期刊文献+
共找到9,566篇文章
< 1 2 250 >
每页显示 20 50 100
Current challenges and solutions of de novo assembly
1
作者 Xingyu Liao Min Li +3 位作者 You Zou Fang-Xiang Wu Yi-Pan Jianxin Wang 《中国电气与电子工程前沿:英文版》 CSCD 2019年第2期90-109,共20页
Background:Next-generation sequencing (NGS) technologies have fostered an unprecedented proliferation of highthroughput sequencing projects and a concomitant development of novel algorithms for the assembly of short r... Background:Next-generation sequencing (NGS) technologies have fostered an unprecedented proliferation of highthroughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads.However,numerous technical or computational challenges in de novo assembly still remain,although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings.Results:In this review,we first briefly introduce some of the major challenges faced by NGS sequence assembly.Then,we analyze the characteristics of various sequencing platforms and their impact on assembly results.After that,we classify de novo assemblers according to their frameworks (overlap graph-based,de Bruijn graph-based and string graph-based),and introduce the characteristics of each assembly tool and their adaptation scene.Next,we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data,single-cell sequencing data and single molecule sequencing data.At last,we discuss the application of SMS long reads in solving problems encountered in NGS assembly.Conclusions:This review not only gives an overview of the latest methods and developments in assembly algorithms,but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type. 展开更多
关键词 next-generation SEQUENCING SINGLE-CELL SEQUENCING SINGLE-MOLECULE SEQUENCING de novo assembly algorithms
SeqSQC:A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data
2
作者 Qian Liu Qiang Hu +7 位作者 Song Yao Marilyn L. Kwan Janise M. Roh Hua Zhao Christine B. Ambrosone Lawrence H. Kushi Song Liu Qianqian Zhu 《基因组蛋白质组与生物信息学报:英文版》 CAS CSCD 2019年第2期211-218,共8页
As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits,a number of packages for checking NGS data quality have sprung up in public dom... As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits,a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data,sample quality issues,such as gender mismatch,abnormal inbreeding coefficient,cryptic relatedness,and population outliers,can also have fundamental impact on downstream analysis. However,there is a lack of tools specialized in identifying problematic samples from NGS data,often due to the limitation of sample size and variant counts. We developed SeqSQC,a Bioconductor package,to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access,and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor. org/packages/SeqSQC. 展开更多
关键词 Next-generation SEQUENCING QUALITY assessment 1000 GENOMES Project Whole-exome SEQUENCING BIOCONDUCTOR PACKAGE
Intestinal toxicity of deoxynivalenol is limited by supplementation with Lactobacillus plantarum JM113 and consequentially altered gut microbiota in broiler chickens 预览
3
作者 Shengru Wu Yanli Liu +5 位作者 Yongle Duan Fangyuan Wang Fangshen Guo Fang Yan Xiaojun Yang Xin Yang 《畜牧与生物技术杂志:英文版》 SCIE CAS CSCD 2019年第1期218-230,共13页
Background: Limited research has focused on the effect of Lactobacillus on the intestinal toxicity of deoxynivalenol(DON).The present study was conducted to investigate the role of Lactobacillus plantarum(L.plantarum)... Background: Limited research has focused on the effect of Lactobacillus on the intestinal toxicity of deoxynivalenol(DON).The present study was conducted to investigate the role of Lactobacillus plantarum(L.plantarum) JM113 in protecting against the intestinal toxicity caused by DON.Methods: A total of 144 one-day-old healthy Arbor Acres broilers were randomly distributed into 3 treatments,including the CON(basal diet),the DON(extra 10 mg/kg deoxynivalenol),and the DL(extra 1 × 109 CFU/kg L.plantarum JM113 based on DON group) treatments.The growth performance,organ indexes,intestinal morphology,pancreatic digestive enzymes,intestinal secreted immunoglobulin A(sIgA),jejunal transcriptome,and intestinal microbiota were evaluated.Results: Compared with the CON and DL groups,the DON supplementation altered intestinal morphology,especially in duodenum and jejunum,where villi were shorter and crypts were deeper(P < 0.05).Meanwhile,the significantly decreased mRNA expression of jejunal claudin-1 and occludin(P < 0.05),ileal rBAT and jejunal GLUT1 of 21-day-old broilers(P < 0.05),as well as duodenal PepT1 and ileal rBAT of 42-day-old broilers were identified in the DON group.Moreover,supplementation with L.plantarum JM113 could increase duodenal expression of IL-10 and IL-12 of 21-dayold broilers,ileal s IgA of 42-day-old broilers,and the bursa of Fabricius index of 21-day-old broilers.Further jejunal transcriptome proved that the genes related to the intestinal absorption and metabolism were significantly reduced in the DON group but a significant increase when supplemented with extra L.plantarum JM113.Furthermore,the bacteria related to nutrient utilization,including the Proteobacteria,Escherichia,Cc-115(P < 0.05),Lactobacillus and Prevotella(P < 0.1) were all decreased in the DON group.By contrast,supplementation with L.plantarum JM113 increased the relative abundance of beneficial bacterium,including the Bacteroidetes,Roseburia,Anaerofustis,Anaerostipe,and Ruminococcus bromi(P < 0.05).Specifically,the increased abun 展开更多
关键词 BROILER CHICKENS DEOXYNIVALENOL Gut microbiota Lactobacillus PLANTARUM JM113 mRNA SEQUENCING 16S rRNA gene SEQUENCING
在线阅读 下载PDF
饲用微生态制剂的生物学功能及其在动物生产中的研究进展
4
作者 吴妍妍 聂存喜 +2 位作者 陈红莉 卢奇成 张文举 《饲料研究》 CAS 北大核心 2019年第5期109-114,共6页
近年来,在畜牧业养殖规模化、集约化不断加快的背景下,抗生素常被用来防治动物疾病,提高动物的生长速度。但抗生素在畜牧业中频繁使用造成了抗生素在环境中及畜产品中残留等问题,危害了畜牧业的健康可持续发展。因此,随着全球范围内禁... 近年来,在畜牧业养殖规模化、集约化不断加快的背景下,抗生素常被用来防治动物疾病,提高动物的生长速度。但抗生素在畜牧业中频繁使用造成了抗生素在环境中及畜产品中残留等问题,危害了畜牧业的健康可持续发展。因此,随着全球范围内禁止使用抗生素生长促进剂(AGPS)的呼声日益高涨,加快畜禽的生长速度、保护其免受病原体感染、提高饲料利用率及畜产品的质量等生产问题不容忽视,导致对寻求替抗的生物制品迫在眉睫,而饲用微生态制剂由于具有绿色、无污染的特点,在促进动物生长、肠道健康等方面的应用取得了前所未有的发展,在操纵宿主的健康轨迹(包括和超越免疫成分)中起着很大的作用,且具有促进营养物质吸收、调节肠道菌群结构及提高畜禽机体免疫力等生物学功能而备受关注。文章从饲用微生态制剂的种类、作用机制及在动物生产中应用研究进行综述。 展开更多
关键词 微生态制剂 生物学功能 作用机制 测序 动物生产
Microbial diversity in Huguangyan Maar Lake of China revealed by high-throughput sequencing 预览
5
作者 HOU Qinghua FANG Zhou +1 位作者 ZHU Qingmei DONG Hongpo 《海洋湖沼学报(英文)》 SCIE CAS CSCD 2019年第4期1245-1257,共13页
Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples fr... Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO^3-, PO4^3-, SiO3^2- and NH4^+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes;however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs. 展开更多
关键词 Huguangyan MAAR LAKE HIGH-THROUGHPUT SEQUENCING MICROBIAL diversity
在线阅读 下载PDF
Evidence for a con served microbiota across the different developmental stages of Plodia interpunctella
6
作者 Valeria Mereghetti Bessem Chouaia +2 位作者 Lidia Limonta Daria Patrizia Locatelli Matteo Montagna 《昆虫科学:英文版》 SCIE CAS CSCD 2019年第3期466-478,共13页
Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmen... Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities world-wide. Using culture-independent approach based on Illumina 16S rRNA gene sequencing we characterized the microbiota of four developmental stages: eggs, first-, and last-instar larvae, and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified microbiota associated to all the analyzed stages. The microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of Proteobacteria. The dominant bacterial genus is represented by Burkholderia (?64%), followed by Propionibacterium, Delftia, Pseudomonas, and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, was detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages. 展开更多
关键词 BURKHOLDERIA Illumina sequencing Indian MEAL MOTH insect SYMBIOSIS PROTEOBACTERIA
Next-generation Sequencing Study of Pathogens in Serum from Patients with Febrile Jaundice in Sierra Leone 预览
7
作者 ZHANG Yi YE Fei +11 位作者 XIA Lian Xu ZHU Ling Wei IDRISSA Laybohr Kamara HUANG Ke Qiang ZHANG Yong LIU Jun BRIMA Kargbo WANG Ji LIANG Mi Fang SONG Jing Dong MA Xue Jun WU Gui Zhen 《生物医学与环境科学:英文版》 SCIE CAS CSCD 2019年第5期363-370,共8页
Objective People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus(YFV) is the only pathogen under surveillance in Sierra Leone owing to the... Objective People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus(YFV) is the only pathogen under surveillance in Sierra Leone owing to the undeveloped medical and public health system there. Most of the results of YFV identification are negative. Elucidation of the pathogen spectrum is required to reduce the prevalence of febrile jaundice. Methods In the present study, we used Ion Torrent semiconductor sequencing to profile the pathogen spectrum in archived YFV‐negative sera from 96 patients in Sierra Leone who presented with unexplained febrile jaundice. Results The most frequently identified sequencing reads belonged to the following pathogens: cytomegalovirus(89.58%), Epstein‐Barr virus(55.21%), hepatitis C virus(34.38%), rhinovirus(28.13%), hepatitis A virus(20.83%), coxsackievirus(10.42%), Ebola virus(8.33%), hepatitis E virus(8.33%), lyssavirus(4.17%), leptospirosis(4.17%), chikungunya virus(2.08%), Crimean‐Congo hemorrhagic fever virus(1.04%), and hepatitis B virus(1.04%). Conclusion The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone. 展开更多
关键词 Sierra Leone FEBRILE JAUNDICE Next‐generation SEQUENCING Virus
在线阅读 下载PDF
Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology 预览
8
作者 Xuchao Zhang Zhiyong Liang +47 位作者 Shengyue Wang Shun Lu Yong Song Ying Cheng Jianming Ying Weiping Liu Yingyong Hou Yangqiu Li Yi Liu Jun Hou Xiufeng Liu Jianyong Shao Yanhong Tai Zheng Wang Li Fu Hui Li Xiaojun Zhou Hua Bai Mengzhao Wang You Lu Jinji Yang Wenzhao Zhong Qing Zhou Xuening Yang Jie Wang Cheng Huang Xiaoqing Liu Xiaoyan Zhou Shirong Zhang Hongxia Tian Yu Chen Ruibao Ren Ning Liao Chunyan Wu Zhongzheng Zhu Hongming Pan Yanhong Gu Liwei Wang Yunpeng Liu Suzhan Zhang Tianshu Liu Gong Chen Zhimin Shao Binghe Xu Qingyuan Zhang Ruihua Xu Lin Shen Yilong Wu 《癌症生物学与医学:英文版》 CAS CSCD 2019年第1期189-204,共16页
Next-generation sequencing(NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously.Therefore, it represents a promising tool for the analysis of molecular targets for the initial ... Next-generation sequencing(NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously.Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology(CSCO) and the China Actionable Genome Consortium(CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians,pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure(SOP), data analysis, report, and NGS platform certification and validation. 展开更多
关键词 Next-generation sequencing TECHNOLOGY CANCER CONSENSUS
在线阅读 下载PDF
GPA:A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation
9
作者 Jiarui Li Pengcheng Du +4 位作者 Adam Yongxin Ye Yuanyuan Zhang Chuan Song Hui Zeng Chen Chen 《基因组蛋白质组与生物信息学报:英文版》 CAS CSCD 2019年第1期106-117,共12页
Identifying antimicrobial resistant(AMR)bacteria in metagenomics samples is essential for public health and food safety.Next-generation sequencing(NGS)technology has provided a powerful tool in identifying the genetic... Identifying antimicrobial resistant(AMR)bacteria in metagenomics samples is essential for public health and food safety.Next-generation sequencing(NGS)technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species.However,for complex bacterial samples,there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations(CNVs)for given genes.Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria,named as Genetic Polymorphisms Assignments(GPA).Simulation results showed that GPA has reduced the false discovery rate(FDR)and mean absolute error(MAE)in CNV and single nucleotide variant(SNV)identification.This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models,and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations.The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains.Also,the framework together with the genome annotation and population comparison tools has been integrated into an application,which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples.The GPA package is available at https://github.com/IID-DTH/GPA-package. 展开更多
关键词 Next-generation sequencing Pool-seq Bayesian model METAGENOMICS Genetic POLYMORPHISMS
一个黎族α-地中海贫血融合基因遗传家系的鉴定
10
作者 胡俊杰 陈鑫苹 +4 位作者 张继业 赵立强 李晓娟 徐卫华 符生苗 《基因组学与应用生物学》 CAS CSCD 北大核心 2019年第4期1525-1531,共7页
鉴定海南黎族人群中发现的一种α-地中海贫血融合基因,并对其家系进行分析,探讨融合基因形成机制及遗传规律。采集先证者及其家系成员外周全血,进行血细胞分析、血红蛋白电泳和地贫常见基因型检测,并采用Gap-PCR法结合特异引物和基因测... 鉴定海南黎族人群中发现的一种α-地中海贫血融合基因,并对其家系进行分析,探讨融合基因形成机制及遗传规律。采集先证者及其家系成员外周全血,进行血细胞分析、血红蛋白电泳和地贫常见基因型检测,并采用Gap-PCR法结合特异引物和基因测序技术对先证者基因型进行鉴定。结果显示先证者基因型为Fusion gene/-α4.2,且该融合基因是由于α珠蛋白基因的α2段与Ψα1段序列发生融合所致。家系遗传分析显示,其祖父基因型为Fusion gene/αα,伯父和父亲的基因型均为Fusion gene/-α4.2,母亲基因型为-α4.2/αwsαws,弟弟基因型为-α4.2/αwsαws。海南省黎族人群中存在有α-地贫融合基因,该发现丰富了黎族地贫基因突变数据库,对遗传咨询及地贫基因诊断和防治具有重要意义。 展开更多
关键词 黎族 血细胞分析 血红蛋白电泳 基因检测 测序
MGMT is down-regulated independently of promoter DNA methylation in rats with all-trans retinoic acidinduced spina bifida aperta 预览
11
作者 He-Nan Zhang Yi Guo +3 位作者 Wei Ma Jia Xue Wei-Lin Wang Zheng-Wei Yuan 《中国神经再生研究:英文版》 SCIE CAS CSCD 2019年第2期361-368,共8页
O6-methylguanine DNA methyltransferase (MGMT), a DNA repair enzyme, has been reported in some congenital malformations, but it is less frequently reported in neural tube defects. This study investigated MGMT mRNA expr... O6-methylguanine DNA methyltransferase (MGMT), a DNA repair enzyme, has been reported in some congenital malformations, but it is less frequently reported in neural tube defects. This study investigated MGMT mRNA expression and methylation levels in the early embryo and in different embryonic stages, as well as the relationship between MGMT and neural tube defects. Spina bifida aperta was induced in rats by a single intragastric administration of all-trans retinoic acid on embryonic day (E) 10, whereas normal control rats received the same amount of olive oil on the same embryonic day. DNA damage was assessed by detecting γ-H2A.X in spina bifida aperta rats. Real time-polymerase chain reaction was used to examine mRNA expression of MGMT in normal control and spina bifida aperta rats. In normal controls, the MGMT mRNA expression decreased with increasing embryonic days, and was remarkably reduced from E11 to E14, reaching a minimum at E18. In the spina bifida aperta model, γ-H2A.X protein expression was increased, and mRNA expression of MGMT was markedly decreased on E14, E16, and E18. Bisulfite sequencing polymerase chain reaction for MGMT promoter methylation demonstrated that almost all CpG sites in the MGMT promoter remained unmethylated in both spina bifida aperta rats and normal controls, and there was no significant difference in methylation level between the two groups on either E14 or E18. Our results show that DNA damage occurs in spina bifida aperta rats. The mRNA expression of MGMT is downregulated, and this downregulation is independent of promoter DNA methylation. 展开更多
关键词 nerve REGENERATION NEURAL tube defects spina bifida aperta spinal cord ALL-TRANS retinoic acid O6-methylguanine DNA methyltransferase gene expression DNA methylation PROMOTER BISULFITE sequencing polymerase chain reaction NEURAL REGENERATION
在线阅读 下载PDF
Association of Gene Mutations with Response to Arsenic-Containing Compound Qinghuang Powder (复方青黄散)in Patients with Myelodysplastic Syndromes
12
作者 ZHAO Pan LIANG Jun-bin +4 位作者 DENG Zhong-yang WANG Ming-jing QIN Jia-yue CHEN Chong-jian HU Xiao-mei 《中国结合医学杂志:英文版》 SCIE CAS CSCD 2019年第6期409-415,共7页
Objective: To in vestigate the relati on ship betwee n gene mutations and resp onse to Compo und Qinghuang Powder (复方青黄散,CQHP) in patients with myelodysplastic syndrome (MDS). Methods: Forty-three MDS patients af... Objective: To in vestigate the relati on ship betwee n gene mutations and resp onse to Compo und Qinghuang Powder (复方青黄散,CQHP) in patients with myelodysplastic syndrome (MDS). Methods: Forty-three MDS patients after treatment with CQHP for 6 months were genotyped by ultra-deep targeted sequencing and the clinical data of patients were collected and the relationship between them was analyzed. Results: Up to 41.86% of patie nts harbored genet mutations, in most cases with more than one mutation. The most comm on mutations were in SF3B1, U2AF1, ASXL1, and DNMT3A. After treatment with CQHP, about 88.00% of patients no longer required blood transfusion, or needed half of prior transfusions. Conlusion: CQHP is an effective treatment for patients with MDS, especially those with gene mutations in SF3B1, DNMT3A, U2AF1, and/or ASXL1. 展开更多
关键词 MYELODYSPLASTIC SYNDROMES arsenic next-generation sequencing REALGAR
Early Detection of Myelodysplastic Syndrome/Leukemia-associated Mutations Using NGS Is Critical in Treating Aplastic Anemia 预览
13
作者 Xiang LI Yao-hui WU +3 位作者 Si-si CAI Wei-ming LI Yong YOU Min ZHANG 《当代医学科学(英文)》 SCIE CAS 2019年第2期217-221,共5页
Distinguishing between aplastic anemia(AA)and hypoblastic myelodysplastic syndrome(hMDS)with a low percentage of bone marrow(BM)blasts(<5%)can be difficult due to the overlap in clonality and a spectrum of genetic ... Distinguishing between aplastic anemia(AA)and hypoblastic myelodysplastic syndrome(hMDS)with a low percentage of bone marrow(BM)blasts(<5%)can be difficult due to the overlap in clonality and a spectrum of genetic alternations between the two subtypes of diseases.However,due to recent advances in DNA sequencing technology,both spectnim and frequency of mutations can be accurately determined and monitored by next-generation sequencing(NGS)at initial diagnosis and during immunosuppressive therapy(1ST)in patients with AA or hMDS.This improvement in acquiring a patient's genetic status and clonal evolution can provide more proper,precise,and on-time information to guide disease management,which is especially helpful in the absence of traditional morphologic/cytogenetic evidence. 展开更多
关键词 APLASTIC ANEMIA hypoblastic MYELODYSPLASTIC syndrome IMMUNOSUPPRESSIVE therapy next-generation sequencing
在线阅读 下载PDF
The diazotrophic community in oat rhizosphere: effects of legume intercropping and crop growth stage
14
作者 Yadong YANG Xiaomin FENG +1 位作者 Yuegao HU Zhaohai ZENG 《农业科学与工程前沿:英文版》 2019年第2期162-171,共10页
In this study, the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil in three cropping systems and at two oat growth stages were investigated using real-time PCR and Illumina MiS... In this study, the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil in three cropping systems and at two oat growth stages were investigated using real-time PCR and Illumina MiSeq sequencing. The nifH gene abundance in oat-soybean intercropping (OSO) and oat-mungbean intercropping (OMO) was significantly greater than that in sole oat (O), but the nifH gene abundance significantly decreased at the later stage in all the treatments. Alpha diversity indices in OSO and OMO were higher at the heading stage, but lower at the maturity stage than that in O. Bradyrhizobium and Skermanella were the dominant genera identified in all samples, with an average proportion of 35.8% and 12.4%, respectively. The proportion of dominant genera showed significant differences and varied with cropping system and growth stage. Principal component analysis showed that growth stage had a stronger effect than intercropping on the diazotrophic community structure. However, Mantel test and redundancy analysis showed there was no environmental factor significantly correlated to the diazotrophic community structure. Our results demonstrate that intercropping had a weaker effect than growth stage on the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil. 展开更多
关键词 COMMUNITY composition Illumina MiSeq sequencing NIFH gene oat-legume INTERCROPPING RHIZOSPHERE soil
Gaucher disease in Montenegro - genotype/phenotype correlations: Five cases report 预览
15
作者 Snezana Vujosevic Sanja Medenica +5 位作者 Vesko Vujicic Milena Dapcevic Nikola Bakic Ruhua Yang Jun Liu Pramod K Mistry 《世界临床病例杂志》 2019年第12期1475-1482,共8页
BACKGROUND The most common lysosomal storage disorder is Gaucher disease (GD). It is a deficiency of lysosomal glucocerebrosidase (GBA) due to biallelic mutations in the GBA gene, characterized by the deposition of gl... BACKGROUND The most common lysosomal storage disorder is Gaucher disease (GD). It is a deficiency of lysosomal glucocerebrosidase (GBA) due to biallelic mutations in the GBA gene, characterized by the deposition of glucocerebroside in macrophage-monocyte system cells. The report targets clinical phenotypes of GD in order to correlate them with GBA gene mutations, as well as to identify GBA gene mutation in patients in Montenegro that are diagnosed with GD. CASES SUMMARY Five patients (4 male, 1 female) of type 1 GD (GD1) are reported. The age at diagnosis ranged from 7 to 40. Patients experienced delays of 1-12 years in diagnosis after the original onset of symptoms. The most common mode of presentation was a variable degree of splenomegaly and thrombocytopenia, while other symptoms included bone pain, hepatomegaly, abdominal pain and fatigue. Osteopenia was present in a majority of the patients: 4/5. All patients were found to have an asymptomatic Erlenmeyer flask deformity of the distal femur. On enzyme replacement therapy (ERT), the hematological and visceral parameters showed significant improvement, but no significant progression in bone mineral density was noticed. GBA gene sequencing revealed homozygosity for the N370S mutation in one patient. The genotypes of the other patients were N370S/55bp deletion, N370S/D409H (2 patients), and H255Q/N370S (1 patient). CONCLUSION The phenotypes of the GD1 encountered in Montenegro were severe but all responded well to ERT. 展开更多
关键词 GAUCHER disease LYSOSOMAL storage disorder Glucocerebrosidase GBA gene sequencing GENOTYPE Case REPORT
在线阅读 免费下载
烟草航天诱变突变体变异检测及分析
16
作者 周世奇 刘东阳 +6 位作者 潘旭浩 屈建康 程立锐 任民 晁江涛 张玉 罗成刚 《植物遗传资源学报》 CAS CSCD 北大核心 2019年第2期377-386,共10页
为预测控制烟草重要性状的关键基因并研究航天诱变机理,对经航天诱变选育的烟草突变体材料NC89-M与野生型NC89进行全基因组重测序,测序深度30×,并对各种类型变异进行检测注释。NC89中检测到单核苷酸多态性位点(SNP,Single nucleoti... 为预测控制烟草重要性状的关键基因并研究航天诱变机理,对经航天诱变选育的烟草突变体材料NC89-M与野生型NC89进行全基因组重测序,测序深度30×,并对各种类型变异进行检测注释。NC89中检测到单核苷酸多态性位点(SNP,Single nucleotide polymorphism)1848013个,小片段插入缺失(Indel,insertion-delection)398922个,结构变异(SV,Structure variation)41969个;NC89-M中检测到SNP 1876219个,Indel 402011个,SV 42699个。NC89-M和NC89对比共得到271655个SNP,分布在8378个基因上,23450个Indel造成2156个基因突变。分析结果表明,NC89-M中SNP变异数目最多,其转换类型和颠换类型的比值为2.053,说明航天诱变对烟草基因组的变异以单碱基突变为主,突变类型以转换为主;在Indel中,插入突变数目明显多于缺失突变,证明航天诱变造成的Indel中以插入突变为主;在SV中,航天诱变主要造成了插入、缺失、倒位、染色体内部迁移和染色体间的迁移5种结构变异类型;变异基因KEGG注释表明,与代谢通路和次生代谢产物合成两方面基因突变数目最多;变异基因功能注释表明,突变体中调控开花时间的MADS-box基因,调控侧生器官发育与叶缘形状的KNOX1基因和萜类化合物合成相关基因等发生了变异。 展开更多
关键词 烟草 航天诱变 重测序 变异分析
Effect of nitrobenzene on the performance and bacterial community in an expanded granular sludge bed reactor treating high-sulfate organic wastewater
17
作者 Jun Li Wentao Li +2 位作者 Gan Luo Yan Li Aimin Li 《中国环境科学与工程前沿:英文版》 SCIE EI CAS CSCD 2019年第1期63-72,共10页
Nitrobenzene (NB) is frequently found in wastewaters containing sulfate and may affect biological sulfate reduction process, but information is limited on the responses of sulfate reduction efficiency and microbial co... Nitrobenzene (NB) is frequently found in wastewaters containing sulfate and may affect biological sulfate reduction process, but information is limited on the responses of sulfate reduction efficiency and microbial community to the increased NB contents. In this study, a laboratory-scale expanded granular sludge bed reactor was operated continuously to treat high-sulfate organic wastewater with increased NB contents. Results successfully demonstrated that the presence of more than 50 mg/L NB depressed sulfate reduction and such inhibition was partly reversible. Bath experiments showed that the maximum specific desulfuration activity (SDA) decreased from 135.80 mg SO4^2-/gVSS/d to 30.78 mg SO4^2-/gVSS/d when the NB contents increased from none to 400 mg/L. High-throughput sequencing showed that NB also greatly affected bacterial community structure. Bcicteroidetes dominated in the bioreactor. The abundance of Proteobacteria increased with NB addition while Firmicutes presented an opposite trend. Proteobacteria gradually replaced Finnicutes for the dominance in response to the increase of influent NB concentrations.The genus Desulfovibrio was the dominant sulfate-reducing bacteria (SRB) with absence or presence of NB, but was inhibited under high content of NB. The results provided better understanding for the biological sulfate reduction under NB stress. 展开更多
关键词 NITROBENZENE (NB) Sulfate-reducing bacteria (SRB) BACTERIAL community SULFATE reduction HIGH-THROUGHPUT SEQUENCING
Dgcr8 deletion in the primitive heart uncovered novel microRNA regulating the balance of cardiac-vascular gene program
18
作者 Xi Chen Lin Wang +8 位作者 Rujin Huang Hui Qiu Peizhe Wang Daren Wu Yonglin Zhu Jia Ming Yangming Wang Jianbin Wang Jie Na 《蛋白质与细胞:英文版》 SCIE CAS CSCD 2019年第5期327-346,共20页
Primitive mammalian heart transforms from a single tube to a four-chambered muscular organ during a short developmental window.We found that knocking out global microRNA by deleting Dgcr8 microprocessor in Mespl cardi... Primitive mammalian heart transforms from a single tube to a four-chambered muscular organ during a short developmental window.We found that knocking out global microRNA by deleting Dgcr8 microprocessor in Mespl cardiovascular progenitor cells lead to the formation of extremely dilated and enlarged heart due to defective cardiomyocyte(CM)differentiation.Transcriptome analysis revealed unusual upregulation of vascular gene expression in Dgcr8 cKO hearts.Single cell RNA sequencing study further confirmed the increase of angiogenesis genes in single Dgcr8 cKO CM.We also performed global microRNA profiling of E9.5 heart for the first time,and identified that miR-541 was transiently highly expressed in E9.5 hearts.Interestingly,introducing miR-541 back into microRNA-free CMs partially rescued their defects,downregulated angiogenesis genes and significantly upregulated cardiac genes.Moreover,miR-541 can target Ctgf and inhibit endothelial function.Our results suggest that micro-RNAs are required to suppress abnormal angiogenesis gene program to maintain CM differentiation. 展开更多
关键词 MICRORNA Dgcr8 Cardiovascular PROGENITOR cells miRNA-541 Single cell RNA sequencing
Characterization and validation of somatic mutation spectrum to reveal heterogeneity in gastric cancer by single cell sequencing
19
作者 Lihua Peng Rui Xing +20 位作者 Dongbing Liu Li Bao Wenxiang Cheng Hongyi Wang Yuan Yu Xiaofeng Liu Lu Jiang Yan Wu Zhongxue An Qiaoyi Liang Ryong Nam Kim Young Kee Shin Huanming Yang Jian Wang Jun Yu Xiuqing Zhang Xun Xu Jiaan Yang Kui Wu Shida Zhu Youyong Lu 《科学通报:英文版》 SCIE EI CSCD 2019年第4期236-244,共9页
Gastric cancer (GC) is a highly heterogeneons disease with multiple cellular types and poor prognosis. However, the cellular evolution and molecular basis of GC at the in dividual intra-tumor level has not bee n well ... Gastric cancer (GC) is a highly heterogeneons disease with multiple cellular types and poor prognosis. However, the cellular evolution and molecular basis of GC at the in dividual intra-tumor level has not bee n well dem on strated. We performed single-cell whole exome sequencing to detect somatic singlenucleotide variants (SNVs) and significantly mutated genes (SMGs) among 34 tumor cells and 9 normal cells from a patient w让h GC. The Complete Prediction for Protein Conformation (CPPC) approach directly predicting the folding con formation of the protein 3D structure with Protein Folding Shape Code, combined with functional experiments were used to confirm the characterization of mutated SMGs in GC cells. We ide ntified 201 somatic SNVs, in eluding 117 non-sy nony mous mutations in GC cells. Further analysis idenrified 24 significant mutated genes (SMGs) in single cells, for which a single amino acid change might affect protein conforniation. Among them, two genes (CDC27 and FLG) that were mutated only in single cells but not in the corresponding tumor tissue, were recurrently present in another GC tissue cohort, and may play a potential role to promote carcinogenesis, as confirmed by functional characterization. Our findings showed a mutational landscape of GC at intra-tumor level for the first time and provided opportunities for understanding the heterogeneity and individualized target therapy for this disease. 展开更多
关键词 Gastric cancer SINGLE-CELL whole EXOME SEQUENCING SNV SIGNIFICANT mutated gene HETEROGENEITY
基于高通量测序的棉花InDel标记开发及其应用 预览
20
作者 陆海燕 陈璐 +2 位作者 王显生 赵涵 沈奇 《棉花学报》 CSCD 北大核心 2019年第4期297-306,共10页
【目的】获得可以用于棉花品种鉴定和纯度检测的二态性InDel标记,提高棉花种子的检验精确度和效率,为棉花的分子育种发挥作用。【方法】基于来源不同的121份棉花全基因组信息,根据高多态性信息含量筛选多态性高的InDel位点,开发二态性In... 【目的】获得可以用于棉花品种鉴定和纯度检测的二态性InDel标记,提高棉花种子的检验精确度和效率,为棉花的分子育种发挥作用。【方法】基于来源不同的121份棉花全基因组信息,根据高多态性信息含量筛选多态性高的InDel位点,开发二态性InDel标记,并在我国66个棉花品种的遗传距离分析和聚类分析中进行应用。【结果】基于121份棉花的二代测序数据获得10967个InDel位点,合成了85对InDel引物,选择其中有效引物64对,其中At亚组的特异引物35对、Dt亚组特异引物29对,At、Dt亚组染色体的平均最小等位频率分别为0.45、0.32,多态信息含量分别为0.49、0.40;所用的66个棉花品种的遗传距离范围是0.04~0.65cM(厘摩),平均为0.39cM,遗传距离最大的2个品种是泗棉3号和中棉所36,遗传距离最小的是徐棉18和徐杂3号。【结论】开发的64个棉花二态性InDel标记能有效地通过揭示品种间的遗传距离反映品种之间的亲缘关系,区分来源不同的棉花品种,具有一定的理论意义和应用价值。 展开更多
关键词 棉花 重测序 INDEL标记 品种鉴定
在线阅读 下载PDF
上一页 1 2 250 下一页 到第
使用帮助 返回顶部 意见反馈