[Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screene...[Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screened by bioinfor- matic analysis method, and carried out real-time PCR expression analysis. [Result] The target gene Bmhsp24.3 expressed in different B. mori materials, but the expres- sion level in different materials significantly varied. The relative expression level of the gene had different degrees of changes under different rearing conditions. With the increase of rearing temperature, the gene expression was upregulated. The ma- terials with better healthiness had remarkable increase in expression of target gene, while the materials with poorer healthiness had less increase in expression of target gene. The expression difference of target gene Bmhsp24.3 was exactly consistent with the healthiness of breeds. [Conclusion] The healthiness of materials had rela- tionship with expression of target gene Bmhsp24.3. the higher the expression of tar- get gene Bmhsp24.3 was, the better the healthiness of materials was; conversely, the lower the expression of target gene Bmhsp24.3 was, the poorer the healthiness of materials was.展开更多
Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiat...Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiation, and development. In humans, this gene plays a vital role in normal brain development and function. Using an in silico approach in combination with 5＇ rapid amplification of cDNA ends （5＇ RACE）, the full-length cDNA of JARIDIC （GenBank accession No. EF139241） from porcine ovary, which contains 5,908 bp nucleotides, with an open reading frame （ORF） of 4,548 bp, has been cloned. The putative porcine JARID 1C protein, which is located in the nucleus, encodes 1,516 amino acids with a molecular weight of 170 kDa and a pI of 5.44. Bioinformatic prediction indicates that the protein contains several conserved domains： a JmjN domain, an ARID domain, a JmjC domain, a C5HC2 zinc finger domain, and a PHD zinc finger domain. Similarity comparisons for nucleic and amino acid sequences reveal that the porcine JARID1C protein shares a high identity with its dog, mouse, rat, and human counterparts. The phylogenetic tree of the JARID1 subfamily proteins has been constructed to reveal the evolutionary relationship of various species. Real-time PCR analysis shows that the JARIDIC gene is expressed in various tissues, but at different levels. The expression levels of this gene are higher in the brain and gonad than in other tissues, suggesting that the JARID1C protein plays a role in porcine brain and gonad functions.展开更多
Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at th...Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at the level of the whole transcriptome can help prevent the progression of HCC. Methods： The aim of this study was to identify differently expressed genes and potent pathways between normal liver and HCC tissues. The gene expression profiles of GSE104627 were downloaded from Gene Expression Omnibus database. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed and protein-protein interaction network of the differentially expressed genes were constructed by Cytoscape software. Results： In total, 880 differently expressed genes were identified between normal and tumor tissues, including 554 up-regulated genes and 326 down-regulated genes. Gene Ontology analysis results showed that the up-regulated genes were significantly enriched in establishment of RNA localization, nucleic acid transport, RNA transport, RNA localization and nucleobase, nucleoside, nucleotide and nucleic acid transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the up-regulated genes were enriched in axon guidance, dorso-ventral axis formation and pathways in cancer. The top 10 hub genes were identified from the protein - protein interaction network, and sub-networks revealed these genes were involved in significant pathways, including G protein-coupled receptors signaling pathway, signaling pathway via MAPK and extracellular matrix organization. Conclusion： The present study described the differently expressed genes between normal tissues and HCC tissues from the level of gene transcription. The possible signaling pathways involved in the development of HCC and related molecules involved were analyzed. However, further laboratory and clinical validation is still needed.展开更多
The total RNA was extracted from Microtusfortis liver tissue which before being infected and after being infected 10 d and 15 d by the Schistosoma japonicum cercariae. Using Rattus norvegicus CD36 gene probe to hybrid...The total RNA was extracted from Microtusfortis liver tissue which before being infected and after being infected 10 d and 15 d by the Schistosoma japonicum cercariae. Using Rattus norvegicus CD36 gene probe to hybridize analysis of CD36 difference expression in the Microtus fortis liver tissues which were infected with Schistosorna japonicum before and after being infected. At the same time, the cDNA sequence and encoded amino acid sequence of the Rattus norvegicus CD36 gene and CD36 protein structural domains were analysized by using bioinformatics. The results showed that the CD36 expression levels in the liver tissue of Microtus fortis after being infected were significantly higher than before being infectied. The Rattus norvegicus CD36 cDNA sequence of a total length is 1625 bp and encoded 472 amino acid residues and Rattus norvegicus CD36 protein containing a CD36 superfamily domain.展开更多
RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies...RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.展开更多
基金Supported by Youth Fund of Provincial Finance for Breeding Project(2010QNJJ-023)Fund Project of Agricultural Science and Technology Achievement Conversion(2010F00080)Science and Technology Supporting Project of Nanchong City(11A0016)~~
文摘[Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screened by bioinfor- matic analysis method, and carried out real-time PCR expression analysis. [Result] The target gene Bmhsp24.3 expressed in different B. mori materials, but the expres- sion level in different materials significantly varied. The relative expression level of the gene had different degrees of changes under different rearing conditions. With the increase of rearing temperature, the gene expression was upregulated. The ma- terials with better healthiness had remarkable increase in expression of target gene, while the materials with poorer healthiness had less increase in expression of target gene. The expression difference of target gene Bmhsp24.3 was exactly consistent with the healthiness of breeds. [Conclusion] The healthiness of materials had rela- tionship with expression of target gene Bmhsp24.3. the higher the expression of tar- get gene Bmhsp24.3 was, the better the healthiness of materials was; conversely, the lower the expression of target gene Bmhsp24.3 was, the poorer the healthiness of materials was.
基金the National High Technology Development Program of China (No. 2006AA10Z136).
文摘Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiation, and development. In humans, this gene plays a vital role in normal brain development and function. Using an in silico approach in combination with 5＇ rapid amplification of cDNA ends （5＇ RACE）, the full-length cDNA of JARIDIC （GenBank accession No. EF139241） from porcine ovary, which contains 5,908 bp nucleotides, with an open reading frame （ORF） of 4,548 bp, has been cloned. The putative porcine JARID 1C protein, which is located in the nucleus, encodes 1,516 amino acids with a molecular weight of 170 kDa and a pI of 5.44. Bioinformatic prediction indicates that the protein contains several conserved domains： a JmjN domain, an ARID domain, a JmjC domain, a C5HC2 zinc finger domain, and a PHD zinc finger domain. Similarity comparisons for nucleic and amino acid sequences reveal that the porcine JARID1C protein shares a high identity with its dog, mouse, rat, and human counterparts. The phylogenetic tree of the JARID1 subfamily proteins has been constructed to reveal the evolutionary relationship of various species. Real-time PCR analysis shows that the JARIDIC gene is expressed in various tissues, but at different levels. The expression levels of this gene are higher in the brain and gonad than in other tissues, suggesting that the JARID1C protein plays a role in porcine brain and gonad functions.
文摘Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at the level of the whole transcriptome can help prevent the progression of HCC. Methods： The aim of this study was to identify differently expressed genes and potent pathways between normal liver and HCC tissues. The gene expression profiles of GSE104627 were downloaded from Gene Expression Omnibus database. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed and protein-protein interaction network of the differentially expressed genes were constructed by Cytoscape software. Results： In total, 880 differently expressed genes were identified between normal and tumor tissues, including 554 up-regulated genes and 326 down-regulated genes. Gene Ontology analysis results showed that the up-regulated genes were significantly enriched in establishment of RNA localization, nucleic acid transport, RNA transport, RNA localization and nucleobase, nucleoside, nucleotide and nucleic acid transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the up-regulated genes were enriched in axon guidance, dorso-ventral axis formation and pathways in cancer. The top 10 hub genes were identified from the protein - protein interaction network, and sub-networks revealed these genes were involved in significant pathways, including G protein-coupled receptors signaling pathway, signaling pathway via MAPK and extracellular matrix organization. Conclusion： The present study described the differently expressed genes between normal tissues and HCC tissues from the level of gene transcription. The possible signaling pathways involved in the development of HCC and related molecules involved were analyzed. However, further laboratory and clinical validation is still needed.
文摘The total RNA was extracted from Microtusfortis liver tissue which before being infected and after being infected 10 d and 15 d by the Schistosoma japonicum cercariae. Using Rattus norvegicus CD36 gene probe to hybridize analysis of CD36 difference expression in the Microtus fortis liver tissues which were infected with Schistosorna japonicum before and after being infected. At the same time, the cDNA sequence and encoded amino acid sequence of the Rattus norvegicus CD36 gene and CD36 protein structural domains were analysized by using bioinformatics. The results showed that the CD36 expression levels in the liver tissue of Microtus fortis after being infected were significantly higher than before being infectied. The Rattus norvegicus CD36 cDNA sequence of a total length is 1625 bp and encoded 472 amino acid residues and Rattus norvegicus CD36 protein containing a CD36 superfamily domain.
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB945401, 2007CB108800)National Natural Science Foundation of China (Grant Nos. 30870575,31071162,31000590)Science and Technology Commission of Shanghai Municipality (Grant No. 11DZ2260300)
文摘RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.
