Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
Recent technological advances in cotton(Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis.High-throughput phenotyping(HTP) is a non-destructive and rapid a...Recent technological advances in cotton(Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis.High-throughput phenotyping(HTP) is a non-destructive and rapid approach of monitoring and measuring multiple phenotypic traits related to the growth,yield,and adaptation to biotic or abiotic stress.Researchers have conducted extensive experiments on HTP and developed techniques including spectral,fluorescence,thermal,and three-dimensional imaging to measure the morphological,physiological,and pathological resistance traits of cotton.In addition,ground-based and aerial-based platforms were also developed to aid in the implementation of these HTP systems.This review paper highlights the techniques and recent developments for HTP in cotton,reviews the potential applications according to morphological and physiological traits of cotton,and compares the advantages and limitations of these HTP systems when used in cotton cropping systems.Overall,the use of HTP has generated many opportunities to accurately and efficiently measure and analyze diverse traits of cotton.However,because of its relative novelty,HTP has some limitations that constrains the ability to take full advantage of what it can offer.These challenges need to be addressed to increase the accuracy and utility of HTP,which can be done by integrating analytical techniques for big data and continuous advances in imaging.展开更多
Abstract： A simple optimized microplate-based method to assay endo-1,4-β-mannosidase activity was described as an improved high-throughput screening method. A series of experimental conditions were optimized. It is ...Abstract： A simple optimized microplate-based method to assay endo-1,4-β-mannosidase activity was described as an improved high-throughput screening method. A series of experimental conditions were optimized. It is revealed that the optimum measurement procedure is as follows： adding 50μL of diluted enzyme sample and 50 μL substrate, incubating at 45 ℃ for exactly 5 min in micro-plate, mixing with 100 μL 3,5-dinitrosalicylic acid （DNS） reagent, maintaining at boiling point for 15 rain, cooling down to room temperature before determining the ABS value at 540 nm using an ELISA micro-plate reader. The reaction volume of the optimized microplate-assay is reduced to 200μL from 2 500 μL used in the standard β-mannanase macro-assay. The optimized micro-assay is significantly more sensitive in all of the 643 candidates during endo-1,4-β-mannosidase screening. Statistical analyses show that the sensitivity of the optimized micro-method is significantly greater than that of the macro-assay. The optimized method is convenient, fast, and cheap for high throughput enzyme screening.展开更多
Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.Thi...Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.展开更多
为研究消毒剂对猪粪厌氧发酵系统的影响,选取不同浓度(质量分数0.02%、0.1%、0.5%)卫可(Virkon^(TM))消毒剂进行试验。结果表明:在高浓度Virkon^(TM)胁迫下,厌氧发酵系统出水中总氮(total nitrogen,TN)、氨氮(ammonia nitrogen,NH_(4)^(...为研究消毒剂对猪粪厌氧发酵系统的影响,选取不同浓度(质量分数0.02%、0.1%、0.5%)卫可(Virkon^(TM))消毒剂进行试验。结果表明:在高浓度Virkon^(TM)胁迫下,厌氧发酵系统出水中总氮(total nitrogen,TN)、氨氮(ammonia nitrogen,NH_(4)^(+)-N)、总磷(total phosphorus,TP)和化学需氧量(chemical oxygen demand,COD)等含量异常剧增,伴随TS和VS的降解率下降。对照组(CK组)和0.02%、0.1%和0.5%Virkon^(TM)试验组(分别记为L组、M组和H组)的最大产CH_(4)速率分别为63.20、71.63、73.10和38.17mL/g且CH_4总产量分别降低4.48%、16.58%(P<0.001)和86.33%(P<0.001)。随着暴露时间的延长,试验组的关键酶活呈先升后降趋势,其中,H组的S-α-GC、S-β-GC、S-ACP、S-NP及S-CAT等土壤酶活被显著性抑制(P<0.05)。进一步结合高通量测序发现,在整个厌氧发酵阶段,H组Ace指数、Chao指数和Shannon指数均显著性低于CK组(P<0.01)。在门水平上,第一优势菌群为厚壁菌门,其次为变形菌门,其中厚壁菌门相对丰度随Virkon^(TM)浓度的上升而降低,而变形菌门则相反;在属水平上,随着厌氧发酵时间的延长,束毛球菌属(Trichococcus)相对丰度均出现不同程度上升,由0.19%~0.39%提升至2.80%~4.20%,而H组中史密斯氏菌属(Smithella)的相对丰度受到极显著性(P<0.001)的抑制,较CK组下降91%。同时通过PICRUSt2功能预测分析发现,各试验组微生物群落COG(clusters of orthologous groups of proteins)功能组成结构差异并不明显,未知功能及氨基酸运输和代谢为主要优势功能;结合KO(KEGG orthology)结果与KEGG(kyoto encyclopedia of genes and genomes)数据库相关基因分析发现,高浓度Virkon^(TM)显著抑制微生物群落的生长代谢活性并削弱厌氧发酵系统的甲烷合成效能,另一方面,却诱导关键功能基因K00531(anfG)的表达活性发生超量级响应,较对照组(CK)激增约272倍。其表达水平的显著上调可能通过强化关键酶活性,使系统对Virkon^(TM)消毒副产物中典型氯代污染物(氯代烷烃及氯代烯烃类化合物)的降解效率获得提升,结果可为猪粪厌氧消化处理提供参考。展开更多
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
文摘Recent technological advances in cotton(Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis.High-throughput phenotyping(HTP) is a non-destructive and rapid approach of monitoring and measuring multiple phenotypic traits related to the growth,yield,and adaptation to biotic or abiotic stress.Researchers have conducted extensive experiments on HTP and developed techniques including spectral,fluorescence,thermal,and three-dimensional imaging to measure the morphological,physiological,and pathological resistance traits of cotton.In addition,ground-based and aerial-based platforms were also developed to aid in the implementation of these HTP systems.This review paper highlights the techniques and recent developments for HTP in cotton,reviews the potential applications according to morphological and physiological traits of cotton,and compares the advantages and limitations of these HTP systems when used in cotton cropping systems.Overall,the use of HTP has generated many opportunities to accurately and efficiently measure and analyze diverse traits of cotton.However,because of its relative novelty,HTP has some limitations that constrains the ability to take full advantage of what it can offer.These challenges need to be addressed to increase the accuracy and utility of HTP,which can be done by integrating analytical techniques for big data and continuous advances in imaging.
基金Project(31000350)supported by the National Natural Science Foundation of China
文摘Abstract： A simple optimized microplate-based method to assay endo-1,4-β-mannosidase activity was described as an improved high-throughput screening method. A series of experimental conditions were optimized. It is revealed that the optimum measurement procedure is as follows： adding 50μL of diluted enzyme sample and 50 μL substrate, incubating at 45 ℃ for exactly 5 min in micro-plate, mixing with 100 μL 3,5-dinitrosalicylic acid （DNS） reagent, maintaining at boiling point for 15 rain, cooling down to room temperature before determining the ABS value at 540 nm using an ELISA micro-plate reader. The reaction volume of the optimized microplate-assay is reduced to 200μL from 2 500 μL used in the standard β-mannanase macro-assay. The optimized micro-assay is significantly more sensitive in all of the 643 candidates during endo-1,4-β-mannosidase screening. Statistical analyses show that the sensitivity of the optimized micro-method is significantly greater than that of the macro-assay. The optimized method is convenient, fast, and cheap for high throughput enzyme screening.
基金Supported by the Natural Science Fund of Heilongjiang Province(LC2016009)(GH)U.S.Department of Energy and U.S.Department of Agricultural Plant Feedstocks Genomics for Bioenergy Program(DE-SC0008338 to XZ and BZ)。
文摘Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.
文摘为研究消毒剂对猪粪厌氧发酵系统的影响,选取不同浓度(质量分数0.02%、0.1%、0.5%)卫可(Virkon^(TM))消毒剂进行试验。结果表明:在高浓度Virkon^(TM)胁迫下,厌氧发酵系统出水中总氮(total nitrogen,TN)、氨氮(ammonia nitrogen,NH_(4)^(+)-N)、总磷(total phosphorus,TP)和化学需氧量(chemical oxygen demand,COD)等含量异常剧增,伴随TS和VS的降解率下降。对照组(CK组)和0.02%、0.1%和0.5%Virkon^(TM)试验组(分别记为L组、M组和H组)的最大产CH_(4)速率分别为63.20、71.63、73.10和38.17mL/g且CH_4总产量分别降低4.48%、16.58%(P<0.001)和86.33%(P<0.001)。随着暴露时间的延长,试验组的关键酶活呈先升后降趋势,其中,H组的S-α-GC、S-β-GC、S-ACP、S-NP及S-CAT等土壤酶活被显著性抑制(P<0.05)。进一步结合高通量测序发现,在整个厌氧发酵阶段,H组Ace指数、Chao指数和Shannon指数均显著性低于CK组(P<0.01)。在门水平上,第一优势菌群为厚壁菌门,其次为变形菌门,其中厚壁菌门相对丰度随Virkon^(TM)浓度的上升而降低,而变形菌门则相反;在属水平上,随着厌氧发酵时间的延长,束毛球菌属(Trichococcus)相对丰度均出现不同程度上升,由0.19%~0.39%提升至2.80%~4.20%,而H组中史密斯氏菌属(Smithella)的相对丰度受到极显著性(P<0.001)的抑制,较CK组下降91%。同时通过PICRUSt2功能预测分析发现,各试验组微生物群落COG(clusters of orthologous groups of proteins)功能组成结构差异并不明显,未知功能及氨基酸运输和代谢为主要优势功能;结合KO(KEGG orthology)结果与KEGG(kyoto encyclopedia of genes and genomes)数据库相关基因分析发现,高浓度Virkon^(TM)显著抑制微生物群落的生长代谢活性并削弱厌氧发酵系统的甲烷合成效能,另一方面,却诱导关键功能基因K00531(anfG)的表达活性发生超量级响应,较对照组(CK)激增约272倍。其表达水平的显著上调可能通过强化关键酶活性,使系统对Virkon^(TM)消毒副产物中典型氯代污染物(氯代烷烃及氯代烯烃类化合物)的降解效率获得提升,结果可为猪粪厌氧消化处理提供参考。
