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Gaizer T, Juhász J, Pillér B, Szakadáti H, Pongor CI, Csikász-Nagy A. Integrative analysis of yeast colony growth. Commun Biol 2024; 7:511. [PMID: 38684888 PMCID: PMC11058853 DOI: 10.1038/s42003-024-06218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Yeast colonies are routinely grown on agar plates in everyday experimental settings to understand basic molecular processes, produce novel drugs, improve health, and so on. Standardized conditions ensure these colonies grow in a reproducible fashion, while in nature microbes are under a constantly changing environment. Here we combine the power of computational simulations and laboratory experiments to investigate the impact of non-standard environmental factors on colony growth. We present the developement and parameterization of a quantitative agent-based model for yeast colony growth to reproduce measurements on colony size and cell number in a colony at non-standard environmental conditions. Specifically, we establish experimental conditions that mimic the effects of humidity changes and nutrient gradients. Our results show how colony growth is affected by moisture changes, nutrient availability, and initial colony inoculation conditions. We show that initial colony spread, not initial cell number have higher impact on the final size and cell number of colonies. Parameters of the model were identified by fitting these experiments and the fitted model gives guidance to establish conditions which enable unlimited growth of yeast colonies.
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Affiliation(s)
- Tünde Gaizer
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
| | - János Juhász
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
- Semmelweis University, Institute of Medical Microbiology, Budapest, Hungary
| | - Bíborka Pillér
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
| | - Helga Szakadáti
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
| | - Csaba I Pongor
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary
| | - Attila Csikász-Nagy
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary.
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2
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Cribb L, Sha R, Yiallourou S, Grima NA, Cavuoto M, Baril AA, Pase MP. Sleep Regularity and Mortality: A Prospective Analysis in the UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.14.23288550. [PMID: 37131603 PMCID: PMC10153326 DOI: 10.1101/2023.04.14.23288550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Background Irregular sleep-wake timing may cause circadian disruption leading to several chronic age-related diseases. We examined the relationship between sleep regularity and risk of all-cause, cardiovascular disease (CVD), and cancer mortality in 88,975 participants from the prospective UK Biobank cohort. Methods The sleep regularity index (SRI) was calculated as the probability of an individual being in the same state (asleep or awake) at any two time points 24 hours apart, averaged over 7-days of accelerometry (range 0-100, with 100 being perfectly regular). The SRI was related to the risk of mortality in time-to-event models. Findings The mean sample age was 62 years (SD, 8), 56% were women, and the median SRI was 60 (SD, 10). There were 3010 deaths during a mean follow-up of 7.1 years. Following adjustments for demographic and clinical variables, we identified a non-linear relationship between the SRI and all-cause mortality hazard (p [global test of spline term] < 0·001). Hazard Ratios, relative to the median SRI, were 1·53 (95% confidence interval [CI]: 1·41, 1·66) for participants with SRI at the 5th percentile (SRI = 41) and 0·90 (95% CI: 0·81, 1·00) for those with SRI at the 95th percentile (SRI = 75), respectively. Findings for CVD mortality and cancer mortality followed a similar pattern. Conclusions Irregular sleep-wake patterns are associated with higher mortality risk. Funding National Health and Medical Research Council of Australia (GTN2009264; GTN1158384), National Institute on Aging (AG062531), Alzheimer's Association (2018-AARG-591358), and the Banting Fellowship Program (#454104).
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Affiliation(s)
- Lachlan Cribb
- Turner Institute for Brain and Mental Health, Monash University, Melbourne Australia
| | - Ramon Sha
- Turner Institute for Brain and Mental Health, Monash University, Melbourne Australia
| | - Stephanie Yiallourou
- Turner Institute for Brain and Mental Health, Monash University, Melbourne Australia
| | - Natalie A Grima
- Turner Institute for Brain and Mental Health, Monash University, Melbourne Australia
| | - Marina Cavuoto
- Turner Institute for Brain and Mental Health, Monash University, Melbourne Australia
- National Ageing Research Institute, Melbourne, Australia
| | - Andree-Ann Baril
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Matthew P Pase
- Turner Institute for Brain and Mental Health, Monash University, Melbourne Australia
- Harvard T.H. Chan School of Public Health, Harvard University, MA, USA
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3
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Palmer BJ, Almgren AS, Johnson CGM, Myers AT, Cannon WR. BMX: Biological modelling and interface exchange. Sci Rep 2023; 13:12235. [PMID: 37507417 PMCID: PMC10382537 DOI: 10.1038/s41598-023-39150-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.
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Affiliation(s)
- Bruce J Palmer
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA
| | - Ann S Almgren
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connah G M Johnson
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA.
| | - Andrew T Myers
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - William R Cannon
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Washington, USA
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4
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Sharma MR, Manjari SR, Agrawal EK, Keshavan P, Koripella RK, Majumdar S, Marcinkiewicz AL, Lin YP, Agrawal RK, Banavali NK. The structure of a hibernating ribosome in a Lyme disease pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.16.537070. [PMID: 37131667 PMCID: PMC10153394 DOI: 10.1101/2023.04.16.537070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The spirochete bacterial pathogen Borrelia ( Borreliella) burgdorferi ( Bbu ) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. We determined the structure of the Bbu 70S ribosome by single particle cryo-electron microscopy (cryo-EM) at a resolution of 2.9 Å, revealing its distinctive features. In contrast to a previous study suggesting that the single hibernation promoting factor protein present in Bbu (bbHPF) may not bind to its ribosome, our structure reveals a clear density for bbHPF bound to the decoding center of the small ribosomal 30S subunit. The 30S subunit has a non-annotated ribosomal protein, bS22, that has been found only in mycobacteria and Bacteroidetes so far. The protein bL38, recently discovered in Bacteroidetes, is also present in the Bbu large 50S ribosomal subunit. The protein bL37, previously seen only in mycobacterial ribosomes, is replaced by an N-terminal α-helical extension of uL30, suggesting that the two bacterial ribosomal proteins uL30 and bL37 may have evolved from one longer uL30 protein. The longer uL30 protein interacts with both the 23S rRNA and the 5S rRNA, is near the peptidyl transferase center (PTC), and could impart greater stability to this region. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energies are predicted for antibiotics, bound to the decoding center or PTC and are in clinical use for Lyme disease, that account for subtle distinctions in antibiotic-binding regions in the Bbu ribosome structure. Besides revealing unanticipated structural and compositional features for the Bbu ribosome, our study thus provides groundwork to enable ribosome-targeted antibiotic design for more effective treatment of Lyme disease.
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5
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Ceriotti G, Borisov SM, Berg JS, de Anna P. Morphology and Size of Bacterial Colonies Control Anoxic Microenvironment Formation in Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17471-17480. [PMID: 36414252 DOI: 10.1021/acs.est.2c05842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial metabolisms using electron acceptors other than oxygen (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and dissolved oxygen (O2) transport by pore water. Such microenvironments allow facultative anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the challenge of directly observing biomass and O2 distributions at the microscale within an opaque sediment matrix. To overcome these limitations, we integrated a microfluidic device with transparent O2 planar optical sensors to measure the temporal behavior of dissolved O2 concentrations and biomass distributions with time-lapse videomicroscopy. Our results reveal that bacterial colony morphology, which is highly variable in flowing porous systems, controls the formation of anoxic microenvironments. We rationalize our observations through a colony-scale Damköhler number comparing dissolved O2 diffusion and a bacterial O2 uptake rate. Our Damköhler number enables us to predict the pore space fraction occupied by anoxic microenvironments in our system for a given bacterial organization.
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Affiliation(s)
- Giulia Ceriotti
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne1015, Switzerland
| | - Sergey M Borisov
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Graz8010, Austria
| | - Jasmine S Berg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne1015, Switzerland
| | - Pietro de Anna
- Institute of Earth Sciences, University of Lausanne, Lausanne1015, Switzerland
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6
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Lin J, Sun H, Dong J. Emergence of sector and spiral patterns from a two-species mutualistic cross-feeding model. PLoS One 2022; 17:e0276268. [PMID: 36260557 PMCID: PMC9581386 DOI: 10.1371/journal.pone.0276268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/04/2022] [Indexed: 11/22/2022] Open
Abstract
The ubiquitous existence of microbial communities marks the importance of understanding how species interact within the community to coexist and their spatial organization. We study a two-species mutualistic cross-feeding model through a stochastic cellular automaton on a square lattice using kinetic Monte Carlo simulation. Our model encapsulates the essential dynamic processes such as cell growth, and nutrient excretion, diffusion and uptake. Focusing on the interplay among nutrient diffusion and individual cell division, we discover three general classes of colony morphology: co-existing sectors, co-existing spirals, and engulfment. When the cross-feeding nutrient is widely available, either through high excretion or fast diffusion, a stable circular colony with alternating species sector emerges. When the consumer cells rely on being spatially close to the producers, we observe a stable spiral. We also see one species being engulfed by the other when species interfaces merge due to stochastic fluctuation. By tuning the diffusion rate and the growth rate, we are able to gain quantitative insights into the structures of the sectors and the spirals.
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Affiliation(s)
- Jiaqi Lin
- Department of Computer Science, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Hui Sun
- Department of Mathematics, California State University, Long Beach, California, United States of America
| | - JiaJia Dong
- Department of Physics & Astronomy, Bucknell University, Lewisburg, Pennsylvania, United States of America
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7
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Hitomi K, Weng J, Ying BW. Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies. Front Microbiol 2022; 13:948657. [PMID: 36081803 PMCID: PMC9448356 DOI: 10.3389/fmicb.2022.948657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Colony growth is a common phenomenon of structured populations dispersed in nature; nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we performed a systematic survey to address the questions of whether and how the spatial distribution of colonies was influenced by the genome and environment. Six Escherichia coli strains carrying either the wild-type or reduced genomes and eight media of varied nutritional richness were used to evaluate the genomic and environmental impacts, respectively. The genome size and nutritional variation contributed to the mean size and total area but not the variation and shape of size distribution of the colonies formed within the identical space and of equivalent spatial density. The spatial analysis by means of the Voronoi diagram found that the Voronoi correlation remained nearly constant in common, in comparison to the Voronoi response decreasing in correlation to genome reduction and nutritional enrichment. Growth analysis at the single colony level revealed positive correlations of the relative growth rate to both the maximal colony size and the Voronoi area, regardless of the genomic and nutritional variety. This result indicated fast growth for the large space assigned and supported homeostasis in the Voronoi correlation. Taken together, the spatial distribution of colonies might benefit efficient clonal growth. Although the mechanisms remain unclear, the findings provide quantitative insights into the genomic and environmental contributions to the growth and distribution of spatially or geographically isolated populations.
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8
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Hydrodynamic Fingering Induced by Gel Film Formation in Miscible Fluid Systems: An Experimental and Mathematical Study. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12105043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hydrodynamic fingering induced by gel formation shares common features with growing biofilms, bacterial colonies, and the instability of a confined chemical garden. Fluid displacement with gel formation is also essential in various engineering applications, including CO2 leakage remediation from storage reservoirs and enhanced oil recovery. We conducted Hele-Shaw cell displacement experiments for a miscible fluid system using skim milk and aqueous citric acid solution. This study aimed to investigate the effects of gel film formation on the fingering instability of a miscible fluid system and develop a mathematical model of the sequential growth of gel film formation at the fingertip. We found that the gel film formation thickens with time, resulting in instability at the interface. A distinctive fingering pattern, resembling tentacles, appears where miscibility is suppressed, and the growth of the finger is localized at the fingertip. The finger width remains constant with increasing flow rate, whereas the number of fingers increases linearly before the fingers merge. The gap width significantly limits the finger width. Finally, a mathematical model of sequential film thickness growth for a bubble-like fingertip structure was developed. This model is based upon the interplay between the diffusion of citric acid through the existing gel film formation and elongation of the fingertip. The model provides an understanding of the fundamental mechanism of the growth of the bubble-like fingertip.
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9
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Bryant AS, Lavrentovich MO. Survival in branching cellular populations. Theor Popul Biol 2022; 144:13-23. [PMID: 35093390 DOI: 10.1016/j.tpb.2022.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/15/2022] [Accepted: 01/15/2022] [Indexed: 10/19/2022]
Abstract
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical model that captures the essential features of the dynamics. Using simulations and analytic approaches, we show that the survival probability of strains within the growing population is sensitive to the branching geometry: Branch bifurcations enhance survival probability due to an overall population growth (i.e., "inflation"), while branch termination and the small effective population size at the growing branch tips increase the probability of strain extinction. We show that the evolutionary dynamics may be captured on a wide range of branch geometries parameterized just by the branch diameter N0 and branching rate b. We find that the survival probability of neutral cell strains is largest at an "optimal" branching rate, which balances the effects of inflation and branch termination. We find that increasing the selective advantage s of the cell strain mitigates the inflationary effect by decreasing the average time at which the mutant cell fate is determined. For sufficiently large selective advantages, the survival probability of the advantageous mutant decreases monotonically with the branching rate.
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Affiliation(s)
- Adam S Bryant
- Department of Physics & Astronomy, University of Tennessee, Knoxville, TN 37966, USA
| | - Maxim O Lavrentovich
- Department of Physics & Astronomy, University of Tennessee, Knoxville, TN 37966, USA.
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10
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Tam AKY, Harding B, Green JEF, Balasuriya S, Binder BJ. Thin-film lubrication model for biofilm expansion under strong adhesion. Phys Rev E 2022; 105:014408. [PMID: 35193209 DOI: 10.1103/physreve.105.014408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
Understanding microbial biofilm growth is important to public health because biofilms are a leading cause of persistent clinical infections. In this paper, we develop a thin-film model for microbial biofilm growth on a solid substratum to which it adheres strongly. We model biofilms as two-phase viscous fluid mixtures of living cells and extracellular fluid. The model explicitly tracks the movement, depletion, and uptake of nutrients and incorporates cell proliferation via a nutrient-dependent source term. Notably, our thin-film reduction is two dimensional and includes the vertical dependence of cell volume fraction. Numerical solutions show that this vertical dependence is weak for biologically feasible parameters, reinforcing results from previous models in which this dependence was neglected. We exploit this weak dependence by writing and solving a simplified one-dimensional model that is computationally more efficient than the full model. We use both the one- and two-dimensional models to predict how model parameters affect expansion speed and biofilm thickness. This analysis reveals that expansion speed depends on cell proliferation, nutrient availability, cell-cell adhesion on the upper surface, and slip on the biofilm-substratum interface. Our numerical solutions provide a means to qualitatively distinguish between the extensional flow and lubrication regimes, and quantitative predictions that can be tested in future experiments.
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Affiliation(s)
- Alexander K Y Tam
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Queensland 4000, Australia
- School of Mathematics and Physics, The University of Queensland, St. Lucia Queensland 4072, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
| | - Brendan Harding
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
| | - J Edward F Green
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
| | - Sanjeeva Balasuriya
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
| | - Benjamin J Binder
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
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11
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Hall R, Charlebois DA. Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology. In Silico Biol 2021; 14:53-69. [PMID: 34924371 PMCID: PMC8842992 DOI: 10.3233/isb-210233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a lattice-based framework to perform spatial-temporal Monte Carlo simulations of budding yeast colonies exposed to different nutrient and magnetic field conditions. The budding patterns of haploid and diploid yeast cells were incorporated into the framework, as well as the filamentous growth that occurs in yeast colonies under nutrient limiting conditions. Simulation of the framework predicted that magnetic fields decrease colony growth rate, solidity, and roundness. Magnetic field simulations further predicted that colony elongation and boundary fluctuations increase in a nutrient- and ploidy-dependent manner. These in-silico predictions are an important step towards understanding the effects of the physico-chemical environment on microbial colonies and for informing bioelectromagnetic experiments on yeast colony biofilms and fungal pathogens.
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Affiliation(s)
- Rebekah Hall
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Daniel A Charlebois
- Department of Physics, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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12
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Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nat Protoc 2021; 16:5030-5082. [PMID: 34635859 PMCID: PMC10824140 DOI: 10.1038/s41596-021-00593-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
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Affiliation(s)
- Ilija Dukovski
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Michael Quintin
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Snorre Sulheim
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kirill S Korolev
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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13
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Kumar A. The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth. Annu Rev Genet 2021; 55:1-21. [PMID: 34280314 DOI: 10.1146/annurev-genet-071719-020249] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic cells are exquisitely responsive to external and internal cues, achieving precise control of seemingly diverse growth processes through a complex interplay of regulatory mechanisms. The budding yeast Saccharomyces cerevisiae provides a fascinating model of cell growth in its stress-responsive transition from planktonic single cells to a filamentous pseudohyphal growth form. During pseudohyphal growth, yeast cells undergo changes in morphology, polarity, and adhesion to form extended and invasive multicellular filaments. This pseudohyphal transition has been studied extensively as a model of conserved signaling pathways regulating cell growth and for its relevance in understanding the pathogenicity of the related opportunistic fungus Candida albicans, wherein filamentous growth is required for virulence. This review highlights the broad gene set enabling yeast pseudohyphal growth, signaling pathways that regulate this process, the role and regulation of proteins conferring cell adhesion, and interesting regulatory mechanisms enabling the pseudohyphal transition. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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14
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Luo N, Wang S, Lu J, Ouyang X, You L. Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa. Mol Syst Biol 2021; 17:e10089. [PMID: 33900031 PMCID: PMC8073002 DOI: 10.15252/msb.202010089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023] Open
Abstract
Branching pattern formation is common in many microbes. Extensive studies have focused on addressing how such patterns emerge from local cell-cell and cell-environment interactions. However, little is known about whether and to what extent these patterns play a physiological role. Here, we consider the colonization of bacteria as an optimization problem to find the colony patterns that maximize colony growth efficiency under different environmental conditions. We demonstrate that Pseudomonas aeruginosa colonies develop branching patterns with characteristics comparable to the prediction of modeling; for example, colonies form thin branches in a nutrient-poor environment. Hence, the formation of branching patterns represents an optimal strategy for the growth of Pseudomonas aeruginosa colonies. The quantitative relationship between colony patterns and growth conditions enables us to develop a coarse-grained model to predict diverse colony patterns under more complex conditions, which we validated experimentally. Our results offer new insights into branching pattern formation as a problem-solving social behavior in microbes and enable fast and accurate predictions of complex spatial patterns in branching colonies.
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Affiliation(s)
- Nan Luo
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
| | - Shangying Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
| | - Jia Lu
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
| | | | - Lingchong You
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Genomic and Computational BiologyDuke UniversityDurhamNCUSA
- Department of Molecular Genetics and MicrobiologyDuke University School of MedicineDurhamNCUSA
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15
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Galdino RV, Benevides CA, Tenório RP. Diffusion maps of Bacillus subtilis biofilms via magnetic resonance imaging highlight a complex network of channels. Colloids Surf B Biointerfaces 2020; 190:110905. [PMID: 32143011 DOI: 10.1016/j.colsurfb.2020.110905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
Bacillus subtilis microorganism when cultivated under chemically-defined conditions developed a biofilm with an unusual pattern of wrinkles on the surface. Some questions were raised about whether there was a special function of these wrinkles for the biofilm itself, since they resembled microchannels that could be involved in the transport of nutrients within the biofilm. Since the diffusion is the main mechanism for nutrient transport to biofilm from the medium, the role of these wrinkled structures in the whole diffusion within the biofilm was investigated using diffusion-weighted magnetic resonance imaging (DW-MRI). Data from these diffusion images was used to generate 2D diffusion maps which highlighted the striking channel features of the biofilm surface. The diffusion maps revealed a network of interconnected channels, with self-diffusion coefficients higher in the microchannels than in other regions of the biofilms. Polar plots made from 2D diffusion maps obtained from the plane of the biofilm show an anisotropy of the diffusion inside the microchannels, with the diffusion higher when along the principal direction of the microchannels. These results agree with the model, that the buckling of the biofilm surface from the B. subtilis creates microchannels that can enhance diffusion throughout the biofilm.
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Affiliation(s)
- Ramon V Galdino
- Centro Regional de Ciências Nucleares do Nordeste, Comissão Nacional de Energia Nuclear, Av. Prof. Luiz Freire, 200, Cidade Universitária, 50740-545 Recife, Pernambuco, Brazil; Agência Pernambucana de Vigilância Sanitária, Secretaria Estadual de Saúde de Pernambuco, Praça Osvaldo Cruz, s/n, Boa Vista, 50050-210 Recife, Pernambuco, Brazil
| | - Clayton A Benevides
- Centro Regional de Ciências Nucleares do Nordeste, Comissão Nacional de Energia Nuclear, Av. Prof. Luiz Freire, 200, Cidade Universitária, 50740-545 Recife, Pernambuco, Brazil
| | - Rômulo P Tenório
- Centro Regional de Ciências Nucleares do Nordeste, Comissão Nacional de Energia Nuclear, Av. Prof. Luiz Freire, 200, Cidade Universitária, 50740-545 Recife, Pernambuco, Brazil.
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16
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Furuichi Y, Yoshimoto S, Inaba T, Nomura N, Hori K. Process Description of an Unconventional Biofilm Formation by Bacterial Cells Autoagglutinating through Sticky, Long, and Peritrichate Nanofibers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2520-2529. [PMID: 31972092 DOI: 10.1021/acs.est.9b06577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this study, we elucidated the formation process of an unconventional biofilm formed by a bacterium autoagglutinating through sticky, long, and peritrichate nanofibers. Understanding the mechanisms of biofilm formation is essential to control microbial behavior and improve environmental biotechnologies. Acinetobacter sp. Tol 5 autoagglutinate through the interaction of the long, peritrichate nanofiber protein AtaA, a trimeric autotransporter adhesin. Using AtaA, without cell growth or extracellular polymeric substances production, Tol 5 cells quickly form an unconventional biofilm. The process forming this unconventional biofilm started with cell-cell interactions, proceeded to cell clumping, and led to the formation of large cell aggregates. The cell-cell interaction was described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory based on a new concept, which considers two independent interactions between two cell bodies and between two AtaA fiber tips forming a discontinuous surface. If cell bodies cannot collide owing to an energy barrier at low ionic strengths but approach within the interactive distance of AtaA fibers, cells can agglutinate through their contact. Cell clumping proceeds following the cluster-cluster aggregation model, and an unconventional biofilm containing void spaces and a fractal nature develops. Understanding its formation process would extend the utilization of various types of biofilms, enhancing environmental biotechnologies.
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Affiliation(s)
- Yoshihide Furuichi
- Department of Biotechnology, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , Aichi 464-8603 , Japan
| | - Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , Aichi 464-8603 , Japan
| | - Tomohiro Inaba
- Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Ibaraki 305-0006 , Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Ibaraki 305-0006 , Japan
- Microbiology Research Center for Sustainability , University of Tsukuba , Tsukuba , Ibaraki 305-8572 , Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , Aichi 464-8603 , Japan
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Tam A, Green JEF, Balasuriya S, Tek EL, Gardner JM, Sundstrom JF, Jiranek V, Binder BJ. A thin-film extensional flow model for biofilm expansion by sliding motility. Proc Math Phys Eng Sci 2019; 475:20190175. [PMID: 31611714 PMCID: PMC6784397 DOI: 10.1098/rspa.2019.0175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/22/2019] [Indexed: 12/17/2022] Open
Abstract
In the presence of glycoproteins, bacterial and yeast biofilms are hypothesized to expand by sliding motility. This involves a sheet of cells spreading as a unit, facilitated by cell proliferation and weak adhesion to the substratum. In this paper, we derive an extensional flow model for biofilm expansion by sliding motility to test this hypothesis. We model the biofilm as a two-phase (living cells and an extracellular matrix) viscous fluid mixture, and model nutrient depletion and uptake from the substratum. Applying the thin-film approximation simplifies the model, and reduces it to one-dimensional axisymmetric form. Comparison with Saccharomyces cerevisiae mat formation experiments reveals good agreement between experimental expansion speed and numerical solutions to the model withO ( 1 ) parameters estimated from experiments. This confirms that sliding motility is a possible mechanism for yeast biofilm expansion. Having established the biological relevance of the model, we then demonstrate how the model parameters affect expansion speed, enabling us to predict biofilm expansion for different experimental conditions. Finally, we show that our model can explain the ridge formation observed in some biofilms. This is especially true if surface tension is low, as hypothesized for sliding motility.
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Affiliation(s)
- Alexander Tam
- School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - J. Edward F. Green
- School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Sanjeeva Balasuriya
- School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ee Lin Tek
- Department of Wine and Food Science, Waite Campus, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Jennifer M. Gardner
- Department of Wine and Food Science, Waite Campus, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Joanna F. Sundstrom
- Department of Wine and Food Science, Waite Campus, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, Waite Campus, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Benjamin J. Binder
- School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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Paul R, Ghosh T, Tang T, Kumar A. Rivalry in Bacillus subtilis colonies: enemy or family? SOFT MATTER 2019; 15:5400-5411. [PMID: 31172158 DOI: 10.1039/c9sm00794f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Two colonies of Bacillus subtilis of identical strains growing adjacent to each other on an agar plate exhibit two distinct types of interactions: they either merge as they grow or demarcation occurs leading to formation of a line of demarcation at the colony fronts. The nature of this interaction depends on the agar concentration in the growth medium and the initial separation between the colonies. When the agar concentration was 0.67% or lower, the two sibling colonies were found to always merge. At 1% or higher concentrations, the colonies formed a demarcation line only when their initial separation was 20 mm or higher. Interactions of a colony with solid structures and liquid drops have indicated that biochemical factors rather than the presence of physical obstacles are responsible for the demarcation line formation. A reaction diffusion model has been formulated to predict if two sibling colonies will form a demarcation line under given agar concentration and initial separation. The model prediction agrees well with experimental findings and generates a dimensionless phase diagram containing merging and demarcation regimes. The phase diagram is in terms of a dimensionless initial separation, d[combining macron], and a dimensionless diffusion coefficient, D[combining macron], of the colonies. The phase boundary between the two interaction regimes can be described by a power law relation between d[combining macron] and D[combining macron].
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Affiliation(s)
- Rajorshi Paul
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada
| | - Tanushree Ghosh
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada
| | - Aloke Kumar
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India.
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Modeling Uniaxial Nonuniform Cell Proliferation. Bull Math Biol 2019; 81:2220-2238. [DOI: 10.1007/s11538-019-00601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
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TAMMiCol: Tool for analysis of the morphology of microbial colonies. PLoS Comput Biol 2018; 14:e1006629. [PMID: 30507938 PMCID: PMC6292648 DOI: 10.1371/journal.pcbi.1006629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/13/2018] [Accepted: 11/08/2018] [Indexed: 01/21/2023] Open
Abstract
Many microbes are studied by examining colony morphology via two-dimensional top-down images. The quantification of such images typically requires each pixel to be labelled as belonging to either the colony or background, producing a binary image. While this may be achieved manually for a single colony, this process is infeasible for large datasets containing thousands of images. The software Tool for Analysis of the Morphology of Microbial Colonies (TAMMiCol) has been developed to efficiently and automatically convert colony images to binary. TAMMiCol exploits the structure of the images to choose a thresholding tolerance and produce a binary image of the colony. The images produced are shown to compare favourably with images processed manually, while TAMMiCol is shown to outperform standard segmentation methods. Multiple images may be imported together for batch processing, while the binary data may be exported as a CSV or MATLAB MAT file for quantification, or analysed using statistics built into the software. Using the in-built statistics, it is found that images produced by TAMMiCol yield values close to those computed from binary images processed manually. Analysis of a new large dataset using TAMMiCol shows that colonies of Saccharomyces cerevisiae reach a maximum level of filamentous growth once the concentration of ammonium sulfate is reduced to 200 μM. TAMMiCol is accessed through a graphical user interface, making it easy to use for those without specialist knowledge of image processing, statistical methods or coding. Many microbes are studied by examining the colony morphology via a two-dimensional top-down image. In order to quantify such images, we typically need to label each pixel as belonging either to the colony or the background, creating a binary image. This task is laborious when performed manually and proves infeasible for large datasets. To overcome this, we have developed the software Tool for Analysis of the Morphology of Microbial Colonies (TAMMiCol), which automatically and efficiently converts colony images to binary. Multiple images may be imported and processed simultaneously, and TAMMiCol exploits the structure of the images to identify an appropriate threshold for the binary conversion of each image. The images produced by TAMMiCol, which take around 20 seconds each to process, compare favourably with images processed manually, which take anywhere up to 15 minutes, while TAMMiCol outperforms several standard image segmentation methods. After processing, the images may be exported as a CSV or MATLAB MAT file for further analysis, or may be quantified by TAMMiCol using the in-built statistics. Using TAMMiCol, we have found that colonies of S. cerevisiae reach a maximum level of filamentous growth once the concentration of ammonium sulfate is reduced to 200 μM.
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Nutrient-limited growth with non-linear cell diffusion as a mechanism for floral pattern formation in yeast biofilms. J Theor Biol 2018; 448:122-141. [DOI: 10.1016/j.jtbi.2018.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 04/01/2018] [Accepted: 04/03/2018] [Indexed: 11/22/2022]
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