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Mariyam Shahina Asif Hameed Shih-Yao Lin Wei-An Lai Yi-Han Hsu Chiu-Chung Young 《Antonie van Leeuwenhoek》2014,106(5):1031-1040
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We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to penalize extreme estimates of the fitnesses, thus correcting overfitting by the previous method. Using a combination of computer simulation and real data analysis, we evaluate the effect of the various penalties on the estimation of the fitnesses and the distribution of S. We show the new method regularizes the estimates of the fitnesses for small, relatively uninformative data sets, but it can still recover the large proportion of deleterious mutations when present in simulated data. Computer simulations indicate that as the number of taxa in the phylogeny or the level of sequence divergence increases, the distribution of S can be more accurately estimated. Furthermore, the strength of the penalty can be varied to study how informative a particular data set is about the distribution of S. We analyze three protein-coding genes (the chloroplast rubisco protein, mammal mitochondrial proteins, and an influenza virus polymerase) and show the new method recovers a large proportion of deleterious mutations in these data, even under strong penalties, confirming the distribution of S is bimodal in these real data. We recommend the use of the new MPL approach for the estimation of the distribution of S in species phylogenies of protein-coding genes. 相似文献
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Mehar H. Asif Shrikant S. Mantri Ayush Sharma Anukool Srivastava Ila Trivedi Priya Gupta Chandra S. Mohanty Samir V. Sawant Rakesh Tuli 《Tree Genetics & Genomes》2010,6(6):941-952
Jatropha curcas is an important non-edible oil seed tree species and is considered a promising source of biodiesel. The complete nucleotide
sequence of J. curcas chloroplast genome (cpDNA) was determined by pyrosequencing and gaps filled by Sanger sequencing. The cpDNA is a circular
molecule of 163,856 bp in length and codes for 110 distinct genes (78 protein coding, four rRNA and 28 distinct tRNA). Genome
organisation and arrangement are similar to the reported angiosperm chloroplast genome. However, in Jatropha, the infA and the rps16 genes are non-functional. The inverted repeat (IR) boundary is within the rpl2 gene, and the 13 nucleotides at the ends of the two duplicate genes are different. Repeat analysis suggests the presence
of 72 repeat regions (>30 bp) apart from the IR; of these, 48 were direct and 24 were palindromic repeats. Phylogenetic analysis
of 81 protein coding chloroplast genes from 65 taxa by maximum parsimony, maximum likelihood and minimum evolution analyses
at 100 bootstraps provide strong support for the placement of inaperturate crotonoids of which Jatropha is a member as sister to articulated crotonoids of which Manihot is a member. 相似文献
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The superior performance of F1 hybrids has a significant impact on agricultural productivity. For commercial application, the availability of an efficient
system for obtaining male-sterile lines of crops is an essential prerequisite. Here we have investigated the use of RNA interference
(RNAi) technology to silence a male-specific gene in the model host tobacco. TA29 is expressed exclusively in anthers at the time of microspore development. About 10 out of 13 tobacco lines transformed with
a hairpin RNAi construct containing TA29 sequences were male sterile. Transgenic plants were phenotypically indistinguishable from non-transgenic plants. At the anthesis
stage, pollen grains from transgenic, male-sterile plants were aborted and lysed in comparison to the round and fully developed
pollen in non-transgenic plants. Microscopic analysis of anthers showed selective degradation of tapetum in transgenic plants
with no microspore development. One week after self-pollination, the ovules of non-transgenic plants were double the size
of those in transgenic plants, due to successful self-fertilization. Male sterile transgenic plants set seed normally, when
cross-pollinated with pollen from non-transgenic plants, confirming no adverse effect on the female parts of the flower. These
results show that silencing of male-specific genes by RNAi is potentially a useful tool for generating male-sterile lines
for producing hybrid seed. 相似文献
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Most, if not all, of the neocortex is multisensory, but the mechanisms by which different cortical areas - association versus sensory, for instance - integrate multisensory inputs are not known. The study by Lakatos et al. reveals that, in the primary auditory cortex, the phase of neural oscillations is reset by somatosensory inputs, and subsequent auditory inputs are enhanced or suppressed, depending on their timing relative to the oscillatory cycle. 相似文献
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Vibha Pandey Yogeshwar Vikram Dhar Parul Gupta Sumit K Bag Neelam Atri Mehar Hasan Asif Prabodh Kumar Trivedi Pratibha Misra 《BMC bioinformatics》2015,16(1)