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21.
Kshitiz?GuptaEmail author Dina?Thomas SV?Vidya KV?VenkateshEmail author S?Ramakumar 《BMC bioinformatics》2005,6(1):105
Background
The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. 相似文献22.
Barysheva EV Selivanov SP Riannel' IuE Velichko SA Usynin EA Usov VIu 《Vestnik rentgenologii i radiologii》1999,(5):32-36
Aiming to evaluate efficiency of 89SrCl (Metastron) in patients with metastatic lesion of the skeleton in prostate cancer we have performed a follow-up scintigraphy of the skeleton with 99mTc-methylendiphosphonate (MDP) and MRI with quantitative study of metastatic foci. 12 patients with prostate cancer (on the average 11 +/- 6 bone metastases were examined using scintigraphy of the skeleton with 99mTc-MDP and MRI study in T1, T2 and proton density modes. Investigations were performed before injected as a single dose of 150 MBq (4 mCi). At all the stages there was made a quantitative study of foci of pathological uptake of 99mTc-MDP compromising numbers of foci, focus parameters, intensity of 99mTc-MDP accumulation in the pathological part relatively the contralateral region as well as quantification of MRI signals from metastatic areas in signal intensity units. In 3 month 4 patients with extensive metastatic skeletal lesion (> 12) showed a considerable decrease of number of foci of pathological 99mTc-MDP uptake (on average to 6 +/- 3). In the remained metastatic foci there was noted a decrease of dimensions and 99mTc-MDP uptake intensity at an average by 29.8 +/- 15%, improvement in T1 intensity by 113 +/- 55.6 units. In 2 patients who initially presented a "superscan" pattern on 99mTc-MDP bone scintigraphy the 89SrCl treatment converted this of low intensity had demonstrated their complete regression. Results of radiologic follow-up of bone metastases in prostate cancer using MRI and bone scintigraphy with 99mTc-MDP argue that systemic radiotherapy with 89SrCl induces significant regress of metastatic process that involves all volume of the metastases. 相似文献
23.
Estimating synonymous and nonsynonymous substitution rates 总被引:8,自引:4,他引:4
Partitioning the total substitution rate into synnonymous and nonsynonymous
components is a key aspect of many analyses in molecular evolution.
Numerous methods exist for estimating these rates. However, until recently
none of the estimation procedures were based on a sound statistical
footing. In this paper, the evolutionary model of Muse and Gaut (1994) is
used as the basis for two sets of parameters quantifying silent and
replacement substitution rates. The parameters are shown to be equal when
the four nucleotides are equally frequent and unequal otherwise.
Maximum-likelihood estimation of these parameters is described, and the
performance of these estimates is compared to that of existing estimation
procedures. It is shown that the estimates of Nei and Gojobori (1986) are
not unbiased for either set of parameters, although they provide very good
estimates for one set as long as sequence divergence is not too high.
However, some disturbing properties are found for the Nei and Gojobori
estimates. In particular, it is shown that the expected value of the Nei
and Gojobori estimate of silent substitution rate is a function of both the
silent and replacement substitution rates. The maximum-likelihood estimates
have no such problems.
相似文献
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A nearly universal feature of intron sequences is that even closely related
species exhibit a large number of insertion/deletion differences. The goal
of the analysis described here is to test whether the observed pattern of
insertion/deletion events in the genealogy of the myosin alkali light chain
(Mlc1) gene is consistent with neutrality, and if not, to determine the
underlying forces of evolutionary change. Mlc1 pre-mRNA is alternatively
spliced, and one constraint is that signals necessary for
tissue-specificity of directed splicing must be conserved. If the total
length of an intron is functionally constrained, then the distribution of
indels on branches of the gene genealogy should reflect a departure from
randomness. Here we perform a phylogenetic analysis, inferring ancestral
states wherever possible on a phylogeny of 29 alleles of Mlc1 from six
species of Drosophila. Observed patterns of indels on the genealogy were
compared to those from simulated data, with the result that we cannot
reject the null hypothesis of neutrality. A clear departure from a neutral
prediction was seen in the excess folding free energy predicted for the
introns flanking the alternatively spliced exon. Relative rate tests also
suggest a retardation in the rate of Mlc1 sequence evolution in the
simulans clade.
相似文献
27.
Kozin S. V. Kravtsov A. A. Elkina A. A. Zlishcheva E. I. Barysheva E. V. Shurygina L. V. Moiseev A. V. Baryshev M. G. 《Biophysics》2019,64(2):272-278
Biophysics - The effect of deuterium-depleted water on oxidative processes in the rat brain under physiological or hypoxic conditions was studied. The results obtained by a tissue culture method... 相似文献
28.
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome 总被引:29,自引:24,他引:5
A model of DNA sequence evolution applicable to coding regions is
presented. This represents the first evolutionary model that accounts for
dependencies among nucleotides within a codon. The model uses the codon, as
opposed to the nucleotide, as the unit of evolution, and is parameterized
in terms of synonymous and nonsynonymous nucleotide substitution rates. One
of the model's advantages over those used in methods for estimating
synonymous and nonsynonymous substitution rates is that it completely
corrects for multiple hits at a codon, rather than taking a parsimony
approach and considering only pathways of minimum change between homologous
codons. Likelihood-ratio versions of the relative-rate test are constructed
and applied to data from the complete chloroplast DNA sequences of Oryza
sativa, Nicotiana tabacum, and Marchantia polymorpha. Results of these
tests confirm previous findings that substitution rates in the chloroplast
genome are subject to both lineage-specific and locus-specific effects.
Additionally, the new tests suggest tha the rate heterogeneity is due
primarily to differences in nonsynonymous substitution rates. Simulations
help confirm previous suggestions that silent sites are saturated, leaving
no evidence of heterogeneity in synonymous substitution rates.
相似文献
29.
ALEKSANDRA I. JOHANSEN ALICE EXNEROVÁ KATEŘINA HOTOVÁ SVÁDOVÁ PAVEL ŠTYS GABRIELLA GAMBERALE‐STILLE BIRGITTA S. TULLBERG 《Ecological Entomology》2010,35(5):602-610
1. Protective coloration in insects may be aposematic or cryptic, and some species change defensive strategy between instars. In Sweden, the adult striated shieldbugs Graphosoma lineatum (Heteroptera: Pentatomidae) undergo a seasonal colour change from pale brown and black striation in the pre‐hibernating adults, to red and black striation in the same post‐hibernating individuals. To the human eye the pre‐hibernating adults appear cryptic against the withered late summer vegetation, whereas the red and black post‐hibernating adults appear aposematic. This suggests a possibility of a functional colour change. However, what is cryptic to the human eye is not necessarily cryptic to a potential predator. 2. Therefore we tested the effect of coloration in adult G. lineatum on their detectability for avian predators. Great tits (Parus major) were trained to eat sunflower seeds hidden inside the emptied exoskeletons of pale or red G. lineatum. Then the detection time for both colour forms was measured in a dry vegetation environment. 3. The birds required a longer time to find the pale form of G. lineatum than the red one. The pale form appears more cryptic on withered late summer vegetation than the red form, not only to the human eye but also to avian predators. The result supports the idea that the adult individuals of G. lineatum undergo a functional change from a cryptic protective coloration to an aposematic one. 相似文献
30.
Gal'chenko V. F. Dulov L. E. Cramer B. Konova N. I. Barysheva S. V. 《Microbiology》2001,70(2):175-185
The biogeochemical processes of methane production and oxidation were studied in the upper horizons of tundra and taiga soils and raised bogs and lake bottom sediments near the Tarko-Sale gas field in western Siberia. Both in dry and water-logged soils, the total methane concentration (in soil particles and gaseous phase) was an order of magnitude higher than in the soil gaseous phase alone (22 and 1.1 nl/cm3, respectively). In bogs and lake bottom sediments methane concentration was as high as 11 l/cm3. Acetate was the major precursor of the newly formed methane. The rate of aceticlastic methanogenesis reached 55 ng C/(cm3day), whereas that of autotrophic methanogenesis was an order of magnitude lower. The most active methane production and oxidation were observed in bogs and lake sediments, where the 13C values of CO2were inversely related to the intensity of bacterial methane oxidation. Methane diffusing from bogs and lake bottom sediments showed 13C values ranging from –78 to –47, whereas the 13C value of carbon dioxide ranged from –18 to –1. In these ecosystems, methane emission comprised from 3 to 206 mg CH4/(m2day). Conversely, the dry and water-logged soils of the tundra and taiga took up atmospheric methane at a rate varying from 0.3 to 5.3 mg CH4/(m2day). Methane consumption in soils was of biological nature. This was confirmed by the radioisotopic method and chamber experiments, in which weighting of methane carbon was observed (the 13C value changed from –51 to –41). 相似文献