Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies

The top-view, two-dimensional spatial patterning of non-uniform growth in a Saccharomyces cerevisiae yeast colony is considered. Experimental images are processed to obtain data sets that provide spatial information on the cell-area that is occupied by the colony. A method is developed that allows for the analysis of the spatial distribution with three metrics. The growth of the colony is quantified in both the radial direction from the centre of the colony and in the angular direction in a prescribed outer region of the colony. It is shown that during the period of 100–200 hours from the start of the growth of the colony there is an increasing amount of non-uniform growth. The statistical framework outlined in this work provides a platform for comparative quantitative assays of strain-specific mechanisms, with potential implementation in inferencing algorithms used for parameter-rate estimation.     

鸟氨酸脱羧酶抗酶抑制因子-1高表达抑制黑素瘤细胞在小鼠体内的生长

鸟氨酸脱羧酶抗酶抑制因子-1(ornithine decarboxylase antienzyme inhibitor-1,OAZI-1)是细胞内调节多胺代谢的重要蛋白质因子。已有研究发现,OAZI-1高表达的黑素瘤细胞在体外能更有效地被抗原提呈细胞识别和吞噬,提示OAZI-1在肿瘤免疫治疗中具有潜在的应用价值。为进一步分析OAZI-1高表达对黑素瘤细胞在小鼠体内生长的影响,高表达OAZI-1的黑素瘤细胞(B16/OAZI-1)被接种到实验小鼠体内,结果发现,接种瘤出现先成瘤随后逐渐消退的现象,至第24 d时,接种瘤的平均体积为36±25 mm3~,而对照细胞接种瘤的平均体积为326±309 mm~3。为探索上述现象的机制,随后分析了B16/OAZI-1在小鼠体内诱导的抗肿瘤免疫效应,结果发现:1)B16/OAZI-1接种显著增加了小鼠脾脏细胞对B16-F1瘤细胞的杀伤活性;2)源于B16-F1的细胞抗原能更有效地促进B16/OAZI-1接种小鼠脾脏细胞的增殖;3)B16/OAZI-1接种小鼠的脾脏细胞具有更强的分泌IFN-γ的能力;4)当在预接种B16/OAZI-1 30 d后的小鼠体内再次接种B16-F1活细胞时,新接种瘤细胞的生长受到显著抑制,小鼠的存活率增加。上述研究结果提示,高表达OAZI-1的黑素瘤细胞在实验动物体内的生长受到显著抑制,其机制可能与OAZI-1能促进肿瘤抗原提呈和诱导抗肿瘤免疫效应相关。     

High-throughput Yeast Plasmid Overexpression Screen

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, including those with direct relevance to human disease. Because of its short generation time and well-characterized genome, a major experimental advantage of the yeast model system is the ability to perform genetic screens to identify genes and pathways that are involved in a given process. Over the last thirty years such genetic screens have been used to elucidate the cell cycle, secretory pathway, and many more highly conserved aspects of eukaryotic cell biology ^1-5. In the last few years, several genomewide libraries of yeast strains and plasmids have been generated ^6-10. These collections now allow for the systematic interrogation of gene function using gain- and loss-of-function approaches ^11-16. Here we provide a detailed protocol for the use of a high-throughput yeast transformation protocol with a liquid handling robot to perform a plasmid overexpression screen, using an arrayed library of 5,500 yeast plasmids. We have been using these screens to identify genetic modifiers of toxicity associated with the accumulation of aggregation-prone human neurodegenerative disease proteins. The methods presented here are readily adaptable to the study of other cellular phenotypes of interest.Download video file.^{(52M, mov)}     

Effects of GPD1 Overexpression in Saccharomyces cerevisiae Commercial Wine Yeast Strains Lacking ALD6 Genes

The utilization of Saccharomyces cerevisiae strains overproducing glycerol and with a reduced ethanol yield is a potentially valuable strategy for producing wine with decreased ethanol content. However, glycerol overproduction is accompanied by acetate accumulation. In this study, we evaluated the effects of the overexpression of GPD1, coding for glycerol-3-phosphate dehydrogenase, in three commercial wine yeast strains in which the two copies of ALD6 encoding the NADP⁺-dependent Mg²⁺-activated cytosolic acetaldehyde dehydrogenase have been deleted. Under wine fermentation conditions, the engineered industrial strains exhibit fermentation performance and growth properties similar to those of the wild type. Acetate was produced at concentrations similar to that of the wild-type strains, whereas sugar was efficiently diverted to glycerol. The ethanol yield of the GPD1 ald6 industrial strains was 15 to 20% lower than that in the controls. However, these strains accumulated acetoin at considerable levels due to inefficient reduction to 2,3-butanediol. Due to the low taste and odor thresholds of acetoin and its negative sensorial impact on wine, novel engineering strategies will be required for a proper adjustment of the metabolites at the acetaldehyde branch point.     

Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

Reversible phosphorylation is one of the major mechanisms of signal transduction, and signaling networks are critical regulators of cell growth and development. However, few of these networks have been delineated completely. Towards this end, quantitative phosphoproteomics is emerging as a useful tool enabling large-scale determination of relative phosphorylation levels. However, phosphoproteomics differs from classical proteomics by a more extensive sampling limitation due to the limited number of detectable sites per protein. Here, we propose a comprehensive quantitative analysis pipeline customized for phosphoproteome data from interventional experiments for identifying key proteins in specific pathways, discovering the protein-protein interactions and inferring the signaling network. We also made an effort to partially compensate for the missing value problem, a chronic issue for proteomics studies. The dataset used for this study was generated using SILAC (Stable Isotope Labeling with Amino acids in Cell culture) technique with interventional experiments (kinase-dead mutations). The major components of the pipeline include phosphopeptide meta-analysis, correlation network analysis and causal relationship discovery. We have successfully applied our pipeline to interventional experiments identifying phosphorylation events underlying the transition to a filamentous growth form in Saccharomyces cerevisiae. We identified 5 high-confidence proteins from meta-analysis, and 19 hub proteins from correlation analysis (Pbi2p and Hsp42p were identified by both analyses). All these proteins are involved in stress responses. Nine of them have direct or indirect evidence of involvement in filamentous growth. In addition, we tested four of our predicted proteins, Nth1p, Pbi2p, Pdr12p and Rcn2p, by interventional phenotypic experiments and all of them present differential invasive growth, providing prospective validation of our approach. This comprehensive pipeline presents a systematic way for discovering signaling networks using interventional phosphoproteome data and can suggest candidate proteins for further investigation. We anticipate the methodology to be applicable as well to other interventional studies via different experimental platforms.     

Tissue Distribution,Gender- and Genotype-Dependent Expression of Autophagy-Related Genes in Avian Species

As a result of the genetic selection of broiler (meat-type breeders) chickens for enhanced growth rate and lower feed conversion ratio, it has become necessary to restrict feed intake. When broilers are fed ad libitum, they would become obese and suffer from several health-related problems. A vital adaptation to starvation is autophagy, a self-eating mechanism for recycling cellular constituents. The autophagy pathway has witnessed dramatic growth in the last few years and extensively studied in yeast and mammals however, there is a paucity of information in avian (non-mammalian) species. Here we characterized several genes involved in autophagosome initiation and elongation in Red Jungle fowl (Gallus gallus) and Japanese quail (coturnix coturnix Japonica). Both complexes are ubiquitously expressed in chicken and quail tissues (liver, leg and breast muscle, brain, gizzard, intestine, heart, lung, kidney, adipose tissue, ovary and testis). Alignment analysis showed high similarity (50.7 to 91.5%) between chicken autophagy-related genes and their mammalian orthologs. Phylogenetic analysis demonstrated that the evolutionary relationship between autophagy genes is consistent with the consensus view of vertebrate evolution. Interestingly, the expression of autophagy-related genes is tissue- and gender- dependent. Furthermore, using two experimental male quail lines divergently selected over 40 generations for low (resistant, R) or high (sensitive, S) stress response, we found that the expression of most studied genes are higher in R compared to S line. Together our results indicate that the autophagy pathway is a key molecular signature exhibited gender specific differences and likely plays an important role in response to stress in avian species.     

Capric Acid Secreted by S. boulardii Inhibits C. albicans Filamentous Growth,Adhesion and Biofilm Formation

Candidiasis are life-threatening systemic fungal diseases, especially of gastro intestinal track, skin and mucous membranes lining various body cavities like the nostrils, the mouth, the lips, the eyelids, the ears or the genital area. Due to increasing resistance of candidiasis to existing drugs, it is very important to look for new strategies helping the treatment of such fungal diseases. One promising strategy is the use of the probiotic microorganisms, which when administered in adequate amounts confer a health benefit. Such a probiotic microorganism is yeast Saccharomyces boulardii, a close relative of baker yeast. Saccharomyces boulardii cells and their extract affect the virulence factors of the important human fungal pathogen C. albicans, its hyphae formation, adhesion and biofilm development. Extract prepared from S. boulardii culture filtrate was fractionated and GC-MS analysis showed that the active fraction contained, apart from 2-phenylethanol, caproic, caprylic and capric acid whose presence was confirmed by ESI-MS analysis. Biological activity was tested on C. albicans using extract and pure identified compounds. Our study demonstrated that this probiotic yeast secretes into the medium active compounds reducing candidal virulence factors. The chief compound inhibiting filamentous C. albicans growth comparably to S. boulardii extract was capric acid, which is thus responsible for inhibition of hyphae formation. It also reduced candidal adhesion and biofilm formation, though three times less than the extract, which thus contains other factors suppressing C. albicans adherence. The expression profile of selected genes associated with C. albicans virulence by real-time PCR showed a reduced expression of HWP1, INO1 and CSH1 genes in C. albicans cells treated with capric acid and S. boulardii extract. Hence capric acid secreted by S. boulardii is responsible for inhibition of C. albicans filamentation and partially also adhesion and biofilm formation.     

Construction of a Gal1-Regulated Yeast Cdna Expression Library and Its Application to the Identification of Genes Whose Overexpression Causes Lethality in Yeast

We have constructed a galactose-inducible expression library by cloning yeast cDNAs unidirectionally under control of the GAL1 promoter in a centromeric shuttle vector. Eleven independent libraries were made each with an average size of about 1 x 10(6) clones, about 50 times larger than the reported mRNA population in a yeast cell. From this library, LEU2 and HIS3 cDNAs were recovered at a frequency of about 1 in 10(4) and in 12 out of 13 cases these were expressed in a galactose-dependent manner. Sequence analysis of leu2 and his3 complementing cDNAs indicates that they contain all the coding sequence and much of the 5' untranslated region. To test the utility of the library for the identification of genes whose overexpression confers a specific phenotype, we screened 25,000 yeast transformants for lethality on galactose. Among 15 clones that showed galactose inducible lethality were cDNAs encoding structural proteins, including ACT1 (actin), TUB2 (beta-tubulin) and ABP1 (actin-binding protein 1), and genes in signal transduction pathways, including TPK1 (a cAMP-dependent protein kinase) and GLC7 (type 1 protein phosphatase). cDNAs overexpressing NHPB (nonhistone protein B) and NSR1 (nuclear sequence recognition protein) were also found to be lethal. Among these, ACT1 was isolated four times, and NSR1 three times. The useful features of this library for cDNA cloning in yeast by complementation, and for the identification of genes whose over-expression confers specific phenotypes, are discussed.     

SIRT3过表达通过调控细胞代谢转换抑制肾肿瘤细胞的增殖

目的:研究SIRT3对肾透明细胞癌(clear cell renal cell carcinoma, ccRCC)769-P细胞增殖和抗氧化能力的影响,并进一步探究其作用机制。方法:在769-P细胞的基础上构建SIRT3过表达稳转细胞系;利用CCK-8试剂检测769-P SIRT3过表达细胞的增殖速度;利用CellROX~Deep Red染料并结合流式细胞分析检测SIRT3过表达对769-P细胞中ROS水平的影响;利用定量蛋白质组学和代谢组学的方法,探究SIRT3对769-P细胞的作用机制。结果:CCK-8实验结果表明,769-P SIRT3过表达细胞的生长速度与对照细胞相比下降了约48%;定量蛋白质组学分析显示,769-P SIRT3过表达细胞中ALDOA、ALDOA、ENO2、PKM、LDHA、LDHB表达量下调约0.4至0.7倍,SDHB和CS上调约1.3倍;代谢组学分析显示,PEP、pyruvic acid、lactate、carnitine水平下降约0.4至0.7倍,isocitric acid和acetyl-CoA水平升高分别约1.3和2.8倍;分析还显示SIRT3过表达上调SOD2、TXN、GPX4和GLRX5的表达量约1.3至2倍,降低ROS水平约40%,增强细胞对过氧化氢的耐受力。结论:SIRT3过表达引起769-P细胞的代谢转换,从而抑制其增殖;且上调769-P细胞中抗氧化酶的表达,降低ROS水平,增强细胞的抗氧化能力。     

Platinum-Induced Filamentous Growth in Escherichia coli

Certain group VIIIB transition metal compounds were found to inhibit cell division in Escherichia coli, causing marked filamentous growth. Gram-negative bacilli were the most sensitive to this effect, whereas gram-positive bacilli responded only at near-toxic levels of the metal. None of the cocci tested showed any apparent effect. Cytokinesis (cross-septation) can be initiated by removal or decrease of platinum, but not by treatment with pantoyl lactone, divalent cations, or a temperature of 42 C.     

Regulation of G2/M Progression by the STE Mitogen-activated Protein Kinase Pathway in Budding Yeast Filamentous Growth

Inoculation of diploid budding yeast onto nitrogen-poor agar media stimulates a MAPK pathway to promote filamentous growth. Characteristics of filamentous cells include a specific pattern of gene expression, elongated cell shape, polar budding pattern, persistent attachment to the mother cell, and a distinct cell cycle characterized by cell size control at G2/M. Although a requirement for MAPK signaling in filamentous gene expression is well established, the role of this pathway in the regulation of morphogenesis and the cell cycle remains obscure. We find that ectopic activation of the MAPK signal pathway induces a cell cycle shift to G2/M coordinately with other changes characteristic of filamentous growth. These effects are abrogated by overexpression of the yeast mitotic cyclins Clb1 and Clb2. In turn, yeast deficient for Clb2 or carrying cdc28-1N, an allele of CDK defective for mitotic functions, display enhanced filamentous differentiation and supersensitivity to the MAPK signal. Importantly, activation of Swe1-mediated inhibitory phosphorylation of Thr-18 and/or Tyr-19 of Cdc28 is not required for the MAPK pathway to affect the G2/M delay. Mutants expressing a nonphosphorylatable mutant Cdc28 or deficient for Swe1 exhibit low-nitrogen-dependent filamentous growth and are further induced by an ectopic MAPK signal. We infer that the MAPK pathway promotes filamentous growth by a novel mechanism that inhibits mitotic cyclin/CDK complexes and thereby modulates cell shape, budding pattern, and cell-cell connections.     

Factors Affecting Filamentous Growth of Sphaerotilus natans

Filamentous growth in cultures of Sphaerotilus natans can be measured and compared with total growth by a standardized procedure of winding filaments around an inoculating needle. Filaments and residual growth are then separately washed on Millipore filters, dried, and weighed. This method has been used to study changes in the growth habit of S. natans elicited by changes in the concentration of nutrients in the medium. The concentration of peptone, in a medium containing a sugar, phosphate buffer, and inorganic salts, has a much greater effect on the proportion of filamentous growth than does the nature or concentration of the carbon source or the concentration of phosphate buffer. Filament formation is significantly inhibited by concentrations of peptone greater than 0.25%; further increases in peptone concentration stimulate the production of large amounts of capsular material. Increasing the concentration of phosphate buffer to 0.05 M almost completely inhibits growth of S. natans.     

Filamentous Growth of Mucor rouxii Under Nitrogen

The form of growth of Mucor rouxii (National Regional Research Laboratory 1894) under nitrogen is dependent on inoculum size. With a large inoculum (10⁶ spores inoculated per ml), the morphology consists mainly of swollen spores with some filaments and yeastlike cells. At lower inoculum levels growth is filamentous. The morphology of this strain on incubation under nitrogen and the dependence of the form of growth on inoculum size are similar to those found previously for other strains of M. rouxii.     

过表达RBP4抑制体外培养的猪前体脂肪细胞分化

为研究视黄醇结合蛋白4(retinol binding protein 4,RBP4)对猪前体脂肪细胞分化的影响,实验构建了RBP4重组腺病毒表达载体,包装并感染猪前体细胞,采用油红O染色和Real-time PCR等方法,检测了过表达RBP4对成脂分化的作用. 研究结果显示,重组腺病毒RBP4载体构建成功,转染猪前体脂肪细胞后,使RBP4的mRNA水平和蛋白水平分别增加了约400倍和20倍. 过表达RBP4能减少脂肪细胞的脂质积累,降低成脂关键基因过氧化物酶体增生物激活受体γ (peroxisome proliferator-activated receptor gamma, PPARγ)和脂肪酸结合蛋白2 (adipocyte protein 2, aP2)的表达. 结果表明,RBP4对猪前体脂肪细胞分化有抑制作用,为进一步研究RBP4对猪前体脂肪细胞分化的作用机制奠定基础.     

过表达miR-455抑制宫颈癌细胞SiHa的生长

研究表明,microRNA(miRNA)可作为癌基因或抑癌基因发挥功能、调控细胞增殖和凋亡等生物学行为,与肿瘤的发生发展密切相关. 在本研究中,我们检测了miR- 455在宫颈癌组织中的表达变化及其对宫颈癌SiHa细胞生物学功能的影响. Real- time PCR实验结果显示,miR-455在宫颈癌组织样本中较正常宫颈组织表达明显降低. 瞬时转染miR-455 mimics使其在SiHa细胞中过表达. CCK-8及流式细胞术分析显示, 过表达miR-455明显抑制细胞增殖,促进细胞凋亡,导致细胞G1/S期阻滞. Real- time PCR分析显示,PI3KR1,BCL2L2 mRNA明显降低.上述研究结果表明, miR-455可显著降低SiHa细胞存活能力,是一个潜在的抑癌基因.     

Bacterial Overexpression of Putative Yeast Mitochondrial Transport Proteins

Thirty-two genes have been identified within the genome of the yeast Saccharomyces cerevisiae which putatively encode mitochondrial transport proteins. We have attempted to overexpress a subset of these genes, namely those which encode mitochondrial transporters of unknown function, and have succeeded in overexpressing 19 of these genes. The overexpressed proteins were then isolated and tested for five well-characterized reconstituted transport activities (i.e., the transport of citrate, dicarboxylates, pyruvate, camitine, and aspartate). Utilizing this approach, we have clearly identified the yeast mitochondrial dicarboxylate transport protein, as well as two additional lower-magnitude transport functions (i.e., tricarboxylate and dicarboxylate transport activities). The implications of these results and the considerations relevant to this approach are discussed.     

丝状真菌瑞氏木霉外源基因表达系统的构建

采用PCR技术体外扩增获得了瑞氏木霉外切葡聚糖纤维二糖水解酶Ⅰ (CBHⅠ )启动子和终止子序列 .并以大肠杆菌质粒pUC1 9为骨架 ,在该启动子和终止子序列间加入多克隆位点 ,构建了瑞氏木霉强表达整合型载体pTRIL .以质粒pAN7 1为模板 ,体外扩增了带有潮霉素磷酸转移酶(hph)基因的DNA片段 ,将hph插入pTRIL的cbh1启动子和终止子序列之间 ,构建了Pcbh1 hph Tcbh1表达盒 .用此表达盒转化瑞氏木霉C30原生质体 ,在潮霉素平板上得到 1 5株抗性转化子 .对其中的H1转化子进行了PCR和Southern印迹分析 ,证实hph基因确实整合到转化子染色体DNA上 ,并在Pcbh1 启动子控制下进行高效表达 .转化子H1对潮霉素抗性达 1 5 0mg L ,比出发菌株提高 2倍 .瑞氏木霉强表达整合型载体pTRIL的构建成功为开展瑞氏木霉分子生物学研究以及进一步的工程菌株构建工作奠定了基础     

RAN1基因过表达抑制嗜热四膜虫大核无丝分裂

Ran GTPase通过RanGTP/RanGDP循环的形式,参与调控多种细胞增殖方式：包括有丝分裂和减数分裂.敲减RAN1基因可导致嗜热四膜虫大核内微管组装紊乱,从而抑制大核无丝分裂.为进一步分析Ran1在无丝分裂中的功能,本研究将野生型Ran1以及模拟GTP（Ran1Q70L）和GDP（Ran1T25N）锁定形式的Ran1突变体在嗜热四膜虫中过量表达,均导致四膜虫细胞增殖速率下降,并引起大核无丝分裂异常,且这种核异常细胞比率与Ran1过表达量呈正相关.免疫荧光定位结果显示,过表达的HA-Ran1在整个细胞中弥散分布,破坏了正常的Ran1分布形式;而过表达的HA-Ran1Q70L明显集中在大核核膜和胞质中,HA-Ran1T25N则主要定位在大核和小核内,分别与Ran1GTP/Ran1GDP循环的辅助调节因子定位模式一致.以上结果表明,过表达Ran1及其突变体可能影响嗜热四膜虫细胞中正常的Ran1GTP/Ran1GDP循环,进而导致大核无 丝分裂异常.