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A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides

Mark AJ Roberts, Elias August, Abdullah Hamadeh, Philip K Maini, Patrick E McSharry, Judith P Armitage, Antonis Papachristodoulou
2009 BMC Systems Biology  
Developing methods for understanding the connectivity of signalling pathways is a major challenge in biological research.  ...  For this purpose, mathematical models are routinely developed based on experimental observations, which also allow the prediction of the system behaviour under different experimental conditions.  ...  The authors would like to thank Dr Marcus Tindall and Dr Steven Porter for useful discussions about this project. The authors would also like to thank the reviewers for their helpful comments.  ... 
doi:10.1186/1752-0509-3-105 pmid:19878602 pmcid:PMC2783038 fatcat:427s3m6rhvawjk2diw4f2cj5ji

Validation and invalidation of systems biology models using robustness analysis

D.G. Bates, C. Cosentino
2011 IET Systems Biology  
In this review, the authors provide a comprehensive overview of the tools and methods that are available for this task, and illustrate the wide range of biological systems to which this approach has been  ...  With the explosive growth in quantitative modelling brought about by Systems Biology, the problem of validating, invalidating and discriminating between competing models of a biological system has become  ...  Finally, in [42] , Papachristodoulou and co-workers applied a novel approach for iteratively invalidating models to the chemotaxis pathway of the bacterium Rhodobacter sphaeroides.  ... 
doi:10.1049/iet-syb.2010.0072 pmid:21823754 fatcat:w6u4sr7k2jeedpcz27r7oadfba

Theoretical insights into bacterial chemotaxis

Marcus J. Tindall, Eamonn A. Gaffney, Philip K. Maini, Judith P. Armitage
2012 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
In this review we highlight the importance that theoretical modeling has played in providing new insight and understanding into bacterial chemotaxis.  ...  We begin with an overview of the bacterial chemotaxis sensory response, before reviewing the role of theoretical modeling in understanding elements of the system on the single cell scale and features underpinning  ...  Recent theoretical work also includes the elucidation of possible signaling cascades within R. sphaeroides by Hamadeh and colleagues 33 who have focused on theoretically inferring the form of intracellular  ... 
doi:10.1002/wsbm.1168 pmid:22411503 fatcat:4sjp4zmyerd4niblhkb2exl75y

Cell biology and molecular basis of denitrification

W G Zumft
1997 Microbiology and Molecular Biology Reviews  
Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.  ...  Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising  ...  A candidate protein for the interaction with N 2 O in the signaling pathway is NosR.  ... 
pmid:9409151 pmcid:PMC232623 fatcat:dl2aoyhjf5agfjmhsev55dyrmq

Exploring the ecology and genomics of globally important nitrite-oxidizing bacteria

Sebastian Lücker
2010 unpublished
N. defluvii to other known NOB in the key enzymes for nitrification, respiration, and autotrophic carbon fixation.  ...  To overcome this limitation, the complete genome sequence of "Candidatus Nitrospira defluvii" was reconstructed using a metagenomic approach. Genome analysis revealed fundamental differences of Ca.  ...  Cy3 and applied simultaneously to increase the signal to background ratio.  ... 
doi:10.25365/thesis.12537 fatcat:jlfigiac5fbofkg55ty2ipiopu

Responses of Pseudomonas aeruginosa to sub-inhibitory antibiotics

Michelle Denise Brazas
Mutants in the R2/F2 pyocin region were found to be resistant to quinolones as well as other DNA damaging agents like mitomycin C, highlighting a role for this region in mediating susceptibility to DNA  ...  A greater understanding of this biological signature will help in evaluating dosing regimes, understanding mechanism of action and in designing new antimicrobials.  ...  Since the relative error increases at low signal intensity where the signal approaches that of the background, data variability increases as the measured signal intensity decreases.  ... 
doi:10.14288/1.0092345 fatcat:rb4mowpb25a3rjnsa3numfijw4