Objective: To clone the human counterpart of rat ZA73, EST cloned from rat tracheal epithelial (RTE) neoplastic transformed cell model induced by (a-particles radiation by using mRNA differential display. Methods: Acc...Objective: To clone the human counterpart of rat ZA73, EST cloned from rat tracheal epithelial (RTE) neoplastic transformed cell model induced by (a-particles radiation by using mRNA differential display. Methods: According to the sequence of rat ZA73, a probe was biotin-labeled to screen human cDNA library, and then the gene sequence was extended by RACE (rapid amplification of cDNA ends). Result: Human gene HRNT-1 (GenBank Accession Number: AF223393) is 4.256 kb in length, with an ORF located in the region between 254 and 3013 bp. 5′ UTS (untranslated sequences) is 253 bp, 3′ UTS is 1243 bp. Conclusion: The combination of cDNA library screening with biotin-labeled probes and RACE is an effective method to clone full-length cDNA, especially for sequences longer than 2 kb.展开更多
The global dissemination of H5 avian influenza viruses represents a significant threat to both human and animal health.In thisstudy,we conducted a genome-wide siRNA library screening against the highly pathogenic H5N1 i...The global dissemination of H5 avian influenza viruses represents a significant threat to both human and animal health.In thisstudy,we conducted a genome-wide siRNA library screening against the highly pathogenic H5N1 influenza virus,leading us tothe identification of 457 cellular cofactors(441 proviral factors and 16 antiviral factors)involved in the virus replication cycle.Gene Ontology term enrichment analysis revealed that the candidate gene data sets were enriched in gene categoriesassociated with mRNA splicing via spliceosome in the biological process,integral component of membrane in the cellularcomponent,and protein binding in the molecular function.Reactome pathway analysis showed that the immune system(up to63 genes)was the highest enriched pathway.Subsequent comparisons with four previous siRNA library screenings revealedthat the overlapping rates of the involved pathways were 8.53%-62.61%,which were significantly higher than those of thecommon genes(1.85%-6.24%).Together,our genome-wide siRNA library screening unveiled a panorama of host cellularnetworks engaged in the regulation of highly pathogenic H5N1 influenza virus replication,which may provide potential targetsand strategies for developing novel antiviral countermeasures.展开更多
Objective To construct and screen the suppression subtractive hybridization (SSH) library of human renal cell carcinoma (RCC). Methods Poly A+ RNA was isolated from RCC lines 786-O(tester) and renal cell(RC) lines HK-...Objective To construct and screen the suppression subtractive hybridization (SSH) library of human renal cell carcinoma (RCC). Methods Poly A+ RNA was isolated from RCC lines 786-O(tester) and renal cell(RC) lines HK-2 ( driver), respectiely. SSH procedure was performed according to the protocol of the PCR-Select cDNA Subtraction Kit ( Clontech), and PCR products were cloned into pT-Adv vector and transformed E. coli TOP10F’. All positive clones picked out were digested and some of which were sequenced. Results The SSH library contained 362 clones with SSH cDNA fragments distributed mainly from 0.3 to 0.9 kb. Among 50 clones sequenced randomly,2 represented unknown genes and the other 48 derived from 36 known genes. Conclusion The quality of the SSH library of human RCC is reliable and is construction is the basis for further screening differentially expressed genes of RCC. 6 refs,4 figs, 1 tab.展开更多
AFLP analysis was performed between a pair of thermo_sensitive genic male sterile (TGMS) rice allelic mutant lines (5460S and 5460F). The reaction conditions for rice AFLP assay were optimized. The relative efficienci...AFLP analysis was performed between a pair of thermo_sensitive genic male sterile (TGMS) rice allelic mutant lines (5460S and 5460F). The reaction conditions for rice AFLP assay were optimized. The relative efficiencies for polymorphism detection of RFLP, RAPD and AFLP were compared. The results indicated that the efficiency for polymorphism detection in rice was in the order of AFLP>RAPD>RFLP, and also indicated that AFLP was a powerful DNA molecular marker technique for polymorphism detection, especially in the case of extremely low polymorphism, such as isogenic lines and allelic mutant lines. Some of the AFLP products between the TGMS rice allelic mutant lines were cloned. Three of them were used as mixed probes to screen BAC library of rice line 5460S. 12 positive clones were screened out. In addition, the advantages and disadvantages of these three molecular marker systems were discussed.展开更多
Metamorphosis is a complex developmental process involving multiple pathways and a large number of genes that are regulated by juvenile hormone(JH)and 20-hydroxyecdysone(20E).Despite important progress in understandin...Metamorphosis is a complex developmental process involving multiple pathways and a large number of genes that are regulated by juvenile hormone(JH)and 20-hydroxyecdysone(20E).Despite important progress in understanding various aspects of silkworm biology,the hormone signaling pathway in the silkworm remains poorly understood.Genome-wide screening using clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)-based libraries has recently emerged as a novel method for analyzing genome function,enabling further research into essential genes,drug targets,and virus-host interaction.Previously,we constructed a genome-wide CRISPR/Cas9-based library of the silkworm(Bombyx mori)and successfully revealed the genes involved in biotic or abiotic stress factor responses.In this study,we used our silkworm CRISPR library and large-scale genome-wide screening to analyze the key genes in the silkworm 20E signaling pathway and their mechanisms of action.Functional annotation showed that 20E regulates key proteins in processes that mainly occur in the cytoplasm and nucleus.Pathway enrichment analysis showed that 20E can activate phosphorylation and may affect innate immunity,interfere with intracellular nutrition and energy metabolism,and eventually cause cell apoptosis.The screening results were experimentally validated by generating cells with knockout alleles of the relevant genes,which had increased tolerance to 20E.Our findings provide a panoramic overview of signaling in response to 20E in the silkworm,underscoring the utility of genome-wide CRISPR mutant libraries in deciphering hormone signaling pathways and the mechanisms that regulate metamorphosis in insects.展开更多
In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After ...In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.展开更多
In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After ...In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.展开更多
HtrA2/Omi is a mammalian mitochondrial serine protease, and was found to have dual roles in mam- malian cells, not only acting as an apoptosis-inducing protein but also maintaining mitochondrial ho- meostasis. PDZ dom...HtrA2/Omi is a mammalian mitochondrial serine protease, and was found to have dual roles in mam- malian cells, not only acting as an apoptosis-inducing protein but also maintaining mitochondrial ho- meostasis. PDZ domain is one of the most important protein-protein interaction modules and is in- volved in a variety of important cellular functions, such as signal transduction, degradation of proteins, and formation of cytoskeleton. Recently, it was reported that the PDZ domain of HtrA2/Omi might regulate proteolytic activity through its interactions with ligand proteins. In this study, we rapidly characterized the binding properties of HtrA2/Omi PDZ domain by validation screening of the PDZ ligand library with yeast two-hybrid approach. Then, we predicted its novel ligand proteins in human proteome and reconfirmed them in the yeast two-hybrid system. Finally, we analyzed the smallest networks bordered by the shortest path length between the protein pairs of novel interactions to evaluate the confidence of the identified interactions. The results revealed some novel binding proper- ties of HtrA2/Omi PDZ domain. Besides the reported Class II PDZ motif, it also binds to Class I and Class III motifs, and exhibits restricted variability at P?3, which means that the P?3 residue is selected according to the composition of the last three residues. Seven novel ligand proteins of HtrA2/Omi PDZ domain were discovered, providing significant clues for further clarifying the roles of HtrA2/Omi. Moreover, this study proves the high efficiency and practicability of the newly developed validation screening of candidate ligand library method for binding property characterization of peptide-binding domains.展开更多
Development and application of phage display technology and research progress of virus affinity peptide were summarized in the paper,and a preliminary outlook for future development was put forward. The paper laid a f...Development and application of phage display technology and research progress of virus affinity peptide were summarized in the paper,and a preliminary outlook for future development was put forward. The paper laid a foundation for development of polypeptide drugs and polypeptide vaccine.展开更多
Analysis of the mitochondrial proteome would provide valuable insight into the function of this important organelle, which plays key roles in energy metabolism, apoptosis, free radical production, thermogenesis, and c...Analysis of the mitochondrial proteome would provide valuable insight into the function of this important organelle, which plays key roles in energy metabolism, apoptosis, free radical production, thermogenesis, and calcium signaling. It could also increase our understanding about the mechanisms that promote mitochondrial disease. To identify proteins that are antigenically dominant in human liver mitochondria, we generated >240 hybridoma cell lines from native mitochondrial proteins after cell fusion, screening, and cloning. Antibodies that recognized mitochondrial proteins were identified by screening human liver cDNA expression libraries. In this study, we identified 6 major antigens that were recognized by at least 2 different monoclonal antibodies (mAbs). The proteins that were antigenically dominant were: acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase), aldehyde dehydrogenase 1 family member A1, carbamoyl phosphate synthetase 1, dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex), enoyl coenzyme A hydratase 1, and hydroxysteroid (11-beta) dehydrogenase 1. We also determined the subcellular localizations of these enzymes within the mitochondria using immunohistocytochemistry. We believe that these well-characterized antibodies will provide a valuable resource for the Human Liver Proteome Project (HLPP), and will make studies aimed at investigating liver mitochondrial function far easier to perform in future. Our results provide strong evidence that, (i) depletion of dominant proteins from liver mitochondrial samples is possible and, (ii) the approaches adopted in this study can be used to explore or validate protein-protein interactions in this important organelle.展开更多
基金China States Key Basic Research Program Grant (No. G1998051208) and National Natural Science Foundation of China (No. 39990600).
文摘Objective: To clone the human counterpart of rat ZA73, EST cloned from rat tracheal epithelial (RTE) neoplastic transformed cell model induced by (a-particles radiation by using mRNA differential display. Methods: According to the sequence of rat ZA73, a probe was biotin-labeled to screen human cDNA library, and then the gene sequence was extended by RACE (rapid amplification of cDNA ends). Result: Human gene HRNT-1 (GenBank Accession Number: AF223393) is 4.256 kb in length, with an ORF located in the region between 254 and 3013 bp. 5′ UTS (untranslated sequences) is 253 bp, 3′ UTS is 1243 bp. Conclusion: The combination of cDNA library screening with biotin-labeled probes and RACE is an effective method to clone full-length cDNA, especially for sequences longer than 2 kb.
基金supported by the National Key Research and DevelopmentProgram of China(2021YFD1800203 and 2021YFD1800204)the National Natural Science Foundation of China(NSFC)(32192453,32272979,and 32172847)+2 种基金the China PostdoctoralScience Foundation(2019M660897)the Innovation Program ofChinese Academy of Agricultural Sciences(CAAS-CSLPDCP-202401)the Earmarked Fund for China Agriculture Re-search System(CARS-41-G12)。
文摘The global dissemination of H5 avian influenza viruses represents a significant threat to both human and animal health.In thisstudy,we conducted a genome-wide siRNA library screening against the highly pathogenic H5N1 influenza virus,leading us tothe identification of 457 cellular cofactors(441 proviral factors and 16 antiviral factors)involved in the virus replication cycle.Gene Ontology term enrichment analysis revealed that the candidate gene data sets were enriched in gene categoriesassociated with mRNA splicing via spliceosome in the biological process,integral component of membrane in the cellularcomponent,and protein binding in the molecular function.Reactome pathway analysis showed that the immune system(up to63 genes)was the highest enriched pathway.Subsequent comparisons with four previous siRNA library screenings revealedthat the overlapping rates of the involved pathways were 8.53%-62.61%,which were significantly higher than those of thecommon genes(1.85%-6.24%).Together,our genome-wide siRNA library screening unveiled a panorama of host cellularnetworks engaged in the regulation of highly pathogenic H5N1 influenza virus replication,which may provide potential targetsand strategies for developing novel antiviral countermeasures.
文摘Objective To construct and screen the suppression subtractive hybridization (SSH) library of human renal cell carcinoma (RCC). Methods Poly A+ RNA was isolated from RCC lines 786-O(tester) and renal cell(RC) lines HK-2 ( driver), respectiely. SSH procedure was performed according to the protocol of the PCR-Select cDNA Subtraction Kit ( Clontech), and PCR products were cloned into pT-Adv vector and transformed E. coli TOP10F’. All positive clones picked out were digested and some of which were sequenced. Results The SSH library contained 362 clones with SSH cDNA fragments distributed mainly from 0.3 to 0.9 kb. Among 50 clones sequenced randomly,2 represented unknown genes and the other 48 derived from 36 known genes. Conclusion The quality of the SSH library of human RCC is reliable and is construction is the basis for further screening differentially expressed genes of RCC. 6 refs,4 figs, 1 tab.
文摘AFLP analysis was performed between a pair of thermo_sensitive genic male sterile (TGMS) rice allelic mutant lines (5460S and 5460F). The reaction conditions for rice AFLP assay were optimized. The relative efficiencies for polymorphism detection of RFLP, RAPD and AFLP were compared. The results indicated that the efficiency for polymorphism detection in rice was in the order of AFLP>RAPD>RFLP, and also indicated that AFLP was a powerful DNA molecular marker technique for polymorphism detection, especially in the case of extremely low polymorphism, such as isogenic lines and allelic mutant lines. Some of the AFLP products between the TGMS rice allelic mutant lines were cloned. Three of them were used as mixed probes to screen BAC library of rice line 5460S. 12 positive clones were screened out. In addition, the advantages and disadvantages of these three molecular marker systems were discussed.
基金This work was supported by grants from the National Natural Science Foundation of China(No.32122084)Chongqing Natural Science Foundation(No.cstc2021ycjh-bgzxm0005)+1 种基金PhD Start-Up Foundation of Southwest University(No.SWU120012)Fundamental Research Funds for the Central Universities(No.SWU-KT22042).None of these fundings played any role in the design of the study,collection,analysis,or interpretation of data or in the writing of the manuscript.
文摘Metamorphosis is a complex developmental process involving multiple pathways and a large number of genes that are regulated by juvenile hormone(JH)and 20-hydroxyecdysone(20E).Despite important progress in understanding various aspects of silkworm biology,the hormone signaling pathway in the silkworm remains poorly understood.Genome-wide screening using clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)-based libraries has recently emerged as a novel method for analyzing genome function,enabling further research into essential genes,drug targets,and virus-host interaction.Previously,we constructed a genome-wide CRISPR/Cas9-based library of the silkworm(Bombyx mori)and successfully revealed the genes involved in biotic or abiotic stress factor responses.In this study,we used our silkworm CRISPR library and large-scale genome-wide screening to analyze the key genes in the silkworm 20E signaling pathway and their mechanisms of action.Functional annotation showed that 20E regulates key proteins in processes that mainly occur in the cytoplasm and nucleus.Pathway enrichment analysis showed that 20E can activate phosphorylation and may affect innate immunity,interfere with intracellular nutrition and energy metabolism,and eventually cause cell apoptosis.The screening results were experimentally validated by generating cells with knockout alleles of the relevant genes,which had increased tolerance to 20E.Our findings provide a panoramic overview of signaling in response to 20E in the silkworm,underscoring the utility of genome-wide CRISPR mutant libraries in deciphering hormone signaling pathways and the mechanisms that regulate metamorphosis in insects.
基金This work was supported by Nationa1 NaturalScience Fundation of China No.39700148 and LifeScience Special fund of CAS supported by ChineseMinisery of Finance.
文摘In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.
文摘In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.
基金the National Basic Research Program (Grant No. 2004CB520804)the National High Technology Research and Development Program (Grant No. 2006AA02Z308)+1 种基金the National Natural Science Foundation of China (Grant Nos. 30270657, 30230150, and 3037030)Beijing Natural Science Foundation (Grant No. 5072037)
文摘HtrA2/Omi is a mammalian mitochondrial serine protease, and was found to have dual roles in mam- malian cells, not only acting as an apoptosis-inducing protein but also maintaining mitochondrial ho- meostasis. PDZ domain is one of the most important protein-protein interaction modules and is in- volved in a variety of important cellular functions, such as signal transduction, degradation of proteins, and formation of cytoskeleton. Recently, it was reported that the PDZ domain of HtrA2/Omi might regulate proteolytic activity through its interactions with ligand proteins. In this study, we rapidly characterized the binding properties of HtrA2/Omi PDZ domain by validation screening of the PDZ ligand library with yeast two-hybrid approach. Then, we predicted its novel ligand proteins in human proteome and reconfirmed them in the yeast two-hybrid system. Finally, we analyzed the smallest networks bordered by the shortest path length between the protein pairs of novel interactions to evaluate the confidence of the identified interactions. The results revealed some novel binding proper- ties of HtrA2/Omi PDZ domain. Besides the reported Class II PDZ motif, it also binds to Class I and Class III motifs, and exhibits restricted variability at P?3, which means that the P?3 residue is selected according to the composition of the last three residues. Seven novel ligand proteins of HtrA2/Omi PDZ domain were discovered, providing significant clues for further clarifying the roles of HtrA2/Omi. Moreover, this study proves the high efficiency and practicability of the newly developed validation screening of candidate ligand library method for binding property characterization of peptide-binding domains.
基金Supported by Scientific and Technological Project of Henan Province(162102110136)Science and Technology Foundation for Outstanding Young Scientists of Henan Academy of Agricultural Sciences(2016YQ28)
文摘Development and application of phage display technology and research progress of virus affinity peptide were summarized in the paper,and a preliminary outlook for future development was put forward. The paper laid a foundation for development of polypeptide drugs and polypeptide vaccine.
基金supported by the National Basic Research Program of China (Grant No. 2006CB910803)the National High Technology Research and Development Program of China (Grant No. 2006AA02A311)
文摘Analysis of the mitochondrial proteome would provide valuable insight into the function of this important organelle, which plays key roles in energy metabolism, apoptosis, free radical production, thermogenesis, and calcium signaling. It could also increase our understanding about the mechanisms that promote mitochondrial disease. To identify proteins that are antigenically dominant in human liver mitochondria, we generated >240 hybridoma cell lines from native mitochondrial proteins after cell fusion, screening, and cloning. Antibodies that recognized mitochondrial proteins were identified by screening human liver cDNA expression libraries. In this study, we identified 6 major antigens that were recognized by at least 2 different monoclonal antibodies (mAbs). The proteins that were antigenically dominant were: acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase), aldehyde dehydrogenase 1 family member A1, carbamoyl phosphate synthetase 1, dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex), enoyl coenzyme A hydratase 1, and hydroxysteroid (11-beta) dehydrogenase 1. We also determined the subcellular localizations of these enzymes within the mitochondria using immunohistocytochemistry. We believe that these well-characterized antibodies will provide a valuable resource for the Human Liver Proteome Project (HLPP), and will make studies aimed at investigating liver mitochondrial function far easier to perform in future. Our results provide strong evidence that, (i) depletion of dominant proteins from liver mitochondrial samples is possible and, (ii) the approaches adopted in this study can be used to explore or validate protein-protein interactions in this important organelle.
