A new approach to species determination for yeast strains: DNA microarray-based comparative genomic hybridization using a yeast DNA microarray with 6000 genes

DNA-DNA hybridization is known as the superior method in the elucidation of relationships between closely related taxa, such as species and strain. For species determination we propose a new DNA-DNA hybridization method: the DNA microarray-based comparative genomic hybridization (CGH) method, using a yeast DNA microarray with approximately 6000 genes. The genome from a yeast strain as a sample strain (Sample) was labelled with Cy3-dye and hybridized to a single DNA microarray, together with the Cy5-labelled genome of S. cerevisiae S288C as a reference strain (Reference). The log2 ratio values [log2[Cy3(Sample)/Cy5(Reference)]: Ratio] of signal intensities of all the gene spots were estimated and divided into the following groups: Ratio < or = -1; -1 < Ratio < 1; 1 < or = Ratio. The hybridization profiles of the genomes of type strains belonging to the genus Saccharomyces were significantly different from that of S. cerevisiae S288C. The Ratio-based grouping allowed us to discriminate between some species from S. cerevisiae more clearly. Furthermore, cluster analysis discriminated between closely related species and strains. Using this method, we were able to not only perform species determination but also to obtain information on alternation in gene copy number of such gene amplifications and deletions with single-gene resolution. These observations indicated that DNA microarray-based CGH is a powerful system for species determination and comparative genome analysis.     

Identification of genes whose expressions are enhanced or reduced in baker's yeast during fed-batch culture process using molasses medium by DNA microarray analysis

Genes whose expression levels are enhanced or reduced during the cultivation process that uses cane molasses in baker's yeast production were identified in this study. The results showed that baker's yeast grown in molasses medium had higher fermentation ability and stress tolerance compared with baker's yeast grown in synthetic medium. Molasses apparently provided not only sugar as a carbon source but also provided functional components that enhanced or reduced expression of genes involved in fermentation ability and stress tolerance. To identify the genes whose expression is enhanced or reduced during cultivation in molasses medium, DNA microarray analysis was then used to compare the gene expression profile of cells grown in molasses with that of cells grown in synthetic medium. To simulate the commercial baker's yeast production process, cells were cultivated using a fed-batch culture system. In molasses medium, genes involved in the synthesis or uptake of vitamins (e.g., biotin, pyridoxine and thiamine) showed enhanced expression, suggesting that vitamin concentrations in molasses medium were lower than those in synthetic medium. Genes involved in formate dehydrogenase and maltose assimilation showed enhanced expression in molasses medium. In contrast, genes involved in iron utilization (e.g., siderophore, iron transporter and ferroxidase) showed enhanced expression in synthetic medium, suggesting that iron starvation occurred. The genes involved in the metabolism of amino acids also showed enhanced expression in synthetic medium. This identification of genes provides information that will help improve the baker's yeast production process.     

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission yeast. The microarray contains DNA fragments, PCR-amplified from a genomic DNA template, that represent > 99% of the 5000 or so annotated fission yeast genes, as well as a number of control sequences. The GenomePRIDE software used attempts to design similarly sized DNA fragments corresponding to gene regions within single exons, near the 3'-end of genes that lack homology to other fission yeast genes. To validate the design and utility of the array, we studied expression changes after a 2 h temperature shift from 25 degrees C to 36 degrees C, conditions widely used when studying temperature-sensitive mutants. Obligingly, the vast majority of genes do not change more than two-fold, supporting the widely held view that temperature-shift experiments specifically reveal phenotypes associated with temperature-sensitive mutants. However, we did identify a small group of genes that showed a reproducible change in expression. Importantly, most of these corresponded to previously characterized heat-shock genes, whose expression has been reported to change after more extreme temperature shifts than those used here. We conclude that the DNA microarray represents a useful resource for fission yeast researchers as well as the broader yeast community, since it will facilitate comparison with the distantly related budding yeast, Saccharomyces cerevisiae. To maximize the utility of this resource, the array and its component parts are fully described in On-line Supplementary Information and are also available commercially.     

DNA microarray analysis suggests that zinc pyrithione causes iron starvation to the yeast Saccharomyces cerevisiae

Zinc pyrithione has been used in anti-dandruff shampoos and in anti-fouling paint on ships. However, little is known of its mode of action. We characterized the effects of sub-lethal concentrations of zinc pyrithione (Zpt) on Saccharomyces cerevisiae using DNA microarrays. The majority of the strongly upregulated genes are related to iron transport, and many of the strongly downregulated genes are related to the biosynthesis of cytochrome (heme). These data suggest that Zpt induces severe iron starvation. To confirm the DNA microarray data, we supplemented cultures containing Zpt with iron, and the growth of the yeast was restored significantly. From these results, we propose that the principal toxicity of zinc pyrithione arises from iron starvation.     

Molecular cloning of verrucosidin-producing Penicillium polonicum genes by differential screening to obtain a DNA probe

A differential molecular screening procedure was developed to obtain DNA clones enriched for verrucosidin-related genes that could be used as DNA probes to detect verrucosidin-producing Penicillium polonicum. Permissive and nonpermissive conditions for verrucosidin production were selected to obtain differentiated poly (A)+ RNA for the cloning strategy. P. polonicum yielded the highest amount of verrucosidin when cultured in malt extract broth at 25 degrees C without shaking. These conditions were selected as verrucosidin permissive conditions. When shaking was applied to the verrucosidin permissive conditions, verrucosidin was not detected. Approximately 5000 transformants were obtained for the library of DNA fragments from verrucosidin-producing P. polonicum and hybridized with cDNA probes obtained from poly (A)+ RNA of permissive and nonpermissive conditions. A total of 120 clones hybridized only with the permissive cDNA probes. From these, eight representative DNA inserts selected on the basis of size and labelled with fluorescein-dUTP were assayed as DNA probes in the second differential screening by Northern hybridization. Probe SVr1 gave a strong hybridization signal selectively with poly (A)+ RNAs from high verrucosidin production. When this probe was assayed by dot blot hybridization with DNA of different moulds species, hybridization was detected only with DNA from the verrucosidin-producing strain. The strategy used in this work has proved to be useful to detect unknown genes related to mycotoxins. In addition, the DNA probe obtained should be considered for the detection of verrucosidin-producing moulds.     

Classification of heavy-metal toxicity by human DNA microarray analysis

Microarray technology is proving to be a useful tool to classify undefined environmental toxicants, to investigate underlying mechanisms of toxicity, and to identify candidate toxicant-specific genetic markers by examining global effects of putative toxicants on gene expression profiles. The aim of this study was to evaluate the toxicities of six heavy metals through the comparison with gene expression patterns induced by well-known chemicals. For this purpose, we first identified the genes altered specifically in HepG2 under the exposure of 2,3-dimethoxy-1,4-naphthoquinone (DMNQ), phenol, and N-nitrosodimethylamine (DMN), which were selected as the model chemicals, using DNA microarray. On the basis of the expression profiles of these genes, toxicities of six heavy metals, arsenic, cadmium, nickel, antimony, mercury, and chromium, were evaluated. The specific gene alteration and hierarchical clustering revealed that biological action of six heavy metals was clearly related to that of DMNQ which has been reported to be a reactive oxygen species (ROS) generating chemical and which induced the genes associated with cell proliferative responses. These results suggest that cell proliferative responses which are probably caused by ROS are a major apparent biological action of high-dose heavy metals, supporting the previous reports. Overall, a mechanism-based classification by DNA microarray would be an efficient method for evaluation of toxicities of environmental samples.     

可视化微阵列蛋白芯片法同时检测蜂蜜中3种农药残留

目的建立可视化微阵列蛋白芯片法同时检测蜂蜜中多菌灵、啶虫脒、蝇毒磷3种农药残留含量的分析方法。方法依次向制备好的微孔板芯片里加入50μL标准品工作液和50μL相应的抗体,在25℃、600 r/min下反应30 min;再向每孔中加入50μL纳米银标记的羊抗鼠IgG, 37℃、600 r/min下反应30 min;最后显色并用芯片专用软件(MiELISA)进行自动化分析。结果该方法对多菌灵、啶虫脒、蝇毒磷的定量检测范围分别为0.4~6.4、0.3~4.8、0.75~12 ng/mL,相关系数r>0.99,检测限分别为3.21、2.47、2.52 ng/mL,准确度为83.6%~126.4%,变异系数均<10%,且三者之间具有极低的交叉反应;向不同种类的空白蜂蜜中添加2种不同浓度的标准品时,检测结果具有较高的准确度和重复性。结论本研究建立的可视化微阵列蛋白芯片检测法操作简便,检测限低,准确度、重复性、特异性均很好,且具有高通量、多指标同时检测等优点,适用于蜂蜜中多菌灵、啶虫脒、蝇毒磷3种农药残留同时检测。     

Effects of dissolved carboxylates and carbonates on the adsorption properties of thiuram disulfate pesticides

The adsorption of thiram and disulfiram onto alpha-Al2O3 and montmorillonite clay has been studied in the presence of small carboxylate anions, bicarbonate, formate, and oxalate. At natural concentrations, HCO3- enhances dramatically the adsorption of both pesticides on alpha-Al2O3 and clay. An analogous significant enhancement of pesticide adsorption is also observed in the presence of formate and oxalate. Density functional theory calculations demonstrate that in solution a stable molecular complex between one molecule of thiram and one molecule of HCO3- is formed with interaction energy -35.6 kcal/mol. In addition, two H20 molecules further stabilize it by an interaction energy of -3.6 kcal/mol. This clustering [thiram- HCO3- -2H2O] leads to a change of the electronic structure and the ultraviolet-visible spectrum of thiram that is observed experimentally. Surface complexation modeling shows that the molecular cluster [thiram-HCO3- -2H2O], which bears a total net charge of -1, is responsible for the observed enhanced adsorption on the charged surface of alumina and clay at pH below their points of zero surface charge. The results reveal a novel pervasive role of carboxylate anions and particularly HCO3- on the adsorption of dithiocarbamate pesticides in natural waters.     

Genome-wide survey of non-essential genes required for slowed DNA synthesis-induced filamentous growth in yeast

We recently discovered that slowed DNA synthesis induces filamentous differentiation in S. cerevisiae. We screened the BY yeast deletion strains and identified four classes of non-essential genes that are required for both slowed DNA-induced filamentous growth and classic forms of filamentous growth: (a) genes encoding regulators of the actin cytoskeleton and cell polarity, ABP1, CAP2 and HUF1 (=YOR300W), in addition to the previously known BNI1, BUD2, PEA2, SPA2 and TPM1; (b) genes that are likely involved in cell wall biosynthesis, ECM25, GAS1 and PRS3; (c) genes encoding possible regulators of protein secretion, SEC66, RPL21A and RPL34B; (d) genes encoding factors for normal mitochondrial function, IML1 and UGO1. These results showed that pseudohyphal formation involves not the only previously known regulation of the actin cytoskeleton/cell polarity but also regulation of cell wall synthesis, protein secretion and mitochondrial function. Identification of multiple classes of genes that are required for both slowed DNA synthesis-induced and classic forms of filamentous growth confirms that slowed DNA synthesis-induced filamentous growth is bone fide filamentous differentiation.     

Effects of phleomycin-induced DNA damage on the fission yeast Schizosaccharomyces pombe cell cycle

The effect of phleomycin, a bleomycin-like antibiotic, has been investigated in the fission yeast, Schizosaccharomyces pombe. We report that in response to phleomycin-induced DNA damage, growth was inhibited and S. pombe cells arrested in the G2-phase of the cell cycle. DNA repair mutants rad9 and rad17 did not arrest and were hypersensitive to phleomycin. Cell cycle mutants that entered mitosis without monitoring the completion of DNA replication also displayed an increased sensitivity to this DNA-damaging agent. Thus, phleomycin could be used as a tool in the fission yeast S. pombe model system for the study of DNA damage and cell cycle checkpoints, or as a new selective agent.     

Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches

Changes in the expression of genes were used to elucidate the metabolic pathways and regulatory mechanisms that respond to environmental or genetic modifications. Results from previously published chemostat datasets were merged with novel data generated in the present study. ORFs displaying significant changes in expression that correlated with those of other ORFs were analysed using GO mapping tools and supplemented by literature information. The strategy developed was used to propose annotations for ORFs of unknown function. The following ORFs were assigned functions as a result of this study: YMR090w, YGL157w, YGR243w, YLR327c, YER121w, YFR017c, YGR067c, YKL187c, YGR236c (SPG1), YMR107w (SPG4), YMR206w, YER067w, YJL103c, YNL175C (NOP13) YJL200C, YDL070C (FMP16) and YGR173W.     

DNA microarray based detection of genes involved in safety and technologically relevant properties of food associated coagulase-negative staphylococci

Aim of the work was to design a polynucleotide based DNA microarray as screening tool to detect genes in food associated coagulase-negative staphylococci (CNS). A focus was laid on genes with potential health concern and technological relevance. The microarray contained 220 probes for genes encoding antibiotic resistances, hemolysins, toxins, amino acid decarboxylases (e.g. biogenic amine formation), binding proteins to extracellular matrix (ECM), lipases, proteases, stress response factors, or nitrate dissimilation. Hybridization of genomic DNA isolated from 32 phenotypically characterized CNS permitted to detect numerous genes, corresponding with the phenotype. However, numerous hybridization signals were obtained for genes without any detectable phenotype. The antibiotic resistance genes blaZ, lnuA, and tetK involved in ?-lactam, lincomycin and tetracycline resistance, respectively, were rarely identified in CNS, however, all species contained some strains with such resistance genes. Decarboxylase genes involved in biogenic amine formation were detected regularly in Staphylococcus carnosus, S. condimenti, S. piscifermentans and S. equorum, but was rarely correlated with the phenotype. The same applied for the fibrinogen (clf) and fibronectin (fbp) binding protein genes, whose phenotype (binding assay) was only correlated in S. equorum and Staphylococcus succinus. Although some CNS showed hemolytic activity and enterotoxin production (Immunoblot) the corresponding genes could not be verified. Technological relevant genes such as proteases or lipases revealed good hybridization signals. In addition, genes involved in nitrate dissimilation (nre, nar, nir), catalase (kat), or superoxide dismutase (sod) were well detected. Interestingly, genes involved in dissimilatory nitrate reduction were more prevalent in strains of S. carnosus, S. condimenti and S. piscifermentans than of S. equorum, S. succinus and S. xylosus.     

利用基因芯片筛选烤烟早花基因初探

为研究与烟草早花有关的基因,本试验利用安捷伦烟草全基因组基因芯片对烤烟品种K326 及其抗早花变异系华烟06、K326LF 花芽分化过程茎尖端基因表达谱进行分析,筛选出其中与花芽分化可能有主要关系的基因:AGL20、CCR2、ELF4、ERD7、CBF1、COR413-PM1、EMF2、VIP4、COL1、AGL17、COL9、FPA、SWN 等,其中COL2、ELF4 的表达差异达到了5倍;AGL62、CBF1、SWN、NAP 与FPA 的差异大于或等于10 倍。该试验可为进一步研究烟草抗早花机理及培育抗早花新品种提供参考。      

气相色谱-高分辨质谱法定性筛查小麦面粉中农药残留

目的 开发和验证用于小麦面粉中农药残留定性筛查的气相高分辨质谱联用方法。方法 小麦面粉样品在乙腈和柠檬酸缓冲液中混匀,加入硫酸镁和氯化钠进行盐析,混匀静置后完成液液萃取。随后上清液经过N-丙基乙二胺和碳十八官能团净化除去杂质,硫酸镁去除水分。再经过氮吹浓缩,进样气相色谱飞行时间质谱进行分析,以全扫描模式进行数据采集。最后通过高分辨质谱数据库比对和质谱工作站的自动积分完成筛查工作。结果 气相色谱飞行时间质谱提供了全面准确的离子扫描结果,当截断值为20%,400种农药都能在4 μg/kg的水平下得到正确的筛查结果,其中假阴性和假阳性率都低于5%。结论 该方法实现了高通量的农药残留筛查,结果准确,适用于小麦面粉样品中的挥发性,半挥发性农药残留的多组分筛查。     

桔子果酒酵母的分离筛选

从腐烂桔子中分离得到35株酿酒酵母,从中筛选出3株发酵性能较优良的菌株.编号为F16菌株在发酵性能及桔子酒的品质方面,总体表现最优,可作为桔子酒发酵用菌种或桔子酒专用菌种选育的出发菌株.     

气相色谱高分辨飞行时间质谱法快速筛查水果中283种农药残留

目的建立气相色谱高分辨飞行时间质谱法(gas chromatography time-of-flight mass spectrometry,GC-TOF/MS)快速筛查水果中283种农药残留量的分析方法。方法利用气相色谱高分辨飞行时间质谱结合MassHunter、PCDL软件建立283种农药的EI精确质量谱库,试样经QuEChERS方法进行萃取净化后,采用EI全扫描监测,通过PCDL谱库全离子筛查模式检索,以保留时间、特征离子精确质量数、分子离子同位素信息等作为定性依据。由谱库选择质量数较大、丰度比较高的精确质量离子为定量离子,进行定量测定。结果在空白苹果、葡萄、橙3种水果中添加10、20、40μg/kg 3个浓度水平下,方法的平均回收率65.9%～129.1%,相对标准偏差(relative standard deviation,RSD)2.8%～11.6%,方法的最低检出浓度可达0.5～10μg/kg。结论该方法简便、快速、灵敏、精密度好,是水果中常见农药残留有效快速筛查技术。     

农药残留快速检测用酶——胆碱酯酶的筛选

在常见易得的前提下,以猪血、鸡血、鸭血、链鱼和鸡肝为实验材料提取胆碱酯酶,通过比较不同来源、不同动物组织胆碱酯酶的活性,并进行了胆碱酯酶对常见农药的敏感性实验,结果表明:鸭血清BChE酶含量丰富、对常见的有机磷农药及氨基甲酸酯类农药较敏感、且来源广泛、廉价易得。可作为果蔬农药残留的快速检测用酶。     

气相色谱-质谱法快速筛查食物中毒中15种农药残留

目的 建立食物中毒后15种农药残留快速定性及半定量的气相色谱-质谱法（gas chromatography-mass spectrometry,GC-MS）。 方法 呕吐物、血液分别采用乙腈、乙酸乙酯溶剂超声萃取,提取液经分散固相萃取法净化,上清液氮吹浓缩至１mL,通过气相色谱-质谱法检测分析。并进行方法学验证。结果 15种农药在0.1~3.0 μg/mL浓度范围内线性关系良好,相关系数为0.992~0.998,检出限为0.001~0.005 μg/mL,样品在0.5、1.0、2.0 μg/mL 3 个加标水平下的平均回收率为73.2% ~ 96.6%,相对标准偏差为1.7 % ~9.4 %。结论 本方法操作过程简便、快速,重复性和准确性较好,适用于食物中毒事件中呕吐物及血液样品中多种农药的检测。     

QuEChERS-三重四极杆液相色谱质谱联用法快速筛查花生中52种农药残留

目的 基于QuEChERS 前处理方法,建立了HPLC-MS/MS快速筛查花生中52种农药残留的筛选和确认。方法 样品经0.1%甲酸乙腈提取,提取液经MgSO4、PSA和C18净化后,采用Waters C18(100 mm×2.1 mm×1.7 μm)色谱柱分离,在三重四级杆正离子反应监测（MRM）测定,基质标准曲线结合外标法定量。结果52种农药在0.001μg/mL~0.1μg/mL范围内线性良好,相关系数均大于0.998,方法的定量限（LOQ）1.0~5.0μg/Kg,通过实际样品加标回收试验,52种农药在10μg/Kg的加标回收率为76.6%~107.6%,相对标准偏差（RSD）为3.5%~12.3%,结论 该方法适用于花生中农药残留的筛查检测及定量分析。