Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli

Background: Efflux is a widespread mechanism of reversible drug resistance in bacteria that can be triggered by environmental stressors, including many classes of drugs. While such chemicals when used alone are typically toxic to the cell, they can also induce the efflux of a broad range of agents and may therefore prove beneficial to cells in the presence of multiple stressors. The cellular response to a combination of such chemical stressors may be governed by a trade-off between the fitness costs due to drug toxicity and benefits mediated by inducible systems. Unfortunately, disentangling the cost-benefit interplay using measurements of bacterial growth in response to the competing effects of the drugs is not possible without the support of a theoretical framework. Results: Here, we use the well-studied multiple antibiotic resistance (MAR) system in E. coli to experimentally characterize the trade-off between drug toxicity (“cost”) and drug-induced resistance (“benefit”) mediated by efflux pumps. Specifically, we show that the combined effects of a MAR-inducing drug and an antibiotic are governed by a superposition of cost and benefit functions that govern these trade-offs. We find that this superposition holds for all drug concentrations, and it therefore allows us to describe the full dose–response diagram for a drug pair using simpler cost and benefit functions. Moreover, this framework predicts the existence of optimal growth at a non-trivial concentration of inducer. We demonstrate that optimal growth does not coincide with maximum induction of the mar promoter, but instead results from the interplay between drug toxicity and mar induction. Finally, we derived and experimentally validated a general phase diagram highlighting the role of these opposing effects in shaping the interaction between two drugs. Conclusions: Our analysis provides a quantitative description of the MAR system and highlights the trade-off between inducible resistance and the toxicity of the inducing agent in a multi-component environment. The results provide a predictive framework for the combined effects of drug toxicity and induction of the MAR system that are usually masked by bulk measurements of bacterial growth. The framework may also be useful for identifying optimal growth conditions in more general systems where combinations of environmental cues contribute to both transient resistance and toxicity.Engineering and Applied SciencesMolecular and Cellular Biolog

Usage-driven problem design for radical innovation in healthcare

While the diffusion and evaluation of healthcare innovations receive a lot of attention, the early design stages are less studied and potential innovators lack methods to identify where new innovations are necessary and to propose concepts relevant to users. To change this, we propose a structured methodology, Radical Innovation Design (RID), which supports designers who want to work on the unstated needs of potential end users in order to create superior value. In this article, the first part of RID is introduced with its two subprocesses: Problem Design and Knowledge Design. In this first period, RID guides innovators to systematically explore users’ problems and evaluate which ones are most pressing in terms of innovation, taking into account existing solutions. The result is an ambition perimeter, composed of a set of value buckets, that is, important usage situations where major problems are experienced and the current solutions provide little or no relief. The methodology then moves on to Solution Design and Business Design (which are not detailed in this article) to address the value buckets identified. With its emphasis on problem exploration, RID differs from methods based on early prototyping. The RID methodology has been validated in various industrial sectors and is well-adapted for healthcare innovation. To exemplify the methodology, we present a case study in dental imagery performed by 10 students in 8 weeks. This example demonstrates how RID favours efficiency in Problem Design and allows designers to explore unaddressed and sometimes undeclared user needs.</jats:p

Adapting the fbs model of designing for usage-driven innovation processes

There has been rising interest in confronting formal models of design with practical design methods, in order to understand better both and to explore how they can improve each other. In this article, we try to map the Radical Innovation Design (RID) methodology in Gero’s Function-Behavior-Structure (FBS) framework. We encounter difficulties in doing so, and propose new constructs extending the FBS framework to account for some processes in RID. For instance, FBS is extended to describe the early stages of RID, where usages are analyzed to identify the appropriate situations and problems on which to innovate. We present a short practical case study to illustrate the relevance of these concepts. Our findings join those of others who have investigated the use of FBS to illustrate innovative projects, where requirements are unclear. We propose perspectives for future research, notably pursuing this work with the situated FBS framework.</jats:p

The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities

Optical microscopy of single bacteria growing on solid agarose support is a powerful method for studying the natural heterogeneity in growth and gene expression. While the material properties of agarose make it an excellent substrate for such studies, the sheer number of exponentially growing cells eventually overwhelms the agarose pad, which fundamentally limits the duration and the throughput of measurements. Here we overcome the limitations of exponential growth by patterning agarose pads on the sub-micron-scale. Linear tracks constrain the growth of bacteria into a high density array of linear micro-colonies. Buffer flow through microfluidic lines washes away excess cells and delivers fresh nutrient buffer. Densely patterned tracks allow us to cultivate and image hundreds of thousands of cells on a single agarose pad over 30-40 generations, which drastically increases single-cell measurement throughput. In addition, we show that patterned agarose can facilitate single-cell measurements within bacterial communities. As a proof-of-principle, we study a community of E. coli auxotrophs that can complement the amino acid deficiencies of one another. We find that the growth rate of colonies of one strain decreases sharply with the distance to colonies of the complementary strain over distances of only a few cell lengths. Because patterned agarose pads maintain cells in a chemostatic environment in which every cell can be imaged, we term our device the single-cell chemostat. High-throughput measurements of single cells growing chemostatically should greatly facilitate the study of a variety of microbial behaviours.Molecular and Cellular Biolog

Uncovering Scaling Laws to Infer Multi-drug Response of Resistant Microbes and Cancer Cells

Drug resistance in bacterial infections and cancers constitutes a major threat to human health. Treatments often include several interacting drugs, but even potent therapies can become ineffective in resistant mutants. Here we simplify the picture of drug resistance by identifying scaling laws that unify the multi-drug responses of drug sensitive and drug resistant cells. Based on these scaling relationships, we are able to infer the two-drug response of resistant mutants in previously unsampled regions of dosage space in clinically relevant microbes such as E. coli, E. faecalis, S. aureus and S. cerevisiae, as well as in human non-small cell lung cancer, melanoma, and breast cancer stem cells. Importantly, we find that scaling relations also apply across evolutionarily close strains. Finally, scaling allows one to rapidly identify new drug combinations and predict potent dosage regimes for targeting resistant mutants without any prior mechanistic knowledge of the specific resistance mechanism.Molecular and Cellular Biolog

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and present some experimental results that show how the study of fluctuation theorems applied to biomolecules contributes to our understanding of the nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India). Invited contributio

Syntectonic mobility of supergene nickel ores of New Caledonia (Southwest Pacific). Evidence from faulted regolith and garnierite veins.

International audienceSupergene nickel deposits of New Caledonia that have been formed in the Neogene by weathering of obducted ultramafic rocks are tightly controlled by fracture development. The relationship of tropical weathering and tectonic structures, faults and tension gashes, have been investigated in order to determine whether fractures have play a passive role only, as previously thought; or alternatively, if brittle tectonics was acting together with alteration. From the observation of time-relationship, textures, and mineralogy of various fracture fills and fault gouges, it may be unambiguously established that active faulting has play a prominent role not only in facilitating drainage and providing room for synkinematic crystallisation of supergene nickel silicate, but also in mobilising already formed sparse nickel ore, giving birth to the very high grade ore nicknamed "green gold"

Near-field interactions between a subwavelength tip and a small-volume photonic-crystal nanocavity

International audienceThe fundamentals of the near-field interaction between a subwavelength metallic tip and a photonic-crystal nanocavity are investigated experimentally and theoretically. It is shown experimentally that the cavity resonance is tuned without any degradation by the presence of the tip and that the reported near-field interaction is strongly related to the field distribution within the nanostructure. Then, in light of a perturbation theory, we show that this interaction is selectively related to the electric field or magnetic field distribution within the cavity, depending on the tip properties