The gene sod in Acidithiobacillusferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria...The gene sod in Acidithiobacillusferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria, a three-dimensional （3D） molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues were identified and spatially clustered. Among them, the residues of Asn38, Glyl03 and Glul61 are randomly scattered throughout the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding and catalytic function.展开更多
AIM： To investigate the expression and significance of caudal-related homeobox transcription factor （Cdx2） in gastric carcinoma （GC） and precancerous lesions. METHODS： The expression of Cdx2 in GC, precancer- ou...AIM： To investigate the expression and significance of caudal-related homeobox transcription factor （Cdx2） in gastric carcinoma （GC） and precancerous lesions. METHODS： The expression of Cdx2 in GC, precancer- ous lesions and normal gastric mucosa were detected using immunohistochemical method. Hematoxylin and eosin staining, alcian blue/periodic acid-schiff and high iron diamine/alcian blue staining were used to classify intestinal metaplasia （IM） and GC. RESULTS： Cdx2 was not detected in normal gas- tric mucosa. Cdx2 expression was detected in 87.1% （101/116） of IM, 50% （36/72） of dysplasia and 48.2% （41/85） of GC. The Cdx2-expressing cells in IM were more prevalent than in dysplasia and carcinoma （P 〈 0.05）. There was no relationship between Cdx2 ex- pression and the classification of IM or the degree of dysplasia. Expression of Cdx2 was significantly higher in intestinal-type carcinoma than in diffuse and mixed- type carcinoma （P 〈 0.05）. Positive expression of Cdx2was mainly found in moderately to well differentiated GC. There was a negative association between nuclear Cdx2 expression and lymph node metastasis and tumor, nodes, metastasis stage of GC （P 〈 0.05）. The patients with Cdx2-positive expression showed a higher survival rate than those with Cdx2-negative expression （P = 0.038）. Multivariate analysis revealed that the expres- sion of Cdx2 and lymph node metastasis were indepen- dent prognostic indicators of GC （P 〈 0.05）.展开更多
DNA methylation plays a vital role in the regulation of gene expression in response to environmental stress. However, little is known about the effect of DNA methylation on the cassava polyploidy. In the present study...DNA methylation plays a vital role in the regulation of gene expression in response to environmental stress. However, little is known about the effect of DNA methylation on the cassava polyploidy. In the present study, methylation-sensitive amplified polymorphisms （MSAP） were used to investigate DNA methylation profiles of cassava polyploidy following cold treatment to identify candidate genes involved in response to cold stress. The result showed that the genome-wide DNA methylation polymorphisms accounted for 34.02%-42.56% in SC8 and its autotetraploid exposed to 5 ~C for 2, 8, 24 and 48 h, respectively. The methylation levels of SC8 at 2 h-cold stress were the highest during 48h under cold treatments. With the time extension within 48 h under cold stress, the methylation levels gradually decreased to the same level as the control but DNA methylation levels of cassava autotetraploid were stable within 48 h. For future analysis of the methylation extent, the cold stress induced more DNA methylation than demethylation in SC8, where DNA methylation was consistent with demethylation in its autotetraploid. The expression analysis demonstrated increase in the transcription of one methylated gene and decrease in the transcription of two demethylated genes. The results revealed that gene methylations in specific sites would be a rapidly epigenetic response to cold stress, further elucidating the methylation functions in its autotetraploid.展开更多
Rad51/RadA paralogs found in eukaryotes and euryarchaea play important roles during recombination and repair,and mutations in one of the human Rad51 paralogs,Rad51C,are associated with breast and ovarian cancers.The h...Rad51/RadA paralogs found in eukaryotes and euryarchaea play important roles during recombination and repair,and mutations in one of the human Rad51 paralogs,Rad51C,are associated with breast and ovarian cancers.The hyperthermophilic crenarchaeon Sulfolobus tokodaii encodes four putative RadA paralogs and studies on these proteins may assist in understanding the functions of human Rad51 paralogs.Here,we report the biochemical characterization of stRadC2,a S.tokodaii RadA paralog.Pull-down assays revealed that the protein was able to interact with the recombinase,RadA,and the Holliday junction endonuclease,Hjc.stRadC2 inhibited the strand exchange activity of RadA and facilitated Hjc-mediated Holliday junction DNA cleavage in vitro.RT-PCR analysis revealed that stRadC2 transcription was immediately reduced after UV irradiation,but was restored to normal levels at the late stages of DNA repair.Our results suggest that stRadC2 may act as an anti-recombination factor in DNA recombinational repair in S.tokodaii.展开更多
基金Project(2004CB619201) supported by the National Basic Research Program of ChinaProject (50321402) supported by the National Natural Science Foundation of China
文摘The gene sod in Acidithiobacillusferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria, a three-dimensional （3D） molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues were identified and spatially clustered. Among them, the residues of Asn38, Glyl03 and Glul61 are randomly scattered throughout the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding and catalytic function.
基金Supported by The Natural Science Foundation of Anhui Province,No. 090413118
文摘AIM： To investigate the expression and significance of caudal-related homeobox transcription factor （Cdx2） in gastric carcinoma （GC） and precancerous lesions. METHODS： The expression of Cdx2 in GC, precancer- ous lesions and normal gastric mucosa were detected using immunohistochemical method. Hematoxylin and eosin staining, alcian blue/periodic acid-schiff and high iron diamine/alcian blue staining were used to classify intestinal metaplasia （IM） and GC. RESULTS： Cdx2 was not detected in normal gas- tric mucosa. Cdx2 expression was detected in 87.1% （101/116） of IM, 50% （36/72） of dysplasia and 48.2% （41/85） of GC. The Cdx2-expressing cells in IM were more prevalent than in dysplasia and carcinoma （P 〈 0.05）. There was no relationship between Cdx2 ex- pression and the classification of IM or the degree of dysplasia. Expression of Cdx2 was significantly higher in intestinal-type carcinoma than in diffuse and mixed- type carcinoma （P 〈 0.05）. Positive expression of Cdx2was mainly found in moderately to well differentiated GC. There was a negative association between nuclear Cdx2 expression and lymph node metastasis and tumor, nodes, metastasis stage of GC （P 〈 0.05）. The patients with Cdx2-positive expression showed a higher survival rate than those with Cdx2-negative expression （P = 0.038）. Multivariate analysis revealed that the expres- sion of Cdx2 and lymph node metastasis were indepen- dent prognostic indicators of GC （P 〈 0.05）.
文摘DNA methylation plays a vital role in the regulation of gene expression in response to environmental stress. However, little is known about the effect of DNA methylation on the cassava polyploidy. In the present study, methylation-sensitive amplified polymorphisms （MSAP） were used to investigate DNA methylation profiles of cassava polyploidy following cold treatment to identify candidate genes involved in response to cold stress. The result showed that the genome-wide DNA methylation polymorphisms accounted for 34.02%-42.56% in SC8 and its autotetraploid exposed to 5 ~C for 2, 8, 24 and 48 h, respectively. The methylation levels of SC8 at 2 h-cold stress were the highest during 48h under cold treatments. With the time extension within 48 h under cold stress, the methylation levels gradually decreased to the same level as the control but DNA methylation levels of cassava autotetraploid were stable within 48 h. For future analysis of the methylation extent, the cold stress induced more DNA methylation than demethylation in SC8, where DNA methylation was consistent with demethylation in its autotetraploid. The expression analysis demonstrated increase in the transcription of one methylated gene and decrease in the transcription of two demethylated genes. The results revealed that gene methylations in specific sites would be a rapidly epigenetic response to cold stress, further elucidating the methylation functions in its autotetraploid.
基金supported by the National Natural Science Foundation of China (Grant Nos. 3093002 and 30870046 to Shen YuLong,and 30700011 to Sheng DuoHong)the Promotive Research Fund for Excellent Young and Middle-aged Scientists of Shandong Province (Grant No. BS2010SW014 to Sheng DuoHong)
文摘Rad51/RadA paralogs found in eukaryotes and euryarchaea play important roles during recombination and repair,and mutations in one of the human Rad51 paralogs,Rad51C,are associated with breast and ovarian cancers.The hyperthermophilic crenarchaeon Sulfolobus tokodaii encodes four putative RadA paralogs and studies on these proteins may assist in understanding the functions of human Rad51 paralogs.Here,we report the biochemical characterization of stRadC2,a S.tokodaii RadA paralog.Pull-down assays revealed that the protein was able to interact with the recombinase,RadA,and the Holliday junction endonuclease,Hjc.stRadC2 inhibited the strand exchange activity of RadA and facilitated Hjc-mediated Holliday junction DNA cleavage in vitro.RT-PCR analysis revealed that stRadC2 transcription was immediately reduced after UV irradiation,but was restored to normal levels at the late stages of DNA repair.Our results suggest that stRadC2 may act as an anti-recombination factor in DNA recombinational repair in S.tokodaii.
