Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs

Objective-To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Sample-Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Procedures-Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. Results-LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Conclusions and Clinical Relevance-Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.     

Reference gene selection for reverse transcription quantitative polymerase chain reaction in chicken hypothalamus under different feeding status

This study was designed to investigate the stability of 10 candidate reference genes, namely ACTB, B2M, GAPDH, HMBS, LBR, POLR2B, RN18S, RPS17, TBP, and YWHAZ for the normalization of gene expression data obtained by quantitative real‐time polymerase chain reaction (qPCR) in studies related to feed intake of chicken. Samples were isolated from hypothalamus under three different nutritional status (ad libitum, fasted for 24 hr, fasted for 24 hr then refed for 2 hr). Five different algorithms were applied for the analysis of reference gene stability: BestKeeper, geNorm, NormFinder, the comparative ΔCt method, and a novel approach using multivariate linear mixed‐effects modelling for stable reference gene selection. TBP and POLR2B were identified as the two most suitable and B2M and RN18S as the two least stable reference genes for normalization. Despite our review, the current literature showing that RN18S is one of the most commonly used reference gene in chicken gene expression studies, its applicability for normalization should be evaluated before each qPCR experiment.     

Reference genes for canine skin when using quantitative real-time PCR

Quantitative real-time PCR (qPCR) facilitates the quantification of mRNA expression. Accurate qPCR analysis of gene expression requires the normalisation of data using a reference or housekeeping gene which is expressed at a similar level in all tissues tested. GAPDH is the most well known and most widely used reference gene but many papers have demonstrated that it is not stably expressed in different tissues. The aim of this study was to measure reference gene stability in canine skin using real-time qPCR. Skin samples from healthy control dogs (n=7) and dogs with atopic dermatitis (lesional skin n=7 and non-lesional skin n=7) were used to quantify seven reference genes (IMP, CG14980, S7, HIRA, GAPDH, RPL13A and SDHA) in canine whole skin. Three different statistical programs (Bestkeeper, GeNorm and Normfinder) were used to assess the stability of the reference genes. The results confirmed that GAPDH is not a stably expressed reference gene in canine skin; this finding may influence interpretation of previous qPCR studies on canine skin using this as a reference gene. RPL13A and CG14980 were found to be the most stably expressed genes in canine whole skin and would be more suitable as reference genes in future studies.     

Reference gene screening for analyzing gene expression in the heart,liver, spleen,lung and kidney of forest musk deer

The screening of reference genes for real-time quantitative PCR (qPCR) in forest musk deer (FMD) tissue is of great significance to the basic research on FMD. However, there are few reports on the stability analysis of FMD reference genes so far. In this study, We used qPCR to detect the expression levels of 11 reference gene candidates (18S rRNA, beta-actin [ACTB], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], TATA box-binding protein [TBP], hypoxanthine phosphoribosyltransferase 1 [HPRT1], tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide [YWHAZ], hydroxymethylbilane synthase [HMBS], eukaryotic translation elongation factor 1 alpha 1 [EEF1A1], succinate dehydrogenase complex flavoprotein subunit A [SDHA], peptidylprolyl isomerase B [PPIB], and ubiquitin C [UBC]) in heart, liver, spleen, lung and kidney of FMD. After removing 18S rRNA on account of its high expression level, geNorm, NormFinder, BestKeeper and ΔCt algorithms were used to evaluate the expression stability of the remaining genes in the five organs, and further comprehensive ranking was calculated by RefFinder. According to the results, the selected reference genes with the most stable expression in the heart of FMD are SDHA and YWHAZ, while in the liver are ACTB and SDHA; in the spleen and lung are YWHAZ and HPRT1; in the kidney are YWHAZ and PPIB. The use of common reference genes in all five organs is not recommended. The analyses showed that tissue is an important variability factor in genes expression stability. Meanwhile, the result can be used as a reference for the selection of reference genes for qPCR in further study.     

Stability of expression of reference genes in porcine peripheral blood mononuclear and dendritic cells

Real-time quantitative PCR (RT-qPCR) is a critical tool used to evaluate changes in gene expression. The precision of this tool is reliant upon the selection of reference genes whose expression remains unaltered in culture conditions and following stimulation. Stably expressed reference genes are used to normalize data so observed changes in expression are not due to artifacts but rather reflect physiological changes. In this study, we examined the expression stability of the porcine genes glyceraldehyde 3-phosphate dehydrogenase (GAPDH), succinate dehydrogenase complex subunit A (SDHA), eukaryotic elongation factor 1 gamma-like protein (eEF1), ribosomal protein L19 (RPL19), beta-actin (ACTB) and ATP synthase mitochondrial F0 complex (ATP5G1) in peripheral blood mononuclear cells (PBMCs), monocytes, monocyte-derived dendritic cells (MoDCs), blood isolated dendritic cells (BDCs) and T cells with or without stimulation with lipolysaccharide (LPS). An M value was used as a measure of gene stability as determined using geNORM software. Recommendations for the use of reference genes include using GAPDH and B-actin in PBMCs: RPL19 and SDHA in T cells; RPL19 and B-actin in monocytes; RPL-19 and SDHA in BDCs: and RPL-19 and ATP5GA in MoDCs.     

模拟增温下短花针茅实时荧光定量内参基因的筛选及验证

本研究以荒漠草原植物短花针茅(Stipa breviflora)为材料,在模拟增温处理下,通过q RT-PCR试验分析9个候选内参基因的表达稳定性,运用Delta-CT法,ge Norm,norm Finder,Bestkeeper软件及Ref Finder在线工具进行候选内参基因的稳定性分析。经普通PCR剔除3个内参基因后,6个候选内参基因表达稳定性由高到低排序为:TLF,18 s r RNA,APRT,TUBα,EF-1α,Actin2。以TLF作为内参基因,在模拟增温下短花针茅转录组数据库中随机选择5个基因进行验证。q RT-PCR结果表明,5个验证基因在增温与对照之间的相对表达量存在倍率变化,且与转录组测序中的变化趋势一致,从而确定TLF为短花针茅增温处理下的最佳内参基因。     

Validation of candidate bovine reference genes for use with real-time PCR

Accurate quantification with real-time PCR requires the use of stable endogenous controls. Recently, there has been much debate concerning the stability of commonly used reference or housekeeping genes. To address this concern, a number of statistical approaches have been designed to analyse data and assist in determining the most appropriate reference genes for experimental comparisons. In this study, three programs, BestKeeper, Norm Finder, and geNorm were used to assess four candidate reference genes: 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), acidic ribosomal protein large (RPLP0) and beta-actin, for use in expression profiling of individuals from divergent cattle genotypes subject to parasitic challenge with the cattle tick Boophilus microplus. Results demonstrated beta-actin and GAPDH were the most suitable reference genes in blood and could be used either individually or combined as an index to normalise data. RPLP0 was identified as the least stable gene, while 18S rRNA was omitted as being too highly expressed. As the recommendations on the most suitable reference genes varied between the programs, it is recommended that more than one should be utilised, to ensure the most robust experimental tools are selected.     

蒙古马高负荷运动训练前后MSTN基因、CKM基因表达量分析

为探讨蒙古马高负荷调教训练前后MSTN、CKM基因的表达情况,实验首先采用SYBR GreenⅠ荧光定量RT-PCR方法对4个常用内参基因(TTN、18s r RNA、GAPDH、β-actin)在臀中肌内的稳定性进行评估;确定内参基因后,对MSTN、CKM基因转录水平进行测定。结果表明:在蒙古马臀中肌中稳定度依次为GAPDH(1.087)β-actin(1.211)TTN(1.285)18s r RNA(1.460),选取稳定度最高的GAPDH基因作为内参基因;高负荷运动训练后MSTN基因m RNA表达量较训练前上调,而CKM基因则下调。本研究为蒙古马运动性能相关基因的研究奠定了基础。     

ASH1L甲基转移酶在牛卵丘细胞中的表达与功能研究

旨在探究缺失、小的、同源异形1（absent，small，or homeotic 1-like，ASH1L）甲基转移酶在牛卵丘细胞中的表达与功能。本研究通过免疫荧光染色在健康母牛卵丘细胞中对ASH1L甲基转移酶进行定位，并分析细胞的组蛋白H3第36位赖氨酸（histone H3 lysine36，H3K36）甲基化修饰模式；合成靶向Ash1L基因的siRNA，对siRNA-1、siRNA-2、siRNA-3及对照组进行荧光定量PCR和蛋白质免疫印迹，筛选有效siRNA；采用荧光定量PCR分析干扰Ash1L表达对处理组及对照组中凋亡相关基因及多梳抑制复合体（polycomb repressive complex 2，PRC2）组成基因的表达水平的影响。结果显示，ASH1L甲基转移酶位于牛卵丘细胞的细胞核中，呈点状分布。成功筛选到能有效干扰牛Ash1L基因的siRNA-2，其干扰效率为60%~70%。将siRNA-2转染卵丘细胞后，该干扰组细胞中H3K36的单甲基化、二甲基化及三甲基化3种甲基化水平均显著低于对照组（P<0.05）；干扰Ash1L导致凋亡相关基因Bax、Bcl-2及caspase-3表达水平显著上调，凋亡基因Bax和caspase-3表达量高于抗凋亡相关基因Bcl-2（1.311和1.179 vs 1.146）；同时，干扰Ash1L基因表达也引起PRC2蛋白亚基EZH2和Suz12基因的mRNA表达量显著升高（P<0.05）。综上所述，本研究探讨了ASH1L甲基转移酶在牛卵丘细胞中的表达和功能，ASH1L在牛卵丘细胞中呈点状分布，且Ash1L基因的抑制导致H3K36me1/2/3水平均显著下降及凋亡基因和PRC2蛋白相关亚基EZH2和Suz12基因表达的升高，为进一步研究其对家畜胚胎的调控作用提供技术和理论基础。     

草地早熟禾荧光定量PCR分析中内参基因的筛选

为筛选出草地早熟禾实时荧光定量中的最适内参基因,利用实时荧光定量PCR技术,分析检测6个传统内参基因ACT、GAPDH、UBQ、EF-1α、18s rRNA和β-tublin在草地早熟禾不同组织器官、叶片不同发育期、非生物胁迫和不同激素诱导下mRNA的表达差异情况。利用geNorm、NormFinder和BestKeeper软件综合评价6个候选内参基因的表达稳定性。结果表明,在不同组织、叶片不同发育期、激素诱导和非生物胁迫下,候选内参基因的表达稳定性存在差异。GAPDH在草地早熟禾不同组织器官中表达最为稳定;EF-1α在非生物胁迫下表达最为稳定;不同激素下首选β-tublin;在叶片不同发育期ACT表达最为稳定。综上所述,通过筛选出不同条件下适宜的内参基因不仅有助于提高草地早熟禾基因表达分析的准确性,也为早熟禾属植物其他内参基因的开发提供了理论参考。     

窄竹叶柴胡内参基因筛选及皂苷合成关键酶基因表达分析

窄竹叶柴胡(Bupleurum marginatum var.stenophyllum)为柴胡属多年生高大型草本植物，以根入药称为藏柴胡，具有较高的药用价值。本试验采用实时荧光定量PCR技术，利用geNorm、NormFinder及BestKeeper3种不同数据分析软件，从5个常用的候选基因(Actin,α-tubulin,β-tubulin,Cyclophilin,EF-1α)筛选出可在窄竹叶柴胡不同器官稳定表达的基因作为内参基因，并利用筛选得到的内参基因分析皂苷合成关键酶基因(HMGR,IPPI,FPS,SS,β-AS)在窄竹叶柴胡不同器官的相对表达量。结果表明β-tubulin基因可作为窄竹叶柴胡不同器官稳定表达的内参基因；皂苷合成关键酶基因在窄竹叶柴胡的不同器官中表达量有显著差异，IPPI基因在种子中表达量最高，其他基因在根中的表达量均高于在其他器官中的表达量，其中HMGR,FPS,SS在侧根的表达量高于主根。因此，窄竹叶柴胡各器官皂苷合成关键酶基因的表达量不同，最适内参基因为β-tubulin基因，本研究为窄竹叶柴胡分子生物学研究提供一定依据，促进其合理开发和利用。     

Intestinal gene expression in pigs experimentally co-infected with PCV2 and PPV

The objective of the present study was to characterize the local immune reaction in the intestine of pigs experimentally infected with PCV2 and PPV. Archived intestinal material from an experimental study in which pigs were co-infected with a Swedish isolate of PCV2 (S-PCV2) and PPV, or a reference isolate of PCV2 (PCV2-1010) and PPV, were used. The intestinal samples were analysed by qPCR for expression of a number of selected cytokines and the overall gene expression in the intestine was screened by cDNA microarray. Analyses by qPCR showed that pigs infected with PCV2-1010/PPV displayed a significantly increased mRNA expression for IL-6 (p<0.05), IL-10 (p<0.05) and IFN-γ (p<0.05). The microarray screening revealed a strong up-regulation of IFITM3 along with several other interferon-stimulated genes (ISGs) in pigs infected with PCV2/PPV. The analyses also indicated differences between the two isolates. Fewer pigs infected with S-PCV2/PPV expressed the cytokines detected by qPCR, compared to pigs infected with PCV2-1010/PPV, and pigs infected with S-PCV2/PPV displayed a higher proportion of down-regulated genes than PCV2-1010/PPV-infected pigs.