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in silico cloning of GDP-D-mannose pyrophosphorylase(GMPase) cDNA from Tomato(Lycopersicon esculentum)

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In Silico Cloning of GDP-D-mannose pyrophosphorylase(GMPase)...

Feasibility Analysis of in silico cloning of Functional Candidate Genes in Tea (Camellia sinensis)

湖北省遗传学会第七次代表大会暨学术讨论会

作者： Liping Zou~1, Hanxia Li~2, Bo Ouyang~1, Junhong Zhang~1, Wei Zhang~1, Zhibiao Ye~(1*) (1. National Key Laboratory of Crop Genetic Improvement, 2. College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070)

Vitamin C (ascorbic acid) is essential to prevent disease associated with connective tissue (e.g., scurvy), improve cardiovascular and immune cell functions, and is used to regenerate α-tocopherol (vitamin E). Although plants and most animals can synthesize ascorbic acid (AsA), human lacks L-gulono-1,4-lactone oxidoreductase, which is required for the final step in AsA synthesis. Because AsA cannot be stored in the body, the vitamin must be acquired regularly from dietary sources, primarily from plants rich in AsA. Tomato

关键词： tomato in silico cloning GDP-D-mannose pyrophosphorylase RT-PCR

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Agricultural Biotechnology 2015年第3期4卷 31-34页

作者： Xiangrui KONG Institute of Tea Research Fujian Academy of Agricultural Sciences

[ Objective ] This study aimed to verify the feasibility of in silico cloning of functional candidate genes in tea. [ Method ] Theobroma cacao caffeine syn- thase gene BCS1 was used as a probe to search the established tea EST database using BLAST; 26 tea ESTs highly homologous to BCS1 were obtained, which were assembled using CAP （contig assembly program） of BioEdit software; subsequently, two EST configs harboring ORF were obtained, which were named TCSnewl and TCSnew2, respectively. Nucleotide sequences and deduced amino acid sequences of theses two genes were compared with those of cDNA of tea caffeine synthase gene TCS in the GenBank database that was cloned with experimental biological method. A phylogenetic tree was constructed for homalogous analysis of the deduced amino acid sequences of theses three genes. [ Result] in silico cloning of functional candidate genes in tea using a homologous gene of distantly related species as a probe is a feasible technical means. [ Conclusion] This study provided the basis for in silico cloning of other functional genes in tea.

关键词： Tea in silico cloning Caffeine synthase gene Phylogenetic tree

Decoding bovine coronavirus immune targets:an epitope informatics approach

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Animal Diseases 2024年第2期4卷 138-153页

作者： Swati Rani Mehnaj Khatoon Jagadish Hiremath Kuralayanapalya Puttahonnappa Suresh Jayashree Anandakumar Nagendra Nath Barman Sheethal Manjunath Yamini Sri S Sharanagouda S.Patil Spatial Epidemiology Lab ICAR-National Institute of Veterinary Epidemiology and Disease InformaticsYelahankaBengaluruKarnataka 560064India College of Veterinary Science Assam Agricultural UniversityGuwahatiAssam 785013India Yuvaraja’s College Mysuru University of MysuruMysuruKarnataka 570005India

Bovine coronavirus(BCoV)poses a significant threat to the global cattle industry,causing both respiratory and gastrointestinal infections in cattle *** necessitates the development of efficacious *** several inactivated and live BCoV vaccines exist,they are predominantly limited to *** immunization of adult cattle is imperative for BCoV infection control,as it curtails viral transmission to calves and ameliorates the impact of enteric and respiratory ailments across all age groups within the *** study presents an in silico methodology for devising a multiepitope vaccine targeting *** spike glycoprotein(S)and nucleocapsid(N)proteins,which are integral elements of the BCoV structure,play pivotal roles in the viral infection cycle and immune *** constructed a remarkably effective multiepitope vaccine candidate specifically designed to combat the BCoV *** immunoinformatics technology,B-cell and T-cell epitopes were predicted and linked together using linkers and adjuvants to efficiently trigger both cellular and humoral immune responses in *** in silico construct was characterized,and assessment of its physicochemical properties revealed the formation of a stable vaccine *** 3D modeling of the vaccine construct,molecular docking revealed a stable interaction with the bovine receptor ***,the viability of the vaccine’s high expression and simple purification was demonstrated by codon optimization and in silico cloning expression into the pET28a(+)*** applying immunoinformatics approaches,researchers aim to better understand the immune response to bovine coronavirus,discover potential targets for intervention,and facilitate the development of diagnostic tools and vaccines to mitigate the impact of this virus on cattle health and the livestock *** anticipate that the design will be useful as a preventive treatment for BCoV sickness in cattle,opening the door for furthe

关键词： Immunoinformatics Bovine coronavirus Multiepitope vaccine Molecular docking in silico cloning

cloning and characterization of a mouse liver-specific gene mfrep-1, up-regulated in liver regeneration

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Cell Research 2002年第Z2期 353-361页

作者： JUN VAN, HAD YING, FBI GU, JIN HE, Yu Li LI, Hm MIN LIU, YONG HUA XU Laboratory of Molecular and Cellular Oncology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China Department of Surgery, Huashan Hospital, Fudan University, Shanghai 200031, China Department of Pathology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China

Human fibrinogen-related protein-1/liver fibrinogen-related protein-1 (HFREP-l/LFIRE-1), a liver-specific protein, is a member of fibrinogen superfamily that exerts various biological activities. However, the function of HFREP-l/LFIRE-1 in liver remains unknown. Here we isolated its mouse ortholog gene-mouse fibrinogen-related protein-1 (mfrep-1), which encoded 314 amino acids, exhibiting 80.4% similarity to HFREP-l/LFIRE-1. Northern blot analysis revealed that 1.2-kb mfrep-1 mRNA was detected selectively in mouse liver. To explore the function of MFREP-1, we examined the levels of mfrep-1 mRNA during regeneration after 70% partial hepatectomy (PHx) in mice, mfrep-1 mRNA increased in the regenerating liver and reached the first shoulder peak at 2-4 h after PHx. Cycloheximide pretreatment could suppress the induction of mfrep-1, indicating the up-regulation of this gene need de novo protein synthesis. Its mRNA continued to elevate at 6 h thereafter and reached the second peak at 24 h. The enhanced express

关键词： mfrep-1 in silico cloning liver regeneration liver-specific expression.

Genome-wide analysis of the AP2/ERF gene family in maize

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Genome-wide analysis of the AP2/ERF gene family in maize

cloning and Identification of A New Na^+/H^+ Antiporter Gene ZmSOS1 in Maize(Zea mays L.)

2012年全国玉米遗传育种学术研讨会暨新品种展示观摩会

作者： Min Huang~(1,2),Shuiyuan Cheng~2,Zuxin Zhang~3,Hewei Du~1 (1.College of life science,Yangtze University,Jingzhou,Hubei 434025,P.R.China 2.Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization,Huanggang Normal Universtiy,Huanggang,Hubei 438000,P.R.China 3.College of plant science and technology,Huazhong Agricultural University,Wuhan 430070,P.R.China)

Plants experience various abiotic stresses during their life cycle,such as drought,salinity,and extreme temperatures, which cause extensive losses to agricultural production *** stress has become one of major limiting factor of crop loss, reducing extensive yields for most major crop plants by more than 50% .Plant adaptation to abiotic stresses is controlled by cascades of molecular *** relatively little is known about these molecular networks of plant tolerance to abiotic stress,a large number of stress - associated genes and signal - transduction systems have been *** researches show that AP2/ERF(APETALA2 /ethylene response factors) subfamily transcription factors play important roles in directing changes of gene expression during abiotic stress. AP2/ERF genes form a large multigene family,containing either one or two AP2 domains,and are classified into five subfamilies: AP2,DREB(dehydration responsive element binding),RAV(related to ABI3/VP),ERF,and others(Sakuma et al.,2002).ERF and DREB subfamily can be further divided into 6 subgroups respectively,ERF with B1-6 6 subgroups,and DREB subfamily with A1-6 6 *** has been demonstrated that AP2/ERF proteins play an important role in regulation of plant growth and development, response to environmental ***2/ERF genes play a variety of roles throughout the plant life cycles,however,few reports of AP2/ERF family are available for maize. In the present report,330 maize AP2/ERF genes were downloaded from PlnTFDB database,and 84 genes were belongs to 35 locus, ***,281 AP2/ERF genes were found from PlnTFDB database.121 maize AP2/ERF genes were obtained from NCBI and Maizesequence database through BLASTP,while 69 of 121 genes have founded in *** 52 of 120 genes were chosen. Above all,333 maize AP2/ERF genes were *** order to exclude false - positive,the amino acid sequence of 330 AP2/ ERF genes was used as a query to search in maiz

关键词： Maize(Zea mays L.) AP2/ERF Transcriptional factor Bioinfomatics in silico cloning

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Agricultural Science & Technology 2009年第6期10卷 57-62,158页

作者：赵祥强南通大学生命科学学院江苏南通226007

[ Objective] The study aimed to clone and identify Na^＋/H^＋ antiporter genes in maize, and provided the information for characterizing the function of such genes in abiotic stress tolerance of maize. Method The in silico cloning, RT-PCR, and bioinformatics analysis were used in this study. Result By in sifico cloning, a plasma membrane Na^＋/H^＋ antiporter gene, named as ZmSOS1 （EMBL accession No. BN001309）, was cloned from maize （ Zea mays L. ）. ZmSOS1 has an open reading frame （ORF） of 3 411 bp which encoded a protein of 1 136 amino acids. By multiple sequence alignment analysis, it showed the predicated peptide of ZmSOS1 were 61% and 82% identities in amino acids to the plasma membrane Na^＋/H^＋ antiporter AtSOS1 and OsSOS1, respectively. The RT-PCR analysis revealed that ZmSOS1 could be significantly up-regulated by salt stress, which indicated ZmSOS1 might play a role in salt tolerance of maize. Conclusion ZmSOS1 is a putative plasma membrane Na^＋/H^＋ antiporter gene and may play a role in abiotic stress tolerance of maize.

关键词： Zea mays Na^+/H^+ antiporter in silico cloning Bioinformatics analysis

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cDNA cloning and Bioinformatic Prediction of TPI Gene from Apis mellifera

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Agricultural Science & Technology 2012年第5期13卷 1097-1100,1126页

作者：王琦李玮妮王荣长治学院生物科学与技术系山西长治046011 福建农林大学生命科学学院福建福州350002 长治卫生学校山西长治046000

[Objective] The aim was to clone triosephosphate isomerase （TPI） gene from Apis mellifera, and predict the properties of TPI protein with bioinformatic meth- ods. [Method] The TPI gene was firstly cloned by in silico cloning based on the ex- pressed sequence tags （ESTs） from Unigene of NCBI. Some characters of the TPI protein including hydrophobicity or hydrophilicity, isoelectric point （pl） and secondary structure were analyzed and predicted by the tools of bioinformatics. [Result] The TPI gene from A. mellifera was 1 768 bp in full length and it contained a complete ORF which encoded 247 amino acids; the pl of TPI protein was 8.515; the TPI protein was a member of ~13-fold family. [Conclusion] The in silico cloning based on the expressed sequence tags is a efficient method in practice, and this study will provide more references for further study on A. mellifera at molecular level.

关键词： Apis mellifera in silico cloning Triosephosphate isomerase (TPI) Bioinformatics

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