G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming ...G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming and resource-intensive.The emergence of artificial intelligence(AI)methods has revolutionized the field of GPCR ligand discovery and has provided valuable tools for accelerating the identification and optimization of GPCR ligands.In this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific applications.First,the online resources that are instrumental in GPCR ligand discovery were summarized,including databases and repositories that contain valuable GPCR-related information and ligand data.Next,GPCR and ligand representation schemes that can convert data into computer-readable formats were introduced.Subsequently,the key applications of AI methods in the different stages of GPCR drug discovery were discussed,ranging from GPCR function prediction to ligand design and agonist identification.Furthermore,an AI-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was proposed.Finally,the challenges and future directions of the application of AI in GPCR research were deliberated.In conclusion,continued advancements in AI techniques coupled with interdisciplina ry collaborations will offer great potential for improving the efficiency of GPCR ligand discovery.展开更多
Urea generation through electrochemical CO_(2) and NO_(3)~-co-reduction reaction(CO_(2)NO_(3)RR)is still limited by either the low selectivity or yield rate of urea.Herein,we report copper carbonate hydroxide(Cu_2(OH)...Urea generation through electrochemical CO_(2) and NO_(3)~-co-reduction reaction(CO_(2)NO_(3)RR)is still limited by either the low selectivity or yield rate of urea.Herein,we report copper carbonate hydroxide(Cu_2(OH)_2CO_(3))as an efficient CO_(2)NO_(3)RR electrocatalyst with an impressive urea Faradaic efficiency of45.2%±2.1%and a high yield rate of 1564.5±145.2μg h~(-1)mg_(cat)~(-1).More importantly,H_(2) evolution is fully inhibited on this electrocatalyst over a wide potential range between-0.3 and-0.8 V versus reversible hydrogen electrode.Our thermodynamic simulation reveals that the first C-N coupling follows a unique pathway on Cu_2(OH)_2CO_(3) by combining the two intermediates,~*COOH and~*NHO.This work demonstrates that high selectivity and yield rate of urea can be simultaneously achieved on simple Cu-based electrocatalysts in CO_(2)NO_(3)RR,and provide guidance for rational design of more advanced catalysts.展开更多
Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases.However,the lack of genomic resources limits the insight into its evolutionary ...Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases.However,the lack of genomic resources limits the insight into its evolutionary and biological characterization.In the present work,we reported the P.tenuifolia genome,the first genome assembly of the Polygalaceae family.We sequenced and assembled this genome by a combination of Illumnina,PacBio HiFi,and Hi-C mapping.The assembly includes 19 pseudochromosomes covering∼92.68%of the assembled genome(∼769.62 Mb).There are 36463 protein-coding genes annotated in this genome.Detailed comparative genome anal-ysis revealed that P.tenuifolia experienced two rounds of whole genome duplication that occurred∼39–44 and∼18–20 million years ago,respectively.Accordingly,we systematically reconstructed ancestral chromosomes of P.tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species.Based on the transcriptomics data,enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P.tenuifolia were identified.Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families,which contributed to the synthesis of triterpenoid saponins.The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae,but also shed light on the synthesis of triterpenoid saponin.展开更多
Objective:This work aimed to report the first complete mitochondrial genome(mitogenome)of Rheum palmatum,summarize the features of Caryophyllales mitogenomes,and to reveal the potential of utilizing the mitogenomes of...Objective:This work aimed to report the first complete mitochondrial genome(mitogenome)of Rheum palmatum,summarize the features of Caryophyllales mitogenomes,and to reveal the potential of utilizing the mitogenomes of R.palmatum and other Caryophyllales species for inferring phylogenetic relationships and species identification.Methods:Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of R.palmatum.A variety of bioinformatics tools were employed to characterize the R.palmatum mitogenome,compare the reported mitogenomes in Caryophyllales and conduct phylogenetic analysis.Results:The mitogenome of R.palmatum was assembled into a single master circle of 302,993 bp,encoding 35 known protein-coding genes,18 transfer RNA genes,and three ribosome RNA genes.A total of 249 long repeats and 49 simple sequence repeats were identified in this mitogenome.The sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 Mb.Among them,23 mitogenomes were circular molecules,one was linear,and one consisted of relaxed circles,linear molecules,and supercoiled DNA.Out of the total mitogenomes,11 were single-chromosome structure,whereas the remaining 14 were multi-chromosomal organizations.The phylogenetic analysis is consistent with both the Engler system(1964)and the Angiosperm Phylogeny Group III system.Conclusions:We obtained the first mitogenome of R.palmatum,which consists of a master circle.Mitogenomes in Caryophyllales have variable genome sizes and structures even within the same species.Circular molecules are still the dominant pattern in Caryophyllales.Single-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales,in contrast to previous studies.It is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.展开更多
基金Natural Science Foundation of Sichuan(2023NSFSC0683)Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine(ZYYCXTD-D202209).
文摘G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming and resource-intensive.The emergence of artificial intelligence(AI)methods has revolutionized the field of GPCR ligand discovery and has provided valuable tools for accelerating the identification and optimization of GPCR ligands.In this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific applications.First,the online resources that are instrumental in GPCR ligand discovery were summarized,including databases and repositories that contain valuable GPCR-related information and ligand data.Next,GPCR and ligand representation schemes that can convert data into computer-readable formats were introduced.Subsequently,the key applications of AI methods in the different stages of GPCR drug discovery were discussed,ranging from GPCR function prediction to ligand design and agonist identification.Furthermore,an AI-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was proposed.Finally,the challenges and future directions of the application of AI in GPCR research were deliberated.In conclusion,continued advancements in AI techniques coupled with interdisciplina ry collaborations will offer great potential for improving the efficiency of GPCR ligand discovery.
基金supported by the Research Grants Council(26206115,16304821 and 16309418)the Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)(SMSEGL20SC01)+2 种基金the Innovation and Technology Commission(grant no.ITC-CNERC14EG03)of the Hong Kong Special Administrative Regionthe Hong Kong Postdoctoral Fellowship Scheme(HKUST PDFS2021-4S12 and HKUST PDFS2021-6S08)the support from the Shenzhen fundamental research funding(JCYJ20210324115809026,20200925154115001,JCYJ20200109141216566)。
文摘Urea generation through electrochemical CO_(2) and NO_(3)~-co-reduction reaction(CO_(2)NO_(3)RR)is still limited by either the low selectivity or yield rate of urea.Herein,we report copper carbonate hydroxide(Cu_2(OH)_2CO_(3))as an efficient CO_(2)NO_(3)RR electrocatalyst with an impressive urea Faradaic efficiency of45.2%±2.1%and a high yield rate of 1564.5±145.2μg h~(-1)mg_(cat)~(-1).More importantly,H_(2) evolution is fully inhibited on this electrocatalyst over a wide potential range between-0.3 and-0.8 V versus reversible hydrogen electrode.Our thermodynamic simulation reveals that the first C-N coupling follows a unique pathway on Cu_2(OH)_2CO_(3) by combining the two intermediates,~*COOH and~*NHO.This work demonstrates that high selectivity and yield rate of urea can be simultaneously achieved on simple Cu-based electrocatalysts in CO_(2)NO_(3)RR,and provide guidance for rational design of more advanced catalysts.
基金supported by the Natural Science Foundation of Sichuan(No.2023NSFSC0683)Innovation Team and Talents Cultivation Program of the National Administration of Traditional Chinese Medicine(No:ZYYCXTD-D-202209)the‘Xinglin Scholar’Discipline Talent Research Promotion Program of Chengdu University of TCM(No.MPRC2021036).
文摘Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases.However,the lack of genomic resources limits the insight into its evolutionary and biological characterization.In the present work,we reported the P.tenuifolia genome,the first genome assembly of the Polygalaceae family.We sequenced and assembled this genome by a combination of Illumnina,PacBio HiFi,and Hi-C mapping.The assembly includes 19 pseudochromosomes covering∼92.68%of the assembled genome(∼769.62 Mb).There are 36463 protein-coding genes annotated in this genome.Detailed comparative genome anal-ysis revealed that P.tenuifolia experienced two rounds of whole genome duplication that occurred∼39–44 and∼18–20 million years ago,respectively.Accordingly,we systematically reconstructed ancestral chromosomes of P.tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species.Based on the transcriptomics data,enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P.tenuifolia were identified.Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families,which contributed to the synthesis of triterpenoid saponins.The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae,but also shed light on the synthesis of triterpenoid saponin.
基金financially supported by the National Natural Science Foundation of China (81874339)Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (2022-I2M-1-018).
文摘Objective:This work aimed to report the first complete mitochondrial genome(mitogenome)of Rheum palmatum,summarize the features of Caryophyllales mitogenomes,and to reveal the potential of utilizing the mitogenomes of R.palmatum and other Caryophyllales species for inferring phylogenetic relationships and species identification.Methods:Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of R.palmatum.A variety of bioinformatics tools were employed to characterize the R.palmatum mitogenome,compare the reported mitogenomes in Caryophyllales and conduct phylogenetic analysis.Results:The mitogenome of R.palmatum was assembled into a single master circle of 302,993 bp,encoding 35 known protein-coding genes,18 transfer RNA genes,and three ribosome RNA genes.A total of 249 long repeats and 49 simple sequence repeats were identified in this mitogenome.The sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 Mb.Among them,23 mitogenomes were circular molecules,one was linear,and one consisted of relaxed circles,linear molecules,and supercoiled DNA.Out of the total mitogenomes,11 were single-chromosome structure,whereas the remaining 14 were multi-chromosomal organizations.The phylogenetic analysis is consistent with both the Engler system(1964)and the Angiosperm Phylogeny Group III system.Conclusions:We obtained the first mitogenome of R.palmatum,which consists of a master circle.Mitogenomes in Caryophyllales have variable genome sizes and structures even within the same species.Circular molecules are still the dominant pattern in Caryophyllales.Single-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales,in contrast to previous studies.It is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.
