Validation of housekeeping genes as internal controls for studying the gene expression in Pyropia haitanensis(Bangiales, Rhodophyta) by quantitative real-time PCR

Pyropia haitanensis is an economically important mariculture crop in China and has a high research value for several life phenomena, for example environmental tolerance. To explore the mechanisms underlying these characteristics, gene expression has been investigated at the whole transcriptome level. Gene expression studies using quantitative real-time PCR should start by selecting an appropriate internal control gene; therefore, the absolute expression abundance of six housekeeping genes （18S rRNA （18S）, ubiquitin-conju-ating enzyme （UBC）, actin （ACT）, β-tubulin （TUB）, elongation factors 2 （EF2）, and glyceraldehyde-3-phos- phate dehydrogenase （GAPDH） examined by the quantitative real-time PCR in samples corresponding to different strains, life-cycle stages and abiotic stress treatments. Their expression stabilities were assessed by the comparative cycle threshold （Ct） method and by two different software packages： geNorm and NormFinder. The most stable housekeeping gene is UBC and the least stable housekeeping is GADPH. Thus, it is proposed that the most appropriate internal control gene for expression analyses in P. haitanensis is UBC. The results pave the way for further gene expression analyses of different aspects of P. haitanensis biology including different strains, life-history stages and abiotic stress responses.

Selection of suitable internal controls for gene expression normalization in rats with spinal cord injury

There is a lack of systematic research on the expression of internal control genes used for gene expression normalization in real-time reverse transcription polymerase chain reaction in spinal cord injury research.In this study,we used rat models of spinal cord hemisection to analyze the expression stability of 13 commonly applied reference genes:Actb,Ankrd27,CypA,Gapdh,Hprt1,Mrpl10,Pgk1,Rictor,Rn18s,Tbp,Ubc,Ubxn11,and Ywhaz.Our results show that the expression of Ankrd27,Ubc,and Tbp were stable after spinal cord injury,while Actb was the most unstable internal control gene.Ankrd27,Ubc,Tbp,and Actb were consequently used to investigate the effects of internal control genes with differing stabilities on the normalization of target gene expression.Target gene expression levels and changes over time were similar when Ankrd27,Ubc,and Tbp were used as internal controls but different when Actb was used as an internal control.We recommend that Ankrd27,Ubc,and Tbp are used as internal control genes for real-time reverse transcription polymerase chain reaction in spinal cord injury research.This study was approved by the Administration Committee of Experimental Animals,Jiangsu Province,China(approval No.20180304-008)on March 4,2018.

Sleep deprivation increase the expression of inducible heat shock protein 70 in rat gastric mucosa

AIM: To investigate if sleep deprivation is able to increase the expression of inducible heat shock protein 70 in gastric mucosa and its possible role in mucosal defense. METHODS: Rats for sleep disruption were placed inside a computerized rotating drum, gastric mucosa was taken from rats with 1, 3 and 7d sleep deprivation. RT-PCR, immunohistochemistry and Western blotting were used to determine the expression of heat shock protein 70. Ethanol (500mL.L(-1), i.g.) was used to induce gastric mucosa damage. RESULTS: RT-PCR, Western blotting and immunostaining confirmed that the sleep deprivation as a stress resulted in significantly greater expression of inducible heat shock protein 70 in gastric mucosa of rats. After the 500mL.L(-1) ethanol challenge, the ulcer area found in the rats with 7d sleep deprivation (19.15 +/- 4.2)mm(2) was significantly lower (P【0.01) than the corresponding control (53.7 +/- 8.1) mm(2). CONCLUSION: Sleep deprivation as a stress, in addition to lowering the gastric mucosal barrier, is able to stimulate the expression of inducible heat shock protein 70 in gastric mucosa of rats, the heat shock protein 70 may play an important role in gastric mucosal protection.

Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

Accurate quantification of transcripts using quantitative real-time polymerase chain reaction （qPCR） depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 （ACT-2）, elongation factor 1 alpha （EF-1α）, elongation factor 1 beta （EF-1β）, glyceraldehyde-3-phosphate dehydrogenase （GAPDH）, ubiquitin （UBQ）, β-tubulin （β-TUB）, and 18 S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene （Gβ） across tissue types was also examined and normalized to the expression of each or both of UBQ andβ-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further fimetional genomics studies in this economically valuable marine bivalve.

Regulation of Expression for the RNP-4F Splicing Assembly Factor in the Fruit-Fly <i>Drosophila melanogaster</i>

Intron splicing in eukaryotic organisms requires the interactions of five snRNAs and numerous different proteins in the spliceosome. Although the molecular mechanism behind splicing has been well studied, relatively little is known about regulation of expression for these splicing factor proteins. One of these proteins is the evolutionarily-conserved Drosophila RNP-4F splicing assembly factor. This protein is transcribed from a single gene into two developmentally regulated mRNAs that differ in their 5’-UTR structure. In the longer isoform, known to be abundant in the developing fly central nervous system, a conserved retained intron which folds into a stem-loop has been implicated in expression control of the mRNA. Here, we describe construction and utilization of several new rnp-4f gene expression study vectors using a GFP reporter in the ΦC31 system. The results confirm our previous observation that presence of the regulatory stem-loop enhances RNP-4F protein expression. However, in that study, the enhancement factor protein was not identified. We show here that overexpression of the RNP-4F transgene compared to the control results in additional translation, as indicated by the GFP reporter in the fluorescent images. These results are interpreted to show that RNP-4F protein acts back on its own mRNA 5’-UTR regulatory region via a feedback pathway to enhance protein synthesis in the developing fly central nervous system. A model is proposed to explain the molecular mechanism behind rnp-4f gene expression control.

乳酸菌Nisin诱导表达载体的构建和鉴定

为构建乳酸菌Nisin诱导表达载体,实现外源目的基因在乳酸菌中的可控表达,本研究以产Nisin乳酸乳球菌染色体DNA为模板,采用PCR技术扩增双组份调控元件nisRK基因和诱导型启动子nisA基因,并克隆至乳酸菌-大肠杆菌穿梭质粒pW425et中,以nisA基因替换原组成型启动子P32,构建乳酸菌Nisin诱导表达载体pW425N。为检测载体的诱导表达功能,以gfp基因作为报告基因,构建重组表达载体pW425N-gfp,以分离自仔猪肠道内嗜酸乳杆菌为受体菌,电转化法制备重组乳酸菌pW425N-gfp/L.acidophilus。结果表明,重组载体能够在Nisin诱导下表达目的荧光蛋白,并且最佳Nisin有效浓度为30 ng/mL,最佳诱导时间为3 h。该表达载体的构建为外源功能性蛋白在乳酸菌中的诱导表达奠定基础。

毛锤角细蜂寄生对黑腹果蝇转录组的影响

黑腹果蝇是水果近成熟期的主要害虫,直接影响葡萄、蓝莓等浆果的品质和商品价值。本研究选用黑腹果蝇蛹期优势寄生蜂——毛锤角细蜂为试材,利用Illumina测序平台的RNA-Seq技术对被毛锤角细蜂寄生6 h和未寄生的黑腹果蝇蛹进行转录组测序分析。结果显示,寄生前后两组样本间共得到294个差异表达基因,其中上调基因98个,下调基因196个;对差异表达基因进行GO和KEGG功能富集分析,并探究寄生对寄主免疫相关基因表达的影响,发现毛锤角细蜂可能属于免疫逃避型寄生蜂。研究结果可为黑腹果蝇的生物防治提供参考。

Identification of stable internal control genes for accurate normalization of real-time quantitative PCR data in testicular tissue from two breeds of cattle

Objective:To assess the stability of 10 candidate internal control genes(ICGs),namely GAPDH,ACTB,RPL23,RPS15A,ATPSF1,GLUT5,HMBS,ATP2B4,PPIA,and BRP to normalize the transcriptional data from testes samples of Zebu and crossbred bulls.Methods:Total RNA was isolated from testicular tissue of Zebu and crossbred bulls(n=6 each)between 2-8 years of age.cDNA was synthesized,and the quantitative real-time polymerase chain reaction(PCR)was performed.The cycle threshold values were used for the analysis of the stability of ICGs.Four different statistical algorithms:geNorm,Normfinder,BestKeeper,and RefFinder,were used to assess the stability of these genes.Results:ATPSF1,HMBS,PPIA,and RPS15A were the most reliable and stable ICGs for Zebu testes,and ATPSF1,RPL23,and PPIA for crossbred testes.Conclusions:A panel of stable ICGs(ATPSF1,HMBS,PPIA,RPS15A for Zebu and ATPSF1,RPL23,and PPIA for crossbred)for normalization of gene expression data in testes samples can be helpful for researchers to conduct functional genomics studies at the testicular level in cattle bulls.

Construction and Control of Genetic Regulatory Networks:A Multivariate Markov Chain Approach

In the post-genomic era, the construction and control of genetic regulatory networks using gene expression data is a hot research topic. Boolean networks (BNs) and its extension Probabilistic Boolean Networks (PBNs) have been served as an effective tool for this purpose. However, PBNs are difficult to be used in practice when the number of genes is large because of the huge computational cost. In this paper, we propose a simplified multivariate Markov model for approximating a PBN The new model can preserve the strength of PBNs, the ability to capture the inter-dependence of the genes in the network, qnd at the same time reduce the complexity of the network and therefore the computational cost. We then present an optimal control model with hard constraints for the purpose of control/intervention of a genetic regulatory network. Numerical experimental examples based on the yeast data are given to demonstrate the effectiveness of our proposed model and control policy.

Energy Signaling in the Regulation of Gene Expression during Stress

Maintenance of homeostasis is pivotal to all forms of life. In the case of plants, homeostasis is constantly threatened by the inability to escape environmental fluctuations, and therefore sensitive mechanisms must have evolved to allow rapid perception of environmental cues and concomitant modification of growth and developmental patterns for adaptation and survival. Re-establishment of homeostasis in response to environmental perturbations requires reprog- ramming of metabolism and gene expression to shunt energy sources from growth-related biosynthetic processes to defense, acclimation, and, ultimately, adaptation. Failure to mount an initial ＇emergency＇ response may result in nutrient deprivation and irreversible senescence and cell death. Early signaling events largely determine the capacity of plants to orchestrate a successful adaptive response. Early events, on the other hand, are likely to be shared by different conditions through the generation of similar signals and before more specific responses are elaborated. Recent studies lend credence to this hypothesis, underpinning the importance of a shared energy signal in the transcriptional response to various types of stress. Energy deficiency is associated with most environmental perturbations due to their direct or indirect deleterious impact on photosynthesis and/or respiration. Several systems are known to have evolved for monitoring the available resources and triggering metabolic, growth, and developmental decisions accordingly. In doing so, energy-sensing systems regulate gene expression at multiple levels to allow flexibility in the diversity and the kinetics of the stress response.

Progress in artificial control system for gene expression

Along with the increasingly wide application of transgenic techniques, new stricter criteria have been raised for controlling the expression of exogenous genes. For these demands, a series of artificial control systems for gene expression have been developed and testified in recent years, which can control exogenous genes expression in exact time and certain level by administration of a specific drug or hormone. The successful construction of these systems offers a practicable method to control precise expression of exogenous gene in organisms, and raises the feasibility of wide application of gene therapy.

Effects and mechanisms of three kinds of chemical inducers on the expression of rat GST-P gene

The expression of rat Glutathione S-transferase P (GST-P) gene can be induced by many kinds of chemical inducers. We have studied the mechanisms of the expression of GST-P gene induced by 3 kinds of Chemical inducers using the induction of the gene expression by chemical inducers, transient transfection, reporter gene assays, electrophoretic mobility shift assays (EMSA) and Northern blot analysis. The results indicate that the effects and mechanisms of chemical inducers on the expression of GS7'-Pgene are different. The interaction of AP-1 or other corresponding transcription factors activated by phorbol ester (TPA) or glycidyl methatylate (GMA) and GPEl enhancer element induces the expression of GST-P gene, while some unknown factors activated by H2O2 interact with GPEII enhancer element.

基因表达转录分析中内参基因的选择

目前基因表达的转录分析多采用单一看家基因作为内参来校正目标基因的表达量.实验中以人肝癌BEL-7402细胞为研究对象,应用实时荧光定量PCR技术,观察了新型三肽化合物酪丝缬肽作用后RPL13A、UBC、EIF4A、B2M、GAPDH和ACTB共6个看家基因mRNA水平的表达情况.经过geNorm程序统计学分析处理,结果表明,这6个看家基因的表达存在差异,确定了RPL13A、UBC2个看家基因用于校正目标基因的表达量.基因表达转录分析中内参基因选择的必要性在实验中得以证明,更重要的是为各种实验因素影响下(尤其是新物质作用下)内参基因的选择介绍和提供了一种行之有效的方法.

甘蔗基因表达定量PCR分析中内参基因的选择

以甘蔗接种黑穗病菌后0、6、12、24、48、60和72h时间点的材料为研究对象,应用实时荧光定量PCR(real-time quantitative PCR,Real-timeqPCR)技术,探讨25SrRNA、GAPDH、β-actin和β-tubulin4个内参基因mRNA水平的表达情况。经geNorm程序统计学分析,4种内参基因的表达稳定性各异,25SrRNA>GAPDH>β-actin>β-tubulin,其中以25SrRNA表达稳定性最好,且根据该基因设计的两对定量PCR引物都是可行的。同时,甘蔗PPO基因表达特性的定量PCR分析也显示,甘蔗PPO基因与植物的抗病性相关。结果显示,研究中所筛选的内参基因是合适的。

白纹伊蚊基因表达定量PCR内参基因的选择

目的筛选白纹伊蚊基因表达定量PCR研究中适合的内参基因。方法采用实时荧光定量PCR技术,对β-ac-tin、BTF3a、rsp5、rsp27a、superoxide、rspL40六个看家基因的mRNA表达水平进行了探讨。结果除rsp27a基因扩增效率高于设定值被剃除外,余5个基因在不同组织中的表达稳定度为rspL40,BTF3a>rsp5>β-actin>superoxide;吸血不同时相表达稳定度为rspL40,rsp5>superoxide>BTF3a>β-actin。结论 rspL40,BTF3在不同组织中表达最稳定;rspL40,rsp5在吸血不同时相表达最稳定。

昆虫表皮蛋白基因研究进展

在昆虫表皮的发生、分化和昆虫躯体外部重要部位及器官的构建中,表皮蛋白是不可或缺的组成元素。本文在简要总结了目前昆虫表皮蛋白鉴定与分类方面研究的基础上,重点对近10年来昆虫表皮蛋白基因的时空表达模式、激素及转录因子对表皮蛋白基因表达的调控、表皮蛋白基因功能的研究进展进行了综述,探讨了其在害虫防治中可能的应用前景,旨在为进一步研究昆虫表皮蛋白基因及其潜在利用价值提供参考。目前报道的昆虫表皮蛋白序列已超过1 400条,分为12个家族,如CPR,CPF,CPFL和Tweedle等。经由蜕皮激素激活的相关转录因子(如βFTZ-F1和BR-C等)作用于表皮蛋白基因上游的顺式作用元件,开启或关闭基因,以调控表皮蛋白基因的表达。表皮蛋白基因在昆虫表皮整合,体形塑造,活动能力,抗逆与抗药性,以及先天免疫等生理现象和生理过程中有不可或缺的作用。因此,如果能够通过抑制关键表皮蛋白基因的表达,或将其从基因组中删除,以阻碍昆虫的发育或扰乱昆虫的繁殖能力,或可为害虫防治策略提供参考。

大豆查尔酮异构酶基因的克隆及乳酸菌表达载体的构建

[目的]将特异存在于豆科植物的II型查尔酮异构酶基因CHI1A构建到目前最有效的食品级乳酸乳球菌NICE诱导表达系统中。[方法]利用RT-PCR技术从大豆总RNA中克隆CHI1A基因,连入pMD18-T克隆载体中并进行测序,然后重组到乳酸乳球菌表达载体PNZ8149-CHI1A,利用电穿孔方法转入乳酸乳球菌NZ3900中。[结果]克隆得到CHI1A完整开放阅读框670bp,与已报导序列(GenBankAY595413)的同源性达到99%;通过PCR和酶切鉴定,成功地将CHI1A导入到NICE表达系统中。[结论]含有CHI1A基因的乳酸乳球菌高效诱导表达载体的构建为利用微生物发酵产生类黄酮奠定基础。

AiiA蛋白的可溶性表达及其抗菌活性研究

AHLs是革兰氏阴性细菌在增殖过程中产生的一类信号分子,与其致病性密切相关。AiiA蛋白作为一种胞内解酯酶。能水解致病菌产生的AHLs分子,使内酯环开环后不能再激活某些胞外酶的表达,从而极大地减弱了细菌的致病性。本研究从苏云金芽孢杆菌LLB15中分离编码aiiA基因的质粒DNA,用PCR方法克隆AiiA基因,并利用pET载体构建6-His融合表达质粒pET29a-aiiA,转化E.coli BL21(DE3)菌株,并筛选得到E.coli BL21(DE3)-pET29a-aiiA工程菌。在20℃的低温和0.8 mmol/L IPTG条件下,经25 h的诱导表达,获得了54.4μg/mL可溶性AiiA蛋白。通过镍柱亲和层析,在国内外首次纯化了带6-His标记的AiiA蛋白。水解活性和抗病性检测表明。该蛋白能水解AHLs分子。对胡萝卜欧文氏软腐病菌具有较强的抗病作用。

5cGy γ射线照射正常人淋巴母细胞基因表达转录谱的变化

应用基因芯片技术分析5 cGy低剂量60Coγ射线照射正常人淋巴母细胞(AHH-1)后基因转录产物水平变化,探讨低剂量辐射对基因表达的影响规律。5 cGy60Coγ射线照射AHH-1细胞后4 h,提取总RNA,用包含有14 112个基因探针的人类cDNA芯片分析基因转录谱,照射组与对照组细胞的基因表达量差异比值大于2或小于0.5,两次检测结果一致的基因点为有效差异表达基因;用RT-PCR进一步验证部分差异表达基因;Western blot分析蛋白表达变化。结果筛选出了11个表达上调基因,9个表达下降基因;RT-PCR检测结果与芯片结果相一致,包括Connexin43、BMPR2、NOL6、LOC51760、LYK5等基因;Westernblot证实Connexin43基因在翻译水平表达亦增加。实验结果表明所筛选出的差异表达基因有助于阐述低剂量辐射生物效应机理,部分基因有可能成为低剂量辐射暴露的生物标志物。

编码1,3-丙二醇氧化还原酶同工酶基因yqhD的克隆与高效表达

利用PCR技术从大肠杆菌(Escherichia coli)中扩增出1.16 kb的编码1,3-丙二醇氧化还原酶同工酶的基因yqhD,将其连接到温控表达载体pHsh,得到重组载体pHsh-yqhD,重组载体在大肠杆菌JM109中得到高效表达。SDS-PAGE分析显示:融合表达产物的相对分子质量均为43 000,同核酸序列测定所推导的值相符。对含有yqhD的基因工程菌进行表达研究表明:42℃诱导4 h,1,3-丙二醇氧化还原酶同工酶的酶活力达到100 IU/mg,而对照菌株的酶活力仅为0.5IU/mg。