镉胁迫后旱柳转录组变化分析

随着重金属镉(Cd)应用范围的扩大,由此引发的土壤镉污染问题日益严重。以具有植物恢复潜力的旱柳Salix matsudana作为研究对象,探究不同浓度的Cd (2.5 mg/L, 50 mg/L)胁迫后旱柳无性系1 d、7 d和30 d后基因表达与代谢通路的变化。转录组测序结果表明:共获得102 595个非冗余基因(Unigenes),相同浓度不同时间的差异基因总数为26 623个和32 154个;相同时间不同浓度的差异基因总数为8 550个、3 444个和11 428个。从中筛选得到与Cd胁迫响应密切相关的基因25个,其中金属硫蛋白、ABC转运蛋白、锌和锰转运蛋白等基因的表达不仅会随着Cd胁迫浓度变化而且同时受到胁迫时间的改变而发生改变;油菜素内酯合成通路的ROT3和黄酮类化合物合成通路的FLS、F3H均明显上调。此外Cd胁迫引起旱柳在代谢过程、细胞过程、膜、细胞器、细胞、细胞部分、催化活化和结合蛋白这8个方面发生改变,参与这些GO条目的差异表达基因数随着Cd浓度和胁迫时间的增加而增加。并对转录组信息的可靠性用RT-PCR和酶活性生理实验数据进行了验证。文中通过转录组测序分析旱柳Cd胁迫后的响应机制,从而为旱柳修复土壤Cd污染提供理论指导。     

Storage Behaviour of Salix alba and Salix matsudana Seeds

Effects of dehydration, storage temperature and humidificationon germination of Salix alba andS. matsudana seeds were studied.Newly released seeds showed 100% germination before and afterdehydration to 11–12% moisture content. Germination ofthe high vigour lot (100% initial normal germination) was notaffected by dehydration to 6.7% moisture content but germinationdecreased with further dehydration to 4.3%. The lower vigourlot (75% initial normal germination) was more susceptible todehydration and germination decreased following dehydrationto 6.7% moisture content. Dry seeds of both species survivedimmersion in liquid nitrogen without loss of viability. Thegermination of seeds stored with 9% moisture content decreasedto 35–40% in 5 months at -20°C or in 2 months at 5°C.However, at 25°C seeds entirely lost viability within 2weeks. Seeds showed improved performance when stored at -70°C> - 20°C > 5°C > 25°C and tolerated dehydrationto a moisture content in equilibrium with 15% relative humidity.Results suggest that they are orthodox in storage behaviouralthough they are short-lived. Humidification treatment of lowvigour seed lots resulted in a remarkable increase in germinationpercentage. Copyright 2000 Annals of Botany Company Salix alba, Salix matsudana, willow, seed storage behaviour, dehydration, humidification, cryopreservation     

Identification of differentially expressed genes in mouse kidney after irradiation using microarray analysis

Irradiation of the kidney induces dose-dependent, progressive renal functional impairment, which is partly mediated by vascular damage. The molecular mechanisms underlying the development of radiation-induced nephropathy are unclear. Given the complexity of radiation-induced responses, microarrays may offer new opportunities to identify a wider range of genes involved in the development of radiation injury. The aim of the present study was to determine whether microarrays are a useful tool for identifying time-related changes in gene expression and potential mechanisms of radiation-induced nephropathy. Microarray experiments were performed using amplified RNA from irradiated mouse kidneys (1 x 16 Gy) and from sham-irradiated control tissue at different intervals (1-30 weeks) after irradiation. After normalization procedures (using information from straight-color, color-reverse and self-self experiments), the differentially expressed genes were identified. Control and repeat experiments were done to confirm that the observations were not artifacts of the array procedure (RNA amplification, probe synthesis, hybridizations and data analysis). To provide independent confirmation of microarray data, semi-quantitative PCR was performed on a selection of genes. At 1 week after irradiation (before the onset of vascular and functional damage), 16 genes were significantly up-regulated and 9 genes were down-regulated. During the period of developing nephropathy (10 to 20 weeks), 31 and 42 genes were up-regulated and 9 and 4 genes were down-regulated. At the later time of 30 weeks, the vast majority of differentially expressed genes (191 out of 203) were down-regulated. Potential genes of interest included TSA-1 (also known as Ly6e) and Jagged 1 (Jag1). Increased expression of TSA-1, a member of the Ly-6 family, has previously been reported in response to proteinuria. Jagged 1, a ligand for the Notch receptor, is known to play a role in angiogenesis, and is particularly interesting in the context of radiation-induced vascular injury. The present study demonstrates the potential of microarrays to identify changing patterns of gene expression in irradiated kidney. Further studies will be required to evaluate functional involvement of these genes in vascular-mediated normal tissue injury.     

Identification of significant periodic genes in microarray gene expression data

Background  

One frequent application of microarray experiments is in the study of monitoring gene activities in a cell during cell cycle or cell division. A new challenge for analyzing the microarray experiments is to identify genes that are statistically significantly periodically expressed during the cell cycle. Such a challenge occurs due to the large number of genes that are simultaneously measured, a moderate to small number of measurements per gene taken at different time points, and high levels of non-normal random noises inherited in the data.     

镉在旱柳中亚细胞分布及存在的化学形态

以2个旱柳无性系幼苗为材料,通过营养液培养并结合差速离心与化学试剂提取法,分析了不同浓度Cd2+胁迫下旱柳叶和根中Cd的亚细胞分布及其存在的化学形态.结果显示,(1)随着培养介质Cd2+浓度升高,旱柳无性系幼苗叶和根中各亚细胞组分Cd含量随之增加.叶片的Cd主要富集于细胞壁、叶绿体和可溶性部分,它们的含量分别占65%～69%、14%～22%、6.8%～7.7%,仅少量Cd发现于膜部分;而根中Cd主要积累于细胞壁和可溶性部分,其中含量分别占59%～66%和14%～25%,Cd在根亚细胞组分中积累量依次为细胞壁>可溶性部分>质体>膜部分.(2)旱柳体内Cd以不同的化学形态存在,大部分为HCl(FHCl)、NaCl(FNaCl)、醋酸(HAC,FHAC)提取态,极少部分为乙醇(EtOH,FEtOH)和水提取态(Fwater),叶和根中5种Cd提取态含量依次为FHCl>FNaCl>FHAC>Fwater>FEtOH,而叶和根中HCl和NaCl提取态Cd占有比例大于30%以上.研究表明,旱柳无性系中Cd主要与蛋白质和有机酸螯合或以金属磷酸盐沉淀的形态存在,其根、叶的细胞壁和液泡在Cd忍耐与解毒中起到重要作用.     

Identification of differentially expressed genes contributing to radioresistance in lung cancer cells using microarray analysis

Radiotherapy has played a key role in the control of tumor growth in many cancer patients. It is usually difficult to determine what fraction of the tumor cell population is radioresistant after a course of radiotherapy. The response of tumor cells to radiation is believed to be accompanied by complex changes in the gene expression pattern. It may be possible to use these to sensitize radioresistant tumor cells and improve radiocurability. Based on the biological effects of ionizing radiation, in the present study, we developed one oligonucleotide microarray to analyze the expression of 143 genes in cells of two lung cancer cell lines with different radiosensitivities. Compared to NCI-H446 cells, expression of 18 genes significantly increased the basal levels in the radioresistant A549 cells, in which eight genes were up-regulated and 10 genes were down-regulated. In A549 cells irradiated with 5 Gy, 22 (19 up-regulated and three down-regulated) and 26 (eight up-regulated and 18 down-regulated) differentially expressed genes were found 6 and 24 h after irradiation, respectively. In NCI-H446 cells, the expression of 17 (nine up-regulated and eight down-regulated) and 18 (six up-regulated and 12 down-regulated) genes was altered 6 and 24 h after irradiation, respectively. RT-PCR was performed, and we found that MDM2, BCL2, PKCZ and PIM2 expression levels were increased in A549 cells and decreased in NCI-H446 cells after irradiation. Genes involved in DNA repair, such as XRCC5, ERCC5, ERCC1, RAD9A, ERCC4 and the gene encoding DNA-PK, were found to be increased to a higher level in A549 cells than in NCI-H446 cells. Antisense suppression of MDM2 resulted in increased radiosensitivity of A549 cells. Taken together, these results demonstrate the possibility that a group of genes involved in DNA repair, regulation of the cell cycle, cell proliferation and apoptosis is responsible for the different radioresistance of these two lung cancer cells. This list of genes may be useful in attempts to sensitize the radioresistant lung cancer cells.     

HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data

MOTIVATION: Recent studies have shown that microarray gene expression data are useful for phenotype classification of many diseases. A major problem in this classification is that the number of features (genes) greatly exceeds the number of instances (tissue samples). It has been shown that selecting a small set of informative genes can lead to improved classification accuracy. Many approaches have been proposed for this gene selection problem. Most of the previous gene ranking methods typically select 50-200 top-ranked genes and these genes are often highly correlated. Our goal is to select a small set of non-redundant marker genes that are most relevant for the classification task. RESULTS: To achieve this goal, we developed a novel hybrid approach that combines gene ranking and clustering analysis. In this approach, we first applied feature filtering algorithms to select a set of top-ranked genes, and then applied hierarchical clustering on these genes to generate a dendrogram. Finally, the dendrogram was analyzed by a sweep-line algorithm and marker genes are selected by collapsing dense clusters. Empirical study using three public datasets shows that our approach is capable of selecting relatively few marker genes while offering the same or better leave-one-out cross-validation accuracy compared with approaches that use top-ranked genes directly for classification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: wyh@cs.dartmouth.edu SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm.     

Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis

To identify fast-evolving genes in reef-building corals, we performed direct comparative sequence analysis with expressed sequence tag (EST) datasets from two acroporid species: Acropora palmata from the Caribbean Sea and A. millepora from the Great Barrier Reef in Australia. Comparison of 589 independent sequences from 1,421 A. palmata contigs, with 10,247 A. millepora contigs resulted in the identification of 196 putative homologues. Most of the homologous pairs demonstrated high amino acid similarities (over 90%). Comparisons of putative homologues showing low amino acid similarities (under 90%) among the Acropora species to the near complete datasets from two other cnidarians (Hydra magnipapillata and Nematostella vectensis) implied that some were non-orthologous. Within 86 homologous pairs, 39 exhibited dN/dS ratios significantly less than 1, suggesting that these genes are under purifying selection associated with functional constraints. Eight independent genes showed dN/dS ratios exceeding 1, while three deviated significantly from 1, suggesting that these genes may play important roles in the adaptive evolution of Acropora. Our results also indicated that CEL-III lectin was under positive selection, consistent with a possible role in immunity or symbiont recognition. Further studies are needed to clarify the possible functions of the genes under positive selection to provide insight into the evolutionary process of corals.     

Identification of two genes potentially associated in iron-heme homeostasis in human carotid plaque using microarray analysis

Classic characteristics are poor predictors of the risk of thromboembolism. Thus, better markers for the carotid atheroma plaque formation and symptom causing are needed. Our objective was to study by microarray analysis gene expression of genes involved in homeostasis of iron and heme in carotid atheroma plaque from the same patient. mRNA gene expression was measured by an Affymetrix GeneChip Human Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA, USA) using RNA prepared from 68 specimens of endarteriectomy from 34 patients. Two genes involved in iron-heme homeostasis, CD163 and heme oxygenase (HO-1), were analysed in 34 plaques. CD163 (2.18, p?=?1.45E?08) and HO-1 (fold-change 2.67, p?=?2.07E?09) mRNAs were induced. We suggest that atheroma plaques show a more pronounced induction of CD163 and HO-1. Although further evidence is needed, our results support previous data. To our knowledge, this is the first report comparing gene expression between intact arterial tissue and carotid plaque using microarray analysis.     

Identification of prior candidate genes for Sclerotinia local resistance in Brassica napus using Arabidopsis cDNA microarray and Brassica-Arabidopsis comparative mapping

Arabidopsis was the leading model of dicot plant. An accomplished platform had been established for functional genomics studies. The platform had largely facilitated molecular biology research of Arabidopsis itself as well as research on its phylogenetic related plants[1,2]. Brassica napus, as an important cooking oil crop, had a close phylogenetic relationship with Arabidopsis[3―5]. In order to take advantage of avail-able Arabidopsis genetic and molecular tools, Girke et al. had explored …     

Identification of mechanosensitive genes in osteoblasts by comparative microarray studies using the rotating wall vessel and the random positioning machine

Weightlessness or microgravity of spaceflight induces bone loss due in part to decreased bone formation by unknown mechanisms. Due to difficulty in performing experiments in space, several ground-based simulators such as the Rotating Wall Vessel (RWV) and Random Positioning Machine (RPM) have become critical venues to continue studying space biology. However, these simulators have not been systematically compared to each other or to mechanical stimulating models. Here, we hypothesized that exposure to RWV inhibits differentiation and alters gene expression profiles of 2T3 cells, and a subset of these mechanosensitive genes behaves in a manner consistent to the RPM and opposite to the trends incurred by mechanical stimulation of mouse tibiae. Exposure of 2T3 preosteoblast cells to the RWV for 3 days inhibited alkaline phosphatase activity, a marker of differentiation, and downregulated 61 and upregulated 45 genes by more than twofold compared to static 1 g controls, as shown by microarray analysis. The microarray results were confirmed by real-time PCR and/or Western blots for seven separate genes and proteins including osteomodulin, runx2, and osteoglycin. Comparison of the RWV data to the RPM microarray study that we previously published showed 14 mechanosensitive genes that changed in the same direction. Further comparison of the RWV and RPM results to microarray data from mechanically loaded mouse tibiae reported by an independent group revealed that three genes including osteoglycin were upregulated by the loading and downregulated by our simulators. These mechanosensitive genes may provide novel insights into understanding the mechanisms regulating bone formation and potential targets for countermeasures against decreased bone formation during space flight and in pathologies associated with lack of bone formation.     

Gene mining: a novel and powerful ensemble decision approach to hunting for disease genes using microarray expression profiling

Current applications of microarrays focus on precise classification or discovery of biological types, for example tumor versus normal phenotypes in cancer research. Several challenging scientific tasks in the post-genomic epoch, like hunting for the genes underlying complex diseases from genome-wide gene expression profiles and thereby building the corresponding gene networks, are largely overlooked because of the lack of an efficient analysis approach. We have thus developed an innovative ensemble decision approach, which can efficiently perform multiple gene mining tasks. An application of this approach to analyze two publicly available data sets (colon data and leukemia data) identified 20 highly significant colon cancer genes and 23 highly significant molecular signatures for refining the acute leukemia phenotype, most of which have been verified either by biological experiments or by alternative analysis approaches. Furthermore, the globally optimal gene subsets identified by the novel approach have so far achieved the highest accuracy for classification of colon cancer tissue types. Establishment of this analysis strategy has offered the promise of advancing microarray technology as a means of deciphering the involved genetic complexities of complex diseases.