Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are n...Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are not currently available in pigs.In this study,based on GBTS technology,we first developed a 50K panel,including 52,000 single-nucleotide polymorphisms(SNPs),in pigs,designated GBTS50K.A total of 6,032 individuals of Large White,Landrace,and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.Our results showed that GBTS50K obtained a high genotyping ability,the SNP and individual call rates of GBTS50K were 0.997–0.998,and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993,respectively,in replicate samples.We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis,selection signature detection,genome-wide association studies(GWAS),genotyped imputation,genetic selection(GS),etc.The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.For example,GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.Particularly,due to the multiple SNPs(mSNPs),GBTS50K generated 100K qualified SNPs without increasing genotyping cost,and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs,and it is also helpful for developing SNP panels for other farm animals.展开更多
为了研究大型肉牛比利时蓝牛生长发育的遗传规律,筛选优异基因,试验基于Illumina Bovine SNP 50K芯片数据,采用PLINK软件对270头比利时蓝牛常染色体数据进行基因组长纯合片段(ROH)检测并基于选择信号分析,通过核苷酸多态性检测取前5%的...为了研究大型肉牛比利时蓝牛生长发育的遗传规律,筛选优异基因,试验基于Illumina Bovine SNP 50K芯片数据,采用PLINK软件对270头比利时蓝牛常染色体数据进行基因组长纯合片段(ROH)检测并基于选择信号分析,通过核苷酸多态性检测取前5%的单核苷酸多态性(single nucleotide polymorphism,SNP)位点,基于牛参考基因组(ARS-UCD1.2)对结果SNPs进行基因注释,对候选基因进行GO功能注释与KEGG信号通路富集分析,并计算染色体上ROH长度占基因组总长度的比例(FROH)。结果表明:在全部270个个体数据中共检测出1893个ROH片段,平均长度13.2311 Mb,平均FROH为0.0392;得到与生长发育相性状相关的基因有NEB、TET2、NEK11、NCKAP1、MYH15、EIF4A2、bta-miR-1248-1、DCAF8、PRORP、DOCK3、SYT15、MYEF2、ZDHHC13,与公牛生育能力相关的基因有CFAP61、DNAL1、BAG1。说明通过对比利时蓝牛生长发育性状相关分子标记的解析可以为比利时蓝牛遗传改良提供理论指导。展开更多
【目的】检测隆林猪的全基因组拷贝数变异。【方法】采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV...【目的】检测隆林猪的全基因组拷贝数变异。【方法】采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV软件分别检测拷贝数变异(copy number variation,CNV),并利用Bedtools软件将CNV合并为拷贝数变异区域(copy number variation region,CNVR),使用Biomart对CNVR进行基因定位,利用David网站对定位到的基因进行GO和KEGG富集分析,使用猪QTL数据库对共同CNVR进行QTL注释。【结果】CNVPartition软件共检测到260个CNVs,合并为47个CNVRs,其中缺失型40个、获得型5个、混合型2个,共定位到84个基因,显著富集到13条信号通路;PennCNV软件共检测到96个CNVs,合并为15个CNVRs,其中缺失型9个、获得型1个、混合型5个,共定位到8个基因,显著富集到8条信号通路;2个软件检测结果定位到的基因主要富集在嗅觉相关通路和G-蛋白偶联相关通路中,其中INPP5B、NEURL1和GAPDHS基因显著富集到精子活力通路;2个软件获得了3个共同CNVRs,其中缺失型、获得型和混合型均为1个,共定位到8个基因,显著富集到涉及嗅觉感官知觉的化学刺激检测通路、嗅觉受体活性通路、嗅觉转导通路、G-蛋白偶联受体活性通路、G-蛋白偶联受体信号通路、膜整体组件通路和质膜通路共7条信号通路;共有130个QTLs与3个共同CNVRs重叠,其中与背膘厚、肉质和乳头数相关的QTLs分别有11、9和6个。【结论】隆林猪CNV可能与嗅觉功能、繁殖性能、背膘厚、肉质和乳头数性状相关。展开更多
Objective To explore the role of extracellular vesicles(EVs)in the pathogenesis of glaucoma caused by E50K mutation.Methods A photoreceptor cell line,RGC-5,was transfected with empty plasmids and plasmids expressing w...Objective To explore the role of extracellular vesicles(EVs)in the pathogenesis of glaucoma caused by E50K mutation.Methods A photoreceptor cell line,RGC-5,was transfected with empty plasmids and plasmids expressing wild-type(WT)optineurin(OPTN)or E50K OPTN to investigate the effects of OPTN glaucoma as well as to identify the role of EVs in glaucoma pathology.The RGC-5 cells were also stimulated with glutamate,and their viability was evaluated using flow cytometry or CCK-8 assay.EVs were extracted,labeled with PKH-26,and added into the medium for normal RGC-5 culture,and the status of the cells was observed thereafter.Results WT OPTN overexpression,E50K OPTN,and glutamate stimulation induced apoptosis of RGC-5 cells.However,when glutamate stimulation was used as an add-on treatment,the degree of apoptosis in WT OPTN-overexpressing RGC-5 cells was significantly lower than that in E50K OPTN-expressing and normal RGC-5 cells.The viability of normal RGC-5 cells was reduced when co-cultured with WT OPTN-overexpressing RGC-5 or E50K OPTN-overexpressing RGC-5.EVs released by the latter two transfected lines similarly reduced normal RGC-5 survival.Conclusion Our results indicate that WT OPTN overexpression may lead to photoreceptor apoptosis.However,overexpression also confers a degree of protection against high concentrations of extracellular glutamate.Additionally,EVs released by transfected RGC-5 cells may regulate the cell state.These findings may improve our understanding of the mechanisms of cell-cell interactions in pathological conditions,providing a basis for the use of EVs as novel targets for early diagnosis and treatment of glaucoma.展开更多
Movies are the better source of entertainment.Every year,a great percentage of movies are released.People comment on movies in the form of reviews after watching them.Since it is difficult to read all of the reviews f...Movies are the better source of entertainment.Every year,a great percentage of movies are released.People comment on movies in the form of reviews after watching them.Since it is difficult to read all of the reviews for a movie,summarizing all of the reviews will help make this decision without wasting time in reading all of the reviews.Opinion mining also known as sentiment analysis is the process of extracting subjective information from textual data.Opinion mining involves identifying and extracting the opinions of individuals,which can be positive,neutral,or negative.The task of opinion mining also called sentiment analysis is performed to understand people’s emotions and attitudes in movie reviews.Movie reviews are an important source of opinion data because they provide insight into the general public’s opinions about a particular movie.The summary of all reviews can give a general idea about the movie.This study compares baseline techniques,Logistic Regression,Random Forest Classifier,Decision Tree,K-Nearest Neighbor,Gradient Boosting Classifier,and Passive Aggressive Classifier with Linear Support Vector Machines and Multinomial Naïve Bayes on the IMDB Dataset of 50K reviews and Sentiment Polarity Dataset Version 2.0.Before applying these classifiers,in pre-processing both datasets are cleaned,duplicate data is dropped and chat words are treated for better results.On the IMDB Dataset of 50K reviews,Linear Support Vector Machines achieve the highest accuracy of 89.48%,and after hyperparameter tuning,the Passive Aggressive Classifier achieves the highest accuracy of 90.27%,while Multinomial Nave Bayes achieves the highest accuracy of 70.69%and 71.04%after hyperparameter tuning on the Sentiment Polarity Dataset Version 2.0.This study highlights the importance of sentiment analysis as a tool for understanding the emotions and attitudes in movie reviews and predicts the performance of a movie based on the average sentiment of all the reviews.展开更多
基金supported by the grants from the Key R&D Program of Shandong Province,China(2022LZGC003)the China Agriculture Research System of MOF and MARA(CARS-35)+1 种基金the National Key Research and Development Project of China(2019YFE0106800)the 2115 Talent Development Program of China Agricultural University。
文摘Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are not currently available in pigs.In this study,based on GBTS technology,we first developed a 50K panel,including 52,000 single-nucleotide polymorphisms(SNPs),in pigs,designated GBTS50K.A total of 6,032 individuals of Large White,Landrace,and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.Our results showed that GBTS50K obtained a high genotyping ability,the SNP and individual call rates of GBTS50K were 0.997–0.998,and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993,respectively,in replicate samples.We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis,selection signature detection,genome-wide association studies(GWAS),genotyped imputation,genetic selection(GS),etc.The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.For example,GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.Particularly,due to the multiple SNPs(mSNPs),GBTS50K generated 100K qualified SNPs without increasing genotyping cost,and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs,and it is also helpful for developing SNP panels for other farm animals.
文摘【目的】检测隆林猪的全基因组拷贝数变异。【方法】采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV软件分别检测拷贝数变异(copy number variation,CNV),并利用Bedtools软件将CNV合并为拷贝数变异区域(copy number variation region,CNVR),使用Biomart对CNVR进行基因定位,利用David网站对定位到的基因进行GO和KEGG富集分析,使用猪QTL数据库对共同CNVR进行QTL注释。【结果】CNVPartition软件共检测到260个CNVs,合并为47个CNVRs,其中缺失型40个、获得型5个、混合型2个,共定位到84个基因,显著富集到13条信号通路;PennCNV软件共检测到96个CNVs,合并为15个CNVRs,其中缺失型9个、获得型1个、混合型5个,共定位到8个基因,显著富集到8条信号通路;2个软件检测结果定位到的基因主要富集在嗅觉相关通路和G-蛋白偶联相关通路中,其中INPP5B、NEURL1和GAPDHS基因显著富集到精子活力通路;2个软件获得了3个共同CNVRs,其中缺失型、获得型和混合型均为1个,共定位到8个基因,显著富集到涉及嗅觉感官知觉的化学刺激检测通路、嗅觉受体活性通路、嗅觉转导通路、G-蛋白偶联受体活性通路、G-蛋白偶联受体信号通路、膜整体组件通路和质膜通路共7条信号通路;共有130个QTLs与3个共同CNVRs重叠,其中与背膘厚、肉质和乳头数相关的QTLs分别有11、9和6个。【结论】隆林猪CNV可能与嗅觉功能、繁殖性能、背膘厚、肉质和乳头数性状相关。
基金supported by grants from the Wuhan Science and Technology Bureau(No.02.07.17040008.05)the Fundamental Research Funds for the Central Universities(2042020kf0099)the Opening Foundation of Hubei Key Laboratory(No.2021KFY054).
文摘Objective To explore the role of extracellular vesicles(EVs)in the pathogenesis of glaucoma caused by E50K mutation.Methods A photoreceptor cell line,RGC-5,was transfected with empty plasmids and plasmids expressing wild-type(WT)optineurin(OPTN)or E50K OPTN to investigate the effects of OPTN glaucoma as well as to identify the role of EVs in glaucoma pathology.The RGC-5 cells were also stimulated with glutamate,and their viability was evaluated using flow cytometry or CCK-8 assay.EVs were extracted,labeled with PKH-26,and added into the medium for normal RGC-5 culture,and the status of the cells was observed thereafter.Results WT OPTN overexpression,E50K OPTN,and glutamate stimulation induced apoptosis of RGC-5 cells.However,when glutamate stimulation was used as an add-on treatment,the degree of apoptosis in WT OPTN-overexpressing RGC-5 cells was significantly lower than that in E50K OPTN-expressing and normal RGC-5 cells.The viability of normal RGC-5 cells was reduced when co-cultured with WT OPTN-overexpressing RGC-5 or E50K OPTN-overexpressing RGC-5.EVs released by the latter two transfected lines similarly reduced normal RGC-5 survival.Conclusion Our results indicate that WT OPTN overexpression may lead to photoreceptor apoptosis.However,overexpression also confers a degree of protection against high concentrations of extracellular glutamate.Additionally,EVs released by transfected RGC-5 cells may regulate the cell state.These findings may improve our understanding of the mechanisms of cell-cell interactions in pathological conditions,providing a basis for the use of EVs as novel targets for early diagnosis and treatment of glaucoma.
文摘Movies are the better source of entertainment.Every year,a great percentage of movies are released.People comment on movies in the form of reviews after watching them.Since it is difficult to read all of the reviews for a movie,summarizing all of the reviews will help make this decision without wasting time in reading all of the reviews.Opinion mining also known as sentiment analysis is the process of extracting subjective information from textual data.Opinion mining involves identifying and extracting the opinions of individuals,which can be positive,neutral,or negative.The task of opinion mining also called sentiment analysis is performed to understand people’s emotions and attitudes in movie reviews.Movie reviews are an important source of opinion data because they provide insight into the general public’s opinions about a particular movie.The summary of all reviews can give a general idea about the movie.This study compares baseline techniques,Logistic Regression,Random Forest Classifier,Decision Tree,K-Nearest Neighbor,Gradient Boosting Classifier,and Passive Aggressive Classifier with Linear Support Vector Machines and Multinomial Naïve Bayes on the IMDB Dataset of 50K reviews and Sentiment Polarity Dataset Version 2.0.Before applying these classifiers,in pre-processing both datasets are cleaned,duplicate data is dropped and chat words are treated for better results.On the IMDB Dataset of 50K reviews,Linear Support Vector Machines achieve the highest accuracy of 89.48%,and after hyperparameter tuning,the Passive Aggressive Classifier achieves the highest accuracy of 90.27%,while Multinomial Nave Bayes achieves the highest accuracy of 70.69%and 71.04%after hyperparameter tuning on the Sentiment Polarity Dataset Version 2.0.This study highlights the importance of sentiment analysis as a tool for understanding the emotions and attitudes in movie reviews and predicts the performance of a movie based on the average sentiment of all the reviews.
