Heterologous hybridization to a complementary DNA microarray reveals the effect of thermal acclimation in the endothermic bluefin tuna (Thunnus orientalis)

The temperature stress that pelagic fishes experience can induce physiological and behavioural changes that leave a signature in gene expression profiles. We used a functional genomics approach to identify genes that were up- or down-regulated following thermal stress in the Pacific bluefin tuna. Following the acclimation period, 113, 81 and 196 genes were found to be differentially expressed between the control (20 °C) and cold (15°) treatment groups, in ventricle, red muscle and white muscle, respectively. The genes whose expression levels were responsive to thermal acclimation varied according to muscle fibre type, perhaps reflecting the tissue-specific degrees of endothermy characteristic of this species.     

缺铁水稻根转录本微点阵分析

水稻不仅是非常重要的粮食作物 ,也是用于研究的模式植物之一 .由于水稻基因组测序的完成 ,用功能基因组学的现代方法来研究缺铁相关基因的表达调控是最高效的方法之一。在前期工作的基础上 ,精心设计了缺铁和EDTA鳌合二价铁诱导5天的水稻根实验 ,并进行了转录水平的微点阵 (microarray)分析。但只获得了第 5天的结果。在 10 5 31个水稻cDNA芯片图谱中 ,缺铁和加铁比较发现了 4 5 1个差异点。对缺铁诱导的 4 5 1个差异cDNA逐一地进行NCBI (美国国家生物技术信息中心 )的BLAST(局部定位排列搜索工具 )数据库检索、分析和归类。发现其中缺铁与加铁 ( -Fe/Fe -EDTAratio)之间的相对表达水平(REL)在 2 - 9.175之间的缺铁诱导上调基因为 2 0 3个 ,缺铁诱导的下调基因为 2 4 8个。对每一类上调基因都逐一地进行了NCBI-PubMed的文献检索。利用国际网络数据库进行了功能鉴定。     

缺铁水稻根转录本组及与膜泡运输相关基因的分析

随着大规模芯片技术(即cDNA微点阵)的开展,这一技术已用于胁迫基因表达的转录本组分析。本论文重点阐述转录 本图谱分析的方法,以及缺铁胁迫下,水稻的基因组表达差异,其中重点是与膜泡运输相关的几个基因。     

Monitoring of Gene Expression Profiles and Isolation of Candidate Genes Involved in Pollination and Fertilization in Rice (Oryza Sativa L.) with a 10K cDNA Microarray

To monitor gene expression profiles during pollination and fertilization in rice at a genome scale, we generated 73,424 high-quality expressed sequence tags (ESTs) derived from the green/etiolated shoot and pistil (0-5 h after pollination, 5hP) of rice, which were subsequently used to construct a cDNA microarray containing ca. 10 000 unique rice genes. This microarray was used to analyze gene expression in pistil unpollinated (UP), 5hP and 5DAP(5 days after pollination), anther, shoot, root, 10-day-old embryo (10EM) and 10-day-old endosperm (10EN). Clustering analysis revealed that the anther has a gene-expression profile more similar to root than to pistil and most pistil-preferentially expressed genes respond to pollination and/or fertilization. There are 253 ESTs exhibiting differential expression (e +/- 2-fold changes) during pollination and fertilization, and about 70% of them can be assigned a putative function. We also recovered 20 genes similar to pollination-related and/or fertility-related genes previously identified as well as genes that were not implicated previously. Microarray and real-time PCR analyses showed that the array sensitivity was estimated at 1-5 copies of mRNA per cell, and the differentially expressed genes showed a high correlation between the two methods. Our results indicated that this cDNA microarray constructed here is reliable and can be used for monitoring gene expression profiles in rice. In addition, the genes that differentially expressed during pollination represent candidate genes for dissecting molecular mechanism of this important biological process in rice.     

低磷胁迫对水稻苗期侧根生长及养分吸收的影响

用蛭石与石英砂作为混合培养介质研究了低磷胁迫对水稻（Oryza sativa L.)苗期侧根发生发育的影响及其与磷吸收的相关关系。结果表明：低磷对水稻的侧根发生发育具有明显的诱导作用及基因型差异。相关性分析表明：单位侧根长度的增加与单位根表面积的增大极显相关,而单位侧根数量的增多与单位根表面积的增大无显的相关性。表明单位根表面积的增加主要来自于单位侧根的伸长。侧根参数与磷含量的相关性分析表明：低磷条件下,侧根总长度和侧根数量都与植株磷含量存在显的正相关,根系总表面积与磷含量存在极显的正相关。表明在低磷条件下,侧根的发生发育对水稻的磷吸收具有重要的作用。根系和地上部的可溶性糖含量分析表明;低磷胁迫改变了同化物在地上部和根系的分配。生物量测定表明：低磷胁迫显增大了植株的根冠比。     

水稻抗稻瘟病近等基因系的cDNA微阵列分析

应用cDNA微阵列对来源于中156／谷梅2号重组自交系的水稻抗稻瘟病近等基因系G205和G71的稻瘟病菌胁迫基因表达谱进行了分析,发现有3个cDNA克隆的表达仅在抗病基因系G205接种病原菌12h后受到诱导,其中两个为功能已知基因,另一个为功能未知的新基因。另有35个差异表达克隆在两个近等基因系中均检测到,其中17个克隆的表达在G205和G71均受到病原菌的诱导,另外18个克隆的表达则在G205和G71均受到病原菌原抑制。序列分析表明,这些稻瘟病菌应答基因分别与防卫反应,信号传递,逆境胁迫和光合作用及糖代谢等功能相关,为植物抗病机制提供了相关信息。另外,Northern还证实了编码富含甘氨酸蛋白基因（Glycinerich protein Grp)的表达受稻瘟病病原菌的诱导,是一个稻瘟病诱导相关基因。     

Microarray Analysis Reveals Similarities and Variations in Genetic Programs Controlling Pollination/Fertilization and Stress Responses in Rice (<Emphasis Type="Italic">Oryza sativa </Emphasis>L.)

Previously, we identified 253 cDNAs that are regulated by pollination/fertilization in rice by using a 10K cDNA microarray. In addition, many of them also appeared to be involved in drought and wounding responses. To investigate this relationship, we obtained their expression profiles after dehydration and wounding treatments in this study. Venn diagram analysis indicated that 53.8% (136/253) and 21% (57/253) of the pollination/fertilization-related genes are indeed regulated by dehydration and wounding, respectively, and nearly half of the genes expressed preferentially in unpollinated pistils (UP) are responsive to dehydration. These results indicated that an extensive gene set is shared among these responses, suggesting that the genetic programs regulating them are likely related. Among them, the genetic network of water stress control may be a key player in pollination and fertilization. Additionally, 39.5% (100/253) cDNAs that are related to pollination/fertilization appear not to be regulated by the stress treatments (dehydration and wounding), suggesting that the existence of additional genetic networks are involved in pollination/fertilization. Furthermore, comparative analysis of the expression profiles of the 253 cDNAs under 18 different conditions (various tissues, treatments and developmental status) revealed that the genetic networks regulating photosynthesis, starch metabolisms, GA- and defense-responses are involved in pollination and fertilization. Taken together, these results provided some clues to elucidate the molecular mechanisms of pollination and fertilization in rice. Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s11103-005-3958-4     

应用基因芯片技术检测肝组织的基因表达

为检测正常肝组织中的基因表达状况,采用cDNA microarray技术对正常肝组织中表达的1500个基因进行定量。结果为97 个基因较高表达,1010个基因中度表达,380个基因低表达。结果是cDNA microarray技术是大规模检测基因表达的有效方法。     

Comparative analysis of amplified and nonamplified RNA for hybridization in cDNA microarray

Limiting amounts of RNA is a major issue in cDNA microarray, especially when one is dealing with fresh tissue samples. Here we describe a protocol based on template switch and T7 amplification that led to efficient and linear amplification of 1300x. Using a glass-array containing 368 genes printed in three or six replicas covering a wide range of expression levels and ratios, we determined quality and reproducibility of the data obtained from one nonamplified and two independently amplified RNAs (aRNA) derived from normal and tumor samples using replicas with dye exchange (dye-swap measurements). Overall, signal-to-noise ratio improved when we used aRNA (1.45-fold for channel 1 and 2.02-fold for channel 2), increasing by 6% the number of spots with meaningful data. Measurements arising from independent aRNA samples showed strong correlation among themselves (r(2)=0.962) and with those from the nonamplified sample (r(2)=0.975), indicating the reproducibility and fidelity of the amplification procedure. Measurement differences, i.e, spots with poor correlation between amplified and nonamplified measurements, did not show association with gene sequence, expression intensity, or expression ratio and can, therefore, be compensated with replication. In conclusion, aRNA can be used routinely in cDNA microarray analysis, leading to improved quality of data with high fidelity and reproducibility.