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
The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(t...The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(the relative)transcription-activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of operons.One complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies.A quantitative model has been developed that captures this information,which tends to be minimized by the current global arrangement of operons in a bacterial(and archaeal)genome compared to possible alternative arrangements.A study is carried out here using this model on a collection of 52 closely related Escherichia coli genomes,which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the(relative)genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change,to maintain the above energy-efficiency property.More specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes(and operons)encoding specific pathways across different genomes.展开更多
Transcriptome profiling has been widely used to analyze transcdptomic variation in plants subjected to abiotic or biotic stresses. Although gene expression changes induced by methyl jasmonate （MeJA） have been profil...Transcriptome profiling has been widely used to analyze transcdptomic variation in plants subjected to abiotic or biotic stresses. Although gene expression changes induced by methyl jasmonate （MeJA） have been profiled in several plant species, no information is available on the MeJA-triggered transcriptome response of Polygonum multiflorum Thunb., a species with highly valuable medicinal properties. In this study, we used transcriptome profiling to investigate transcdptome changes in roots of P. mu/tiflorum seedlings subjected to a 0.25 mmol/L-MeJA rootirrigation treatment. A total of 18 677 differentially expressed genes （DEGs） were induced by MeJA treatment, of which 4535 were up-regulated and 14 142 were down-ragulated compared with controls. These DEGs were associated with 125 metabolic pathways. In addition to various common primary and secondary metabolic pathways, several sec- ondary metabolic pathways related to components with significant pharmacological effects were enriched by MeJA, including arachidonic acid metabolism, linoleic acid metabolism, and stilbenoid biosynthesis. The MeJA-induced transcdptome changes uncovered in this study provide a solid foundation for future study of functional genes controlling effective components in secondary metabolic pathways of P. multiflorum.展开更多
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）.
基金supported in part by National Science Foundation (#NSF DEB-0830024 and NSF MCB-0958172)the US Department of Energy’s BioEnergy Science Center grant through the Office of Biological and Environmental Research+1 种基金The BioEnergy Science Center is a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of ScienceFunding for open access charge: US Department of Energy’s BioEnergy Science Center
文摘The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they are.We have previously discovered that(the relative)transcription-activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of operons.One complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies.A quantitative model has been developed that captures this information,which tends to be minimized by the current global arrangement of operons in a bacterial(and archaeal)genome compared to possible alternative arrangements.A study is carried out here using this model on a collection of 52 closely related Escherichia coli genomes,which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the(relative)genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change,to maintain the above energy-efficiency property.More specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes(and operons)encoding specific pathways across different genomes.
基金supported by the Double-Support Plan of Sichuan Agricultural University(No.03570313),China
文摘Transcriptome profiling has been widely used to analyze transcdptomic variation in plants subjected to abiotic or biotic stresses. Although gene expression changes induced by methyl jasmonate （MeJA） have been profiled in several plant species, no information is available on the MeJA-triggered transcriptome response of Polygonum multiflorum Thunb., a species with highly valuable medicinal properties. In this study, we used transcriptome profiling to investigate transcdptome changes in roots of P. mu/tiflorum seedlings subjected to a 0.25 mmol/L-MeJA rootirrigation treatment. A total of 18 677 differentially expressed genes （DEGs） were induced by MeJA treatment, of which 4535 were up-regulated and 14 142 were down-ragulated compared with controls. These DEGs were associated with 125 metabolic pathways. In addition to various common primary and secondary metabolic pathways, several sec- ondary metabolic pathways related to components with significant pharmacological effects were enriched by MeJA, including arachidonic acid metabolism, linoleic acid metabolism, and stilbenoid biosynthesis. The MeJA-induced transcdptome changes uncovered in this study provide a solid foundation for future study of functional genes controlling effective components in secondary metabolic pathways of P. multiflorum.
