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21.
The results of the plasmid screening of Yersinia pestis strains isolated from four autonomous focuses on the northern border of the Central Asian zone of plague natural focality are presented. The plasmid profile of Yersinia pestis strains from the focuses is characterized as stable and independent of the source and time of strain isolation. The peculiar characteristic of the strains isolated in Tuva is the presence of an "additional" 15-16 Md plasmid in those strains. 相似文献
22.
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
23.
V D Brikman S V Balakhonov L P Mironova G P Aparin 《Zhurnal mikrobiologii, epidemiologii, i immunobiologii》1989,(7):3-7
112 newly isolated clinical cultures of Y. pseudotuberculosis have been studied. The strains have been characterized by the presence of plasmids and pathogenicity signs associated with plasmids. The results of the study have confirmed the decisive role of the plasmid with a molecular weight of 44-48 MD in the virulence of Y. pseudotuberculosis. The plasmid with a molecular weight of 82 MD, previously attributed the role of an epidemic marker, has also been found to be widely spread. Our study has revealed no specific features in the plasmid composition of the strains isolated under the conditions of sporadic and epidemic pseudotuberculosis morbidity. The results of the study of the pathogenicity of isogenic derivatives differing by the presence of pXV indicate that the role of plasmids with molecular weights of 3.8 and 82 MD in this process is not essential in the model systems, traditional for enteroinvasive Yersinia. 相似文献
24.
M. V. Afanas’ev S. V. Balakhonov E. G. Tokmakova V. S. Polovinkina E. A. Sidorova V. V. Sinkov 《Russian Journal of Genetics》2016,52(9):899-906
This paper studies a full nucleotide sequence of cryptic plasmid pTP33, which was isolated from the typical plague strain of the Tuvinian natural focus, Yersinia pestis I-2638. Sequencing was carried out using the 454 GS Junior platform (Roche). In analysis using the software package GS De Novo Assembler v. 2.7 (Roche) and the algorithm Newbler v. 2.7, 1855 nucleotide reads, which contained 1101246 nucleotides, were assembled to a contig of 33 978 bp. The GC content of the obtained nucleotide sequence was 50.25%. During annotation, we found 56 open reading frames. Homologs of the predicted reading frames were sought in the BLAST databases. We detected 22 reading frames coding hypothetical proteins, 23 frames coding phagerelated proteins, and 11 frames coding proteins with known functions, including toxin–antitoxin system YefM-YoeB, nucleic acids and polysaccharides metabolism proteins (exopolysaccharide production protein ExoZ, exodeoxyribonuclease VIII), and replication proteins (ParA). Some predicted pTP33 proteins were found to be homologs (from 45 to 75%) with sequences of phage-related proteins of certain microorganisms—endosymbionts of insects (Sodalis glossinidius) and endosymbionts of entomopathogenic nematodes (Photorhabdus luminescens, P. asymbiotica, Xenorhabdus bovienii). 相似文献
25.
S V Balakhonov S Tséndzhav A Erdénébat 《Molekuliarnaia genetika, mikrobiologiia i virusologiia》1991,(11):27-29
The plasmid spectres of 122 strains of Yersinia pestis isolated in Mongolia from patients, wild mammals and arthropods were studied. The populations of three plasmidovars of Yersinia pestis were found to be circulating in the natural foci of plague in Mongolia. The first plasmidovar harbours three plasmids with mol masses 6, 47, 65 Md. The second and third plasmidovars contain the plasmids with mol masses 6, 16, 47, 65 Md and 8, 47, 75-80 Md. 相似文献
26.
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
27.
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
28.
Rebekka?K?SchneiderEmail author Susanne?Ziegler Isabelle?Leisten Monica?SV?Ferreira Anne?Schumacher Bj?rn?Rath Dirk?Fahrenkamp Gerhard?Müller-Newen Martina?Crysandt Stefan?Wilop Edgar?Jost Steffen?Koschmieder Ruth?Knüchel Tim?H?Brümmendorf Patrick?Ziegler 《Journal of hematology & oncology》2014,7(1):92
We characterized bone marrow stromal cells (BMSC) from patients with pre-fibrotic myeloproliferative neoplasms (MPN). MPN-BMSC showed decreased capacity to stimulate the proliferation of colony-forming units of normal hematopoietic stem and progenitor cells and displayed increased matrix remodelling (in particular fibronectin deposition) compared to control BMSC. This finding was confirmed in pre-fibrotic MPN bone marrow biopsies in a tissue microarray (n?=?34), which stained positive for fibronectin in the absence of reticulin as a standard myelofibrosis marker. Fibronectin expression correlated significantly with reduced haemoglobin levels in MPN-patients (p?=?0.007; R2?=?0.42). Our data show significant cell-intrinsic alterations in MPN-MSC and suggest that Fibronectin expression might be applicable as a biomarker for the identification of early myelofibrotic transformation in reticulin-negative MPN. 相似文献
29.
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
30.
Mitchell SV Elkind Kristen Coates Wanling Tai Myunghee C Paik Bernadette Boden-Albala Ralph L Sacco 《BMC neurology》2006,6(1):37-6