首页 > 最新文献

Hereditas最新文献

英文 中文
Effect on the expression of drd2 and drd3 after neonatal lesion in the lymphocytes, nucleus accumbens, hippocampus and prefrontal cortex: comparative analysis between juvenile and adult Wistar rats 新生儿损伤后淋巴细胞、伏隔核、海马和前额皮质中drd2和drd3表达的影响:幼鼠与成年Wistar大鼠的比较分析
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-11-22 DOI: 10.1186/s41065-016-0018-9
A. Genis-Mendoza, C. Tovilla-Zárate, Lilia López-Narváez, P. Mendoza-Lorenzo, P. Ostrosky-Wegman, H. Nicolini, T. González-Castro, Yazmín Hernández-Díaz
{"title":"Effect on the expression of drd2 and drd3 after neonatal lesion in the lymphocytes, nucleus accumbens, hippocampus and prefrontal cortex: comparative analysis between juvenile and adult Wistar rats","authors":"A. Genis-Mendoza, C. Tovilla-Zárate, Lilia López-Narváez, P. Mendoza-Lorenzo, P. Ostrosky-Wegman, H. Nicolini, T. González-Castro, Yazmín Hernández-Díaz","doi":"10.1186/s41065-016-0018-9","DOIUrl":"https://doi.org/10.1186/s41065-016-0018-9","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0018-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Efficient callus formation and plant regeneration are heritable characters in sugar beet (Beta vulgaris L.) 甜菜(Beta vulgaris L.)愈伤组织形成和植株再生的遗传特性
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-11-15 DOI: 10.1186/s41065-016-0015-z
Hiroyo Kagami, K. Taguchi, Takumi Arakawa, Y. Kuroda, H. Tamagake, T. Kubo
{"title":"Efficient callus formation and plant regeneration are heritable characters in sugar beet (Beta vulgaris L.)","authors":"Hiroyo Kagami, K. Taguchi, Takumi Arakawa, Y. Kuroda, H. Tamagake, T. Kubo","doi":"10.1186/s41065-016-0015-z","DOIUrl":"https://doi.org/10.1186/s41065-016-0015-z","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0015-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections 全基因组SNP分型调查医疗保健提供者中耐甲氧西林金黄色葡萄球菌携带作为多个手术部位感染的来源
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-11-14 DOI: 10.1186/s41065-016-0017-x
Chandler C. Roe, Kim Horn, E. Driebe, J. Bowers, J. Terriquez, P. Keim, D. Engelthaler
{"title":"Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections","authors":"Chandler C. Roe, Kim Horn, E. Driebe, J. Bowers, J. Terriquez, P. Keim, D. Engelthaler","doi":"10.1186/s41065-016-0017-x","DOIUrl":"https://doi.org/10.1186/s41065-016-0017-x","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0017-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden. 瑞典东南部Alternaria solani分离物的遗传多样性和F129L置换的发生。
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-09-23 eCollection Date: 2016-01-01 DOI: 10.1186/s41065-016-0014-0
Firuz Odilbekov, Eva Edin, Larisa Garkava-Gustavsson, Helena Persson Hovmalm, Erland Liljeroth

Background: Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides.

Results: Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin.

Conclusions: Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.

背景:由Alternaria solani真菌引起的马铃薯早疫病主要发生在瑞典的东南部地区,但也发生在瑞典的其他地区。本研究的目的是利用 AFLP 标记分析法研究来自瑞典东南部不同马铃薯种植区的 A. solani 群体的遗传多样性。此外,还检测了培养分离物中编码细胞色素 b 的基因是否发生了替代,这与对 QoI 杀菌剂丧失敏感性有关:瑞典种群的内氏基因多样性指数(Nei's gene diversity index)显示基因多样性高达 0.20。瑞典东南部不同地区的 A. solani 种群之间也存在基因差异。对 A. solani 分离物的线粒体基因型进行了测定,在分离物中发现了两种已知的基因型:GI(基因型 1)和 GII(基因型 2)。在 GII 型分离物中证实了 F129L 替代的发生,它对石硫合剂失去了敏感性。体外分生孢子萌发试验证实,含有 F129L 替代的分离株对唑菌酰胺的敏感性降低,对吡唑醚菌酯的敏感性也有所降低:结论:瑞典东南部的茄属真菌分离物的遗传多样性相对较高。在田间种群中已经发现了 F129L 替代,这种替代会导致对石硫合剂的敏感性降低,这可能会对 QoI 杀菌剂的未来药效产生影响。
{"title":"Genetic diversity and occurrence of the F129L substitutions among isolates of <i>Alternaria solani</i> in south-eastern Sweden.","authors":"Firuz Odilbekov, Eva Edin, Larisa Garkava-Gustavsson, Helena Persson Hovmalm, Erland Liljeroth","doi":"10.1186/s41065-016-0014-0","DOIUrl":"10.1186/s41065-016-0014-0","url":null,"abstract":"<p><strong>Background: </strong>Early blight, caused by the fungus <i>Alternaria solani,</i> occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of <i>A. solani</i> populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome <i>b</i>, associated with loss of sensitivity against QoI fungicides.</p><p><strong>Results: </strong>Nei's gene diversity index for the Swedish populations of <i>A. solani</i> revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of <i>A. solani</i> from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of <i>A. solani</i> was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin.</p><p><strong>Conclusions: </strong>Genetic diversity was relatively high among isolates of <i>A. solani</i> in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5226105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Increasing the efficiency of homologous recombination vector-mediated end joining repair by inhibition of Lig4 gene using siRNA in sheep embryo fibroblasts. 利用siRNA抑制Lig4基因提高羊胚胎成纤维细胞同源重组载体介导的末端连接修复效率。
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-09-01 DOI: 10.16288/j.yczz.16-074
Wei Wang, Yu-shuang Wang, Lan-lan Huang, Zi-jian Jian, Xin-Hua Wang, Shou-ren Liu, Wen-hui Pi
In animal cells, inhibition of non-homologous end joining (NHEJ) pathway improves the efficiency of homologous recombination (HR)-mediated double-strand brakes (DSBs) repair. To improve the efficiency of HR in sheep embryo fibroblasts, the NHEJ key molecule DNA ligase 4 (Lig4) was suppressed by siRNA interference. Four pairs of siRNA targeting Lig4 were designed and chemically synthesized. These siRNA were electro-transferred into sheep embryo fibroblasts respectively. Compared with the control groups, two pairs of siRNA were identified to effectively inhibit the expression of sheep Lig4 gene by qRT-PCR and Western blotting. The plasmid rejoining assay was adopted for examining the efficiency of HR-mediated DSB repair. I-SceⅠ endonuclease linearized vector and siRNA were co-transfected into sheep embryo fibroblasts. Flow cytometry analysis of cells after transfection for 72 h showed that suppression of Lig4 using siRNAs increased the rejoining efficiency of HR vector by 3-4 times compared with the control groups. Therefore, enhanced HR vector rejoining frequency by instant inhabition of Lig4 gene provides theoretical basis for improving gene targeting efficiency of sheep embryo fibroblasts.
在动物细胞中,抑制非同源末端连接(non-homologous end joining, NHEJ)途径可提高同源重组(homologous recombination, HR)介导的双链刹车(double-strand brakes, DSBs)修复效率。为了提高绵羊胚胎成纤维细胞的HR效率,通过siRNA干扰抑制NHEJ关键分子DNA连接酶4 (Lig4)。设计并化学合成了4对靶向Lig4的siRNA。这些siRNA分别被电转移到绵羊胚胎成纤维细胞中。与对照组相比,通过qRT-PCR和Western blotting鉴定出两对能有效抑制绵羊Lig4基因表达的siRNA。采用质粒重连接法检测hr介导的DSB修复效率。将I-SceⅠ核酸内切酶线性化载体与siRNA共转染羊胚成纤维细胞。转染72 h后的细胞流式细胞术分析显示,与对照组相比,使用sirna抑制Lig4可使HR载体的重连接效率提高3-4倍。因此,通过瞬时转染Lig4基因提高HR载体的重连接频率,为提高羊胚成纤维细胞的基因靶向效率提供了理论依据。
{"title":"Increasing the efficiency of homologous recombination vector-mediated end joining repair by inhibition of Lig4 gene using siRNA in sheep embryo fibroblasts.","authors":"Wei Wang, Yu-shuang Wang, Lan-lan Huang, Zi-jian Jian, Xin-Hua Wang, Shou-ren Liu, Wen-hui Pi","doi":"10.16288/j.yczz.16-074","DOIUrl":"https://doi.org/10.16288/j.yczz.16-074","url":null,"abstract":"In animal cells, inhibition of non-homologous end joining (NHEJ) pathway improves the efficiency of homologous recombination (HR)-mediated double-strand brakes (DSBs) repair. To improve the efficiency of HR in sheep embryo fibroblasts, the NHEJ key molecule DNA ligase 4 (Lig4) was suppressed by siRNA interference. Four pairs of siRNA targeting Lig4 were designed and chemically synthesized. These siRNA were electro-transferred into sheep embryo fibroblasts respectively. Compared with the control groups, two pairs of siRNA were identified to effectively inhibit the expression of sheep Lig4 gene by qRT-PCR and Western blotting. The plasmid rejoining assay was adopted for examining the efficiency of HR-mediated DSB repair. I-SceⅠ endonuclease linearized vector and siRNA were co-transfected into sheep embryo fibroblasts. Flow cytometry analysis of cells after transfection for 72 h showed that suppression of Lig4 using siRNAs increased the rejoining efficiency of HR vector by 3-4 times compared with the control groups. Therefore, enhanced HR vector rejoining frequency by instant inhabition of Lig4 gene provides theoretical basis for improving gene targeting efficiency of sheep embryo fibroblasts.","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67512674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Research advances on microbial genetics in China in 2015. 2015年中国微生物遗传学研究进展。
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-09-01 DOI: 10.16288/J.YCZZ.16-305
X. Jianping, H. Yubo, L. Gang, B. Linquan
In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled. We also illustrated the biosynthetic pathways and regulators of multiple microbial compounds, novel enzyme reactions, and new mechanisms regulating microbial gene expression. And new findings were obtained in the microbial development, evolution and population genetics. For the industrial microbiology, more understanding on the molecular basis of the microbial factory has been gained. For the pathogenic microbiology, the genetic circuits of several pathogens were depicted, and significant progresses were achieved for understanding the pathogen-host interaction and revealing the genetic mechanisms underlying antimicrobial resistance, emerging pathogens and environmental microorganisms at the genomic level. In future, the genetic diversity of microbes can be used to obtain specific products, while gut microbiome is gathering momentum.
2015年,中国微生物遗传学在许多方面都取得了重大进展。为了展示中国科学家在微生物遗传学方面的贡献,本文综述了中国科学家在微生物遗传学方面取得的一些显著进展,并重点介绍了一些重要发现。在微生物遗传学的基础上,许多参与基因表达调控的大分子复合物的组成、结构和功能已经被阐明。此外,揭示了微生物免疫系统识别外来核酸的分子基础。我们还阐述了多种微生物化合物的生物合成途径和调节因子,新的酶反应,以及调节微生物基因表达的新机制。在微生物发育、进化、群体遗传学等方面有了新的发现。对于工业微生物学,对微生物工厂的分子基础有了更多的了解。在病原微生物学方面,描述了几种病原菌的遗传回路,并在基因组水平上对病原菌-宿主相互作用的理解和耐药性、新发病原菌和环境微生物的遗传机制的揭示取得了重大进展。未来,微生物的遗传多样性可以用来获得特定的产品,而肠道微生物组正在积聚动力。
{"title":"Research advances on microbial genetics in China in 2015.","authors":"X. Jianping, H. Yubo, L. Gang, B. Linquan","doi":"10.16288/J.YCZZ.16-305","DOIUrl":"https://doi.org/10.16288/J.YCZZ.16-305","url":null,"abstract":"In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled. We also illustrated the biosynthetic pathways and regulators of multiple microbial compounds, novel enzyme reactions, and new mechanisms regulating microbial gene expression. And new findings were obtained in the microbial development, evolution and population genetics. For the industrial microbiology, more understanding on the molecular basis of the microbial factory has been gained. For the pathogenic microbiology, the genetic circuits of several pathogens were depicted, and significant progresses were achieved for understanding the pathogen-host interaction and revealing the genetic mechanisms underlying antimicrobial resistance, emerging pathogens and environmental microorganisms at the genomic level. In future, the genetic diversity of microbes can be used to obtain specific products, while gut microbiome is gathering momentum.","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.16288/J.YCZZ.16-305","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67512879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Insight into the genetic variability analysis and cultivar identification of tall fescue by using SSR markers 利用SSR标记分析高羊茅的遗传变异及品种鉴定
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-08-11 DOI: 10.1186/s41065-016-0013-1
Kaixin Fu, Zhihui Guo, Xinquan Zhang, Yan Fan, Wendan Wu, Daxu Li, Yan Peng, Linkai Huang, Ming-Mao Sun, S. Bai, Xiao Ma
{"title":"Insight into the genetic variability analysis and cultivar identification of tall fescue by using SSR markers","authors":"Kaixin Fu, Zhihui Guo, Xinquan Zhang, Yan Fan, Wendan Wu, Daxu Li, Yan Peng, Linkai Huang, Ming-Mao Sun, S. Bai, Xiao Ma","doi":"10.1186/s41065-016-0013-1","DOIUrl":"https://doi.org/10.1186/s41065-016-0013-1","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0013-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Genetic structure of Mount Huang honey bee (Apis cerana) populations: evidence from microsatellite polymorphism 黄山蜜蜂群体遗传结构:来自微卫星多态性的证据
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-07-06 DOI: 10.1186/s41065-016-0010-4
Fang Liu, Tengfei Shi, Sisi Huang, Linsheng Yu, S. Bi
{"title":"Genetic structure of Mount Huang honey bee (Apis cerana) populations: evidence from microsatellite polymorphism","authors":"Fang Liu, Tengfei Shi, Sisi Huang, Linsheng Yu, S. Bi","doi":"10.1186/s41065-016-0010-4","DOIUrl":"https://doi.org/10.1186/s41065-016-0010-4","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0010-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Assessment of diversity and genetic relationships of Neonectria ditissima: the causal agent of fruit tree canker 果树溃疡病病原新树蝇的多样性及亲缘关系评价
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-07-01 DOI: 10.1186/s41065-016-0011-3
M. Ghasemkhani, L. Garkava-Gustavsson, E. Liljeroth, H. Nybom
{"title":"Assessment of diversity and genetic relationships of Neonectria ditissima: the causal agent of fruit tree canker","authors":"M. Ghasemkhani, L. Garkava-Gustavsson, E. Liljeroth, H. Nybom","doi":"10.1186/s41065-016-0011-3","DOIUrl":"https://doi.org/10.1186/s41065-016-0011-3","url":null,"abstract":"","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s41065-016-0011-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines. eRFSVM:预测增强子的混合分类器--集成随机森林与支持向量机。
IF 2.7 3区 生物学 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2016-06-30 eCollection Date: 2016-01-01 DOI: 10.1186/s41065-016-0012-2
Fang Huang, Jiawei Shen, Qingli Guo, Yongyong Shi

Background: Enhancers are tissue specific distal regulation elements, playing vital roles in gene regulation and expression. The prediction and identification of enhancers are important but challenging issues for bioinformatics studies. Existing computational methods, mostly single classifiers, can only predict the transcriptional coactivator EP300 based enhancers and show low generalization performance.

Results: We built a hybrid classifier called eRFSVM in this study, using random forests as a base classifier, and support vector machines as a main classifier. eRFSVM integrated two components as eRFSVM-ENCODE and eRFSVM-FANTOM5 with diverse features and labels. The base classifier trained datasets from a single tissue or cell with random forests. The main classifier made the final decision by support vector machines algorithm, with the predicting results of base classifiers as inputs. For eRFSVM-ENCODE, we trained datasets from cell lines including Gm12878, Hep, H1-hesc and Huvec, using ChIP-Seq datasets as features and EP300 based enhancers as labels. We tested eRFSVM-ENCODE on K562 dataset, and resulted in a predicting precision of 83.69 %, which was much better than existing classifiers. For eRFSVM-FANTOM5, with enhancers identified by RNA in FANTOM5 project as labels, the precision, recall, F-score and accuracy were 86.17 %, 36.06 %, 50.84 % and 93.38 % using eRFSVM, increasing 23.24 % (69.92 %), 97.05 % (18.30 %), 76.90 % (28.74 %), 4.69 % (89.20 %) than the existing algorithm, respectively.

Conclusions: All these results demonstrated that eRFSVM was a better classifier in predicting both EP300 based and FAMTOM5 RNAs based enhancers.

背景:增强子是组织特异性远端调控元件,在基因调控和表达中发挥着重要作用。增强子的预测和识别是生物信息学研究中重要但具有挑战性的问题。现有的计算方法大多是单一分类器,只能预测基于转录辅激活因子 EP300 的增强子,而且泛化性能较低:eRFSVM 集成了 eRFSVM-ENCODE 和 eRFSVM-FANTOM5 两个具有不同特征和标签的组件。基础分类器使用随机森林训练来自单一组织或细胞的数据集。主分类器以基础分类器的预测结果为输入,通过支持向量机算法做出最终决定。对于 eRFSVM-ENCODE,我们以 ChIP-Seq 数据集为特征,以基于 EP300 的增强子为标签,训练了来自 Gm12878、Hep、H1-hesc 和 Huvec 等细胞系的数据集。我们在 K562 数据集上测试了 eRFSVM-ENCODE,结果预测精度为 83.69%,远远优于现有的分类器。对于 eRFSVM-FANTOM5,以 FANTOM5 项目中 RNA 鉴定出的增强子为标签,eRFSVM 的精确度、召回率、F-score 和准确率分别为 86.17 %、36.06 %、50.84 % 和 93.38 %,比现有算法分别提高了 23.24 %(69.92 %)、97.05 %(18.30 %)、76.90 %(28.74 %)、4.69 %(89.20 %):所有这些结果表明,eRFSVM 在预测基于 EP300 和基于 FAMTOM5 RNAs 的增强子方面是一种更好的分类器。
{"title":"eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines.","authors":"Fang Huang, Jiawei Shen, Qingli Guo, Yongyong Shi","doi":"10.1186/s41065-016-0012-2","DOIUrl":"10.1186/s41065-016-0012-2","url":null,"abstract":"<p><strong>Background: </strong>Enhancers are tissue specific distal regulation elements, playing vital roles in gene regulation and expression. The prediction and identification of enhancers are important but challenging issues for bioinformatics studies. Existing computational methods, mostly single classifiers, can only predict the transcriptional coactivator EP300 based enhancers and show low generalization performance.</p><p><strong>Results: </strong>We built a hybrid classifier called eRFSVM in this study, using random forests as a base classifier, and support vector machines as a main classifier. eRFSVM integrated two components as eRFSVM-ENCODE and eRFSVM-FANTOM5 with diverse features and labels. The base classifier trained datasets from a single tissue or cell with random forests. The main classifier made the final decision by support vector machines algorithm, with the predicting results of base classifiers as inputs. For eRFSVM-ENCODE, we trained datasets from cell lines including Gm12878, Hep, H1-hesc and Huvec, using ChIP-Seq datasets as features and EP300 based enhancers as labels. We tested eRFSVM-ENCODE on K562 dataset, and resulted in a predicting precision of 83.69 %, which was much better than existing classifiers. For eRFSVM-FANTOM5, with enhancers identified by RNA in FANTOM5 project as labels, the precision, recall, F-score and accuracy were 86.17 %, 36.06 %, 50.84 % and 93.38 % using eRFSVM, increasing 23.24 % (69.92 %), 97.05 % (18.30 %), 76.90 % (28.74 %), 4.69 % (89.20 %) than the existing algorithm, respectively.</p><p><strong>Conclusions: </strong>All these results demonstrated that eRFSVM was a better classifier in predicting both EP300 based and FAMTOM5 RNAs based enhancers.</p>","PeriodicalId":55057,"journal":{"name":"Hereditas","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2016-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5226099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65774437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Hereditas
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1