[Objectives]This study was conducted to detect and analyze tomato leaf curl New Delhi virus(ToLCNDV).[Methods]Through PCR detection,sequence analysis,and pathogenicity verification,tomato leaf curl New Delhi virus(ToL...[Objectives]This study was conducted to detect and analyze tomato leaf curl New Delhi virus(ToLCNDV).[Methods]Through PCR detection,sequence analysis,and pathogenicity verification,tomato leaf curl New Delhi virus(ToLCNDV)was identified in zucchini exhibiting systemic disease symptoms during a 2024 outbreak in Qingzhou City,Shandong Province,and was designated as ToLCNDV-SD.[Results]Specific primer amplification showed that all eight diseased samples produced bands of 504 bp(DNA-A)and 892 bp(DNA-B).Sequencing analysis revealed that ToLCNDV-SD DNA-A shared 96.10%homology with an Indonesian melon isolate(LC421834.1),while DNA-B showed 88.31%homology with a Malaysian bitter gourd isolate(MW248678.1).Phylogenetic analysis indicated its closest relationship with Southeast Asian cucurbit-infecting isolates.Friction transmission tests confirmed that the virus could spread mechanically,inducing typical symptoms 14 d after inoculation with positive PCR detection.[Conclusions]This study provides important insights for understanding the epidemic mechanisms and control strategies of ToLCNDV in China.展开更多
Root rot is a prevalent soil-borne fungal disease in citrus.Citron C-05(Citrus medica)stands out as a germplasm within Citrus spp.due to its complete resistance to citrus canker and favorable characteristics such as s...Root rot is a prevalent soil-borne fungal disease in citrus.Citron C-05(Citrus medica)stands out as a germplasm within Citrus spp.due to its complete resistance to citrus canker and favorable characteristics such as single embryo and easy rooting.However,Citron C-05 was found to be highly susceptible to root rot during cultivation,with the specific pathogens previously unknown.In this study,four candidate fungal species were isolated from Citron C-05 roots.Sequence analysis of ITS,EF-1a,RPB1,and RPB2 identified two Fusarium solani strains,Rr-2 and Rr-4,as the candidates causing root rot in Citron C-05.Resistance tests showed these two pathogens increased root damage rate from 10.30%to 35.69%in Citron C-05,sour orange(Citrus aurantium),sweet orange(Citrus sinensis)and pummelo(Citrus grandis).F.solani exhibited the weak pathogenicity towards trifoliate orange(Poncirus trifoliata).DAB staining revealed none of reddish-brown precipitation in the four susceptible citrus germplasm after infection with F.solani,while trifoliate orange exhibited significant H2O2 accumulation.Trypan blue staining indicated increased cell death in the four susceptible citrus germplasm following infection with these two pathogens but not in trifoliate orange.These findings provide a comprehensive understanding of citrus root rot and support future research on the mechanisms of root rot resistance in citrus.展开更多
In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology bas...In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.展开更多
Tannases produced by filamentous fungi are in a family of important hydrolases of gallotannins and have broad industry applications.But until now,the 3-D structures of fungi tannases have not been reported.The protein...Tannases produced by filamentous fungi are in a family of important hydrolases of gallotannins and have broad industry applications.But until now,the 3-D structures of fungi tannases have not been reported.The protein sequence deduced from the cDNA sequence obtained using RT-PCR amplification was identified as tannase through sequence alignment and phylogenetic analysis.Structure models based on the tannase sequence were collected using I-TASSER,and the model with the best match to the surface charge density-pH titration profile was selected as the final structure for tannase from Aspergillusniger N5-5.This work provides an effective method for protein structure research.The structure constructed in this work should be very important to understand the enzyme bioactivities and further developments of fungi tannases.展开更多
Background Breed identification is useful in a variety of biological contexts.Breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are se...Background Breed identification is useful in a variety of biological contexts.Breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are several methods proposed.However,what is the optimal combination of these methods remain unclear.In this study,using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project,we compared the combinations of three methods(Delta,FST,and In)for breed-informative SNP detection and five machine learning methods(KNN,SVM,RF,NB,and ANN)for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs.In addition,we evaluated the accuracy of breed identification using SNP chip data of different densities.Results We found that all combinations performed quite well with identification accuracies over 95%in all scenarios.However,there was no combination which performed the best and robust across all scenarios.We proposed to inte-grate the three breed-informative detection methods,named DFI,and integrate the three machine learning methods,KNN,SVM,and RF,named KSR.We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99%in most cases and was very robust in all scenarios.The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases.Conclusions The current study showed that the combination of DFI and KSR was the optimal strategy.Using sequence data resulted in higher accuracies than using chip data in most cases.However,the differences were gener-ally small.In view of the cost of genotyping,using chip data is also a good option for breed identification.展开更多
The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detecti...The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detection scheme for the satellite-based AIS signal transmitted over the white Gaussian noise channel. Based on the maximum likelihood estimation and a Viterbi decoder, the proposed scheme is capable of tolerating a frequency offset up to 5% of the symbol rate. The complexity of the proposed scheme is reduced by the state-complexity reduction, which is based on per-survivor processing. Simulation results prove that the proposed non-coherent sequence detection scheme has high robustness to frequency offset compared to the relative scheme when messages collision exists.展开更多
The sequences which consist of any segment of a chaos sequence are called asC-sequences. These sequences could be used as a kind of input signals to replace M-sequences in theprocess identification. This substitution ...The sequences which consist of any segment of a chaos sequence are called asC-sequences. These sequences could be used as a kind of input signals to replace M-sequences in theprocess identification. This substitution is theoretically proved to be feasible. InverseC-sequences are created in a way similar to inverse M-sequences to solve the problem thatC-sequences have non-ideal balance property, that is, the numbers of '0' and '1' are unequal.Besides its good pseudo-random property, the sequences have other advantages such as easy togenerate, varieties of the segment and adjustable cycle time.展开更多
A new method for identifying nonlinear time varying systems with unknown structure is presented. The method extends the application area of basis sequence identification. The essential idea is to utilize the learning ...A new method for identifying nonlinear time varying systems with unknown structure is presented. The method extends the application area of basis sequence identification. The essential idea is to utilize the learning and nonlinear approximating ability of neural networks to model the non linearity of the system, characterize time varying dynamics of the system by the time varying parametric vector of the network, then the parametric vector of the network is approximated by a weighted sum of known basis sequences. Because of black box modeling ability of neural networks, the presented method can identify nonlinear time varying systems with unknown structure. In order to improve the real time capability of the algorithm, the neural network is trained by a simple fast learning algorithm based on local least squares presented by the authors. The effectiveness and the performance of the method are demonstrated by some simulation results.展开更多
In this study,we performed amplificaion and sequence analysis of exon7 of gene Badh2 of 12 fragrant rice materials,and identified the aroma of fragrant rice materials by the method of seed chewing and KOH soaking,so a...In this study,we performed amplificaion and sequence analysis of exon7 of gene Badh2 of 12 fragrant rice materials,and identified the aroma of fragrant rice materials by the method of seed chewing and KOH soaking,so as to analyze the sequence mutation of exon 7 in the Badh2 gene of rice material and its corresponding relation with the flavor character.The results showed that an 8 bp deletion(aaaa--t---ggc)and a mutation of SNP(g→t)in exon 7 of Badh2 gene were found in 10 materials,including Xiangnuo,Lvjinxiang,Meixiangzhan 2,Huaxiang,Yuexiangxuan 1,Hongyuxiang,Meixiangxuan 1,Baxiangxuan 1,Taixiangxuan 1,Taixiangxuan 2.This mutation was consistent with the mutation of EU155083 sequence in GenBank and was reported for the first time in Chinese rice materials.In these 10 fragrant rice materials with mutation,Huaxiang and Meixiangxuan 1 were identified as the heterozygote genotype,and Hongyuxiang was identified as non-fragrant rice,so the sequence mutation in exon 7 of Badh2 gene in fragrant rice materials did not correspond to aroma traits one by one;and 7 materials were identified as fragrant rice,and the brown rice of Meixiangzhan 2 and Yuexiangyuan 1 had sweet taste.The results could provide a reference for the research on the genetic mechanism of rice aroma character and the promotion of fragrant rice varieties.展开更多
Identifying the contents of processed food products is essential to correct labelling. In processed foodstuffs, species identification through morphological analysis is difficult. Several factors hinder the identifica...Identifying the contents of processed food products is essential to correct labelling. In processed foodstuffs, species identification through morphological analysis is difficult. Several factors hinder the identification of fish species in processed foods: proteins or other materials subjected to analysis may be denatured during heat treatments;the presence of other ingredients (e.g., olive and other vegetable oils) may interfere with the analysis. Consequently, possible frauds perpetrated by replacing valuable species with less precious ones may go undetected. In most processed samples (e.g. canned products), DNA is degraded into small fragments, which considerably reduces the sensitivity of molecular analysis. The main goal of our research was to develop an analytical method able to identify fish species in highly processed products, such as canned fish. The assay was developed by combining an effective method of DNA recovery from samples with the detection of small-sized sequences of the mitochondrial Cytb gene. This method appears particularly suitable when morphological characterization is difficult, to carry out such as in canned products where DNA is degraded or present in small quantities. We have analyzed 60 samples of seafood commercial products identifying 3 different genera and five different species. All analyzed samples revealed a correct species declaration, for one sample we highlighted important commercial fraud. We also used bio-informatic identification systems for the Sequence Alignment and the construction of phylogenetic tree to better confirm the revealed fraud.展开更多
Dilated cardiomyopathy（DCM）is characterized by the dilated heart chambers and reduced systolic function in the absence of specific aetiology[1].Approximately one third of DCM cases are hereditary.In recent years,DCM...Dilated cardiomyopathy（DCM）is characterized by the dilated heart chambers and reduced systolic function in the absence of specific aetiology[1].Approximately one third of DCM cases are hereditary.In recent years,DCM concomitant with arrhythmias and sudden death resulting from gene mutation has been widely展开更多
[Objective] The study aimed to identify woltberry （Lycium Linn.） germplasm resources at molecular level by analyzing the nrDNA ITS sequence. [Method] Genomic DNA from woltberry leaves extracted by modified CTAB meth...[Objective] The study aimed to identify woltberry （Lycium Linn.） germplasm resources at molecular level by analyzing the nrDNA ITS sequence. [Method] Genomic DNA from woltberry leaves extracted by modified CTAB method were regarded as templates for PCR amplification by specific primer, clone and sequencing. [Result] The nrDNA ITS sequences were obtained and then differentiated among three tested materials. [Conclusion] PCR amplification and sequencing on nrDNA ITS is a feasible approach to identify different woltberry germplasm resources.展开更多
[ Objective ] The study aimed to identify Lycium Linn. at molecular level. [ Method ] The nrDNA ITS sequence of 5 edible Lycium Linn. germplasm resources were investigated. [ Result ] The nrDNA ITS regions of five edi...[ Objective ] The study aimed to identify Lycium Linn. at molecular level. [ Method ] The nrDNA ITS sequence of 5 edible Lycium Linn. germplasm resources were investigated. [ Result ] The nrDNA ITS regions of five edible Lycium Liun. germplasm resources were sequenced. The whole sequences varied from 628 bp to 632 bp, with the average length of 630 bp. Total 79 variation sites were observed in the sequences, which accounts for 12. 5%. [ Conclusion] Sequence analysis based on nrDNA sequencing provides a new approach to identify edible Lycium Linn. germplasm resources.展开更多
Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992...Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992）. Cotton fibers are single-celled trichomes that emerge from the ovule epidermal cells. Indexed by the number of days post-anthesis （dpa）, fiber morphogenesis includes four distinct but overlapping steps： initiation （0-3 dpa）, elongation （3-20 dpa）, secondary cell wall thickening （15-45 dpa） and maturation （40-60 dpa） （Yang et al., 2008, Du et al., 2013）. The efficiency and duration of each morphogenesis stage is important to the quality attributes of the mature fiber. Cell elongation is critical for fiber length, whereas secondary cell wall thickening is important for fiber fineness and strength （Meinert and Delmer, 1977）.展开更多
The diagnosis of bacterial or fungal infections requires the identification of the pathogen etiology in the shortest time possible. Although some biomarkers are used as indicators of bacterial infections, their specif...The diagnosis of bacterial or fungal infections requires the identification of the pathogen etiology in the shortest time possible. Although some biomarkers are used as indicators of bacterial infections, their specificity and sensitivity are highly variable, and there is no direct relationship between the level increase of these biomarkers for mycosis. It is common to obtain negative microbiological cultures in patients infected by non-culturable, intracellular bacteria or mycosis, even though there is a high clinical suspicion of infection. This study identifies the pathogen present in critically infected patients through 16S and 18S/eEF1 genes detection by polymerase chain reaction (PCR) coupled with Sanger sequencing. Thirty clinical samples were evaluated by PCR, of which 40% were positive for fungi, 23.33% for bacteria, 26.7% for fungi and bacteria, and 10% for no pathogen. The PCRs outcomes period for bacteria or fungi was one day compared to seven and up to 14 days (on average) of microbiological culture for bacteria and fungi. Then, we assessed the relationship with the most used biomarkers (procalcitonin, C-reactive protein, globular sedimentation velocity, and the neutrophil-lymphocyte index). This combination of molecular techniques has been shown as helpful in identifying intracellular bacteria and fungi that are difficult to culture by conventional methods. Screening with genomic markers 16S and 18S/eEF1 by PCR allowed us to optimize the time to obtain the result of the infection caused by bacteria or fungi. Also, identifying the specific etiological microorganism by Sanger sequencing was very helpful in avoiding the progression of the disease and setting targeted treatment with better clinical outcomes.展开更多
This paper presents a case study for a complex contaminated groundwater site impacted by a historical release of chlorinated solvents in Silicon Valley, California. The original conceptual site model (CSM) inferred a ...This paper presents a case study for a complex contaminated groundwater site impacted by a historical release of chlorinated solvents in Silicon Valley, California. The original conceptual site model (CSM) inferred a contaminant migration pathway based on the groundwater gradient interpreted from groundwater elevation data, which is based on the underlying assumption that the subsurface conditions are homogeneous. However, the buried channel deposits render the underlying geology highly heterogeneous, and this heterogeneity plays a significant role in the subsurface migration of contaminants. Chemical fingerprinting evidence suggested that contamination at the downgradient property boundary was related to an off-site contaminant source. But, this alone was not a compelling argument. However, Environmental Sequence Stratigraphy (ESS), a geology-based environmental forensic technique, was applied to define the permeability architecture or the “plumbing” that controls subsurface fluid flow and contaminant migration. First, the geologic and depositional setting was synthesized based on regional geologic data, and representative facies models were identified for the site. Second, the existing CSM and site lithology data were reviewed and existing lithology data were graphically presented to display vertical grain-size patterns. This analysis focused on the nexus between the depositional environment and the site-specific subsurface data resulting in correlations/interpretations between and beyond data points that are based on established stratigraphic principles. The depositional environment results in buried river channels as the primary control on subsurface fluid flow, which defines hydrostratigraphic units (or HSUs). Finally, a hydrostratigraphic CSM that includes maps and cross sections was constructed to depict the HSUs present as a framework to integrate hydro-geology and chemistry data. This study demonstrates that: 1) Highly per-meable buried river channel deposits control subsurface fluid flow and contaminant transport, and have distinct chemical constituents and concentrations (i.e., they represent distinct HSUs), 2) Mapping of such HSUs is feasible with existing boring log data, 3) In settings such as the Santa Clara Valley where groundwater flow is governed by subsurface channel deposits, a hydrostratigraphic mapping approach is superior to a depth-based aquifer zonation approach, and 4) For heterogeneous subsurface, a detailed geology-based definition of the subsurface is an integral component of an environmental forensic analyses to determine contaminant source(s) and pathways.展开更多
The rapid identification of lactic acid bacteria,which are essential microorganisms in the food industry,is of great significance for industrial applications.The identification of lactic acid bacteria traditionally re...The rapid identification of lactic acid bacteria,which are essential microorganisms in the food industry,is of great significance for industrial applications.The identification of lactic acid bacteria traditionally relies on the isolation and identification of pure colonies.While this method is well-established and widely used,it is not without limitations.The subjective judgment inherent in the isolation and purification process introduces potential for error,and the incomplete nature of the isolation process can result in the loss of valuable information.The advent of next generation sequencing has provided a novel approach to the rapid identification of lactic acid bacteria.This technology offers several advantages,including rapidity,accuracy,high throughput,and low cost.Next generation sequencing represents a significant advancement in the field of DNA sequencing.Its ability to rapidly and accurately identify lactic acid bacteria strains in samples with insufficient information or in the presence of multiple lactic acid bacteria sets it apart as a valuable tool.The application of this technology not only circumvents the potential errors inherent in the traditional method but also provides a robust foundation for the expeditious identification of lactic acid bacteria strains and the authentication of bacterial powder in industrial applications.This paper commences with an overview of traditional and molecular biology methods for the identification of lactic acid bacteria.While each method has its own advantages,they are not without limitations in practical application.Subsequently,the paper provides an introduction of the principle,process,advantages,and disadvantages of next generation sequencing,and also details its application in strain identification and rapid identification of lactic acid bacteria.The objective of this study is to provide a comprehensive and reliable basis for the rapid identification of industrial lactic acid bacteria strains and the authenticity identification of bacterial powder.展开更多
Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequ...Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.展开更多
[Objective] The research aimed to distinguish Chinese herb Qingjiao from its botanical origin plants by comparing different DNA sequences,so as to provide a molecular basis for origin identification and quality evalua...[Objective] The research aimed to distinguish Chinese herb Qingjiao from its botanical origin plants by comparing different DNA sequences,so as to provide a molecular basis for origin identification and quality evaluation.[Method] The cpDNA psbA-trnH and nrDNA ITS sequences of five Chinese herb Qingjiao plants,including Gentiana macrophylla pall.,Gentiana straminea Maxim.,Gentiana crassicaulis Duthie ex Burk.,Gentiana dahurica Fisch and Gentiana officinalis H.Smith,were amplified with PCR,and then sequenced by direct PCR sequencing method for homologous analysis.[Results] The length of cpDNA psbA-trnH of five plants was 316-318 bp;there were seven different haplotypes and seven variable sites;the GC content of the sequence was 21.2%;the phylogenetic clustering showed the same result as haplotype analysis.The length of nrDNA ITS sequence of five plants was 624-625 bp,there were five different haplotypes and 13 variable sites;the GC content of the sequence was 59.3%.The result of phylogenetic clustering suggested that G.dahurica and G.straminea,G.macrophylla and G.officinalis clustered together as sister clades,respectively.[Conclusion] The nucleotide differences of nrDNA ITS regions could be used for distinguishing botanical origin in Chinese herb Qingjiao.展开更多
MicroRNAs (miRNAs) are a class of ~22 nucleotides long non coding RNA molecules which play an important role in gene regulation at the post transcriptional level. The conserved nature of miRNAs provides the basis of n...MicroRNAs (miRNAs) are a class of ~22 nucleotides long non coding RNA molecules which play an important role in gene regulation at the post transcriptional level. The conserved nature of miRNAs provides the basis of new miRNA identification through homology search. In an attempt to identify new conserved miRNAs in tea, previously known plant miRNAs were used for searching their homolog in a tea Expressed Sequence Tags and full length nucleotide sequence database. The sequences showing homolog no more than four mismatches were predicted for their fold back structures and passed through a series of filtration criteria, finally led us to identify 13 conserved miRNAs in tea belonging to 9 miRNA families. A total of 37 potential target genes in Arabidopsis were identified subsequently for 7 miRNA families based on their sequence complementarity which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%). Overall, our findings will accelerate the way for further researches of miRNAs and their functions in tea.展开更多
基金Supported by Taishan Industry Leading Talent Program in Shandong Province(tscx202306156)Weifang Science and Technology Development Program(2024GX073).
文摘[Objectives]This study was conducted to detect and analyze tomato leaf curl New Delhi virus(ToLCNDV).[Methods]Through PCR detection,sequence analysis,and pathogenicity verification,tomato leaf curl New Delhi virus(ToLCNDV)was identified in zucchini exhibiting systemic disease symptoms during a 2024 outbreak in Qingzhou City,Shandong Province,and was designated as ToLCNDV-SD.[Results]Specific primer amplification showed that all eight diseased samples produced bands of 504 bp(DNA-A)and 892 bp(DNA-B).Sequencing analysis revealed that ToLCNDV-SD DNA-A shared 96.10%homology with an Indonesian melon isolate(LC421834.1),while DNA-B showed 88.31%homology with a Malaysian bitter gourd isolate(MW248678.1).Phylogenetic analysis indicated its closest relationship with Southeast Asian cucurbit-infecting isolates.Friction transmission tests confirmed that the virus could spread mechanically,inducing typical symptoms 14 d after inoculation with positive PCR detection.[Conclusions]This study provides important insights for understanding the epidemic mechanisms and control strategies of ToLCNDV in China.
基金supported by Joint Funds of the National Natural Science Foundation of China(Grant No.U21A20228).
文摘Root rot is a prevalent soil-borne fungal disease in citrus.Citron C-05(Citrus medica)stands out as a germplasm within Citrus spp.due to its complete resistance to citrus canker and favorable characteristics such as single embryo and easy rooting.However,Citron C-05 was found to be highly susceptible to root rot during cultivation,with the specific pathogens previously unknown.In this study,four candidate fungal species were isolated from Citron C-05 roots.Sequence analysis of ITS,EF-1a,RPB1,and RPB2 identified two Fusarium solani strains,Rr-2 and Rr-4,as the candidates causing root rot in Citron C-05.Resistance tests showed these two pathogens increased root damage rate from 10.30%to 35.69%in Citron C-05,sour orange(Citrus aurantium),sweet orange(Citrus sinensis)and pummelo(Citrus grandis).F.solani exhibited the weak pathogenicity towards trifoliate orange(Poncirus trifoliata).DAB staining revealed none of reddish-brown precipitation in the four susceptible citrus germplasm after infection with F.solani,while trifoliate orange exhibited significant H2O2 accumulation.Trypan blue staining indicated increased cell death in the four susceptible citrus germplasm following infection with these two pathogens but not in trifoliate orange.These findings provide a comprehensive understanding of citrus root rot and support future research on the mechanisms of root rot resistance in citrus.
基金financially supported by National Key R&D Program(2021YFF0701905)。
文摘In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.
基金the National Natural Science Foundation of China (No. 21374117)the 100 Talents Program of Chinese Academy of Sciences for financial support
文摘Tannases produced by filamentous fungi are in a family of important hydrolases of gallotannins and have broad industry applications.But until now,the 3-D structures of fungi tannases have not been reported.The protein sequence deduced from the cDNA sequence obtained using RT-PCR amplification was identified as tannase through sequence alignment and phylogenetic analysis.Structure models based on the tannase sequence were collected using I-TASSER,and the model with the best match to the surface charge density-pH titration profile was selected as the final structure for tannase from Aspergillusniger N5-5.This work provides an effective method for protein structure research.The structure constructed in this work should be very important to understand the enzyme bioactivities and further developments of fungi tannases.
基金funded by National Key Research and Development Program of China(2021YFD1200404)the Yangzhou University Interdisciplinary Research Foundation for Animal Science Discipline of Targeted Support(yzuxk202016)the Project of Genetic Improvement for Agricultural Species(Dairy Cattle)of Shandong Province(2019LZGC011).
文摘Background Breed identification is useful in a variety of biological contexts.Breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are several methods proposed.However,what is the optimal combination of these methods remain unclear.In this study,using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project,we compared the combinations of three methods(Delta,FST,and In)for breed-informative SNP detection and five machine learning methods(KNN,SVM,RF,NB,and ANN)for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs.In addition,we evaluated the accuracy of breed identification using SNP chip data of different densities.Results We found that all combinations performed quite well with identification accuracies over 95%in all scenarios.However,there was no combination which performed the best and robust across all scenarios.We proposed to inte-grate the three breed-informative detection methods,named DFI,and integrate the three machine learning methods,KNN,SVM,and RF,named KSR.We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99%in most cases and was very robust in all scenarios.The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases.Conclusions The current study showed that the combination of DFI and KSR was the optimal strategy.Using sequence data resulted in higher accuracies than using chip data in most cases.However,the differences were gener-ally small.In view of the cost of genotyping,using chip data is also a good option for breed identification.
文摘The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detection scheme for the satellite-based AIS signal transmitted over the white Gaussian noise channel. Based on the maximum likelihood estimation and a Viterbi decoder, the proposed scheme is capable of tolerating a frequency offset up to 5% of the symbol rate. The complexity of the proposed scheme is reduced by the state-complexity reduction, which is based on per-survivor processing. Simulation results prove that the proposed non-coherent sequence detection scheme has high robustness to frequency offset compared to the relative scheme when messages collision exists.
基金This work was financially supported by the National Natural Science Foundation of China (No.70071047, No.10247005)the Postdoctoral Science Foundation of China (No.2002032129)
文摘The sequences which consist of any segment of a chaos sequence are called asC-sequences. These sequences could be used as a kind of input signals to replace M-sequences in theprocess identification. This substitution is theoretically proved to be feasible. InverseC-sequences are created in a way similar to inverse M-sequences to solve the problem thatC-sequences have non-ideal balance property, that is, the numbers of '0' and '1' are unequal.Besides its good pseudo-random property, the sequences have other advantages such as easy togenerate, varieties of the segment and adjustable cycle time.
文摘A new method for identifying nonlinear time varying systems with unknown structure is presented. The method extends the application area of basis sequence identification. The essential idea is to utilize the learning and nonlinear approximating ability of neural networks to model the non linearity of the system, characterize time varying dynamics of the system by the time varying parametric vector of the network, then the parametric vector of the network is approximated by a weighted sum of known basis sequences. Because of black box modeling ability of neural networks, the presented method can identify nonlinear time varying systems with unknown structure. In order to improve the real time capability of the algorithm, the neural network is trained by a simple fast learning algorithm based on local least squares presented by the authors. The effectiveness and the performance of the method are demonstrated by some simulation results.
基金Earmarked Fund for China Agriculture Research System(CARS-01-89)Fundamental Scientific Research Fund of Hainan Academy of Agricultural Sciences(JBKYYWF2020-03)Science and Technology Innovation Project of Hainan Academy of Agricultural Sciences(KJCX-2020-11)。
文摘In this study,we performed amplificaion and sequence analysis of exon7 of gene Badh2 of 12 fragrant rice materials,and identified the aroma of fragrant rice materials by the method of seed chewing and KOH soaking,so as to analyze the sequence mutation of exon 7 in the Badh2 gene of rice material and its corresponding relation with the flavor character.The results showed that an 8 bp deletion(aaaa--t---ggc)and a mutation of SNP(g→t)in exon 7 of Badh2 gene were found in 10 materials,including Xiangnuo,Lvjinxiang,Meixiangzhan 2,Huaxiang,Yuexiangxuan 1,Hongyuxiang,Meixiangxuan 1,Baxiangxuan 1,Taixiangxuan 1,Taixiangxuan 2.This mutation was consistent with the mutation of EU155083 sequence in GenBank and was reported for the first time in Chinese rice materials.In these 10 fragrant rice materials with mutation,Huaxiang and Meixiangxuan 1 were identified as the heterozygote genotype,and Hongyuxiang was identified as non-fragrant rice,so the sequence mutation in exon 7 of Badh2 gene in fragrant rice materials did not correspond to aroma traits one by one;and 7 materials were identified as fragrant rice,and the brown rice of Meixiangzhan 2 and Yuexiangyuan 1 had sweet taste.The results could provide a reference for the research on the genetic mechanism of rice aroma character and the promotion of fragrant rice varieties.
文摘Identifying the contents of processed food products is essential to correct labelling. In processed foodstuffs, species identification through morphological analysis is difficult. Several factors hinder the identification of fish species in processed foods: proteins or other materials subjected to analysis may be denatured during heat treatments;the presence of other ingredients (e.g., olive and other vegetable oils) may interfere with the analysis. Consequently, possible frauds perpetrated by replacing valuable species with less precious ones may go undetected. In most processed samples (e.g. canned products), DNA is degraded into small fragments, which considerably reduces the sensitivity of molecular analysis. The main goal of our research was to develop an analytical method able to identify fish species in highly processed products, such as canned fish. The assay was developed by combining an effective method of DNA recovery from samples with the detection of small-sized sequences of the mitochondrial Cytb gene. This method appears particularly suitable when morphological characterization is difficult, to carry out such as in canned products where DNA is degraded or present in small quantities. We have analyzed 60 samples of seafood commercial products identifying 3 different genera and five different species. All analyzed samples revealed a correct species declaration, for one sample we highlighted important commercial fraud. We also used bio-informatic identification systems for the Sequence Alignment and the construction of phylogenetic tree to better confirm the revealed fraud.
基金the funds of "the Youth Fund of Nantong Health Bureau 2015",ID:WQ2015009
文摘Dilated cardiomyopathy（DCM）is characterized by the dilated heart chambers and reduced systolic function in the absence of specific aetiology[1].Approximately one third of DCM cases are hereditary.In recent years,DCM concomitant with arrhythmias and sudden death resulting from gene mutation has been widely
基金Supported by Natural Science foundation of Ningxia Hui Antonomous Region(NZ0769)~~
文摘[Objective] The study aimed to identify woltberry （Lycium Linn.） germplasm resources at molecular level by analyzing the nrDNA ITS sequence. [Method] Genomic DNA from woltberry leaves extracted by modified CTAB method were regarded as templates for PCR amplification by specific primer, clone and sequencing. [Result] The nrDNA ITS sequences were obtained and then differentiated among three tested materials. [Conclusion] PCR amplification and sequencing on nrDNA ITS is a feasible approach to identify different woltberry germplasm resources.
基金Natural Science Foundation of Ningxia Hui Autonomous Region(NZ0769)~~
文摘[ Objective ] The study aimed to identify Lycium Linn. at molecular level. [ Method ] The nrDNA ITS sequence of 5 edible Lycium Linn. germplasm resources were investigated. [ Result ] The nrDNA ITS regions of five edible Lycium Liun. germplasm resources were sequenced. The whole sequences varied from 628 bp to 632 bp, with the average length of 630 bp. Total 79 variation sites were observed in the sequences, which accounts for 12. 5%. [ Conclusion] Sequence analysis based on nrDNA sequencing provides a new approach to identify edible Lycium Linn. germplasm resources.
基金supported by the grants from the State Key Basic Research and Development Plan (No. 2010CB126003)the National Transgenic Animals and Plants Research Project (Nos. 2011ZX08005-003 and 2011ZX08009-003)
文摘Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992）. Cotton fibers are single-celled trichomes that emerge from the ovule epidermal cells. Indexed by the number of days post-anthesis （dpa）, fiber morphogenesis includes four distinct but overlapping steps： initiation （0-3 dpa）, elongation （3-20 dpa）, secondary cell wall thickening （15-45 dpa） and maturation （40-60 dpa） （Yang et al., 2008, Du et al., 2013）. The efficiency and duration of each morphogenesis stage is important to the quality attributes of the mature fiber. Cell elongation is critical for fiber length, whereas secondary cell wall thickening is important for fiber fineness and strength （Meinert and Delmer, 1977）.
文摘The diagnosis of bacterial or fungal infections requires the identification of the pathogen etiology in the shortest time possible. Although some biomarkers are used as indicators of bacterial infections, their specificity and sensitivity are highly variable, and there is no direct relationship between the level increase of these biomarkers for mycosis. It is common to obtain negative microbiological cultures in patients infected by non-culturable, intracellular bacteria or mycosis, even though there is a high clinical suspicion of infection. This study identifies the pathogen present in critically infected patients through 16S and 18S/eEF1 genes detection by polymerase chain reaction (PCR) coupled with Sanger sequencing. Thirty clinical samples were evaluated by PCR, of which 40% were positive for fungi, 23.33% for bacteria, 26.7% for fungi and bacteria, and 10% for no pathogen. The PCRs outcomes period for bacteria or fungi was one day compared to seven and up to 14 days (on average) of microbiological culture for bacteria and fungi. Then, we assessed the relationship with the most used biomarkers (procalcitonin, C-reactive protein, globular sedimentation velocity, and the neutrophil-lymphocyte index). This combination of molecular techniques has been shown as helpful in identifying intracellular bacteria and fungi that are difficult to culture by conventional methods. Screening with genomic markers 16S and 18S/eEF1 by PCR allowed us to optimize the time to obtain the result of the infection caused by bacteria or fungi. Also, identifying the specific etiological microorganism by Sanger sequencing was very helpful in avoiding the progression of the disease and setting targeted treatment with better clinical outcomes.
文摘This paper presents a case study for a complex contaminated groundwater site impacted by a historical release of chlorinated solvents in Silicon Valley, California. The original conceptual site model (CSM) inferred a contaminant migration pathway based on the groundwater gradient interpreted from groundwater elevation data, which is based on the underlying assumption that the subsurface conditions are homogeneous. However, the buried channel deposits render the underlying geology highly heterogeneous, and this heterogeneity plays a significant role in the subsurface migration of contaminants. Chemical fingerprinting evidence suggested that contamination at the downgradient property boundary was related to an off-site contaminant source. But, this alone was not a compelling argument. However, Environmental Sequence Stratigraphy (ESS), a geology-based environmental forensic technique, was applied to define the permeability architecture or the “plumbing” that controls subsurface fluid flow and contaminant migration. First, the geologic and depositional setting was synthesized based on regional geologic data, and representative facies models were identified for the site. Second, the existing CSM and site lithology data were reviewed and existing lithology data were graphically presented to display vertical grain-size patterns. This analysis focused on the nexus between the depositional environment and the site-specific subsurface data resulting in correlations/interpretations between and beyond data points that are based on established stratigraphic principles. The depositional environment results in buried river channels as the primary control on subsurface fluid flow, which defines hydrostratigraphic units (or HSUs). Finally, a hydrostratigraphic CSM that includes maps and cross sections was constructed to depict the HSUs present as a framework to integrate hydro-geology and chemistry data. This study demonstrates that: 1) Highly per-meable buried river channel deposits control subsurface fluid flow and contaminant transport, and have distinct chemical constituents and concentrations (i.e., they represent distinct HSUs), 2) Mapping of such HSUs is feasible with existing boring log data, 3) In settings such as the Santa Clara Valley where groundwater flow is governed by subsurface channel deposits, a hydrostratigraphic mapping approach is superior to a depth-based aquifer zonation approach, and 4) For heterogeneous subsurface, a detailed geology-based definition of the subsurface is an integral component of an environmental forensic analyses to determine contaminant source(s) and pathways.
基金Supported by Special Project of"Grassland Talents"in Inner Mongolia.
文摘The rapid identification of lactic acid bacteria,which are essential microorganisms in the food industry,is of great significance for industrial applications.The identification of lactic acid bacteria traditionally relies on the isolation and identification of pure colonies.While this method is well-established and widely used,it is not without limitations.The subjective judgment inherent in the isolation and purification process introduces potential for error,and the incomplete nature of the isolation process can result in the loss of valuable information.The advent of next generation sequencing has provided a novel approach to the rapid identification of lactic acid bacteria.This technology offers several advantages,including rapidity,accuracy,high throughput,and low cost.Next generation sequencing represents a significant advancement in the field of DNA sequencing.Its ability to rapidly and accurately identify lactic acid bacteria strains in samples with insufficient information or in the presence of multiple lactic acid bacteria sets it apart as a valuable tool.The application of this technology not only circumvents the potential errors inherent in the traditional method but also provides a robust foundation for the expeditious identification of lactic acid bacteria strains and the authentication of bacterial powder in industrial applications.This paper commences with an overview of traditional and molecular biology methods for the identification of lactic acid bacteria.While each method has its own advantages,they are not without limitations in practical application.Subsequently,the paper provides an introduction of the principle,process,advantages,and disadvantages of next generation sequencing,and also details its application in strain identification and rapid identification of lactic acid bacteria.The objective of this study is to provide a comprehensive and reliable basis for the rapid identification of industrial lactic acid bacteria strains and the authenticity identification of bacterial powder.
基金supported by the Genetically Modified Organisms Breeding Major Projects of China (2016ZX08011-003)China Agriculture Research System (CARS-04)CAAS Agricultural Science and Technology Innovation Project
文摘Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.
基金Supported by Science Foundation for the Excellent Youth and Middle-aged Scholars in Qinghai University(2009-QY-19)~~
文摘[Objective] The research aimed to distinguish Chinese herb Qingjiao from its botanical origin plants by comparing different DNA sequences,so as to provide a molecular basis for origin identification and quality evaluation.[Method] The cpDNA psbA-trnH and nrDNA ITS sequences of five Chinese herb Qingjiao plants,including Gentiana macrophylla pall.,Gentiana straminea Maxim.,Gentiana crassicaulis Duthie ex Burk.,Gentiana dahurica Fisch and Gentiana officinalis H.Smith,were amplified with PCR,and then sequenced by direct PCR sequencing method for homologous analysis.[Results] The length of cpDNA psbA-trnH of five plants was 316-318 bp;there were seven different haplotypes and seven variable sites;the GC content of the sequence was 21.2%;the phylogenetic clustering showed the same result as haplotype analysis.The length of nrDNA ITS sequence of five plants was 624-625 bp,there were five different haplotypes and 13 variable sites;the GC content of the sequence was 59.3%.The result of phylogenetic clustering suggested that G.dahurica and G.straminea,G.macrophylla and G.officinalis clustered together as sister clades,respectively.[Conclusion] The nucleotide differences of nrDNA ITS regions could be used for distinguishing botanical origin in Chinese herb Qingjiao.
文摘MicroRNAs (miRNAs) are a class of ~22 nucleotides long non coding RNA molecules which play an important role in gene regulation at the post transcriptional level. The conserved nature of miRNAs provides the basis of new miRNA identification through homology search. In an attempt to identify new conserved miRNAs in tea, previously known plant miRNAs were used for searching their homolog in a tea Expressed Sequence Tags and full length nucleotide sequence database. The sequences showing homolog no more than four mismatches were predicted for their fold back structures and passed through a series of filtration criteria, finally led us to identify 13 conserved miRNAs in tea belonging to 9 miRNA families. A total of 37 potential target genes in Arabidopsis were identified subsequently for 7 miRNA families based on their sequence complementarity which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%). Overall, our findings will accelerate the way for further researches of miRNAs and their functions in tea.
