Murine expression and mutation analyses of the prostate androgen-regulated mucin-like protein 1 (Parm1) gene, a candidate for human epispadias

Background

Epispadias is the mildest phenotype of the human bladder exstrophy–epispadias complex (BEEC), and presents with varying degrees of severity. This urogenital birth defect results from a disturbance in the septation process, during which separate urogenital and anorectal components are formed through division of the cloaca. This process is reported to be influenced by androgen signaling. The human PARM1 gene encodes the prostate androgen-regulated mucin-like protein 1, which is expressed in heart, kidney, and placenta.

Methods

We performed whole mount in situ hybridization analysis of Parm1 expression in mouse embryos between gestational days (GD) 9.5 and 12.5, which are equivalent to human gestational weeks 4–6. Since the spatio-temporal localization of Parm1 corresponded to tissues which are affected in human epispadias, we sequenced PARM1 in 24 affected patients.

Results

We found Parm1 specifically expressed in the region of the developing cloaca, the umbilical cord, bladder anlage, and the urethral component of the genital tubercle. Additionally, Parm1 expression was detected in the muscle progenitor cells of the somites and head mesenchyme. PARM1 gene analysis revealed no alterations in the coding region of any of the investigated patients.

Conclusions

These findings suggest that PARM1 does not play a major role in the development of human epispadias. However, we cannot rule out the possibility that a larger sample size would enable detection of rare mutations in this gene.     

IGFBP-3 and IGFBP-10 (CYR61) up-regulation during the development of Barrett's oesophagus and associated oesophageal adenocarcinoma: potential biomarkers of disease risk

Dys-regulation of the insulin-like growth factor (IGF) system increases the risk of a number of malignancies. The aim of this study was to investigate the role of members of the IGF binding protein (IGFBP) superfamily in the development of oesophageal adenocarcinoma (EAC) and their possible use as markers of disease risk. Expression of IGFBP-2, IGFBP-3, IGFBP-4, and IGFBP-10/CYR61 was assessed using Real-Time-polymerase chain reaction (PCR) and immunohistochemistry in oesophageal tissues from Barrett's oesophagus (BE) patients with and without associated EAC, and in control subjects. IGFBP-3, IGFBP-4, and IGFBP-10/CYR61 mRNA levels were up-regulated in Barrett's (n=17) and tumour tissue of EAC patients (n=18) compared with normal tissue of control subjects without BE or EAC (n=18) (p<0.001). Over-expression of IGFBP-3 and IGFBP-10/CYR61 proteins was observed in Barrett's, dysplastic and tumour tissue of EAC cases (n=47 for IGFBP-10; n=39 for IGFBP-3) compared with adjacent normal epithelium (p<0.050). Notably, IGFBP-3, IGFBP-4, and IGFBP-10/CYR61 expression in Barrett's tissue of EAC cases (n=17) was significantly (p<0.001) higher than in Barrett's tissue of BE patients with no sign of progression to cancer (n=15). Overall, the results suggest that members of the IGFBP superfamily are up-regulated during oesophageal carcinogenesis and merit further investigation as markers of EAC risk.     

Comparative studies of zebrafish Danio rerio lipoprotein lipase (lpl) and hepatic lipase (lipc) genes belonging to the lipase gene family: evolution and expression pattern

In this study, bioinformatics analysis, tissue distribution and developmental expression pattern of lipoprotein lipase (lpl) and hepatic lipase (lipc) in zebrafish Danio rerio are reported. In adult D. rerio, lpl was highly expressed in liver. This is remarkably different from the tissue expression pattern of LPL in mammals, which is not detected in the adult liver. The expression of lipc was liver specific, which is consistent with that in mammals. During embryogenesis, lpl mRNA was increased gradually in concentration from 0·5 hpf (hour post fertilization) to 6 dpf (days post fertilization), but lipc was not expressed at the early stage of the embryo until 3 dpf. In situ hybridization further displayed the expression pattern of lpl mainly restricted to the head region including cells surrounding the mouth opening, branchial arches, pectoral fin and lateral line neuromast, whereas lipc was mainly restricted to the liver and part of head regions including lens. This lays a foundation for further investigation of lpl or lipc function and evolution in fishes.     

斜纹夜蛾普通气味结合蛋白GOBP1基因的表达定位分析

气味调控斜纹夜蛾Spodoptera litura（鳞翅目,夜蛾科）的交配和产卵行为,而嗅觉气味结合蛋白（OBP）是昆虫与外界环境进行化学信息交流中的一种重要蛋白。本研究基于已报道的斜纹夜蛾普通气味结合蛋白GOBP1基因cDNA序列（GenBank登录号为EF159978）设计引物,通过RT-PCR法分析了GOBP1 mRNA的组织特异性表达情况,并对GOBP1基因条带进行了克隆、测序和Blast比对。此外,再通过RNA原位杂交的方法进一步分析了GOBP1 mRNA在触角中的表达定位。结果表明:GOBP1只在斜纹夜蛾的触角组织中表达,而且GOBP1转录本较多分布于靠近嗅觉感受器即触角边缘部位。这些结果进一步说明GOBP1是斜纹夜蛾嗅觉过程中的重要蛋白,同时为深入研究GOBP1与其他蛋白的相互空间定位关系、GOBP1的功能等奠定了基础。     

Post-meiotic expression of the mouse dihydropyrimidinase-related protein 3 (DRP-3) gene during spermiogenesis

The dihydropyrimidinase-related protein (DRP) family, originally identified in humans by their homology to dihydropyrimidinase, contains at least four members. Genes of this family, and their counterparts in other mammals and chickens, are expressed mainly in fetal and neonatal brain, suggesting that the encoded proteins have a physiological role in the development of the central nervous system. In addition, the DRP-3 gene is expressed in testis as a shorter mRNA than the brain form. As a first step in understanding the extra-neuronal function of DRP-3, the structure and expression of testis DRP-3 were examined. Testis DRP-3 cDNA showed the same sequence as brain DRP-3 cDNA, except for the 5′-terminal end, which encodes a 5′-untranslated region and the 11 N-terminal amino acid residues, indicating that the two forms of DRP-3 mRNA were transcribed from a single copy gene. Northern blotting analysis detected DRP-3 mRNA in 30-, 40- and 70-day-old, but not in 10- and 20-day-old testes. In situ hybridization analysis indicated that the expression of DRP-3 in testis is restricted to post-meiotic round spermatids. This is the first report of the expression of DRP genes in extra-neuronal cells. Mol. Reprod. Dev. 51:105–111, 1998. © 1998 Wiley-Liss, Inc.     

A genome-wide survey of maize lipid-related genes: candidate genes mining,digital gene expression profiling and co-location with QTL for maize kernel oil

Lipids play an important role in plants due to their abundance and their extensive participation in many metabolic processes. Genes involved in lipid metabolism have been extensively studied in Arabidopsis and other plant species. In this study, a total of 1003 maize lipid-related genes were cloned and annotated, including 42 genes with experimental validation, 732 genes with full-length cDNA and protein sequences in public databases and 229 newly cloned genes. Ninety-seven maize lipid-related genes with tissue-preferential expression were discovered by in silico gene expression profiling based on 1984483 maize Expressed Sequence Tags collected from 182 cDNA libraries. Meanwhile, 70 QTL clusters for maize kernel oil were identified, covering 34.5% of the maize genome. Fifty-nine (84%) QTL clusters co-located with at least one lipid-related gene, and the total number of these genes amounted to 147. Interestingly, thirteen genes with kernel-preferential expression profiles fell within QTL clusters for maize kernel oil content. All the maize lipid-related genes identified here may provide good targets for maize kernel oil QTL cloning and thus help us to better understand the molecular mechanism of maize kernel oil accumulation.     

棉卷叶野螟泛素基因的克隆、序列分析及原核表达

本研究用RT-PCR方法,克隆了棉卷叶野螟Haritalodes derogata (Fabricius)泛素基因编码区,GenBank登录号为EU580145。序列分析表明,该编码区长228 bp,编码76个氨基酸,推测的编码蛋白的相对分子质量和等电点分别为8.53 kD和5.83。同源性比较发现,棉卷叶野螟泛素基因与其他10种昆虫泛素基因在氨基酸水平上具有93%以上的相似性。系统发育树显示棉卷叶野螟与斜纹夜蛾Spodoptera litura (Fabricius)遗传距离较近,通过同源建模获得了该棉卷叶野螟基因编码蛋白的理论三维结构。将棉卷叶野螟泛素基因与pET-32a(+)连接,构建原核表达载体pET-32a-ub,经IPTG诱导,棉卷叶野螟泛素基因在大肠杆菌BL21(DE3) 中高效表达。本研究成功克隆了棉卷叶野螟泛素基因的编码区,并经Western blotting分析证明实现了该基因的原核表达,为进一步研究其在该昆虫体内的作用机理奠定了基础。     

孟氏隐唇瓢虫气味结合蛋白ComOBP1基因的克隆和时空表达

采用RT-PCR和RACE技术,从孟氏隐唇瓢虫Cryptolaemus montrouzieri Mulsant中成功克隆出气味结合蛋白(Com OBP1)基因的全序列(Genbank登陆号:KU170686)。Com OBP1基因全长922 bp,包括5'端长为40 bp的非编码区域(UTR),及3'端长为462 bp的UTR,开放阅读框ORF长为420 bp,编码139个氨基酸,预测的分子量为15.516 k Da,等电点p I为6.57,存在AATAAA加尾信号。N-末端疏水区包含由20个氨基酸构成的信号肽,无跨膜结构,有4个保守的半胱氨酸,属于Minus-C OBP,也是在孟氏隐唇瓢虫中发现的第一个Minus-C OBP。氨基酸序列中有且仅有一个N-糖基化位点为62 NLSA,并存在2个潜在的磷酸化位点。与其它昆虫的Minus-C OBPs进行同源性比较并构建系统发育树,发现与同为鞘翅目Coleoptera昆虫的同源性较高。利用Real-time PCR、RT-PCR技术对Cmon OBP1基因在孟氏隐唇瓢虫不同发育阶段,不同组织,不同营养条件及不同食性下的表达水平进行了测定,结果显示,Cmon OBP1基因在整个发育阶段均有表达,雄性成虫期具有最高表达量,且多在成虫的头部及翅部表达。当营养条件发生变化时,表达丰度不会发生变化,当猎物由天然猎物柑橘粉蚧Planococcus citri Risso变成碗豆修尾蚜Megoura japonica Matsumura时,表达量会明显下降。该结果表明,孟氏隐唇瓢虫的不同发育阶段、不同组织及猎物种类会影响Cmon OBP1基因的表达,从而进一步影响其嗅觉行为。同时,Cmon OBP1基因可能在雄虫相关的信息素感受过程中发挥着重要作用。     

粘虫类钙粘蛋白基因的克隆、序列分析及时空表达

昆虫中肠膜类钙粘蛋白（cadherin-like protein, CLP）是苏云金芽孢杆菌Bacillus thuringiensis (Bt)毒素的重要受体之一, 与Bt毒素的杀虫作用机制以及昆虫对Bt毒素的抗性等密切相关。本研究应用RT-PCR和RACE技术, 克隆了迁飞性重要害虫粘虫Mythimna separata类钙粘蛋白基因全长cDNA序列（命名为Msclp, GenBank登录号为JF951432）, 全长5 642 bp, 编码1 757个氨基酸, 推导的氨基酸序列具有昆虫类钙粘蛋白的特征结构, 包括1个信号肽、 1个前蛋白区、 12个钙粘蛋白重复、 1个近膜区、 1个跨膜区和1个胞质区。预测的分子量和等电点分别为196.786 kD和4.5。该蛋白与同科的烟夜蛾Helicoverpa assulta、 烟芽夜蛾Heliothis virescens、 棉铃虫Helicoverpa armigera及甜菜夜蛾Spodoptera exigua的类钙粘蛋白亲缘关系最近, 氨基酸序列一致性分别为61.77%, 61.66%, 61.26%和58.14%。荧光定量RT-PCR分析表明, 该类钙粘蛋白基因在不同龄期的粘虫幼虫中表达量差异极显著(P<0.01), 其中4龄幼虫相对表达量最高, 但与3龄、 6龄幼虫并没有显著性差异; 1和2龄幼虫表达量最低; 表达部位主要在粘虫中肠, 在中肠以外的虫体其他部位表达量极低。这些结果对于揭示转Bt作物对非靶标、 迁飞性粘虫的杀虫作用机制以及评价其潜在的对Bt毒素抗性机制等奠定了基础。     

Characterization of human reflex tear proteome reveals high expression of lacrimal proline‐rich protein 4 (PRR4)

In‐depth studies on the proteome of reflex tears are still inadequate. Hence, further studies on this subject will unravel the key proteins which are conjectured to possess vital functions in the protection of the ocular surface. Therefore, this study investigated the differences in the expression levels in proteome of reflex compared to basal tears. Basal (n = 10) and reflex (n = 10) tear samples from healthy subjects were collected employing the capillary method, subsequently pooled and the proteomes were characterized employing 1DE combined with LC‐ESI‐MS/MS strategy for label‐free quantitative (LFQ) analysis. The differentially expressed proteins were validated by 2DE combined with LC‐ESI‐MS/MS and targeted‐MS approach called accurate inclusion mass screening (AIMS) strategies. The analysis of the reflex tear proteome demonstrated increased abundance in proline‐rich protein 4 (PRR4) and zymogen granule protein 16 homolog B (ZG16B) for the first time. Other abundant lacrimal proteins, e.g. lactotransferrin and lysozyme remained constant. Predominantly, the lacrimal gland‐specific PRR4 represents the major increased protein in reflex tears in an attempt to wash out irritants that come into contact with the eye. Conversely, decreased abundance in Ig alpha‐1 chain C, polymeric immunoglobulin receptor, cystatin S/SN, clusterin and mammaglobin were observed. This study had further unraveled the intricate proteome regulation during reflex tearing, especially the potential role of PRR4, which may be the key player in the protection and maintenance of dynamic balance of the ocular surface.     

PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants

Normalization of quantitative gene expression data with a suitable reference gene is essential for accurate and reliable results. However, the availability and choice of most suitable reference gene(s) showing uniform expression across all the experimental conditions remain a drawback. We have developed a web server, PlantRGS (http://www.nipgr.res.in/PlantRGS), for the identification of most suitable candidate reference gene(s) at the whole-genome level using microarray data for quantitative gene expression studies in plants. Microarray data from more than 11 000 tissue samples for nine plant species have been included in the PlantRGS for meta-analysis. The web server provides a user-friendly graphical user interface-based analysis tool for the identification of most suitable reference genes in the selected plant species under user-defined experimental conditions. Various parameter options and output formats will help users to investigate desired number of most suitable reference genes with wide range of expression levels. Validation of results revealed that novel reference genes identified by the PlantRGS outperforms the traditionally used reference genes in terms of expression stability. We anticipate that the PlantRGS will provide a platform for the identification of most suitable reference gene(s) under given experimental conditions and facilitate quantitative gene expression studies in plants.     

Promoter characterization and expression of the gene coding for the human GM2 activator protein

Type 2 diabetes (or non-insulin dependent diabetes mellitus, NIDDM) is a common metabolic disease in man. The Goto–Kakizaki (GK) rat has been designed as a NIDDM model. Previous studies with this strain have shown differences at the mitochondrial level. The mitochondrial permeability transition (MPT) is a widely studied phenomenon but yet poorly understood, that leads to mitochondrial dysfunction and cell death. The aim of this work was to compare the differences in susceptibility of induction of the MPT with calcium phosphate in GK and Wistar rats. Our results show that heart mitochondria from GK rats are less susceptible to the induction of MPT, and show a larger calcium accumulation before the overall loss of mitochondrial impermeability.     

The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis

We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (ACT), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Results are accompanied by estimates of the statistical significance of the correlation relationships, expressed as probability (P) and expectation (E) values. Additionally, highly ranked genes on a correlation list can be examined using the novel clique finder tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots, and dissection into cliques of co-regulated genes. We illustrate the applications of the software by analysing genes encoding functionally related proteins, as well as pathways involved in plant responses to environmental stimuli. These analyses demonstrate novel biological relationships underlying the observed gene co-expression patterns. To demonstrate the ability of the software to develop testable hypotheses on gene function within a defined biological process we have used the example of cell wall biosynthesis genes. The resource is freely available at http://www.arabidopsis.leeds.ac.uk/ACT/     

朱砂叶螨HSP90基因克隆及原核表达

采用RT-PCR及RACE技术克隆朱砂叶螨Tetranychus cinnabarinus的热激蛋白90(HSP90)基因, 并进行序列分析, 得到一条长2 595 bp的cDNA序列, 该序列开放阅读框（open reading frame, ORF）为2 169 bp, 编码722个氨基酸, 分子量约为83.45 kDa, 理论等电点为4.81, 3′非编码区（untranslated region, UTR）为249 bp, 5′UTR为177 bp。通过Antheprot分析发现5个HSP90家族的签名序列及胞质HSP90特征序列MEEVD。同源性分析表明, 朱砂叶螨HSP90编码区核苷酸序列和其他已知的HSP90, 尤其是节肢动物昆虫的HSP90, 具有很高的相似性。将鉴定正确的原核重组表达质粒pET43a-TcHSP90, 转化大肠杆菌Escherichia coli BL21(origami) 进行原核表达, 应用SDS-PAGE和Western blotting技术分离并检测融合蛋白, 结果表明构建的原核表达质粒可以在宿主菌中稳定、正确表达。朱砂叶螨TcHSP90基因的克隆、原核表达, 为进一步研究HSP90的性质和功能的研究提供有用的实验材料。