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29959篇 您的检索式:期刊名="Genomics"
    题名 作者 年代 出处 被引量
1KaKs_Calculator:Calculating Ka and Ks Through Model Selection and Model Averaging显示文摘KaKs_Calculator is a software package that calculates nonsynonymous (Ka) andsynonymous (Ks) substitution rates through model selection and model averag-ing. Since existing methods for this estimation adopt their specific mutation(substitution) models that consider different evolutionary features, leading todiverse estimates, KaKs Calculator implements a set of candidate models in amaximum likelihood framework and adopts the Akaike information criterion tomeasure fitness between models and data, aiming to include as many featuresas needed for accurately capturing evolutionary information in protein-coding se-quences. In addition, several existing methods for calculating Ka and Ks arealso incorporated into this software. KaKs Calculator, including source codes,compiled executables, and documentation, is freely available for academic use athttp://gffzz5c65aa98f6514e89hv5xkw66fwcbk6fcq.ffgz.tsg.suse.edu.cn/software.htm.Zhang Zhang Jun Li Xiao-Qian Zhao Jun Wang Gane Ka-Shu Wong Jun Yu 2006Genomics, Proteomics & Bioinformatics2006,4,4:86
2Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System显示文摘Transcription activator-like effector nucleases(TALENs) and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated(Cas) systems have emerged as powerful tools for genome editing in a variety of species. Here, we report, for the first time, targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. We designed five TALENs targeting 4 genes, namely ZmPDS, ZmIPK1A, ZmIPK, ZmMRP4, and obtained targeting efficiencies of up to 23.1% in protoplasts, and about 13.3% to 39.1% of the transgenic plants were somatic mutations. Also, we constructed two gRNAs targeting the ZmIPK gene in maize protoplasts, at frequencies of 16.4% and 19.1%, respectively. In addition, the CRISPR/Cas system induced targeted mutations in Z. mays protoplasts with efficiencies(13.1%) similar to those obtained with TALENs(9.1%). Our results show that both TALENs and the CRISPR/Cas system can be used for genome modification in maize.Zhen Liang Kang Zhang Kunling Chen Caixia Gao 2014Journal of Genetics and Genomics2014,41,2:136
3Exosome and Exosomal MicroRNA: Trafficking, Sorting, and Function显示文摘Exosomes are 40–100 nm nano-sized vesicles that are released from many cell types into the extracellular space. Such vesicles are widely distributed in various body fluids. Recently,m RNAs and micro RNAs(mi RNAs) have been identified in exosomes, which can be taken up by neighboring or distant cells and subsequently modulate recipient cells. This suggests an active sorting mechanism of exosomal mi RNAs, since the mi RNA profiles of exosomes may differ from those of the parent cells. Exosomal mi RNAs play an important role in disease progression, and can stimulate angiogenesis and facilitate metastasis in cancers. In this review, we will introduce the origin and the trafficking of exosomes between cells, display current research on the sorting mechanism of exosomal mi RNAs, and briefly describe how exosomes and their mi RNAs function in recipient cells.Finally, we will discuss the potential applications of these mi RNA-containing vesicles in clinical settings.Jian Zhang Sha Li Lu Li Meng Li Chongye Guo Jun Yao Shuangli Mi 2015Genomics, Proteomics & Bioinformatics2015,13,1:162
4PacBio Sequencing and Its Applications显示文摘Single-molecule, real-time sequencing developed by Pacific Bio Sciences offers longer read lengths than the second-generation sequencing(SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using Pac Bio sequencing can close gaps in current reference assemblies and characterize structural variation(SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with diseases. Moreover, Pac Bio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes,due to its ability to sequence full-length transcripts or fragments with significant lengths. Additionally, Pac Bio's sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using Pac Bio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with Pac Bio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using Pac Bio Sequencing alone. The advent of Pac Bio sequencing has made available much information that could not be obtained via SGS alone.Anthony Rhoads Kin Fai Au 2015Genomics, Proteomics & Bioinformatics2015,13,5:107
5KaKs_Calculator 2.0:A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies显示文摘We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version.It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates;among them,we added our modified versions of several widely used methods as the gamma series including γ-NG,γ-LWL,γ-MLWL,γ-LPB,γ-MLPB,γ-YN and γ-MYN,which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version.The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5' to 3' direction of protein-coding sequences,and have improved the overall performance on sequence analysis for evolution studies.A toolbox,including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction,is downloadable from the website for academic purpose at http://gffzz6ccd80d7270b40f2sv5xkw66fwcbk6fcq.ffgz.tsg.suse.edu.cn/projects/kakscalculator2/.Dapeng Wang Yubin Zhang Zhang Zhang Jiang Zhu Jun Yu 2010Genomics, Proteomics & Bioinformatics2010,8,1:79
6Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer显示文摘Long non-coding RNAs(lnc RNAs) play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a variety of chromatin-based mechanisms and via cross-talk with other RNA species. lnc RNAs can function as decoys, scaffolds, and enhancer RNAs. This review summarizes the characteristics of lnc RNAs, including their roles, functions, and working mechanisms, describes methods for identifying and annotating lnc RNAs, and discusses future opportunities for lnc RNA-based therapies using antisense oligonucleotides.Yiwen Fang Melissa J. Fullwood 2016Genomics, Proteomics & Bioinformatics2016,14,1:63
7Transcriptional and Post-transcriptional Gene Regulation by Long Non-coding RNA显示文摘Advances in genomics technology over recent years have led to the surprising discovery that the genome is far more pervasively transcribed than was previously appreciated.Much of the newly-discovered transcriptome appears to represent long non-coding RNA(lncRNA),a heterogeneous group of largely uncharacterised transcripts.Understanding the biological function of these molecules represents a major challenge and in this review we discuss some of the progress made to date.One major theme of lncRNA biology seems to be the existence of a network of interactions with microRNA(miRNA) pathways.lnc RNA has been shown to act as both a source and an inhibitory regulator of mi RNA.At the transcriptional level,a model is emerging whereby lnc RNA bridges DNA and protein by binding to chromatin and serving as a scaffold for modifying protein complexes.Such a mechanism can bridge promoters to enhancers or enhancer-like non-coding genes by regulating chromatin looping,as well as conferring specificity on histone modifying complexes by directing them to specific loci.Iain M.Dykes Costanza Emanueli 2017Genomics, Proteomics & Bioinformatics2017,15,3:71
8Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis显示文摘The heat shock transcription factors (HSFs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (HSPs), which are critical in the protection against stress damage and many other important biological processes. Study of the HSF gene family is important for understanding the mechanism by which plants respond to stress. The completed genome sequences of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) constitute a valuable resource for comparative genomic analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. The identification of phylogenetic relationships among HSF proteins in these species is a fundamental step to unravel the functionality of new and yet uncharacterized genes belonging to this family.In this study, the full complement of HSF genes in rice and Arabidopsis has probably been identified through the genome-wide scan. Phylogenetic analyses resulted in the identification of three major clusters of orthologous genes that contain members belonging to both species, which must have been represented in their common ancestor before the taxonomic splitting of the angiosperms. Further analysis of the phylogenetic tree reveals a possible dicot specific gene group. We also identified nine pairs of paralogs, as evidence for studies on the evolution history of rice HSF family and rice genome evolution. Expression data analysis indicates that HSF proteins are widely expressed in plants. These results provide a solid base for future functional genomic studies of the HSF gene family in rice and Arabidopsis.Jingkang Guo Jian Wu Qian Ji Chao Wang Lei Luo Yi Yuan Yonghua Wang Jian Wang 2008Journal of Genetics and Genomics2008,35,2:52
9A Brief Review on the Mechanisms of miRNA Regulation显示文摘MicroRNAs (miRNAs) are a class of short,endogenously-initiated non-coding RNAs that post-transcriptionally control gene expression via either translational repression or mRNA degradation.It is becoming evident that miRNAs are playing significant roles in regulatory mechanisms operating in various organisms,including developmental timing and host-pathogen interactions as well as cell differentiation,proliferation,apoptosis and tumorigenesis.Likewise,as a regulatory element,miRNA itself is coordinatively modulated by multifarious effectors when carrying out basic functions,such as SNP,miRNA editing,methylation and circadian clock.This mini-review summarized the current understanding of interactions between miRNAs and their targets,including recent advancements in deciphering the regulatory mechanisms that control the biogenesis and functionality of miRNAs in various cellular processes.Yimei Cai Xiaomin Yu Songnian Hu Jun Yu 2009Genomics, Proteomics & Bioinformatics2009,7,4:55
10Cytological analysis and genetic control of rice anther development显示文摘Microsporogenesis and male gametogenesis are essential for the alternating life cycle of flowering plants between diploid sporophyte and haploid gametophyte generations.Rice(Oryza saliva) is the world's major staple food,and manipulation of pollen fertility is particularly important for the demands to increase rice grain yield.Towards a better understanding of the mechanisms controlling rice male reproductive development,we describe here the cytological changes of anther development through 14 stages,including cell division,differentiation and degeneration of somatic tissues consisting of four concentric cell layers surrounding and supporting reproductive cells as they form mature pollen grains through meiosis and mitosis.Furthermore,we compare the morphological difference of anthers and pollen grains in both monocot rice and eudicot Arabidopsis thaliana.Additionally,we describe the key genes identified to date critical for rice anther development and pollen formation.Dabing Zhang Xue Luo Lu Zhu 2011Journal of Genetics and Genomics2011,38,9:56
11TALEN or Cas9-Rapid,Efficient and Specific Choices for Genome Modifications显示文摘Precise modifications of complex genomes at the single nucleotide level have been one of the big goals for scientists working in basic and applied genetics,including biotechnology,drug development,gene therapy and synthetic biology.However,the relevant techniques for making these manipulations in model organisms and human cells have been lagging behind the rapid high throughput studies in the post-genomic era with a bottleneck of low efficiency,time consuming and laborious manipulation,and off-targeting problems.Recent discoveries of TALEs(transcription activator-like effectors) coding system and CRISPR(clusters of regularly interspaced short palindromic repeats) immune system in bacteria have enabled the development of customized TALENs(transcription activator-like effector nucleases) and CRISPR/Cas9 to rapidly edit genomic DNA in a variety of cell types,including human cells,and different model organisms at a very high efficiency and specificity.In this review,we first briefly summarize the development and applications of TALENs and CRISPR/Cas9-mediated genome editing technologies;compare the advantages and constraints of each method;particularly,discuss the expected applications of both techniques in the field of site-specific genome modification and stem cell based gene therapy;finally, propose the future directions and perspectives for readers to make the choices.Chuanxian Wei Jiyong Liu Zhongsheng Yu Bo Zhang Guanjun Gao Renjie Jiao 2013Journal of Genetics and Genomics2013,40,6:52
12Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana显示文摘Abiotic stresses cause serious crop losses. Knowledge on genes functioning in plant responses to adverse growth conditions is essential for developing stress tolerant crops. Here we report that transgenic expression of MYB15, encoding a R2R3 MYB transcription factor in Arabidopsis thaliana, conferred hypersensitivity to exogenous abscisic acid (ABA) and improved tolerance to drought and salt stresses. The promoter of MYB15 was active in not only vegetative and reproductive organs but also the guard cells of stomata. Its transcript level was substantially upregulated by ABA, drought or salt treatments. Compared with wild type (WT) control, MYB15 overexpression lines were hypersensitive to ABA in germination assays, more susceptible to ABA-elicited inhibition of root elongation, and more sensitive to ABA-induced stomatal closure. In line with the above findings, the transcript levels of ABA biosynthesis (ABA1, ABA2), signaling (ABI3), and responsive genes (AtADH1, RD22, RD29B, AtEM6) were generally higher in MYB15 overexpression seedlings than in WT controls after treatment with ABA. MYB15 overexpression lines displayed improved survival and reduced water loss rates than WT control under water deficiency conditions. These overexpression lines also displayed higher tolerance to NaCl stress. Collectively, our data suggest that overexpression of MYB15 improves drought and salt tolerance in Arabidopsis possibly by enhancing the expression levels of the genes involved in ABA biosynthesis and signaling, and those encoding the stress-protective proteins.Zhenhua Ding Shiming Li Xueli An Xin Liu Huanju Qin Daowen Wang 2009Journal of Genetics and Genomics2009,36,1:42
13Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers显示文摘The genetic diversity of 118 accessions of broomcorn millet(Panicum miliaceum L.),collected from various ecological areas,was analyzed.Using 46 SSR(Simple Sequence Repeat) polymorphic markers from rice,wheat,oat and barley,a total of 226 alleles were found,which exhibited moderate level of diversity.The number of alleles per primer ranged from two to nine,with an average of 4.91.The range of polymorphism information content(PIC) was 0.284-0.980(average,0.793).The expected heterozygosity(He) varied from 0.346 to 0.989,with an average of 0.834.The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609,and it ranged from 0.461 to 0.851.The UPGMA(Unweight Pair Group Method with Arithmetic Mean) clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups.Mantel test meant that geographical origin and genetic distance presented positive correlation.The clustering results were consistent with known information on ecological growing areas.The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes.It indicates that the highest level of genetic diversity occurred in the Loess Plateau,which is probably the original site of Panicum miliaceum.Xingyu Hu Jianfei Wang Ping Lu Hongsheng Zhang 2009Journal of Genetics and Genomics2009,36,8:44
14A Pid3 allele from rice cultivar Gumei2 confers resistance to Magnaporthe oryzae显示文摘瑞斯强风,由 Magnaporthe oryzae 引起了,是大多数破坏疾病之一。用基于地图的策略并且在 silico 途径,我们孤立新米饭(Oryza sativa L.) Pid3 的强风抵抗等位基因,指明的 Pi25,从稳定的强风抵抗栽培变种 Gumei2。在表示上分析和互补测试证明 Pi25 授与强风抵抗到 M。oryzae 孤立 js001-20。顺序分析证明 Pi25 是有与在核苷酸位置的 Pid3 相比的单个核苷酸替换的 2772 核苷酸的 intronless 基因 459 并且述词地编码了典型卷的 coilnucleotide 绑定 siteleucine 有到 Pid3 的 100% 身份的 924 氨基酸剩余的富有的重复(CCNBSLRR ) 蛋白质通常认为的蛋白质。在 Nipponbare 的易受影响的等位基因 pi25 在核苷酸位置包含了一个胡说八道变化 2209 与 736 氨基酸剩余导致截断的蛋白质。另外,导致 10 氨基酸替换的 14 核苷酸替换在 Pi25 和在上游的 pi25 之间被识别在易受影响的等位基因的早熟的站 codon。尽管 Pi25/Pid3-mediated 抵抗的机制需要进一步被调查,等位基因的隔离将在经由转基因的途径引起节目的米饭强风抵抗便于 Pi25/Pid3 的利用,标记帮助选择。Jie Chen Yongfeng Shi Wenzheng Liu Rongyao Chai Yaping Fu Jieyun Zhuang Jianli Wu 2011Journal of Genetics and Genomics2011,38,5:45
15Efficient and Specific Modifications of the Drosophila Genome by Means of an Easy TALEN Strategy显示文摘技术开发总是是在生物医学的研究驾驶突破的力量之一。自从托马斯·摩根的时间起,一步一步地, Drosophilists 为操作并且机能上地把开发了强大的基因工具为改进这些技术并且开发新技术的果蝇染色体,而是房间仍然大,今天特别作为生物学家开始系统地学习不同模型有机体的功能的 genomics ,包括人,以一种高产量的方式。这里,我们报导,第一次在果蝇,为借助于改进抄写在很高的效率修改果蝇染色体的一个快速、容易、高度特定的方法像使活跃之物的受动器核酸酶(TALEN ) 策略。我们利用了最近发达的单位集会策略装配设计修改黄基因的二特定的 TALEN (在性染色体上) 并且新奇正染色体的基因。TALEN 的 mRNAs 随后被注入果蝇胚胎。从 31.2% 注射 F0 肥沃的苍蝇,我们检测了包含黄基因的可继承的修正。从到可继承的修正的察觉的特定的 TALEN 的建设的全部过程能在一个月以内被完成。在果蝇的这个调停 TALEN 的染色体修正方法的潜在的应用程序被讨论。Jiyong Liu Changqing Li Zhongsheng Yu Peng Huang Honggang Wu Chuanxian Wei Nannan Zhu Yan Shen Yixu Chen Bo Zhang Wu-Min Deng Renjie Jiao 2012Journal of Genetics and Genomics2012,39,5:43
16Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice显示文摘Most of the important agronomic traits in crop plants,such as yield,quality and stress response,are quantitative and jointly controlled by many genomic loci or major genes.Improving these complex traits depends on the combination of beneficial alleles at the quantitative trait loci(QTLs).However,the conventional cross breeding method is extremely time-consuming and laborious for pyramiding multiple QTLs.In certain cases,this approachRongfang Xu Yachun Yang Ruiying Qin Hao Li Chunhong Qiu Li Li Pengcheng Wei Jianbo Yang 2016Journal of Genetics and Genomics2016,43,8:47
17Oxford Nanopore MinION Sequencing and Genome Assembly显示文摘The revolution of genome sequencing is continuing after the successful secondgeneration sequencing(SGS) technology. The third-generation sequencing(TGS) technology, led by Pacific Biosciences(Pac Bio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the Min ION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies(ONT). Min ION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability,affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer Min ION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.Hengyun Lu Francesca Giordano Zemin Ning 2016Genomics, Proteomics & Bioinformatics2016,14,5:41
18Human Gut Microbiota and Gastrointestinal Cancer显示文摘Human gut microbiota play an essential role in both healthy and diseased states of humans.In the past decade,the interactions between microorganisms and tumors have attracted much attention in the efforts to understand various features of the complex microbial communities,as well as the possible mechanisms through which the microbiota are involved in cancer prevention,carcinogenesis,and anti-cancer therapy.A large number of studies have indicated that microbial dysbiosis contributes to cancer susceptibility via multiple pathways.Further studies have suggested that the microbiota and their associated metabolites are not only closely related to carcinogenesis by inducing in?ammation and immune dysregulation,which lead to genetic instability,but also interfere with the pharmacodynamics of anticancer agents.In this article,we mainly reviewed the in?uence of gut microbiota on cancers in the gastrointestinal(GI)tract(including esophageal,gastric,colorectal,liver,and pancreatic cancers)and the regulation of microbiota by diet,prebiotics,probiotics,synbiotics,antibiotics,or the Traditional Chinese Medicine.We also proposed some new strategies in the prevention and treatment of GI cancers that could be explored in the future.We hope that this review could provide a comprehensive overview of the studies on the interactions between the gut microbiota and GI cancers,which are likely to yield translational opportunities to reduce cancer morbidity and mortality by improving prevention,diagnosis,and treatment.Changting Meng Chunmei Bai Thomas D. Brown Leroy E. Hood Qiang Tian 2018Genomics, Proteomics & Bioinformatics2018,16,1:43
19Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat显示文摘Quantitative trait loci (QTLs) for plant height in wheat (Triticum aestivum L.) were studied using a set of 168 doubled haploid (DH) lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai’an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions (QEs). Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rht1 and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection (MAS).Kunpu Zhang Jichun Tian Liang Zhao Shanshan Wang 2008Journal of Genetics and Genomics2008,35,2:36
20Thinopyrum ponticum and Th. intermedium: the promising source of resistance to fungal and viral diseases of wheat显示文摘Thinopyrum ponticum and Th. intermedium provide superior resistance against various diseases in wheat (Ttricum aestivum). Because of their readily crossing with wheat, many genes for disease resistance have been introduced from the wheatgrasses into wheat. Genes for resistance to leaf rust, stem rust, powdery mildew, Barley yellow dwarf virus, Wheat streak mosaic virus, and its vector, the wheat curl mite, have been transferred into wheat by producing chromosome translocations. These genes offer an opportunity to improve resistance of wheat to the diseases; some of them have been extensively used in protecting wheat from damage of the diseases. Moreover, new resistance to diseases is continuously detected in the progenies of wheat-Thinopyrum derivatives. The present article summaries characteri-zation and application of the genes for fungal and viral diseaseresistance derived from Th. ponticum and Th. intermedium.Hongjie Li Xiaoming Wang 2009Journal of Genetics and Genomics2009,36,9:35
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