Identification of m RNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng

Increasing evidence suggests that long non-coding RNAs(lnc RNAs) play significant roles in plants.However,little is known about lnc RNAs in Panax ginseng C.A.Meyer,an economically significant medicinal plant species.A total of3,688 m RNA-like non-coding RNAs(mlnc RNAs),a class of lnc RNAs,were identified in P.ginseng.Approximately 40% of the identified mlnc RNAs were processed into small RNAs,implying their regulatory roles via small RNA-mediated mechanisms.Eleven mi RNA-generating mlnc RNAs also produced si RNAs,suggesting the coordinated production of mi RNAs and si RNAs in P.ginseng.The mlnc RNA-derived small RNAs might be 21-,22-,or 24-nt phased and could be generated from both or only one strand of mlnc RNAs,or from super long hairpin structures.A full-length mlnc RNA,termed MAR(multiple-function-associated mlnc RNA),was cloned.It generated the most abundant si RNAs.The MAR si RNAs were Researchpredominantly 24-nt and some of them were distributed in a phased pattern.A total of 228 targets were predicted for 71 MAR si RNAs.Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways,suggesting the significance of MAR in P.ginseng.Consistently,MAR was detected in all tissues analyzed and responded to methyl jasmonate(Me JA) treatment.It sheds light on the function of mlncRNAs in plants.     

家蚕Bcl-2家族基因 BmBuffy 的克隆及表达分析

【目的】本研究旨在获得家蚕 Bombyx mori Bcl-2家族同源基因,并分析其在不同组织和发育阶段的时空表达模式及功能。【方法】用cDNA末端快速扩增方法（rapid amplification of cDNA ends, RACE）克隆家蚕Bcl-2家族基因BmBuffy,利用SSR分子标记连锁分析确定其染色体定位。同时,用RT-PCR和qPCR技术分析该基因在家蚕幼虫及变态期间不同组织中的表达。【结果】克隆获得全长家蚕Bcl-2家族同源基因 BmBuffy,证明该基因位于第 4号染色体上,开放阅读框长879 bp,编码292 aa,预测其分子量大小为32.4 kDa,等电点为9.94,且第130-231位氨基酸之间存在1个Bcl-2_like Superfamily结构域。系统进化发育树表明,其与黑腹果蝇Drosophila melanogaster的DmBuffy关系最近,氨基酸序列一致性为27%。BmBuffy在幼虫组织中的表达结果显示,其在马氏管中表达量最高,而且在不同组织变态期的关键时间点均有明显变化。【结论】家蚕BmBuffy具有Bcl-2家族典型结构域,BmBuffy定位于第 4号染色体上,BmBuffy在家蚕变态期的组织生理变化中起到一定作用。本文为进一步研究家蚕Bcl-2家族基因的功能奠定基础。     

家蚕醛氧化酶基因（BmAOXs）的鉴定与表达分析

醛氧化酶（aldehyde oxidases, AO, EC 1.2.3.1）是属于钼-黄素酶（molybdo-flavoenzymes, MFEs）家族的一类蛋白酶。为了探讨该酶在家蚕Bombyx mori中的功能, 本研究对家蚕醛氧化酶基因（BmAOXs）家族进行了鉴定和分析。以其他物种AO基因序列检索家蚕全基因组数据库, 获得了8个BmAOX候选基因, 均具有醛氧化酶保守的功能域。进化分析表明, BmAOX与其他昆虫AO聚为一簇。RT-PCR分析结果显示: BmAOX1, BmAOX2, BmAOX3, BmAOX5具有很强的组织特异性; 而BmAOX4, BmAOX6, BmAOX7, BmAOX8则在蛹和成虫的多个组织中均有表达, 提示它们在家蚕生理代谢活动中起重要作用。利用Native PAGE和活性染色方法, 对BmAOX编码的蛋白进行检测, 结果表明: 家蚕蛹中有5种有活性的醛氧化酶, 而成虫中有6种, 各组织中均有有活性的BmAOX, 只是种类和活性水平有所不同。本研究结果为深入探讨BmAOX家族的功能奠定了基础。     

猪L-FABP基因的克隆、表达特征及遗传多态性研究

FABPs属于脂结合蛋白超家族成员,是一类分子量较小而对脂肪酸有高亲和力的蛋白质,广泛存在于脊椎动物和非脊椎动物的细胞质中.FABPs担当细胞内脂肪酸的运输任务,它们与脂肪酸结合将其运输到脂肪酸氧化的位置、脂肪酸脂化成甘油三醋或磷脂的位置,或者进入细胞核内发挥其可能的调控功能.因此FABPs对脂类代谢具有重要的调控作用.本研究把L-FABP基因作为影响猪肌内脂肪含量的候选基因.为此,利用cDNA末端快速扩增(RACE)和PCR技术,克隆到猪肝脏型脂肪酸结合蛋白基因(L-FABP)的全长cDNA序列(GenBank登录号AY960623)和部分基因组序列(GenBank登录号DQ182323).猪L-FABP基因的cDNA序列全长518 bp,该序列包括起始密码子TGA和38 bp的5'末端非编码区(5'URT),终止密码子TAG和99 bp的3'末端非编码区(3'URT),在3'URT结构区域中包含polyA加尾信号序列AATAAA.猪L-FABP基因与其他FABPs基因一样,也由4个外显子(67 bp、173 bp、93 bp和51 bp)和3个内含子组成,内含子1和3的大小是1 679bp和565 bp,没有获得内含子2的序列,外显子和内含子剪接处符合GT/AG规律.应用Clustal W/X程序对猪L-FABP与其他物种的L-FABP进行多重序列比对,发现猪L-FABP与人、大鼠、鸡的L-FABP的相似性分别为89.8%、81.9%和72.4%.亲水性分析表明,猪L-FABP也是一个潜在的跨膜蛋白,在氨基酸残基57-65之间有一个明显的跨膜α螺旋.应用半定量RT-PCR分析发现,猪L-FABP在猪体组织中广泛存在,但在肝脏和小肠组织中表达量最为丰富.分析还发现,所克隆得到的编码区核苷酸序列与已知猪L-FABP基因的编码区核苷酸序列存在一定的变异,分别是外显子2中T→C(116位)、C→T(231位)、C→A(236位)和A→C(258位),演绎成氨基酸在Leu74Met存在差异.为进一步证实这些突变位点在猪群中真实存在,利用PCR-SSCP检测方法对4个猪种(藏猪、大河猪、雅南猪和约克夏)的157头个体的外显子2全序列进行SNP位点多态性片段的基因型分型,结果发现一个C→T的单核苷酸多态,等位基因频率在中国地方猪种(藏猪、大河猪、雅南猪)与国外约克夏猪种间存在极显著的差异(P＜0.01).连锁分析发现,基因型CC的肌内脂肪含量(4.86±0.22%)显著的高于基因型CT(4.16±0.23%)和TT(4.05±0.27%)的肌内脂肪含量(P＜0.05).因此,推测L-FABP基因可能是影响猪肌内脂肪含量的主效基因或与主效基因紧密连锁的标记基因,并且能够在分子标记辅助选择中用于对猪肌内脂肪含量的遗传改良.     

基于荧光微球液相基因表达阵列的建立

建立基于荧光微球的液相基因表达阵列,用于特定基因组合的表达谱分析.采用带有不同强度荧光鉴别信号的羧基化微球,与氨基修饰的不同标签寡核苷酸序列化学偶联,制成微球阵列.多重连接依赖的探针扩增技术(MLPA)用于扩增靶基因核苷酸序列,即通过RNA标本六随机引物逆转成cDNA,与不同基因特异性的一对探针杂交,耐高温的连接酶联接,最后采用生物素标记的同一对引物扩增.PCR产物与微球阵列液相杂交,加入链亲和素标记的PE染料,上流式细胞仪检测.应用这一系统检测骨髓增生异常综合症中难治性贫血(RA)、难治性贫血伴原始细胞增多(RAEB)、难治性贫血伴转化中原始细胞增多(RAEBt)、急性髓细胞性白血病(AML)和其他组(包括再生障碍性贫血、血小板减少、巨幼贫、溶贫等)差异表达谱,差异表达结果用实时荧光定量PCR验证.共建立了5个基因的微球阵列,分别为Rap1GAP、RAC2、SPA1、RhoBTB3和内参GAPDH,每个基因检测的线性范围为0.002 5～0.1μmol,液相表达阵列具有良好的特异性和重复性(P<0.001).检测RA、RAEB、RAEBt、AML和其他组差异表达发现,RAC2、RhoBTB3、SPA-1和Rap1GAP各组间有显著性差异性存在(分别为P<0.000 1,P=0.049 1,P=0.020 6和P=0.004 6),其差异显著性与实时荧光定量PCR一致,泊松相关系数分别为0.930,0.946,0.945和0.921,具显著性(P<0.001).结果表明,成功建立了基于荧光微球的液相基因表达阵列,其敏感性高、特异性强、重复性好.     

Gene expression profiling of gut mucosa and mesenteric lymph nodes in simian immunodeficiency virus-infected macaques with divergent disease course

BACKGROUND: Although the majority of drug-na?ve HIV-infected patients develop acquired immunodeficiency syndrome (AIDS), a small percentage remains asymptomatic without therapeutic intervention. METHODS: We have utilized the simian immunodeficiency virus (SIV)-infected rhesus macaque model to gain insights into the molecular mechanisms of long-term protection against simian AIDS. RESULTS: Chronically SIV-infected macaques with disease progression had high viral loads and CD4(+) T-cell depletion in mucosal tissue and peripheral blood. These animals displayed pathologic changes in gut-associated lymphoid tissue (GALT) and mesenteric lymph node that coincided with increased expression of genes associated with interferon induction, inflammation and immune activation. In contrast, the animal with long-term asymptomatic infection suppressed viral replication and maintained CD4(+) T cells in both GALT and peripheral blood while decreasing expression of genes involved in inflammation and immune activation. CONCLUSIONS: Our findings suggest that reduced immune activation and effective repair and regeneration of mucosal tissues correlate with long-term survival in SIV-infected macaques.     

Genomic structure, promoter analysis, and expression of the porcine (Sus scrofa) Mx1 gene

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus could improve the innate resistance of pigs to natural influenza infections. Several issues need to be resolved before efficient large scale screening of the allelic polymorphism at the porcine (Sus scrofa) Mx1 locus can be implemented. First, the Mx1 genomic structure has to be established and sufficient flanking intronic sequences have to be gathered to enable simple PCR amplification of the coding portions of the gene. Then, a basic knowledge of the promoter region needs to be obtained as an allelic variation there can significantly alter absolute levels and/or tissue-specificity of MX protein expression. The results gathered here show that the porcine Mx1 gene and promoter share the major structural and functional characteristics displayed by their homologs described in cattle, mouse, chicken, and man. The crucial function of the proximal interferon-sensitive response elements motif for gene expression is also demonstrated. The sequence data compiled here will allow an extensive analysis of the polymorphisms present among the widest spectrum possible of porcine breeds with the aim to identify an Mx1 allele providing antiviral resistance.     

沙葱萤叶甲钙结合蛋白基因的鉴定及表达谱分析

【目的】沙葱萤叶甲Galeruca daurica是一种近年来在内蒙古草原上猖獗成灾的新害虫。本研究旨在克隆沙葱萤叶甲钙结合蛋白(calcium-binding protein, CaBP)基因,分析其在沙葱萤叶甲成虫不同发育阶段及不同温度下的表达谱,为进一步探究其在沙葱萤叶甲生长发育及滞育过程中的作用奠定基础。【方法】根据沙葱萤叶甲转录组和蛋白质组数据,筛选CaBP基因序列信息,应用RT-PCR技术克隆获得CaBP基因的开放阅读框(ORF)全长序列,并对其进行生物信息学分析;通过qPCR检测其在沙葱萤叶甲成虫不同日龄(羽化后3, 7, 10, 15, 20, 30, 40, 60, 90和110 d)及3日龄成虫在不同温度(0, 5, 10,15, 20, 25, 30和35℃)下处理1 h后的表达水平。【结果】克隆得到4条具有完整ORF的沙葱萤叶甲CaBP基因cDNA序列,分别命名为GdCaM, GdCAPSL, GdTnCl和GdCRT(GenBank登录号: MN695412-695415),ORF全长分别为480, 648, 516和1 209 bp,分别编码149, 215, 171和402个氨基酸;只有GdCRT拥有信号肽。同源序列比对和系统发育分析表明,GdCaM, GdCAPSL, GdTnCl和GdCRT分别与玉米根萤叶甲Diabroticavirgifera virgifera的CaM, CAPSL, TnCl及马铃薯甲虫Leptinotarsa decemlineata CRT的氨基酸序列一致性最高,分别为100.0%, 74.0%, 88.2%和92.5%。qPCR结果表明,4个CaBP基因在沙葱萤叶甲不同日龄成虫中均差异表达,且表达模式不同。GdCaM在成虫滞育前(羽化后3 d)表达量较高,进入滞育后(羽化后7 d)表达量降低,在滞育期间(羽化后7-60 d)表达量变化较小,而解除滞育后(羽化后90 d)表达量进一步下调。GdCAPSL在滞育初期(羽化后10 d)维持在最低水平,进入滞育中后期(羽化后40和60 d)开始回升,滞育解除后又突然下调至最低水平,而羽化后110 d急剧上升至最高水平。GdTnCl在滞育初期(羽化后15-20 d)高表达,进入滞育中后期(羽化后30-60 d)急剧下降至最低水平,滞育解除后再次上调,但羽化后110 d突然下调至最低水平。GdCRT在进入滞育后表达量开始逐渐下调,在滞育维持期间(羽化后15-60 d)维持在低水平,滞育解除后又开始上升。温度对3日龄成虫中除GdCRT外的其他3个CaBP基因的表达有显著影响。温度低于20℃时,GdCaM的表达量随温度的降低而升高,但0℃时突然下降;温度高于20℃时,GdCaM的表达量随着温度的升高而上升。GdCAPSL的表达量随着温度的升高而呈现上升的趋势,25℃时达到最高,然后下降。GdTnCl随着温度的升高,表达量呈现下降的趋势。【结论】钙结合蛋白可能在沙葱萤叶甲成虫生长发育及夏滞育调控过程中发挥着重要作用。     

Molecular analysis of early rice stamen development using organ-specific gene expression profiling

Elucidating the regulatory mechanisms of plant organ formation is an important component of plant developmental biology and will be useful for crop improvement applications. Plant organ formation, or organogenesis, occurs when a group of primordial cells differentiates into an organ, through a well-orchestrated series of events, with a given shape, structure and function. Research over the past two decades has elucidated the molecular mechanisms of organ identity and dorsalventral axis determinations. However, little is known about the molecular mechanisms underlying the successive processes. To develop an effective approach for studying organ formation at the molecular level, we generated organ-specific gene expression profiles (GEPs) reflecting early development in rice stamen. In this study, we demonstrated that the GEPs are highly correlated with early stamen development, suggesting that this analysis is useful for dissecting stamen development regulation. Based on the molecular and morphological correlation, we found that over 26 genes, that were preferentially up-regulated during early stamen development, may participate in stamen development regulation. In addition, we found that differentially expressed genes during early stamen development are clustered into two clades, suggesting that stamen development may comprise of two distinct phases of pattern formation and cellular differentiation. Moreover, the organ-specific quantitative changes in gene expression levels may play a critical role for regulating plant organ formation. Electronic Supplementary Material Supplementary material is available for this article at Xiao-Chun Lu, Hua-Qin Gong contributed equally to this work.     

Effects of antidepressant treatment on gene expression profile in mouse brain: cell type-specific transcription profiling using laser microdissection and microarray analysis

A gene expression study of mice treated with the tricyclic antidepressant amitriptyline was performed. To enable the detection of cell type-specific expression changes, laser-microdissected nucleus accumbens was analysed after 4 and 28 days of treatment. After 4 days of treatment no significantly regulated genes could be detected in this study. In contrast, 95 genes exhibited different expression levels in animals treated for 28 days with amitrityline compared with sham animals. This observation reflects the long-term effects and adaptation processes observed in patients treated with this drug. Among the regulated genes are receptors belonging to the dopamine-dependent signalling cascade, ion channels (mainly voltage-dependent potassium and calcium channels) potentially involved in signalling cascades and neuropeptides. The results support the hypothesis that the therapeutic effect of this antidepressant is much more complex and not confined to a reuptake inhibition of neurotransmitters. Paradigms inducing only weak expression changes, which may be limited to certain cell types within the highly complex brain structure, can therefore be reliably investigated by applying a cell type-specific expression profiling technique based on laser microdissection and subsequent RNA amplification followed by DNA microarray analysis.     

松墨天牛OBP基因MaltOBP2和MaltOBP6的克隆、序列分析及组织表达谱和原核表达研究

【目的】本研究旨在探索松墨天牛Monochamus alternatus Hope在嗅觉识别寄主植物过程中扮演重要角色的气味结合蛋白(odorant binding proteins,OBPs)的结构及功能。【方法】利用生物信息学方法对得到的Malt OBP2和Malt OBP6基因序列和蛋白结构进行分析,并通过实时荧光定量PCR分析Malt OBP2和Malt OBP6在松墨天牛雄虫不同组织和时空中的表达差异,利用p ET32a(+)原核表达载体对Malt OBP2和Malt OBP6进行了诱导蛋白表达。【结果】本研究得到两个松墨天牛气味结合蛋白基因——Malt OBP2(Gen Bank登录号:KP120891)和Malt OBP6(Gen Bank登录号:KP120892),ORF长度分别为402 bp和408 bp,翻译的氨基酸序列均含有4个保守的半胱氨酸位点,表明得到的两个OBP基因的编码蛋白均属于Minus-C OBP亚家族;推导的两个OBP蛋白均有6个α螺旋区域,且α螺旋区域在两个蛋白的位置非常相似,但是两个OBP蛋白推测的配体结合位点和位点极性却完全不同。组织表达模式表明,Malt OBP2和Malt OBP6在成虫头部、触角、下颚(唇)须、腹部末端和足中均有表达,表达程度不一,但都在头部显著表达,触角中的表达量相比其他组织中较低或只是持平。发育表达结果表明,Malt OBP2在蛹触角中的表达量最高,而Malt OBP6在幼虫头部的表达量最高。本研究成功构建了原核表达载体p ET32aMalt OBP2和p ET32a-Malt OBP6,并进行了OBP蛋白诱导表达,低温(16℃和20℃)条件利于蛋白表达在上清液中,延长诱导表达时间(12 h)可以增加蛋白的表达量。【结论】本研究从松墨天牛体内得到了Minus-C OBP蛋白亚家族的两个基因Malt OBP2和Malt OBP6,通过配体结合位点推测它们具有不同的生理功能;通过组织表达谱结果推测这两个OBP基因在松墨天牛中的功能不仅仅局限于嗅觉识别,或还有味觉感受、化学感受等其他生理功能。本研究结果为两个OBP蛋白的结构和功能研究奠定了基础,为探索松墨天牛的化学感受机制提供了条件。     

家蚕非编码RNA在神经系统中的表达分析

【目的】非编码RNA(non-coding RNA,ncRNA)在家蚕Bombyx mori发育过程中具有重要调控作用。本研究旨在探索ncRNA参与家蚕神经系统发育的分子机理。【方法】采用实时荧光定量PCR技术对22个中等长度的ncRNA及3个ncRNA的邻近编码基因在家蚕幼虫神经系统中的表达水平进行检测。【结果】8个ncRNA(包括1个C/D box snoRNA,4个H/ACA box snoRNA和3个不能归类的ncRNA)在家蚕5龄幼虫神经组织和非神经组织中均有表达,且在胸腹神经中的表达量明显高于头部神经中的表达量。其中,snoRNA Bm-51,Bm-18和Bm-86在胸腹神经中的表达量分别是头部神经中的23,5和4.7倍。进一步研究发现,这3个内含子起源的ncRNA与其宿主基因在家蚕神经系统中的表达趋势一致,宿主基因在胸腹神经中的表达量也明显高于头部神经中的表达量。【结论】本研究筛选到的在家蚕不同神经部位存在差异表达的ncRNA,特别是在胸腹神经中高表达的ncRNA可能协同其邻近编码基因,参与家蚕神经发育或神经活动过程。该结果为研究ncRNA参与家蚕神经系统发育提供了分子依据,为从非编码RNA角度探索鳞翅目害虫防治提供了新的思路。