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11.
Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference 总被引:2,自引:0,他引:2
Brauer MJ Holder MT Dries LA Zwickl DJ Lewis PO Hillis DM 《Molecular biology and evolution》2002,19(10):1717-1726
We investigated the usefulness of a parallel genetic algorithm for phylogenetic inference under the maximum-likelihood (ML) optimality criterion. Parallelization was accomplished by assigning each "individual" in the genetic algorithm "population" to a separate processor so that the number of processors used was equal to the size of the evolving population (plus one additional processor for the control of operations). The genetic algorithm incorporated branch-length and topological mutation, recombination, selection on the ML score, and (in some cases) migration and recombination among subpopulations. We tested this parallel genetic algorithm with large (228 taxa) data sets of both empirically observed DNA sequence data (for angiosperms) as well as simulated DNA sequence data. For both observed and simulated data, search-time improvement was nearly linear with respect to the number of processors, so the parallelization strategy appears to be highly effective at improving computation time for large phylogenetic problems using the genetic algorithm. We also explored various ways of optimizing and tuning the parameters of the genetic algorithm. Under the conditions of our analyses, we did not find the best-known solution using the genetic algorithm approach before terminating each run. We discuss some possible limitations of the current implementation of this genetic algorithm as well as of avenues for its future improvement. 相似文献
12.
Microorganisms originating from a soil contaminated by low levels of polycyclic aromatic hydrocarbons (PAHs) were enriched
with three- and four-ring PAHs as primary substrates in the presence of benzo[a]pyrene (BaP). Most enrichment cultures, isolated in the presence or absence of a sorptive matrix, significantly transformed
BaP. Evidence of BaP mineralization was obtained with cultures enriched on phenanthrene and anthracene. Our findings supplement
literature data suggesting the wide occurrence of microbial activity against BaP. Journal of Industrial Microbiology & Biotechnology (2002) 28, 70–73 DOI: 10.1038/sj/jim/7000211
Received 11 December 2000/ Accepted in revised form 04 September 2001 相似文献
13.
High critical temperature above T(g) may contribute to the stability of biological systems
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Buitink J van den Dries IJ Hoekstra FA Alberda M Hemminga MA 《Biophysical journal》2000,79(2):1119-1128
In this study, we characterized the molecular mobility around T(g) in sugars, poly-L-lysine and dry desiccation-tolerant biological systems, using ST-EPR, (1)H-NMR, and FTIR spectroscopy, to understand the nature and composition of biological glasses. Two distinct changes in the temperature dependence of the rotational correlation time (tau(R)) of the spin probe 3-carboxy-proxyl or the second moment (M(2)) were measured in sugars and poly-L-lysine. With heating, the first change was associated with the melting of the glassy state (T(g)). The second change (T(c)), at which tau(R) abruptly decreased over several orders of magnitude, was found to correspond with the so-called cross-over temperature, where the dynamics changed from solid-like to liquid-like. The temperature interval between T(g) and T(c) increased in the order of sucrose < trehalose < raffinose = staychose < poly-L-lysine < biological tissues, from 17 to >50 degrees C, implying that the stability above T(g) improved in the same order. These differences in temperature-dependent mobilities above T(g) suggest that proteins rather than sugars play an important role in the intracellular glass formation. The exceptionally high T(c) of intracellular glasses is expected to provide excellent long-term stability to dry organisms, maintaining a slow molecular motion in the cytoplasm even at temperatures far above T(g). 相似文献
14.
Aerial dispersal plasticity under different wind velocities in a salt marsh wolf spider 总被引:1,自引:0,他引:1
Dispersal can be regarded as a process operating both betweenand within patches of suitable habitat. For uncontrolled dispersalprocesses, the risk of crossing the borders of the habitat patchand arriving in the unsuitable landscape matrix will increasewith decreasing patch area, in particular when the distancebetween isolated habitat patches is larger than the species'average dispersal capacity. Ballooning dispersal in spiderscan be considered as a passive dispersal process, in which disperseddistances depend on the prevalent wind velocity. We executeda reaction norm analysis to analyze how dispersal propensityof the salt marsh wolf spider Pardosa purbeckensis dependedon population characteristics (patch size) and the environment(wind velocity). Dispersal propensity was affected by the interactionbetween wind velocity and maternal patch size. Ballooning propensitiesdecreased with decreasing salt marsh size. Interestingly, genotypesfrom large salt marshes show higher ballooning propensitiesunder higher wind velocities, whereas those from small habitatpatches show their highest dispersal propensity under low windvelocities. Crossing reaction norms and subsequently stronggenotype x environment interaction variation was observed inall populations but tended to be lower in genotypes from largesalt marshes. It is likely that this pattern results from differencesin wind velocityrelated costs of within-habitat dispersalin salt marshes of different sizes. 相似文献
15.
Boyen P Van Dyck D Neven F van Ham RC van Dijk AD 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2011,8(5):1344-1357
Correlated motif mining (cmm) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for cmm thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that cmm is an np-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic slider which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that slider outperforms existing motif-driven cmm methods and scales to large protein-protein interaction networks. The slider-implementation and the data used in the experiments are available on http://bioinformatics.uhasselt.be. 相似文献
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Alvarez M Huygens D Díaz LM Villanueva CA Heyser W Boeckx P 《Plant, cell & environment》2012,35(1):126-135
Acid phosphatase (ACP) enzymes are involved in the mobilization of soil phosphorus (P) and polyphosphate accumulated in the fungal tissues of ectomycorrhizal roots, thereby influencing the amounts of P that are stored in the fungus and transferred to the host plant. This study evaluated the effects of ectomycorrhizal morphotype and soil fertility on ACP activity in the extraradical mycelium (ACP(myc)), the mantle (ACP(mantle)) and the Hartig net region (ACP(Hartig)) of ectomycorrhizal Nothofagus obliqua seedlings. ACP activity was quantified in vivo using enzyme-labelled fluorescence-97 (ELF-97) substrate, confocal laser microscopy and digital image processing routines. There was a significant effect of ectomycorrhizal morphotype on ACP(myc), ACP(mantle) and ACP(Hartig), while soil fertility had a significant effect on ACP(myc) and ACP(Hartig). The relative contribution of the mantle and the Hartig net region to the ACP activity on the ectomycorrhizal root was significantly affected by ectomycorrhizal morphotype and soil fertility. A positive correlation between ACP(Hartig) and the shoot P concentration was found, providing evidence that ACP activity at the fungus:root interface is involved in P transfer from the fungus to the host. It is concluded that the spatial distribution of ACP in ectomycorrhizas varies as a function of soil fertility and colonizing fungus. 相似文献
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Kevin Lambeets Frederik Hendrickx Stijn Vanacker Kris Van Looy Jean-Pierre Maelfait Dries Bonte 《Biodiversity and Conservation》2008,17(13):3133-3148
We assessed the composition of spider and carabid beetle assemblages along river banks from the Common Meuse (Belgium) to
determine their relationships with local topographical and landscape-related characteristics. Data were gathered with pitfall
traps in 1998 and explored by ordination and grouping methods. Our analysis revealed that the presence of xerothermic spider
species was limited to scarcely covered, less dynamic gravel banks. Riparian spider species were found on frequently flooded
as well as on rather elevated and high gravel banks, while riparian carabid beetles were dominant on all sampled banks. The
level of flooding disturbance, the vegetation density and the presence of silt appeared to be the most important environmental
determinants of spider and carabid beetle assemblage structure. Consequently, local environmental factors influence species
occurrence patterns in a similar way for the two investigated arthropod groups. Nevertheless, distinct ecological groups are
differently ordered along the prime environmental gradients. Nature management should therefore consider the conservation,
restoration and connectivity of both dynamic and more elevated banks in order to obtain a high degree of local and regional
heterogeneity throughout the river system. 相似文献