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31.
Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites 总被引:23,自引:9,他引:14
This paper presents a maximum likelihood approach to estimating the
variation of substitution rate among nucleotide sites. We assume that the
rate varies among sites according to an invariant+gamma distribution, which
has two parameters: the gamma parameter alpha and the proportion of
invariable sites theta. Theoretical treatments on three, four, and five
sequences have been conducted, and computer program have been developed. It
is shown that rho = (1 + theta alpha)/(1 + alpha) is a good measure for the
rate heterogeneity among sites. Extensive simulations show that (1) if the
proportion of invariable sites is negligible, i.e., theta = 0, the gamma
parameter alpha can be satisfactorily estimated, even with three sequences;
(2) if the proportion of invariable sites is not negligible, the
heterogeneity rho can still be suitably estimated with four or more
sequences; and (3) the distances estimated by the proposed method are
almost unbiased and are robust against violation of the assumption of the
invariant + gamma distribution.
相似文献
32.
H A Ludlam B Nwachukwu W C Noble A V Swan I Phillips 《The Journal of applied bacteriology》1989,67(4):417-423
The preservation of micro-organisms that may be found on the skin was studied by storage in liquid media at--70 degrees C. In the first part of the study the performance of 12 varieties of suspending media was evaluated with pure cultures of 17 species of micro-organisms maintained in the laboratory. After storage for 1 year the best medium (Oxoid Nutrient Broth with 15% glycerol) showed a mean survival for all organisms studied of 83.8%, with no significant differences between organisms. Even the worst medium (distilled water) permitted greater than 40% survival at 1 year. No changes in the characteristics of these micro-organisms were detected after 6 months storage in glycerol broth. In the second part of the study nose swabs were suspended in one representative medium (Bacto Nutrient Broth containing 7% glycerol). The mean percentage survival of staphylococci in these suspensions after 1 year's storage at - 70 degrees C was 75.4%. These results indicate that coagulase-negative coagulase-negative staphylococci in samples of skin flora may be stored under these conditions for long periods, greatly reducing the work-load in epidemiological studies of infection. 相似文献
33.
34.
The cDNA cloning and molecular evolution of reptile and pigeon lactate dehydrogenase isozymes 总被引:1,自引:0,他引:1
The cDNAs encoding lactate dehydrogenase isozymes LDH-A (muscle) and LDH-B
(heart) from alligator and turtle and LDH-A, LDH-B, and LDH-C (testis) from
pigeon were cloned and sequenced. The evolutionary relationships among
vertebrate LDH isozymes were analyzed. Contrary to the traditional belief
that the turtle lineage branched off before the divergence between the
lizard/alligator and bird lineages, the turtle lineage was found to be
clustered with either the alligator lineage or the alligator-bird clade,
while the lizard lineage was found to have branched off before the
divergence between the alligator/turtle and bird lineages. The pigeon
testicular LDH-C isozyme was evidently duplicated from LDH-B (heart), so it
is not orthologous to the mammalian testicular LDH-C isozymes.
相似文献
35.
Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies 总被引:10,自引:9,他引:1
The statistical properties of the paralinear and LogDet distances under
nonstationary nucleotide frequencies were studied. First, we developed
formulas for correcting the estimation biases of the paralinear and LogDet
distances, i.e., the bias-corrected distance is estimated by dc = d -
2var(d), where d and var(d) are the estimated distance and sampling
variance, respectively. The performances of these formulas and the formulas
for sampling variances were examined by computer simulation. Second, we
developed a method for estimating the variance- covariance matrix of
paralinear distances, so that statistical tests of DNA phylogenies can be
conducted in the nonstationary case. Third, a new LogDet-based method for
testing the molecular clock hypothesis was developed under nonstationary
nucleotide frequencies.
相似文献
36.
Caffeoyl-coenzyme A (CoA) O-methyltransferase (CCoAOMT) has been proposed to be involved in an alternative methylation pathway of lignin biosynthesis. However, no direct evidence has been available to confirm that CCoAOMT is essential for lignin biosynthesis. To understand further the methylation steps in lignin biosynthesis, we used an antisense approach to alter O-methyltransferase (OMT) gene expression and investigated the consequences of this alteration. We generated transgenic tobacco plants with a substantial reduction in CCoAOMT as well as plants with a simultaneous reduction in both CCoAOMT and caffeic acid O-methyltransferase (CAOMT). Lignin analysis showed that the reduction in CCoAOMT alone resulted in a dramatic decrease in lignin content. The reduction in CCoAOMT also led to a dramatic alteration in lignin composition. Both guaiacyl lignin and syringyl lignin were reduced in the transgenic plants. However, guaiacyl lignin was preferentially reduced, which resulted in an increase in the S/G (syringl/guaiacyl) ratio. We have also analyzed lignin content and composition in transgenic plants having a simultaneous reduction in both CCoAOMT and CAOMT. The reduction in both OMTs resulted in a further decrease in total lignin content. This is in sharp contrast to the effect that resulted from the reduction in CAOMT alone, which only decreased the syringl lignin unit without a reduction in overall lignin content. These results unequivocally demonstrate that methylation reactions in lignin biosynthesis are catalyzed by both CCoAOMT and CAOMT. 相似文献
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39.
Peter Sörös Faisal Al-Otaibi Savio WH Wong J Kevin Shoemaker Seyed M Mirsattari Vladimir Hachinski Ruth E Martin 《BMC neurology》2011,11(1):20
Background
Various functional resonance imaging, magnetoencephalographic and lesion studies suggest the involvement of the insular cortex in the control of swallowing. However, the exact location of insular activation during swallowing and its functional significance remain unclear. 相似文献40.
Anderson DJ Durieux JK Song K Alvarado R Jackson PK Hatzivassiliou G Ludlam MJ 《PloS one》2011,6(8):e22607
Oncogenic mutations in the mitogen activated protein kinase (MAPK) pathway are prevalent in human tumors, making this pathway a target of drug development efforts. Recently, ATP-competitive Raf inhibitors were shown to cause MAPK pathway activation via Raf kinase priming in wild-type BRaf cells and tumors, highlighting the need for a thorough understanding of signaling in the context of small molecule kinase inhibitors. Here, we present critical improvements in cell-line engineering and image analysis coupled with automated image acquisition that allow for the simultaneous identification of cellular localization of multiple MAPK pathway components (KRas, CRaf, Mek1 and Erk2). We use these assays in a systematic study of the effect of small molecule inhibitors across the MAPK cascade either as single agents or in combination. Both Raf inhibitor priming as well as the release from negative feedback induced by Mek and Erk inhibitors cause translocation of CRaf to the plasma membrane via mechanisms that are additive in pathway activation. Analysis of Erk activation and sub-cellular localization upon inhibitor treatments reveals differential inhibition and activation with the Raf inhibitors AZD628 and GDC0879 respectively. Since both single agent and combination studies of Raf and Mek inhibitors are currently in the clinic, our assays provide valuable insight into their effects on MAPK signaling in live cells. 相似文献