Expressed Repeat Elements Improve RT-qPCR Normalization across a Wide Range of Zebrafish Gene Expression Studies

The selection and validation of stably expressed reference genes is a critical issue for proper RT-qPCR data normalization. In zebrafish expression studies, many commonly used reference genes are not generally applicable given their variability in expression levels under a variety of experimental conditions. Inappropriate use of these reference genes may lead to false interpretation of expression data and unreliable conclusions. In this study, we evaluated a novel normalization method in zebrafish using expressed repetitive elements (ERE) as reference targets, instead of specific protein coding mRNA targets. We assessed and compared the expression stability of a number of EREs to that of commonly used zebrafish reference genes in a diverse set of experimental conditions including a developmental time series, a set of different organs from adult fish and different treatments of zebrafish embryos including morpholino injections and administration of chemicals. Using geNorm and rank aggregation analysis we demonstrated that EREs have a higher overall expression stability compared to the commonly used reference genes. Moreover, we propose a limited set of ERE reference targets (hatn10, dna15ta1 and loopern4), that show stable expression throughout the wide range of experiments in this study, as strong candidates for inclusion as reference targets for qPCR normalization in future zebrafish expression studies. Our applied strategy to find and evaluate candidate expressed repeat elements for RT-qPCR data normalization has high potential to be used also for other species.     

Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles

Background

Ulcerative colitis (UC) was the most frequently diagnosed inflammatory bowel disease (IBD) and closely linked to colorectal carcinogenesis. By far, the underlying mechanisms associated with the disease are still unclear. With the increasing accumulation of microarray gene expression profiles, it is profitable to gain a systematic perspective based on gene regulatory networks to better elucidate the roles of genes associated with disorders. However, a major challenge for microarray data analysis is the integration of multiple-studies generated by different groups.

Methodology/Principal Findings

In this study, firstly, we modeled a signaling regulatory network associated with colorectal cancer (CRC) initiation via integration of cross-study microarray expression data sets using Empirical Bayes (EB) algorithm. Secondly, a manually curated human cancer signaling map was established via comprehensive retrieval of the publicly available repositories. Finally, the co-differently-expressed genes were manually curated to portray the layered signaling regulatory networks.

Results

Overall, the remodeled signaling regulatory networks were separated into four major layers including extracellular, membrane, cytoplasm and nucleus, which led to the identification of five core biological processes and four signaling pathways associated with colorectal carcinogenesis. As a result, our biological interpretation highlighted the importance of EGF/EGFR signaling pathway, EPO signaling pathway, T cell signal transduction and members of the BCR signaling pathway, which were responsible for the malignant transition of CRC from the benign UC to the aggressive one.

Conclusions

The present study illustrated a standardized normalization approach for cross-study microarray expression data sets. Our model for signaling networks construction was based on the experimentally-supported interaction and microarray co-expression modeling. Pathway-based signaling regulatory networks analysis sketched a directive insight into colorectal carcinogenesis, which was of significant importance to monitor disease progression and improve therapeutic interventions.     

Control of Adenovirus Gene Expression: Cellular Gene Products Restrict Expression of Adenovirus Host Range Mutants in Nonpermissive Cells

Adenovirus type 5 (Ad5) host range mutants dl312 and hr-1, with lesions in region E1A (0 to 4.5 map units) of the viral genome, fail to accumulate virus-specific early RNA during infection in HeLa cells. In a recent report, we showed that the addition of anisomycin, a stringent inhibitor of protein synthesis, at 1 h after infection of HeLa cells with hr-1 virus resulted in the accumulation of properly spliced and translatable mRNA from all early regions (M. G. Katze, H. Persson, and L. Philipson, Mol. Cell. Biol. 1:807-813, 1981). Based on these results we proposed a model in which expression of early mutant RNA was achieved through inactivation of a cellular protein normally causing a reduction in the amount of viral RNA. These studies have been extended in the present report, which shows that early viral proteins can be detected in Ad5 dl312- and Ad5 hr-1-infected HeLa cells which have been treated for several hours with anisomycin either shortly after infection or before infection. A pulse of drug treatment also resulted in expression of substantial amounts of adenovirus structural proteins after infection with both Ad5 hr-1 and Ad5 dl312, whereas in drug-free controls no late proteins were detected. The Ad5 hr-1 virus previously reported to be DNA replication negative in nonpermissive HeLa cells was found to replicate its DNA, albeit at low levels, when anisomycin was present either from 1 to 5 h postinfection or for 5 h before infection. When infectious virus production was examined in mutant-infected cells the titer of Ad5 dl312 virus was found to increase at least 500-fold in anisomycin-treated HeLa cells. Taken together, these and our previous results suggest that the block in gene expression characteristic for complementation group I Ad5 host range mutants in HeLa cells can be overcome by inactivating cellular gene products serving as negative regulators of viral gene expression.     

显性白毛调控基因在不同毛色羊驼皮肤中表达差异的研究

为了研究KIT基因对羊驼毛色的影响及在不同毛色羊驼皮肤中的表达差异,实验在分析羊驼KIT基因结构的基础上,自行设计表达引物,将羊驼KIT基因exon10-exon14成功定向克隆入原核表达载体pET-32a( )中,构建了KIT基因的重组表达质粒pET-32a( )-KIT.同时进行诱导表达,并以纯化的重组蛋白为免疫原,采喟长程免疫程序免疫兔子,成功制备兔抗羊驼多克隆抗体,从而进行免疫组化分析.结果表明:(1)羊驼KIT基因exon10-exon14编码含138个氨基酸残基的蛋白;(2)SDS-PAGE电泳结果显示重组表达质粒pET-32a( )-KIT诱导下,表达的KIT蛋白为可溶性蛋白;(3)免疫组化研究表明,白毛色羊驼皮肤毛囊内根鞘周围组织有KIT蛋白的表达,外根鞘和结缔组织也有少量表达,而黄色羊驼皮肤毛囊周围即内外根鞘则不表达KIT蛋白.     

‘红巴梨’果皮UFGT基因的克隆及表达分析

以‘巴梨’红色芽变品种‘红巴梨’果皮为材料,采用同源克隆技术和RACE结合的方法,克隆了UFGT(UDP-葡萄糖:类黄酮3-O-葡萄糖基转移酶)蛋白的部分cDNA,命名为Pc UFGT。结果表明:该cDNA片段长为1 089 bp,与苹果UFGT基因序列一致性达89%,氨基酸序列同源性为85%,含有糖基转移酶的UDPGT、COG1819和MGT等保守域。荧光实时定量PCR分析表明,该基因在‘红巴梨’幼果期表达强度约为‘巴梨’的2倍,而果实成熟期表达强度略低于‘巴梨’;该基因在‘红巴梨’果肉中不表达。     

Lef-1基因在棕色和白色羊驼皮肤差异表达

本实验旨在研究Lef-1在不同毛色羊驼皮肤中的表达和定位,探索其与毛色间的关系.采用实时荧光定量PCR、Western blotting以及免疫组织化学方法,研究白色和棕色羊驼皮肤中的mRNA、蛋白表达水平和定位.实时荧光定量PCR结果显示,Lef-1在棕色羊驼皮肤组织相对基因表达量是3.3727±0.1989,在白色羊驼皮肤组织是1.0003±0.0227; Western blotting结果显示,在羊驼皮肤组织总蛋白中存在分子量约44 KD与兔抗Lef-1多克隆抗体发生免疫阳性反应的蛋白条带,棕色羊驼平均蛋白表达量显著高于白色羊驼;免疫组织化学结果显示,在棕色羊驼皮肤组织中多表达在毛球部、表皮也有分布,在白色羊驼皮肤组织中多表达在表皮,在棕色和白色羊驼皮肤组织中外根鞘都有较强表达.结果显示Lef-1在棕色和白色羊驼皮肤的定位和含量存在差异,提示Lef-1可能影响了羊驼被毛颜色的形成.     

羊驼皮肤中核糖体蛋白L34（RPL34）基因表达的分析

从羊驼皮肤eDNA文库中筛选到冗P￡34的克隆,经PCR鉴定并测序得知：一种克隆的大小为270bp（命名为尺P躬4,）,另一种克隆的大小为470bp（命名为RPL34Ⅱ）。序列分析发现,RPL34Ⅰ和Ⅱ在核苷酸水平上,5’UTR区不具有同源性,3’UTR区具有同源性;在氨基酸水平上,部分具有高度同源性;分子进化树分析表明二者具有不同的进化速率。此外,RPL34Ⅰ和Ⅱ对应于不同的转录本。通过以上结果分析,认为RPL34Ⅰ和RPL34Ⅱ二者同时在羊驼皮肤中表达,可能是RPIJ34的两个剪接体,发挥不同的生物学功能。     

Wnt通路中的部分基因在绒山羊胚胎皮肤毛囊中的表达分析

已知绒山羊毛囊的发育受Wnt等信号通路控制,但Wnt通路相关基因在绒山羊胚胎毛囊启动和生长发育过程中的表达及作用机制尚不清楚。本文采用RNA-Seq技术对45 d,55 d和65 d的绒山羊胚胎体侧皮肤进行了转录组测序,鉴定Wnt通路相关基因的表达。 RNA- Seq技术结合blast搜索,将转录组有效测序数据与云南黑山羊参考基因组序列(http://goat. kiz.ac. cn/GGD/download.htm)比对,获得了已知的Wnt通路（pathway hsa04310）中的123个相关基因（86.0%）。进而采用实时荧光定量PCR技术检测,验证了差异表达的Sfrp4、Wnt3、Wnt10a（上调）和Apc2（下调）基因在绒山羊胚胎不同时期皮肤中的表达量,初步探索了绒山羊毛囊在胚胎期启动、发育过程中,Wnt通路部分基因的表达模式,为进一步研究Wnt通路部分基因在绒山羊胚胎毛囊启动、发育过程中的作用机制提供了有意义的线索。     

Rapidly Shifting Sex Ratio across a Species Range

Sex ratios are subject to distortion by a range of inherited parasites [1]. Although it has been predicted that the presence of these elements will result in spatial and temporal variation in host sex ratio [2], [3] and [4], testing of this hypothesis has been constrained by availability of historical data. We here determine spatial and temporal variation in sex ratio in a interaction between a butterfly and male-killing Wolbachia bacteria [5] by assaying infection presence in museum specimens, and from this inferring infection prevalence and phenotype in historical populations. Comparison of contemporary and museum samples revealed profound change in four of five populations examined. Two populations become extremely female biased, associated with spread of the male-killer bacterium. One evolved from extremely female biased to a sex ratio near parity, resulting from the infection losing male-killing activity. The final population fluctuated widely in sex ratio, associated with varying frequency of the male killer. We conclude that asynchronous invasion and decline of sex-ratio distorters combines with the evolution of host suppressors to produce a rapidly changing mosaic of sex ratio. As a consequence, the reproductive ecology of the host species is likely to be fundamentally altered over short time scales [6]. Further, the study demonstrates the utility of museum specimens as “silent witnesses” of evolutionary change.     

Wnt5a Exhibits Layer-Specific Expression in Adult Skin,Is Upregulated in Psoriasis,and Synergizes with Type 1 Interferon

Background

Wnt5a is a member of the wingless-type patterning regulators important in pre-natal development. The expression and distribution of Wnt5a and its receptors frizzled (fzd) 3 and fzd 5 in adult human skin have not been comprehensively studied to date.

Methodology/Principal Findings

We here show that Wnt5a, fzd3, fzd5, as well as fzd6 are restricted to specific layers in normal epidermis, analogous to their zonal distribution in hair follicles, suggesting a role in adult skin differentiation. In line, Wnt5a and fzd5 are both overexpressed and re-distributed in the epidermis of psoriasis which involves disturbed keratinocyte differentiation. Functionally, Wnt5a lowers the concentration of IFN required to induce target genes, and increases the magnitude of IFN target gene induction, suggesting a molecular mechanism underlying IFN hypersensitivity in psoriasis. Finally, we identify nedd8 and the amyloid precursor APP, previously shown to be upregulated in psoriasis, as targets of synergistic IFNα/Wnt5a induction.

Conclusions/Significance

The present data (i) suggest that Wnt5a regulates epidermal differentiation even in adult skin and (ii) identify synergistic induction of type 1 IFN target genes as a novel mode of Wnt5a action. Targeting Wnt5a in the skin may reduce IFN hypersensitivity and be of therapeutical value.     

CD57 Expression and Cytokine Production by T Cells in Lesional and Unaffected Skin from Patients with Psoriasis

Background

The immunopathogenic mechanisms leading to psoriasis remain unresolved. CD57 is a marker of replicative inability and immunosenescence on CD8+ T cells and the proportion of CD57 expressing CD8+ T cells is increased in a number of inflammatory conditions.

Methodology

We examined the expression of CD57 on T cells in the skin of patients affected with psoriasis, comparing lesional and unaffected skin. We also assessed functionality of the T cells by evaluating the secretion of several inflammatory cytokines (IL-17A, IFN-gamma, IL-2, IL-33, TNF-alpha, IL-21, IL-22, and IL-27), from cell-sorted purified CD4+ and CD8+ T cells isolated from lesional and unaffected skin biopsies of psoriasis patients.

Principal Findings

We observed that the frequency of CD57+CD4+ and CD57+CD8+ T cells was significantly higher in unaffected skin of psoriasis patients compared to lesional skin. Sorted CD4+ T cells from psoriatic lesional skin produced higher levels of IL-17A, IL-22, and IFN-gamma compared to unaffected skin, while sorted CD8+ T cells from lesional skin produced higher levels of IL-17, IL-22, IFN-gamma, TNF-alpha, and IL-2 compared to unaffected skin.

Conclusions/Significance

These findings suggest that T cells in unaffected skin from psoriasis patients exhibit a phenotype compatible with replicative inability. As they have a lower replicative capacity, CD57+ T cells are less frequent in lesional tissue due to the high cellular turnover.     

Sarcoptes scabiei Mites Modulate Gene Expression in Human Skin Equivalents

The ectoparasitic mite, Sarcoptes scabiei that burrows in the epidermis of mammalian skin has a long co-evolution with its hosts. Phenotypic studies show that the mites have the ability to modulate cytokine secretion and expression of cell adhesion molecules in cells of the skin and other cells of the innate and adaptive immune systems that may assist the mites to survive in the skin. The purpose of this study was to identify genes in keratinocytes and fibroblasts in human skin equivalents (HSEs) that changed expression in response to the burrowing of live scabies mites. Overall, of the more than 25,800 genes measured, 189 genes were up-regulated >2-fold in response to scabies mite burrowing while 152 genes were down-regulated to the same degree. HSEs differentially expressed large numbers of genes that were related to host protective responses including those involved in immune response, defense response, cytokine activity, taxis, response to other organisms, and cell adhesion. Genes for the expression of interleukin-1α (IL-1α) precursor, IL-1β, granulocyte/macrophage-colony stimulating factor (GM-CSF) precursor, and G-CSF precursor were up-regulated 2.8- to 7.4-fold, paralleling cytokine secretion profiles. A large number of genes involved in epithelium development and keratinization were also differentially expressed in response to live scabies mites. Thus, these skin cells are directly responding as expected in an inflammatory response to products of the mites and the disruption of the skin’s protective barrier caused by burrowing. This suggests that in vivo the interplay among these skin cells and other cell types, including Langerhans cells, dendritic cells, lymphocytes and endothelial cells, is responsible for depressing the host’s protective response allowing these mites to survive in the skin.