Mathematical modeling, simulation and analysis of metabolic oscillations in Bacillus subtilis biofilms

Metabolic oscillations in biofilms of Bacillus subtilis have been reported as periodic halting of growth in the expansion of the colony growing in a microfluidics chamber by Liu et al (2015). This thesis is aimed at understanding these oscillations through minimal dynamic model involving three ordinary differential equations (ODEs). The model is first applied in its basic form in order to describe the oscillations. Next, various modifications of the model are discussed in detail and the results of each modification are viewed in light of the underlying biology. The four modifications investigate the mechanism of oscillations with respect to spatial effects, reversible reactions and more robust reaction kinetics. Finally, we apply the minimal model in a broader perspective in order to understand population dynamics in a typical community of a social organism. We consider three interacting subpopulations of a species that have their own distinct phenotypes. None of the subpopulations have an absolute advantage over the other two. This gives rise to cyclic dynamics like the rock paper scissors game which is analysed using evolutionary game theory. We also present an asymmetrical two-player two- strategy game describing the same system, where the phenotype of each subpopulation is considered as a strategy. This investigation tests the ideal strategies for three different levels of antibiotic stress. We observe bet-hedging in the form of production of resistant cells which are a costly choice in the absence of the antibiotic stress. Although the population dynamics study is described with a broad range of applicability, we also discuss its applications in the B. subtilis biofilm

Evolutionary games on graphs

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first three sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fourth section surveys the topological complications implied by non-mean-field-type social network structures in general. The last three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.Comment: Review, final version, 133 pages, 65 figure

Competitive intransitivity, population interaction structure, and strategy coexistence

Sherpa Romeo green journal. Permission to archive accepted author manuscriptIntransitive competition occurs when competing strategies cannot be listed in a hierarchy, but rather form loops – as in the game Rock-Paper-Scissors. Due to its cyclic competitive replacement, competitive intransitivity promotes strategy coexistence, both in Rock-Paper-Scissors and in higher-richness communities. Previous work has shown that this intransitivity-mediated coexistence is strongly influenced by spatially explicit interactions, compared to when populations are well mixed. Here, we extend and broaden this line of research and examine the impact on coexistence of intransitive competition taking place on a continuum of small-world networks linking spatial lattices and regular random graphs. We use simulations to show that the positive effect of competitive intransitivity on strategy coexistence holds when competition occurs on networks toward the spatial end of the continuum. However, in networks that are sufficiently disordered, increasingly violent fluctuations in strategy frequencies can lead to extinctions and the prevalence of monocultures. We further show that the degree of disorder that leads to the transition between these two regimes is positively dependent on population size; indeed for very large populations, intransitivity-mediated strategy coexistence may even be possible in regular graphs with completely random connections. Our results emphasize the importance of interaction structure in determining strategy dynamics and diversity

Colicin E1 addition to the swine diet prevents post weaning diarrhea

Post-weaning diarrhea remains a threat to swine production in the US despite the use of antibiotic feed additives and other alternative therapies utilized in post-weaning diets. Colicins are proteins produced by, and effective against E. coli, including the enterotoxigenic Escherichia coli (ETEC) responsible for post-weaning diarrhea. The addition of 16.5 of a mg/kg highly purified Colicin E1 (ColE1) to a post-weaning ration reduced the duration and severity of diarrhea caused by a combination of two F18+ ETEC strains over a five day study. Semi-quantitative real time PCR of the ileum revealed lower levels of mRNA expression for inflammatory cytokines IL-1beta and TNFbeta in the 16.5 mg/kg ColE1 fed group as compared to the control animals. These data, taken together with a lower number of ETEC challenge bacteria recovered from ColE1 fed animals 24 hours after oral challenge, suggests that the dietary ColE1 was able to reduce the numbers of ETEC able to colonize the ileum, thereby rendering it unable to cause diarrhea.;In a longer duration study that lasted 4 weeks, a more natural seeder pig challenge model was utilized, and ColE1 addition was also efficacious. This study utilized a post weaning diet containing thought to be protective against PWD such as spray dried plasma and whey protein for the first two weeks. To this diet, 20 mg/kg ColE1 was added. Exposure to the seeder animal without dietary ColE1 supplementation resulted in similar rates of PWD as those achieved by direct oral challenge in the previous study. Much lower rates of diarrhea were noted in the ColE1 fed group (18%) as compared to the control animals (80%) between days 4 and 10 after exposure to the sick animal. Body weight gains were significantly higher in the ColE1 fed pigs as a result, compared to those without the dietary addition at weeks 1 and 2. In a group of pigs not exposed to ETEC challenge, no body weight differences were noted when ColE1 was added to the diet. Semi quantitative real time PCR analysis of ileum mucosa showed higher levels of TNFalpha in the challenged, non-treated animals than those with the ColE1 addition and both diets in the non-challenged room 4 weeks after exposure to the seeder animal. Levels of COX-2 and PGHS, enzymes responsible for maintenance of immune function and barrier function in the intestine, were higher in the ColE1 fed, challenged animals than any other group.;Overall, the addition of the ColE1 purified from a Colicin E1 producing E. coli culture reduced the incidence and severity of PWD in both an oral challenge model and a seeder pig challenge model. The expense required to purify the ColE1 used in this study makes it cost prohibitive for use as an additive in swine feed at this time. For this reason, we have utilized recombinant yeast technology to express the ColE1. This method requires no purification cost because intracellular expression of the ColE1 enables the yeast cell to be directly fed to the pigs

Prevalence of Shiga-toxin producing Escherichia coli in Alberta beef cattle and characteristics of non-pathogenic microcin producing Escherichia coli champion battling bacterial virulence

Zoonotic pathogens, like Shiga toxin-producing Escherichia coli (STEC) are a food safety and health risk. Among STEC, O157 is considered a major pathogen; however, globally the number of outbreaks with new emerging STEC strains is rising. Here, quantitative data on STEC O157 were gathered for western-Canada beef cattle and compared to emerging STEC. Quantitative data revealed; O178 is 4-times more numerous than O157 and high Shiga-toxin events are often not attributed to O157. Results suggest current surveillance likely misses emerging STEC due to restricted O-serogroup screening. Secondly, an alternate STEC mitigation strategy was investigated as an alternative approach to use of antibiotics which is controversial in human and animal therapeutics. Competition experiments identified a strong E. coli O103F which incapacitated STEC growth by producing a diffusible antimicrobial, most likely a microcin. The antimicrobial revealed tremendous potential for use along the farm-to-fork continuum or in human intervention to mitigate STEC

Cooperative and harmful behaviour in the bacterial world

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2017Bacteria are social organisms capable of displaying a multiplicity of complex behaviours, some of them with a significant impact on human lives. Antibiotic resistance, for one, is currently a major health menace and is typically envisioned as an asocial behaviour. Yet, sensitive bacteria can survive the action of antibiotics, given that their social entourage gathers the right characteristics. In this thesis social behaviour of bacteria, ranging from altruistic to spiteful, are shown to affect not only their survival, but also their ability to counterattack the invasion of competing bacteria, and ensure the preservation of social traits, such as antibiotic resistance. To ascertain the complexity and relevance of social behaviours on the bacterial world we studied two types of Escherichia coli mobile genetic elements: bacteriophages and plasmids. Such elements, are not only able to transmit horizontally between different bacterial lineages, but are also able to promote social behaviour in bacteria. In this thesis, both a temperate bacteriophage and three different conjugative plasmids were shown to act as promotors of bacterial social behaviours – both cooperative and harmful. Lysogenic bacteria were shown to use the λ bacteriophage as an allelopathic agent able to harm susceptible cells in their vicinity. This behaviour is of a spiteful nature towards the killed susceptible cells, but also proves to be altruistic towards surviving lysogenic bacteria in the population. Similarly, ampicillin-resistant bacteria, carrying conjugative plasmids, were able to cooperate in the detoxification of ampicillin enriched environments, which led to the survival of genetically sensitive bacteria. However, such sensitive hitchhikers did not remain unharmed for long. In fact, the resistant bacteria were able to use plasmids as a mechanism to harm plasmid-free bacteria and also to restore the cooperative antibiotic-resistance in the population. There is a great need to increase the general knowledge about bacterial social behaviours, since they are involved in well-known threats to public’s health. As far as bacteria are concerned, especially pathogenic bacteria, it is urgent to understand how social behaviours influence the ability of strains to survive the action of antibiotics, but also how they are able to cope when competing against non-pathogenic strains.As bactérias são organismos sociais capazes de desempenhar uma multiplicidade de comportamentos complexos, alguns dos quais com um impacto significativo na vida dos seres humanos. A resistência a antibióticos, por exemplo, é uma das maiores ameaças à saúde pública da atualidade e é tipicamente vista como um comportamento associal. Porém, bactérias sensíveis podem sobreviver à ação de antibióticos, se o seu enquadramento social reunir as características necessárias. Nesta tese, mostra-se que comportamentos sociais bacterianos, desde altruísmo a malícia, são capazes de afetar não só a sua sobrevivência como também a sua habilidade de contra-atacar a invasão de bactérias competidoras, assegurando a preservação de traços sociais, tais como a resistência a antibiótico. Por forma a desenvolver os conhecimentos relativos à complexidade e relevância dos comportamentos sociais no “mundo bacteriano”, estudamos dois tipos de elementos genéticos móveis de Escherchia coli: bacteriófagos e plasmídeos. Esses elementos são, não só capazes de ser transferidos horizontalmente entre diferentes linhagens bacterianas, como também são capazes de promover comportamentos sociais em populações bacterianas. Nesta tese, demonstra-se que, tanto um bacteriófago temperado como três plasmídeos conjugativos, atuam como promotores de comportamentos sociais – sejam cooperativos ou prejudiciais. É demonstrado que bactérias lisogénicas podem usar o fago λ como um agente alelopático capaz de prejudicar células suscetíveis na sua vizinhança. Este comportamento é de uma natureza maliciosa do ponto de vista das bactérias suscetíveis, mas também se mostra altruístico para com as outras bactérias lisogénicas que existem na população. Da mesma forma que bactérias resistentes a ampicilina, que possuem plasmídeos conjugativos, foram capazes de cooperar na destoxificação de um ambiente suplementado com ampicilina, o que por sua vez levou à sobrevivência de bactérias geneticamente sensíveis à ampicilina. No entanto, essas bactérias sensíveis oportunistas não permaneceram impunes por muito tempo. De facto, as bactérias resistentes foram capazes de usar os plasmídeos como uma forma de prejudicar as bactérias inicialmente sem plasmídeo e também como forma de restaurar o comportamento cooperativo de resistência a antibióticos na população. Existe uma grande necessidade em aumentar o conhecimento geral acerca de comportamentos sociais bacterianos, uma vez que estes organismos estão envolvidos em ameaças à saúde pública bem conhecidos. Em relação a bactérias, especialmente bactérias patogénicas, é urgente perceber como é que comportamentos sociais influenciam a capacidade de sobrevivência de estirpes à ação de antibióticos, mas também como é que elas essas estirpes são capazes de lidar quando em competição com bactérias não patogénicas

The ecology and evolution of diversity and cooperation in bacterial public-goods

Explaining why cooperation exists despite the persistent advantage of cheats has been the focus of much theoretical and empirical attention in biology. Using the bacterium Pseudomonas aeruginosa as a model system for the evolution of cooperation, I investigate two distinct phenomena which may develop our understanding of how cooperation is maintained; 1) tag-based cooperation and diversity; and 2) environmental heterogeneity. The first investigates how diversity in cooperative systems may be a response to the selective pressure exerted by cheating, and how cheats may then regulate communities to maintain diversity: I demonstrate that in competition, tag-based cooperation is able to evade parasitism, provided the public-good is only accessible to producer strains, i.e., the cheat possesses the “wrong” tag. I also demonstrate that cheats can have a marked influence on diversity: In a community of two producer strains with different tags, if a third cheater strain is introduced, it will drive both its own producer and itself extinct. I do not find that the presence of cheats maintains diversity in either structured or unstructured environments, and discuss the possible causes of this. In the second topic of this thesis, I investigate the effect of environmental heterogeneity in resource availability, through space and time, on the evolution of cooperation. Environmental heterogeneity is a ubiquitous feature of natural landscapes, yet its effect on the evolution of cooperation has not been extensively studied. I demonstrate that resource availability heterogeneity, in both time and space, acts to maintain cooperation at higher levels than homogeneous environments of the same total resource value. This effect is due to the covariance between productivity and the cost of cooperation: high resource availability periods and spaces are highly productive, and also incur a relatively lower cost of cooperation.BBSR