Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries

Background

Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences.

Results

Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research.

Conclusion

GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.     

Effect of starving and dowex 50 treatment on growth of normal and x-irradiated yeast

1. Effects of starvation or treatment with a cation exchange resin, dowex 50, parallel in some respects those seen earlier on the respiration and fermentation of bakers' yeast receiving 90,000 r of 250 kv. x-rays. Starvation increased the radiosensitivity of cell division processes whether measured by colony formation or by turbidimetric determination of growth in a liquid medium. The dowex 50 enhanced the radiation effect by the latter measure but appeared to increase colony formation of irradiated yeast. 2. The effects on growth differ from those on respiration and fermentation in that the exchange resin treatment did not inhibit colony formation further, and neither starvation nor resin appreciably altered the growth of non-irradiated yeast. 3. Two effects of radiation are seen in these experiments: (a) a permanent inhibition of growth, and (b) a temporary inhibition of the remaining cells resulting in delay of growth. 4. The irradiated cell is more dependent on certain aspects of its environment in terms of growth responses as well as in terms of metabolism (i.e. respiration and fermentation). Whether or not potassium plays a role in the growth response as it does in the metabolic response cannot be ascertained from the present data.     

The amoebal cell of Physarum polycephalum: colony formation and growth.

Two stages of colony growth were observed during microscopic studies of Physarum polycephalum amoebae. During the first stage, “spreading growth,” the colony is composed of dispersed single cells. During the second stage, “aggregate growth,” most of the active cells in a colony are aggregated in a ring at the colony boundary. Measurements of cell movement as a function of bacterial concentration indicate that, during both spreading and aggregate growth, cell movements are not affected by changes in bacterial concentration but that the transition from spreading to aggregate growth occurs earlier on plates with lower bacterial concentrations. These results indicate that autonomous characteristics of the amoebae are more important for the determination of colony form than local variations in the concentrations of nutrients.The genetic determination of colony form is demonstrated by the existence of mutants that display specific alterations in colony morphology. Because the aggregate rings of these mutants move at an increased rate, mutant clones appear as variant sectors of wild-type colonies. The increased rate of mutant ring movement suggests that this selection method may be a useful technique for isolating mutant myxamoebae with defects in movement and behavior.     

A method for radioprotective effect evaluation

The method here proposed is based on the prevention of photodynamic yeast cell damage by substances possessing radioprotective activity.The photodynamic yeast inactivation was achieved with Toluidine Blue as the photosensitizer and white exciting light. The model radioprotectors tested, namely, WR2721 [S-2(3-aminopropylamino)ethylphosphorothioic acid] and AET [2-aminoethylisothiouronium bromide], were applied at concentrations ranging from 0 to 200 mg/L. Under the conditions of photodynamic damage WR2721 and AET demonstrated a protective effect as evaluated by the enhancement of the cell survival and colony formation. The protection achieved by AET was more effective. The dependence of the protective effect on the concentration of both agents was linear in the low concentrations range.Experiments with radioprotective preparations of yeast origin demonstrated a similar relationship between the concentration and cell survival.These results indicate that the prevention of the photodynamic yeast cell damage by radioprotectors can find an application as a method for determination of radioprotective effects demonstrated by biotechnologically obtained substances in the course of their production and purification.     

Mouse polyomavirus large T antigen inhibits cell growth and alters cell and colony morphology in Saccharomyces cerevisiae

The gene for mouse polyomavirus large tumor (LT) antigen, a potent oncoprotein, was expressed in Saccharomyces cerevisiae from the inducible GAL1 promoter. Substantial cell growth inhibition as well as colony and cell morphology changes dependent on cyclic adenosine monophosphate (cAMP) were observed. In contrast to cell and colony morphology alterations, the growth inhibition appeared to be transient, thus indicating the existence of an active adaptation of yeast cells to the LT antigen presence.     

Extracting information on the evolution of living- and dead-cell fractions of Salmonella Typhimurium colonies in gelatin gels based on microscopic images and plate-count data

Aims:  The aim of this study was to extract information on cell number and colony volume dynamics of Salmonella Typhimurium colonies.
Methods and Results:  Both cell number and colony volume of Salmonella Typhimurium in gelatin were monitored during the exponential and the stationary phase with varying pH and water activity, by plate counts and microscopic image analysis respectively. The exponential growth rates of cell numbers and colony volumes were correlated. The exponential growth rate of cell numbers was estimated based on this correlation and a secondary model that describes the effect of pH and water activity on the growth rate of the colony volumes. During the stationary phase, the cell number was constant, while colony volume increased, thus indicating the formation of a dead fraction. Models were developed to describe the living and dead population.
Conclusions:  By comparing colony volumes and cell numbers, the formation of dead fraction can be noticed from the beginning of the stationary phase, which indicates that the stationary phase is a dynamic – including both cell death and cell growth – rather than a static phase.
Significance and Impact of the Study:  This study was the first to investigate the proportion of living and dead bacteria within a stationary colony quantitatively.     

Direct identification of pure Penicillium species using image analysis

This paper presents a method for direct identification of fungal species solely by means of digital image analysis of colonies as seen after growth on a standard medium. The method described is completely automated and hence objective once digital images of the reference fungi have been established. Using a digital image it is possible to extract precise information from the surface of the fungal colony. This includes color distribution, colony dimensions and texture measurements. For fungal identification, this is normally done by visual observation that often results in a very subjective data recording. Isolates of nine different species of the genus Penicillium have been selected for the purpose. After incubation for 7 days, the fungal colonies are digitized using a very accurate digital camera. Prior to the image analysis each image is corrected for self-illumination, thereby gaining a set of directly corresponding images with respect to illumination. A Windows application has been developed to locate the position and size of up to three colonies in the digitized image. Using the estimated positions and sizes of the colonies, a number of relevant features can be extracted for further analysis. The method used to determine the position of the colonies will be covered as well as the feature selection. The texture measurements of colonies of the nine species were analyzed and a clustering of the data into the correct species was confirmed. This indicates that it is indeed possible to identify a given colony merely by macromorphological features. A classifier (in the normal distribution) based on measurements of 151 colonies incubated on yeast extract sucrose agar (YES) was used to discriminate between the species. This resulted in a correct classification rate of 100% when used on the training set and 96% using cross-validation. The same methods applied to 194 colonies incubated on Czapek yeast extract agar (CYA) resulted in a correct classification rate of 98% on the training set and 71% using cross-validation.     

Rapid determination of plasmid-carrying yeast cells by using an imaging sensor system

A novel imaging sensor system for the determination of plasmid carrying yeast cells was developed. The sensor system consisted of an Silicon Intensifier Target (SIT) video camera, a fluorescent microscope, and a personal computer system equipped with an image memory board. This system was based on the fact that the membrane integrity of only plasmid-carrying cells is lost following cell growth in 5-fluoro-orotic acid (5-FOA) containing medium, and consequently these target cell can be stained with fluorescent probes and detected. In this study, plasmid-carrying cells were detected and their fraction determined in a mixture of both plasmid-carring and plasmid-free cells. A good correlation was observed between the values determined by this sensor system and the conventional method in the 30%-80% range, and one assay was possible within 4 h. This sensor system could be used for the monitoring of plasmid-carrying fraction in recombinant yeast cells during cultivation.     

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.     

A simple and rapid method for screening transformant yeast colonies using PCR.

A simple and rapid procedure for screening transformant yeast colonies is described. In this method, a trace amount of plasmid DNA is isolated from a small amount of yeast cell mass; then, the presence of the exogenous DNA in each yeast colony is detected by PCR amplification.     

<Emphasis Type="Italic">ScreenMill</Emphasis>: A freely available software suite for growth measurement,analysis and visualization of high-throughput screen data

Background  

Many high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data points, making data analysis a time consuming and painstaking process. Here we describe ScreenMill, a new software suite that automates image analysis and simplifies data review and analysis for high-throughput biological experiments.     

渗透剂对酿酒酵母生长的影响及其模型分析

考察了Saccharomyces cerevisiae FL1酵母菌株在固体平板上的生长动力学过程及2种渗透剂对不同生理阶段的酵母细胞增殖行为的影响．建立了一个数学模型,该模型可以预测固体培养过程中生物量随时间的变化情况,结果表明,模型预测值与实际值能够很好符合,将该模型应用于考察氯化钠和甘油对细胞增殖行为的影响,结果揭示,氯化钠显著抑制指数生长期和平衡期细胞分裂,降低酵母比生长速率和生物量;甘油对平衡期细胞增殖有促进作用,提高比生长速率和生物量;甘油与氯化钠之间存在协同作用,0．15M甘油不能减弱高盐的应激作用。     

Analysis of synchronous photon emissions from the bacterium Photobacterium phosphoreum during colony formation from a single cell

Light emission from Photobacterium phosphoreum was analysed during cell growth on an agar plate from a single cell to colony formation. Temporal analysis of image intensified light was set so that a quadratic window covered a single cell. Intensity of light emission from a single cell through colony formation showed an initial decrease, a prolonged lag phase, and then a rapid increase. These responses on an agar plate were similar to those from liquid cultures. The image analysis showed repeated bursts of light emission in the phases when light was increasing and decreasing. Statistical analysis of light emission also emphasized the presence of bursts of light emission, suggesting the metabolic synchronism of luciferase reactions in either a single cell or synchronously divided cells. The repetitive bursts of light occurred in a single cell and continued during the growth phase in which the cell population and the light emission was increasing. In a single cell, however, periodicity of light emission was not defined directly from fast Fourier transformation, although it was indicated on oscillation of mean level of fluctuated light emission, at initial phase of culture on agar plate.     

The effect of sodium chloride concentration and pH on the growth of Salmonella typhimurium colonies on solid medium

The growth of Salmonella typhimurium colonies on a model food system (agar solidified culture medium) was followed. Colony radius, determined using computer image analysis (IA) techniques, and viable cell number per colony were measured as indices of colony growth, and the effect of [NaCl] (0.5–3.5% (w/v)) and pH (7.0–5.0) on colony growth at 30°C was observed; colonies were point inoculated from serial dilutions. Colony growth (between 13 and 26 h after inoculation) was linear when expressed in terms of radius, and exponential when expressed in terms of viable cell number per colony. Overall, both increasing the [NaCl] and decreasing the pH had little effect on colony growth, other than to delay the onset of linear radial growth. Initial specific growth rate (μ) ranged from 0.73 to 0.87 h⁻¹. Thin films of agar medium on microscope slides allowed the growth of microcolonies to be observed after just 4 h incubation. A greater understanding of the growth kinetics of bacterial colonies, and the effects of environment on such data, may enable better control of foodborne bacterial pathogens, and consequently an improvement in food product safety.     

Application of an automated colony counter for evaluation of the viability of a yeast culture

Application of an automated colony counter for evaluation of the viability of microbial cultures was investigated with yeast cultures as a model. Statistical comparison of the results of automated and visual (“manual”) colony counting is presented, as well as the results of the application of the bundled software to digital images obtained by light microscopy for determination of the cell concentration in suspensions. Automated counting is concluded to significantly accelerate the evaluation of culture viability by colony-forming capacity, provided that a certain requirements of sample preparation and analysis are observed.     

大丽轮枝菌VdSCH9基因的功能研究

大丽轮枝菌是一种土传性植物病原真菌,可侵染多种植物并引发黄萎病。目前,人们关于大丽轮枝菌的侵染和致病机制的了解还很不深入。本文通过敲除大丽轮枝菌编码丝氨酸/苏氨酸的蛋白激酶基因VdSCH9,阐明了其在大丽轮枝菌生长发育及致病过程中的作用。SCH9基因在酵母中的表达与cAMP-PKA途径和TOR信号通路相关,对酵母的生长、压力响应和寿命等有重要作用。大丽轮枝菌VdSCH9敲除突变体的生长速率显著下降,菌落边缘菌丝更为稀疏,菌丝分枝减少,对棉花植株为害的平均病情指数为56.6,显著低于野生型和互补突变体的平均病情指数90.5和82.8,对茄子植株为害的平均病情指数为65.9,也显著低于野生型和互补突变体的平均病情指数91.1和89.8。另外,敲除突变体对于高渗透压、氧化还原压力、细胞膜和细胞壁完整性等压力条件的敏感性增强。因此,VdSCH9对于大丽轮枝菌的生长、压力响应及致病力均有重要作用。     

Mathematical modeling of regulatory mechanisms in yeast colony development

In the present study, yeast colony development serves as a model system to study growth of fungal populations with negligible nutrient and signal transport within the mycelium. Mathematical simulations address the question whether colony development is governed by diffusional limitation of nutrients. A hybrid one-dimensional cellular automaton model was developed that describes growth of discrete cells based upon microscopic interaction rules in a continuous field of nutrient and messenger. The model is scaled for the geometry of the experimental setup, cell size, growth- and substrate uptake rates. Therefore, calculated cell density profiles and nutrient distributions can be compared to experimental results and the model assumptions can be verified. In the physiologically relevant parameter range, simulations show an exponentially declining cell density along the median axis of the colonies in case of a diffusion limited growth scenario. These results are in good agreement with cell density profiles obtained in cultivations of the yeast Candida boidinii with glucose as the limiting carbon source but stand in contrast to the constant cell density profile estimated for Yarrowia lipolytica grown under the same conditions. While from the comparison of experimental results and simulations a diffusion limited growth mechanism is proposed for glucose limited C. boidinii colonies, this hypothesis is rejected for the growth of Y. lipolytica. As an alternative, a quorum sensing model was developed that can explain the evolution of constant cell density profiles based on the effect of a not further characterized unstable or volatile messenger.     

On the suitability of gelatin for plate cultures. II

Summary In continuation of our investigation into the factors which determine the suitability of gelatin for colony formation it was demonstrated that surface tension lowering substances added in small concentrations to plate media prepared with a poor gelatin have a decidedly favourable effect. Especially Tweens were examined. An addition of 0.01% Tween 60 or 80 to the gelatin media was sufficient to bring about growth of typical lobated colonies of bothBacterium coli andFlavobacterium aquatile. In none of the experiments made did the Tweens, in the low concentrations applied, exhibit any toxic effect. No direct method for the determination of the surface tension of gels being available, we resorted to the determination of the wettability of the various gelatin gels. With the aid of this method it was found that the contact angle of water droplets on 10% gelatin gels correlated satisfactory with colony appearance. It seems probable that gelatins of good quality contain some constituent which increases the wettability of the gel. Finally it was shown that addition of Tweens to agar gels produces analogous effects on colony growth.     

A novel concentration and viability detection method for <Emphasis Type="Italic">Brettanomyces</Emphasis> using the Cellometer image cytometry

Brettanomyces spp. can present unique cell morphologies comprised of excessive pseudohyphae and budding, leading to difficulties in enumerating cells. The current cell counting methods include manual counting of methylene blue-stained yeasts or measuring optical densities using a spectrophotometer. However, manual counting can be time-consuming and has high operator-dependent variations due to subjectivity. Optical density measurement can also introduce uncertainties where instead of individual cells counted, an average of a cell population is measured. In contrast, by utilizing the fluorescence capability of an image cytometer to detect acridine orange and propidium iodide viability dyes, individual cell nuclei can be counted directly in the pseudohyphae chains, which can improve the accuracy and efficiency of cell counting, as well as eliminating the subjectivity from manual counting. In this work, two experiments were performed to demonstrate the capability of Cellometer image cytometer to monitor Brettanomyces concentrations, viabilities, and budding/pseudohyphae percentages. First, a yeast propagation experiment was conducted to optimize software counting parameters for monitoring the growth of Brettanomyces clausenii, Brettanomyces bruxellensis, and Brettanomyces lambicus, which showed increasing cell concentrations, and varying pseudohyphae percentages. The pseudohyphae formed during propagation were counted either as multiple nuclei or a single multi-nuclei organism, where the results of counting the yeast as a single multi-nuclei organism were directly compared to manual counting. Second, a yeast fermentation experiment was conducted to demonstrate that the proposed image cytometric analysis method can monitor the growth pattern of B. lambicus and B. clausenii during beer fermentation. The results from both experiments displayed different growth patterns, viability, and budding/pseudohyphae percentages for each Brettanomyces species. The proposed Cellometer image cytometry method can improve efficiency and eliminate operator-dependent variations of cell counting compared with the traditional methods, which can potentially improve the quality of beverage products employing Brettanomyces yeasts.