The safety of traditional Chinese medicine(TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products ha...The safety of traditional Chinese medicine(TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the ‘bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.展开更多
For the protection of consumers and developments of relevant industry, authentication of medicinal plants is a critical issue. This review covers various aspects of authentication methods and techniques based on molec...For the protection of consumers and developments of relevant industry, authentication of medicinal plants is a critical issue. This review covers various aspects of authentication methods and techniques based on molecular biology and genomics with special emphasis on molecular biology techniques including genome-based authentication, microchip-based authentication, DNA barcoding, and their applications.展开更多
Central to the core principle of cell theory,depicting cells'history,state and fate is a fundamental goal in modern biology.By leveraging clonal analysis and sin-gle-cell RNA-seq technologies,single-cell lineage t...Central to the core principle of cell theory,depicting cells'history,state and fate is a fundamental goal in modern biology.By leveraging clonal analysis and sin-gle-cell RNA-seq technologies,single-cell lineage trac-ing provides new opportunities to interrogate both cell states and lineage histories.During the past few years,many strategies to achieve lineage tracing at single-cell resolution have been developed,and three of them(in-tegration barcodes,polylox barcodes,and CRISPR barcodes)are noteworthy as they are amenable in experimentally tractable systems.Although the above strategies have been demonstrated in animal develop-ment and stem cell research,much care and effort are still required to implement these methods.Here we review the development of single-cell lineage tracing,major characteristics of the cell barcoding strategies,applications,as well as technical considerations and limitations,providing a guide to choose or improve the single-cell barcoding lineage tracing.展开更多
Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy.Accurate species quantification remains challenging,as current methods often yield in...Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy.Accurate species quantification remains challenging,as current methods often yield inconsistent results.This study introduces a novel pyrosequencing-based technique,termed herb molecular quantification(Herb-Q),designed to precisely quantify herbal products.We evaluated its effectiveness using Pinellia ternata and five of its adulterants.Initially,we assessed commonly used DNA barcodes with sequences from a public database,identifying two candidate regions,Maturase K(matK)and internal transcribed spacer 2(ITS2),for screening specific single nucleotide polymorphism(SNP)loci,allowing for species-specific identification.These loci were validated by amplifying and sequencing genomic material from collected samples.Our validation studies showed that Herb-Q demonstrated excellent linearity,accuracy,repeatability,and detection limits.We established quantitative standard curves with high R^(2)values(>0.99)to enable precise species quantification,which were combined with external standards to provide clear and accurate visual quantification results.The average bias in quantifying the tuber of P.ternata was 2.38%,confirming that Herb-Q can accurately identify and quantify herbal product constituents.Moreover,the entire quantification process took less than 4 h.This study presents a novel,rapid method for accurately quantifying species in herbal products and advances the application of DNA barcoding from species identification to quantitative detection.展开更多
Micro/nanoscale photonic barcodes hold great potential for broad applications in items tracking,mul-tiplexed bioassays and anti-counterfeiting.The ever-increasing demand in advanced anti-counterfeiting applications ca...Micro/nanoscale photonic barcodes hold great potential for broad applications in items tracking,mul-tiplexed bioassays and anti-counterfeiting.The ever-increasing demand in advanced anti-counterfeiting applications calls for micro/nanoscale barcodes with accurate recognition,large encoding capacity and high security level.Here,we proposed a strategy to construct the dual-stimuli responsive photonic barcodes based on the perovskite quantum dots(PQDs)doped polymer whispering-gallery-mode(WGM)microcavities via swelling-deswelling method.Benefiting from the well-defined spherical microcavities,the photoluminescence(PL)spectra of as-prepared composites exhibit a series of sharp peaks characteristics resulting from the effective WGM modulation,which constitutes the fingerprint of a specific resonator and thus allows a definition of photonic barcodes.On this basis,we achieved responsive photonic barcodes based on the volatile polar-solvent-controlled luminescence in the mi-crospheres benefitting from the space-confined microcavities and the ionic feature of the PQDs.More-over,the light-controlled photonic barcodes have further been acquired through reversibly regulating the inactivation and activation of the energy transfer(ET)process between the PQDs and photochromic dyes.The well-established protocols of PQDs@WGM enable the development of distinct responsive barcodes with multi-responsive features,which will pave an avenue to new types of flexible WGM-based components for optical data recording and security labels.展开更多
Molecular markers provide a useful method for genotype characterization and allow a high precision determination of the genetic relationship between cultivars and varieties. A system based on DNA sequences—which is k...Molecular markers provide a useful method for genotype characterization and allow a high precision determination of the genetic relationship between cultivars and varieties. A system based on DNA sequences—which is known as DNA barcoding—will choose one or several standard loci which can be sequenced and compared to differentiate between species. In this research, the ITS, matK, and trnH-psbA sequences were evaluated for the molecular identification of seven F. carica genotypes, generating complete sequences for the first two loci, but unable to produce bidirectional sequences by using the trnH-psbA sequence. The ITS sequence presented the highest variation rates, while the phylogeny constructed with the matK sequence obtained the highest percentage of solved monophyletic groups. Through Pearson’s correlation analysis, it was possible to determine the existence of a significant correlation between the ITS region and psbA-trnH, and the matK and psbA-trnH sequences, but not between ITS and matK. The phylogenies constructed with the ITS + matK barcodes and ITS + matK + psbA-trnH presented the highest percentage for resolution. However, considering the cost efficiency and the facilitated recovery by using PCR, the matK + ITS combination is recommended.展开更多
Deploying and Implementing RFID Systems for tracking and controlling products in supply chain management is not affordable for small and midsized companies due to its complexity, cost, and difficulties pertaining data...Deploying and Implementing RFID Systems for tracking and controlling products in supply chain management is not affordable for small and midsized companies due to its complexity, cost, and difficulties pertaining data management and maintenance. Cloud computing can be used to mitigate the risks associated with the implementation and deployment of RFID based on system in supply chain management because the complex system for data filtering, management and maintenance can be implemented on the cloud that otherwise requires the purchase of new hardware, staff and professional services.展开更多
To determine the role of mitochondrial COⅠgene in classification and identification of species,a total of 39 single individuals from nine species pertaining to two genera of Cynoglossidae in the Yangtze Estuary were ...To determine the role of mitochondrial COⅠgene in classification and identification of species,a total of 39 single individuals from nine species pertaining to two genera of Cynoglossidae in the Yangtze Estuary were barcoded by COⅠ,sequenced and compared with that of other Cynoglossidae species recorded in the Gen Bank. Total genomic DNA was extracted from each scale sample using the classic phenol / chloroform extraction method. Six hundred and fifty base pairs( bp)COⅠfragments were amplified using the primers ’i. e. ’ F1: 5’- TCA ACC AAC CAC AAA GAC ATT GGC AC- 3’,R1: 5’- TAG ACT TCT GGG TGG CCA AAG AAT CA- 3’. Every PCR amplification was performed in a total volume of 50 μL of PCR mixture. PCR products were purified and then sequenced in both forward and reverse directions using an ABI PRISMTM 3730 XL Automated Sequencer. DNA sequences were aligned with clustal W using default parameters. Base composition,variable and parsimony informative sites were determined using MEGA 5. 0. Neighbor- joining( NJ) and Maximum parsimony( MP) phylogenetic trees were constructed for COⅠhaplotypes( Kimura 2 Parameter substitution model,K2P; 1 000 bootstraps pseudoreplications) using MEGA 5. 0. Using the MEGA5. 0 software for statistical analysis,the averaged AT content was greater than the GC content( Tab. 2). The GC content of codon position 1 averaged 53. 8%( 51. 8%-57. 3%),which of position 2 for 42. 0%,and that of position 3 ranged from 28. 1% to 37. 8% in average of 32. 4%( Tab. 4). The transitional pairs( si) was slightly more than the transversional pairs( sv),and the ratio( R = si/sv) was 1. 45( Tab. 3). Analysis of the frequency of amino acids in COⅠgene encoding protein showed that the highest frequency of amino acid was leucine,and the lowest frequency of amino acid was tryptophan( Tab. 5). The average K2 P distances pairwise-species and within-species were 0. 191 and 0. 003,respectively( Tab. 6). The K2 P distance pairwise-species was 63. 7 times of that within-species. According to the MP and展开更多
Three newly recorded species in the order Acerentomata in Protura from China are described:Filientomon duodecimsetosum Nakamura,2004,Verrucoentomon anatoli Shrubovych & Bernard,2012 and Verrucoentomon louisanne Sh...Three newly recorded species in the order Acerentomata in Protura from China are described:Filientomon duodecimsetosum Nakamura,2004,Verrucoentomon anatoli Shrubovych & Bernard,2012 and Verrucoentomon louisanne Shrubovych & Bernard,2012.The important morphological characters of Chinese specimens are described in detail.An updated key to Chinese Verrucoentomon species is provided.In addition,their DNA barcodes are sequenced and analyzed.展开更多
Optical barcodes have demonstrated a great potential in multiplexed bioassays and cell tracking for their distinctive spectral fingerprints.The vast majority of optical barcodes were designed to identify a specific ta...Optical barcodes have demonstrated a great potential in multiplexed bioassays and cell tracking for their distinctive spectral fingerprints.The vast majority of optical barcodes were designed to identify a specific target by fluorescence emission spectra,without being able to characterize dynamic changes in response to analytes through time.To overcome these limitations,the concept of the bioresponsive dynamic photonic barcode was proposed by exploiting interfacial energy transfer between a microdroplet cavity and binding molecules.Whispering-gallery modes resulting from cavity-enhanced energy transfer were therefore converted into photonic barcodes to identify binding activities,in which more than trillions of distinctive barcodes could be generated by a single droplet.Dynamic spectral barcoding was achieved by a significant improvement in terms of signal-to-noise ratio upon binding to target molecules.Theoretical studies and experiments were conducted to elucidate the effect of different cavity sizes and analyte concentrations.Timeresolved fluorescence lifetime was implemented to investigate the role of radiative and non-radiative energy transfer.Finally,microdroplet photonic barcodes were employed in biodetection to exhibit great potential in fulfilling biomedical applications.展开更多
DNA barcoding provides accurate stages. Single-gene-targeted metagenomic analysis identification of zooplankton species through all life based on DNA barcode databases can facilitate long- term monitoring of zooplankt...DNA barcoding provides accurate stages. Single-gene-targeted metagenomic analysis identification of zooplankton species through all life based on DNA barcode databases can facilitate long- term monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang （Yangtze） River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitocbondrial cytochrome oxidase subunit 1 （coxl） gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units （MOTUs）. Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species （similarity〉96%） or genus level （similarity〈96%）. Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.展开更多
This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi.It focuses on 25 phytopathogenic genera:Alternaria,Bipolaris,Boeremia,Botryosphaeria,Calonectria,Co...This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi.It focuses on 25 phytopathogenic genera:Alternaria,Bipolaris,Boeremia,Botryosphaeria,Calonectria,Coniella,Corticiaceae,Curvularia,Elsinoe,Entyloma,Erythricium,Fomitiporia,Fulviformes,Laetisaria,Limonomyces,Neofabraea,Neofusicoccum,Phaeoacremonium,Phellinotus,Phyllosticta,Plenodomus,Pseudopyricularia,Tilletia,Venturia and Waitea,using recent molecular data,up to date names and the latest taxonomic insights.For each genus a taxonomic background,diversity aspects,species identification and classification based on molecular phylogeny and recommended genetic markers are provided.In this study,varieties of the genus Boeremia have been elevated to species level.Botryosphaeria,Bipolaris,Curvularia,Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries,as many new species have been introduced to these genera.展开更多
The genus Munidopsis has high biodiversity in seamount habitats.In this study,two new Munidopsis species,Munidopsis ahyongi sp.nov.and Munidopsis carolinensis sp.nov.from the Caroline Ridge in the tropical western Pac...The genus Munidopsis has high biodiversity in seamount habitats.In this study,two new Munidopsis species,Munidopsis ahyongi sp.nov.and Munidopsis carolinensis sp.nov.from the Caroline Ridge in the tropical western Pacific Ocean were described.M.ahyongi sp.nov.is very similar to a group of species in the M.serricornis complex,but can be readily distinguished from the related species in having the oblique posterior orbital margins,2 spines on the lateral carapace margin,and a relatively longer rostral median spine.M.carolinensis sp.nov.is different from two related species primarily in having oblique frontal margins,blunt outer orbital angles,straight lateral margins of the rostrum,scale-like rugae on sternites 5-7,and less spinose pereopod 1(chelipeds,P1)merus and carpus.Aside from the morphological comparisons,DNA barcode analysis and phylogenetic analysis based on the cytochrome c oxidase subunit I gene(COI)were employed for the identification of these new species.展开更多
Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylo...Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylogenetic approaches currently used to discriminating these species remain unsatisfactory.In this study,we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria.Each Gaultheria plastome contained 110 unique genes(76 protein-coding,30 tRNA,and four rRNA genes).Duplication of trnfM,rps14,and rpl23 genes were detected,while all plastomes lacked ycf1 and ycf2 genes.Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene.Moreover,plastomes of Gaultheria leucocarpa var.yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene.Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales.Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species.Additionally,seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens.Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria.In addition,our findings provide important resources for identification of Chinese medicinal wintergreens.展开更多
基金supported by National Natural Science Foundation of China (No. 81473303)the Major Scientific and Technological Special Project for ‘Significant New Drugs Creation’ (No. 2014ZX09304307001)
文摘The safety of traditional Chinese medicine(TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the ‘bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.
基金National Science and Technology Major Program (2008ZX 10005-004)Liaoning Education Department (2009A120)China Postdoctoral Science Foundation (20080440019 and 200902069)
文摘For the protection of consumers and developments of relevant industry, authentication of medicinal plants is a critical issue. This review covers various aspects of authentication methods and techniques based on molecular biology and genomics with special emphasis on molecular biology techniques including genome-based authentication, microchip-based authentication, DNA barcoding, and their applications.
基金supported in part by National Key R&D Program of China(2018YFA0801402,2018YFA0107200)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16020404)+3 种基金Guangdong Basic and Applied Basic Research Foundation(2019B151502054)Frontier Research Program of Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory,2018GZR110105013)Jiazi Research Innovative Project of Bioland Laboratory(2019GZR110108001)Science and Technology Planning Project of Guangdong Province(2020B1212060052).
文摘Central to the core principle of cell theory,depicting cells'history,state and fate is a fundamental goal in modern biology.By leveraging clonal analysis and sin-gle-cell RNA-seq technologies,single-cell lineage trac-ing provides new opportunities to interrogate both cell states and lineage histories.During the past few years,many strategies to achieve lineage tracing at single-cell resolution have been developed,and three of them(in-tegration barcodes,polylox barcodes,and CRISPR barcodes)are noteworthy as they are amenable in experimentally tractable systems.Although the above strategies have been demonstrated in animal develop-ment and stem cell research,much care and effort are still required to implement these methods.Here we review the development of single-cell lineage tracing,major characteristics of the cell barcoding strategies,applications,as well as technical considerations and limitations,providing a guide to choose or improve the single-cell barcoding lineage tracing.
基金supported by the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences(Nos.CI2021A04106 and CI2021A03910)the National Key Research and Development Program of China(No.2019YFC1710601)+3 种基金the Fundamental Research Funds for the Central Public Welfare Research Institutes of China(Nos.ZZ15-YQ-033,ZXKT21026 and ZXKT23004)the Major Special Project of Scientific and Technological Cooperation of Bijie(No.2021-02)the Advantageous Chinese Medicinal Materials R&D Talent Base Project of Bijie,Guizhou Province(No.RCJD2020-21)Bijie Technology Innovation Platform and Talent Team(Bikehe[2023]No.66-BJZDSYS 2024-05).
文摘Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy.Accurate species quantification remains challenging,as current methods often yield inconsistent results.This study introduces a novel pyrosequencing-based technique,termed herb molecular quantification(Herb-Q),designed to precisely quantify herbal products.We evaluated its effectiveness using Pinellia ternata and five of its adulterants.Initially,we assessed commonly used DNA barcodes with sequences from a public database,identifying two candidate regions,Maturase K(matK)and internal transcribed spacer 2(ITS2),for screening specific single nucleotide polymorphism(SNP)loci,allowing for species-specific identification.These loci were validated by amplifying and sequencing genomic material from collected samples.Our validation studies showed that Herb-Q demonstrated excellent linearity,accuracy,repeatability,and detection limits.We established quantitative standard curves with high R^(2)values(>0.99)to enable precise species quantification,which were combined with external standards to provide clear and accurate visual quantification results.The average bias in quantifying the tuber of P.ternata was 2.38%,confirming that Herb-Q can accurately identify and quantify herbal product constituents.Moreover,the entire quantification process took less than 4 h.This study presents a novel,rapid method for accurately quantifying species in herbal products and advances the application of DNA barcoding from species identification to quantitative detection.
基金supported financially by the Ministry of Science and Technology of China(2017YFA0204502)the National Natural Science Foundation of China(NSFC)(22275104,21905145)+1 种基金the project ZR2021YQ06 supported by Shandong Provincial Natural Science FoundationScientific Research Foundation in Qilu University of Technology(Shandong Academy of Sciences)(2022PY013).
文摘Micro/nanoscale photonic barcodes hold great potential for broad applications in items tracking,mul-tiplexed bioassays and anti-counterfeiting.The ever-increasing demand in advanced anti-counterfeiting applications calls for micro/nanoscale barcodes with accurate recognition,large encoding capacity and high security level.Here,we proposed a strategy to construct the dual-stimuli responsive photonic barcodes based on the perovskite quantum dots(PQDs)doped polymer whispering-gallery-mode(WGM)microcavities via swelling-deswelling method.Benefiting from the well-defined spherical microcavities,the photoluminescence(PL)spectra of as-prepared composites exhibit a series of sharp peaks characteristics resulting from the effective WGM modulation,which constitutes the fingerprint of a specific resonator and thus allows a definition of photonic barcodes.On this basis,we achieved responsive photonic barcodes based on the volatile polar-solvent-controlled luminescence in the mi-crospheres benefitting from the space-confined microcavities and the ionic feature of the PQDs.More-over,the light-controlled photonic barcodes have further been acquired through reversibly regulating the inactivation and activation of the energy transfer(ET)process between the PQDs and photochromic dyes.The well-established protocols of PQDs@WGM enable the development of distinct responsive barcodes with multi-responsive features,which will pave an avenue to new types of flexible WGM-based components for optical data recording and security labels.
文摘Molecular markers provide a useful method for genotype characterization and allow a high precision determination of the genetic relationship between cultivars and varieties. A system based on DNA sequences—which is known as DNA barcoding—will choose one or several standard loci which can be sequenced and compared to differentiate between species. In this research, the ITS, matK, and trnH-psbA sequences were evaluated for the molecular identification of seven F. carica genotypes, generating complete sequences for the first two loci, but unable to produce bidirectional sequences by using the trnH-psbA sequence. The ITS sequence presented the highest variation rates, while the phylogeny constructed with the matK sequence obtained the highest percentage of solved monophyletic groups. Through Pearson’s correlation analysis, it was possible to determine the existence of a significant correlation between the ITS region and psbA-trnH, and the matK and psbA-trnH sequences, but not between ITS and matK. The phylogenies constructed with the ITS + matK barcodes and ITS + matK + psbA-trnH presented the highest percentage for resolution. However, considering the cost efficiency and the facilitated recovery by using PCR, the matK + ITS combination is recommended.
文摘Deploying and Implementing RFID Systems for tracking and controlling products in supply chain management is not affordable for small and midsized companies due to its complexity, cost, and difficulties pertaining data management and maintenance. Cloud computing can be used to mitigate the risks associated with the implementation and deployment of RFID based on system in supply chain management because the complex system for data filtering, management and maintenance can be implemented on the cloud that otherwise requires the purchase of new hardware, staff and professional services.
基金Fund on the Special Fund for Agro-scientific Research in the Public Interest(No.201203065)Special Fund for Ecological Restoration in Adjacent Waters of Grass Sand Reservoir
文摘To determine the role of mitochondrial COⅠgene in classification and identification of species,a total of 39 single individuals from nine species pertaining to two genera of Cynoglossidae in the Yangtze Estuary were barcoded by COⅠ,sequenced and compared with that of other Cynoglossidae species recorded in the Gen Bank. Total genomic DNA was extracted from each scale sample using the classic phenol / chloroform extraction method. Six hundred and fifty base pairs( bp)COⅠfragments were amplified using the primers ’i. e. ’ F1: 5’- TCA ACC AAC CAC AAA GAC ATT GGC AC- 3’,R1: 5’- TAG ACT TCT GGG TGG CCA AAG AAT CA- 3’. Every PCR amplification was performed in a total volume of 50 μL of PCR mixture. PCR products were purified and then sequenced in both forward and reverse directions using an ABI PRISMTM 3730 XL Automated Sequencer. DNA sequences were aligned with clustal W using default parameters. Base composition,variable and parsimony informative sites were determined using MEGA 5. 0. Neighbor- joining( NJ) and Maximum parsimony( MP) phylogenetic trees were constructed for COⅠhaplotypes( Kimura 2 Parameter substitution model,K2P; 1 000 bootstraps pseudoreplications) using MEGA 5. 0. Using the MEGA5. 0 software for statistical analysis,the averaged AT content was greater than the GC content( Tab. 2). The GC content of codon position 1 averaged 53. 8%( 51. 8%-57. 3%),which of position 2 for 42. 0%,and that of position 3 ranged from 28. 1% to 37. 8% in average of 32. 4%( Tab. 4). The transitional pairs( si) was slightly more than the transversional pairs( sv),and the ratio( R = si/sv) was 1. 45( Tab. 3). Analysis of the frequency of amino acids in COⅠgene encoding protein showed that the highest frequency of amino acid was leucine,and the lowest frequency of amino acid was tryptophan( Tab. 5). The average K2 P distances pairwise-species and within-species were 0. 191 and 0. 003,respectively( Tab. 6). The K2 P distance pairwise-species was 63. 7 times of that within-species. According to the MP and
基金supported by the National Natural Science Foundation of China(31471958,31272298)the Youth Innovation Promotion Association of the CAS(2013183)the Open Project of Key Laboratory of Insect Developmental and Evolutionary Biology,CAS(2009DP17321409)
文摘Three newly recorded species in the order Acerentomata in Protura from China are described:Filientomon duodecimsetosum Nakamura,2004,Verrucoentomon anatoli Shrubovych & Bernard,2012 and Verrucoentomon louisanne Shrubovych & Bernard,2012.The important morphological characters of Chinese specimens are described in detail.An updated key to Chinese Verrucoentomon species is provided.In addition,their DNA barcodes are sequenced and analyzed.
基金We would like to thank the Centre of Bio-Devices and Bioinformatics and CNRS International—Nanyang Technological University-Thales Research Alliance(CINTRA)for lab supportWe would also like to thank NTU for the startup grant(SUG-M4082308.040).
文摘Optical barcodes have demonstrated a great potential in multiplexed bioassays and cell tracking for their distinctive spectral fingerprints.The vast majority of optical barcodes were designed to identify a specific target by fluorescence emission spectra,without being able to characterize dynamic changes in response to analytes through time.To overcome these limitations,the concept of the bioresponsive dynamic photonic barcode was proposed by exploiting interfacial energy transfer between a microdroplet cavity and binding molecules.Whispering-gallery modes resulting from cavity-enhanced energy transfer were therefore converted into photonic barcodes to identify binding activities,in which more than trillions of distinctive barcodes could be generated by a single droplet.Dynamic spectral barcoding was achieved by a significant improvement in terms of signal-to-noise ratio upon binding to target molecules.Theoretical studies and experiments were conducted to elucidate the effect of different cavity sizes and analyte concentrations.Timeresolved fluorescence lifetime was implemented to investigate the role of radiative and non-radiative energy transfer.Finally,microdroplet photonic barcodes were employed in biodetection to exhibit great potential in fulfilling biomedical applications.
基金Supported by the National Natural Science Foundation of China(No.41230963)the National Basic Research Program of China(973 Program)(No.2011CB403604)+2 种基金the"135"Fund of Institute of Oceanology,Chinese Academy of Sciences(No.2012I0060102)the Innovative Research Group Funding of the National Natural Science Foundation of China(No.41121064)the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDA11020305)
文摘DNA barcoding provides accurate stages. Single-gene-targeted metagenomic analysis identification of zooplankton species through all life based on DNA barcode databases can facilitate long- term monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang （Yangtze） River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitocbondrial cytochrome oxidase subunit 1 （coxl） gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units （MOTUs）. Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species （similarity〉96%） or genus level （similarity〈96%）. Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.
基金funded by the grants of the National Natural Science Foundation of China(NSFC Grant Nos.31670027,31460011 and 30870009)the National Research Council of Thailand grants Thailands’Fungal Diversity,Solving Problems and Creating Biotechnological Products(Grant No.61201321016)+11 种基金Taxonomy,Diversity,Phylogeny and Evolution of fungi in Capnodiales(Grant No.61215320024)"the future of specialist fungi in a changing climate:baseline data for generalist and specialist fungi associated with ants,Rhododendron species and Dracena species"(Grant No.DBG6080013)"Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion"(RDG6130001)Mae Fah Luang University and University of Mauritius for research supportthe support from Biosystems and Integrative Sciences Institute(BioISI,FCT/UID/Multi/04046/2013)Associacao Nordesta for field support,Capes-SIU(008/13)and Fundacao de Amparo a Ciencia e Technologia de Pernambuco(FACEPE,APQ-0375-2.03/15)for financial supportthe Conselho Nacional de Desenvolvimento Cientifico e Technologico(CNPq)(307601/2015-3 and 312186/2016-9)for scholarshipsthe University of Queensland Development Fellowships(UQFEL1718905)support from the Department of the Environment and Energy under the Australian Biological Resources Study(Grant No.RG18-43)the Royal Golden Jubilee PhD program under Thailand Research Fund for a personal grant(RGJ scholarship no.PHD/0002/2560)the National Natural Science Foundation of China(Project ID:NSF31500017 to Huang Zhang)CAS President’s International Fellowship Initiative(PIFI)for funding his postdoctoral research(number 2019PC0008)the National Science Foundation of China and the Chinese Academy of Sciences for financial support under the following grants:41761144055,41771063 and Y4ZK111B01.
文摘This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi.It focuses on 25 phytopathogenic genera:Alternaria,Bipolaris,Boeremia,Botryosphaeria,Calonectria,Coniella,Corticiaceae,Curvularia,Elsinoe,Entyloma,Erythricium,Fomitiporia,Fulviformes,Laetisaria,Limonomyces,Neofabraea,Neofusicoccum,Phaeoacremonium,Phellinotus,Phyllosticta,Plenodomus,Pseudopyricularia,Tilletia,Venturia and Waitea,using recent molecular data,up to date names and the latest taxonomic insights.For each genus a taxonomic background,diversity aspects,species identification and classification based on molecular phylogeny and recommended genetic markers are provided.In this study,varieties of the genus Boeremia have been elevated to species level.Botryosphaeria,Bipolaris,Curvularia,Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries,as many new species have been introduced to these genera.
基金the Science&Technology Basic Resources Investigation Program of China(No.2017FY100804)the National Natural Science Foundation of China(Nos.31572229,41876178)+1 种基金the Senior User Project of R/V Kexue(No.KEXUE2018G25)。
文摘The genus Munidopsis has high biodiversity in seamount habitats.In this study,two new Munidopsis species,Munidopsis ahyongi sp.nov.and Munidopsis carolinensis sp.nov.from the Caroline Ridge in the tropical western Pacific Ocean were described.M.ahyongi sp.nov.is very similar to a group of species in the M.serricornis complex,but can be readily distinguished from the related species in having the oblique posterior orbital margins,2 spines on the lateral carapace margin,and a relatively longer rostral median spine.M.carolinensis sp.nov.is different from two related species primarily in having oblique frontal margins,blunt outer orbital angles,straight lateral margins of the rostrum,scale-like rugae on sternites 5-7,and less spinose pereopod 1(chelipeds,P1)merus and carpus.Aside from the morphological comparisons,DNA barcode analysis and phylogenetic analysis based on the cytochrome c oxidase subunit I gene(COI)were employed for the identification of these new species.
基金the National Natural Science Foundation of China(31960080,41671052 and 42175139)the Reserve Talents of Young and Middle-aged Academic and Technical Leaders in Yunnan province(202005AC160020)the Program Innovative Research Team in Science and Technology in Yunnan Province(202005AE160004).
文摘Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylogenetic approaches currently used to discriminating these species remain unsatisfactory.In this study,we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria.Each Gaultheria plastome contained 110 unique genes(76 protein-coding,30 tRNA,and four rRNA genes).Duplication of trnfM,rps14,and rpl23 genes were detected,while all plastomes lacked ycf1 and ycf2 genes.Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene.Moreover,plastomes of Gaultheria leucocarpa var.yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene.Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales.Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species.Additionally,seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens.Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria.In addition,our findings provide important resources for identification of Chinese medicinal wintergreens.
