images than with conventional T2-weighted images or proton-density images. In a cerebral contusion patient, the FLAIR images revealed a lobulated structure with the residual cortex appearing as high-signal areas. The lesions surrounding the cystic change were imaged as high-signal areas. These structural changes were demonstrated better with FLAIR images than with conventional T2-weighted sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1991

Nucleotide sequence analysis of the inversion termini located within IS3 elements alpha 3 beta 3 and beta 5 alpha 5 of Escherichia coli K-12.

This paper presents the first detailed structural analysis of termini of an inversion mediated by recombination between Escherichia coli native IS elements. The complete nucleotide sequence of the inversion termini in the lactose region of Escherichia coli K-12 confirms our previous suggestion that the inversion occurred by homologous recombination between alpha 3 beta 3 and beta 5 alpha 5 IS3 elements (D. J. Savic, J. Bacteriol. 140:311-319, 1979; D. J. Savic, S. Romac, and S. D. Ehrlich, J. Bacteriol. 155:943-946, 1983). The data show a slight structural divergence of alpha 3 beta 3 and beta 5 alpha 5 elements, but they do not reveal new sequences within recombined IS3 elements that could influence the expression of nearby genes.

Base Sequence↗

PubMed1990

Sequence analysis of the inversion region containing the pilin genes of Moraxella bovis.

Moraxella bovis EPP63 is able to produce two antigenically distinct pili called Q and I pili (previously called beta and alpha pili). Hybridization studies have shown that the transition between the types is due to inversion of a 2.1-kilobase segment of chromosomal DNA. We present the sequence of a 4.1-kilobase region of cloned DNA spanning the entire inversion region in orientation 1 (Q pilin expressed). Comparison of this sequence with the sequence of the polymerase chain reaction-amplified genomic DNA from orientation 2 (I pilin expressed) allows the site-specific region of recombination to be localized to a 26-base-pair region in which sequence similarity to the left inverted repeat of the Salmonella typhimurium hin system was previously noted. In addition, 50% sequence similarity was seen in a 60-base-pair segment of our sequence to the recombinational enhancer of bacteriophage P1, an inversion system related to the hin system of S. typhimurium. Finally, two open reading frames representing potential genes were identified.

Amino Acid Sequence↗

PubMed1999

[Use of fluid-attenuated inversion recovery (FLAIR) images in brain check-up].

Fluid-attenuated inversion recovery (FLAIR) images are magnetic resonance (MR) images obtained with an inversion recovery sequence having a long inversion time (T 1) and a long echo time (TE). The purpose of this study was to evaluate the utility of FLAIR images in brain check-up. 320 healthy adults (229 males, 91 females) were examined with FLAIR sequences of several types having repetitive time (TR) of 7000 msec, inversion times of 1700 msec and echo times (TE) of 110 msec. All studies were performed on a SHIMAZU MAGNEX 100 HP 1.0 T imaging system. FLAIR images were useful in detecting cortical and subcortical lesions near the brain surface, which were unclear in the conventional T 2 weighted images. FLAIR images were useful in evaluation of periventricular hyperintensity area (PVH). Frequency and degree of PVH were increased in aging. FLAIR images were useful in the differential diagnosis of lacuna and perivascular space. In conclusion, FLAIR images were very sensitive for the detection of brain lesions in brain check-up.

Adult↗

PubMed2001

Effect of chondrocalcinosis on the MR imaging of knee menisci.

OBJECTIVE: Our goal was to determine the influence of chondrocalcinosis on MR imaging in the detection of meniscal tears. MATERIALS AND METHODS: A retrospective review was performed of knee MR imaging and arthroscopy records from two university hospitals between 1996 and 1998. Seventy individuals had radiographic evidence of chondrocalcinosis and underwent knee MR imaging. Thirty-seven of these individuals had undergone arthroscopy for further evaluation of their symptoms. MR imaging sensitivity and specificity in the detection of medial and lateral meniscal tears were calculated in these 37 patients who had radiographic evidence of chondrocalcinosis and in a control group of 34 patients who underwent MR imaging and arthroscopy but did not have knee chondrocalcinosis. RESULTS: In the chondrocalcinosis group, MR imaging sensitivity, specificity, and accuracy for meniscal tear were 78%, 71%, and 78%, respectively, for the lateral meniscus, and 89%, 72%, and 81% for the medial meniscus. The control group showed sensitivity, specificity, and accuracy of 93%, 100%, and 97%, respectively, for the lateral meniscus and 100% in all cases for the medial meniscus. The MR imaging detection of meniscal tears in both the lateral and medial compartments combined is significantly poorer in the presence of chondrocalcinosis (p < 0.005). CONCLUSION: MR imaging sensitivity and specificity for detection of meniscal tear is decreased in the presence of meniscal chondrocalcinosis. Chondrocalcinosis appeared as a high-signal-intensity region on T1-weighted, intermediate-weighted, and inversion recovery sequences. The high signal of chondrocalcinosis on inversion recovery sequence is an interesting observation that to our knowledge has not been previously reported. Radiographic correlation with the MR imaging examination can help prevent overdiagnosing meniscal tears.

Adult↗

PubMed2003

Myocardial viability: rapid assessment with delayed contrast-enhanced MR imaging with three-dimensional inversion-recovery prepared pulse sequence.

Contrast-enhanced magnetic resonance (MR) imaging allows detection of nonviable myocardium. The authors compared a one-breath-hold three-dimensional inversion-recovery gradient-echo MR sequence with a multiple-breath-hold two-dimensional inversion-recovery gradient-echo MR sequence for the detection of nonviable myocardium. On the basis of a quantitative and qualitative approach, total myocardial area and contrast material-enhanced area, as well as the presence and spatial extent of hyperenhancement, were analyzed separately for each MR image obtained with each sequence in 10 patients with chronic ischemic heart disease. Findings for total myocardial area and contrast-enhanced area agreed well between the two sequences. A high level of agreement was also found for the presence of hyperenhancement (kappa = 0.84), while agreement was poor for the transmural extent of hyperenhancement (kappa = 0.32), which was attributed to the blurred appearance of the three-dimensional MR images. Findings with the one-breath-hold three-dimensional MR sequence allow assessment of nonviable myocardium with good agreement with those with the multiple-breath-hold two-dimensional MR sequence.

Adult↗

PubMedDate not supplied

Fast inversion recovery for myelin suppression (FIRMS). A new MRI pulse sequence for highlighting cerebral gray matter.

The purpose of this study is to test a new pulse sequence, fast inversion recovery for myelin suppression (FIRMS) for its ability to improve the conspicuity of gray matter. Twenty-six seizure patients were scanned with FIRMS as well as standard sequences. Gray matter conspicuity was evaluated objectively using region-of-interest calculations, including image contrast, contrast ratios, and contrast:noise (C/N). In evaluation of the hippocampus and cortex, all objective measurements of conspicuity were highest for FIRMS. In five clinical cases of suspected cortical dysplasia, FIRMS improved delineation of pathology in positive cases and ruled out the diagnosis in negative cases. In a case of hippocampal sclerosis, FIRMS was able to demonstrate atrophy of the alveus. Fast inversion recovery for myelin suppression holds promise for its ability to highlight the cerebral cortex and hippocampus.

Cerebral Cortex↗

PubMed1987

Venous clots: evaluation with MR imaging.

In vitro and in vivo studies were performed to determine the proton relaxation and imaging characteristics of static blood and acute and organized clot in canine jugular veins. In vivo, it was found that two inversion recovery sequences using a short inversion time (100 msec) demonstrated better differentiation of signal intensity of intravascular clot from surrounding soft tissues than did standard T1- and T2-weighted sequences. In vitro, quantitative measurements showed marked reduction of both T1 and T2 relaxation time of acute clot compared with stagnant blood. In addition, the T1 relaxation time, and to a lesser extent the T2 relaxation time, shortened as the clot aged, indicating a potential role for magnetic resonance imaging in determining the age of venous thrombi.

Animals↗

PubMed1996

[FLAIR images of cerebral and brain stem infarction].

FLAIR (fluid-attenuated inversion recovery) images are MR images obtained with an inversion recovery sequence having a long inversion time (TI) and a long echo time (TE). We examined 47 cases (56 graphics) of lacunar infarction (LI), 28 cases (32 graphics) of cortical infarction (CI) and 16 cases (23 graphics) of stem infarction (SI) with a FLAIR sequence having a repetitive time (TR) of 6500 msec, a TI of 1700 msec and a TE of 110 msec, and compared these graphics with T2-weighted images by spin-echo sequence (TR 2500 msec, TE 90 msec). LI and CI were better demonstrated with FLAIR images than with conventional T2-weighted images. FLAIR images were very useful in detecting lesions adjacent to the lateral ventricles and the cerebral sulci in particular, because the cerebrospinal fluid signals in the lateral ventricles and the cerebral sulci were low-intensity, with brain tissue appearing as high-intensity areas. In a number of old infarctions, FLAIR images revealed cystic structures, constructed out of internal low-intensity areas and peripheral high-intensity areas. These structural changes suggested that FLAIR images can provide information on pathological changes.

Aged↗

PubMed1993

Imaging of human brain activity at 0.15 T using fluid attenuated inversion recovery (FLAIR) pulse sequences.

A 3-4% change in signal intensity correlated with visual stimulation was observed in the occipital lobes of three normal volunteers examined with MRI at 0.15 T using fluid attenuated inversion recovery pulse sequences. Similar results were observed at 1.0 T. A double difference technique in which difference images are themselves opposed provided an increase in sensitivity.

Brain↗

PubMed1993

In vivo and in vitro studies of a copy number mutation of the RepA replication protein of plasmid pSC101.

The RepA replication protein of plasmid pSC101 binds as a monomer to three repeated sequences (RS1, RS2, and RS3) in the replication origin of the plasmid to initiate duplication and binds as a dimer to two inversely repeated sequences (IR1 and IR2) in its promoter region (D. Manen, L. C. Upegui-Gonzalez, and L. Caro, Proc. Natl. Acad. Sci. USA 89:8923-8927, 1992). The binding to IR2 autoregulates repA transcription (P. Linder, G. Churchward, G. X. Xia, Y. Y. Yu, and L. Caro, J. Mol. Biol. 181:383-393, 1985). A mutation in the protein RepA(cop) that affects a single amino acid increases the plasmid copy number fourfold. In vivo experiments show that, when provided in trans under a foreign promoter, the RepA(cop) protein increases the replication of a plasmid containing the origin of replication without repA, whereas it decreases the repression of its own promoter. In vitro experiments show that the purified RepA(cop) protein binds more efficiently to the repeated sequences within the origin than does RepA and that its binding to these sequences is more specific than that of RepA. Binding to an inversely repeated sequence within the repA promoter gives opposite results: the wild-type protein binds efficiently to that sequence, whereas the mutated protein binds less efficiently and less specifically. Footprint experiments confirmed these results and, in addition, showed a difference in the pattern of protection of the inversely repeated sequences by the mutant protein. Equilibrium binding experiments showed that the formation of protein-probe complexes at increasing concentrations of protein had a sigmoidal shape for binding to RS sequences and a hyperbolic shape for binding to IR sequences. The results, together with earlier work (G.-X. Xia, D. Manen, T. Goebel, P. Linder, G. Churchward, and L. Caro, Mol. Microbiol. 5:631-640, 1991), confirm that the binding of RepA to RS sequences plays a crucial role in the regulation of plasmid replication and that its binding to IR sequences plays a role in the autoregulation of RepA expression. They also demonstrate that the two separate functions of the protein are effected by two different forms of binding to the target sites.

Amino Acid Sequence↗

PubMed1988

Rearrangement of the bacterial chromosome: forbidden inversions.

The order of genes in the chromosome of enteric bacteria has been evolutionarily conserved despite the existence of mechanisms for rearrangement. Homologous chromosomal sequences in the same orientation recombine to form deletions or duplications. When homologous sequences in inverse orientation recombine, one expects to form an inversion of the intervening chromosomal segment. This expectation was tested by placing pairs of homologous sequences in inverse order at various points in the chromosome. Sequences at many pairs of sites (permissive) do recombine to generate the expected inversion, while the same sequences placed at other pairs of sites (nonpermissive) do not form an inversion. For the one nonpermissive interval tested, the missing inversion type can be constructed by an alternative transductional method; strains with this inversion are viable. Thus mechanistic limitations must prevent sequences at particular sites from undergoing the recombination event required to form an inversion.

Chromosome Inversion↗

PubMed2007

Inhibition of Sonic hedgehog signaling leads to posterior digit loss in Ambystoma mexicanum: parallels to natural digit reduction in urodeles.

Molecular mechanisms patterning the tetrapod limb, including anterior-posterior axis determination involving Sonic hedgehog (Shh), have received much attention, particularly in amniotes. Anterior-posterior patterning in urodele amphibians differs radically from that of amniotes in that it shows a pronounced anterior-to-posterior sequence of digit development. In contrast, amniotes develop their digits almost simultaneously with a slight posterior-to-anterior polarity. Here we use cyclopamine, an inhibitor of the Hedgehog signaling pathway, to investigate the role of Shh in anterior-posterior patterning in the urodele limb. Inhibition of Shh signal transduction affects digit number long before their morphological appearance. In accordance with the apparently derived order of digit development in urodeles, exposure reproducibly removes digits in a posterior-to-anterior sequence, the inverse of their developmental sequence. This pattern of digit loss mimics the order of digit loss in natural variation. We suggest that variation in Shh expression and/or signal transmission may explain natural variation in digit number in urodeles.

Ambystoma mexicanum↗

PubMed1994

Genomic polymorphism in the T-even bacteriophages.

We have compared the genomes of 49 bacteriophages related to T4. PCR analysis of six chromosomal regions reveals two types of local sequence variation. In four loci, we found only two alternative configurations in all the genomes that could be analyzed. In contrast, two highly polymorphic loci exhibit variations in the number, the order and the identity of the sequences present. In phage T4, both highly polymorphic loci encode internal proteins (IPs) that are encapsidated in the phage particle and injected with the viral DNA. Among the various T4-related phages, 10 different ORFs have been identified in the IP loci; their amino acid sequences have the characteristics of internal proteins. At the beginning of each of these coding sequences is a highly conserved 11 amino acid leader motif. In addition, both 5' and 3' to most of these ORFs, there is a approximately 70 bp sequence that contains a T4 early promoter sequence with an overlapping inversely repeated sequence. The homologies within these flanking sequences may mediate the recombinational shuffling of the IP sequences within the locus. A role for the new IP-like sequences in determining the phage host range is proposed since such a role has been previously demonstrated for the IP1 gene of T4.

Amino Acid Sequence↗

PubMed2003

[CT and MRI characteristics of tumours of the temporal bone and the cerebello-pontine angle].

Tumours lesions of the temporal bone and of the cerebello-pontine angle are rare. This tumours can be separated into benign and malignant lesions. In this paper the CT and MRI characteristics of tumours of the temporal bone and the cerebello-pontane angle will be demonstrated. High resolution CT (HRCT) as usually performed in the axial plane are using a high resolution bone window level setting, coronal planes are the reconstructed from the axial data set or will be obtained directly. With the MRI FLAIR sequence in the axial plane the whole brain will be scanned either to depict or exclude a tumour invasion into the brain. After this,T2-weighted fast spin echo sequences or fat suppressed inversion recovery sequences in high resolution technique in the axial plane will be obtained from the temporal bone and axial T1-weighted spin echo sequences before and after the intravenous application of contrast material will be obtained of this region. Finally T1-weighted spin echo sequences in high resolution technique with fat suppression after the intravenous application of contrast material will be performed in the coronal plane. HRCT and MRI are both used to depict the most exact tumorous borders. HRCT excellently depicts the osseous changes for example exostosis of the external auditory canal, while also with HRCT osseous changes maybe characterized into more benign or malignant types. MRI has a very high soft tissue contrast and may therefore either characterize vascular space-occupying lesions for example glomus jugulare tumours or may differentiate between more benign or malignant lesions. In conclusion HRCT and MRI of the temporal bone are excellent methods to depict and mostly characterize tumour lesions and can help to differentiate between benign and malignant lesion. These imaging methods shall be used complementary and may have a great impact for the therapeutic planning.

Adenocarcinoma↗

PubMed2000

MR imaging of septic sacroiliitis.

OBJECTIVE: To investigate the diagnostic value of magnetic resonance (MR) imaging in detecting septic sacroiliitis and to determine whether the MR characteristics allow this entity to be differentiated from sacroiliitis in spondylarthropathy (SpA). PATIENTS AND DESIGN: The imaging findings of 11 patients with septic sacroiliitis were retrospectively analyzed by two experienced radiologists. Radiographic surveys of the pelvis as well as computed tomography (CT) and MR images of the sacroiliac joints were available in all cases. Seven of the patients additionally underwent a follow-up MR examination. The MR imaging protocol comprised combinations of coronal and transverse T1-weighted spin-echo (SE) or fast SE sequences, T2-weighted gradient-echo (GE) sequences and short tau inversion recovery sequence (STIR) sequences as well as dynamic contrast-enhanced T1-weighted acquisitions. RESULTS: Three patients with a short disease history showed anterior and/or posterior subperiosteal infiltrations ("lava cleft phenomenon"), transcapsular infiltrations of juxtaarticular muscle layers, which obscured the fasciae, and periarticular bone marrow edema. The eight patients with more advanced stages of sacroiliitis additionally showed abscess formation, sequestration, and erosion. At follow-up MR examination (n=7) under systemic antibiotic treatment, the morphologic characteristics showed progression (n=1), regression (n=4), unchanged findings (n=1), or a mixed response (n=1). Clinical improvement precedes resolution of the MR findings. CONCLUSIONS: Anterior and/or posterior subperiosteal infiltrations and transcapsular infiltrations of juxtaarticular muscle layers were depicted in all patients. These MR imaging findings are characteristic of septic sacroiliitis and may be used to differentiate this entity from sacroiliitis in SpA.

Adolescent↗