The coronavirus disease 2019(COVID-19)coronavirus is a new strain of coronavirus that had not been previously detected in humans.As its severe pathogenicity is concerned,it is important to study it thoroughly to aid i...The coronavirus disease 2019(COVID-19)coronavirus is a new strain of coronavirus that had not been previously detected in humans.As its severe pathogenicity is concerned,it is important to study it thoroughly to aid in the discovery of a cure.In this study,the microRNAs(miRNAs)of COVID-19 were annotated to provide a powerful tool for the study of this novel coronavirus.We obtained 16 novel coronavirus genome sequences and the mature sequences of all viruses in the microRNA database(miRbase),and then used the miRNA matures sequences of the virus to perform the Basic Local Alignment Search Tool(BLAST)analysis in the coronavirus genome,extending the matched regions of approximately 20 bp to two segments by 200 bp.Six sequences were obtained after deleting redundant sequences.Then,the hairpin structures of the mature miRNAs were determined using RNAfold.The mature sequence on one hairpin arm was selected into a total of 4 sequences,and finally the relevant miRNA precursor prediction tools were used to verify whether the selected sequences are miRNA precursor sequences of the novel coronavirus.The miRNAs of the novel coronavirus were annotated by our newly developed method,which will lay the foundation for further study of this virus.展开更多
Non-Camellia tea is a part of the colorful Chinese tea culture,and is also widely used as beverage and medicine in folk for disease prevention and treatment.In this study,37 samples were collected,including 33 kinds o...Non-Camellia tea is a part of the colorful Chinese tea culture,and is also widely used as beverage and medicine in folk for disease prevention and treatment.In this study,37 samples were collected,including 33 kinds of non-Camellia teas and 4 kinds of teas(Camellia).Traditional functions of non-Camellia teas were investigated.Furthermore,non-Camellia teas of original plants were characterized and identified by molecular methods.Four candidate regions(rbcL,matK,ITS2,psbA-trnH)were amplified by polymerase chain reaction.In addition,DNA barcodes were used for the first time to discriminate the commercial non-Camellia tea and their adulterants,and to evaluate their safety.This study showed that BLASTN and the relevant phylogenetic tree are efficient tools for identification of the commercial non-Camellia tea and their adulterants.However,some sequences from original plants have not been found and there is a limitation of sequence number of original plants in GenBank.Submitting more original plant sequences to the GenBank will be helpful for evaluating the safety of non-Camellia teas.展开更多
Microbial activities impact arsenic(As) transformation in mine tailings substantially, yet little is understood on the functional diversity of As metabolism genes. This study explored this issue using a metagenomic ap...Microbial activities impact arsenic(As) transformation in mine tailings substantially, yet little is understood on the functional diversity of As metabolism genes. This study explored this issue using a metagenomic approach coupled by a local BLASTN procedure established in our recent studies. An assembled metagenome, recovered from hypersaline and sulfidic mine tailings, was screened for As metabolism genes aio A, arr A, ars C and ars M. This was done using a local BLASTN procedure against databases of the As metabolism genes built in this study. Putative As metabolism genes detected in the assembled metagenome included 11 ars M, 20 ars C and 1 arr A full-length sequences. Together with the rRNA-based phylogenetic profiling results, a picture depicting microbial As cycling in the tailings to the genus level was obtained. It was found that most of the dominant genera in the tailings potentially harboured the genes for As reduction and/or methylation. In particular, a typical pyrite-eater present in the tailings, Thioalkalivibrio sp., was found to harbour not only ars C and ars M, but also arr A. These results highlight the unexpected diversity of As metabolism genes in the tailings, especially considering the extremely low species diversity therein. The microbial As cycling picture established here has potential use for guiding the purposeful manipulation of As biogeochemistry in the tailings.展开更多
基金the National Natural Science Foundation of China under Grants No.31572618 and No.31972791.
文摘The coronavirus disease 2019(COVID-19)coronavirus is a new strain of coronavirus that had not been previously detected in humans.As its severe pathogenicity is concerned,it is important to study it thoroughly to aid in the discovery of a cure.In this study,the microRNAs(miRNAs)of COVID-19 were annotated to provide a powerful tool for the study of this novel coronavirus.We obtained 16 novel coronavirus genome sequences and the mature sequences of all viruses in the microRNA database(miRbase),and then used the miRNA matures sequences of the virus to perform the Basic Local Alignment Search Tool(BLAST)analysis in the coronavirus genome,extending the matched regions of approximately 20 bp to two segments by 200 bp.Six sequences were obtained after deleting redundant sequences.Then,the hairpin structures of the mature miRNAs were determined using RNAfold.The mature sequence on one hairpin arm was selected into a total of 4 sequences,and finally the relevant miRNA precursor prediction tools were used to verify whether the selected sequences are miRNA precursor sequences of the novel coronavirus.The miRNAs of the novel coronavirus were annotated by our newly developed method,which will lay the foundation for further study of this virus.
基金This research was financially supported by the“Twelfth Five-year Plan”Program supported by the Ministry of Science and Technology(2012BAI28B02).
文摘Non-Camellia tea is a part of the colorful Chinese tea culture,and is also widely used as beverage and medicine in folk for disease prevention and treatment.In this study,37 samples were collected,including 33 kinds of non-Camellia teas and 4 kinds of teas(Camellia).Traditional functions of non-Camellia teas were investigated.Furthermore,non-Camellia teas of original plants were characterized and identified by molecular methods.Four candidate regions(rbcL,matK,ITS2,psbA-trnH)were amplified by polymerase chain reaction.In addition,DNA barcodes were used for the first time to discriminate the commercial non-Camellia tea and their adulterants,and to evaluate their safety.This study showed that BLASTN and the relevant phylogenetic tree are efficient tools for identification of the commercial non-Camellia tea and their adulterants.However,some sequences from original plants have not been found and there is a limitation of sequence number of original plants in GenBank.Submitting more original plant sequences to the GenBank will be helpful for evaluating the safety of non-Camellia teas.
基金financially supported by The University of Queensland Postdoctoral Fund and Mount Isa Mines, Glencore Ltd. (formerly Xstrata Copper Ltd.), Australia
文摘Microbial activities impact arsenic(As) transformation in mine tailings substantially, yet little is understood on the functional diversity of As metabolism genes. This study explored this issue using a metagenomic approach coupled by a local BLASTN procedure established in our recent studies. An assembled metagenome, recovered from hypersaline and sulfidic mine tailings, was screened for As metabolism genes aio A, arr A, ars C and ars M. This was done using a local BLASTN procedure against databases of the As metabolism genes built in this study. Putative As metabolism genes detected in the assembled metagenome included 11 ars M, 20 ars C and 1 arr A full-length sequences. Together with the rRNA-based phylogenetic profiling results, a picture depicting microbial As cycling in the tailings to the genus level was obtained. It was found that most of the dominant genera in the tailings potentially harboured the genes for As reduction and/or methylation. In particular, a typical pyrite-eater present in the tailings, Thioalkalivibrio sp., was found to harbour not only ars C and ars M, but also arr A. These results highlight the unexpected diversity of As metabolism genes in the tailings, especially considering the extremely low species diversity therein. The microbial As cycling picture established here has potential use for guiding the purposeful manipulation of As biogeochemistry in the tailings.
