A 1 539 by squalene synthase (AaSQS) cDNA was cloned from a high-yield Artemisia annua L. strain 001 by reverse transcription-polymerise chain reaction (RT-PCR). The amino acid sequence of AaSQS is 70%, 77%, 44% and 3...A 1 539 by squalene synthase (AaSQS) cDNA was cloned from a high-yield Artemisia annua L. strain 001 by reverse transcription-polymerise chain reaction (RT-PCR). The amino acid sequence of AaSQS is 70%, 77%, 44% and 39%a identical to that of squalene synthases from Arabidopsis thaliana, tobacco, human and yeast, respectively. The AaSQS genomic DNA has a complex organization containing 14 exons and 13 introns. Full-length or C-terminal truncated cDNA was subcloned into prokaryotic expression vector pET30a and the constructed plasmid was introduced to Escherichia coli strain BL21 (DE3) for induced overexpression. No squalene synthase protein with expected molecular mass was observed in E. cola containing the putative full-length squalene synthase cDNA, however, overexpression in E. coli was achieved by truncating 30 amino acids of hydrophobic region at the carboxy terminus.展开更多
Objective: To establish a rabbit atrial fibrillation model with rapid atrial pacing (RAP) and investigate its ultrastructural changes and expressions of L-type calcium channel subunits and potassium channel Kv4. 3. Me...Objective: To establish a rabbit atrial fibrillation model with rapid atrial pacing (RAP) and investigate its ultrastructural changes and expressions of L-type calcium channel subunits and potassium channel Kv4. 3. Methods: Thirty-six rabbits were performed electrical stimulation through bipolar endo-cardial led by surgical technique. 600 beat per min from 0 to 48 h. Atrial ultrastructure was observed by transmission electron microscope (TEM) after different pacing times. mRNA were measured by reverse transcription-polymera.se chain reaction (RT-PCR). Results: Atrial ultrastructure had alteration after 3 hours' pacing, such as mitochondria vacuolization, myofilament lysis and glucogen aggregation. The mRNA of the Ca2+ channel β1 and α1 subunits began to decrease after pacing of 6 h. which were paralleled with the change of Kv4. 3 mRNA. But the auxiliary subunit α2 were not affected. Conclusion: Ultrastructural changes and mRNA levels of L-type calcium channel subunits and potassium channel Kv4. 3 are decreased after RAP. with a mechanism of transcriptional down-regulation of underlying ion channels due to calcium overloading after RAP.展开更多
Objective:To establish a systematic framework for selecting the best clustering algorithm and provide an evaluation method for clustering analyses of gene expression data. Methods: Based on data structure (internal in...Objective:To establish a systematic framework for selecting the best clustering algorithm and provide an evaluation method for clustering analyses of gene expression data. Methods: Based on data structure (internal information) and function classification (external information), the evaluation of gene expression data analyses were carried out by using 2 approaches. Firstly, to assess the predictive power of clusteringalgorithms, Entropy was introduced to measure the consistency between the clustering results from different algorithms and the known and validated functional classifications. Secondly, a modified method of figure of merit (adjust-FOM) was used as internal assessment method. In this method, one clustering algorithm was used to analyze all data but one experimental condition, the remaining condition was used to assess the predictive power of the resulting clusters. This method was applied on 3 gene expression data sets (2 from the Lyer's Serum Data Sets, and 1 from the Ferea's Saccharomyces Cerevisiae Data Set). Results: A method based on entropy and figure of merit (FOM) was proposed to explore the results of the 3 data sets obtained by 6 different algorithms, SOM and Fuzzy clustering methods were confirmed to possess the highest ability to cluster. Conclusion: A method based on entropy is firstly brought forward to evaluate clustering analyses.Different results are attained in evaluating same data set due to different function classification. According to the curves of adjust_FOM and Entropy_FOM, SOM and Fuzzy clustering methods show the highest ability to cluster on the 3 data sets.展开更多
Spatial expression patterns of homeobox （HOX） genes delineate positional identity of primary fibroblasts from different topo- graphic sites. The molecular mechanism underlying the establishing or maintaining of HOX ...Spatial expression patterns of homeobox （HOX） genes delineate positional identity of primary fibroblasts from different topo- graphic sites. The molecular mechanism underlying the establishing or maintaining of HOX gene expression pattern remains an attractive developmental issue to be addressed. Our previous work suggested a critical role of CTCF/cobesin-mediated high- er-order chromatin structure in RA-induced HOXA activation in human teratocarcinoma NT2/D1 cells. This study investigated the recruitment of CTCF and cohesin, and the higher-order chromatin structure of the HOXA locus in fetal lung and adult foreskin fibroblasts, which display complementary HOXA gene expression patterns. Chromatin contacts between the CTCF-binding sites were observed with lower frequency in human foreskin fibroblasts. This observation is consistent with the lower level of cohesin recruitment and 5＇ HOXA gene expression in the same cells. We also showed that CTCF-binding site A56 （CBSA56） related chromatin structures exhibit the most notable changes in between the two types of cell, and hence may stand for one of the key CTCF-binding sites for cell-type specific chromatin structure organization. Together, these results im- ply that CTCF/cohesin coordinates HOXA cluster higher-order chromatin structure and expression during development, and provide insight into the relationship between cell-type specific chromatin organization and the spatial collinearity.展开更多
Magnetoreception is a hallmark ability of animals for orientation and migration via sensing and utilizing geomagnetic fields.Magnetoreceptor(MagR) and cryptochromes(Cry) have recently been identified as the basis for ...Magnetoreception is a hallmark ability of animals for orientation and migration via sensing and utilizing geomagnetic fields.Magnetoreceptor(MagR) and cryptochromes(Cry) have recently been identified as the basis for magnetoreception in Drosophila.However,it has remained unknown whether MagR and Cry have conserved roles in diverse animals.Here we report the identification and expression of magr and cry genes in the fish medaka(Oryzias latipes).Cloning and sequencing identified a single magr gene,four cry genes and one cry-like gene in medaka.By sequence alignment,chromosomal synteny and gene structure analysis,medaka cry2 and magr were found to be the orthologs of human Cry2 and Magr,with cry1 aa and crylab being coorthologs of human Cry1.Therefore,magr and cry2 have remained as single copy genes,whereas cry1 has undergone two rounds of gene duplication in medaka.Interestingly,magr and cry genes were detected in various stages throughout embryogenesis and displayed ubiquitous expression in adult organs rather than specific or preferential expression in neural organs such as brain and eye.Importantly,magr knockdown by morpholino did not produce visible abnormality in developing embryos,pointing to the possibility of producing viable magr knockouts in medaka as a vertebrate model for magnet biology.展开更多
文摘A 1 539 by squalene synthase (AaSQS) cDNA was cloned from a high-yield Artemisia annua L. strain 001 by reverse transcription-polymerise chain reaction (RT-PCR). The amino acid sequence of AaSQS is 70%, 77%, 44% and 39%a identical to that of squalene synthases from Arabidopsis thaliana, tobacco, human and yeast, respectively. The AaSQS genomic DNA has a complex organization containing 14 exons and 13 introns. Full-length or C-terminal truncated cDNA was subcloned into prokaryotic expression vector pET30a and the constructed plasmid was introduced to Escherichia coli strain BL21 (DE3) for induced overexpression. No squalene synthase protein with expected molecular mass was observed in E. cola containing the putative full-length squalene synthase cDNA, however, overexpression in E. coli was achieved by truncating 30 amino acids of hydrophobic region at the carboxy terminus.
基金Supported by National Natural Science Foundation of China (No.30370583)
文摘Objective: To establish a rabbit atrial fibrillation model with rapid atrial pacing (RAP) and investigate its ultrastructural changes and expressions of L-type calcium channel subunits and potassium channel Kv4. 3. Methods: Thirty-six rabbits were performed electrical stimulation through bipolar endo-cardial led by surgical technique. 600 beat per min from 0 to 48 h. Atrial ultrastructure was observed by transmission electron microscope (TEM) after different pacing times. mRNA were measured by reverse transcription-polymera.se chain reaction (RT-PCR). Results: Atrial ultrastructure had alteration after 3 hours' pacing, such as mitochondria vacuolization, myofilament lysis and glucogen aggregation. The mRNA of the Ca2+ channel β1 and α1 subunits began to decrease after pacing of 6 h. which were paralleled with the change of Kv4. 3 mRNA. But the auxiliary subunit α2 were not affected. Conclusion: Ultrastructural changes and mRNA levels of L-type calcium channel subunits and potassium channel Kv4. 3 are decreased after RAP. with a mechanism of transcriptional down-regulation of underlying ion channels due to calcium overloading after RAP.
文摘Objective:To establish a systematic framework for selecting the best clustering algorithm and provide an evaluation method for clustering analyses of gene expression data. Methods: Based on data structure (internal information) and function classification (external information), the evaluation of gene expression data analyses were carried out by using 2 approaches. Firstly, to assess the predictive power of clusteringalgorithms, Entropy was introduced to measure the consistency between the clustering results from different algorithms and the known and validated functional classifications. Secondly, a modified method of figure of merit (adjust-FOM) was used as internal assessment method. In this method, one clustering algorithm was used to analyze all data but one experimental condition, the remaining condition was used to assess the predictive power of the resulting clusters. This method was applied on 3 gene expression data sets (2 from the Lyer's Serum Data Sets, and 1 from the Ferea's Saccharomyces Cerevisiae Data Set). Results: A method based on entropy and figure of merit (FOM) was proposed to explore the results of the 3 data sets obtained by 6 different algorithms, SOM and Fuzzy clustering methods were confirmed to possess the highest ability to cluster. Conclusion: A method based on entropy is firstly brought forward to evaluate clustering analyses.Different results are attained in evaluating same data set due to different function classification. According to the curves of adjust_FOM and Entropy_FOM, SOM and Fuzzy clustering methods show the highest ability to cluster on the 3 data sets.
基金supported by the National Natural Science Foundation of China(31030026)the National Basic Research Program(2011CB-965203)the PUMC Youth funds(3332013138)
文摘Spatial expression patterns of homeobox （HOX） genes delineate positional identity of primary fibroblasts from different topo- graphic sites. The molecular mechanism underlying the establishing or maintaining of HOX gene expression pattern remains an attractive developmental issue to be addressed. Our previous work suggested a critical role of CTCF/cobesin-mediated high- er-order chromatin structure in RA-induced HOXA activation in human teratocarcinoma NT2/D1 cells. This study investigated the recruitment of CTCF and cohesin, and the higher-order chromatin structure of the HOXA locus in fetal lung and adult foreskin fibroblasts, which display complementary HOXA gene expression patterns. Chromatin contacts between the CTCF-binding sites were observed with lower frequency in human foreskin fibroblasts. This observation is consistent with the lower level of cohesin recruitment and 5＇ HOXA gene expression in the same cells. We also showed that CTCF-binding site A56 （CBSA56） related chromatin structures exhibit the most notable changes in between the two types of cell, and hence may stand for one of the key CTCF-binding sites for cell-type specific chromatin structure organization. Together, these results im- ply that CTCF/cohesin coordinates HOXA cluster higher-order chromatin structure and expression during development, and provide insight into the relationship between cell-type specific chromatin organization and the spatial collinearity.
基金supported by the National Research Foundation of Singapore(NRF-CRP7-2010-03)
文摘Magnetoreception is a hallmark ability of animals for orientation and migration via sensing and utilizing geomagnetic fields.Magnetoreceptor(MagR) and cryptochromes(Cry) have recently been identified as the basis for magnetoreception in Drosophila.However,it has remained unknown whether MagR and Cry have conserved roles in diverse animals.Here we report the identification and expression of magr and cry genes in the fish medaka(Oryzias latipes).Cloning and sequencing identified a single magr gene,four cry genes and one cry-like gene in medaka.By sequence alignment,chromosomal synteny and gene structure analysis,medaka cry2 and magr were found to be the orthologs of human Cry2 and Magr,with cry1 aa and crylab being coorthologs of human Cry1.Therefore,magr and cry2 have remained as single copy genes,whereas cry1 has undergone two rounds of gene duplication in medaka.Interestingly,magr and cry genes were detected in various stages throughout embryogenesis and displayed ubiquitous expression in adult organs rather than specific or preferential expression in neural organs such as brain and eye.Importantly,magr knockdown by morpholino did not produce visible abnormality in developing embryos,pointing to the possibility of producing viable magr knockouts in medaka as a vertebrate model for magnet biology.
