The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combinin...The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.展开更多
The ribosomal proteins are crucial for the maintenance of ribosomal translational efficiency and fidelity.In the study,we characterized the ribosomal protein S30(RPS30)gene from Arachis hypogaea that has been isolated...The ribosomal proteins are crucial for the maintenance of ribosomal translational efficiency and fidelity.In the study,we characterized the ribosomal protein S30(RPS30)gene from Arachis hypogaea that has been isolated through Genefishing analysis during defense responses to Ralstonia solanacearum.The cDNA of RPS 30 contained a 189 base pair(bp)open-reading frame encoding 62 amino acids.The genomic DNA consists of 272 bp containing two exons and one 83 bp intron.The RPS 30 mRNA transcript was mainly expressed in roots and leaves.The expression level of the RPS 30 mRNA transcripts was up-regulated sharply 6 h after bacterial challenge and was 12 times greater than that of the control group.The phylogenetic analysis for genes encoding proteins showed that RPS30 were conserved within dicotyledonous and monocotyledonous plants.d S extremely exceeded d N in all branches of the tree(d N/d S<1.0),indicating that functional constraint have acted on RPS 30 throughout evolution.展开更多
目的：研究核糖体蛋白S15a（ribosomal protein S15a RPS15a）基因在胃癌及癌旁组织中表达差异，为进一步了解胃癌发生、发展的分子机制提供帮助。方法应用荧光定量PCR等方法进一步验证该基因在胃癌及癌旁组织中的表达差异，并在多种肿...目的：研究核糖体蛋白S15a（ribosomal protein S15a RPS15a）基因在胃癌及癌旁组织中表达差异，为进一步了解胃癌发生、发展的分子机制提供帮助。方法应用荧光定量PCR等方法进一步验证该基因在胃癌及癌旁组织中的表达差异，并在多种肿瘤细胞中的表达量进行比较。结果该基因在胃癌组织中的表达量高于其对应的癌旁组织，但在多种肿瘤细胞中的表达量无显著差异。结论 RPS15a基因在胃癌中呈高表达，说明其可能与细胞恶性生物学行为相关。在多种肿瘤细胞中表达量无显著差异，推测其可能在恶性肿瘤中的高表达具有普遍性。展开更多
Different fused-core stationary phase chemistries（C18,Amide,Phenyl-hexyl and Peptide ES-C18） were used for the analysis of 21 structurally representative model peptides.In addition,the effects of the mobile phase co...Different fused-core stationary phase chemistries（C18,Amide,Phenyl-hexyl and Peptide ES-C18） were used for the analysis of 21 structurally representative model peptides.In addition,the effects of the mobile phase composition（ACN or MeOH as organic modifier;formic acid or acetic acid,as acidifying component） on the column selectivity,peak shape and overall chromatographic performance were evaluated.The RP-amide column,combined with a formic acid-acetonitrile based gradient system,performed as best.A peptide reversed-phase retention model is proposed,consisting of 5 variables：log SumAA,log Sv,clog P,log nHDon and log nHAcc.Quantitative structure-retention relationship（QSRR） models were constructed for 16 different chromatographic systems.The accuracy of this peptide retention model was demonstrated by the comparison between predicted and experimentally obtained retention times,explaining on average 86% of the variability.Moreover,using an external set of 5 validation peptides,the predictive power of the model was also demonstrated.This peptide retention model includes the novel in-silico calculated amino acid descriptor,AA,which was calculated from log P,3D-MoRSE,RDF and WHIM descriptors.展开更多
Ribosomally synthesized and post-translationally modified peptides(RiPPs)are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity.Recent advances in genomics and sy...Ribosomally synthesized and post-translationally modified peptides(RiPPs)are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity.Recent advances in genomics and synthetic biology,are facilitating us to discover a large number of new ribosomal natural products,including lanthipeptides,lasso peptides,sactipeptides,thiopeptides,microviridins,cyanobactins,linear thiazole/oxazole-containing peptides and so on.In this review,we summarize bioinformatic strategies that have been developed to identify and prioritize biosynthetic gene clusters(BGCs)encoding RiPPs,and the genome mining-guided discovery of novel RiPPs.We also prospectively provide a vision of what genomics-guided discovery of RiPPs may look like in the future,especially the discovery of RiPPs from dominant but uncultivated microbes,which will be promoted by the combinational use of synthetic biology and metagenome mining strategies.展开更多
基金supported by the National Natural Science Foundation of China(grantno.30670152)the National Infrastructure of Natural Resources for Science and Technology(grant no.2005DKA21403)the Natural Science Foundation of Hebei Province,China(no.C2008000158)
文摘The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.
基金Natural Science Funds for Young Scholar of Shandong Academy of Agricultural Sciences,China(No.2015YQN13)Natural Science Foundation of Shandong Province,China(ZR2015YL064)+2 种基金Qingdao Science and Technology Plan Basic Research Project,China(No.12-1-4-11-(1)-jch)China Agricultural Research System(No.CARS-13)Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(No.CXGC2018E21)
文摘The ribosomal proteins are crucial for the maintenance of ribosomal translational efficiency and fidelity.In the study,we characterized the ribosomal protein S30(RPS30)gene from Arachis hypogaea that has been isolated through Genefishing analysis during defense responses to Ralstonia solanacearum.The cDNA of RPS 30 contained a 189 base pair(bp)open-reading frame encoding 62 amino acids.The genomic DNA consists of 272 bp containing two exons and one 83 bp intron.The RPS 30 mRNA transcript was mainly expressed in roots and leaves.The expression level of the RPS 30 mRNA transcripts was up-regulated sharply 6 h after bacterial challenge and was 12 times greater than that of the control group.The phylogenetic analysis for genes encoding proteins showed that RPS30 were conserved within dicotyledonous and monocotyledonous plants.d S extremely exceeded d N in all branches of the tree(d N/d S<1.0),indicating that functional constraint have acted on RPS 30 throughout evolution.
文摘目的：研究核糖体蛋白S15a（ribosomal protein S15a RPS15a）基因在胃癌及癌旁组织中表达差异，为进一步了解胃癌发生、发展的分子机制提供帮助。方法应用荧光定量PCR等方法进一步验证该基因在胃癌及癌旁组织中的表达差异，并在多种肿瘤细胞中的表达量进行比较。结果该基因在胃癌组织中的表达量高于其对应的癌旁组织，但在多种肿瘤细胞中的表达量无显著差异。结论 RPS15a基因在胃癌中呈高表达，说明其可能与细胞恶性生物学行为相关。在多种肿瘤细胞中表达量无显著差异，推测其可能在恶性肿瘤中的高表达具有普遍性。
基金funded by a Ph.D.grant of "Institute for the Promotion of Innovation through Science and Technology in Flanders(IWT-Vlaanderen)"(No.091241 for MD and 073402 for SVD)the Special Research Fund of the Ghent University (Grant no.BOF 01J22510 for EW and BOF 01D38811 for SS)
文摘Different fused-core stationary phase chemistries（C18,Amide,Phenyl-hexyl and Peptide ES-C18） were used for the analysis of 21 structurally representative model peptides.In addition,the effects of the mobile phase composition（ACN or MeOH as organic modifier;formic acid or acetic acid,as acidifying component） on the column selectivity,peak shape and overall chromatographic performance were evaluated.The RP-amide column,combined with a formic acid-acetonitrile based gradient system,performed as best.A peptide reversed-phase retention model is proposed,consisting of 5 variables：log SumAA,log Sv,clog P,log nHDon and log nHAcc.Quantitative structure-retention relationship（QSRR） models were constructed for 16 different chromatographic systems.The accuracy of this peptide retention model was demonstrated by the comparison between predicted and experimentally obtained retention times,explaining on average 86% of the variability.Moreover,using an external set of 5 validation peptides,the predictive power of the model was also demonstrated.This peptide retention model includes the novel in-silico calculated amino acid descriptor,AA,which was calculated from log P,3D-MoRSE,RDF and WHIM descriptors.
基金Z.Zhong,B.He,and Y-X Li acknowledge a partial financial support from the National Key R&D Program of China(2018YFA0903200)Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)(SMSEGL20SC01)J.Li acknowledges a partial financial support by a National Institutes of Health(NIH)grant P20GM103641 and a National Science Foundation EPSCoR Program OIA-1655740.
文摘Ribosomally synthesized and post-translationally modified peptides(RiPPs)are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity.Recent advances in genomics and synthetic biology,are facilitating us to discover a large number of new ribosomal natural products,including lanthipeptides,lasso peptides,sactipeptides,thiopeptides,microviridins,cyanobactins,linear thiazole/oxazole-containing peptides and so on.In this review,we summarize bioinformatic strategies that have been developed to identify and prioritize biosynthetic gene clusters(BGCs)encoding RiPPs,and the genome mining-guided discovery of novel RiPPs.We also prospectively provide a vision of what genomics-guided discovery of RiPPs may look like in the future,especially the discovery of RiPPs from dominant but uncultivated microbes,which will be promoted by the combinational use of synthetic biology and metagenome mining strategies.
