基本局部比对搜索工具(basic local alignment search tool,BLAST)是核酸或蛋白质序列相似性分析最常用的工具之一。因为程序涉及参数较多,一些学生和研究者有时不根据实际情况也不阅读说明书就直接选择默认参数,可能会得出错误结论。BL...基本局部比对搜索工具(basic local alignment search tool,BLAST)是核酸或蛋白质序列相似性分析最常用的工具之一。因为程序涉及参数较多,一些学生和研究者有时不根据实际情况也不阅读说明书就直接选择默认参数,可能会得出错误结论。BLAST可以进行核酸、蛋白质序列及其相互间的比对,一些低年级学生会有困惑,不知如何进行程序的选择等问题。鉴于这些情况,笔者尝试用2020年初网络的热议话题"新冠病毒极有可能源于实验室"作为引子吸引学生注意力,通过复现并从理论上初步分析其错误,以及产生错误的原因来达到让本科生快速熟悉BLAST的使用及易错点,达到BLAST理论教学的目的。在实验课中,虚构恐龙基因,即一个小组在基因中插入"密码",由另一小组解开"密码",通过小组间利用BLAST工具进行加密与解密的趣味活动,从而加深对程序正确选择的理解,同时巩固了理论教学内容。此教学设计利用当下新冠病毒起源的热点话题不仅提高了学生的学习兴趣,同时也帮助他们利用该工具解决实际问题,培养了学生利用专业知识进行言论分辨的能力。希望此文能对BLAST工具的正确使用和新医科背景下生物医学教学有所启发和帮助。展开更多
目的设计单纯疱疹病毒2型(HSV-2)诊断芯片的O ligo探针。方法利用BLA ST软件对HSV-2的DNA序列进行序列比对,得到有意义的特异序列;用生物学软件O ligo6.0设计特异性高、Tm值相近、长度均一的O ligo探针。结果获得13条60-m er O ligo探...目的设计单纯疱疹病毒2型(HSV-2)诊断芯片的O ligo探针。方法利用BLA ST软件对HSV-2的DNA序列进行序列比对,得到有意义的特异序列;用生物学软件O ligo6.0设计特异性高、Tm值相近、长度均一的O ligo探针。结果获得13条60-m er O ligo探针。结论利用BLA ST系统和生物学软件O ligo6.0设计HSV-2诊断芯片的探针,可为后期打印成DNA芯片,用于HSV-2的检测打下基础。展开更多
We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species.Ten reverse species-specific primers designed from the 16 S rRNA gene,in combination with one forward...We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species.Ten reverse species-specific primers designed from the 16 S rRNA gene,in combination with one forward universal primer,generated PCR fragments of ca.270 bp length for each species.The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species.Amplification was observed in specific species only.The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber,and was proven to be a useful,rapid,and low-cost technique to identify the origin of the sea cucumber product.展开更多
We examined salt tolerance responsive genes in Pak-choi under salt stress and analyze their potential function. The LRNA differential display was used to screen the transcript derived fragments （TDFs） related to sal...We examined salt tolerance responsive genes in Pak-choi under salt stress and analyze their potential function. The LRNA differential display was used to screen the transcript derived fragments （TDFs） related to salinity tolerance in tolerant and Loderately tolerant Pak-choi germplasm. Seventy-eight primer combinations generated 101 differential eDNA fragments, which ere divided into 10 expression types. Seven cDNA sequences （GenBank accession Nos. DQ006915-DQ006921） obtained and ,~quenced were highly homologous to some known expression genes or the genes related to the signaling pathways in plants under ifferent abiotic stress.展开更多
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
文摘基本局部比对搜索工具(basic local alignment search tool,BLAST)是核酸或蛋白质序列相似性分析最常用的工具之一。因为程序涉及参数较多,一些学生和研究者有时不根据实际情况也不阅读说明书就直接选择默认参数,可能会得出错误结论。BLAST可以进行核酸、蛋白质序列及其相互间的比对,一些低年级学生会有困惑,不知如何进行程序的选择等问题。鉴于这些情况,笔者尝试用2020年初网络的热议话题"新冠病毒极有可能源于实验室"作为引子吸引学生注意力,通过复现并从理论上初步分析其错误,以及产生错误的原因来达到让本科生快速熟悉BLAST的使用及易错点,达到BLAST理论教学的目的。在实验课中,虚构恐龙基因,即一个小组在基因中插入"密码",由另一小组解开"密码",通过小组间利用BLAST工具进行加密与解密的趣味活动,从而加深对程序正确选择的理解,同时巩固了理论教学内容。此教学设计利用当下新冠病毒起源的热点话题不仅提高了学生的学习兴趣,同时也帮助他们利用该工具解决实际问题,培养了学生利用专业知识进行言论分辨的能力。希望此文能对BLAST工具的正确使用和新医科背景下生物医学教学有所启发和帮助。
文摘目的设计单纯疱疹病毒2型(HSV-2)诊断芯片的O ligo探针。方法利用BLA ST软件对HSV-2的DNA序列进行序列比对,得到有意义的特异序列;用生物学软件O ligo6.0设计特异性高、Tm值相近、长度均一的O ligo探针。结果获得13条60-m er O ligo探针。结论利用BLA ST系统和生物学软件O ligo6.0设计HSV-2诊断芯片的探针,可为后期打印成DNA芯片,用于HSV-2的检测打下基础。
基金Supported by the National Natural Science Foundation of China(No.31201999)the Natural Science Foundation of Guangdong Province,China(No.S2011040000463)+4 种基金the Foundation for Distinguished Young Talents in Higher Education of Guangdong,China(No.LYM11086)the Key Laboratory Program of Tropical Marine Bio-Resources and Ecology,Chinese Academy of Science(No.LMB111004)the China Spark Program(Nos.2012GA780007,2012GA780020,2012GA780008)the National Students'Innovation and Entrepreneurship Training Project(No.201210579031)the Zhanjiang Foundation for Science and Technology,China(Nos.2011C3104009,2011D0244,2012C3102018)
文摘We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species.Ten reverse species-specific primers designed from the 16 S rRNA gene,in combination with one forward universal primer,generated PCR fragments of ca.270 bp length for each species.The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species.Amplification was observed in specific species only.The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber,and was proven to be a useful,rapid,and low-cost technique to identify the origin of the sea cucumber product.
基金Project supported by the National "the Tenth Five-Year-Plan" Key Program (No. 2004BA525B08)China and the Key Laboratory of Vegetable Genetics and Physiology, Ministry of Agriculture, China
文摘We examined salt tolerance responsive genes in Pak-choi under salt stress and analyze their potential function. The LRNA differential display was used to screen the transcript derived fragments （TDFs） related to salinity tolerance in tolerant and Loderately tolerant Pak-choi germplasm. Seventy-eight primer combinations generated 101 differential eDNA fragments, which ere divided into 10 expression types. Seven cDNA sequences （GenBank accession Nos. DQ006915-DQ006921） obtained and ,~quenced were highly homologous to some known expression genes or the genes related to the signaling pathways in plants under ifferent abiotic stress.
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.
