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differential expression of MicroRNAs in Response to Drought Stress in Maize

Journal of Integrative Agriculture 2013年第8期12卷 1414-1422页

作者： LI Jing-sheng FU Feng-ling AN Ming ZHOU Shu-feng SHE Yue-hui LI Wan-chen Maize Research Institute Sichuan Agricultural University Agronomy Faculty Sichuan Agricultural University

Drought is one of the major abiotic stresses that limit maize productivity. Apart from the principal transcriptional regulation, post-transcriptional regulation mediated by microRNAs appears to be the prevalent response of plants to abiotic stress. In this study, the differential expression of microRNAs in the previously evaluated drought-tolerant inbred lines R09 under drought stress was detected by microarray hybridization. The target genes of the differentially-expressed microRNAs were predicted by bioinformatics software WMD3 for plant target gene prediction. The possible regulation of the differentially-expressed microRNAs as well as their target genes in maize response to drought stress was analysed according to Gene Ontology. Sixty-eight microRNAs in 29 microRNA families were detected to be differentially expressed in the seedling of the drought-tolerant inbred line R09, accounting for 5.97% of the total number of the probes. The expression profiles were different between the two time points of the drought stress. The functions of the genes targeted by the differentially-expressed microRNAs involve multiple physiological and biochemical pathways of response to abiotic stress, such as transcription regulation, metabolism, signal transduction, hormone stimulation, and transmembrane transport. Under drought stress, the differential expression of microRNAs regulates the expression of their target genes, resulting in multiple responses of physiological and biochemical pathways relative to drought tolerance of maize, miR156, miR159 and miR319 families may play more important roles. The different members of the same family may play similar regulation effects in most cases.

关键词： differential expression drought maize microarray microRNA target gene

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differential expression analysis of Liprin-α2 in hibernating bat (Rhinolophus ferrumequinum)

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Progress in Natural Science:Materials International 2008年第1期18卷 27-32页

作者： Lihong Yuan a,b,c, Xueguo Zuo a, Jinping Chen d, Benfu Lin e, Junpeng Zhang b, Min Sun e, Shuyi Zhang a,* a School of Life Science, East China Normal University, Shanghai 200062, China b Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China c Graduate University of Chinese Academy of Sciences, Beijing 100080, China d Guangdong Entomological Institute, Guangzhou 510260, China e Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China School of Life Science East China Normal University Shanghai 200062 China Institute of Zoology Chinese Academy of Sciences Beijing 100080 China Graduate University of Chinese Academy of Sciences Beijing 100080 China Guangdong Entomological Institute Guangzhou 510260 China Guangzhou Institute of Biomedicine and Health Chinese Academy of Sciences Guangzhou 510663 China

A PCR-based subtractive hybridization technique was used to identify genes up-regulated in the hibernating bat brain to explore the molecular mechanism of hibernation. Three genes, Liprin-a2, PTP4A2 and CAMKKb were difierentially expressed in hibernating bat brain tissue compared to active bat brain tissue. One of them, Liprin-a2, which has recently been shown to have the key function in the organization of presynaptic and postsynaptic multiprotein complexes was studied in detail. We demonstrated that the expression level of Liprin-a2 was up-regulated almost 4-fold in hibernating bat brains by RT-PCR compared to levels in active bats. The difierential expression pattern of Liprin-a2 was also detected in muscle, fat, brain and heart tissue of hibernating bats by real-time quantitative PCR. The result indicated that Liprin-a2 was over-expressed in brain and heart tissue and down-regulated in muscle and fat. In brain tissue of hibernating bats, Liprin-a2 expression was statistically significantly higher than in brain tissue of active controls (P = 0.029). The precise control of transcriptional level and the distinctively difierential expression pattern of Liprin-a2 in difierent organs during circ- annual hibernation may have important physiological significance, not only in maintaining normal function of many key organs but also in effectively conserving limited energy resources without physiological damage.

关键词： Bat differential expression Hibernation Liprin-a2

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differential expression analyses for single-ce RNA-Seq： old questions on new data

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Frontiers of Electrical and Electronic Engineering in China 2016年第4期4卷 243-260页

作者： Zhun Miao Xuegong Zhang MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic & Systems Biology TNLIST Department of Automation Tsinghua University Beijing 100084 China School of Life Sciences Tsinghua University Beijing 100084 China

Single-cell RNA sequencing （scRNA-seq） is an emerging technology that enables high resolution detection of heterogeneities between ceils. One important application of scRNA-seq data is to detect differential expression （DE） of genes. Currently, some researchers still use DE analysis methods developed for bulk RNA-Seq data on single-cell data, and some new methods for scRNA-seq data have also been developed. Bulk and single-cell RNA-seq data have different characteristics. A systematic evaluation of the two types of methods on scRNA-seq data is needed. Results： In this study, we conducted a series of experiments on scRNA-seq data to quantitatively evaluate 14 popular DE analysis methods, including both of traditional methods developed for bulk RNA-seq data and new methods specifically designed for scRNA-seq data. We obtained observations and recommendations for the methods under different situations. Conclusions： DE analysis methods should be chosen for scRNA-seq data with great caution with regard to different situations of data. Different strategies should be taken for data with different sample sizes and/or different strengths of the expected signals. Several methods for scRNA-seq data show advantages in some aspects, and DEGSeq tends to outperform other methods with respect to consistency, reproducibility and accuracy of predictions on scRNA-seq data.

关键词： single-cell RNA-Seq differential expression

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differential expression Analysis of Genic Male Sterility A／B Lines in Chinese Cabbage—Pak—Choi（Brassica campestris *** Makino）

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Agricultural Sciences in China 2003年第2期2卷 195-199页

作者： WANGYong－qin CAOJia－shu 等 InstituteofVegetableScience ZhejiangUniversityHangzhou310029P.R.China

To determine differential expression of genie male sterility A/B lines in Chinese cabbage-pak-choi (Brassica campestris ssp. chinensis Makino var. communis Tsen et Lee), we used the RNA fingerprinting technique, cDNA-AFLP analysis, in different developmental stages and different tissues. While no obvious differential expressions were observed in rosette leaves, florescence leaves, and scapes, some differential expressions were found in alabstrums of A/B lines and among leaves, scapes and alabstrums. We analyzed the al-abstrums collected in different developmental stages with 10 primer combinations. We got a unique band between middle size alabstrums and large alabstrums in B line in one of the ten pair primers, and in another one pair, one band reflecting a higher gene-expression level in A line than that in B line was obtained. No unique bands were found with the other primer combinations. The bands reflecting different gene-expression level were confirmed by Northern hybridization. The results indicated that cDNA-AFLP was a suitable tool for studying differential expression of genie male sterility in plants. SDS-polyacrylamide gel electrophoresis patterns of soluble proteins further verified the difference in A/B lines.

关键词： Chinese cabbage Brassica campestris L. (syn. B. rapa L.) Genie male sterility differential expression cDNA-AFLP SDS-PAGE

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The impact of allelochemicals on the differential expression of symbiotic bacteria in cotton aphids

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Journal of Integrative Agriculture 2018年第8期17卷 1815-1821页

作者： LIU Ying LIANG Ping-zhuo LI Fen MA Kang-sheng CHEN Xue-wei CHEN An-qi LIANG Pei GAO Xi-wu Department of Entomology China Agricultural UniversityBeijing 100193P.P.China

Insects have developed a good adaptive mechanism in response to environmental stresses in the long-term evolution. They have developed a helpful metabolism system to resist plant allelochemicals. Insects also harbor different kinds of symbiotic bacteria, which provide them a competitive advantage. Here, using cotton aphid as an example, we investigated the effects of four plant allelochemicals on the differential expression of symbiotic bacteria based on transcriptome data. We also studied the composition of symbiotic bacteria and function on pathway level in three kinds of aphids. We found that the bacteria have a significant role in resisting the plant allelochemicals stress and host plant selection by aphids. These results should be useful to investigate the environmental adaption mechanism of aphids in the view of symbiotic bacteria. These results would offer a new insight for improving strategy of aphids and developing new pest control systems.

关键词： Aphis gossypii plant allelochemicals differential expression symbiotic bacteria

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A Study on the Activity of Carboxylesterase and the differential expression of Its Gene in the Midguts of Bombyx mori Resistant to BmDNV-Z

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Agricultural Sciences in China 2007年第8期6卷 1018-1026页

作者： GAO Gui-tian CHEN Ke-ping YAO Qin CHEN Hui-qing WANG Lin-ling XU Jia-ping ZHAO Yuan WANG Yong-jie Institute of Life Sciences Jiangsu University Zhenjiang 212013 P.R.China Department of Food Enginneering Shaanxi Normal University Xi＇an 710062 P.R.China

This study was to discuss the relationship among the change in the activity of Bombyx mori carboxylesterase （BmCarE） in the midguts, the differential expression of BmCarE gene （bmcare） in the midguts, and the ability of Bombyx mori resistant to densonucleosis virus （BmDNV）, and to elucidate the molecular mechanism of resistance to BmDNV-Z. With two silkworm strains, HUABA, which is susceptible to BmDNV-Z, and BC8 （a near isogenic line of HUABA）, which is completely resistant to the same virus, as materials, the activity of BmCarE in the midgut was determined by Bio-Tek Synergy, and the differential expression of bmcare between the two strains was investigated by real-time fluorescence quantitative PCR, both at 12, 36, and 72 h post oral inoculation of the two strains with virus （hereafter referred as inoculation）. While the activity of BmCarE in the midguts of BC8 inoculation group at 12 h post inoculation was higher than that in the BC8 control group, the HUABA inoculated group, and the HUABA control group by 3.28, 2.26, and 3.02 times, respectively, with the difference being highly significant （P 〈 0.01）, there was no statistical difference among the other groups. The relative expression level of bmcare in the midguts of BC8 inoculation group at 12 h post inoculation was higher than that in the BC8 control group, the HUABA inoculation group, and the HUABA control group by 17.714, 21.76, and 15.09 times, respectively, with the difference being highly significant （P 〈 0.01）, and there was no statistical difference among other groups. The elevation of BmCarE activity and expression level of bmcare in the resistant strain at 12 h post inoculation may relate to the resistant gene （nsd/nsd） and the stimulation of BmDNV-Z. The molecular basis for the elevation of BmCarE activity in the resistant strain BC8 may be the change in the expression level of bmcare.

关键词： Bombyx mori resistance BmDNV-Z midgut carboxylesterase enzyme activity differential expression

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differential expression of miRNAs in Rice under High Temperature Stress

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Agricultural Biotechnology 2015年第4期4卷 6-9,15页

作者： Guangmin XU Xiaofang YANG Rong ZHANG Qiao LI Juan LI College of Life Science Anhui Agricultural University Biotechnology Center Anhui Agricultural University

The growth and development of rice are closely related with temperature. In order to clarify the mechanism of high temperature resistance in riee, in this study, using high temperature-resistant Indian rice cultivar N22 as the experimental material, Osa-rniR159c, Osa-miR159d, Osa-miR159f, Osa-miR164d, Osa- rrdR529b and Osa-miR166h-3p obtained by high-throughput sequencing as target genes, the expression patterns of these genes in young panicles of rice under high temperature stress were analyzed by RNA-tailing and primer-extension RT-PCR, which provided theoretical basis for breeding high temperature-resistant rice eultivars.

关键词： Rice High temperature stress miRNAs qRT-PCR differential expression

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differential expression analysis of microRNAs and their potential target genes responding to infection of Cucumber green mottle mosaic virus in cucumber

Differential expression analysis of microRNAs and their pote...

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中国植物病理学会2015年学术年会

作者： LIANG Chao-qiong LIU Hua-wei MENG Yan LUO Lai-xin LI Jian-qiang Department of Plant Pathology China Agricultural University/Key laboratory of Plant PathologyMinistry of Agriculture Beijing Engineering Research Center of Seed and Plant Health/Beijing Key Laboratory of Seed Disease Testing and Control Molecular Plant Pathology United States Department of AgricultureAgricultural Research Service

Cucumber green mottle mosaic virus（CGMMV） is a mainly emerged Cucurbitaceaeinfecting Tobamo- virus that has spread fast in *** serious virus disease often disorders the natural grown processes and leds cucumber to produce sterile flower or abnormal fruit,so eventually devastates Cucurbitaceae ***（miRNAs） are comprised by a large group of 21-24 nt RNA molecules that are important regulators of plant development processes and stress *** this study,relative expression levels of 6 miRNAs（miR159,miR169,miR172,miR838,miR854 and miR5658） and their corresponding 6 putative target genes（Csa4M002940.1,Csa4 MO 15840.1,Csa5M175970.1,Csa6M520360.1,Csa2M224260.1 and CsalM470280.1） were detected at 1,7,14,21,28,35 and 42 dpi in the leaf,stem and root tissues of cucumber infected with CGMMV by quantitative real-time PCR（qRT-PCR）.The results showed that miR159,miR172 and miR5658 were significantly down-regulated in leaf and stem tissues,while miR169,miR838 and miR854 were only significantly down-regulated in leaf at 28 *** expression level of miR172 was found to be positively correlated with its targets（Csa5M175970.1） during 1-42 dpi in leaf *** in more cases,the correlative relationship of miR159,miRl 69,miR838,miR854 and miR- 5658 and their respective targets varied in different inoculation *** has been proposed that those 6 putative targets genes were likely to associate with *** results provide insights into miRNA-mediated interactions of CGMMV and cucumber.

关键词： microRNA targets Cucumber green mottle mosaic virus cucumber differential expression

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differential expression of genetic loci underlying above-and below-ground lignin contents and Cell wall constituents in poplars

Differential expression of genetic loci underlying above-and...

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第二届中国林业学术大会——S2 功能基因组时代的林木遗传与改良

作者： Gerald A. Tuskan Mark Davis Lee Gunter Ranjan Priya Environmental Sciences Division Oak Ridge National Laboratory National Bioenery Center National Renewable Energy Laboratory

In this study, we establish a comprehensive genetic map with a large number of progeny from a three generation intercross hybrid poplars, and phenotype the lignin content, S/G ratio and 28 cell wall constituents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content in stem is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations were only observed among components within organs. Altogether 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci with 27 of these loci are pleiotropic. The majority of the detected genetic loci were found to express differentially in stem and root. This study provides desirable genetic information and will enhance our ability to breed and engineer genotypes improved for pulp, paper, cellulosic ethanol, and carbon sequestration.

关键词： Lignin Cell wall constituent Quantitative trait loci differential expression

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differential expression of wnt1, wnt2, wnt4, wnt5 and wnt11A/b in protoscoleces and adult of Echinococcus granulosus

Differential Expression of wnt1, wnt2, wnt4, wnt5 and wnt11A...

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中国动物学会寄生虫学专业委员会第十届全国寄生虫学青年工...

作者： WANG Zheng-rong ZHANG Yan-yan BO Xin-wen XU Xue-ping XU Chun-sheng Xinjiang Academy of Agricultural and Reclamation Science Shehezi University

Objective To investigate the differential expression of wnt gene family wnt1、wnt2、wnt4、wnt5 and wnt11A/B in protoscoleces and adult of ***. Methods The SYBR Green Ⅰreal-time quantitative PCR and whole-mount in situ hybridization methods were applied to analyze the differential transcription and positioning of these genes in protoscoleces and adult of ***. Results The quantitative results showed that the wnt gene family were transcribed in both protoscoleces and adult of ***. The transcription of wnt1 and wnt2 were higher in adult of *** than protoscoleces, On the contrary, the transcription of wnt4、wnt5 and wnt11A/B were higher in protoscoleces than adult of ***. The whole-mount in situ hybridization results showed that the wnt gene family mRNA were mainly distributed in rostellum、suckers、hooks and margins of protoscoleces. Conclusion Based on these findings, the transcription and distribution of wnt1、wnt2、wnt4、wnt5 and wnt11 B in differential stages of *** has certain regularity, which laid down the foundation for further research of the roles of wnt gene family and wnt signal during the development of ***.

关键词： Echinococcus granlosus wnt gene protoscoleces adult differential expression

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