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51.
Dyson MT Jones JK Kowalewski MP Manna PR Alonso M Gottesman ME Stocco DM 《Biology of reproduction》2008,78(2):267-277
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Sampling properties of DNA sequence data in phylogenetic analysis 总被引:20,自引:6,他引:20
We inferred phylogenetic trees from individual genes and random samples of
nucleotides from the mitochondrial genomes of 10 vertebrates and compared
the results to those obtained by analyzing the whole genomes. Individual
genes are poor samples in that they infrequently lead to the whole-genome
tree. A large number of nucleotide sites is needed to exactly determine the
whole-genome tree. A relatively small number of sites, however, often
results in a tree close to the whole-genome tree. We found that blocks of
contiguous sites were less likely to lead to the whole-genome tree than
samples composed of sites drawn individually from throughout the genome.
Samples of contiguous sites are not representative of the entire genome, a
condition that violates a basic assumption of the bootstrap method as it is
applied in phylogenetic studies.
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Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies. 总被引:22,自引:4,他引:18 下载免费PDF全文
DNA-dependent protein kinase (DNA-PK or the scid factor) and Ku are critical for DNA end-joining in V(D)J recombination and in general non-homologous double-strand break repair. One model for the function of DNA-PK is that it forms a complex with Ku70/86, and this complex then binds to DNA ends, with Ku serving as the DNA-binding subunit. We find that DNA-PK can itself bind to linear DNA fragments ranging in size from 18 to 841 bp double-stranded (ds) DNA, as indicated by: (i) mobility shifts; (ii) crosslinking between the DNA and DNA-PK; and (iii) atomic-force microscopy. Binding of the 18 bp ds DNA to DNA-PK activates it for phosphorylation of protein targets, and this level of activation is not increased by addition of purified Ku70/86. Ku can stimulate DNA-PK activity beyond this level only when the DNA fragments are long enough for the independent binding to the DNA of both DNA-PK and Ku. Atomic-force microscopy indicates that under such conditions, the DNA-PK binds at the DNA termini, and Ku70/86 assumes a position along the ds DNA that is adjacent to the DNA-PK. 相似文献
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Grzegorz A. Kowalewski Ryszard Kornijów Suzanne McGowan Anna Kaczorowska Krystyna Bałaga Tadeusz Namiotko Michał Gąsiorowski Agnieszka Wasiłowska 《Hydrobiologia》2016,763(1):301-312
Shallow lakes are susceptible to catastrophic regime shifts characterised by the presence or absence or macrophytes. However, the long-term controls on macrophyte succession in shallow lakes are incompletely understood. To investigate this, we analysed multiple sediment proxies in Lake Rotcze (Eastern Poland), a small, shallow and densely macrophyte-covered lake to (1) reconstruct the ‘reference conditions’ (sensu WFD) and development of the lake in recent centuries, (2) compare historical evidence with the sedimentary record, and (3) identify the natural and anthropogenic drivers of macrophyte succession. Before the twentieth century, conditions in the lake may be referred to as ‘reference conditions’. Subsequently forest clearance in the catchment resulted in lower water transparency, but concurrent catchment drainage lowered water levels and increased macrophyte development. Since 1950 elevated nutrient supply and climatically driven increases in water levels led to the deterioration of water transparency and partial macrophyte withdrawal. At the end of the twentieth century lake-level drawdown led to low phytoplankton biomass and clear water creating a novel ecosystem where macrophytes invade the whole lake. These patterns suggest that both natural and anthropogenically induced water level fluctuations have been critical drivers of macrophyte development. 相似文献
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