Various active components have been extracted from the root of Polygonum cuspidatum.However,the genetic basis for their activity is virtually unknown.In this study,25600002 short reads (2.3 Gb) of P.cuspidatum root tr...Various active components have been extracted from the root of Polygonum cuspidatum.However,the genetic basis for their activity is virtually unknown.In this study,25600002 short reads (2.3 Gb) of P.cuspidatum root transcriptome were obtained via Illumina HiSeq 2000 sequencing.A total of 86418 unigenes were assembled de novo and annotated.Twelve,18,60 and 54 unigenes were respectively mapped to the mevalonic acid (MVA),methyl-D-erythritol 4-phosphate (MEP),shikimate and resveratrol biosynthesis pathways,suggesting that they are involved in the biosynthesis of pharmaceutically important anthraquinone and resveratrol.Eighteen potential UDP-glycosyltransferase unigenes were identified as the candidates most likely to be involved in the biosynthesis of glycosides of secondary metabolites.Identification of relevant genes could be important in eventually increasing the yields of the medicinally useful constituents of the P.cuspidatum root.From the previously published transcriptome data of 19 non-model plant taxa,1127 shared orthologs were identified and characterized.This information will be very useful for future functional,phylogenetic and evolutionary studies of these plants.展开更多
Clematis is a botanical source for various pharmaceutically active components,which has long been used in conventional medicine since the beginning of Chinese civilization.Increasing interest in Clematis medicinal res...Clematis is a botanical source for various pharmaceutically active components,which has long been used in conventional medicine since the beginning of Chinese civilization.Increasing interest in Clematis medicinal resources has led to additional discoveries of triterpenoid saponins,flavonoids,coumarins,alkaloids and many other compounds in various Clematis species,and to investigations on their chemotaxonomy,molecular phylogeny and pharmacology.In continuation with our studies on Clematis chemistry and biology,we review the chemistry,chemotaxonomy,molecular biology and phylogeny of Clematis and their relevance to drug efficacy and drug development.Various databases and technology have been used in literature search in order to characterize the global scientific effort.It is essential to study more species for both the sustainable utilization of Clematis medicinal resources and finding novel compounds with potential clinical utility.Systems biology and omics technologies will play an increasingly important role in future medicinal research involving bioactive compounds of Clematis.展开更多
Agilawood is a costly heartwood medicine obtained from Aquilaria sinensis with active ingredients mainly composed of volatile and semi-volatile substances. However, the formation time of agilawood is quite long and li...Agilawood is a costly heartwood medicine obtained from Aquilaria sinensis with active ingredients mainly composed of volatile and semi-volatile substances. However, the formation time of agilawood is quite long and little is known about its formation mechanism. Two highly active fungi obtained from natural agilawood were inoculated on A. sinensis trees to understand their interaction processes and elucidate the transformation rules of induced chemical compositions within different test periods. The results demonstrated that the fungi could successfully colonize living tissues and cells and activate the host defense system, resulting in agilawood accumulation. With increasing time, the main components of A. sinensis converted into constituents or analogs of agilawood and the host exhibited "self-injury" to prevent fungal intrusion and protect other tissues. The data presented here could provide scientific basis for producing agilawood with the two new fungi in a safe, feasible, and sustainable manner without destroying rare Aquilaria plants.展开更多
This study was carried out to understand and establish the changes in physicochemical properties of starch extracted from Chinese yam (Dioscorea opposita Thunb.) after acetylation. Yam starch acetates with different d...This study was carried out to understand and establish the changes in physicochemical properties of starch extracted from Chinese yam (Dioscorea opposita Thunb.) after acetylation. Yam starch acetates with different degrees of substitution (DS) were prepared by the reaction of yam starch with glacial acetic acid/acetic anhydride using sulfuric acid as the catalyst. Their formation was confirmed by the presence of the carbonyl signal around 1750 cm-1 in the Fourier transform infrared (FT-IR) spectra. The thermal behavior of the native starch and starch acetate were investigated using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The results reveal that the starch acetates are more thermally stable than the native starch. The starch esters showed 50% weight loss at tem- peratures from 328℃ to 372 ℃ , while the native starch underwent 50% weight loss at 325℃ . The glass transition temperature (Tg) of the starch decreased from 273℃ to 226℃. The X-ray diffraction (XRD) patterns could be classified as typical of the C-type for yam starch. X-ray diffraction also showed the loss of the ordered C-type starch crystalline structure and the degree of crystallinity of starch de- creased from 36.10% to 10.96% with the increasing DS. The scanning electron microscopy (SEM) sug- gested that the most of the starch granules disintegrated with many visible fragments with the in- creasing DS.展开更多
Nonsynonymous single nucleotide polymorphisms (nsSNPs) in coding regions can lead to amino acid changes that might alter the protein’s function and account for susceptibility to disease and altered drug/xenobiotic re...Nonsynonymous single nucleotide polymorphisms (nsSNPs) in coding regions can lead to amino acid changes that might alter the protein’s function and account for susceptibility to disease and altered drug/xenobiotic response. Many nsSNPs have been found in genes encoding human phase II metabolizing enzymes; however, there is little known about the relationship between the genotype and phenotype of nsSNPs in these enzymes. We have identified 923 validated nsSNPs in 104 human phase II enzyme genes from the Ensembl genome database and the NCBI SNP database. Using PolyPhen, Panther, and SNAP algorithms, 44%?59% of nsSNPs in phase II enzyme genes were predicted to have functional impacts on protein function. Predictions largely agree with the available experimental annotations. 68% of deleterious nsSNPs were correctly predicted as damaging. This study also identified many amino acids that are likely to be functionally critical, but have not yet been studied experimentally. There was significant concordance between the predicted results of Panther and PolyPhen, and between SNAP non-neutral predictions and PolyPhen scores. Evolutionarily non-neutral (destabilizing) amino acid substitutions are thought to be the pathogenetic basis for the alteration of phase II enzyme activity and to be associated with disease susceptibility and drug/xenobiotic toxicity. Furthermore, the molecular evolutionary patterns of phase II enzymes were characterized with regards to the predicted deleterious nsSNPs.展开更多
Flavin-containing monooxygenase (FMO), like cytochrome P450 (CYP), is a monooxygenase that uses the reducing equivalents of NADPH to reduce one atom of molecular oxygen to water, while the other atom is used to oxidiz...Flavin-containing monooxygenase (FMO), like cytochrome P450 (CYP), is a monooxygenase that uses the reducing equivalents of NADPH to reduce one atom of molecular oxygen to water, while the other atom is used to oxidize the substrate. Recently, it was shown that some CYP isoforms have been subject to positive selection. However, it is unknown whether the highly conserved phase I detoxification enzyme, FMO, has undergone similar positive Darwinian selection. We used maximum-likelihood models of codon substitution, evolutionary fingerprinting, and cross species comparison to investigate the occurrence of adaptive evolution in FMO sequences. We used recent genomic data from a range of species, including vertebrates and invertebrates. We present the evidence for the occurrence of adaptive evolution in mammalian FMO 3, 4, 5, and fugu FMOs but not in mammalian FMO 1, FMO 2, frog FMOs, other fish FMOs and invertebrate FMOs. The sites under adaptive evolution were significantly associated with the insertion domain in mammalian FMO 5. We identified specific amino acid sites in FMOs 3–5 that are likely targets for selection based on the patterns of parallel amino acid change. The most likely role of adaptive evolution is the repair of mutations that permitted optimal NADP+ binding and improved catalytic efficiency. The occurrence of positive selection during the evolution of phase I detoxification enzymes such as FMOs 3–5 and fugu FMO suggests the occurrence of both high selection pressure acting on species within their unique habitats and significant changes in intensity and direction (forms of xenobiotics and drugs) resulting from changes in microhabitat and food.展开更多
基金supported by the National Science and Technology Major Program (Grant No.2008ZX10005-004)
文摘Various active components have been extracted from the root of Polygonum cuspidatum.However,the genetic basis for their activity is virtually unknown.In this study,25600002 short reads (2.3 Gb) of P.cuspidatum root transcriptome were obtained via Illumina HiSeq 2000 sequencing.A total of 86418 unigenes were assembled de novo and annotated.Twelve,18,60 and 54 unigenes were respectively mapped to the mevalonic acid (MVA),methyl-D-erythritol 4-phosphate (MEP),shikimate and resveratrol biosynthesis pathways,suggesting that they are involved in the biosynthesis of pharmaceutically important anthraquinone and resveratrol.Eighteen potential UDP-glycosyltransferase unigenes were identified as the candidates most likely to be involved in the biosynthesis of glycosides of secondary metabolites.Identification of relevant genes could be important in eventually increasing the yields of the medicinally useful constituents of the P.cuspidatum root.From the previously published transcriptome data of 19 non-model plant taxa,1127 shared orthologs were identified and characterized.This information will be very useful for future functional,phylogenetic and evolutionary studies of these plants.
基金supported by Dalian Jiaotong University and Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine,Ministry of Education,China
文摘Clematis is a botanical source for various pharmaceutically active components,which has long been used in conventional medicine since the beginning of Chinese civilization.Increasing interest in Clematis medicinal resources has led to additional discoveries of triterpenoid saponins,flavonoids,coumarins,alkaloids and many other compounds in various Clematis species,and to investigations on their chemotaxonomy,molecular phylogeny and pharmacology.In continuation with our studies on Clematis chemistry and biology,we review the chemistry,chemotaxonomy,molecular biology and phylogeny of Clematis and their relevance to drug efficacy and drug development.Various databases and technology have been used in literature search in order to characterize the global scientific effort.It is essential to study more species for both the sustainable utilization of Clematis medicinal resources and finding novel compounds with potential clinical utility.Systems biology and omics technologies will play an increasingly important role in future medicinal research involving bioactive compounds of Clematis.
基金supported by the National Natural Science Foundation of China (31170016, 31270383)
文摘Agilawood is a costly heartwood medicine obtained from Aquilaria sinensis with active ingredients mainly composed of volatile and semi-volatile substances. However, the formation time of agilawood is quite long and little is known about its formation mechanism. Two highly active fungi obtained from natural agilawood were inoculated on A. sinensis trees to understand their interaction processes and elucidate the transformation rules of induced chemical compositions within different test periods. The results demonstrated that the fungi could successfully colonize living tissues and cells and activate the host defense system, resulting in agilawood accumulation. With increasing time, the main components of A. sinensis converted into constituents or analogs of agilawood and the host exhibited "self-injury" to prevent fungal intrusion and protect other tissues. The data presented here could provide scientific basis for producing agilawood with the two new fungi in a safe, feasible, and sustainable manner without destroying rare Aquilaria plants.
基金the funds for New Century Elite of Education Ministry (Grant No. E105001)the funds from the Tianjin Municipal Science and Technology Commis-sion (Grant No. 07JCZDJC05400)Natural Science Foundation of Tianjin Mu-nicipal (Grant No. 08JCZDJC15300)
文摘This study was carried out to understand and establish the changes in physicochemical properties of starch extracted from Chinese yam (Dioscorea opposita Thunb.) after acetylation. Yam starch acetates with different degrees of substitution (DS) were prepared by the reaction of yam starch with glacial acetic acid/acetic anhydride using sulfuric acid as the catalyst. Their formation was confirmed by the presence of the carbonyl signal around 1750 cm-1 in the Fourier transform infrared (FT-IR) spectra. The thermal behavior of the native starch and starch acetate were investigated using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The results reveal that the starch acetates are more thermally stable than the native starch. The starch esters showed 50% weight loss at tem- peratures from 328℃ to 372 ℃ , while the native starch underwent 50% weight loss at 325℃ . The glass transition temperature (Tg) of the starch decreased from 273℃ to 226℃. The X-ray diffraction (XRD) patterns could be classified as typical of the C-type for yam starch. X-ray diffraction also showed the loss of the ordered C-type starch crystalline structure and the degree of crystallinity of starch de- creased from 36.10% to 10.96% with the increasing DS. The scanning electron microscopy (SEM) sug- gested that the most of the starch granules disintegrated with many visible fragments with the in- creasing DS.
基金supported by the Major National Science and Technology Program (Grant No. 2008ZX10005-004)the Liaoning Education Depart-ment (Grant No. 2009A120)the China Postdoctoral Science Founda-tion (Grant Nos. 20080440019 and 200902069)
文摘Nonsynonymous single nucleotide polymorphisms (nsSNPs) in coding regions can lead to amino acid changes that might alter the protein’s function and account for susceptibility to disease and altered drug/xenobiotic response. Many nsSNPs have been found in genes encoding human phase II metabolizing enzymes; however, there is little known about the relationship between the genotype and phenotype of nsSNPs in these enzymes. We have identified 923 validated nsSNPs in 104 human phase II enzyme genes from the Ensembl genome database and the NCBI SNP database. Using PolyPhen, Panther, and SNAP algorithms, 44%?59% of nsSNPs in phase II enzyme genes were predicted to have functional impacts on protein function. Predictions largely agree with the available experimental annotations. 68% of deleterious nsSNPs were correctly predicted as damaging. This study also identified many amino acids that are likely to be functionally critical, but have not yet been studied experimentally. There was significant concordance between the predicted results of Panther and PolyPhen, and between SNAP non-neutral predictions and PolyPhen scores. Evolutionarily non-neutral (destabilizing) amino acid substitutions are thought to be the pathogenetic basis for the alteration of phase II enzyme activity and to be associated with disease susceptibility and drug/xenobiotic toxicity. Furthermore, the molecular evolutionary patterns of phase II enzymes were characterized with regards to the predicted deleterious nsSNPs.
基金supported by the National Science and Technology Major Project of the Ministry of Science and Technology of China (2008ZX10005-004)Educational Commission of Liaoning Province of China (2009A120)China Postdoctoral Science Foundation (20080440019 and 200902069)
文摘Flavin-containing monooxygenase (FMO), like cytochrome P450 (CYP), is a monooxygenase that uses the reducing equivalents of NADPH to reduce one atom of molecular oxygen to water, while the other atom is used to oxidize the substrate. Recently, it was shown that some CYP isoforms have been subject to positive selection. However, it is unknown whether the highly conserved phase I detoxification enzyme, FMO, has undergone similar positive Darwinian selection. We used maximum-likelihood models of codon substitution, evolutionary fingerprinting, and cross species comparison to investigate the occurrence of adaptive evolution in FMO sequences. We used recent genomic data from a range of species, including vertebrates and invertebrates. We present the evidence for the occurrence of adaptive evolution in mammalian FMO 3, 4, 5, and fugu FMOs but not in mammalian FMO 1, FMO 2, frog FMOs, other fish FMOs and invertebrate FMOs. The sites under adaptive evolution were significantly associated with the insertion domain in mammalian FMO 5. We identified specific amino acid sites in FMOs 3–5 that are likely targets for selection based on the patterns of parallel amino acid change. The most likely role of adaptive evolution is the repair of mutations that permitted optimal NADP+ binding and improved catalytic efficiency. The occurrence of positive selection during the evolution of phase I detoxification enzymes such as FMOs 3–5 and fugu FMO suggests the occurrence of both high selection pressure acting on species within their unique habitats and significant changes in intensity and direction (forms of xenobiotics and drugs) resulting from changes in microhabitat and food.
