Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcrib...Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.展开更多
CRISPR-Cas （Clustered, Regularly Interspaced, Short Palindromic Repeats - CRISPR-associated （Cas）） RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has bec...CRISPR-Cas （Clustered, Regularly Interspaced, Short Palindromic Repeats - CRISPR-associated （Cas）） RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has become the most exciting and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9 system has been demonstrated in many species, and several laboratories have established CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to sbRNA screening. At least three companies have been founded to leverage this technology for therapeutic uses. To facilitate the implementation of this technology, many software tools have been developed to identify guide RNAs that effectively target a desired genomic region. Here, I provide an overview of the technology, focusing on guide RNA design principles, available software tools and their strengths and weaknesses.展开更多
[Objective] To examine the grammar model based on lexical substring exac- tion for RNA secondary structure prediction. [Method] By introducing cloud model into stochastic grammar model, a machine learning algorithm su...[Objective] To examine the grammar model based on lexical substring exac- tion for RNA secondary structure prediction. [Method] By introducing cloud model into stochastic grammar model, a machine learning algorithm suitable for the lexicalized stochastic grammar model was proposed. The word grid mode was used to extract and divide RNA sequence to acquire lexical substring, and the cloud classifier was used to search the maximum probability of each lemma which was marked as a certain sec- ondary structure type. Then, the lemma information was introduced into the training stochastic grammar process as prior information, realizing the prediction on the sec- ondary structure of RNA, and the method was tested by experiment. [Result] The experimental results showed that the prediction accuracy and searching speed of stochastic grammar cloud model were significantly improved from the prediction with simple stochastic grammar. [Conclusion] This study laid the foundation for the wide application of stochastic grammar model for RNA secondary structure prediction.展开更多
Researchers reporting in the Nature journal Scientific Reports haveused next generation sequencing and quantitative reverse transcriptase PCR （RT-PCR） technology to profile plasma microRNA （miRNA） expression in co...Researchers reporting in the Nature journal Scientific Reports haveused next generation sequencing and quantitative reverse transcriptase PCR （RT-PCR） technology to profile plasma microRNA （miRNA） expression in cohorts of men with and without late-onset hypogonadism （LOH）. The study proposes a panel of three miRNAs as novel biomarkers to aid in the diagnosis of LOH.展开更多
Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate b...Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops(not individuals) are the basic players. We thus redefine quasispecies as RNA quasispecies consortia(qs-c) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competencenot error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity(immunity) functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. Fromsuch qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs.展开更多
An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFGs can include sta...An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFGs can include statistical biases that often occur in RNA sequences, necessary to profile specific RNA structures for structural homology search. In this paper, a succinct stochastic grammar model is introduced for RNA that has competitive search effectiveness. More importantly, the profiling model can be easily extended to include pseudoknots, structures that are beyond the capability of profile SCFGs. In addition, the model allows heuristics to be exploited, resulting in a significant speed-up for the CYK algorithm-based search.展开更多
基金The work was supported by the National Natural Science Foundation of China (Grant No. 39730070).
文摘Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.
文摘CRISPR-Cas （Clustered, Regularly Interspaced, Short Palindromic Repeats - CRISPR-associated （Cas）） RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has become the most exciting and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9 system has been demonstrated in many species, and several laboratories have established CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to sbRNA screening. At least three companies have been founded to leverage this technology for therapeutic uses. To facilitate the implementation of this technology, many software tools have been developed to identify guide RNAs that effectively target a desired genomic region. Here, I provide an overview of the technology, focusing on guide RNA design principles, available software tools and their strengths and weaknesses.
基金Supported by the Science Foundation of Hengyang Normal University of China(09A36)~~
文摘[Objective] To examine the grammar model based on lexical substring exac- tion for RNA secondary structure prediction. [Method] By introducing cloud model into stochastic grammar model, a machine learning algorithm suitable for the lexicalized stochastic grammar model was proposed. The word grid mode was used to extract and divide RNA sequence to acquire lexical substring, and the cloud classifier was used to search the maximum probability of each lemma which was marked as a certain sec- ondary structure type. Then, the lemma information was introduced into the training stochastic grammar process as prior information, realizing the prediction on the sec- ondary structure of RNA, and the method was tested by experiment. [Result] The experimental results showed that the prediction accuracy and searching speed of stochastic grammar cloud model were significantly improved from the prediction with simple stochastic grammar. [Conclusion] This study laid the foundation for the wide application of stochastic grammar model for RNA secondary structure prediction.
文摘Researchers reporting in the Nature journal Scientific Reports haveused next generation sequencing and quantitative reverse transcriptase PCR （RT-PCR） technology to profile plasma microRNA （miRNA） expression in cohorts of men with and without late-onset hypogonadism （LOH）. The study proposes a panel of three miRNAs as novel biomarkers to aid in the diagnosis of LOH.
文摘Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops(not individuals) are the basic players. We thus redefine quasispecies as RNA quasispecies consortia(qs-c) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competencenot error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity(immunity) functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. Fromsuch qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs.
文摘An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFGs can include statistical biases that often occur in RNA sequences, necessary to profile specific RNA structures for structural homology search. In this paper, a succinct stochastic grammar model is introduced for RNA that has competitive search effectiveness. More importantly, the profiling model can be easily extended to include pseudoknots, structures that are beyond the capability of profile SCFGs. In addition, the model allows heuristics to be exploited, resulting in a significant speed-up for the CYK algorithm-based search.
