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61.
In order to reconstruct phylogenetic trees from extremely dissimilar
sequences it is necessary to estimate accurately the extent of sequence
divergence. In this paper a new method of sequence analysis, Markov triple
analysis, is developed for determining the relative frequencies of
nucleotide substitutions within the three branches of a three-taxon
dendrogram. Assuming that nucleotide sites are independently and
identically distributed and assuming a Markov model for nucleotide (or
protein) evolution, it is shown that the unique Markov matrices can be
reconstructed given only the joint probability distribution relating three
taxa. (In the much simpler case involving only two taxa and two character
states, Markov matrices can also be reconstructed, provided symmetry
assumptions are placed on the elements of the matrices.) The method is
illustrated using sequence data from the combined first and second codon
positions derived from complete human, mouse, and cow mitochondrial
sequences.
相似文献
62.
DNA hybridization evidence for the principal lineages of hummingbirds (Aves:Trochilidae) 总被引:3,自引:0,他引:3
The spectacular evolutionary radiation of hummingbirds (Trochilidae) has
served as a model system for many biological studies. To begin to provide a
historical context for these investigations, we generated a complete matrix
of DNA hybridization distances among 26 hummingbirds and an outgroup swift
(Chaetura pelagica) to determine the principal hummingbird lineages. FITCH
topologies estimated from symmetrized delta TmH-C values and subjected to
various validation methods (bootstrapping, weighted jackknifing, branch
length significance) indicated a fundamental split between hermit
(Eutoxeres aquila, Threnetes ruckeri; Phaethornithinae) and nonhermit
(Trochilinae) hummingbirds, and provided strong support for six principal
nonhermit clades with the following branching order: (1) a predominantly
lowland group comprising caribs (Eulampis holosericeus) and relatives
(Androdon aequatorialis and Heliothryx barroti) with violet-ears (Colibri
coruscans) and relatives (Doryfera ludovicae); (2) an Andean-associated
clade of highly polytypic taxa (Eriocnemis, Heliodoxa, and Coeligena); (3)
a second endemic Andean clade (Oreotrochilus chimborazo, Aglaiocercus
coelestis, and Lesbia victoriae) paired with thorntails (Popelairia
conversii); (4) emeralds and relatives (Chlorostilbon mellisugus, Amazilia
tzacatl, Thalurania colombica, Orthorhyncus cristatus and Campylopterus
villaviscensio); (5) mountain-gems (Lampornis clemenciae and Eugenes
fulgens); and (6) tiny bee-like forms (Archilochus colubris, Myrtis fanny,
Acestrura mulsant, and Philodice mitchellii). Corresponding analyses on a
matrix of unsymmetrized delta values gave similar support for these
relationships except that the branching order of the two Andean clades (2,
3 above) was unresolved. In general, subsidiary relationships were
consistent and well supported by both matrices, sometimes revealing
surprising associations between forms that differ dramatically in plumage
and bill morphology. Our results also reveal some basic aspects of
hummingbird ecologic and morphologic evolution. For example, most of the
diverse endemic Andean assemblage apparently comprises two genetically
divergent clades, whereas the majority of North American hummingbirds
belong a single third clade. Genetic distances separating some
morphologically distinct genera (Oreotrochilus, Aglaiocercus, Lesbia;
Myrtis, Acestrura, Philodice) were no greater than among congeneric
(Coeligena) species, indicating that, in hummingbirds, morphological
divergence does not necessarily reflect level of genetic divergence.
相似文献
63.
64.
65.
Despite their remoteness from sources of atmospheric pollutant emissions, the Afromontane tarns in the Maloti-Drakensberg region are perfect candidates to study the negative effects of acidifying atmospheric pollution, because mountain lakes are widely recognised as sentinel ecosystems, unimpacted by direct human disturbance within their catchments. Thirty-four tarns were sampled in the Maloti-Drakensberg region and most were found to be extremely sensitive to acidic deposition, as indicated by their low acid neutralising capacity. There are very few studies of freshwater critical loads for any region within South Africa. The steady-state water chemistry model (SSWC) was adapted and used to determine critical loads, whereas exceedance was estimated relative to modelled regional deposition data, in order to understand the risk of harmful effects to aquatic ecosystems. Seventy-six percent of sampled sites across the Maloti-Drakensberg would exceed critical loads even at the lowest modelled deposition levels, but there are no current measured deposition data for the region. The sensitivity of the Maloti-Drakensberg tarns needs to be considered in future policy formulation regarding acceptable levels of acidifying atmospheric pollution from South Africa’s energy sector and indicates the need for assessing aquatic ecosystem impacts in other regions of South Africa. 相似文献
66.
E C Castro JA Diaz GomezDe Ferreyra C R De Castro N D'Acosta C M De Fenos 《Biochemical and biophysical research communications》1973,50(2):337-343
There is a higher activity of ethyl morphine N-demethylase (EM-ase) and cytochrome P-450 (P-450) reductase as well as higher P-450 content in the smooth endoplasmic reticulum (SER) than in the rough endoplasmic reticulum (RER). The extent of the irreversible binding of the14C from14CCl4 to lipids and proteins, as well as the CCl4-induced destruction of P-450 is more intense in SER than in RER while the opposite was found for glucose 6-phosphatase (G6P-ase) destruction. CCl4-induced lipid peroxidation is as intense in SER as is in RER.14C from14CCl4 gets irreversibly bound to ribosomal proteins. 相似文献
67.
Peter Thorpe Sophie Mantelin Peter JA Cock Vivian C Blok Mirela C Coke Sebastian Eves-van den Akker Elena Guzeeva Catherine J Lilley Geert Smant Adam J Reid Kathryn M Wright Peter E Urwin John T Jones 《BMC genomics》2014,15(1)
Background
The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium.Results
The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure.Conclusion
This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-923) contains supplementary material, which is available to authorized users. 相似文献68.
Daiane D Hartwig Thaís L Oliveira Fabiana K Seixas Karine M Forster Caroline Rizzi Cláudia P Hartleben Alan JA McBride Odir A Dellagostin 《Microbial cell factories》2010,9(1):98
Background
Leptospirosis, a zoonosis caused by Leptospira spp., is recognized as an emergent infectious disease. Due to the lack of adequate diagnostic tools, vaccines are an attractive intervention strategy. Recombinant proteins produced in Escherichia coli have demonstrated promising results, albeit with variable efficacy. Pichia pastoris is an alternative host with several advantages for the production of recombinant proteins. 相似文献69.
70.
Lucas A Smolders Bj?rn P Meij David Onis Frank M Riemers Niklas Bergknut Richard Wubbolts Guy CM Grinwis Martin Houweling Marian JA Groot Koerkamp Dik van Leenen Frank CP Holstege Herman AW Hazewinkel Laura B Creemers Louis C Penning Marianna A Tryfonidou 《Arthritis research & therapy》2013,15(1):R23