Comparative analysis of gene expression between Babesia bovis blood stages and kinetes allowed by improved genome annotation

Throughout their life cycle, Babesia parasites alternate between a mammalian host, where they cause babesiosis, and the tick vector. Transition between hosts results in distinct environmental signals that influence patterns of gene expression, consistent with the morphological and functional changes operating in the parasites during their life stages. In addition, comparing differential patterns of gene expression among mammalian and tick parasite stages can provide clues for developing improved methods of control. Hereby, we upgraded the genome assembly of Babesia bovis, a bovine hemoparasite, closing a 139 kbp gap, and used RNA-Seq datasets derived from mammalian blood and tick kinete stages to update the genome annotation. Of the originally annotated genes, 1,254 required structural changes, and 326 new genes were identified, leading to a different predicted proteome compared to the original annotation. Next, the RNA-Seq data was used to identify B. bovis genes that were differentially expressed in the vertebrate and arthropod hosts. In blood stages, 28% of the genes were upregulated up to 300 fold, whereas 26% of the genes in kinetes, a tick stage, were upregulated up to >19,000 fold. We thus discovered differentially expressed genes that may play key biological roles and serve as suitable targets for the development of vaccines to control bovine babesiosis.     

基于基因表达谱的疾病亚型特征基因挖掘方法

在本研究中,提出了一种基于基因表达谱的疾病亚型特征基因挖掘方法,该方法基于过滤后基因表达谱,融合无监督聚类识别疾病亚型技术和提出的衡量特征基因对疾病亚型鉴别能力的模式质量测度,以嵌入的方式实现特征基因挖掘。最后将提出的方法应用于40例结肠癌组织与22例正常结肠组织中2000个基因的表达谱实验数据,结果显示:提出的方法是一种可行的疾病亚型特征基因挖掘方法,方法的优势在于可并行实现疾病亚型划分和特征基因识别。     

Factors affecting gene expression of patatin and proteinase-inhibitor-II gene families in detached potato leaves:

In whole intact potato (Solanum tuberosum L.) plants, the gene families of class-I patatin and proteinase inhibitor II (Pin 2) are constitutively expressed in the tubers. However, they are also induced in detached potato leaves in the presence of light. To further characterize this light action, the detached leaves were subjected to monochromatic light of different wavelengths and to darkness in the presence of metabolites and inhibitors. Patatin genes could be induced by the simultaneous application of sucrose (sugars) and glutamine in darkness. Neither of these metabolites was active when supplied alone. When photosynthesis was blocked by 3-(3,4-Di-chlorophenyl)-1, 1-dimethylurea (DCMU) in the light, patatin genes were not expressed; however, the inhibition was overcome in the presence of sucrose. This indicates that besides its role in photosynthetic carbohydrate production, light may be essential for the supply of amino acids (or reduced nitrogen). Unlike patatin, Pin 2 genes were, to a small extent, also active in darkness, and sucrose weakly enhanced this expression. However, DCMU did not affect Pin 2 expression in the light. Both abscisic acid and methyl jasmonate strongly promoted the accumulation of Pin 2 mRNA independent of the light conditions, indicating that the gene family is probably under hormonal control. The phytohormones did not affect patatin gene expression. Inhibitors of cytosolic (cycloheximide) and organellar (chloramphenicol) translation had opposite effects on the two gene families. Careful evaluation of the inhibitors' action indicates that protein synthesis (cytosol) is required for the expression of Pin 2 genes but not for the patatin genes. These results clearly demonstrate that, although in situ both gene families are constitutively expressed in the same plant organ (tuber) in intact plants, their expression is mediated by different factors.Abbreviations ABA cis-abscisic acid - DCMU 3-(3,4-dichlorphenyl)-1,1-dimethylurea - GUS -glucuronidase activity - MeJA methyl jasmonate - Pin 2 proteinase inhibitor II We thank Beate Küsgen and Regina Breitfeld for the greenhouse work. This work was supported by a grant from the Bundesministerium für Forschung und Technologie.     

Vascular expression of the grp1.8 promoter is controlled by three specific regulatory elements and one unspecific activating sequence

The bean grp1.8 full-length promoter is specifically active in vascular tissue during normal development of tobacco. Deletion of a negative regulatory element resulted in ectopic activity of the promoter in cortical cells of hypocotyls, roots and stems. A 169 bp fragment (–205 to –36) of the grp1.8 promoter conferred vascular-specific expression to CaMV 35S minimal promoters whereas a 141 bp fragment (–205 to –64) strongly activated these minimal promoters both in vascular and cortical cells. These experiments defined a new regulatory element (VSE) that is essential for vascular-specific expression and is located between –64 and –36. The 141 bp grp1.8 promoter sequence had enhancer-like properties as it was active in both orientations. A 24 bp sequence (bp –119 to –96, corresponding to the SE1 regulatory element) enhanced expression from several minimal promoters strongly but unspecifically, whereas a 26 bp sequence (–98 to –73, corresponding to the RSE regulatory element) induced vascular-specific expression. Thus, the grp1.8 promoter is regulated by a combinatorial mechanism that can integrate the action of different, non-additively acting regulatory elements into vascular-specific expression.     

The gene expression sequence of radiated mucosa in an animal mucositis model

Abstract. Oral mucositis is a common, dose-limiting, acute toxicity of radiation therapy administered for the treatment of cancers of the head and neck. Accumulating data would suggest that the pathogenesis of mucositis is complex and involves the sequential interaction of all cell types of the oral mucosa, as well as a number of cytokines and elements of the oral environment. While a number of studies have reported on gene expression of particular cell types in response to radiation, the overall response of irradiated mucosa has only been evaluated in a limited way. The present study was undertaken to evaluate the expression of a target group of genes using RNA quantification assays and, more broadly, to assess patterns of mucosal gene expression using DNA microarray hybridization. Our results demonstrate the sequential upregulation of a series of genes that, when taken collectively, suggest an intricate functional interaction.     

中华蜜蜂性信息素结合蛋白ASP1的原核表达及配基结合特性分析

【目的】研究中华蜜蜂Apis cerana cerana信息素结合蛋白ASP1与蜜蜂信息素及某些植物挥发物分子的结合功能。【方法】构建中蜂ASP1的原核表达载体, 对其进行重组蛋白的诱导表达和分离纯化, 并得到具有生化活性的中蜂ASP1重组蛋白, 最后以1-NPN作为荧光报告探针, 通过荧光竞争结合实验研究中蜂重组ASP1蛋白与蜜蜂信息素及其他气味分子的结合功能。【结果】在22种潜在信息气味物质中, 有7种与中蜂ASP1有较强的结合能力, 能将1-NPN的相对荧光强度降至50%以下。其中发现蜂王信息素两种成分对 羟基苯甲酸甲酯和香草醇的竞争能力最强, 可分别引起1-NPN相对荧光值下降99.31%和95.50%, 解离常数K_D分别为13.39和98.44 μmol/L; 而与除蜂王信息素外的其他信息素如幼虫信息素和工蜂信息素等分子均不结合。此外中蜂ASP1对于水杨酸甲酯、 苯乙醛、 3, 4-二甲基苯甲醛4-烯丙基藜芦醚和β-紫罗兰酮等5种植物挥发物质能产生强度不一的结合。【结论】中蜂信息素结合蛋白ASP1对蜂王信息素具有非常强的特异性, 同时也能结合某些植物挥发性气味分子, 暗示中蜂ASP1是一种以蜂王信息素识别为主要功能、 植物挥发物识别为次要功能的多功能信息素结合蛋白。     

Gene expression profiling of human diseases by serial analysis of gene expression

Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases.     

普通烟草LBD基因家族的全基因组序列鉴定与表达分析

LBD是一类具有LOB(lateral organ boundaries)结构域的基因家族,在植物发育过程中起到非常重要的作用。采用生物信息学方法,根据拟南芥LBD基因序列鉴定了普通烟草基因组中的LBD基因,并对家族成员进行了序列特征、系统发育和表达谱分析。结果表明:普通烟草基因组中共有98个LBD基因成员,其基因结构相对简单,一般含有1~3个外显子。LBD基因家族可分成I和II两大类,两类均含有CX_2CX_6CX_3C保守结构域,但II类不含有LX_6LX_3LX_6L形成的"卷曲螺旋"二级结构,根据与拟南芥LBD蛋白构建的系统发育树则可细分成5个亚家族(Ia、Ib、Ic、Id和II)。将LBD基因与表达序列标签(EST)比对,发现36个基因有EST证据;EST、芯片数据和转录组数据分析表明:LBD基因具有不同的组织表达模式,部分基因表现出组织特异性。这些研究结果为普通烟草LBD基因家族功能的深入研究奠定了基础。     

The Chlorella virus adenine methyltransferase gene promoter is a strong promoter in plants

An upstream region isolated from a eukaryotic algal virus adenine methyltransferase gene was tested for promoter function in plants. Fusion of this region to the chloramphenicol acetyltransferase reporter gene resulted in significantly higher expression than fusion with the cauliflower mosaic virus 35S promoter. Strong levels of expression were also found in electroporated monocot plant cells. The promoter activity in transgenic tobacco plants showed tissue-specific expression. Leaves had the highest expression followed by stems and flowers. The promoter activity was not detected in root tissue. Environmental cues, such as light, and the phytohormones auxin and cytokinines had no effect on the promoter's expression. This promoter might be utilized to achieve high levels of expression of introduced genes in higher plants.