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A Formal Model for the Simulation and Analysis of Early Biofilm Formation

Antonio Cerone, Enrico Marsili
2020 International Conference on Information and Knowledge Management  
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

João B. Xavier, Esteban Martinez‐Garcia, Kevin R. Foster
2009 American Naturalist  
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

J.B. Xavier, C. Picioreanu, M.C.M. van Loosdrecht
2004 Water Science and Technology  
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

David Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak
2019 BMC Bioinformatics  
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

Natsuko Rivera-Yoshida, Marta Bottagisio, Davide Attanasi, Paolo Savadori, Elena De Vecchi, Alessandro Bidossi, Alessio Franci
2022 Microorganisms  
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

Guo-Bing Xiong, Sheng-Hua Xie, Ai-Bo Liu
2021 Annals of Palliative Medicine  
(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

Chandrabose Selvaraj, Jeyachandran Sivakamavalli, Baskaralingam Vaseeharan, Poonam Singh, Sanjeev Kumar Singh
2014 Molecular Biosystems  
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

Carey D Nadell, Joao B Xavier, Simon A Levin, Kevin R Foster, Nancy A Moran
2008 PLoS Biology  
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

C. Picioreanu, J. B. Xavier, M. C. M. van Loosdrecht
2004 Biofilms  
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

Noor Buchholz, Alberto Budia, Julia de la Cruz, Wolfgang Kram, Owen Humphreys, Meital Reches, Raquel Valero Boix, Federico Soria
2022 Polymers  
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

Monica Licker, Roxana Moldovan, Elena Hogea, Delia Muntean, Florin Horhat, Luminița Baditoiu, Alexandru Florin Rogobete, Emil Tîrziu, Csilla Zambori
2017 Romanian Journal of Laboratory Medicine  
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

Jair Carrazco-Palafox, Blanca Estela Rivera-Chavira, Jaime Raúl Adame-Gallegos, Luz María Rodríguez-Valdez, Erasmo Orrantia-Borunda, Guadalupe Virginia Nevárez-Moorillón
2021 Coatings  
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

Ozlem Altay, Cheng Zhang, Hasan Turkez, Jens Nielsen, Mathias Uhlén, Adil Mardinoglu
2021 Metabolites  
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


2019 International Journal of Applied Pharmaceutics  
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

Marco Artini, Alexandros Patsilinakos, Rosanna Papa, Mijat Božović, Manuela Sabatino, Stefania Garzoli, Gianluca Vrenna, Marco Tilotta, Federico Pepi, Rino Ragno, Laura Selan
2018 Molecules  
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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