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A Formal Model for the Simulation and Analysis of Early Biofilm Formation
2020
International Conference on Information and Knowledge Management
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We exploit the model-checking features of Real-time Maude to formally prove that a regular cleaning or replacement of the infrastructure prevents the biofilm formation. ...
An important challenge is to predict the time needed for the formation of a biofilm on a specific surface, in order to plan when the material infrastructure that comprises such a surface needs to be cleaned ...
Conclusion and Future Work We have used Real-Time Maude to define an approach for the formal modelling and analysis of early biofilm formation. ...
doi:10.1007/978-3-030-70650-0_9
dblp:conf/cikm/CeroneM20
fatcat:5iocglw5uja4hpalxmp5v42wk4
Social Evolution of Spatial Patterns in Bacterial Biofilms: When Conflict Drives Disorder
2009
American Naturalist
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We present a mechanistic model of cell growth at a surface, and we show that tension between growth and competition for nutrients can explain how empirically observed patterns emerge in biofilms. ...
Our theory provides a formal link between higher-level patterning and the potential for evolutionary conflict by showing that both can arise from a single set of scale-dependent processes. ...
Shimizu, and D. Sumpter for comments on the manuscript. We also thank E. Alpkvist for valuable help with the numeric methods. ...
doi:10.1086/599297
pmid:19456262
fatcat:sdfnmejhwzhrrnhmuedz5zapnm
Assessment of three-dimensional biofilm models through direct comparison with confocal microscopy imaging
2004
Water Science and Technology
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This work assesses the capability of a state-of-the-art technique for three-dimensional (3D) modeling of biofilm structure, individual based modeling (IbM), to quantitatively describe the early development ...
The mathematical modeling of spatial biofilm formation that provides the capability to predict biofilm structure from first principles has been in development for the past six years. ...
Acknowledgements Financial support by the F.C.T./M.C.T., Portugal, through the grant SFRH/BPD/11485/2002 is thankfully acknowledged. ...
doi:10.2166/wst.2004.0834
pmid:15303739
fatcat:nhxqllldjje2hhrlzdkojy6tdq
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking
2019
BMC Bioinformatics
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Conclusions: The advantages of our modelling and analysis approach are the description of quorum sensing and associated biofilm formation over two phases of bacterial growth, taking into account bacterial ...
Our simulation results support the expected behaviour that biofilm formation is increased in areas of higher bacterial colony size and density. ...
Acknowledgements We would like to thank Christian Rohr for his assistance during model construction. ...
doi:10.1186/s12859-019-2690-z
fatcat:bvshsyxdkzho3e7paihqdosttu
Host Environment Shapes S. aureus Social Behavior as Revealed by Microscopy Pattern Formation and Dynamic Aggregation Analysis
2022
Microorganisms
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Besides providing a new tool for biofilm phenotypic analysis, our results suggest new insights into the social behavior of S. aureus in physiological conditions and highlight the inadequacy of commonly ...
By means of optical and confocal microscopy, image pattern analysis, and mathematical modeling, we show that planktonic biofilm-like aggregates and sessile biofilm lifestyles are two co-existing and interacting ...
-Y. thanks Programa de Becas Posdoctorales UNAM-DGAPA for a postdoctoral fellowship.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/microorganisms10030526
pmid:35336102
pmcid:PMC8949161
fatcat:teb2xydm6vcoziaxrznytd5t34
In vitro dynamic bladder models for studying urinary tract infections: a narrative review
2021
Annals of Palliative Medicine
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(V) Research analysis: 45 studies investigated the bacterial biofilm formation in the bladder model. ...
Our analysis showed for the first time that in vitro dynamic bladder models could provide new ideas for exploring the mechanism and prevention of bacterial biofilm infection in urinary implanted biomaterials ...
biofilm formation as that in the static system Dynamic model Crystal violet and fluorescence image analysis showed that the formation of acylase coated bacterial biofilm was inhibited by 80% when Pseudomonas ...
doi:10.21037/apm-20-2061
pmid:33691461
fatcat:gu6ghs66dzgz5dag63lr3ost7m
Structural elucidation of SrtA enzyme in Enterococcus faecalis: an emphasis on screening of potential inhibitors against the biofilm formation
2014
Molecular Biosystems
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Present work is an inclusive report of structural elucidation in SrtA and screening of potent inhibitors targeting E. faecalis through computational and experimental methodologies. ...
microscopy (SEM): For SEM analysis, biofilms containing glass pieces were fixed for 1 h in a 2.5% glutaraldehyde. ...
Formerly, the role of sortase gene (SrtA) in monospecies biofilm formation was investigated in Streptococcus mutans and it was observed that inactivation of SrtA caused a decrease in biofilm formation ...
doi:10.1039/c3mb70613c
pmid:24718729
fatcat:r3h25o63z5cpbi47teq55yc6wm
The Evolution of Quorum Sensing in Bacterial Biofilms
2008
PLoS Biology
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A key example of such group behavior is biofilm formation, in which communities of cells attach to a surface and envelope themselves in secreted polymers. ...
Here, we investigate this striking variation in the first evolutionary model of quorum sensing in biofilms. ...
CDN, JBX, and KRF designed simulations. CDN and JBX performed simulations. CDN, JBX, and KRF analyzed data. JBX contributed analytical tools. CDN, JBX, SAL, and KRF wrote the paper. ...
doi:10.1371/journal.pbio.0060014
pmid:18232735
pmcid:PMC2214811
fatcat:vpez6ntm4bddfm4yliq5cmvyeu
Advances in mathematical modeling of biofilm structure
2004
Biofilms
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Mathematical modeling of biofilm structure 1 2 C. Picioreanu et al. ...
The individual based model for biofilms was adapted (Martins et al., 2004b) to simulate the formation of activated sludge flocs, including two different bacterial morphotypes: floc-forming bacteria and ...
terms of physical processes involved in their formation and Results from simulations carried out for a two-species biofilm where the competition between PHB-producing and EPS-producing heterotrophic microorganisms ...
doi:10.1017/s1479050505001572
fatcat:mx2hhu7ccja6rfi6vskaj7hf2i
Urinary Stent Development and Evaluation Models: In Vitro, Ex Vivo and In Vivo—A European Network of Multidisciplinary Research to Improve Urinary Stents (ENIUS) Initiative
2022
Polymers
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Lastly, the third part lists and discusses the pros and cons of available animal models for urinary stent evaluation, this being the final step before human trials. ...
In the second part, we provide a step-by-step guide on what to consider when setting up an ex vivo model for stent evaluation on the example of a biodegradable stent. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/polym14091641
pmid:35566810
pmcid:PMC9102855
fatcat:cnlro2oimzceta25cvpoisfrmu
Microbial biofilm in human health - an updated theoretical and practical insight
2017
Romanian Journal of Laboratory Medicine
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The role of microbial biofilms in medical pathology is a subject that raises interest for both researchers and clinicians in order to establish new methods for prevention and treatment of biofilms. ...
The risk of microbial biofilm development exists for a long list of medical devices and equipment, as well as in certain diseases such as cystic fibrosis. ...
In vivo tissue -biofilm models Infections related to biofilm growth and development have been simulated in living tissues, resulting in the design of biofilm models, with the purpose of overcoming the ...
doi:10.1515/rrlm-2017-0001
fatcat:tnzc54g4czhlzpmk7bedzk3m2i
Rhamnolipids from Pseudomonas aeruginosa Rn19a Modifies the Biofilm Formation over a Borosilicate Surface by Clinical Isolates
2021
Coatings
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E26, Enterococcus faecalis I27 on borosilicate coupons inside a Center for Disease Control and Prevention (CDC) reactor. ...
The Enterococcus faecalis I27 isolate decreased its biofilm formation ability in 2.2 log CFU/cm2 in static conditions by the addition of rhamnolipids and 3.0 log units in dynamic conditions. ...
Acknowledgments: Jair Carrazco-Palafox acknowledges the School of Medicine and Biomedical Sciences, Universidad Autónoma de Chihuahua for supporting his doctoral studies. ...
doi:10.3390/coatings11020136
fatcat:45h4j523nves7fwrxvkfdod4yi
Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling
2021
Metabolites
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Altogether, our integrative systems biology analysis revealed the interactions between the bacteria and its microenvironment and enabled the discovery of antimicrobial targets for biofilm-related diseases ...
Here, we integrated transcriptomics data of bacterial cells grown on exponential and biofilm conditions into a manually curated GEM of B. cenocepacia. ...
Acknowledgments: The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project snic2019-35-23. ...
doi:10.3390/metabo11040221
pmid:33916474
pmcid:PMC8067366
fatcat:u7r2matoxrfu3m3ypma3svd32u
CHEWING GUM CONTAINING PROPOLIS WAX FROM APIS MELLIFERA BEES FOR PREVENTION OF DENTAL CARIES DISEASE
2019
International Journal of Applied Pharmaceutics
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formation, which is an early disease stage of dental caries.Characterization of jelutong latex using differential scanning calorimetry and thermogravimetric analysis shows that the latex has glass transitiontemperatures ...
chewing gum was formulated using latex from the jelutong tree (Dyera costuata) with the addition of propolis wax(1–5%) as an antibacterial agent to inhibit the activity of S. mutans and prevent biofilm ...
ACKNOWLEDGMENT The author would like to thank Universitas Indonesia for their financial support in the form of the Grant of Indexed International Publication of Student Final Project (PITTA). ...
doi:10.22159/ijap.2019.v11s1.15941
fatcat:6gtrrdxf7vb5fcn557drz3naku
Antimicrobial and Antibiofilm Activity and Machine Learning Classification Analysis of Essential Oils from Different Mediterranean Plants against Pseudomonas aeruginosa
2018
Molecules
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The interest in the development of new approaches for the prevention and treatment of biofilm formation has recently increased. ...
The aim of this study was to seek new non-biocidal agents able to inhibit biofilm formation, in order to counteract virulence rather than bacterial growth and avoid the selection of escape mutants. ...
Acknowledgments: Rino Ragno is thankful to Virgina Filacchione for having checked the manuscript's style and grammar. ...
doi:10.3390/molecules23020482
pmid:29473844
fatcat:6gmpkhvebfc4rigmvwswyt6u5i
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