AIM:To investigate the variability of the main immunodominant motifs of hepatitis B virus(HBV) core gene by ultra-deep-pyrosequencing(UDPS).METHODS:Four samples(2 genotype A and 2 genotype D) from 4 treatment-na ve pa...AIM:To investigate the variability of the main immunodominant motifs of hepatitis B virus(HBV) core gene by ultra-deep-pyrosequencing(UDPS).METHODS:Four samples(2 genotype A and 2 genotype D) from 4 treatment-na ve patients were assessed for baseline variability.Two additional samples from one patient(patient 4,genotype D) were selected for analysis:one sample corresponded to a 36-mo treatment-free period from baseline and the other to the time of viral breakthrough after 18 mo of lamivudine treatment.The HBV region analyzed covered amino acids 40 to 95 of the core gene,and included the two main epitopic regions,Th50-69 and B74-84.UDPS was carried out in the Genome Sequencer FLX system(454 Life Sciences,Roche).After computer filtering of UDPS data based on a Poisson statistical model,122 813 sequences were analyzed.The most conserved position detected by UDPS was analyzed by site-directed mutagenesis and evaluated in cell culture.RESULTS:Positions with highest variability rates were mainly located in the main core epitopes,confirming their role as immune-stimulating regions.In addition,the distribution of variability showed a relationship with HBV genotype.Patient 1(genotype A) presented the lowest variability rates and patient 2(genotype A) had 3 codons with variability higher than 1%.Patient 3 and 4(both genotype D) presented 5 and 8 codons with variability higher than 1%,respectively.The median baseline frequencies showed that genotype A samples had higher variability in epitopic positions than in the other positions analyzed,approaching significance(P = 0.07,sample 1 and P = 0.05,sample 2).In contrast,there were no significant differences in variability between the epitopic and other positions in genotype D cases.Interestingly,patient 1 presented a completely mutated motif from amino acid 64 to 67(E 64 LMT 67),which is commonly recognized by T helper cells.Additionally,the variability observed in all 4 patients was particularly associated with the E 64 LMT 67 motif.Codons 78 and 79 were highly conserved in all samples,in keeping with their involvement in the interaction between the HBV virion capsid and the surface antigens(HBsAg).Of note,codon 76 was even more conserved than codons 78 and 79,suggesting a possible role in HBsAg interactions or even in hepatitis B e antigen conformation.Sequential analysis of samples from patient 4(genotype D) illustrated the dynamism of the HBV quasispecies,with strong selection of one minor baseline variant coinciding with a decrease in core variability during the treatment-free and lamivudinetreated period.The drop in variability seemed to result from a "steady state" situation of the HBV quasispecies after selection of the variant with greatest fitness.CONCLUSION:Host immune pressure seems to be the main cause of HBV core evolution.UDPS analysis is a useful technique for studying viral quasispecies.展开更多
As a good method to solve the problem of high methane on the workface and inthe goaf,drawing coal strata methane through a surface borehole is used.However,theexcavation affected the overlying rock strata greatly.When...As a good method to solve the problem of high methane on the workface and inthe goaf,drawing coal strata methane through a surface borehole is used.However,theexcavation affected the overlying rock strata greatly.When the excavation face passedthrough the surface borehole position,the surface borehole fractures fast.This problemwas seriously related to the unformed squeeze effect.Therefore,a squeezing deformationfracture model based on the rock strata squeezing effect was set up.At the same time,a3DEC simulation model is presented to confirm the theory.The result shows that the modelis reliable and has a good engineering application value.展开更多
Using first-principles calculations, we studied the interaction of methanol with the Pt（100） surface based on generalized gradient approximation. We found that top sites of Pt（100） surface are the favored adsorpti...Using first-principles calculations, we studied the interaction of methanol with the Pt（100） surface based on generalized gradient approximation. We found that top sites of Pt（100） surface are the favored adsorptive positions in energy, and methanol molecule interacts with the Pt surface through oxygen atoms. Moreover, we also explored the possible dissociation pathways of methanol on the Pt surface, and suggested that the products of dissociation can be controlled by the external manipulation.展开更多
基金Supported by A Grant from the Spanish Ministry of Health and Consumer Affairs,No. FIS PS09/00899 and SAF 2009-10403CIBERehd Funded by Instituto CarlosⅢ,Ministry of Health and Consumer Affairs
文摘AIM:To investigate the variability of the main immunodominant motifs of hepatitis B virus(HBV) core gene by ultra-deep-pyrosequencing(UDPS).METHODS:Four samples(2 genotype A and 2 genotype D) from 4 treatment-na ve patients were assessed for baseline variability.Two additional samples from one patient(patient 4,genotype D) were selected for analysis:one sample corresponded to a 36-mo treatment-free period from baseline and the other to the time of viral breakthrough after 18 mo of lamivudine treatment.The HBV region analyzed covered amino acids 40 to 95 of the core gene,and included the two main epitopic regions,Th50-69 and B74-84.UDPS was carried out in the Genome Sequencer FLX system(454 Life Sciences,Roche).After computer filtering of UDPS data based on a Poisson statistical model,122 813 sequences were analyzed.The most conserved position detected by UDPS was analyzed by site-directed mutagenesis and evaluated in cell culture.RESULTS:Positions with highest variability rates were mainly located in the main core epitopes,confirming their role as immune-stimulating regions.In addition,the distribution of variability showed a relationship with HBV genotype.Patient 1(genotype A) presented the lowest variability rates and patient 2(genotype A) had 3 codons with variability higher than 1%.Patient 3 and 4(both genotype D) presented 5 and 8 codons with variability higher than 1%,respectively.The median baseline frequencies showed that genotype A samples had higher variability in epitopic positions than in the other positions analyzed,approaching significance(P = 0.07,sample 1 and P = 0.05,sample 2).In contrast,there were no significant differences in variability between the epitopic and other positions in genotype D cases.Interestingly,patient 1 presented a completely mutated motif from amino acid 64 to 67(E 64 LMT 67),which is commonly recognized by T helper cells.Additionally,the variability observed in all 4 patients was particularly associated with the E 64 LMT 67 motif.Codons 78 and 79 were highly conserved in all samples,in keeping with their involvement in the interaction between the HBV virion capsid and the surface antigens(HBsAg).Of note,codon 76 was even more conserved than codons 78 and 79,suggesting a possible role in HBsAg interactions or even in hepatitis B e antigen conformation.Sequential analysis of samples from patient 4(genotype D) illustrated the dynamism of the HBV quasispecies,with strong selection of one minor baseline variant coinciding with a decrease in core variability during the treatment-free and lamivudinetreated period.The drop in variability seemed to result from a "steady state" situation of the HBV quasispecies after selection of the variant with greatest fitness.CONCLUSION:Host immune pressure seems to be the main cause of HBV core evolution.UDPS analysis is a useful technique for studying viral quasispecies.
基金Supported by the National Great Research Foundation of China(973)(2005CB221504)the National Natural Science Foundation of China(50534080)the National Key Technology R&D Program(2006BAK03B03)
文摘As a good method to solve the problem of high methane on the workface and inthe goaf,drawing coal strata methane through a surface borehole is used.However,theexcavation affected the overlying rock strata greatly.When the excavation face passedthrough the surface borehole position,the surface borehole fractures fast.This problemwas seriously related to the unformed squeeze effect.Therefore,a squeezing deformationfracture model based on the rock strata squeezing effect was set up.At the same time,a3DEC simulation model is presented to confirm the theory.The result shows that the modelis reliable and has a good engineering application value.
文摘Using first-principles calculations, we studied the interaction of methanol with the Pt（100） surface based on generalized gradient approximation. We found that top sites of Pt（100） surface are the favored adsorptive positions in energy, and methanol molecule interacts with the Pt surface through oxygen atoms. Moreover, we also explored the possible dissociation pathways of methanol on the Pt surface, and suggested that the products of dissociation can be controlled by the external manipulation.
