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41.
MOTIVATION: Recently, we described a Maximum Weighted Matching (MWM) method
for RNA structure prediction. The MWM method is capable of detecting
pseudoknots and other tertiary base-pairing interactions in a
computationally efficient manner (Cary and Stormo, Proceedings of the Third
International Conference on Intelligent Systems for Molecular Biology, pp.
75-80, 1995). Here we report on the results of our efforts to improve the
MWM method's predictive accuracy, and show how the method can be extended
to detect base interactions formerly inaccessible to automated RNA modeling
techniques. RESULTS: Improved performance in MWM structure prediction was
achieved in two ways. First, new ways of calculating base pair likelihoods
have been developed. These allow experimental data and combined statistical
and thermodynamic information to be used by the program. Second, accuracy
was improved by developing techniques for filtering out spurious base pairs
predicted by the MWM program. We also demonstrate here a means by which the
MWM folding method may be used to detect the presence of base triples in
RNAs. AVAILABILITY: http://www.cshl.org/mzhanglab/tabaska/j axpage. html
CONTACT: tabaska@cshl.org
相似文献
42.
Contrasting levels of DNA polymorphism at the autosomal and X-linked visual color pigment loci in humans and squirrel monkeys 总被引:1,自引:0,他引:1
The X-linked color pigment (opsin) locus is known to be highly polymorphic
in the squirrel monkey and other New World monkeys. To see whether this is
also the case for the autosomal (blue) opsin locus, we obtained 32 squirrel
monkey and 30 human blue opsin gene sequences. No amino acid polymorphism
was found in either the squirrel monkey sample or the human sample,
contrary to the situation at the X-linked opsin locus. This sharp contrast
in the level of polymorphism might be due to differences in gene expression
between the autosomal and the X-linked loci. At the X-linked locus,
heterozygote advantage can occur because, owing to X-inactivation, the two
alleles in a heterozygote are expressed in different cone cells, producing
two types of cone cell, whereas at the autosomal locus, heterozygote
advantage cannot occur because the two alleles in a heterozygote are
expressed in the same cone cells, producing only one type of cone cell
(i.e., phenotypically a homozygote). From the sequence data, the levels of
nucleotide diversity (pi, i.e., the number of nucleotide differences per
site) are estimated: for the human sample, pi = 0.00% per nondegenerate
site, 0.00% per twofold degenerate site, and 0.04% per fourfold degenerate
site in the coding regions and 0.01% per site in intron 4; for the squirrel
monkey sample, pi = 0.00% per nondegenerate site, 0.00% per twofold
degenerate site, and 0.15% per fourfold degenerate site in the coding
regions and 0.17% per site in intron 4. The blue opsin genes from the
common and pygmy chimpanzees, the gorilla, the capuchin, and the howler
monkey were also sequenced. Features critical to the function of the opsin
are well conserved in all known mammalian sequences. However, the
interhelical loops are, on average, actually more conservative than the
transmembrane helical regions. In addition, these sequence data and those
from some other genes indicate that the common and pygmy chimpanzees are
not closely related, their divergence data being from one third to one half
the date of the human-chimpanzee divergence.
相似文献
43.
The Effect of Benzimidazole and Red Light on the Senescence of Detached Leaves of Oryza sativa cv. Ratna 总被引:1,自引:0,他引:1
Excised rice leaves (Oryza sativa L. cv. Ratna) werefloated on a 10–3M solution of benzirnidazole under dark or continuous red light. Compared to the water control a degradation of chlorophyll, protein, RNA, DNA and a decrease in the activity of alkaline inorganic pyrophosphatase was delayed at the same time as an increase of α-amino nitrogen and the activity of acid inorganic pyrophosphatase occurred, Benzimidazole was more effective under red light than in the dark in retarding senescence. The possible role of inorganic pyrophosphatases is discussed with respect to biosynthesis during leaf senescence. 相似文献
44.
Background
Bacillus organisms are common laboratory contaminants. The majority of Bacillus bacteraemias are transient and not clinically significant. Clinically significant infection due to Bacillus species is rare and mostly due to Bacillus cereus infections in immuno-compromised hosts.Case presentation
We report a case of central venous catheter infection with Bacillus pumilus in an immunocompetent child with tufting enteropathy on long-term parenteral nutrition (PN). There were three episodes of central venous catheter infection with Bacillus pumilus in three months. Despite adequate and appropriate use of intravenous antibiotics, the infection failed to clear resulting in the need for removal of the catheter for complete cure.Conclusion
Bacillus species can cause clinically significant central venous catheter infection, even in an immunocompetent host. Despite adequate antibiotic treatment, the central venous catheter may need removal for complete cure. 相似文献45.
Integrated and biological control of gladiolus corm rot and wilt caused by Fusarium oxysporum f.sp. gladioli 总被引:2,自引:0,他引:2
An isolate of Trichoderma virens Miller, Giddens & Foster, carboxin and a combination of both were evaluated for the control of gladiolus corm rot and wilt caused by Fusarium oxysporum f.sp. gladioli in glasshouse and field experiments. All treatments significantly reduced disease incidence in both glasshouse and field conditions. T. virens gave control at least as good as carboxin in all experiments. Control was significantly improved in two field experiments by combining the biological and chemical treatments. 相似文献
46.
Maria D. Van Kerkhove Tommi Asikainen Niels G. Becker Steven Bjorge Jean-Claude Desenclos Thais dos Santos Christophe Fraser Gabriel M. Leung Marc Lipsitch Ira M. Longini Jr Emma S. McBryde Cathy E. Roth David K. Shay Derek J. Smith Jacco Wallinga Peter J. White Neil M. Ferguson Steven Riley for the WHO Informal Network for Mathematical Modelling for Pandemic Influenza HN 《PLoS medicine》2010,7(6)
47.
48.
Growth and iron oxidation by Thiobacillus ferrooxidans are affected by the presence of silver, molybdenum, uranium and copper. Growth is more sensitive to the presence of these metals than the iron oxidation system of the bacterium. Silver toxicity is much more specific than molybdenum and uranium. Iron oxidation is inhibited at only 0.1 parts/106 of silver which is 300 and 5000 times less than the minimum inhibitory concentration of molybdenum and uranium, respectively. Copper and zinc at concentrations as high as 2000 and 15 000 parts/106 , respectively, have no influence on the iron oxidation rate. In the presence of silver, molybdenum, uranium and copper below their minimum inhibitory concentrations as well as in the absence of nitrogen, phosphorus and potassium, iron oxidation is not coupled to growth. 相似文献
49.
Long-term responses of zooplankton to invasion by a planktivorous fish in a subarctic watercourse 总被引:1,自引:0,他引:1
1. Introduced or invading predators may have strong impacts on prey populations of the recipient community mediated by direct and indirect interactions. The long-term progression of predation effects, covering the invasion and establishment phase of alien predators, however, has rarely been documented.
2. This paper documents the impact of an invasive, specialized planktivorous fish on its prey in a subarctic watercourse. Potential predation effects on the crustacean plankton, at the community, population and individual levels, were explored in a long-term study following the invasion by vendace ( Coregonus albula ).
3. Over the 12-year period, the density and species richness of zooplankton decreased, smaller species became more abundant and Daphnia longispina , one of the largest cladocerans, was eliminated from the zooplankton community.
4. Within the dominant cladocerans, including Daphnia spp., Bosmina longispina and Bosmina longirostris , the body size of ovigerous females and the size at first reproduction decreased after the arrival of the new predator. The clutch sizes of Daphnia spp. and B. longirostris also increased.
5. Increased predation pressure following the vendace invasion induced many effects on the crustacean zooplankton, and we document comprehensive and strong direct and indirect long-term impacts of an introduced non-native predator on the native prey community. 相似文献
2. This paper documents the impact of an invasive, specialized planktivorous fish on its prey in a subarctic watercourse. Potential predation effects on the crustacean plankton, at the community, population and individual levels, were explored in a long-term study following the invasion by vendace ( Coregonus albula ).
3. Over the 12-year period, the density and species richness of zooplankton decreased, smaller species became more abundant and Daphnia longispina , one of the largest cladocerans, was eliminated from the zooplankton community.
4. Within the dominant cladocerans, including Daphnia spp., Bosmina longispina and Bosmina longirostris , the body size of ovigerous females and the size at first reproduction decreased after the arrival of the new predator. The clutch sizes of Daphnia spp. and B. longirostris also increased.
5. Increased predation pressure following the vendace invasion induced many effects on the crustacean zooplankton, and we document comprehensive and strong direct and indirect long-term impacts of an introduced non-native predator on the native prey community. 相似文献
50.
Inter‐simple sequence repeat (ISSR) analysis and aggressiveness assays were used to investigate genetic variability within a global collection of Fusarium culmorum isolates. A set of four ISSR primers were tested, of which three primers amplified a total of 37 bands out of which 30 (81%) were polymorphic. The intraspecific diversity was high, ranging from four to 28 different ISSR genotypes for F. culmorum depending on the primer. The combined analysis of ISSR data revealed 59 different genotypes clustered into seven distinct clades amongst 75 isolates of F. culmorum examined. All the isolates were assayed to test their aggressiveness on a winter wheat cv. ‘Armada’. A significant quantitative variation for aggressiveness was found among the isolates. The ISSR and aggressiveness variation existed on a macro‐ as well as micro‐geographical scale. The data suggested a long‐range dispersal of F. culmorum and indicated that this fungus may have been introduced into Canada from Europe. In addition to the high level of intraspecific diversity observed in F. culmorum, the index of multilocus association calculated using ISSR data indicated that reproduction in F. culmorum cannot be exclusively clonal and recombination is likely to occur. 相似文献