Shaping bacterial population behavior through computer-interfaced control of individual cells

This is the final version. Available from Springer Nature via the DOI in this record.Strains and data are available from the authors upon request. Custom scripts for the described setup are available as Supplementary Software.Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.European Union's Seventh Frame ProgrammeAustrian Science FundAgence Nationale de la RechercheAgence Nationale de la RechercheAgence Nationale de la Recherch

A framework for the integration of green and lean six sigma for superior sustainability performance

Evidence suggests that Lean, Six Sigma and Green approaches make a positive contribution to the economic, social and environmental (i.e. sustainability) performance of organizations. However, evidence also suggests that organizations have found their integration and implementation challenging. The purpose of this research is therefore to present a framework that methodically guides companies through a five stages and sixteen steps process to effectively integrate and implement the Green, Lean and Six Sigma approaches to improve their sustainability performance. To achieve this, a critical review of the existing literature in the subject area was conducted to build a research gap, and subsequently develop the methodological framework proposed. The paper presents the results from the application of the proposed framework in four organizations with different sizes and operating in a diverse range of industries. The results showed that the integration of Lean Six Sigma and Green helped the organizations to averagely reduce their resources consumption from 20% to 40% and minimize the cost of energy and mass streams by 7-12%. The application of the framework should be gradual, the companies should assess their weaknesses and strengths, set priorities, and identify goals for successful implementation. This paper is one of the very first researches that presents a framework to integrate Green and Lean Six Sigma at a factory level, and hence offers the potential to be expanded to multiple factories or even supply chains

Multidrug efflux pumps:structure, function and regulation

Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities

Lean manufacturers transcendence to green manufacturing: Correlating the diffusion of lean and green manufacturing systems

Scientific evidence of human impact on the natural environment, such as global warming, continues to mount. Green manufacturing systems that focus on minimizing environmental impact of manufacturing processes and products are ever more important to our sustainable future. Green manufacturing systems are slow to gain acceptance as manufacturers are focused on implementing Lean manufacturing systems, generally considered the most competitive manufacturing systems in the world. In recent years, researchers and the US Environmental Protection Agency (EPA) have sought to build a bridge between Lean and Green manufacturing systems, in hopes that the rapid expanse of Lean can serve as a catalyst to the implementation of Green manufacturing systems.This study contributes to this growing body of knowledge by determining if leading Lean manufacturers are transcending beyond the traditional limits of Lean and implementing Green manufacturing systems as part of their overallwaste reduction strategy. In this work Lean manufacturing plants that have been evaluated by a panel of experts from the Shingo Prize for Excellence in Manufacturing are surveyed on the diffusion of Green manufacturing system practices throughout their operation. A full system correlation analysis is performed utilizing forty-eight measures of Lean and Green manufacturing systems under the categories of management system, waste reducing techniques, and results. Data analysis indicates that known Lean manufacturers are significantly Greener than the general population of manufacturers in twenty-five of twenty-six measures of Green manufacturing. Lean manufacturers who implement Green manufacturing systems have the strongest results in both Lean and Green result areas, particularly cost reduction, indicating synergy between Lean and Green manufacturing systems. Manufacturing plants that choose to vertically integrate versus horizontally integrate their Lean systems transcend to Green manufacturing. Mexican plants in the study practice significantly higher levels of material resource efficiency and are more inclined to develop industrial partnerships to resolve environmental issues. The study also identifies a critical need for integrating Lean and Green management systems to drive synergistic waste reducing techniques throughout the operation. An integrated Lean and Green manufacturing system model, dubbed Zero Waste Manufacturing , is proposed as a solution for economically and environmentally sustainable manufacturing

Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations

The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin-antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.status: publishe

The antibiotic dosage of fastest resistance evolution: gene amplifications underpinning the inverted-U (dataset)

The article associated with this dataset is located in ORE at: http://hdl.handle.net/10871/124652This is the dataset used for the Reding et al. (2021) article "The Antibiotic Dosage of Fastest Resistance Evolution: gene amplifications underpinning the inverted-U" published in Molecular Biology and Evolution.Engineering and Physical Sciences Research Council (EPSRC)Ramón Areces Postdoctoral FellowshipMinisterio de Ciencia, Innovación y Universidades/FEDE