Dual Fluorochrome Flow Cytometric Assessment of Yeast Viability

A novel staining protocol is reported for the assessment of viability in yeast, specifically the biocontrol yeast, Pichia anomala. Employing both the red fluorescent membrane potential sensitive oxonol stain DiBAC₄(5) (Bis-(1,3-dibutylbarbituric acid)pentamethine oxonol), a structural analog of the commonly used DiBAC₄(3) (Bis-(1,3-dibutylbarbituric acid)trimethine oxonol), with one of the esterase dependent green fluorogenic probes such as CFDA-AM (5-Carboxyfluorescein diacetate, acetoxymethyl ester) or Calcein-AM (Calcein acetoxymethyl ester), a two-color flow cytometric method was developed, which yields rapid quantitative information on the vitality and vigor of yeast cell cultures. The method was validated by cell sorting and analysis of live, heat killed, and UV-treated yeast.     

Aptamer Selection Express: A Novel Method for Rapid Single-Step Selection and Sensing of Aptamers

Here we describe a new DNA capture element (DCE) sensing system, based on the quenching and dequenching of a double-stranded aptamer. This system shows very good sensitivity and thermal stability. While quenching, dequenching, and separating the DCE systems made from different aptamers (all selected by SELEX), an alternative method to rapidly select aptamers was developed—the Aptamer Selection Express (ASExp). This process has been used to select aptamers against different types of targets (Bacillus anthracis spores, Bacillus thuringiensis spores, MS-2 bacteriophage, ovalbumin, and botulinum neurotoxin). The DCE systems made from botulinum neurotoxin aptamers selected by ASExp have been investigated. The results of this investigation indicate that ASExp can be used to rapidly select aptamers for the DCE sensing system.     

Improved Flow Cytometric Analysis of the Budding Yeast Cell Cycle

The budding yeast, Saccharomyces cerevisiae has been a remarkably useful model system for the study of eukaryotic cell cycle regulation. Flow cytometric analysis of DNA content in budding yeast has become a standard tool for the analysis of cell cycle progression. However, popular protocols utilizing the DNA binding dye, propidium iodide, suffer from a number of drawbacks that confound accurate analysis by flow cytometry. Here we show the utility of the DNA binding dye, SYTOX Green, in the cell cycle analysis of yeast. Samples analyzed using SYTOX Green exhibited better coefficients of variation, improved linearity between DNA content and fluorescence, and decreased peak drift associated with changes in dye concentration, growth conditions or cell size.

Key Words:

Flow cytometry, Cell cycle, Saccharomyces cerevisiae, SYTOX Green, Propidium iodide     

Selection of Ethanol-Tolerant Yeast Hybrids in pH-Regulated Continuous Culture

Hybrids between naturally occurring wine yeast strains and laboratory strains were formed as a method of increasing genetic variability to improve the ethanol tolerance of yeast strains. The hybrids were subjected to competition experiments under continuous culture controlled by pH with increasing ethanol concentrations over a wide range to select the fastest-growing strain at any concentration of ethanol. The continuous culture system was obtained by controlling the dilution rate of a chemostat connected to a pH-meter. The nutrient pump of the chemostat was switched on and off in response to the pH of the culture, which was thereby kept near a critical value (pH_c). Under these conditions, when the medium was supplemented with ethanol, the ethanol concentration of the culture increased with each pulse of dilution. A hybrid strain was selected by this procedure that was more tolerant than any of the highly ethanol-tolerant wine yeast strains at any concentration of ethanol and was able to grow at up to 16% (vol/vol) ethanol. This improvement in ethanol tolerance led to an increase in both the ethanol production rate and the total amount of ethanol produced.     

A Rapid Method for Protein Extraction from Fission Yeast

Researchers working with fission yeast conduct protein extraction widely and frequently, but this includes the handling of glass beads, and hence is laborious and cumbersome, especially when dealing with a large number of samples. Here we describe a rapid and reliable method for preparing protein extract from fission yeast, one which is applicable to routine western blotting.     

A Rapid Chromosome-Mapping Method for Cloned Fragments of Yeast DNA

A rapid and generally applicable method is described for mapping a cloned yeast DNA segment to the chromosome(s) from which it originated. The method is based upon the recent finding that the integration into a yeast chromosome of a segment of the 2 mu plasmid DNA results, in heterozygous diploids, in the specific loss of genetic information from the chromosome into which the 2 mu DNA was integrated (Falco et al. 1982). After verification of the accuracy of the method using several genes whose position was known in advance, the method was used to locate the yeast actin gene, which lies on the left arm of chromosome VI, about 50 cM distal to CDC4.     

A Novel Flow Cytometric Hemozoin Detection Assay for Real-Time Sensitivity Testing of Plasmodium falciparum

Resistance of Plasmodium falciparum to almost all antimalarial drugs, including the first-line treatment with artemisinins, has been described, representing an obvious threat to malaria control. In vitro antimalarial sensitivity testing is crucial to detect and monitor drug resistance. Current assays have been successfully used to detect drug effects on parasites. However, they have some limitations, such as the use of radioactive or expensive reagents or long incubation times. Here we describe a novel assay to detect antimalarial drug effects, based on flow cytometric detection of hemozoin (Hz), which is rapid and does not require any additional reagents. Hz is an optimal parasite maturation indicator since its amount increases as the parasite matures. Due to its physical property of birefringence, Hz depolarizes light, hence it can be detected using optical methods such as flow cytometry. A common flow cytometer was adapted to detect light depolarization caused by Hz. Synchronized in vitro cultures of P. falciparum were incubated for 48 hours with several antimalarial drugs. Analysis of depolarizing events, corresponding to parasitized red blood cells containing Hz, allowed the detection of parasite maturation. Moreover, chloroquine resistance and the inhibitory effect of all antimalarial drugs tested, except for pyrimethamine, could be determined as early as 18 to 24 hours of incubation. At 24 hours incubation, 50% inhibitory concentrations (IC50) were comparable to previously reported values. These results indicate that the reagent-free, real-time Hz detection assay could become a novel assay for the detection of drug effects on Plasmodium falciparum.     

A Novel,Rapid Method to Quantify Intraplatelet Calcium Dynamics by Ratiometric Flow Cytometry

Cytosolic free calcium ions represent important second-messengers in platelets. Therefore, quantitative measurement of intraplatelet calcium provides a popular and very sensitive tool to evaluate platelet activation and reactivity. Current protocols for determination of intracellular calcium concentrations in platelets have a number of limitations. Cuvette-based methods do not allow measurement of calcium flux in complex systems, such as whole blood, and therefore require isolation steps that potentially interfere with platelet activation. Flow cytometry has the potential to overcome this limitation, but to date the application of calibrated, quantitative readout of calcium kinetics has only been described for Indo-1. As excitation of Indo-1 requires a laser in the ultraviolet range, such measurements cannot be performed with a standard flow cytometer. Here, we describe a novel, rapid calibration method for ratiometric calcium measurement in platelets using both Ar⁺-laser excited fluorescence dyes Fluo-4 and Fura Red. We provide appropriate equations that allow rapid quantification of intraplatelet calcium fluxes by measurement of only two standardisation buffers. We demonstrate that this method allows quantitative calcium measurement in platelet rich plasma as well as in whole blood. Further, we show that this method prevents artefacts due to platelet aggregate formation and is therefore an ideal tool to determine basal and agonist induced calcium kinetics.     

利用流式细胞术测定CTL活性方法在EIAV免疫学中的应用

利用PKH 26和CFSE两种荧光染料对靶细胞染色,建立了一种通过流式细胞术进行马传染性贫血症病毒(Equine infectious anemia virus,EIAV)抗原特异性细胞毒性T淋巴细胞(Cytotoxic T lymphocytes,CTL)反应的新方法,避免了经典的Cr51释放法对检测人员的放射线威胁,降低了本底释放,提高了检测的灵敏度.将该检测方法用于检测EIAV疫苗毒接种马和嵌合克隆接种马的细胞免疫反应变化趋势,数据显示细胞免疫反应在接种后3个月达到成熟阶段而后保持在较高的反应水平.该方法的成功建立和应用为研究EIAV减毒疫苗的免疫机制提供了好的研究手段,也为其他病毒的免疫学研究提供了新的参考方法.     

利用流式细胞术测定CTL活性方法在EIAV免疫学中的应用

利用PKH-26和CFSE两种荧光染料对靶细胞染色,建立了一种通过流式细胞术进行马传染性贫血症病毒 (Equine infectious anemia virus,EIAV)抗原特异性细胞毒性T淋巴细胞(Cytotoxic T lymphocytes,CTL)反应的 新方法,避免了经典的Cr51释放法对检测人员的放射线威胁,降低了本底释放,提高了检测的灵敏度。将该检测方 法用于检测EIAV疫苗毒接种马和嵌合克隆接种马的细胞免疫反应变化趋势,数据显示细胞免疫反应在接种后3 个月达到成熟阶段而后保持在较高的反应水平。该方法的成功建立和应用为研究EIAV减毒疫苗的免疫机制提 供了好的研究手段,也为其他病毒的免疫学研究提供了新的参考方法。     

Rapid Method for Measuring Extracellular Water in Yeast Preparations

A rapid procedure for the quantitative determination of extracellular water in bulk bakers' yeast was developed on the basis of the solute dilution principle. A reagent is prepared by synthesizing the diazonium ion of p-aminobenzoic acid and coupling it to peptone. This "azopeptone reagent" permits direct colorimetric measurement, which accounts for the rapidity and simplicity of the test. Potential errors due to osmotic effects are avoided by supplementing the reagent with saline and, more importantly, minimizing the duration of contact between reagent and cells. The new method has acceptable accuracy and precision, and may also be suitable for use with other microorganisms.     

A Novel Flow Cytometric High Throughput Assay for a Systematic Study on Molecular Mechanisms Underlying T Cell Receptor-Mediated Integrin Activation

Lymphocyte function-associated antigen 1 (LFA-1), a member of β2-integrin family, exerts multiple roles in host T cell immunity and has been identified as a useful drug-development target for inflammatory and autoimmune diseases. Applying the findings that primary resting T cells absorb nanometric membrane vesicles derived from antigen presenting cells (APC) via dual receptor/ligand interactions of T cell receptor (TCR) with cognate peptide-major histocompatibility complex (MHC) complex (pMHC) and LFA-1 with its ligand, intercellular adhesion molecule-1 (ICAM-1), and that signaling cascades triggered by TCR/pMHC interaction take a part in the vesicle-absorption, we established a cell-based high throughput assay for systematic investigation, via isolation of small molecules modulating the level of vesicle-absorption, of molecular mechanisms underlying the T cell absorption of APC-derived vesicles, i.e., structural basis of TCR/pMHC and LFA-1/ICAM-1 interactions and TCR-mediated LFA-1 activation. As primary T cells along with physiological ligands expressed in biological membrane are used and also individual cells in assay samples are analyzed by flow cytometry, results obtained using the assay system hold superior physiological and therapeutic relevance as well as statistical precision.     

一种快速筛选酵母高表达菌株的新方法

为建立一种快速筛选酵母高表达菌株的方法,将生长在固体培养基上的新转化的表达菌落原位转移到醋酸纤维素薄膜上,再利用硝酸纤维素薄膜原位捕获醋酸纤维素薄膜上的蛋白,然后用免疫印迹的方法检测原位转印到硝酸纤维素膜上菌落分泌蛋白,根据免疫印迹的强弱进行高表达菌株的筛选。结果显示,经过菌落原位转印和免疫印迹显色,显色信号强的菌落表达量相对较高。因此,双膜法原位检测是一种快速、高效的筛选酵母高表达菌株的方法。     

Flow Cytometric Analysis of Bimolecular Fluorescence Complementation: A High Throughput Quantitative Method to Study Protein-protein Interaction

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC is based on the production of fluorescence using two non-fluorescent fragments of a fluorescent protein (Venus, a Yellow Fluorescent Protein variant, is used here). Non-fluorescent Venus fragments (VN and VC) are fused to two interacting proteins (in this case, AKAP-Lbc and PDE4D3), yielding fluorescence due to VN-AKAP-Lbc-VC-PDE4D3 interaction and the formation of a functional fluorescent protein inside cells.BiFC provides information on the subcellular localization of protein complexes and the strength of protein interactions based on fluorescence intensity. However, BiFC analysis using microscopy to quantify the strength of protein-protein interaction is time-consuming and somewhat subjective due to heterogeneity in protein expression and interaction. By coupling flow cytometric analysis with BiFC methodology, the fluorescent BiFC protein-protein interaction signal can be accurately measured for a large quantity of cells in a short time. Here, we demonstrate an application of this methodology to map regions in PDE4D3 that are required for the interaction with AKAP-Lbc. This high throughput methodology can be applied to screening factors that regulate protein-protein interaction.     

Flow Cytometric Method Using Fluorescent Microspheres to Measure Reticuloendothelial Function or Particulate Translocation

The reticuloendothelial system (RES) influences the outcome of vascular shock and environmental stress. We describe a procedure that employs flow cytometry and 1 μm fluorescent microspheres (FM) to study RES function. FM (2 × 10¹⁰ beads/kg) were administered via a jugular cannula in Sprague-Dawley rats. After 15 min, blood and tissues were collected and digested in 15% KOH. Phycoerythrin 1 μm beads were added to each sample as an internal standard and analyzed by flow cytometry. FM were preferentially cleared by the spleen, liver and lung. Clearance was confirmed by fluorescent photomicroscopy. Addition of the internal standard to determine accurately aspiration volume enhanced precision. This procedure offers advantages over other RES clearance methods including bacterial, radioactive or carbon clearance assays. Moreover, this method could enhance accuracy, reproducibility and speed of data collection in particulate transport studies that are based on manual microscopic scanning and FM counting.     

一种新的cDNA末端快速扩增获取全长cDNA的方法

为克隆精子发生相关基因的全长cDNA,根据mRNA差异显示获得的ESTs设计引物。利用一种新的cDNA末端快速扩增方法（SMART RACE）扩增该EST的5′末端,并进行克隆测序,与cDNA差异显示获得ESTs拼接后,获得了三个新的全长cDNA。结果表明：SMAR RACE是一种简便、有效的克隆cDNA5′末端未知序列的技术。     

A Flow Cytometry Method for Rapid Detection and Enumeration of Total Bacteria in Milk

Application of flow cytometry (FCM) to microbial analysis of milk is hampered by the presence of milk proteins and lipid particles. Here we report on the development of a rapid (≤1-h) FCM assay based on enzymatic clearing of milk to determine total bacteria in milk. When bacteria were added to ultra-heat-treated milk, a good correlation (r ≥ 0.98) between the FCM assay and the more conventional methods of plating and direct microscopic counting was achieved. Raw milk data showed a significant correlation (P < 0.01) and a good agreement (r = 0.91) between FCM and standard plate count methods. The detection limit of the FCM assay was ≤10⁴ bacteria ml of milk⁻¹. This limit is below the level of detection required to satisfy legislation in many countries and states.     

一种简便的适用于酵母双杂交系统的酵母质粒提取方法

目的:建立一种适用于酵母双杂交系统的简便快捷的酵母质粒提取方法。方法:以酿酒酵母为供试材料,用玻璃珠振荡法破除酵母细胞壁,提取酵母总DNA,最后通过电转化大肠杆菌DH10B获得目的质粒。结果:粗提得到的质粒可直接转化DH10B,作为模板用于PCR分析及酵母双杂交后续的序列分析等,大大降低了工作量。结论:该方法简便快捷,经济实用,降低了成本,提高了效率,可以作为一种实验室酵母质粒提取方法。     

A Novel Method Incorporating Gene Ontology Information for Unsupervised Clustering and Feature Selection

Background

Among the primary goals of microarray analysis is the identification of genes that could distinguish between different phenotypes (feature selection). Previous studies indicate that incorporating prior information of the genes'' function could help identify physiologically relevant features. However, current methods that incorporate prior functional information do not provide a relative estimate of the effect of different genes on the biological processes of interest.

Results

Here, we present a method that integrates gene ontology (GO) information and expression data using Bayesian regression mixture models to perform unsupervised clustering of the samples and identify physiologically relevant discriminating features. As a model application, the method was applied to identify the genes that play a role in the cytotoxic responses of human hepatoblastoma cell line (HepG2) to saturated fatty acid (SFA) and tumor necrosis factor (TNF)-α, as compared to the non-toxic response to the unsaturated FFAs (UFA) and TNF-α. Incorporation of prior knowledge led to a better discrimination of the toxic phenotypes from the others. The model identified roles of lysosomal ATPases and adenylate cyclase (AC9) in the toxicity of palmitate. To validate the role of AC in palmitate-treated cells, we measured the intracellular levels of cyclic AMP (cAMP). The cAMP levels were found to be significantly reduced by palmitate treatment and not by the other FFAs, in accordance with the model selection of AC9.

Conclusions

A framework is presented that incorporates prior ontology information, which helped to (a) perform unsupervised clustering of the phenotypes, and (b) identify the genes relevant to each cluster of phenotypes. We demonstrate the proposed framework by applying it to identify physiologically-relevant feature genes that conferred differential toxicity to saturated vs. unsaturated FFAs. The framework can be applied to other problems to efficiently integrate ontology information and expression data in order to identify feature genes.