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81.
Vincens P; Buffat L; Andre C; Chevrolat JP; Boisvieux JF; Hazout S 《Bioinformatics (Oxford, England)》1998,14(8):715-725
MOTIVATION: Complete genomic sequences will become available in the future.
New methods to deal with very large sequences (sizes beyond 100 kb)
efficiently are required. One of the main aims of such work is to increase
our understanding of genome organization and evolution. This requires
studies of the locations of regions of similarity. RESULTS: We present here
a new tool, ASSIRC ('Accelerated Search for SImilarity Regions in
Chromosomes'), for finding regions of similarity in genomic sequences. The
method involves three steps: (i) identification of short exact chains of
fixed size, called 'seeds', common to both sequences, using hashing
functions; (ii) extension of these seeds into putative regions of
similarity by a 'random walk' procedure; (iii) final selection of regions
of similarity by assessing alignments of the putative sequences. We used
simulations to estimate the proportion of regions of similarity not
detected for particular region sizes, base identity proportions and seed
sizes. This approach can be tailored to the user's specifications. We
looked for regions of similarity between two yeast chromosomes (V and IX).
The efficiency of the approach was compared to those of conventional
programs BLAST and FASTA, by assessing CPU time required and the regions of
similarity found for the same data set. AVAILABILITY: Source programs are
freely available at the following address: ftp://ftp.biologie.ens.
fr/pub/molbio/assirc.tar.gz CONTACT: vincens@biologie.ens.fr,
hazout@urbb.jussieu.fr
相似文献
82.
Gill Furze Alun Roebuck Peter Bull Robert JP Lewin David R Thompson 《BMC cardiovascular disorders》2002,2(1):1-5
Background
Systolic compression of a coronary artery by overlying myocardial tissue is termed myocardial bridging. Myocardial bridging usually has a benign prognosis, but some cases resulting in myocardial ischemia, infarction and sudden cardiac death have been reported. We are reporting a case of myocardial bridging which was complicated with acute myocardial infarction associated with inappropriate blood donation.Case presentation
A 33 year-old-man was admitted to our emergency with acute anteroseptal myocardial infarction after a blood donation. The electrocardiography showed sinus rhythm and was consistent with an acute anteroseptal myocardial infarction. We decided to perform primary percutanous intervention (PCI). Myocardial bridging was observed in the mid segment of the left anterior descending coronary artery on coronary angiogram. PCI was canceled and medical follow up was decided. Blood transfusion was made because he had a deep anemia. A normal hemaglobin level and clinical reperfusion was achieved after ten hours by blood transfusion. At the one year follow up visit, our patient was healthy and had no cardiac complaints.Conclusions
Myocardial bridging may cause acute myocardial infarction in various clinical conditions. Although the condition in this case caused profound anemia related acute myocardial infarction, its treatment and management was unusual. 相似文献83.
Pannequin J Kovac S Tantiongco JP Norton RS Shulkes A Barnham KJ Baldwin GS 《The Journal of biological chemistry》2004,279(4):2453-2460
Although bismuth salts have been used for over two centuries for the treatment of various gastrointestinal disorders, the mechanism of their therapeutic action remains controversial. Because gastrins bind two trivalent ferric ions with high affinity, and because ferric ions are essential for the biological activity of glycine-extended gastrin 17, we have investigated the hypothesis that trivalent bismuth ions influence the biological activity of gastrins. Binding of bismuth ions to gastrins was measured by fluorescence quenching and NMR spectroscopy. The effects of bismuth ions on gastrin-stimulated biological activities were measured in inositol phosphate, cell proliferation, and cell migration assays. Fluorescence quenching experiments indicated that both glycine-extended and amidated gastrin 17 bound two bismuth ions. The NMR spectral changes observed on addition of bismuth ions revealed that Glu-7 acted as a ligand at the first bismuth ion binding site. In the presence of bismuth ions the ability of glycine-extended gastrin 17 to stimulate inositol phosphate production, cell proliferation, and cell migration was markedly reduced. In contrast, bismuth ions had little effect on the affinity of the CCK-2 receptor for amidated gastrin 17, or on the stimulation of inositol phosphate production by amidated gastrin 17. We conclude that bismuth ions may act, at least in part, by blocking the effects of glycine-extended gastrin 17 on cell proliferation and cell migration in the gastrointestinal tract. This is the first report of a specific inhibitory effect of bismuth ions on the action of a gastrointestinal hormone. 相似文献
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Background
Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods randomly generate a new trial conformation, which is either accepted or rejected according to a criterion based on energy calculations and stochastic rules. These simulation trials are generated using a method based on crankshaft motion that, apart from some slight improvements, has remained the same for many years.Results
In this paper, we present a new algorithm for the deformation of plasmid DNA molecules for Monte Carlo simulations. The move underlying our algorithm preserves the size and connectivity of straight-line segments of the plasmid DNA skeleton. We also present the results of three experiments comparing our deformation move with the standard and biased crankshaft moves in terms of acceptance ratio of the trials, energy and temperature evolution, and average displacement of the molecule. Our algorithm can also be used as a generic geometric algorithm for the deformation of regular polygons or polylines that preserves the connections and lengths of their segments.Conclusion
Compared with both crankshaft moves, our move generates simulation trials with higher acceptance ratios and smoother deformations, making it suitable for real-time visualization of plasmid DNA coiling. For that purpose, we have adopted a DNA assembly algorithm that uses nucleotides as building blocks. 相似文献90.