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PubMed1987

[Optimization of examining sequences in MR tomography using isosignal displays].

Contrast performance in MR tomography is influenced by the choice of technical parameters such as pulse repetition time (TR), echo time (TE) and inversion time (TI) in the same manner as by differences in the tissue parameters relaxation time and proton density. To optimise image contrast it is therefore suggested to preselect the imaging sequence. Such presselection is possible on the basis of isosignal visualisations S(T1, T2). In the inversion recovery sequence (IR) the isosignal images obtained with the parameters TE, TI, TR enable determination of relaxation time T1 by graphic representation, from the time of zero passage of the longitudinal tissue magnetisation.

Humans↗
PubMed2003

Comparing Levovist-enhanced pulse inversion harmonic imaging and ferumoxides-enhanced MR imaging of hepatic metastases.

OBJECTIVE: The aim of this study was to compare the sensitivity of pulse inversion harmonic digital sonography, unenhanced transabdominal sonography, and ferumoxides-enhanced MR imaging in the depiction of liver metastases. In addition, pulse inversion harmonic digital sonography was performed at different scanning times after Levovist injection to define the best phase for depiction. SUBJECTS AND METHODS: Twenty-six consecutive patients with findings of extrahepatic primary malignancies and liver metastases suspected on transabdominal sonography were examined with both pulse inversion harmonic imaging and ferumoxides-enhanced MR imaging within a 7-day period. Pulse inversion harmonic imaging was performed before and at 20, 100, and 180 sec after a bolus injection of Levovist. MR imaging was performed before and after ferumoxides administration, using breath-hold gradient-recalled echo T1-weighted and turbo spin-echo short tau inversion recovery T2-weighted sequences. Two radiologists independently evaluated image quality, and the number, location, and diameter of lesions scanned using both techniques. Intraoperative sonography or at least 8-month follow-up confirmed the lesions depicted. Analyses included Wilcoxon's signed rank test and Interclass correlation test. RESULTS: Levovist-enhanced pulse inversion harmonic imaging revealed 104 metastases on the first scan after contrast injection, 126 on the second scan, and 118 on the third, compared with 66 on the unenhanced scan. Pulse inversion harmonic digital sonography depicted 90% of lesions shown on ferumoxides-enhanced MR imaging (140 metastases) (p = 0.001). CONCLUSION: Levovist-enhanced pulse inversion harmonic digital sonography is a sensitive technique for depiction of liver metastases. Pulse inversion harmonic digital sonography may have a potential role in imaging patients with possible metastatic involvement of the liver. Further studies are needed to define its place in the workup of these patients. At present, ferumoxides-enhanced MR imaging, being more sensitive, must be performed in all patients in whom pulse inversion harmonic digital sonography is not conclusive or when after pulse inversion harmonic digital sonography, patients remain eligible for surgery.

Adult↗
PubMed2000

Conventional high resolution versus fast T(2)-weighted MR imaging of the heart: assessment of reperfusion induced myocardial injury in an animal model.

Cardiac image quality in terms of spatial resolution and signal contrast was assessed for conventional and newly developed T(2)-weighted fast spin-echo imaging with high k-space segmentation. The capability in revealing regional myocardial edema and cellular damage was examined by a porcine model using histopathologic correlation. Twelve porcine hearts were excised from slaughtered animals and instantly perfused with 1000 mL cold cardioplegic solution. After 4 h of cold ischemia the hearts were reperfused for one hour using a "Langendorff" perfusion model followed by MR imaging at 1.5 Tesla. Three additional pig hearts served as controls and were studied by MR directly after harvesting. Histopathological analysis of regional tissue changes was performed macro- and microscopically. Short axis T(2)-weighted (3000/45 and 90) high quality fast spin-echo (FSE) images were recorded without cardiac action and signal intensity was correlated with histology. These images also served as gold standard for evaluation of newly developed faster sequences allowing measuring times shorter than 20 s. Fast T(2)-weighted imaging comprised single-slice fast spin echo (moderate echo train length of 23 echoes, FSE(m)), and multi-slice single-shot half-Fourier fast spin-echo (71 echoes, FSE(HASTE)) sequences, supplemented by versions with inversion recovery preparation (FSE(m)IR and FSE(HASTE)IR). Systolic function after reperfusion was restored in 10 porcine hearts. Tissue alterations included myocardial edema and contraction band necrosis which was found to be most severe in myocardium with maximum T(2) SI. Especially FSE(m) and FSE(m)IR sequences allowed differentiation of all categories of tissue damage on a high level of significance. In contrast, single-shot FSE(HASTE) and FSE(HASTE)IR sequences did not provide sufficient image quality to discriminate moderate and severe myocardial damage (p > 0.05). Different degrees of myocardial injury after ischemia and reperfusion can be staged by MR imaging, especially using conventional high resolution T(2)-weighted FSE sequences. The animal study indicates that fast T(2)-weighted FSE(m) and FSE(m)IR sequences lead to superior image quality and diagnostic accuracy compared to FSE(HASTE) and FSE(HASTE)IR imaging.

Analysis of Variance↗
PubMed1998

Optimizing potentials for the inverse protein folding problem.

Inverse protein folding, which seeks to identify sequences that fold into a given structure, has been approached by threading candidate sequences onto the structure and scoring them with database-derived potentials. The sequences with the lowest energies are predicted to fold into that structure. It has been argued that the limited success of this type of approach is not due to the discrepancy between the scoring potential and the true potential but is rather due to the fact that sequences choose their lowest-energy structure rather than structures choosing the lowest-energy sequences. Here we develop a non-physical potential scheme optimized for the inverse folding problem. We maximize the average probability of success for a set of lattice proteins to obtain the optimal potential energy function, and show that the potential obtained by our method is more likely to produce successful predictions than the true potential.

Protein Folding↗
PubMed1991

Identification of two functional regions in Fis: the N-terminus is required to promote Hin-mediated DNA inversion but not lambda excision.

The Fis protein of E. coli binds to a recombinational enhancer sequence that is required to stimulate Hin-mediated DNA inversion. Fis is also required for efficient lambda prophase excision in vivo. The properties of mutant Fis proteins were examined in vivo and in vitro with respect to their stimulatory effects on these two different site-specific DNA recombination reactions. Both recombination reactions are dramatically affected by mutations altering a helix-turn-helix DNA binding motif located near the Fis C-terminus (residues 74-93). These mutations invariably decrease DNA binding affinity and some cause reduced DNA bending. Mutations in the Fis N-terminal region reduce or abolish the stimulation of Hin-mediated DNA recombination by Fis, but have little or no effect on DNA binding or lambda excision. We conclude that there are at least two functionally distinct domains in Fis: a C-terminal DNA binding region that is required for promoting both DNA recombination reactions and an N-terminal region that is uniquely required for Hin-mediated inversion.

Amino Acid Sequence↗
PubMed1998

Hydrophobic free energy eigenfunctions of pore, channel, and transporter proteins contain beta-burst patterns.

Hydropathy plots are often used in place of missing physical data to model transmembrane proteins that are difficult to crystallize. The sequential maxima of their graphs approximate the number and locations of transmembrane segments, but potentially useful additional information about sequential hydrophobic variation is lost in this smoothing procedure. To explore a broader range of hydrophobic variations without loss of the transmembrane segment-relevant sequential maxima, we utilize a sequence of linear decompositions and transformations of the n-length hydrophobic free energy sequences, Hi, i = 1...n, of proteins. Constructions of hydrophobic free energy eigenfunctions, psil, from M-lagged, M x M autocovariance matrices, CM, were followed by their all-poles, maximum entropy power spectral, Somega(psil), and Mexican Hat wavelet, Wa,b(psil), transformations. These procedures yielded graphs indicative of inverse frequencies, omega-1, and sequence locations of hydrophobic modes suggestive of secondary and supersecondary protein structures. The graphs of these computations discriminated between Greek Key, Jelly Role, and Up and Down categories of antiparallel beta-barrel proteins. With these methods, examples of porins, connexins, hexose transporters, nuclear membrane proteins, and potassium but not sodium channels appear to belong to the Up and Down antiparallel beta-barrel variety.

Carrier Proteins↗
PubMed1995

Complete sequence of a mariner transposable element from the predatory mite Metaseiulus occidentalis isolated by an inverse PCR approach.

Degenerate primers designed and synthesized based on two conserved regions of the mariner transposase open reading frame were used to amplify a 454 bp DNA fragment from M. occidentalis. Two inverse primers were then synthesized and used to amplify flanking genomic DNA fragments from M. occidentalis by a ligation-mediated inverse PCR. The complete mariner element (Moc1) was 1284 bp long, including the imperfect 28 bp inverted terminal repeat sequences, and shared 59% similarity to an active 1286 bp long D. mauritiana mariner element (Mos1). Insertions, deletions and substitutions were observed in the Moc1 sequence at several positions. No intact open reading frame was detected and the Moc1 element is considered inactive. Stringent Southern blot hybridizations revealed at least twelve copies of mariner sequences similar to Moc1 in the colonies tested.

Animals↗
PubMed1989

[Experimental determination of weighting functions in magnetic resonance tomography].

Weighting functions are defined and calculated for the pulse sequences spin-echo and inversion recovery. These weighting functions make possible a qualitative discussion of the term "weighting" in MR imaging. Furthermore, a new method has been developed to determine weighting functions experimentally. A comparison between the results obtained and the theoretical predictions shows a sufficiently good agreement. This method can also be applied with other pulse sequences.

Humans↗
PubMed1992

A combination inversion and translocation in Neurospora crassa with inviable deficiency progeny that can be rescued in heterokaryons.

Chromosome rearrangement In(IL;IR)T(IL;IIIR)SLm-1, has a pericentric inversion in linkage group I associated with a reciprocal translocation between I and III. The rearrangement was identified cytologically in pairing with normal sequence chromosomes at pachynema. Rearrangement breakpoints were mapped genetically in IL, IR and IIIR by crosses with normal sequence strains and in crosses with an inversion that partially overlaps the SLm-1 inversion. When rearrangement SLm-1 is crossed to parents with normal sequence chromosomes, one class among the progeny has a small chromosome deficiency and large duplication. The ascospores containing this deficiency/duplication die either before germination or just after, when growth commences. Germ tubes of the deficiency/duplication progeny, which start to grow then stop, resemble the aborted growth of auxotrophic mutants germinated on minimal medium. Efforts to correct the deficiency with nutritional supplements were not successful. However, the defective class can be rescued by fusing the germinating hyphae of the deficiency ascospore with a complementary auxotrophic mutant to form a heterokaryon. A deficiency/duplication nucleus that is rescued in a heterokaryon can serve as a fertilizing nucleus in crosses with a normal sequence parent. One half of their progeny have the normal chromosome sequence and one half have the chromosome deficiency syndrome and die at germination.

Chromosome Inversion↗
PubMed1997

Double-strand breaks may initiate the inversion mutation causing the Hunter syndrome.

We have previously shown that patients with the Hunter syndrome frequently have suffered from a recombination event between the IDS gene and its putative pseudogene, IDS-2, resulting in an inversion of the intervening DNA. The inversion, which might be the consequence of an intrachromosomal mispairing, is caused by homologous recombination between sequences located in intron 7 of the IDS gene and sequences located distal of exon 3 in IDS-2. In order to gain insight into the mechanisms causing the inversion, we have isolated both inversion junctions in six unrelated patients. DNA sequence analysis of the junctions showed that all recombinations have taken place within a 1 kb region where the sequence identity is >98%. An interesting finding was the identification of regions with alternating IDS gene and IDS-2 sequences present at one inversion junction, suggesting that the recombination event has been initiated by a double-strand break in intron 7 of the IDS gene. The results from this study suggest that homologous recombination in man could be explained by mechanisms similar to those described for Saccharomyces cerevisiae. The results also have practical implications for diagnosis of patients with the Hunter syndrome.

Chromosome Inversion↗
PubMed2001

Rapid hemophilia A molecular diagnosis by a simple DNA sequencing procedure: identification of 14 novel mutations.

We here describe a simple, efficient DNA sequencing procedure for hemophilia A molecular diagnosis. In severe patients we first test for the presence of factor VIII gene intron 22 inversion using a recently described single-tube PCR method. In moderate, mild, or inversion-negative severe patients we systematically sequence the promoter, all exons and splice junctions of factor VIII gene. Specially designed primers allow amplification of 23 PCR products under the same salt conditions and thermocycling parameters. The whole sequencing procedure, from blood extraction to mutation identification, can be readily done within 42 h when using regular instruments or in just 14 h when using a high-throughput sequencer. Thus, this is a versatile and cost-effective strategy with little hands-on time requirements. Since its implementation we have identified mutations in 45/46 hemophilia A patients, 14 of which are novel. Once the genetic defect has been identified, accurate genetic counseling is then easily performed.

Amino Acid Substitution↗
PubMed1980

Sequencing the DNA of recombinant chromosomes.

With contemporary molecular cloning and DNA sequencing techniques, deriving the primary structure of higher cell genes is now routine. This publication reviews the chemical DNA sequencing method, and suggests strategies for sequencing recombinant DNA, whether arising naturally by chromosome rearrangement in vivo or created experimentally by gene splicing in vitro. One such strategy prepares end-labeled restriction fragments from an inserted or rearranged DNA region, for sequencing by the chemical method. Another maps the point at which the sequences of two related DNA regions diverge, and indicates which restriction endonucleases would be useful for sequencing across that point. These techniques can facilitate sequencing of DNA integrations, excisions, translocations, inversions, and introns in cloned chromosomal segments.

Animals↗
PubMed1983

The FLP protein of the yeast 2-microns plasmid: expression of a eukaryotic genetic recombination system in Escherichia coli.

The FLP gene of the yeast 2-microns plasmid is involved in a site-specific recombination event that results in the inversion of a set of sequences within the plasmid. This gene has been cloned and expressed in Escherichia coli. Expression of the FLP gene results in efficient recombination within the bacterial cell, which is specific for plasmids containing at least one 2-microns plasmid recombination site. This work demonstrates that (i) FLP protein is actively involved in 2-microns plasmid recombination; (ii) no other factors specific to yeast are required for the reaction; (iii) FLP protein acts efficiently in trans; (iv) FLP protein will promote site-specific insertion and deletion reactions in addition to the inversion reaction; and (v) FLP-promoted recombination is not dependent upon any DNA structural features unique to yeast chromatin.

Base Sequence↗
PubMed1998

Chromosome translocation based on illegitimate recombination in human tumors.

Recurrent chromosome translocations in nonhematological tumors are restricted to specific subtypes, and their mechanism is currently unknown. Analysis of the sequence data of 113 interchromosomal junctions derived from 77 Ewing's tumors carrying the characteristic t(11;22) translocation indicate that, in this tumor, translocations are initiated independently on each chromosome in regions that lack site specific recombination signal. Local sequence duplications, deletions, and, most importantly, inversions that are diagnostic of DNA hairpin formation indicate that, at the breakpoint, single-stranded DNA ends are processed individually before interchromosomal joining. Taken together, these observations suggest that chromosome translocations in Ewing's tumors are mediated through a genuine illegitimate recombination mechanism.

Base Sequence↗
PubMed2005

Salivary polytene chromosome mapping of Anopheles (Cellia) subpictus Grassi (Culicidae: Diptera).

With the introduction of molecular taxonomy of mosquitoes, polytene chromosome maps have become indispensable as standard references for locating genes, puffs, and inversion breakpoints of unique DNA sequences. We present a line map and a photomap of the salivary polytene chromosomes of Anopheles (Cellia) subpictus Grassi, an important emerging vector of malaria in India. In addition, we discuss the nature of this species complex consisting of sibling species A, B, C, and D. The comparative study is in relevance to the X chromosome heterozygous inversion differences between 2 allopatric populations of the species and the recognition of 4 X-chromosome inversion genotypes viz: species A-X(+a+b), B-X(ab), C-X(a+b) and D-X(+ab).

Animals↗
PubMed2005

Full-brain T1 mapping through inversion recovery fast spin echo imaging with time-efficient slice ordering.

Brain T1 mapping has important clinical applications in detecting brain disorders. Conventional T1 mapping techniques are usually based on inversion recovery spin echo (IRSE) imaging or its more time-efficient counterpart inversion recovery fast spin echo (IRFSE) imaging because they can deliver good image quality. Multiple inversion times are required to accurately estimate T1 over a wide range of values. Without acquisition optimization, both the IRSE and the IRFSE T1 mapping techniques require long scan times to image the whole brain. To reduce the scan time and maintain the quality of the T1 maps, we propose a new full-brain T1 mapping pulse sequence based on a multislice inversion recovery fast spin echo imaging using a time-efficient slice ordering technique.

Adult↗
PubMed1998

Identification of 5' flanking sequence of RH50 gene and the core region for erythroid-specific expression.

The Rh blood group antigens are carried by two distinct but homologous membrane proteins encoded by two closely related genes, RCHE and RHD. Rh50 glyco-protein is the membrane protein tightly associated with Rh polypeptides and is critical for expression of Rh antigens. The amino acid sequence and predicted membrane topology of Rh50 glycoprotein are significantly homologous with those of the Rh proteins. Northern blot analysis of leukemic cell lines showed that expression of RH50 gene is restricted to cells with erythroid features. HEL and K562 cells showed a transcription levels ratio of 1 to 9.9 for Rh50, and 12.3 to 1 for Rh. The nucleotide sequence of 5' flanking region of RH50 gene and functional promoter assays also supported the erythroid-specific regulation of the gene, whereas the sequence had lower homology with the promoter sequence of RH genes. Seven GATAs, nine E-boxes, two CACCCs, one YY1, and one October motif were identified in the 1868bp 5' flanking sequence. The core promoter of RH50 gene was located within 68bp length from the translation start position, which included an inverse GATA motif, although obvious motifs for Sp1 or erythroid Krüppel-like factor were lacking. The inverse GATA motif was the target sequence of GATA-1 protein, and disruption of the motif abolished the transactivating activity of erythroid cells. These studies confirm the erythroid-specific expression of Rh antigens, but suggest distinct regulatory mechanisms for RH vs RH50 genes.

Amino Acid Sequence↗
PubMed2002

Genome sequence of Yersinia pestis KIM.

We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing surprising amounts of locally colinear "backbone," or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of E. coli pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.

Bacteriophages↗