Solutions of most nonlinear differential equations have to be obtained numerically. The time series obtained by numerical integration will be a solution of the differential equation only if it is independent of the in...Solutions of most nonlinear differential equations have to be obtained numerically. The time series obtained by numerical integration will be a solution of the differential equation only if it is independent of the integration step h. A numerical solution is considered to have converged, when the difference between the time series for steps h and h/2 becomes smaller as h decreases. Unfortunately, this convergence criterium is unsuitable in the case of a chaotic solution, due to the extreme sensitivity to initial conditions that is characteristic of this kind of solution. We present here a criterium of convergence that involves the comparison of the attractors associated to the time series for integration time steps h and h/2. We show that the probability that the chaotic attractors associated to these time series are the same increases monotonically as the integration step h is decreased. The comparison of attractors is made using 1) the method of correlation integral, and 2) the method of statistical distance of probability distributions.展开更多
Background:A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position.However,it has been observed that ribosomes can misinterpret the stop codon and continue t...Background:A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position.However,it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3′UTR region.This phenomenon is called stop codon read-through(SCR).It has been suggested that these events would occur on a programmed basis,but the underlying mechanisms are still not well understood.Methods:Here,we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles.The associated ribosomal leak rate was estimated for every event identified.A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed.Results:The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon,suggesting the existence of at least two mechanisms that could alter the translational termination process.Furthermore,a linear regression models for each of the three stop codons was developed,and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon.Conclusions:We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.展开更多
文摘Solutions of most nonlinear differential equations have to be obtained numerically. The time series obtained by numerical integration will be a solution of the differential equation only if it is independent of the integration step h. A numerical solution is considered to have converged, when the difference between the time series for steps h and h/2 becomes smaller as h decreases. Unfortunately, this convergence criterium is unsuitable in the case of a chaotic solution, due to the extreme sensitivity to initial conditions that is characteristic of this kind of solution. We present here a criterium of convergence that involves the comparison of the attractors associated to the time series for integration time steps h and h/2. We show that the probability that the chaotic attractors associated to these time series are the same increases monotonically as the integration step h is decreased. The comparison of attractors is made using 1) the method of correlation integral, and 2) the method of statistical distance of probability distributions.
基金LIE is funded by CONICET Ph.D.Fellowship.AMA and LD are researchers of CONICET(Argentina).JRR is Full Professor at the UNLP(Argentina).This work was supported by CONICET,Argentina(PIP2017-00059).
文摘Background:A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position.However,it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3′UTR region.This phenomenon is called stop codon read-through(SCR).It has been suggested that these events would occur on a programmed basis,but the underlying mechanisms are still not well understood.Methods:Here,we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles.The associated ribosomal leak rate was estimated for every event identified.A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed.Results:The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon,suggesting the existence of at least two mechanisms that could alter the translational termination process.Furthermore,a linear regression models for each of the three stop codons was developed,and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon.Conclusions:We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.
