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51.
Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa 总被引:13,自引:5,他引:8
The reconstruction of phylogenetic history is predicated on being able to
accurately establish hypotheses of character homology, which involves
sequence alignment for studies based on molecular sequence data. In an
empirical study investigating nucleotide sequence alignment, we inferred
phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based
on complete small-subunit rDNA sequences, using six different
multiple-alignment procedures: manual alignment based on the secondary
structure of the 18S rRNA molecule, and automated similarity-based
alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM
computer programs. Trees were constructed using neighboring-joining,
weighted-parsimony, and maximum- likelihood methods. All of the multiple
sequence alignment procedures yielded the same basic structure for the
estimate of the phylogenetic relationship among the taxa, which presumably
represents the underlying phylogenetic signal. However, the placement of
many of the taxa was sensitive to the alignment procedure used; and the
different alignments produced trees that were on average more dissimilar
from each other than did the different tree-building methods used. The
multiple alignments from the different procedures varied greatly in length,
but aligned sequence length was not a good predictor of the similarity of
the resulting phylogenetic trees. We also systematically varied the gap
weights (the relative cost of inserting a new gap into a sequence or
extending an already-existing gap) for the ClustalW program, and this
produced alignments that were at least as different from each other as
those produced by the different alignment algorithms. Furthermore, there
was no combination of gap weights that produced the same tree as that from
the structure alignment, in spite of the fact that many of the alignments
were similar in length to the structure alignment. We also investigated the
phylogenetic information content of the helical and nonhelical regions of
the rDNA, and conclude that the helical regions are the most informative.
We therefore conclude that many of the literature disagreements concerning
the phylogeny of the Apicomplexa are probably based on differences in
sequence alignment strategies rather than differences in data or
tree-building methods.
相似文献
52.
Structural comparison of fibroblast growth factor-specific heparan sulfates derived from a growing or differentiating neuroepithelial cell line 总被引:3,自引:1,他引:2
Brickman YG; Nurcombe V; Ford MD; Gallagher JT; Bartlett PF; Turnbull JE 《Glycobiology》1998,8(5):463-471
Heparan sulfate (HS) glycosaminoglycans are essential modulators of
fibroblast growth factor (FGF) activity both in vivo and in vitro, and
appear to act by cross-linking particular forms of FGF to appropriate FGF
receptors. We have recently isolated and characterized two separate HS
pools derived from immortalized embryonic day 10 mouse neuroepithelial 2.3D
cells: one from cells in log growth phase, which greatly potentiates the
activity of FGF-2, and the other from cells undergoing contact-inhibition
and differentiation, which preferentially activates FGF-1. These two pools
of HS have very similar functional activities to those species isolated
from primary neuroepithelial cells at corresponding stages of active
proliferation or differentiation. We present here a structural comparison
between these cell line HS species to establish the nature of the changes
that occur in the biosynthesis of HS. A combination of chemical and
enzymatic cleavage, low pressure chromatography and strong anion-exchange
HPLC were used to generate full chain models of each species. Overall, the
HS pools synthesized in the dividing cell line pools possessed less complex
sulfation than those derived from more differentiated, growth arrested
cells.
相似文献
53.
DNA-protein cross-links are generated by both endogenous and exogenous DNA damaging agents, as intermediates during normal DNA metabolism, and during abortive base excision repair. Cross-links are relatively common lesions that are lethal when they block progression of DNA polymerases. DNA-protein cross-links may be broadly categorized into four groups by the DNA and protein chemistries near the cross-link and by the source of the cross-link: DNA-protein cross-links may be found (1) in nicked DNA at the 3' end of one strand (topo I), (2) in nicked DNA at the 5' end of one strand (pol beta), (3) at the 5' ends of both strands adjacent to nicks in close proximity (topo II; Spo 11), and (4) in one strand of duplex DNA (UV irradiation; bifunctional carcinogens and chemotherapeutic agents). Repair mechanisms are reasonably well-defined for groups 1 and 3, and suggested for groups 2 and 4. Our work is focused on the recognition and removal of DNA-protein cross-links in duplex DNA (group 4). 相似文献
54.
Cross-hybridizing snake satellite, Drosophila, and mouse DNA sequences may have arisen independently 总被引:2,自引:0,他引:2
Previous reports have interpreted hybridization between snake satellite DNA
and DNA clones from a variety of distant taxonomic groups as evidence for
evolutionary conservation, which implies common ancestry (homology) and/or
convergence (analogy) to produce the cross- hybridizing sequences. We have
isolated 11 clones from a genomic library of Drosophila melanogaster, using
a cloned 2.5-kb snake satellite probe of known nucleotide sequence. We have
also analysed published sequence data from snakes, mice, and Drosophila.
These data show that (1) all of the cross-hybridization between the snake,
fly, and mouse clones can be accounted for by the presence of either of two
tandem repeats, [GATA]n and [GACA]n and (2) these tandem repeats are
organized differently among the different species. We find no evidence that
these sequences are homologous apart from the existence of the simple
repeat itself, although their divergence from a common ancestral sequence
cannot be ruled out. The sequences contain a variety of homogeneous
clusters of tandem repeats of CATA, GA, TA, and CA, as well as GATA and
GACA. We suggest that these motifs may have arisen by a self-accelerating
process involving slipped-strand mispairing of DNA. Homogeneity of the
clusters might simply be the result of a rate of accumulation of tandem
repeats that exceeds that of other mutations.
相似文献
55.
Olivier JT Briët Gawrie NL Galappaththy Flemming Konradsen Priyanie H Amerasinghe Felix P Amerasinghe 《Malaria journal》2005,4(1):1-11
In Vietnam, a large proportion of all malaria cases and deaths occurs in the central mountainous and forested part of the country. Indeed, forest malaria, despite intensive control activities, is still a major problem which raises several questions about its dynamics. A large-scale malaria morbidity survey to measure malaria endemicity and identify important risk factors was carried out in 43 villages situated in a forested area of Ninh Thuan province, south central Vietnam. Four thousand three hundred and six randomly selected individuals, aged 10–60 years, participated in the survey. Rag Lays (86%), traditionally living in the forest and practising "slash and burn" cultivation represented the most common ethnic group. The overall parasite rate was 13.3% (range [0–42.3] while Plasmodium falciparum seroprevalence was 25.5% (range [2.1–75.6]). Mapping of these two variables showed a patchy distribution, suggesting that risk factors other than remoteness and forest proximity modulated the human-vector interactions. This was confirmed by the results of the multivariate-adjusted analysis, showing that forest work was a significant risk factor for malaria infection, further increased by staying in the forest overnight (OR= 2.86; 95%CI [1.62; 5.07]). Rag Lays had a higher risk of malaria infection, which inversely related to education level and socio-economic status. Women were less at risk than men (OR = 0.71; 95%CI [0.59; 0.86]), a possible consequence of different behaviour. This study confirms that malaria endemicity is still relatively high in this area and that the dynamics of transmission is constantly modulated by the behaviour of both humans and vectors. A well-targeted intervention reducing the "vector/forest worker" interaction, based on long-lasting insecticidal material, could be appropriate in this environment. 相似文献
56.
57.
58.
Dialyzed extracts of Bacillus megaterium KM contain thymidine, deoxyadenosine, and deoxyguanosine kinase activities. Thymidine kinase activity is best with deoxyadenosine triphosphate or deoxyguanosine triphosphate (dGTP) as the phosphoryl donor, whereas the best deoxyadenosine kinase activity is obtained with dGTP or adenosine triphosphate. Deoxyguanosine kinase activity functions optimally with deoxycytidine triphosphate as the donor. Although the thymidine kinase activity of crude extracts does not have a demonstrable divalent cation requirement, the addition of Mg(2+) or Mn(2+) is necessary for the formation of thymidine di- and triphosphates. The synthesis of thymidine kinase appears to be partially derepressed by thymine starvation. Incubation of extracts with deoxyadenosine and dGTP results in the substantial accumulation of deoxyadenosine di- and triphosphates. Extracts deaminate deoxycytidine to deoxyuridine, presumably as a consequence of the action of deoxycytidine deaminase, and then convert deoxyuridine to deoxyuridylic acid. B. megaterium extracts do not contain any detectable deoxycytidine kinase activity. 相似文献
59.
Wachsman, J. T. (University of Illinois, Urbana), S. Kemp, and L. Hogg. Comparative effects of 5-fluorouracil on strains of Bacillus megaterium. J. Bacteriol. 87:1011-1018. 1964.-Growth of Bacillus megaterium strain KM is severely inhibited by 5-fluorouracil (FU). Both thymidine and uridine are required to overcome this inhibition. The addition of uridine alone to a FU-inhibited culture permits good ribonucleic acid (RNA) and protein synthesis for the first 2 hr, but rather poor deoxyribonucleic acid synthesis. Uridine enhances the bactericidal effect of FU, promoting a decrease in the viable count of from 4 to 5 decades in 5 hr. Death begins after a 1-hr lag and is accompanied by hydrolysis of RNA and cell lysis, commencing during the 2- to 5-hr interval. The combination of FU and uridine is not bactericidal, when a methionine auxotroph is deprived of its required amino acid. Substrains of KM, partially resistant to FU, were isolated. Strain T(2) requires only thymidine to overcome the inhibitory effects of FU, whereas strain FU/2 requires only uridine. With a uridine auxotroph of strain KM, FU partially replaces uridine by permitting a small, but reproducible, increase in the amount of protein. 相似文献
60.
Carmen Lai Hugo M Horlings Marc J van de Vijver Eric H van Beers Petra M Nederlof Lodewyk FA Wessels Marcel JT Reinders 《BMC bioinformatics》2007,8(1):422