A cDNA library was successfully constructed from Anip973, a human lung adenocarcinoma cell line with high metastatic potential. NIH3T3 cells were stably transfected using this cDNA library and screened for morphologic...A cDNA library was successfully constructed from Anip973, a human lung adenocarcinoma cell line with high metastatic potential. NIH3T3 cells were stably transfected using this cDNA library and screened for morphological changes in a soft agar assay. Genomic DNA was isolated from putative clones and the integrated sequence was retrieved by PCR and sequencing. Three known genes, ribosomal protein L23, hypothetical protein FLJ22104, and serine protease inhibitor, kazal type 6 and a number of 5＇-terminally truncated sequences were identified. Furthermore, cells transfected with ribosomal protein L23 was highly invasive compared with the empty vector as control （P 〈 0.02）. These results indicate that the expression cloning of cDNA libraries in NIH3T3 cells and subsequent screening for loss of contact inhibition in soft agar is a viable tool for identifying tumor-related genes and ribosomal protein L23 gene plays a role in cell movement and metastasis.展开更多
A full length cDNA named HongrESl was isolated and cloned by screening rat epididymis cDNA library using a mouse EST as a probe and 5'RACE followed. It contained 1590bp nucleotides and its predicted protein had 41...A full length cDNA named HongrESl was isolated and cloned by screening rat epididymis cDNA library using a mouse EST as a probe and 5'RACE followed. It contained 1590bp nucleotides and its predicted protein had 415 amino acid residues including a serpin (serine protease inhibitor) conserved domain. Tissue distribution pattern showed it was specifically expressed in adult rat epididymis; moreover, in situ hybridyza-tion indicated this gene was expressed in a limited region of the cauda epididymis near vas deference. Such kind of expression pattern sugested that HongrESl had potential function in male reproduction.展开更多
Tetrahymena thermophila is a model eukaryotic organism. Functional genomic analyses in Tetrahymena present rich opportunities to address fundamental questions of cell and molecular biology. The Tetrahymena Gene Expres...Tetrahymena thermophila is a model eukaryotic organism. Functional genomic analyses in Tetrahymena present rich opportunities to address fundamental questions of cell and molecular biology. The Tetrahymena Gene Expression Database (TGED; available at http://tged.ihb.ac.cn) is the first expression database of a ciliated protozoan. It covers three major physiological and developmental states: growth, starvation, and conjugation, and can be accessed through a user-friendly web interface. The gene expression profiles and candidate co-expressed genes for each gene can be retrieved using Gene ID or Gene description searches. Descriptions of standardized methods of sample preparation and the opportunity to add new Tetrahymena microarray data will be of great interest to the Tetrahymena research community. TGED is intended to be a resource for all members of the scientific research community who are interested in Tetrahymena and other ciliates.展开更多
Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available ...Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available to provide the association information between gene over- or under-expression and various diseases. In this study, we presented a comprehensive disease-associated over- and under-expressed gene database （OUGene） based on our proposed text mining pipeline and several open curated databases. It contains total 41,269 unique associa- tions between 7,238 over- or under-expressed genes and 1,480 diseases, which are supported by 81,974 evidence sentences from 56,442 articles. The OUGene is compre- hensive and covers most important therapeutic areas. Meanwhile a new scoring system is designed to rank the associations based on benchmarking against hand-curated data. OUGene provides an easy-of-use web interface for researchers to analyze these data and visualize the associ- ated networks, which can give insights to the complex relationships between over- and under-expressed genes and diseases at a system level. It is available at www.csbio.sjtu. edu.cn/bioinf/OUGene/.展开更多
Objective： To clone and identify one novel regeneration related gene H3 （CA854305） from the differential expression genes library we had set up before. Methods： Use the method of Northern blot to detect the diffe...Objective： To clone and identify one novel regeneration related gene H3 （CA854305） from the differential expression genes library we had set up before. Methods： Use the method of Northern blot to detect the different expressions of the novel gene under different situations, employ the technique of in silico cloning to scan the span of the novel gene, and analyze their sequences. Also we used reverse transcription PCR to validate the largest open reading frame. Results：Northern blotting results of H3 （ CA854305 ） showed that the transplanted group had more efficient and extensive expression than untreated and uninjured groups 5 days after spinal cord injury, while the untreated group had more extensive expression than uninjured group. It implied that H3 might have some relationship with nerve regeneration after spinal cord injury. From the results of in silico cloning we got a longest contig of 1635 bp and an largest open reading frame of 542 bp from 49 to 591 bp correspondent with the Cozak rules. Reverse transcription PCR validated the largest open reading frame sequence primarily. Conclusions： We got the sequence of novel gene H3 which might be one of the regeneration-related penes.展开更多
基金This work was supported by Returning Scholars Fund of Heilongjiang Province (No. LC04C02) the Department of Education Overseas Researcher Fund of Heilongjiang Province (No. 1054HZ013).
文摘A cDNA library was successfully constructed from Anip973, a human lung adenocarcinoma cell line with high metastatic potential. NIH3T3 cells were stably transfected using this cDNA library and screened for morphological changes in a soft agar assay. Genomic DNA was isolated from putative clones and the integrated sequence was retrieved by PCR and sequencing. Three known genes, ribosomal protein L23, hypothetical protein FLJ22104, and serine protease inhibitor, kazal type 6 and a number of 5＇-terminally truncated sequences were identified. Furthermore, cells transfected with ribosomal protein L23 was highly invasive compared with the empty vector as control （P 〈 0.02）. These results indicate that the expression cloning of cDNA libraries in NIH3T3 cells and subsequent screening for loss of contact inhibition in soft agar is a viable tool for identifying tumor-related genes and ribosomal protein L23 gene plays a role in cell movement and metastasis.
基金supported by the Special Funds for Major State Basic Research Project(“973”No.G1999055901)State 863 High Technology R and D Project of China(No.2001AA221211)+3 种基金Shanghai Development Foundation of Science and Technology(No.01JC14046)Director foundation of Chinese Academy of Sciences,National Natural Science Foundation(No.30100064&39893320)Special funds of Biological Science and Technology from Chinese Academy of Science,NIH Forgarty International Center Grant 1-R03-TW01490-01A,CFDA No.93.934CAS knowledge creative program(KSCX2-SW-201).
文摘A full length cDNA named HongrESl was isolated and cloned by screening rat epididymis cDNA library using a mouse EST as a probe and 5'RACE followed. It contained 1590bp nucleotides and its predicted protein had 415 amino acid residues including a serpin (serine protease inhibitor) conserved domain. Tissue distribution pattern showed it was specifically expressed in adult rat epididymis; moreover, in situ hybridyza-tion indicated this gene was expressed in a limited region of the cauda epididymis near vas deference. Such kind of expression pattern sugested that HongrESl had potential function in male reproduction.
基金supported by the National Natural Science Foundation of China (Grant Nos. 30870356 and 30970424)the Knowledge Innovation Program of Chinese Academy of Sciences (Grant No. KSCX2-YW-G-072)the National Institutes of Health (Grant Nos. GM021793 and GM072752)
文摘Tetrahymena thermophila is a model eukaryotic organism. Functional genomic analyses in Tetrahymena present rich opportunities to address fundamental questions of cell and molecular biology. The Tetrahymena Gene Expression Database (TGED; available at http://tged.ihb.ac.cn) is the first expression database of a ciliated protozoan. It covers three major physiological and developmental states: growth, starvation, and conjugation, and can be accessed through a user-friendly web interface. The gene expression profiles and candidate co-expressed genes for each gene can be retrieved using Gene ID or Gene description searches. Descriptions of standardized methods of sample preparation and the opportunity to add new Tetrahymena microarray data will be of great interest to the Tetrahymena research community. TGED is intended to be a resource for all members of the scientific research community who are interested in Tetrahymena and other ciliates.
文摘Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available to provide the association information between gene over- or under-expression and various diseases. In this study, we presented a comprehensive disease-associated over- and under-expressed gene database （OUGene） based on our proposed text mining pipeline and several open curated databases. It contains total 41,269 unique associa- tions between 7,238 over- or under-expressed genes and 1,480 diseases, which are supported by 81,974 evidence sentences from 56,442 articles. The OUGene is compre- hensive and covers most important therapeutic areas. Meanwhile a new scoring system is designed to rank the associations based on benchmarking against hand-curated data. OUGene provides an easy-of-use web interface for researchers to analyze these data and visualize the associ- ated networks, which can give insights to the complex relationships between over- and under-expressed genes and diseases at a system level. It is available at www.csbio.sjtu. edu.cn/bioinf/OUGene/.
基金he National Natural Science Foundation of China(No.30000173)
文摘Objective： To clone and identify one novel regeneration related gene H3 （CA854305） from the differential expression genes library we had set up before. Methods： Use the method of Northern blot to detect the different expressions of the novel gene under different situations, employ the technique of in silico cloning to scan the span of the novel gene, and analyze their sequences. Also we used reverse transcription PCR to validate the largest open reading frame. Results：Northern blotting results of H3 （ CA854305 ） showed that the transplanted group had more efficient and extensive expression than untreated and uninjured groups 5 days after spinal cord injury, while the untreated group had more extensive expression than uninjured group. It implied that H3 might have some relationship with nerve regeneration after spinal cord injury. From the results of in silico cloning we got a longest contig of 1635 bp and an largest open reading frame of 542 bp from 49 to 591 bp correspondent with the Cozak rules. Reverse transcription PCR validated the largest open reading frame sequence primarily. Conclusions： We got the sequence of novel gene H3 which might be one of the regeneration-related penes.
