The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(t...The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(the relative)transcription-activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of operons.One complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies.A quantitative model has been developed that captures this information,which tends to be minimized by the current global arrangement of operons in a bacterial(and archaeal)genome compared to possible alternative arrangements.A study is carried out here using this model on a collection of 52 closely related Escherichia coli genomes,which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the(relative)genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change,to maintain the above energy-efficiency property.More specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes(and operons)encoding specific pathways across different genomes.展开更多
The quasinormal mode frequencies can be understood from the massless particles trapped at the unstable circular null geodesics and slowly leaking out to infinity. Based on this viewpoint, in this paper, we semiclassic...The quasinormal mode frequencies can be understood from the massless particles trapped at the unstable circular null geodesics and slowly leaking out to infinity. Based on this viewpoint, in this paper, we semiclassically construct the entropy spectrum of the static and stationary black holes from the null geodesics. The result shows that the spacing of the entropy spectrum only depends on the property of the black hole in the eikonal limit. Moreover, for a black hole far from the extremal case, the spacing is found to be smaller than 2π for any dimension, which is very different from the result of the previous work by using the usual quasinormal mode frequencies.展开更多
基金supported in part by National Science Foundation (#NSF DEB-0830024 and NSF MCB-0958172)the US Department of Energy’s BioEnergy Science Center grant through the Office of Biological and Environmental Research+1 种基金The BioEnergy Science Center is a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of ScienceFunding for open access charge: US Department of Energy’s BioEnergy Science Center
文摘The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(the relative)transcription-activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of operons.One complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies.A quantitative model has been developed that captures this information,which tends to be minimized by the current global arrangement of operons in a bacterial(and archaeal)genome compared to possible alternative arrangements.A study is carried out here using this model on a collection of 52 closely related Escherichia coli genomes,which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the(relative)genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change,to maintain the above energy-efficiency property.More specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes(and operons)encoding specific pathways across different genomes.
基金supported by the National Natural Science Foundation of China(Grant Nos.1120507411375075 and 11522541)the Fundamental Research Funds for the Central Universities(Grant No.lzujbky-2015-jl01)
文摘The quasinormal mode frequencies can be understood from the massless particles trapped at the unstable circular null geodesics and slowly leaking out to infinity. Based on this viewpoint, in this paper, we semiclassically construct the entropy spectrum of the static and stationary black holes from the null geodesics. The result shows that the spacing of the entropy spectrum only depends on the property of the black hole in the eikonal limit. Moreover, for a black hole far from the extremal case, the spacing is found to be smaller than 2π for any dimension, which is very different from the result of the previous work by using the usual quasinormal mode frequencies.
