scholarly journals Collective sensing and collective responses in quorum-sensing bacteria

2015 ◽  
Vol 12 (103) ◽  
pp. 20140882 ◽  
Author(s):  
R. Popat ◽  
D. M. Cornforth ◽  
L. McNally ◽  
S. P. Brown
Keyword(s):  
Quorum Sensing ◽  
Molecular Mechanisms ◽  
Environmental Parameters ◽  
Nutrient Concentrations ◽  
Environmental Challenges ◽  
Theoretical Approaches ◽  
Complex Decision Making ◽  
Evolution Of Resistance ◽  
Complex Decision ◽  
Antibacterial Chemotherapy

Bacteria often face fluctuating environments, and in response many species have evolved complex decision-making mechanisms to match their behaviour to the prevailing conditions. Some environmental cues provide direct and reliable information (such as nutrient concentrations) and can be responded to individually. Other environmental parameters are harder to infer and require a collective mechanism of sensing. In addition, some environmental challenges are best faced by a group of cells rather than an individual. In this review, we discuss how bacteria sense and overcome environmental challenges as a group using collective mechanisms of sensing, known as ‘quorum sensing’ (QS). QS is characterized by the release and detection of small molecules, potentially allowing individuals to infer environmental parameters such as density and mass transfer. While a great deal of the molecular mechanisms of QS have been described, there is still controversy over its functional role. We discuss what QS senses and how, what it controls and why, and how social dilemmas shape its evolution. Finally, there is a growing focus on the use of QS inhibitors as antibacterial chemotherapy. We discuss the claim that such a strategy could overcome the evolution of resistance. By linking existing theoretical approaches to data, we hope this review will spur greater collaboration between experimental and theoretical researchers.

scholarly journals In silicobacteria evolve robust cooperation via complex quorum-sensing strategies

2019 ◽  
Author(s):  
Yifei Wang ◽  
Jennifer B. Rattray ◽  
Stephen A. Thomas ◽  
James Gurney ◽  
Sam P. Brown
Keyword(s):  
Quorum Sensing ◽  
Experimental Evolution ◽  
Molecular Mechanisms ◽  
Bacterial Species ◽  
Critical Role ◽  
Experimental Studies ◽  
Environmental Drivers ◽  
High Signal ◽  
Environmental Challenges ◽  
Digital Organisms

AbstractMany species of bacteria collectively sense and respond to their social and physical environment via ‘quorum sensing’ (QS), a communication system controlling extracellular cooperative traits. Despite detailed understanding of the mechanisms of signal production and response, there remains considerable debate over the functional role(s) of QS: in short, what is it for? Experimental studies have found support for diverse functional roles: density sensing, mass-transfer sensing, genotype sensing, etc. While consistent with theory, these results cannot separate whether these functions were drivers of QS adaption, or simply artifacts or ‘spandrels’ of systems shaped by distinct ecological pressures. The challenge of separating spandrels from drivers of adaptation is particularly hard to address using extant bacterial species with poorly understood current ecologies (let alone their ecological histories). To understand the relationship between environmental challenges and trajectories of QS evolution, we used an agent-based simulation modeling approach. Given genetic mixing, our simulations produce behaviors that recapitulate features of diverse microbial QS systems, including coercive (high signal / low response) and generalized reciprocity (signal auto-regulation) strategists — that separately and in combination contribute to QS-dependent resilience of QS-controlled cooperation in the face of diverse cheats. We contrast ourin silicoresults with bacterial QS architectures that have evolved under largely unknown ecological contexts, highlighting the critical role of genetic constraints in shaping the shorter term (experimental evolution) dynamics of QS. More broadly, we see experimental evolution of digital organisms as a complementary tool in the search to understand the emergence of complex QS architectures and functions.Author summaryBacteria communicate and cooperate using complex cell-cell signaling systems known as quorum-sensing (QS). While the molecular mechanisms are often well understood, the reasons why bacteria use QS are less clear — how has QS aided survival and growth? The answer to this question is dependent on the environment of adaptation, and unfortunately our current understanding of QS bacterial ecology is broadly lacking. To address this gap, we studied the evolution of ‘digital organisms’, individual-based computer simulations of bacterial populations evolving under defined environmental contexts. Our results pinpoint how simple environmental challenges (variable density and genetic mixing) can lead to the emergence of complex strategies that recapitulate features of bacterial QS, and open a path towards reverse-engineering the environmental drivers of QS.

scholarly journals A Delphi Study Investigating Clinicians’ Views on Access to, Delivery of, and Adaptations of MBCT in the UK Clinical Settings

Mindfulness ◽  
2021 ◽  
Author(s):  
Kate Williams ◽  
Samantha Hartley ◽  
Peter Taylor
Keyword(s):  
Delphi Study ◽  
Good Practice ◽  
Evidence Base ◽  
Clinical Settings ◽  
Training Support ◽  
Decision Making Processes ◽  
Complex Decision Making ◽  
Complex Decision ◽  
The Uk ◽  
Clinical Populations

Abstract Objectives Mindfulness-based cognitive therapy (MBCT) is a well-evidenced relapse-prevention intervention for depression with a growing evidence-base for use in other clinical populations. The UK initiatives have outlined plans for increasing access to MBCT in clinical settings, although evidence suggests that access remains limited. Given the increased popularity and access to MBCT, there may be deviations from the evidence-base and potential risks of harm. We aimed to understand what clinicians believe should be best clinical practice regarding access to, delivery of, and adaptations to MBCT. Methods We employed a two-stage Delphi methodology. First, to develop statements around best practices, we consulted five mindfulness-based experts and reviewed the literature. Second, a total of 59 statements were taken forward into three survey rating rounds. Results Twenty-nine clinicians completed round one, with 25 subsequently completing both rounds two and three. Forty-four statements reached consensus; 15 statements did not. Clinicians agreed with statements regarding sufficient preparation for accessing MBCT, adherence to the evidence-base and good practice guidelines, consideration of risks, sufficient access to training, support, and resources within services, and carefully considered adaptations. The consensus was not reached on statements which reflected a lack of evidence-base for specific clinical populations or the complex decision-making processes involved in delivering and making adaptations to MBCT. Conclusions Our findings highlight the delicate balance of maintaining a client-centred and transparent approach whilst adhering to the evidence-base in clinical decisions around access to, delivery of, and adaptations in MBCT and have important wide-reaching implications.

scholarly journals The YadA Protein of Yersinia pseudotuberculosis Mediates High-Efficiency Uptake into Human Cells under Environmental Conditions in Which Invasin Is Repressed

2002 ◽  
Vol 70 (9) ◽  
pp. 4880-4891 ◽  
Author(s):  
Julia Eitel ◽  
Petra Dersch
Keyword(s):  
Extracellular Matrix ◽  
Mammalian Cells ◽  
Yersinia Pseudotuberculosis ◽  
High Efficiency ◽  
Environmental Parameters ◽  
Infection Process ◽  
Nutrient Concentrations ◽  
Integrin Receptors ◽  
Uptake Process ◽  
High Level

ABSTRACT The YadA protein is a major adhesin of Yersinia pseudotuberculosis that promotes tight adhesion to mammalian cells by binding to extracellular matrix proteins. In this study, we first addressed the possibility of competitive interference of YadA and the major invasive factor invasin and found that expression of YadA in the presence of invasin affected neither the export nor the function of invasin in the outer membrane. Furthermore, expression of YadA promoted both bacterial adhesion and high-efficiency invasion entirely independently of invasin. Antibodies against fibronectin and β1 integrins blocked invasion, indicating that invasion occurs via extracellular-matrix-dependent bridging between YadA and the host cell β1 integrin receptors. Inhibitor studies also demonstrated that tyrosine and Ser/Thr kinases, as well as phosphatidylinositol 3-kinase, are involved in the uptake process. Further expression studies revealed that yadA is regulated in response to several environmental parameters, including temperature, ion and nutrient concentrations, and the bacterial growth phase. In complex medium, YadA production was generally repressed but could be induced by addition of Mg2+. Maximal expression of yadA was obtained in exponential-phase cells grown in minimal medium at 37°C, conditions under which the invasin gene is repressed. These results suggest that YadA of Y. pseudotuberculosis constitutes another independent high-level uptake pathway that might complement other cell entry mechanisms (e.g., invasin) at certain sites or stages during the infection process.

scholarly journals Goal-driven active learning

2021 ◽  
Vol 35 (2) ◽  
Author(s):  
Nicolas Bougie ◽  
Ryutaro Ichise
Keyword(s):  
Decision Making ◽  
Reinforcement Learning ◽  
Learning Process ◽  
Real World ◽  
Imitation Learning ◽  
Learning Approaches ◽  
Wide Range ◽  
Fixed Set ◽  
Complex Decision Making ◽  
Complex Decision

AbstractDeep reinforcement learning methods have achieved significant successes in complex decision-making problems. In fact, they traditionally rely on well-designed extrinsic rewards, which limits their applicability to many real-world tasks where rewards are naturally sparse. While cloning behaviors provided by an expert is a promising approach to the exploration problem, learning from a fixed set of demonstrations may be impracticable due to lack of state coverage or distribution mismatch—when the learner’s goal deviates from the demonstrated behaviors. Besides, we are interested in learning how to reach a wide range of goals from the same set of demonstrations. In this work we propose a novel goal-conditioned method that leverages very small sets of goal-driven demonstrations to massively accelerate the learning process. Crucially, we introduce the concept of active goal-driven demonstrations to query the demonstrator only in hard-to-learn and uncertain regions of the state space. We further present a strategy for prioritizing sampling of goals where the disagreement between the expert and the policy is maximized. We evaluate our method on a variety of benchmark environments from the Mujoco domain. Experimental results show that our method outperforms prior imitation learning approaches in most of the tasks in terms of exploration efficiency and average scores.

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

scholarly journals Cross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Orit Malka ◽  
Dorin Kalson ◽  
Karin Yaniv ◽  
Reut Shafir ◽  
Manikandan Rajendran ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Gut Microbiome ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
Human Microbiome ◽  
Cell Communication ◽  
Probiotic Yeast ◽  
Gut Pathogen ◽  
Cell Cell

Abstract Background Probiotic milk-fermented microorganism mixtures (e.g., yogurt, kefir) are perceived as contributing to human health, and possibly capable of protecting against bacterial infections. Co-existence of probiotic microorganisms are likely maintained via complex biomolecular mechanisms, secreted metabolites mediating cell-cell communication, and other yet-unknown biochemical pathways. In particular, deciphering molecular mechanisms by which probiotic microorganisms inhibit proliferation of pathogenic bacteria would be highly important for understanding both the potential benefits of probiotic foods as well as maintenance of healthy gut microbiome. Results The microbiome of a unique milk-fermented microorganism mixture was determined, revealing a predominance of the fungus Kluyveromyces marxianus. We further identified a new fungus-secreted metabolite—tryptophol acetate—which inhibits bacterial communication and virulence. We discovered that tryptophol acetate blocks quorum sensing (QS) of several Gram-negative bacteria, particularly Vibrio cholerae, a prominent gut pathogen. Notably, this is the first report of tryptophol acetate production by a yeast and role of the molecule as a signaling agent. Furthermore, mechanisms underscoring the anti-QS and anti-virulence activities of tryptophol acetate were elucidated, specifically down- or upregulation of distinct genes associated with V. cholerae QS and virulence pathways. Conclusions This study illuminates a yet-unrecognized mechanism for cross-kingdom inhibition of pathogenic bacteria cell-cell communication in a probiotic microorganism mixture. A newly identified fungus-secreted molecule—tryptophol acetate—was shown to disrupt quorum sensing pathways of the human gut pathogen V. cholerae. Cross-kingdom interference in quorum sensing may play important roles in enabling microorganism co-existence in multi-population environments, such as probiotic foods and the gut microbiome. This discovery may account for anti-virulence properties of the human microbiome and could aid elucidating health benefits of probiotic products against bacterially associated diseases.

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