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81.
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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83.
H. Lemriss Martins Sim?es P S. Lemriss M. Butin A. Ibrahimi S. El Kabbaj JP Rasigade F. Laurent 《Standards in genomic sciences》2014,9(3):1118-1127
Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the human microflora. Recently, a clonal population of Staphylococcus capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis (LOS) in several neonatal intensive care units in France. Here, we report the complete genome sequence and annotation of the prototype Staphylococcus capitis NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids) exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA genes and 4 rRNA genes. 相似文献
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GRÉGOIRE M. HUMMEL ULRICH SCHURR IAN T. BALDWIN & ACHIM WALTER 《Plant, cell & environment》2009,32(2):134-143
Root growth in Nicotiana attenuata is transiently reduced after application of oral secretions (OS) of Manduca sexta larvae to wounds in leaves. Feeding of M. sexta or OS elicitation is known to result in jasmonic acid (JA) and ethylene bursts, and activates a suite of defence responses. Because both plant hormones are known to strongly reduce root growth, their activation might account for the observed reduction of root growth following herbivory. To test this hypothesis, we measured primary root growth with digital image sequence processing at high temporal resolution in antisense- lipoxygenase 3 (as LOX3 ) and inverted repeat- coronatin-insensitive 1 (ir COI1 ) seedlings which are impaired in JA biosynthesis and perception, respectively, and wild-type (WT) seedlings. Higher root growth rates in ir COI1 compared with WT were observed after OS elicitation. The dynamics of wound-induced root growth reduction coincide with the dynamics of root growth reduction induced by external application of methyl JA. In an experiment with 1-methylcyclopropen (1-MCP), a potent ethylene receptor blocker, no wounding-specific difference between growth of 1-MCP-treated plants and non-treated plants was observed, suggesting that wound-induced endogenous JA and not ethylene mediates the wounding-specific reduction in root growth. Yet, inhibiting the ethylene response by applying 1-MCP led to markedly increased root growth compared with that of control plants, indicating that ethylene normally suppresses plant growth in N. attenuata seedlings. 相似文献
87.
JP Valde LG Lawson A Lindberg JF Agger H Saloniemi O Østerås 《Acta veterinaria Scandinavica》2004,45(4):201-210
Data from the national dairy cow recording systems during 1997 were used to calculate lactation-specific cumulative risk of mastitis treatments and cumulative risk of removal from the herds in Denmark, Finland Norway and Sweden. Sweden had the lowest risk of recorded mastitis treatments during 305 days of lactation and Norway had the highest risk. The incidence risk of recorded mastitis treatments during 305 days of lactation in Denmark, Finland, Norway and Sweden was 0.177, 0.139, 0.215 and 0.127 for first parity cows and 0.228, 0.215, 0.358 and 0.204 for parities higher than three, respectively. The risk of a first parity cow being treated for mastitis was almost 3 times higher at calving in Norway than in Sweden. The period with the highest risk for mastitis treatments was from 2 days before calving until 14 days after calving and the highest risk for removal was from calving to 10 days after calving in all countries.The study clearly demonstrated differences in bovine mastitis treatment patterns among the Nordic countries. The most important findings were the differences in treatment risks during different lactations within each country, as well as differences in strategies with respect to the time during lactation mastitis was treated. 相似文献
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James?F?MeschiaEmail author Thomas?G?Brott Robert?D?BrownJr Richard?JP?Crook Michael?Frankel John?Hardy José?G?Merino Stephen?S?Rich Scott?Silliman Bradford?Burke?Worrall 《BMC neurology》2003,3(1):4
Background
The molecular basis for the genetic risk of ischemic stroke is likely to be multigenic and influenced by environmental factors. Several small case-control studies have suggested associations between ischemic stroke and polymorphisms of genes that code for coagulation cascade proteins and platelet receptors. Our aim is to investigate potential associations between hemostatic gene polymorphisms and ischemic stroke, with particular emphasis on detailed characterization of the phenotype. 相似文献89.
90.
Gill Furze Alun Roebuck Peter Bull Robert JP Lewin David R Thompson 《BMC cardiovascular disorders》2002,2(1):1-5