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PubMed2003

Coronary MR imaging using free-breathing 3D steady-state free precession with radial k-space sampling.

PURPOSE: To investigate the potential of free-breathing 3D steady-state free precession (SSFP) imaging with radial k-space sampling for coronary MR-angiography (MRA), coronary projection MR-angiography and coronary vessel wall imaging. MATERIALS AND METHODS: A navigator-gated free-breathing T2-prepared 3D SSFP sequence (TR = 6.1 ms, TE = 3.0 ms, flip angle = 120 degrees, field-of-view = 360 mm(2)) with radial k-space sampling (384 radials) was implemented for coronary MRA. For projection coronary MRA, this sequence was combined with a 2D selective aortic spin tagging pulse. Coronary vessel wall imaging was performed using a high-resolution inversion-recovery black-blood 3D radial SSFP sequence (384 radials, TR = 5.3 ms, TE = 2.7 ms, flip angle = 55 degrees, reconstructed resolution 0.35 x 0.35 x 1.2 mm(3)) and a local re-inversion pulse. Six healthy volunteers (two for each sequence) were investigated. Motion artifact level was assessed by two radiologists. RESULTS: In coronary MRA, the coronary lumen was displayed with a high signal and high contrast to the surrounding lumen. Projection coronary MRA demonstrated selective visualization of the coronary lumen while surrounding tissue was almost completely suppressed. In coronary vessel wall imaging, the vessel wall was displayed with a high signal when compared to the blood pool and the surrounding tissue. No visible motion artifacts were seen. CONCLUSION: 3D radial SSFP imaging enables coronary MRA, coronary projection MRA and coronary vessel wall imaging with a low motion artifact level.

Adult↗
PubMed1996

"Black blood" T2-weighted inversion-recovery MR imaging of the heart.

PURPOSE: To develop a short-inversion-time inversion-recovery (STIR) magnetic resonance imaging pulse sequence for evaluating the myocardium that is relatively free of flow and motion artifact. MATERIALS AND METHODS: The authors implemented a breath-hold, cardiac-triggered STIR sequence with preparatory radio-frequency pulses to eliminate signal from flowing blood. A segmented rapid acquisition with relaxation enhancement (turbo spin echo) readout was used, with the inversion-recovery delay adjusted to null fat. The sequence was implemented at 1.0 and 1.5 T and tested in phantoms, five healthy volunteers, and three patients. RESULTS: Phantom studies confirmed the expected behavior of the sequence. In the volunteers, fat-suppressed images of the heart with STIR contrast were generated in a breath-hold period. Blood in the heart chambers was uniformly nulled, and motion artifacts were effectively suppressed. Focal high signal intensity consistent with edema was seen in two patients with acute myocardial infarction; in a third patient, a paracardiac mass was visualized and sharply demarcated relative to normal myocardium. CONCLUSION: Fast STIR imaging of the heart with effective suppression of flow and motion artifacts was implemented. The approach has much potential for high-contrast imaging in a variety of diseases affecting the heart and mediastinum.

Adult↗
PubMed1988

A comparison of one-shot and recovery methods in T1 imaging.

Spin-lattice (T1) relaxation times are conventionally estimated using inversion recovery or saturation recovery sequences. Such "recovery" methods are limited in magnetic resonance imaging by the long times required to collect multiple points along the T1 relaxation curve. This problem can be overcome by the use of "one-shot" methods, which collect all points along the relaxation curve in a single excitation. We have compared the relative efficiency of these methods, on the basis of the signal-to-noise ratio obtained in the calculated T1 image from an exam time of fixed duration. We have found that a one-shot method using stimulated echoes has a poor efficiency. However, a method based on a technique first proposed by Look and Locker has an efficiency that is almost equal to the inversion recovery method and therefore possesses highly favorable properties for T1 imaging.

Magnetic Resonance Imaging↗
PubMed2004

The evolutionary history of human chromosome 7.

We report on a comparative molecular cytogenetic and in silico study on evolutionary changes in human chromosome 7 homologs in all major primate lineages. The ancestral mammalian homologs comprise two chromosomes (7a and 7b/16p) and are conserved in carnivores. The subchromosomal organization of the ancestral primate segment 7a shared by a lemur and higher Old World monkeys is the result of a paracentric inversion. The ancestral higher primate chromosome form was then derived by a fission of 7b/16p, followed by a centric fusion of 7a/7b as observed in the orangutan. In hominoids two further inversions with four distinct breakpoints were described in detail: the pericentric inversion in the human/African ape ancestor and the paracentric inversion in the common ancestor of human and chimpanzee. FISH analysis employing BAC probes confined the 7p22.1 breakpoint of the pericentric inversion to 6.8 Mb on the human reference sequence map and the 7q22.1 breakpoint to 97.1 Mb. For the paracentric inversion the breakpoints were found in 7q11.23 between 76.1 and 76.3 Mb and in 7q22.1 at 101.9 Mb. All four breakpoints were flanked by large segmental duplications. Hybridization patterns of breakpoint-flanking BACs and the distribution of duplicons suggest their presence before the origin of both inversions. We propose a scenario by which segmental duplications may have been the cause rather than the result of these chromosome rearrangements.

Animals↗
PubMed1984

Location and analysis of nucleotide sequences at one end of a putative lac transposon in the Escherichia coli chromosome.

A segment of Escherichia coli DNA that contained a discontinuity of homology with Salmonella typhimurium DNA was isolated. The segment, 1,430 base pairs long, was derived from one end of the lac "loop," a region of about 12 kilobase pairs of E. coli DNA, including the lac operon which has no detectable homology with S. typhimurium DNA (K. Lampel and M. Riley, Mol. Gen. Genet. 186:82-86, 1982). The nucleotide sequence of the 1,430-base-pair segment of DNA was determined. The location of the junction of discontinuity of homology within the segment was established by hybridization experiments. Nucleotide sequences at or near the junction were determined to be similar to sequences that are involved in site-specific inversion in S. typhimurium, E. coli, phage P1, and phage Mu. Similar sequences are also present within the terminal inverted repeat sequences of transposon Tn5 and at the V-D-J joining sequences of eucaryotic immunoglobulin genes. Therefore, the lac operon, together with flanking DNA, may have been inserted into the E. coli chromosome at one time via a site-specific recombination event. Rearrangement events of this kind undoubtedly have played a significant role in the evolutionary divergence of chromosomal DNAs.

Base Composition↗
PubMed2003

Chromosomal arm replacement in Streptomyces griseus.

UV irradiation of Streptomyces griseus 2247 yielded a new chromosomal deletion mutant, MM9. Restriction and sequencing analysis revealed that homologous recombination between two similar lipoprotein-like open reading frames, which are located 450 and 250 kb from the left and right ends, respectively, caused chromosomal arm replacement. As a result, new 450-kb terminal inverted repeats (TIRs) were formed in place of the original 24-kb TIRs. Frequent homologous recombinations in Streptomyces strains suggest that telomere deletions can usually be repaired by recombinational DNA repair functioning between the intact and deleted TIR sequences on the same chromosome.

Base Sequence↗
PubMed1994

[An introduction to fast and ultrafast sequences in magnetic resonance].

The main limitations of magnetic resonance imaging (MRI) are due to the long acquisition time needed for data sampling. Fast and ultrafast sequences, thanks to progress in hardware and software technology, allow the acquisition times to be dramatically reduced. Such improvements will definitely increase MR capabilities and make MRI a fast and dynamic technique no longer depending on patients' cooperation and limited by patients' conditions--e.g., trauma, pediatric, or claustrophobic patients--or even by the anatomic features of the region of interest. The latest experimental studies are aimed at increasing the clinical applications and the perspectives of clinical MRI and at such ambitious goals as MR-fluoroscopy, interventional MRI, total body examination in less than one minute and functional MRI. In this paper the technical principles and the main indications of this new kind of sequences are reported, with a special emphasis on Gradient-Echo (GE), Turbo Spin-Echo (turbo SE) or Fast Spin-Echo (fast SE), Turbo FLASH and Echo Planar (EP) sequence. A smaller flip angle (FA) and the substitution of the 180 degrees RF pulse with a gradient reversal are the main differences of GE from SE sequences. From GE sequences, several fast sequences are derived, such as angiographic and turbo FLASH sequences. The latter, thanks to 180 degrees preinversion RF pulse, using idoneous inversion times (IT), provide flexible contrast. Turbo SE sequences, which are directly derived from conventional SE sequence, allow the acquisition time to be markedly shortened, by acquiring several Fourier lines of K-space for each TR. The repetition of several 180 degrees pulses following the excitatory 90 degrees RF pulse does the trick through the creation of multiple echoes for a single TR. EP sequences are the fastest ones currently available: with them, an image can be acquired in 30-100 ms. However, the limited availability of the relative hardware and the need of both quality implementation and the definition of clinical indications are major obstacles to the widespread use of these sequences. The SE T2-weighted sequence, the main responsible for the long examination time, will be replaced soon. Further implementation of these sequences will make MRI a fast, flexible and adaptable method to any exam and patient disability.

Echo-Planar Imaging↗
PubMed2004

A conserved tripeptide in CNG and HCN channels regulates ligand gating by controlling C-terminal oligomerization.

Cyclic nucleotides directly enhance the opening of the tetrameric CNG and HCN channels, although the mechanism remains unclear. We examined why HCN and certain CNG subunits form functional homomeric channels, whereas other CNG subunits only function in heteromeric channels. The "defect" in the CNGA4 subunit that prevents its homomeric expression was localized to its C-linker, which connects the transmembrane domain to the binding domain and contains a tripeptide that decreases the efficacy of ligand gating. Remarkably, replacement of the homologous HCN tripeptide with the CNGA4 sequence transformed cAMP into an inverse agonist that inhibits HCN channel opening. Using analytical ultracentrifugation, we identified the structural basis for this gating switch: whereas cAMP normally enhances the assembly of HCN C-terminal domains into a tetrameric gating ring, inclusion of the CNGA4 tripeptide reversed this action so that cAMP now causes gating ring disassembly. Thus, ligand gating depends on the dynamic oligomerization of C-terminal binding domains.

Amino Acid Sequence↗
PubMed1992

Characterization of an inversion on the long arm of chromosome 10 juxtaposing D10S170 and RET and creating the oncogenic sequence RET/PTC.

RET/PTC is a transforming sequence created by the fusion of the tyrosine kinase domain of the RET protooncogene with the 5' end of the locus D10S170 designated by probe H4 and is frequently found activated in human papillary thyroid carcinomas. RET and D10S170 have been mapped to contiguous regions of the long arm of chromosome 10: q11.2 and q21, respectively. To identify the mechanism leading to the generation of the oncogenic sequence RET/PTC, a combined cytogenetic and molecular analysis of several cases of papillary thyroid carcinomas was done. In four cases the results indicated that these tumors had RET/PTC activation and a paracentric inversion of the long arm of chromosome 10, inv(10)(q11.2q21), with breakpoints coincident with the regions where RET and D10S170 are located. Therefore, a chromosome 10q inversion provides the structural basis for the D10S170-RET fusion that forms the hybrid transforming sequence RET/PTC.

Blotting, Southern↗
PubMed2004

Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA.

Adaptive changes in nature occur by a variety of mechanisms, and Drosophila chromosomal inversions was one of the first studied examples. However, the precise genetic causes of the adaptive value of inversions remain uncertain. Here we investigate the impact of the widespread inversion 2j of Drosophila buzzatii on the expression of the CG13617 gene, whose coding region is located only 12 bp away from the inversion proximal breakpoint. This gene is transcribed into a 2.3-kb mRNA present in all D. buzzatii developmental stages. More importantly, the expression level of CG13617 is reduced 5-fold in embryos of lines homozygous for the 2j inversion compared with lines without the inversion. An antisense RNA that originates in the Foldback-like transposon Kepler inserted at the breakpoint junction in all of the 2j lines and that forms duplexes with the CG13617 mRNA in 2j embryos is most likely responsible for the near silencing of the gene. Few examples of RNA interference caused by transposable elements (TEs) have been previously described, but this mechanism might be prevalent in many organisms and illustrates the potential of TEs as a major source of genetic variation. In addition, because chromosomal rearrangements are usually induced by TEs, position effects might be more common than previously recognized and contribute significantly to the evolutionary success of inversions.

Animals↗
PubMed2004

Correlation between magnetic resonance angiography (MRA) and quantitative coronary angiography (QCA) in ectatic coronary vessels.

Coronary artery ectasia (CAE) is defined as a dilatation of an arterial segment to a diameter at least 1.5 times that of the adjacent normal artery. The correct follow-up of ectatic vessels is hampered by the need for repeat angiograms. In this work we compared quantitative coronary angiography (QCA) measurements of the diameter of the proximal most ectatic part of coronary vessels, with corresponding measurements obtained by magnetic resonance angiography (MRA) using both gradient echo and turbo spin echo imaging sequences. Fifteen patients (14 male), aged 45-65 years, with known CAE were prospectively studied. Two electrocardiogram (ECG)-triggered pulse sequences were implemented for coronary magnetic resonance angiography. The first was a three-dimensional (3D), segmented, k-space gradient-echo sequence, employing a T2-weighted preparation prepulse and a frequency-selective, fat-saturation prepulse to enhance "white blood" (WB) contrast of the coronary arteries. The second sequence was an M2D dual Inversion Recovery (IR) Turbo Spin-Echo with a linear k-space acquisition scheme, providing "black-blood" (BB) contrast of the coronaries. All scans were carried out with the patient free breathing using a 2D, real-time Navigator beam, for respiratory motion tracking and gating. All patients underwent QCA, and the diameter of the proximal most ectatic part of each vessel was measured and compared with "white-blood" and "black-blood" MRA measurements. The average length of continuously visualized LM, LAD, LCx, and RCA by MRA was 2.5 +/- 0.3, 5.8 +/- 0.8, 3.9 +/- 1.0, and 7.2 +/- 1.2 cm, respectively. There were no statistically significant differences between diameter measurements of the proximal most ectatic part of each vessel, obtained with WB and BB sequences. There was a close correlation between MRA and QCA measurements (r = 0.87, p < 0.001). Bland-Altman analysis showed no systematic differences between the examined methods, over the whole range of vessel diameters measured. Coronary MRA is in close correlation with QCA for CAE detection. Magnetic resonance angiography, being noninvasive, may prove of significant value for the efficient follow-up of these patients.

Aged↗
PubMed2005

Long-term changes in sequence of atrial activation and refractory periods: no evidence for "atrial memory".

OBJECTIVES: The purpose of this study was to test whether the spatial distribution of the atrial refractory period (AERP) and the vulnerability to atrial fibrillation (AF) are altered by long-term changes in the sequence of atrial activation. BACKGROUND: The spatial distribution of the AERP plays an important role in AF. Changes in the activation sequence have been postulated to modulate atrial repolarization ("atrial memory"). METHODS: Six goats were chronically instrumented with epicardial atrial electrodes to determine activation time and AERP at 11 different areas of the right (RA) and left (LA) atrium and the Bachmann bundle. Activation time and AERP were measured during sinus rhythm and during prolonged RA and LA pacing (1 week RA pacing, 2 weeks LA pacing, 1 week RA pacing; 150 bpm). Inducibility of AF was determined by the number of atrial sites where single premature stimuli induced AF paroxysms >1 second. RESULTS: During sinus rhythm (106 +/- 4 bpm), AERP was longest at the Bachmann bundle and shortest at the LA free wall (185 +/- 6 ms and 141 +/- 5 ms, P < .001). In five of six goats, an inverse correlation between local activation time and AERP was found during sinus rhythm (r = -0.53 +/- 0.05; P < .05). The increase in atrial rate during RA and LA pacing caused an overall shortening of AERP from 167 +/- 6 ms to 140 +/- 6 ms (P < .001). However, a switch between long-term RA and LA pacing did not significantly change AERP at any of the 11 atrial regions and had no significant effect on AF inducibility. CONCLUSIONS: During sinus rhythm, an inverse relationship exists between the sequence of atrial activation and the local refractory period. However, long-term changes in the sequence of atrial activation do not alter the spatial distribution of AERP or the inducibility of AF.

Action Potentials↗
PubMed1998

The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases.

BACKGROUND: Conservative site-specific recombination is responsible for the resolution of cointegrates which result during the transposition of class II transposable elements. Resolution is catalysed by a transposon-encoded recombinase, resolvase, that belongs to a large family of recombinases, including DNA invertases. Resolvases and the related invertases are likely to employ similar reaction mechanisms during recombination. There are important differences, however. Resolvases require two accessory DNA binding sites within each of the two directly repeated recombination sites. Invertases instead need a host factor, Fis, and an enhancer type DNA sequence, in addition to two inversely orientated recombination sites. RESULTS: The resolvase encoded by transposable element ISXc5 from the gram-negative phytopathogen Xanthomonas campestris shows two features which distinguish it from other known resolvases. First, it is more closely phylogenetically related to invertases than other resolvases. In particular, two functionally important regions seem highly conserved between this resolvase and members of the invertase subfamily. Second, the enzyme exhibits a large extension of its carboxy-terminal domain with unknown function. We purified ISXc5 resolvase and analysed its resolution reaction in vitro. Our biochemical and DNA topological analysis reveals that critical features of resolution are similar, if not identical, to that carried out by gammadelta resolvase. However, despite its apparent similarity to invertases, we were unable to detect recombination on standard substrates for DNA inversion, in either the presence or absence of Fis. CONCLUSIONS: ISXc5 resolvase employs a reaction mechanism which is common to members of the resolvase family. Its position near the evolutionary borderline to invertases and its high degree of identity within two functionally important regions with members of the DNA invertase subfamily suggest that only a few replacements of critical residues may suffice to convert this resolvase into a functional, possibly Fis-dependent invertase.

Amino Acid Sequence↗
PubMed2002

Sequence variations within protein families are linearly related to structural variations.

It is commonly believed that similarities between the sequences of two proteins infer similarities between their structures. Sequence alignments reliably recognize pairs of protein of similar structures provided that the percentage sequence identity between their two sequences is sufficiently high. This distinction, however, is statistically less reliable when the percentage sequence identity is lower than 30% and little is known then about the detailed relationship between the two measures of similarity. Here, we investigate the inverse correlation between structural similarity and sequence similarity on 12 protein structure families. We define the structure similarity between two proteins as the cRMS distance between their structures. The sequence similarity for a pair of proteins is measured as the mean distance between the sequences in the subsets of sequence space compatible with their structures. We obtain an approximation of the sequence space compatible with a protein by designing a collection of protein sequences both stable and specific to the structure of that protein. Using these measures of sequence and structure similarities, we find that structural changes within a protein family are linearly related to changes in sequence similarity.

Amino Acid Sequence↗
PubMed1989

The transcriptional control regions of the copia retrotransposon.

We have analysed the sequence elements that control expression of the copia retrotransposon. Expression of copia fusion constructs containing DNA sequence deletions and rearrangements was assayed by transient expression analysis. Progressive deletion and linker substitution identifies two regions on either side of the major transcriptional start sites in the copia long terminal repeat These regions are both required for high level expression in a cultured Drosophila melanogaster cell line but only the upstream region is required for copia expression in a Drosophila hydei cell line. A third control region lies downstream of the long terminal repeat in a region previously believed to contain no cis-acting regulatory sequences. We show by displacement and inversion of this region that it contains a transcriptional enhancer.

Animals↗
PubMed2000

Selective sweep near the In(2L)t inversion breakpoint in an African population of Drosophila melanogaster.

Chromosomal inversions largely inhibit recombination and may be associated with selective forces, such as hitch-hiking effects: the effect of positive selection on linked loci. A West African population of Drosophila melanogaster showed a high frequency (0.61) of the In(2L)t inversion. Departure from neutrality statistically associated with the inversion polymorphism was previously recorded at Su(H), a locus distant from the proximal breakpoint of the inversion. These results were consistent with hitch-hiking effects with recombination. The present sequence polymorphism survey involves a 1 kb fragment of the Vha68-1 locus located closer to the proximal breakpoint of the inversion. It shows a significant deficit of polymorphism with respect to divergence when compared with other loci studied in the same population, thus suggesting selective effects. Only 11 polymorphic sites are present in a sample of 20 chromosomes and these sites present a significant excess of rare-frequency variants. The major haplotype shows an unexpectedly high frequency. Our estimate of the background selection effect is not sufficient to account for the observed reduction of polymorphism. Intraspecific variation is structured between inverted and standard chromosomes; there are no shared polymorphisms but also no fixed differences between them. This pattern, together with that found on other loci previously studied near this inversion breakpoint, suggests hitch-hiking effects enhanced by the inversion.

Animals↗
PubMed1997

Unusual feature of the T-cell receptor genes in T-lineage acute lymphoblastic leukemia.

We characterized the T-cell receptor (TCR) gene rearrangements and sequences in 15 T-lineage acute lymphoblastic leukemia (T-ALL) and seven adult T-cell leukemia (ATL) samples. Southern blot analysis showed that neither of the two TCR delta alleles was deleted in two T-ALL samples, suggesting that the TCR alpha loci have a germ line configuration. The TCR alpha and beta sequences were cloned and sequenced by reverse transcriptase-inverse polymerase chain reaction. Two T-ALL samples had a long complementarity determining region (CDR), three of the alpha chain and the other two T-ALL samples had long CDR3 of the beta chain, compared with normal peripheral blood lymphocytes (PBL). Thus, a total of six T-ALL samples had unusual TCR gene structure, which was unrelated to the immunophenotype. On the other hand, CDR3 length in ATL samples was similar to normal PBL. These data suggest that T-ALL is derived from an immature T-cell repertoire which undergoes TCR gene rearrangement or has not been negatively selected.

Adolescent↗
PubMed2006

Isolation of aminopeptidase N genes of food associated propionibacteria and observation of their transcription in skim milk and acid whey.

In this study consensus oligonucleotides PN5/PN3 were designed by aligning the aminopeptidase N genes (pepN) of various actinobacteria and applied to the isolation of the pepN genes of dairy propionibacteria (PAB) and closely related species associated with food. This allowed sequencing of a pepN gene region from Propionibacterium jensenii LMG 16541. The sequence of this gene was completed by inverse PCR. Consensus primer pairs NU1/D1 and NU2/D1 were derived from the alignment of the new sequence with its homologues in Propionibacterium acnes and other actinobacteria; these were used to start sequencing of the pepN genes of Propionibacterium freudenreichii, Propionibacterium thoenii, Propionibacterium microaerophilum, Propionibacterium acidipropionici, Propioni bacterium cyclohexanicum and Propionibacterium microaerophilum. Reverse transcription coupled with PN5/PN3 and NU1/D1 PCR tests indicated that the pepN genes of P. jensenii and P. freudenreichii are expressed during growth in skim milk and acid whey.

Amino Acid Sequence↗