Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systema...Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.展开更多
The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrat...The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrated with microfluidics,typically comprises barcode array,sample loading,and reaction unit array chips.Here,we present a review of microfluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and single cells,including protein biomarkers,microRNA(miRNA),circulating tumor DNA(ctDNA),single-cell secreted proteins,single-cell exosomes,and cell interactions.We begin with an overview of current high-throughput detection and analysis approaches.Following this,we outline recent improvements in microfluidic devices for biomolecule and single-cell detection,highlighting the benefits and limitations of these devices.This paper focuses on the research and development of microfluidic barcode biochips,covering their self-assembly substrate materials and their specific applications with biomolecules and single cells.Looking forward,we explore the prospects and challenges of this technology,with the aim of contributing toward the use of microfluidic barcode detection biochips in medical diagnostics and therapies,and their large-scale commercialization.展开更多
This study introduces a lightweight deep learning model and a novel synthetic dataset designed to restore damaged one-dimensional(1D)barcodes and Quick Response(QR)codes,addressing critical challenges in logistics ope...This study introduces a lightweight deep learning model and a novel synthetic dataset designed to restore damaged one-dimensional(1D)barcodes and Quick Response(QR)codes,addressing critical challenges in logistics operations.The proposed solution leverages an efficient Pix2Pix-based framework,a type of conditional Generative Adversarial Network(GAN)optimized for image-to-image translation tasks,enabling the recovery of degraded barcodes and QR codes with minimal computational overhead.A core contribution of this work is the development of a synthetic dataset that simulates realistic damage scenarios frequently encountered in logistics environments,such as low contrast,misalignment,physical wear,and environmental interference.By training on this diverse and realistic dataset,the model demonstrates exceptional performance in restoring readability and decoding accuracy.The lightweight architecture,featuring a U-Net-based encoder-decoder with separable convolutions,ensures computational efficiency,making the approach suitable for real-time deployment on embedded and resource-constrained devices commonly used in logistics systems.Experimental results reveal significant improvements:QR code decoding ratios increased from 14%to 99%on training data and from 15%to 68%on validation data,while 1D barcode decoding ratios improved from 7%to 73%on training data and from 9%to 44%on validation data.By providing a robust,resource-efficient solution for restoring damaged barcodes and QR codes,this study offers practical advancements for enhancing the reliability of automated scanning systems in logistics operations,particularly under challenging conditions.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
DNA barcoding is a powerful technique for species identification with little morphological knowledge, by using short sections of DNA from a specific region of the genome. Two core barcode markers, rbcL and matK, and a...DNA barcoding is a powerful technique for species identification with little morphological knowledge, by using short sections of DNA from a specific region of the genome. Two core barcode markers, rbcL and matK, and a supplementary nuclear ribosomal internal transcribed spacer region were used to examine the effectiveness of the markers for Poaceae barcoding using 133 individuals of 36 taxa across 23 genera of Korean Panicoideae. We also aimed to establish a DNA barcode database for the major weeds of Korean Panicoideae. All three markers revealed a good level of amplification and sequencing success. As a single DNA marker, the ITS region achieved the highest species resolution, followed by matK. Resolving power was increased when nrlTS was incorporated into the core barcode markers. The best resolving power was obtained with a combination of matK ＋ ITS with 89.7%, followed by rbcL ＋ matK ＋ ITS with 89.3%. Thus, rbcL may be not necessary as a DNA barcode for Panicoideae species identification, when considering cost and effectiveness. Instead, a combination of matK ＋ ITS is proposed as the most suitable DNA barcode for the species identification of Panicoideae, Poaceae. We conclude that DNA barcoding using a combination of matK ＋ ITS could be one of powerful techniques for the identification of Poaceae species, The barcode sequences were deposited to the National Center for Biotechnology Information （NCBI） database for public use.展开更多
[Objective] The study aimed to solve the problem of morphological identi- fication difficulties and propose solutions for the identification of foreign mosquitoes that are difficult to identify. [Method] Based on the ...[Objective] The study aimed to solve the problem of morphological identi- fication difficulties and propose solutions for the identification of foreign mosquitoes that are difficult to identify. [Method] Based on the sequencing, alignment and anal- ysis of COl gene fragment, DNA barcode technology was used to identify 7 exotic mosquitoes, and the phylogenetic analysis was performed using MEGA6.0 and DNASTAR software. Then the morphological characteristics of the mosquitoes were reviewed. [Result[ These mosquitoes were Armigeres subalbatus, Culex gefidus, Anopheles gambiae, and Culiseta incidens. [Conclusion] DNA barcode technology is a useful supplement to the morphological classification method of mosquitoes.展开更多
Salvia plebeia has been in use as traditional Chinese medicine(TCM)for more than 500 years.In this study,the complete chloroplast(cp)genome of S.plebeia was sequenced,assembled and compared to those of other five publ...Salvia plebeia has been in use as traditional Chinese medicine(TCM)for more than 500 years.In this study,the complete chloroplast(cp)genome of S.plebeia was sequenced,assembled and compared to those of other five published Salvia cp genomes.It was found that the cp genome structure of S.plebeia was well conserved and had a total size of 151062 bp.Four parameters were used to display the usage conditions of the codons of the amino acids in Salvia genus.Although the number of protein-coding genes in each species was the same,the total number of codons was different.Except for amino acids Trp and Met whose Relative Synonymous Codon Usage(RSCU)value of one condon was equal to 1,the remaining 19 amino acids had 1-3 preferred codons.The preferred codon names of each amino acid were coincident.The period size for the tandem repeats of six species ranged from 9 to 410 bp.Salvia cp genomes mainly possessed tandem repeats with a copy number less than or equal to 3.The sequence length of tandem repeats of the six species ranged from 25 to 824 bp.Highly viarable regions including four intergenic spacers and six partial genes were discovered as potential specific barcodes for Salvia species through cp genome-wide comparison.Finally,we performed phylogenetic analyses based on the complete cp genome and coding sequences respectively.These results provide information to help construct the cp genome library for Salvia,which may support studies of phylogenetics,DNA barcoding,population and transplastomics.展开更多
Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use o...Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. Methods Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure： reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide （random hexamer or non-ribosomal hexanucleotide） primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline. Results NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease （HFMD） and identified other potential viruses or differentiated misdiagnosis events. Conclusion The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.展开更多
Two-dimensional(2D) barcode technology is an electronic tagging technology based on combination of computer and optical technology. It is an important way of information collection and input. 2D barcode technology has...Two-dimensional(2D) barcode technology is an electronic tagging technology based on combination of computer and optical technology. It is an important way of information collection and input. 2D barcode technology has been widely used in various fields of logistics,production automation,and e-commerce,but it also has brought about a series of safety problems. Based on evolutionary encryption technology,this paper improved algorithm of traditional 2D barcode generation,to improve forgery- proof performance of 2D barcode. This algorithm is applied to agricultural products quality and safety traceability system and the results show that it is effective.展开更多
基金supported by the National Natural Science Foundation of China(32371700,32071670 and 31870196)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)+4 种基金the Science and Technology Basic Resources Investigation Program of China(2021FY100200)Yunnan Revitalization Talent Support Program“Young Talent”and“Innovation Team”Projects(202405AS350019)the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Science(XTBG-1450101)the Key R&D program of Yunnan Province,China(202103AC100003)the Key Basic Research program of Yunnan Province,China(202101BC070003).
文摘Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.
基金supported by the National Key Research and Development Plan of China(2023YFB3210400)the Natural Science Innovation Group Foundation of China(T2321004)+3 种基金the National Natural Science Foundation of China(62174101)Shandong University Integrated Research and Cultivation Project(2022JC001)Key Research and Development Plan of Shandong Province(Major Science and Technology Innovation Project2022CXGC020501).
文摘The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrated with microfluidics,typically comprises barcode array,sample loading,and reaction unit array chips.Here,we present a review of microfluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and single cells,including protein biomarkers,microRNA(miRNA),circulating tumor DNA(ctDNA),single-cell secreted proteins,single-cell exosomes,and cell interactions.We begin with an overview of current high-throughput detection and analysis approaches.Following this,we outline recent improvements in microfluidic devices for biomolecule and single-cell detection,highlighting the benefits and limitations of these devices.This paper focuses on the research and development of microfluidic barcode biochips,covering their self-assembly substrate materials and their specific applications with biomolecules and single cells.Looking forward,we explore the prospects and challenges of this technology,with the aim of contributing toward the use of microfluidic barcode detection biochips in medical diagnostics and therapies,and their large-scale commercialization.
基金supported by the Scientific and Technological Research Council of Turkey(TÜB˙ITAK)through the Industrial R&D Projects Grant Program(TEYDEB)under Project No.3211077(grant recipient:Metin Kahraman)。
文摘This study introduces a lightweight deep learning model and a novel synthetic dataset designed to restore damaged one-dimensional(1D)barcodes and Quick Response(QR)codes,addressing critical challenges in logistics operations.The proposed solution leverages an efficient Pix2Pix-based framework,a type of conditional Generative Adversarial Network(GAN)optimized for image-to-image translation tasks,enabling the recovery of degraded barcodes and QR codes with minimal computational overhead.A core contribution of this work is the development of a synthetic dataset that simulates realistic damage scenarios frequently encountered in logistics environments,such as low contrast,misalignment,physical wear,and environmental interference.By training on this diverse and realistic dataset,the model demonstrates exceptional performance in restoring readability and decoding accuracy.The lightweight architecture,featuring a U-Net-based encoder-decoder with separable convolutions,ensures computational efficiency,making the approach suitable for real-time deployment on embedded and resource-constrained devices commonly used in logistics systems.Experimental results reveal significant improvements:QR code decoding ratios increased from 14%to 99%on training data and from 15%to 68%on validation data,while 1D barcode decoding ratios improved from 7%to 73%on training data and from 9%to 44%on validation data.By providing a robust,resource-efficient solution for restoring damaged barcodes and QR codes,this study offers practical advancements for enhancing the reliability of automated scanning systems in logistics operations,particularly under challenging conditions.
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.
文摘DNA barcoding is a powerful technique for species identification with little morphological knowledge, by using short sections of DNA from a specific region of the genome. Two core barcode markers, rbcL and matK, and a supplementary nuclear ribosomal internal transcribed spacer region were used to examine the effectiveness of the markers for Poaceae barcoding using 133 individuals of 36 taxa across 23 genera of Korean Panicoideae. We also aimed to establish a DNA barcode database for the major weeds of Korean Panicoideae. All three markers revealed a good level of amplification and sequencing success. As a single DNA marker, the ITS region achieved the highest species resolution, followed by matK. Resolving power was increased when nrlTS was incorporated into the core barcode markers. The best resolving power was obtained with a combination of matK ＋ ITS with 89.7%, followed by rbcL ＋ matK ＋ ITS with 89.3%. Thus, rbcL may be not necessary as a DNA barcode for Panicoideae species identification, when considering cost and effectiveness. Instead, a combination of matK ＋ ITS is proposed as the most suitable DNA barcode for the species identification of Panicoideae, Poaceae. We conclude that DNA barcoding using a combination of matK ＋ ITS could be one of powerful techniques for the identification of Poaceae species, The barcode sequences were deposited to the National Center for Biotechnology Information （NCBI） database for public use.
文摘[Objective] The study aimed to solve the problem of morphological identi- fication difficulties and propose solutions for the identification of foreign mosquitoes that are difficult to identify. [Method] Based on the sequencing, alignment and anal- ysis of COl gene fragment, DNA barcode technology was used to identify 7 exotic mosquitoes, and the phylogenetic analysis was performed using MEGA6.0 and DNASTAR software. Then the morphological characteristics of the mosquitoes were reviewed. [Result[ These mosquitoes were Armigeres subalbatus, Culex gefidus, Anopheles gambiae, and Culiseta incidens. [Conclusion] DNA barcode technology is a useful supplement to the morphological classification method of mosquitoes.
基金supported by the Key Research Project of China Academy of Chinese Medical Sciences of the 13th Five-Year Plan(No.ZZ10-007)the National Key Research and Development Plan of China(Nos.2017YFB1002303 and 2019YFC1710601)。
文摘Salvia plebeia has been in use as traditional Chinese medicine(TCM)for more than 500 years.In this study,the complete chloroplast(cp)genome of S.plebeia was sequenced,assembled and compared to those of other five published Salvia cp genomes.It was found that the cp genome structure of S.plebeia was well conserved and had a total size of 151062 bp.Four parameters were used to display the usage conditions of the codons of the amino acids in Salvia genus.Although the number of protein-coding genes in each species was the same,the total number of codons was different.Except for amino acids Trp and Met whose Relative Synonymous Codon Usage(RSCU)value of one condon was equal to 1,the remaining 19 amino acids had 1-3 preferred codons.The preferred codon names of each amino acid were coincident.The period size for the tandem repeats of six species ranged from 9 to 410 bp.Salvia cp genomes mainly possessed tandem repeats with a copy number less than or equal to 3.The sequence length of tandem repeats of the six species ranged from 25 to 824 bp.Highly viarable regions including four intergenic spacers and six partial genes were discovered as potential specific barcodes for Salvia species through cp genome-wide comparison.Finally,we performed phylogenetic analyses based on the complete cp genome and coding sequences respectively.These results provide information to help construct the cp genome library for Salvia,which may support studies of phylogenetics,DNA barcoding,population and transplastomics.
基金supported by the China Mega-Project for Infectious Disease(2016ZX10004-101,2016ZX10004-215)Beijing Municipal Science&Technology Commission Project(D151100002115003)Guangzhou Municipal Science&Technology Commission Project(2015B2150820)
文摘Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. Methods Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure： reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide （random hexamer or non-ribosomal hexanucleotide） primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline. Results NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease （HFMD） and identified other potential viruses or differentiated misdiagnosis events. Conclusion The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.
基金Supported by National Key Technology Research and Development Program of the Ministry of Science and Technology of China(2012BAD35B04)
文摘Two-dimensional(2D) barcode technology is an electronic tagging technology based on combination of computer and optical technology. It is an important way of information collection and input. 2D barcode technology has been widely used in various fields of logistics,production automation,and e-commerce,but it also has brought about a series of safety problems. Based on evolutionary encryption technology,this paper improved algorithm of traditional 2D barcode generation,to improve forgery- proof performance of 2D barcode. This algorithm is applied to agricultural products quality and safety traceability system and the results show that it is effective.
