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
We are far from knowing all species living on the planet.Understanding biodiversity is demanding and requires time and expertise.Most groups are understudied given problems of identifying and delimiting species.DNA ba...We are far from knowing all species living on the planet.Understanding biodiversity is demanding and requires time and expertise.Most groups are understudied given problems of identifying and delimiting species.DNA barcoding emerged to overcome some of the difficulties in identi-fying species.Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups.Here,we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the south-ern Appalachian Mountains(USA).We used 3 reference databases and several automated classification methods on a data set including several arthropod groups.Acari,Araneae,Collembola,Coleoptera,Diptera,and Hymenoptera were well represented,showing different performances across methods and databases.Spiders performed the best,with correct identification rates to species and genus levels of~50%across data-bases.Springtails performed poorly,no barcodes were identified to species or genus.Other groups showed poor to mediocre performance,from around 3%(mites)to 20%(beetles)correctly identified barcodes to species,but also with some false identifications.In general,BOLD-based identification offered the best identification results but,in all cases except spiders,performance is poor,with less than a fifth of specimens correctly identified to genus or species.Our results indicate that the soil arthropod fauna is still insufficiently documented,with many species unrepresented in DNA barcode libraries.More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNAbarcoding as a universally applicable identification method.展开更多
Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research ha...Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.展开更多
DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Jugl...DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification(AFRAID)method of species identification,a novel approach for precise species identification in plants.Specifically,we determined(1)the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae,(2)the minimum size of chloroplast dataset for species discrimination,and(3)minimum amount of next generation sequencing(NGS)data required for species identification.We found that species identification rates were highest when whole chloroplast genomes were used,followed by taxon-specific DNA barcodes,and then universal DNA barcodes.Species identification of 100%was achieved when chloroplast genome sequence coverage reached 20%and the original sequencing data reached 500,000 reads.AFRAID accurately identified species for all samples tested after 500,000 clean reads,with far less computing time than common approaches.These results provide a new approach to accurately identify species,overcoming limitations of traditional DNA barcodes.Our method,which uses next generation sequencing to generate partial chloroplast genomes,reveals that DNA barcode regions are not necessarily fixed,accelerating the process of species identification.展开更多
The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term o...The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term overfishing,the ichthyoplankton structure has been dramatically altered.Understanding the species composition and distribution of fish eggs and larvae is one of the most essential tasks to accurately regulate fishery resources and formulate effective management policies;however,little is known about the ichthyoplankton in this region.In this study,an integrated strategy of morphology identification(MI)and mitochondrial COI DNA barcoding was used to identify species of fish eggs and larvae collected from the ECSCZA.MI revealed 15 fish egg species belonging to 12 families and 12 fish larva species belonging to 12 families;in contrast,DNA barcoding altogether identified 30 species,including 18 fish egg species and 13 fish larva species.One species was shared between the egg and larva samples.Our study offers useful tools and critical scientific information for further understanding the diversity,distribution,and conservation management of various ichthyoplankton species in the marine environment.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
[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
Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the perfo...Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes （motK, rbcL, and ITS） were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment （PWG） distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method.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
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funded by the U.S.National Science Foundation(Award DEB-1916263 to M.S.C.)the Clemson University Experiment Station(SC-1700596 to M.S.C.).
文摘We are far from knowing all species living on the planet.Understanding biodiversity is demanding and requires time and expertise.Most groups are understudied given problems of identifying and delimiting species.DNA barcoding emerged to overcome some of the difficulties in identi-fying species.Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups.Here,we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the south-ern Appalachian Mountains(USA).We used 3 reference databases and several automated classification methods on a data set including several arthropod groups.Acari,Araneae,Collembola,Coleoptera,Diptera,and Hymenoptera were well represented,showing different performances across methods and databases.Spiders performed the best,with correct identification rates to species and genus levels of~50%across data-bases.Springtails performed poorly,no barcodes were identified to species or genus.Other groups showed poor to mediocre performance,from around 3%(mites)to 20%(beetles)correctly identified barcodes to species,but also with some false identifications.In general,BOLD-based identification offered the best identification results but,in all cases except spiders,performance is poor,with less than a fifth of specimens correctly identified to genus or species.Our results indicate that the soil arthropod fauna is still insufficiently documented,with many species unrepresented in DNA barcode libraries.More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNAbarcoding as a universally applicable identification method.
基金supported by grants from Key Research&Development Project of Nanhua Biomedical Co.,Ltd.(No.H202191490139)National Natural Science Foundation of China(No.31872866)+1 种基金China Postdoctoral Science Foundation(Nos.2021M701160 and 2022M721101)Funds of Hunan university(521119400156).
文摘Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
基金supported by the funds from Natural Science Foundation of Hebei Province(C2022402017).
文摘DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification(AFRAID)method of species identification,a novel approach for precise species identification in plants.Specifically,we determined(1)the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae,(2)the minimum size of chloroplast dataset for species discrimination,and(3)minimum amount of next generation sequencing(NGS)data required for species identification.We found that species identification rates were highest when whole chloroplast genomes were used,followed by taxon-specific DNA barcodes,and then universal DNA barcodes.Species identification of 100%was achieved when chloroplast genome sequence coverage reached 20%and the original sequencing data reached 500,000 reads.AFRAID accurately identified species for all samples tested after 500,000 clean reads,with far less computing time than common approaches.These results provide a new approach to accurately identify species,overcoming limitations of traditional DNA barcodes.Our method,which uses next generation sequencing to generate partial chloroplast genomes,reveals that DNA barcode regions are not necessarily fixed,accelerating the process of species identification.
文摘The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term overfishing,the ichthyoplankton structure has been dramatically altered.Understanding the species composition and distribution of fish eggs and larvae is one of the most essential tasks to accurately regulate fishery resources and formulate effective management policies;however,little is known about the ichthyoplankton in this region.In this study,an integrated strategy of morphology identification(MI)and mitochondrial COI DNA barcoding was used to identify species of fish eggs and larvae collected from the ECSCZA.MI revealed 15 fish egg species belonging to 12 families and 12 fish larva species belonging to 12 families;in contrast,DNA barcoding altogether identified 30 species,including 18 fish egg species and 13 fish larva species.One species was shared between the egg and larva samples.Our study offers useful tools and critical scientific information for further understanding the diversity,distribution,and conservation management of various ichthyoplankton species in the marine environment.
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[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 Fundamental Research Funds for the Central Universities(grant no.TD2012-04)the Scientific Research Foundation of the State Human Resource Ministry and the Education Ministry for Returned Chinese Scholars(to L.Xie)+2 种基金the State Key Laboratory Program from the State Key Laboratory of Systematic and Evolutionary Botany(grant no.LSEB2011-07)the Main Direction Program of Knowledge Innovation of the Chinese Academy of Sciences(grant no.KSCX2-EW-Z-1)the National Natural Science Foundation of China(grant nos.31170201,81072317,31110103911)
文摘Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes （motK, rbcL, and ITS） were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment （PWG） distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method.
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.
