应用表达谱基因芯片筛选植物激活蛋白处理水稻相关差异基因

应用基因表达谱检测植物激活蛋白处理水稻相关差异基因的表达,建立相关基因表达谱。用Cy5和Cy3分别标记激活蛋白处理和对照cDNA,将两种荧光探针混合,与载有10368位点的水稻表达谱cDNA基因芯片进行杂交,并用芯片扫描系统进行扫描,通过Cy5与Cy3信号强度比值的计算研究基因的表达差异。共获得97个差异表达基因,其中上调基因4个,下调基因93个。应用基因表达谱芯片成功筛选了植物激活蛋白处理水稻差异表达的基因,为深入揭示该激活蛋白的作用机制研究提供依据。     

XCRK基因在水稻与细菌性条斑病菌互作中的功能解析

XCRK(Xoc-associated receptor-like kinase)基因是对水稻细菌性条斑病(bacterial leaf streak,BLS)致病菌侵染应答的差异蛋白质组学研究中发现的一个拟抗病基因.生物信息学分析显示该基因位于水稻的1号染色体上,编码一个含有322个氨基酸的蛋白激酶.组织表达分析显示XCRK基因在根、茎、叶、花序等组织中均有表达,且其表达受高盐、H2O2和脱落酸(ABA)的诱导.为了探究XCRK基因在水稻BLS中的作用,通过PCR扩增XCRK基因编码区,构建超量表达载体,并转化水稻愈伤组织获得了超量表达XCRK基因的转基因水稻植株;同时构建了RNA干扰(RNAi)表达载体,并获得了抑制表达XCRK基因的转基因水稻植株.对T1代转基因植株进行了BLS抗性分析,结果显示:超量表达XCRK基因明显增强了转基因水稻对BLS致病菌的抗性;相反地,抑制表达XCRK基因的转基因水稻对BLS致病菌的敏感性则略有增强.综上结果表明XCRK基因正调控水稻对BLS的抗性,这为进一步研究该基因的作用机制提供了理论依据.     

杨树LEA基因家族全基因组鉴定及表达分析

从杨树基因组中鉴定LEA蛋白家族成员,并分析基因在杨树各组织以及在种子形成、吸涨及萌发过程中的表达情况.从NCBI下载拟南芥、水稻以及大豆等植物的LEA蛋白家族成员,通过blastP程序从杨树基因组中鉴定出候选基因,并采用pfam程序进行进一步筛选获得杨树LEA蛋白基因,最后通过芯片以及EST数据分析基因的表达量.通过对杨树LEA蛋白基因家族在全基因组水平上的搜索,确定了杨树LEA蛋白家族8个亚家族,共87个成员,发现在花中有16个基因高量表达,且其中8个基因具有很高的组织特异性.在吸涨种子中,PtLEA1.1和PtLEA3.1有高量的表达,LEAⅣ,LEAⅤ,LEAⅥ及SMP亚家族成员都具有特异的表达.12个基因在萌发种子中有高量的表达,其中4个基因特异表达,5个基因在种子萌发过程中可能受到光照的影响.此外,3个基因在成熟叶片中出现了下调表达,8个基因在根中具有高量表达,3个基因的高量表达在木质部中被发现.杨树LEA蛋白不同亚家族成员可能参与了植物种子的生长发育、种子的萌发及对胁迫的响应等多种生理功能.     

禾本科植物β-淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析

 β-淀粉酶(beta-amylase,BAM)是一类关键的淀粉水解酶,在禾谷类作物生长发育过程中起着重要作用,与植物多种非生物胁迫响应相关.本研究通过系统发育分析,将水稻、玉米、高粱、谷子、二穗短柄草5 种禾本科植物中共54 个BAM 基因分为10 个同源基因簇,每个同源基因簇都涵盖了这5 个物种,因此推测在禾本科祖先物种中至少含有10 个BAM 基因,并且在禾本科植物分化后没有发生明显的基因丢失事件.基于对编码蛋白质序列的功能分化分析,表明同源基因簇间存在明显的进化速率的差异.对10 个同源基因簇进行了适应性进化检测,发现有3 个同源簇在禾本科植物的进化过程中经历了适应性进化.此外,对水稻β-淀粉酶的表达分析发现,一些β-淀粉酶具有组织特异性表达特征,并且至少有5 个水稻的β-淀粉酶基因具有受到非生物逆境的胁迫而表现出不同的表达模式.本研究结果为进一步探讨禾本科BAM 基因的生物学功能提供了一定的理论基础.     

水稻全基因组磷脂酶家族蛋白筛选及其生物信息学分析

利用已鉴定磷脂酶基因同源筛选的方法对水稻全基因组范围的磷脂酶基因进行鉴定与筛选,有助于研究其家族基因的各种功能.通过对水稻全基因组进行分析,筛选鉴定磷脂酶家族成员,并对编码蛋白的跨膜区、等电点、分子量等理化性质以及进化、基因组定位、表达特征进行生物信息分析.结果表明：水稻磷脂酶家族基因分为3个亚组,亚组内基因表现出明显相似的结构及进化特征,且磷脂酶家族基因编码蛋白具有相同的3个保守基序,染色体上的磷脂酶家族基因表现出了明显的不均衡性,磷脂酶家族大部分基因表达量偏低,部分表现出了组织表达偏好性,少部分基因在水稻各个组织或生育阶段表达量比较高,可能同水稻发育相关.     

超级杂交水稻LYP9及其亲本的转录组学分析研究

虽然杂交优势在农业生产上得到广泛应用，但其遗传基础和分子机理仍不甚明晰，是一个经典的科学难题。根据已知和预测的籼稻基因，中科院遗传与发育生物学研究所朱立煌研究组和未祯研究组与中科院北京基因组学研究所于军研究组以及湖南杂交水稻中心袁隆平研究组合作，设计了全基因组寡聚核苷酸芯片，并利用这种芯片研究了超级杂交稻LYP9及其亲本株93—11和PA64s发育过程中叶与花序的转录组情况。研究发现，AL7种组织（育秧和耕种期的叶，孕穗期、抽穗期、开花期和灌浆期的剑叶，灌浆期的花序）分离的共计36926个基因中有22266个在上述样本组织中表达。     

利用小样本表达谱数据构造前列腺癌基因网络

用25张前列腺癌芯片表达谱数据,基于基因间的表达相似性和基因的差异表达程度,筛选出287条基因,用模糊聚类的方法将其聚成65个类,用贝叶斯模型构造了一个大型的基因网络,并对这个网络的有效性进行了验证.结果表明,基于本文提出的策略,利用小样本量的表达谱数据构造大型基因网络是可行的.     

丙型肝炎病毒5＇NCR转基因细胞模型及在反义核酸药物筛选和评价中的应用

为了进行以基因为靶的抗丙型肝炎病毒(HCV)药物的筛选及评价,将HCV5＇NCR-C基因与荧光素酶基因的融合基因片段插入pCI-neo表达载体,通过PCR扩增、酶切反应及荧光素酶瞬间表达活性鉴定,获得HCV5＇NCR调控荧光素酶的稳定表达质粒pHCV-ne04,将其转染HepG2细胞,经GA18筛选,从150个克隆中获得一个高荧光素酶活性表达的细胞株HepG2.9706.该株细胞内HCV片段的DNA及mRNA检测均呈阳性,转基因拷贝数为140.利用该细胞株,通过脂质体介导,对3条针对HCV调控基因的反义寡核苷酸(ASODNs)即HCV363,HCV349,HCV279进行了活性评价,结果显示,三种ASODNs均具有特异性的剂量依赖性抑制活性,浓度在0.5μmol/L时,三者对HCV5＇NCR调控荧光素酶表达抑制率分别为61%,55%及48%.该研究提示反义寡核苷酸有可能成为治疗HCV的新途径.     

水稻染色质重塑因子OsSWIB1的表达分析及其突变体的创建

SWI/SNF家族是ATP依赖的染色质重塑复合物，对基因的表达调控具有重要作用.为了探究水稻中染色质重塑因子OsSWIB1的功能，对OsSWIB1基因表达模式进行分析.结果表明：OsSWIB1在水稻的叶、叶鞘及穗中表达量较高，而在茎、茎顶端分生组织及根中表达量较低；在水稻不同的生长发育时期，除在苗期表达量较低外，OsSWIB1在分蘖期、孕穗期、抽穗期及灌浆期均有较高表达.此外，OsSWIB1在短日照条件下的表达明显高于在长日照条件下的表达.利用CRISPR-Cas9技术对OsSWIB1基因进行靶向编辑，共获得20株T₀代转基因植株，通过测序分析，鉴定出3个纯合编辑的突变体.对1个杂合编辑突变体的后代进行分离，获得了1个缺失200 bp的纯合突变体.     

利用寡核苷酸芯片进行拟南芥SO2胁迫基因表达谱分析

运用拟南芥寡核苷酸芯片ATH1,分析SO2胁迫对拟南芥基因表达谱的影响.在22 810个探针中共检出30 mg*m-3SO2胁迫组与对照组间表达改变1倍以上的基因494个,其中上调220个,下调表达274个,主要涉及与细胞代谢(189个)、结合(177个)、转录调控(74个)、结构分子(55个)、信号转导(53个)、物质运输(39个)等功能相关的基因.胁迫组中与细胞防御相关的基因,包括防御酶基因、病程相关蛋白PRs和细胞壁防御相关基因等表达上调.结果表明,SO2胁迫时植物细胞能够通过对基因转录的调控,从分子水平上改变细胞的生理过程,提高植株对逆境的适应性.     

Expression profile analysis of 9 heat shock protein genes throughout the life cycle and under abiotic stress in rice

Plant heat shock proteins (Hsps) facilitate protein folding or assembly under diverse developmental and adverse environmental conditions. Nine OsHsps were identified in our previous study from a proteomic analysis of rice cv. IRAT 109 leaf samples at the seedling stage under drought stress. To obtain additional information on the 9 OsHsp genes, this study focused on an expression profile analysis at different development stages throughout the life cycle of rice, and under different abiotic stresses and phyto-hormone treatments. The 9 genes exhibited distinctive expression patterns in different organs or development stages. Five of the genes (OsHsp72.90, OsHsp72.57, OsHsp71.18, OsHsp24.15 and OsHsp18.03) showed high expression in the endosperm, indicating that OsHsp genes may play important roles in rice seed development. All 9 OsHsps were up-regulated under heat, polyethylene glycol, and abscisic acid treatment, whereas salt stress caused up-regulation of 6 genes (OsHsp93.04, OsHsp71.10, OsHsp71.18, OsHsp72.57, OsHsp24.15 and OsHsp18.03) and cold stress resulted in down-regulation of OsHsp93.04 and OsHsp72.57. These diverse expression profiles imply potential functional diversity of the Hsp gene family in rice.     

Involvement of Jasmonate-signaling pathway in the herbivore-induced rice plant defense

The expression patterns of eight defense- related genes in the herbivore-infested and jasmonate- treated (jasmonic acid, JA and its derivative MeJA) rice leaves were analyzed using RT-PCR. The results showed that Spodoptera litura Fabricius (Lepidoptera: Noctuidae) herbi-vory induced the expression of lipoxygenase (LOX) and al-lene oxide synthase (AOS) genes that are involved in the jasmonate-signaling pathway. Moreover, S. litura damage resulted in the expression of farnesyl pyrophosphate syn-thase (FPS), Bowman-birk proteinase inhibitor (BBPI), phenylalanine ammonia-lyase (PAL) and other rice defense- related genes that were also induced by aqueous JA treat-ment or gaseous MeJA treatment. These indicated that in rice leaves, the JA-related signaling pathway was involved in the S. litura-induced chemical defense. Mechanical damage and brown planthopper (BPH), Nilaparvata lugens (St錶) (Homoptera: Delphacidae) damage induced the expression of LOX gene, but both treatments did not induce the expression of AOS gene. However, BPH damage induced the expression of acidic pathogen-related protein 1 (PR-1a), Chitinase (PR-3), and PAL genes, which is involved in the salicylate- signaling pathway. It was suggested that salicylate-related signaling pathway or other pathways, rather than jas-monate-signaling pathway was involved in the BPH-induced rice plant defense.     

Blast fungus-induction and developmental and tissue-specific expression of a rice P450<Emphasis Type="Italic">CYP72A</Emphasis> gene cluster

Cytochrome P450 gene superfamily is widely involved in diverse processes of plant development and environmental responses including defense response to pathogens.We previously isolated a rice cDNA fragment in a DD-PCR screening for blast fungus-induced genes. In the current study, we isolated a CYP72A gene cluster consisting of 7 P450 CYP72A genes (CYP72A17-23) with the conserved cDNA sequence through the public rice genome data. There are total 14 putative CYP72A members in the rice genome, with high diversity at N-terminal sequences while high homology at C-terminal sequences of those 14 putative proteins. We analyzed expression profiles of the cloned 7 CYP72A genes during pathogen infection and development. The results showed that expression of CYP72A18, 19, 22 and 23 was differentially regulated in the incompatible and compatible interactions between rice and blast fungus. Except CYP72A20, a pseudogene, other 6 CYP72A genes also exhibited temporal and spatial expression patterns, respectively.These findings provide fundamental data for rice P450 gene function analysis.     

差异展示法鉴定GA3诱导的水稻差异表达的mRNA

赤霉素是植物生长发育过程中一类重要的调节激素，在水稻不育系上喷施合适浓度的ＧＡ３（赤霉素的一种）可以克服其包颈现象。运用反转录和聚合酶链式反应建立了一套旨在分离差异表达ｃＤＮＡ的差异展示方法。     

Transgenic rice homozygous lines expressing GNA showed enhanced resistance to rice brown planthopper

Mature seed-derived calli from two elite Chinese japonica rice (Oryza sativa L.) cultivars Eyi 105 and Ewan 5 were co-transformed with two plasmids, pWRG1515 and pRSSGNA1, containing the selectable marker hygromycin phosphotransferase gene (hpt), the reporter β-glucuronidase gene (gusA) and the snowdrop (Galanthus nivalis) lectin gene (gna) via particle bombardment. 61 independent transgenic rice plants were regenerated from 329 bombarded calli. 79% transgenic plants contained all the three genes, revealed by PCR/Southern blot analysis. Western blot analysis revealed that 36 out of 48 gna-containing transgenic plants expressed GNA (75%) at various levels with the highest expression being approximately 0.5% of total soluble protein. Genetic analysis confirmed Mendelian segregation of transgenes in progeny. From the R2 generations whose R1 parent plants showing 3:1 Mendelian segregation patterns, we identified five independent homozygous lines containing and expressing all the three transgenes. Insect bioassay and feeding tests showed that these homozygous lines had significant inhibition to rice brown planthopper (Nilaparvata lugens, BPH) by decreasing BPH survival and overall fecundity, retarding BPH development and declining BPH feeding. These BPH-resistant lines have been incorporated into rice insect resistance breeding program. This is the first report that homozygous transgenic rice lines expressing GNA, developed by genetic transformation and through genetic analysis-based selection, conferred enhanced resistance to BPH, one of the most damaging insect pests in rice.     

水稻中两个同源异型结构域转录因子的亚细胞定位

为了对水稻同源异型结构域转录因子HD-ZipⅢ家族中的HDZ1和HDZ2进行亚细胞定位,利用RT-PCR技术从水稻cDNA中扩增HDZ1和HDZ2的编码区(去除终止密码子序列),与绿色荧光蛋白GFP编码框融合,构建2个转录因子的瞬时表达载体,采用农杆菌介导的转化方法转化至烟草中进行瞬时表达分析.结果表明:PCR扩增所得为目的基因片段HDZ1和HDZ2;二者与载体质粒pCAMBIA35S-GFP连接获得的融合表达载体成功移至烟草中并表达;确定HDZ1主要定位于烟草叶片的气孔中,而HDZ2定位于烟草表皮细胞的细胞膜上.二者在亚细胞中的定位不同,可能在水稻生长发育中所起的作用也不相同.     

Proteomic analysis of blast-resistant near-isogenic lines derived from japonica rice,var. Yunyin,infected with Magnaporthe oryzae

Rice blast is one of the most devastating dis- eases in the world and outbreaks occur frequently. The differences in protein expression between blast resistant and susceptible near-isogenic lines （NILs） of japonica rice var. Yunyin infected with Magnaporthe oryzae were ana- lyzed using proteomics, indicated that 67 different proteins were identified from 75 obtained proteins using the matrix- assisted laser desorption/ionization time-of-flight mass spectrometry technique. Seven specific expression proteins, 43 up-regulated proteins and 17 down-regulated proteins were identified among the 67 proteins. The bioinformatical analysis demonstrated that these 67 different proteins were involved in many biological physiological processes including five proteins related to photosynthesis, 25 pro- teins related to metabolism, six proteins related to anti- oxidants, 10 proteins related to protein synthesis and modification, five proteins related to signal transduction,four proteins related to adversity stress and 12 non-func- tional proteins. These identified proteins were directly or indirectly related to stress. Five proteins related to different physiological processes were selected. Their cDNA sequences were predicted and their expression patterns were analyzed using real-time PCR, demonstrated that the genes would response to M. oryzae and the response blindingly different between blast resistant and blast sus- ceptible NILs.     

甲基乙二醛诱导牙周膜成纤维细胞基因表达与分析

运用基因芯片研究甲基乙二醛诱导人牙周膜成纤维细胞基因表达谱的变化。原代培养人牙周膜成纤维细胞,诱导组以终质量浓度为0.1 g/L的甲基乙二醛刺激培养细胞,对照组不含甲基乙二醛。24 h后收获细胞,提取mRNA,逆转录cDNA时用Cy3和Cy5荧光染料标记,制备成cDNA探针,与表达谱芯片进行杂交、扫描和分析。芯片检测结果用实时定量聚合酶链反应验证和生物信息学分析。结果共有18条基因显著差异表达,其中上调基因有11条,下调基因有7条,差异性表达的基因按功能可分为程序性细胞死亡、信号转导、细胞因子、代谢酶类、载体蛋白和未知基因等。与程序性细胞死亡、信号转导和细胞因子相关基因的差异表达可能是甲基乙二醛通过线粒体信号通路,诱导人牙周膜成纤维程序性细胞死亡,破坏牙周组织增生,从而导致牙周病发生的机制。     

水稻整体原位杂交实验技术方法的改进

以检测水稻SUPERWOMAN1(SPW1)/OsMADS16基因的表达模式为例,通过对杂交探针的制备、材料的固定及解离通透、显色等方面进行优化,获得背景值低、特异性高的SPW1/OsMADS16基因特异性表达结果.建立一套针对水稻的整体原位杂交技术,方法简单,费用低廉,可在离心管中多种材料同时进行.主要实验步骤包括探...