Morphological Instabilities in a Growing Yeast Colony: Experiment and Theory

Sams, Thomas; Sneppen, Kim; Jensen, Mogens H.; Ellegaard, C.; Christensen, Bjørn Eggert; Thrane, Ulf

doi:10.1103/physrevlett.79.313

Cited by 33 publications

(30 citation statements)

References 25 publications

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“…Recently, López and Jensen [36] introduced a class of models for the growth of colonial organisms, such as fungi and bacteria. The models are motivated by recent experiments [37] with the yeast Pichia membranaefaciens on solidified agarose film. Depending on the concentration of polluting metabolites, different front morphologies were observed.…”

Section: Models For Fungal Growthmentioning

confidence: 99%

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Nonequilibrium critical behavior in unidirectionally coupled stochastic processes

Goldschmidt

Hinrichsen

Howard³

et al. 1999

Phys. Rev. E

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Phase transitions from an active into an absorbing, inactive state are generically described by the critical exponents of directed percolation (DP), with upper critical dimension d(c)=4. In the framework of single-species reaction-diffusion systems, this universality class is realized by the combined processes A-->A+A, A+A-->A, and A-->0. We study a hierarchy of such DP processes for particle species A,B,..., unidirectionally coupled via the reactions A-->B, ...(with rates mu(AB),...). When the DP critical points at all levels coincide, multicritical behavior emerges, with density exponents beta(i) which are markedly reduced at each hierarchy level i> or =2. This scenario can be understood on the basis of the mean-field rate equations, which yield beta(i)=1/2(i-1) at the multicritical point. Using field-theoretic renormalization-group techniques in d=4-epsilon dimensions, we identify a new crossover exponent phi, and compute phi=1+O(epsilon(2)) in the multicritical regime (for small mu(AB)) of the second hierarchy level. In the active phase, we calculate the fluctuation correction to the density exponent on the second hierarchy level, beta(2)=1/2-epsilon/8+O(epsilon(2)). Outside the multicritical region, we discuss the crossover to ordinary DP behavior, with the density exponent beta(1)=1-epsilon/6+O(epsilon(2)). Monte Carlo simulations are then employed to confirm the crossover scenario, and to determine the values for the new scaling exponents in dimensions d< or =3, including the critical initial slip exponent. Our theory is connected to specific classes of growth processes and to certain cellular automata, and the above ideas are also applied to unidirectionally coupled pair annihilation processes. We also discuss some technical as well as conceptual problems of the loop expansion, and suggest some possible interpretations of these difficulties.

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Section: Models For Fungal Growthmentioning

confidence: 99%

“…However, random sequential updates seem to be a more appropriate description of the experiments in Ref. [37], since realistic cells do not divide synchronously. Therefore it is still unclear to what extent the roughening transition of the model in Ref.…”

Section: Models For Fungal Growthmentioning

confidence: 99%

Nonequilibrium critical behavior in unidirectionally coupled stochastic processes

Goldschmidt

Hinrichsen

Howard³

et al. 1999

Phys. Rev. E

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“…Agarose is agar that has been purified to remove agaropectin (a poorly defined, complex polysaccharide with sulfate or pyruvate side groups) (16). It has been used as a microbial substrate (19)(20)(21)(22) but is much more commonly used as a matrix for gel electrophoresis (23). Noble agar is a bleached and washed derivative of agar, resulting in a whiter gel (24), and is occasionally used as a growth substrate (25,26).…”

mentioning

confidence: 99%

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

Jaeger

McElfresh

Wong

et al. 2015

Appl Environ Microbiol

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c Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. Single-cell organisms such as bacteria and yeasts have been used extensively to study genes and genome organization, proteins and protein interactions, biological pathways, and cellular structure and to address numerous other fundamental biological questions (1, 2). Many microbes, especially the species Escherichia coli and Saccharomyces cerevisiae, combine numerous beneficial properties that make them ideal model organisms: easy laboratory cultivation, easy genetic manipulation, short generation time, and safe handling. Microbial cultures can be maintained in liquid growth medium or on solid/semisolid gel substrates (3). Liquid colony maintenance allows the microbial cultures to expand rapidly and is used in screens that rely on optical density measurements to extract kinetic growth parameters or use downstream liquid-based assays such as flow cytometry or high-throughput microscopy (4-7). While throughput in liquid is generally bound to a maximum of 96 or 384 samples per plate, solid-substrate colony maintenance has the advantage that individual cell clones can be readily separated and that colony parameters such as color, shape, structure, and size can be extracted easily using digital image acquisition (8-10). Additionally, advances in robotic pinning devices allow for much higher throughput on solid substrate, with close to 25,000 colonies possible on a single microtiter footprintsized gel plate (11). This much higher density has led to solidsubstrate screening being the method of choice for many current high-throughput applications (12)(13)(14).Historically, agar has been the predominant gelling agent in microbial research. Agar is a mixture of polysaccharides f...

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“…These petals can potentially structure the colony by allowing it to concentrate growth to specific zones or form channels for nutrient excess and metabolite removal. A detailed analysis of this and more complex morphologies in giant yeast colonies has revealed that the likely determinants of the ultimate shape assumed include the nutrient and metabolite concentrations, the mechanical interaction with the underlying substratum, and potentially secreted ligands (Sams, 1997;A. Levchenko, unpublished results).…”

Section: From Cell Regulation Network To Cell -Cell Communication Nementioning

confidence: 99%

Dynamical and integrative cell signaling: challenges for the new biology

Levchenko

2003

Biotech & Bioengineering

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Years of careful experimental analysis have revealed that signaling molecules are organized into complex networks of biochemical reactions exquisitely regulated in time and space to provide a cell with highfidelity information about an extremely noisy and volatile environment. A new view of signaling networks as systems consisting of multiple complex elements interacting in a multifarious fashion is emerging, a view that conflicts with the single-gene or protein-centric approach common in biological research. The postgenomic era has brought about a different, network-centric methodology of analysis, suddenly forcing researchers toward the opposite extreme of complexity, where the networks being explored are, to a certain extent, intractable and uninterpretable. Both the cartoons of simple pathways and the very large ''hair-ball'' diagrams of large intracellular networks are also representations of static worlds, superficially devoid of dynamics and chemistry. These representations are often viewed as being analogous to stably linked computer and neural networks rather than dynamically changing networks of chemical interactions, where the notions of concentration, compartmentalization, and diffusion may be the primary determinants of connectivity. Arguably, the systems biology approach, relying on computational modeling coupled with various experimental techniques and methodologies, will be an essential component of analysis of the behavior of signal transduction pathways. Combining the dynamical view of rapidly evolving responses and the structural view arising from high-throughput analyses of the interacting species will be the best approach toward efforts toward greater understanding of intracellular signaling processes. B

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Morphological Instabilities in a Growing Yeast Colony: Experiment and Theory

Cited by 33 publications

References 25 publications

Nonequilibrium critical behavior in unidirectionally coupled stochastic processes

Nonequilibrium critical behavior in unidirectionally coupled stochastic processes

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

Dynamical and integrative cell signaling: challenges for the new biology

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