scholarly journals New Insights into the Dynamics of Swarming Bacteria: A Theoretical Study

2016 ◽  
Author(s):  
David Hansmann ◽  
Guido Fier ◽  
Rubén C. Buceta
Keyword(s):  
Inelastic Collision ◽  
Theoretical Study ◽  
Rotational Diffusion ◽  
Agar Plate ◽  
Soft Agar ◽  
E Coli ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
K 12 ◽  
Swarming Behaviour

In the present work we simulate the basic two-dimensional dynamics of swarmingE. colibacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with each other only through inelastic collision and with the highly viscous environment through damping forces. The motion of single agents is modelled closely corresponding to the behaviour of swimming bacteria. The dynamics of the model were adjusted to reproduce the experimental measurements of swimmingE. coliK-12. Accordingly, simulations with loosely packed agents (ρ≈0) show typical run-and-tumble statistics. In contrast, simulations with densely packed agents (ρ≈0.3-0.7) are dominated by interactions (collisions) between agents which lead to the emergence of swarming behaviour. In addition, we model the motion of single agents on the base of modified run-and-tumble dynamics, where the bacteria do not turn actively during the tumble. We show that simulations with densely packed modified agents lead as well the emergence of swarming behaviour, if rotational diffusion is considered.

scholarly journals Stochastic Model for Direction Changes of Swimming Bacteria

2016 ◽  
Author(s):  
G. Fier ◽  
D. Hansmann ◽  
R. C. Buceta
Keyword(s):  
Stochastic Model ◽  
Control Parameter ◽  
Rotational Diffusion ◽  
Steady State Solution ◽  
E Coli ◽  
Isotropic Media ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
The Green Function ◽  
Centers Of Mass

AbstractIn this work we introduce a stochastic model to describe directional changes in the movement of swimming bacteria. We use the probability density function (PDF) of turn angles, measured on tumbling E. coli wild-type, to build a Langevin equation for the deflection of the bacterial body swimming in isotropic media. We solved analytically this equation by means of the Green function method and show that three parameters are sufficient to describe the movement: a characteristic time, the steady-state solution and a control parameter. We conclude that the tumble motion, which is manifested as abrupt turns, is primarily caused by the rotational boost generated by the flagellar motor and complementarily by the rotational diffusion introduced by noise. We show that, in the tumble motion, the deflection is a non-stationary stochastic processes during times where the tumble occurs. By tuning the control parameter our model is able to explain small turns of the bacteria around their centers of mass along the run. We show that the deflection during the run is an Ornstein-Uhlenbeck process, which for typical run times is stationary. We conclude that, along the run, the rotational boosts do not exist or are neglectable and that only the rotational diffusion remains. Thus we have a single model to explain the turns of the bacterium during the run or tumble movements, through a control parameter that can be tuned through a critical value that can explain the transition between the two turn behaviours. This model is also able to explain very satisfactory all available statistical experimental data, such as PDFs and average values of turning angles and times, of both run and tumble motions.

scholarly journals Modelling and analysis of bacterial tracks suggest an active reorientation mechanism in Rhodobacter sphaeroides

2014 ◽  
Vol 11 (97) ◽  
pp. 20140320 ◽  
Author(s):  
Gabriel Rosser ◽  
Ruth E. Baker ◽  
Judith P. Armitage ◽  
Alexander G. Fletcher
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Computational Algorithm ◽  
Rotational Diffusion ◽  
Particle Model ◽  
Cell Geometry ◽  
Brownian Rotation ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
Open Question ◽  
Straight Lines

Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly understood reorientation mechanism in the monoflagellate species Rhodobacter sphaeroides . The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable reorientation. When rotation restarts the cell body usually points in a new direction. It has been assumed that the new direction is simply the result of Brownian rotation. We consider three variants of a self-propelled particle model of bacterial motility. The first considers rotational diffusion only, corresponding to a non-chemotactic mutant strain. Two further models incorporate stochastic reorientations, describing ‘run-and-tumble’ motility. We derive expressions for key summary statistics and simulate each model using a stochastic computational algorithm. We also discuss the effect of cell geometry on rotational diffusion. Working with a previously published tracking dataset, we compare predictions of the models with data on individual stopping events in R. sphaeroides . This provides strong evidence that this species undergoes some form of active reorientation rather than simple reorientation by Brownian rotation.

scholarly journals Contribution of the Twin Arginine Translocation System to the Virulence of Enterohemorrhagic Escherichia coli O157:H7

2003 ◽  
Vol 71 (9) ◽  
pp. 4908-4916 ◽  
Author(s):  
Nathalie Pradel ◽  
Changyun Ye ◽  
Valérie Livrelli ◽  
Jianguo Xu ◽  
Bernard Joly ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Immunoblot Analysis ◽  
Vero Cells ◽  
Soft Agar ◽  
Enterohemorrhagic Escherichia Coli ◽  
E Coli ◽  
Twin Arginine Translocation ◽  
Tat System ◽  
K 12

ABSTRACT Shiga toxin-producing Escherichia coli O157:H7 is a major food-borne infectious pathogen. In order to analyze the contribution of the twin arginine translocation (TAT) system to the virulence of E. coli O157:H7, we deleted the tatABC genes of the O157:H7 EDL933 reference strain. The mutant displayed attenuated toxicity on Vero cells and completely lost motility on soft agar plates. Further analyses revealed that the ΔtatABC mutation impaired the secretion of the Shiga toxin 1 (Stx1) and abolished the synthesis of H7 flagellin, which are two major known virulence factors of enterohemorrhagic E. coli O157:H7. Expression of the EDL933 stxAB 1 genes in E. coli K-12 conferred verotoxicity on this nonpathogenic strain. Remarkably, cytotoxicity assay and immunoblot analysis showed, for the first time, an accumulation of the holotoxin complex in the periplasm of the wild-type strain and that a much smaller amount of StxA1 and reduced verotoxicity were detected in the ΔtatC mutant cells. Together, these results establish that the TAT system of E. coli O157:H7 is an important virulence determinant of this enterohemorrhagic pathogen.

scholarly journals Cluster II che Genes from Pseudomonas aeruginosa Are Required for an Optimal Chemotactic Response

2002 ◽  
Vol 184 (16) ◽  
pp. 4374-4383 ◽  
Author(s):  
Abel Ferrández ◽  
Andrew C. Hawkins ◽  
Douglas T. Summerfield ◽  
Caroline S. Harwood
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Gene Clusters ◽  
Soft Agar ◽  
Chemotactic Response ◽  
Wild Type ◽  
E Coli ◽  
Chemotaxis Proteins ◽  
Complete Set ◽  
K 12

ABSTRACT Pseudomonas aeruginosa, a γ-proteobacterium, is motile by means of a single polar flagellum and is chemotactic to a variety of organic compounds and phosphate. P. aeruginosa has multiple homologues of Escherichia coli chemotaxis genes that are organized into five gene clusters. Previously, it was demonstrated that genes in cluster I and cluster V are essential for chemotaxis. A third cluster (cluster II) contains a complete set of che genes, as well as two genes, mcpA and mcpB, encoding methyl-accepting chemotaxis proteins. Mutations were constructed in several of the cluster II che genes and in the mcp genes to examine their possible contributions to P. aeruginosa chemotaxis. A cheB2 mutant was partially impaired in chemotaxis in soft-agar swarm plate assays. Providing cheB2 in trans complemented this defect. Further, overexpression of CheB2 restored chemotaxis to a completely nonchemotactic, cluster I, cheB-deficient strain to near wild-type levels. An mcpA mutant was defective in chemotaxis in media that were low in magnesium. The defect could be relieved by the addition of magnesium to the swarm plate medium. An mcpB mutant was defective in chemotaxis when assayed in dilute rich soft-agar swarm medium or in minimal-medium swarm plates containing any 1 of 60 chemoattractants. The mutant phenotype could be complemented by the addition of mcpB in trans. Overexpression of either McpA or McpB in P. aeruginosa or Escherichia coli resulted in impairment of chemotaxis, and these cells had smooth-swimming phenotypes when observed under the microscope. Expression of P. aeruginosa cheA2, cheB2, or cheW2 in E. coli K-12 completely disrupted wild-type chemotaxis, while expression of cheY2 had no effect. These results indicate that che cluster II genes are expressed in P. aeruginosa and are required for an optimal chemotactic response.

scholarly journals Modelling and analysis of bacterial tracks suggest an active reorientation mechanism inRhodobacter sphaeroides

2014 ◽  
Author(s):  
Gabriel Rosser ◽  
Ruth E. Baker ◽  
Judith P. Armitage ◽  
Alexander George Fletcher
Keyword(s):  
Computational Algorithm ◽  
Rotational Diffusion ◽  
Particle Model ◽  
Summary Statistics ◽  
Cell Geometry ◽  
Brownian Rotation ◽  
Swimming Bacteria ◽  
Run And Tumble ◽  
Open Question ◽  
Straight Lines

Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly-understood reorientation mechanism in the monoflagellate speciesRhodobacter sphaeroides. The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable reorientation. When rotation restarts the cell body usually points in a new direction. It has been assumed that the new direction is simply the result of Brownian rotation. We consider three variants of a self-propelled particle model of bacterial motility. The first considers rotational diffusion only, corresponding to a non-chemotactic mutant strain. A further two models also include stochastic reorientations, describing 'run-and-tumble' motility. We derive expressions for key summary statistics and simulate each model using a stochastic computational algorithm. We also discuss the effect of cell geometry on rotational diffusion. Working with a previously published tracking dataset, we compare predictions of the models with data on individual stopping events inR. sphaeroides. This provides strong evidence that this species undergoes some form of active reorientation rather than simple reorientation by Brownian rotation.

The Order in Which Antibiotics are Administered Affects the Fitness Costs of Adherent-Invasive E. coli (AIEC) Strains

2019 ◽  
Author(s):  
Jordan B Gregg
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Combination Therapy ◽  
Agar Plate ◽  
Sequential Therapy ◽  
Negative Control ◽  
Clinical Settings ◽  
Fitness Costs ◽  
Inflammatory Gene Expression ◽  
E Coli

AIEC-LF82 is a strain of bacteria that is surmised to have a role in causing IBD and Crohn’s disease by activating pro-inflammatory gene expression in organisms. Using antibiotics via combination therapy has been a technique used in clinical settings in an attempt to treat the strains, however, the attempts have not been that effective nor efficient in terms of completely halting the growth and colonization of AIEC to treat IBD and Crohn's disease patients. Research has shown that regarding hindering or preventing the colonization bacterial colonies, sequential therapy tends to be more effective and time-efficient than combination therapy, with fewer adverse effects. To test if this is also the case with the AIEC-LF82 strain of bacteria, I first tested AIEC’s response to combination therapy using the Penicillin-Streptomycin, Kanamycin-Chloramphenicol, antimicrobial peptide (AMP), Kanamycin, SPE phase and LB agar plates, all of which were experimental plates other than the LB agar plate that acted as the negative control. I then tested AIEC-LF82’s response to sequential therapy using the LB+ Kan + Spe, LB + AMP + Spe, LB+ Kan/Cam + Spe, LB + P/S + Spe, LB + P/S + Kan and LB + P/S + AMP and one LB agar plate acting as the negative control. The only differences between sets a and b were the order in which antibiotics were administered in the six aforementioned treatment sets. Ultimately, I found that set b of sequential therapy, strong-weak antibiotic treatments, was the most effective treatment but that set a regarding sequential therapy was actually the least effective of all of the treatments. In conclusion, using strong-weak sequential antibiotic therapy treatments appears to be a potentially promising option to treat patients suffering from Crohn's disease and IBD.

scholarly journals Tailoring a Global Iron Regulon to a Uropathogen

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Rajdeep Banerjee ◽  
Erin Weisenhorn ◽  
Kevin J. Schwartz ◽  
Kevin S. Myers ◽  
Jeremy D. Glasner ◽  
...  
Keyword(s):  
Amino Acids ◽  
Urinary Tract ◽  
Amino Acid ◽  
Regulatory Network ◽  
Iron Homeostasis ◽  
Iron Limitation ◽  
Content Type ◽  
E Coli ◽  
General Stress ◽  
K 12

ABSTRACT Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O2-dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O2 to produce aerobactin. IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.

scholarly journals Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Carlos-Francisco Méndez-Cruz ◽  
Antonio Blanchet ◽  
Alan Godínez ◽  
Ignacio Arroyo-Fernández ◽  
Socorro Gama-Castro ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Knowledge Extraction ◽  
Biomedical Literature ◽  
Main Role ◽  
E Coli ◽  
Bacterial Transcription ◽  
Manual Curation ◽  
New Knowledge ◽  
Serovar Typhimurium ◽  
K 12

Abstract Transcription factors (TFs) play a main role in transcriptional regulation of bacteria, as they regulate transcription of the genetic information encoded in DNA. Thus, the curation of the properties of these regulatory proteins is essential for a better understanding of transcriptional regulation. However, traditional manual curation of article collections to compile descriptions of TF properties takes significant time and effort due to the overwhelming amount of biomedical literature, which increases every day. The development of automatic approaches for knowledge extraction to assist curation is therefore critical. Here, we show an effective approach for knowledge extraction to assist curation of summaries describing bacterial TF properties based on an automatic text summarization strategy. We were able to recover automatically a median 77% of the knowledge contained in manual summaries describing properties of 177 TFs of Escherichia coli K-12 by processing 5961 scientific articles. For 71% of the TFs, our approach extracted new knowledge that can be used to expand manual descriptions. Furthermore, as we trained our predictive model with manual summaries of E. coli, we also generated summaries for 185 TFs of Salmonella enterica serovar Typhimurium from 3498 articles. According to the manual curation of 10 of these Salmonella typhimurium summaries, 96% of their sentences contained relevant knowledge. Our results demonstrate the feasibility to assist manual curation to expand manual summaries with new knowledge automatically extracted and to create new summaries of bacteria for which these curation efforts do not exist. Database URL: The automatic summaries of the TFs of E. coli and Salmonella and the automatic summarizer are available in GitHub (https://github.com/laigen-unam/tf-properties-summarizer.git).

scholarly journals Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12.

Genetics ◽  
1990 ◽  
Vol 125 (4) ◽  
pp. 691-702 ◽  
Author(s):  
B L Berg ◽  
V Stewart
Keyword(s):  
Escherichia Coli ◽  
Nitrate Reductase ◽  
Formate Dehydrogenase ◽  
Recombinant Dna ◽  
Structural Genes ◽  
Respiratory Pathway ◽  
E Coli ◽  
Formate Oxidation ◽  
Operon Expression ◽  
K 12

Abstract Formate oxidation coupled to nitrate reduction constitutes a major anaerobic respiratory pathway in Escherichia coli. This respiratory chain consists of formate dehydrogenase-N, quinone, and nitrate reductase. We have isolated a recombinant DNA clone that likely contains the structural genes, fdnGHI, for the three subunits of formate dehydrogenase-N. The fdnGHI clone produced proteins of 110, 32 and 20 kDa which correspond to the subunit sizes of purified formate dehydrogenase-N. Our analysis indicates that fdnGHI is organized as an operon. We mapped the fdn operon to 32 min on the E. coli genetic map, close to the genes for cryptic nitrate reductase (encoded by the narZ operon). Expression of phi(fdnG-lacZ) operon fusions was induced by anaerobiosis and nitrate. This induction required fnr+ and narL+, two regulatory genes whose products are also required for the anaerobic, nitrate-inducible activation of the nitrate reductase structural gene operon, narGHJI. We conclude that regulation of fdnGHI and narGHJI expression is mediated through common pathways.

Sign in / Sign up

Export Citation Format

Share Document