Modeling of Actual Eukaryotic Control Gene Subnetworks Based on the Method of Generalized Threshold Models

Mathematical and computational means are developed that take into consideration the specifics of control processes at the molecular level and allow one to obtain both qualitative and quantitative patterns of gene network dynamics. Using the method of generalized threshold models, models are constructed for the Arabidopsis thalianaflower morphogenesis control subsystem and gene subnetwork controlling the Drosophila melanogasterearly ontogeny. The dynamics of these systems are investigated: kinetic curves are computed for molecular components (RNA, proteins), possible modes of functioning and steady states of the nets are revealed and biologically interpreted. The models are shown to be adequate to the real processes. The effectiveness of the generalized threshold model method is evaluated in the analysis of the actual eukaryotic gene networks.     

拟南芥不同组织基因表达及可变剪接差异分析

可变剪接是转录后重要的基因表达调控方式,也是转录组和蛋白质组多样性的重要来源. 近年来随着拟南芥、水稻、玉米等植物转录组测序的完成,研究人员发现植物pre-mRNA可变剪接的发生与组织分化、发育等生物学过程密切相关. 本工作基于GEO数据库的RNA-seq数据,使用高通量测序数据分析常用的Trimmomatic、Salmon、DESeq2、SUPPA2等工具,识别了拟南芥的种子、根、叶、花、花梗、节间、长角果共7种组织的表达基因和可变剪接事件,以及7种组织间的差异表达基因和差异可变剪接事件,并以叶和花为例展示了相应的生物学功能分析. 该工作系统地研究了拟南芥基因表达和可变剪接发生的组织特异性,有助于进一步阐明植物基因组的基因表达调控机制.     

Identification of One Intron Loss and Phylogenetic Evolution of Dfak Gene in the Drosophila melanogaster Species Group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5–10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.     

GFP基因在新疆小拟南芥和拟南芥中的表达分析

以质粒pMCB30为模板,扩增GFP基因,连接到载体pCMBIA2300-35S-OCS上,构建过量表达载体p35S:GFP,将其转入农杆菌GV3101.通过农杆菌介导法将p35S:GFP载体分别转入新疆特色植物小拟南芥和拟南芥中.T0代经含有卡那霉素的1/2MS培养基筛选,获得了T1代转基因小拟南芥2株,T1代转基因拟南芥9株.通过激光共聚焦显微镜观察,在转基因小拟南芥和拟南芥的根尖细胞中均可检测到GFP绿色荧光蛋白;对转基因植株进行PCR扩增,均可检测到GFP基因,表明GFP基因已成功转入小拟南芥和拟南芥中.该研究建立了小拟南芥的遗传转化体系,为进一步利用GFP基因和进一步研究小拟南芥的功能基因奠定基础.     

拟南芥叶形态建成基因ABL1的图位克隆及鉴定

前期研究表明ABL1可能在植物叶发育过程中扮演重要的角色,其突变表现为叶片生长迟缓、成熟叶片叶缘缺刻明显等生长缺陷特征。该研究利用图位克隆及其精细定位技术,将ABL1基因锁定在2个SSLP标记T23K8和T8F5之间,该区间包含44个基因。通过生物信息学成功找到ABL1突变基因为拟南芥FAS1,该基因编码染色质组装因子CAF1的一个亚基,在植物顶端分生组织生长调控中扮演重要角色。RT-PCR结果显示,该基因表达受阻,功能互补实验证实abl1突变体的确是FAS1基因的一个新等位突变。研究结果暗示,ABL1/FAS1在植物叶形态建成中也起着重要作用。     

Construction of targeting vectors to disruptPAT1 gene inArabidopsis Trp1-100

To develop the gene targeting system by homologous recombination inArabidopsis thaliana, we constructed two targeting vectors and showed the reliability of the scheme which is based on genetic complementation of phosphoribosylanthranilate transferase (PAT1) gene. ThePAT1 gene, which is essential for tryptophan biosynthesis, was selected as a target gene because the loss of function leads to fluorescence phenotype due to the accumulation of anthranilic acid derivatives. pHS113 containsPAT1 gene surrounding 5′ and 3′ flanking portions, but the most coding region of thePAT1 gene is replaced by the neomycin phosphotransferase gene (NPTII). pHS117 consists of 1.1 kb internal fragment of genomicPAT1 gene following withNPTII gene. In this targeting strategy,Arabidopsis PAT1 gene can be disrupted by single-step of transformation experiment.     

拟南芥表皮毛发育突变体abt3-1的基因定位及表型分析

在发掘和鉴定调控植物表皮毛发育的新因子过程中,获得了一个表皮毛发育异常的拟南芥隐性突变体abt3-1(aberrantly branched trichome 3-1)。与野生型拟南芥(Col-0)相比,其表皮毛分支数目明显增加。另外,abt3-1还表现出植株小、叶形宽、叶色发灰、主根短等发育缺陷。利用图位克隆技术将该突变基因ABT3定位在1号染色体上,分子标记在F28G11#3与F4N21#1之间,物理距离为134kb。该研究将为进一步克隆ABT3基因及研究其在调控植物生长发育过程中的作用奠定基础。     

拟南芥角质层发育突变体中WBC11基因的分析与鉴定

从拟南芥(Arabidopsis thaliana L.)突变体库中筛选到一个发育突变体ku7fy1,其突变表型为叶片狭长,生长缓慢。该研究利用图位克隆技术和候选基因测序鉴定出ku7fy1角质层发育基因(white-brown complex11,WBC11)有一个点突变。对该突变体cDNA测序结果显示,WBC11基因的突变导致其第7个内含子在形成成熟mRNA时无法被正常剪切,使该突变体内WBC11的mRNA大量降解并在翻译时提前引入终止密码子。甲苯胺蓝染色实验显示,突变体叶片表面角质层有缺陷;遗传互补实验进一步证明,突变体ku7fy1中的突变基因是WBC11,ku7fy1表型是由WBC11突变造成的。     

转甜瓜CmSAMDC基因拟南芥的获得及其耐盐性研究

该研究以哥伦比亚生态型野生拟南芥为材料,将甜瓜CmSAMDC基因构建到植物双元表达载体pCAMBIA1304上,采用农杆菌介导法转入拟南芥,在含有50mg/L潮霉素(Hyg)MS固体培养基上筛选转基因后代,并利用T3代转基因幼苗进行耐盐性分析。结果显示:(1)成功构建了植物超表达载体35S∷CmSAMDC,并经农杆菌介导法转化拟南芥,潮霉素抗性筛选后获得了转CmSAMDC基因拟南芥T3代植株。(2)转CmSAMDC基因拟南芥T3代幼苗在含100、150、200mmol/L NaCl培养基中,侧根长势比野生型植株更为健壮;在200mmol/L NaCl浇灌处理后,转CmSAMDC基因T3代植株仍能维持正常生长,而野生型植株的生长明显受到抑制;在400mmol/L NaCl浇灌处理后16d,野生型植株逐渐死亡,而转基因植株仍能继续存活;对盐胁迫后植株的脂质过氧化程度(MDA)测定显示,野生型植株MDA水平较转基因植株上升更为明显。研究表明,过表达甜瓜CmSAMDC基因增强了转基因拟南芥的耐盐性。     

携带IL-2/NK4双基因减毒沙门氏菌TPIN的遗传稳定性研究

对携带IL-2/NK4双基因减毒沙门氏菌TPIN的遗传稳定性进行研究。将TPIN连续传40代,取10代、20代、30代、40代菌落进行鉴定,包括菌落和菌体的形态、质粒的纯度和浓度、目的基因片段、双酶切结果及转染人肝癌细胞(HepG2)后目的基因体外表达活性。结果表明,每10代的菌落和菌体形态一致,其所含质粒的纯度和浓度在传代过程中无明显变化,PCR扩增的目的基因条带大小一致,双酶切鉴定结果正确,转染HepG2细胞后,每代间所表达目的蛋白浓度无明显差异。TPIN作为消化道肿瘤的生物治疗药物,在遗传方面有较好的稳定性,可进一步进行大量生产。     

An approach to study the evolution of theDrosophila 5S ribosomal genes using P-element transformation

Summary The P-element-mediated gene transfer system was used to introduceDrosophila teissieri 5S genes into theDrosophila melanogaster genome. Eight transformedD. melanogaster strains that carryD. teissieri 5S mini-clusters consisting of 9–21 adjacent 5S units were characterized. No genetic exchanges betweenD. melanogaster andD. teissieri 5S clusters were detected over a 2-year survey of the eight strains. The occurrence of small rearrangements within theD. melanogaster 5S cluster was demonstrated in one of the transformed strains.     

互花米草NHX2基因的克隆与功能鉴定

NHX2属于CPA1基因家族,编码Na~+/H~+逆向转运蛋白,控制液泡膜中活性K~+的摄取,同时调节气孔的关闭。该研究以耐盐植物互花米草为材料,采用PCR技术克隆NHX2基因,并将其转入拟南芥进行相关功能鉴定。结果显示:(1)成功克隆获得互花米草NHX2基因CDS序列(1 602 bp),命名为SaNHX2,该基因编码533个氨基酸,SaNHX2蛋白的分子量约为58.65 kD,定位于细胞核和细胞膜,表明SaNHX2基因可能发挥转录调控的功能。(2) qRT-PCR结果显示,在ABA、NaCl和干旱胁迫处理下,互花米草叶和根中SaNHX2基因的表达量均上调。(3)为进一步鉴定其功能,成功构建植物表达载体,将SaNHX2基因转入拟南芥;经RT-PCR检测结果显示,SaNHX2基因在转基因植株中过表达;高盐胁迫处理后,转SaNHX2基因拟南芥的主根长度、叶绿素总量和相关胁迫应答基因表达量均高于转空载拟南芥,表明转SaNHX2基因拟南芥的耐盐能力显著增强。研究表明,SaNHX2基因可能在盐胁迫调节机制中发挥调控作用,可作为改良农作物耐盐的重要候选基因。     

Distribution of polymorphic gene duplication at theGpdh locus in natural populations ofDrosophila melanogaster

Summary The glycerol-3-phosphate dehydrogenase (GPDH, E. C. 1.1.1.8) gene ofDrosophila melanogaster contains a tandem duplication of a 4.5-kb-long DNA fragment. Survey of theGpdh gene region by the Southern blot analysis revealed the following features of this gene duplication: (1) The duplication was not observed in chromosome lines that carryIn(2L)t, a cosmopolitan chromosomal inversion in this species. The duplication and the inversion are in linkage disequilibrium. (2) The duplication is polymorphic in the Japan and US natural populations examined. Its frequency is 0.26 on an average inIn(2L)t-free chromosomes. (3) Triplication is absent or has not become frequent in the populations surveyed. Possible evolutionary factors of this duplication polymorphism are discussed.     

siRNA介导的ERA1表达下调对拟南芥抗旱性的影响

ERA1是控制植物气孔开闭的一个重要基因,根据其保守域构建RNA干扰(RNAi)载体并转化拟南芥,考察转基因植株的生长、气孔导度、离体叶片失水率以及ERA1和相关基因表达,探讨siRNA介导的ERA1表达下调对拟南芥抗旱性的影响。结果表明:转基因拟南芥株系中ERA1的表达受到明显抑制,其离体叶片失水率低于野生型,但并未出现ERA1缺失突变体的负面生长表型;转基因株系对ABA处理比野生型更敏感,其ABA处理株的根长显著变短,气孔孔径更小;转基因株ABI1、ABI2、ATHB6的表达量降低,而RAB18、RD29B、ADH1的表达量升高,siRNA介导的ERA1表达下调可能会激活RAB18、RD29B等逆境响应元件。研究发现,采用RNAi技术可以有效下调ERA1表达,在没有过多负面生长表型的前提下提高拟南芥的抗旱性,且ERA1表达下调可能通过ABA途径正面影响拟南芥的抗旱性。     

Effects of cytokinin and senescence-inducing factors on expression of P ARR5 -GUS gene construct during leaf senescence in transgenic Arabidopsis thaliana plants

ARR5-gene expression was studied in the course of natural leaf senescence and detached leaf senescence in the dark using Arabidopsis thaliana plants transformed with the P _ARR5 -GUS gene construct. GUS-activity was measured as a marker of ARR5-gene expression. Chlorophyll and total protein amounts were also estimated to evaluate leaf senescence. Natural leaf senescence was accompanied by the progressive decline in the GUS-activity in leaves of the 2nd and 3rd nodes studied, and this shift of GUS-activity was more pronounced than the loss of chlorophyll content. The ability of the ARR5-gene promoter to respond to cytokinin was not eliminated during natural leaf senescence, as was demonstrated by a cytokinin-induced increase in GUS activity in leaves after their detachment and incubation on benzyladenine (BA, 5 × 10⁻⁶ M) in the dark. Leaf senescence in the dark was associated with the further decrease in the GUS-activity. The ARR5-gene promoter response to cytokinin was enhanced with the increase of the age of plants, taken as a source of leaves for cytokinin treatments. Hence, although the expression of the ARR5 gene reduces during natural and dark/detached leaf senescence, the ARR5-gene sensitivity to cytokinin was maintained in both cases and even increased with the leaf age. This data suggest that the ARR5 gene, which belongs to the type-A negative regulators of plant response to cytokinin, could be a feedback regulator able to prevent retardation by cytokinin of leaf senescence when it is important for plant life. Growth regulators either reduced ARR5 gene response to cytokinin during senescence of mature detached leaves in the dark (SA, meJA, ABA, SP) or increased it (IAA), thus modifying the resulting rate of its expression.