Interferon-induced protein with tetratricopeptide repeats 1(IFIT1), also known as interferon-induced protein 56(IFI56) or Interferon-stimulated protein 56(ISG56), was originally identified as a protein induced upon tr...Interferon-induced protein with tetratricopeptide repeats 1(IFIT1), also known as interferon-induced protein 56(IFI56) or Interferon-stimulated protein 56(ISG56), was originally identified as a protein induced upon treatment with interferon and inhibited by viral replication and translational initiation. In this study, Epinephelus lanceolatus IFIT1(ELIFIT1) gene was cloned for the first time. The complete cDNA of El IFIT1 gene includes 2921 nucleotides, and encodes a 437-amino acid(AA) protein. The putative ELIFIT1 protein has 9 TRP domains and is highly similar with IFIT1 proteins in other teleosts. In healthy fish, ELIFIT1 gene was highly expressed in the blood, which indicate its specific function in the peripheral immune system. Its expression was also observed in various immunity-related tissues including spleen, intestine, and kidney, Inducted with spotted knifejaw iridovirus(SKIV), ELIFIT1 gene expression was upregulated in the spleen, kidney, and liver 24 h after induction and reached its peak at 72 h, indicating that ELIFIT1 may play an important role in antivirus. These findings contribute to the understanding of the antiviral regulation of ELIFIT1 gene in teleost.展开更多
The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper, we introduce the motif tracking algorithm （MTA）, a novel immune inspired （IS）...The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper, we introduce the motif tracking algorithm （MTA）, a novel immune inspired （IS） pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases, the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilization of an intuitive symbolic representation. The resulting population of motifs is shown to have considerable potential value for other applications such as forecasting and algorithm seeding.展开更多
Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as...Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433,782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya.展开更多
The functionality of a gene or a protein depends on codon repeats occurring in it.As a consequence of their vitality in protein function and apparent involvement in causing diseases,an interest in these repeats has de...The functionality of a gene or a protein depends on codon repeats occurring in it.As a consequence of their vitality in protein function and apparent involvement in causing diseases,an interest in these repeats has developed in recent years.The analysis of genomic and proteomic sequences to identify such repeats requires some algorithmic support from informatics level.Here,we proposed an offline stand-alone toolkit Repeat Searcher and Motif Detector（RSMD）,which uncovers and employs few novel approaches in identification of sequence repeats and motifs to understand their functionality in sequence level and their disease causing tendency.The tool offers various features such as identifying motifs,repeats and identification of disease causing repeats.RSMD was designed to provide an easily understandable graphical user interface（GUI）,for the tool will be predominantly accessed by biologists and various researchers in all platforms of life science.GUI was developed using the scripting language Perl and its graphical module PerlTK.RSMD covers algorithmic foundations of computational biology by combining theory with practice.展开更多
【目的】利用P2C可以定向进入卵巢以及Gal4蛋白可与UAS序列稳定结合的特点,在中华按蚊Anopheles sinensis中建立高效的非胚胎期外源DNA投递技术系统。【方法】注射P2C-Gal4-DsRed重组蛋白至吸血后20 h时的中华按蚊雌成蚊腹部,通过冰冻...【目的】利用P2C可以定向进入卵巢以及Gal4蛋白可与UAS序列稳定结合的特点,在中华按蚊Anopheles sinensis中建立高效的非胚胎期外源DNA投递技术系统。【方法】注射P2C-Gal4-DsRed重组蛋白至吸血后20 h时的中华按蚊雌成蚊腹部,通过冰冻切片荧光观察和Western blot检测分析重组蛋白P2C-Gal4-DsRed在卵巢中的投递效率;制备P2C-Gal4 DNA BINDING重组蛋白,构建包含12×UAS重复基序的转基因质粒和辅助质粒,通过电泳迁移实验分析重组蛋白P2C-Gal4 DNA BINDING和12×UAS重复基序间的体外结合;分别将体外孵育的P2C-Gal4 DNA BINDING+辅助质粒ITF36-12×UAS和P2C-Gal4 DNA BINDING+转基因质粒ITF2-12×UAS afm复合物注射入吸血后20 h时的中华按蚊雌成蚊腹部,于血餐后40 h时提取其卵巢组织DNA,并通过特异性引物PCR扩增和测序分析外源DNA在活体中的投递情况。【结果】100%注射P2C-Gal4-DsRed的中华按蚊雌成蚊卵巢在绿色滤光片下呈现明显的红色荧光,表明P2C-Gal4-DsRed重组蛋白能够被高效地导入雌成蚊卵巢中;P2C-Gal4 DNA BINDING重组蛋白能够与12×UAS重复基序以及含有该重复基序片段的质粒稳定结合;分别有91%和93%的注射了P2C-Gal4 DNA BINDING+ITF36-12×UAS和P2C-Gal4 DNA BINDING+ITF2-12×UAS afm的雌成蚊卵巢组织中能够检测到外源DNA片段。【结论】在中华按蚊中成功建立了基于P2C卵巢导向肽和Gal4-12×UAS重复基序结合特性的外源DNA投递技术体系;通过此技术平台能够便捷、快速和高效地实现质粒等DNA分子在中华按蚊卵巢中的投递,这为进一步简化转基因、过表达及基因敲入等遗传操作奠定了基础。展开更多
粘虫 Mythimna separata（Walker）是一种迁飞性害虫，严重危害玉米、水稻、小麦等粮食作物。 SSR 是指以1～6个核苷酸为基本重复单位的串联重复 DNA 序列。 SSR 位点的信息分析为粘虫扩散、迁飞和交配等行为分子机制的研究以及粘虫的...粘虫 Mythimna separata（Walker）是一种迁飞性害虫，严重危害玉米、水稻、小麦等粮食作物。 SSR 是指以1～6个核苷酸为基本重复单位的串联重复 DNA 序列。 SSR 位点的信息分析为粘虫扩散、迁飞和交配等行为分子机制的研究以及粘虫的综合防治奠定理论基础。本研究基于高通量测序获得的粘虫转录组数据，利用软件 msatcom‐mander 发掘粘虫 SSR 位点。结果从20776条转录组 Unigenes 中共搜索出400个 SSR ，分布于372条 Unigenes 中。在粘虫转录组 SSR 中，三核苷酸重复的数量最为丰富，有271个；其次是二核苷酸和单核苷酸重复，分别是70个和49个；四至六核苷酸重复的数量都很少，共10个。粘虫转录组 SSR 共包含24种重复基元，其中 CCG／CGG 是优势重复基元类型，有69个；其次是 AAG／CTT ，有57个。 CG／CG 有18个，在二核苷酸重复基元中所占的比例达到25.7％。此研究发掘到的 SSR 位点将为粘虫遗传图谱的构建、遗传多样性分析、亲缘关系分析等提供丰富的分子标记。展开更多
基金supported by the Shandong Breeding Project (No. 2016LZGC009)the Projects from Laboratory for Marine Fisheries Science and Food Production Processes+2 种基金Pilot National Laboratory for Marine Science and Technology (Qingdao)(Nos. 2018-MFS-T08, 2017A STCP-OS15)the Central Public-interest Scientific Institution Basal Research Fund,CAFS (No. 2020TD20)the Central Public-Interest Scientific Institution Basal Re-search Fund,YSFRI,CAFS (No. 20603022018026)。
文摘Interferon-induced protein with tetratricopeptide repeats 1(IFIT1), also known as interferon-induced protein 56(IFI56) or Interferon-stimulated protein 56(ISG56), was originally identified as a protein induced upon treatment with interferon and inhibited by viral replication and translational initiation. In this study, Epinephelus lanceolatus IFIT1(ELIFIT1) gene was cloned for the first time. The complete cDNA of El IFIT1 gene includes 2921 nucleotides, and encodes a 437-amino acid(AA) protein. The putative ELIFIT1 protein has 9 TRP domains and is highly similar with IFIT1 proteins in other teleosts. In healthy fish, ELIFIT1 gene was highly expressed in the blood, which indicate its specific function in the peripheral immune system. Its expression was also observed in various immunity-related tissues including spleen, intestine, and kidney, Inducted with spotted knifejaw iridovirus(SKIV), ELIFIT1 gene expression was upregulated in the spleen, kidney, and liver 24 h after induction and reached its peak at 72 h, indicating that ELIFIT1 may play an important role in antivirus. These findings contribute to the understanding of the antiviral regulation of ELIFIT1 gene in teleost.
文摘The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper, we introduce the motif tracking algorithm （MTA）, a novel immune inspired （IS） pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases, the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilization of an intuitive symbolic representation. The resulting population of motifs is shown to have considerable potential value for other applications such as forecasting and algorithm seeding.
文摘Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433,782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya.
文摘The functionality of a gene or a protein depends on codon repeats occurring in it.As a consequence of their vitality in protein function and apparent involvement in causing diseases,an interest in these repeats has developed in recent years.The analysis of genomic and proteomic sequences to identify such repeats requires some algorithmic support from informatics level.Here,we proposed an offline stand-alone toolkit Repeat Searcher and Motif Detector（RSMD）,which uncovers and employs few novel approaches in identification of sequence repeats and motifs to understand their functionality in sequence level and their disease causing tendency.The tool offers various features such as identifying motifs,repeats and identification of disease causing repeats.RSMD was designed to provide an easily understandable graphical user interface（GUI）,for the tool will be predominantly accessed by biologists and various researchers in all platforms of life science.GUI was developed using the scripting language Perl and its graphical module PerlTK.RSMD covers algorithmic foundations of computational biology by combining theory with practice.
文摘【目的】利用P2C可以定向进入卵巢以及Gal4蛋白可与UAS序列稳定结合的特点,在中华按蚊Anopheles sinensis中建立高效的非胚胎期外源DNA投递技术系统。【方法】注射P2C-Gal4-DsRed重组蛋白至吸血后20 h时的中华按蚊雌成蚊腹部,通过冰冻切片荧光观察和Western blot检测分析重组蛋白P2C-Gal4-DsRed在卵巢中的投递效率;制备P2C-Gal4 DNA BINDING重组蛋白,构建包含12×UAS重复基序的转基因质粒和辅助质粒,通过电泳迁移实验分析重组蛋白P2C-Gal4 DNA BINDING和12×UAS重复基序间的体外结合;分别将体外孵育的P2C-Gal4 DNA BINDING+辅助质粒ITF36-12×UAS和P2C-Gal4 DNA BINDING+转基因质粒ITF2-12×UAS afm复合物注射入吸血后20 h时的中华按蚊雌成蚊腹部,于血餐后40 h时提取其卵巢组织DNA,并通过特异性引物PCR扩增和测序分析外源DNA在活体中的投递情况。【结果】100%注射P2C-Gal4-DsRed的中华按蚊雌成蚊卵巢在绿色滤光片下呈现明显的红色荧光,表明P2C-Gal4-DsRed重组蛋白能够被高效地导入雌成蚊卵巢中;P2C-Gal4 DNA BINDING重组蛋白能够与12×UAS重复基序以及含有该重复基序片段的质粒稳定结合;分别有91%和93%的注射了P2C-Gal4 DNA BINDING+ITF36-12×UAS和P2C-Gal4 DNA BINDING+ITF2-12×UAS afm的雌成蚊卵巢组织中能够检测到外源DNA片段。【结论】在中华按蚊中成功建立了基于P2C卵巢导向肽和Gal4-12×UAS重复基序结合特性的外源DNA投递技术体系;通过此技术平台能够便捷、快速和高效地实现质粒等DNA分子在中华按蚊卵巢中的投递,这为进一步简化转基因、过表达及基因敲入等遗传操作奠定了基础。
文摘粘虫 Mythimna separata（Walker）是一种迁飞性害虫，严重危害玉米、水稻、小麦等粮食作物。 SSR 是指以1～6个核苷酸为基本重复单位的串联重复 DNA 序列。 SSR 位点的信息分析为粘虫扩散、迁飞和交配等行为分子机制的研究以及粘虫的综合防治奠定理论基础。本研究基于高通量测序获得的粘虫转录组数据，利用软件 msatcom‐mander 发掘粘虫 SSR 位点。结果从20776条转录组 Unigenes 中共搜索出400个 SSR ，分布于372条 Unigenes 中。在粘虫转录组 SSR 中，三核苷酸重复的数量最为丰富，有271个；其次是二核苷酸和单核苷酸重复，分别是70个和49个；四至六核苷酸重复的数量都很少，共10个。粘虫转录组 SSR 共包含24种重复基元，其中 CCG／CGG 是优势重复基元类型，有69个；其次是 AAG／CTT ，有57个。 CG／CG 有18个，在二核苷酸重复基元中所占的比例达到25.7％。此研究发掘到的 SSR 位点将为粘虫遗传图谱的构建、遗传多样性分析、亲缘关系分析等提供丰富的分子标记。
