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In this Timeline article, Collins and colleagues chart the history of synthetic biology since its inception just over a decade ago, with a focus on both the cultural and scientific progress that has been made as well as on key breakthroughs and areas for future development.

Bacterial responses to antibiotics are complex and involve many genetic and biochemical pathways. This Review describes the effects of bactericidal antibiotics on bacterial cellular processes, the associated responses that contribute to killing and recent insights into these processes revealed through the study of biological networks.

Advances in the synthetic biology field are allowing an expansion beyond small gene networks towards larger biological programs that hold promise for a wide range of applications, including biosensing, therapeutics and the production of biofuels, pharmaceuticals and biomaterials.

Indole, secreted by E. coli, induces oxidative-stress and phage-shock pathway genes to increase persistence, a phenomenon in which dormant bacteria are resistant to antibiotics.

Bacteria regularly evolve antibiotic resistance, but little is known about this process at the population level. Here, a continuous culture of Escherichia coli facing increasing antibiotic levels is followed. Most isolates taken from this population are less antibiotic resistant than the population as a whole. A few highly resistant mutants provide protection to the less resistant constituents, in part by producing the signalling molecule indole, which serves to turn on drug efflux pumps and oxidative-stress protective mechanisms.

Mouse induced pluripotent stem (iPS) cells have been shown to retain an epigenetic 'memory' of their cell type of origin. Kim et al. study this question in human cells and document both incomplete erasure of methylation and aberrant de novo methylation during reprogramming.

A unique multiple cloning site (MCS) and defined genetic components without MCS restriction sites allow for the rapid construction and iterative tuning of synthetic genetic circuits.

Two studies find that programmable RNA-processing tools counter the problem of context-dependence in the construction of synthetic biology circuits.

Despite our continued efforts to assert control over pathogens, more and more bacteria are saying “no” to drugs. It is becoming increasingly apparent that microbial environments, influenced by intracellular and extracellular metabolic processes, modulate antibiotic susceptibility in bacteria. A deeper understanding of these environmental processes may prove crucial for the development of new antibacterial therapies.

This study uses single-cell expression profiling of pluripotent stem cells after various perturbations, and uncovers a high degree of variability that can be inherited through cell divisions—modulating microRNA or external signalling pathways induces a ground state with reduced gene expression heterogeneity and a distinct chromatin profile.

Bone marrow formed in a cylindrical PDMS device implanted in a mouse can be surgically removed and cultured for a week in vitro without losing any of the hallmarks of in vivo bone marrow niches.

Patrick Sullivan and colleagues report a multi-stage genome-wide association study for schizophrenia in a Swedish population. They identify 13 loci newly associated with schizophrenia.

Hermaphrodites develop and maintain male and female reproductive organs in a single individual. Chong et al. show that a DM domain transcription factor is required for male germ cell regeneration and maintains ‘maleness’ in a hermaphrodite, the planarian flatworm Schmidtea mediterranea.

Disparate modes of suppression of the let-7 microRNA family are selectively and inversely related in neuroblastoma.

Ellis et al. describe a strategy for rationally assembling gene networks with predictable behaviors. Using mathematical models, they predict the responses of complex synthetic gene networks built from quantitatively characterized promoter libraries, and harness these networks to regulate an industrially relevant yeast phenotype.

A zinc finger–based modular DNA sequence–recognition system produces a customizable response signal that can induce apoptosis or detect virus-infected cells.

Synthetic biology has expanded the availability of engineered bacterial systems for diverse applications and is now developing safeguards for their effective and secure use. The report of two synthetic gene circuit ‘kill switches’ provides new biocontainment mechanisms for engineered Escherichia coli.

By exploring the phageome in mice, antibiotic treatment is shown to lead to enrichment of phage-encoded genes that are related to antibiotic resistance.

James Collins and colleagues explore the role of the bacterial epigenome in antibiotic stress survival. They find that Escherichia coli survival under antibiotic pressure is strongly compromised in the absence of adenine methylation at GATC sites, suggesting that targeting adenine methylation might be a viable approach to enhance antibiotic activity.

NRAS-driven melanomas have limited therapeutic options. Combining genetically engineered models and oncogenic signaling inhibitors with rational systems-biology approaches, the authors compare the effects of genetic extinction of NRAS to that of chemical pathway inhibition targeting downstream MEK. The differences provide actionable targets by revealing that NRAS signaling operates as a gated output and that MEK inhibition, although inducing apoptosis, is not able to achieve further inhibition of NRAS-induced outputs such as cell-cycle progression. A combination of MEK and CDK4 inhibitors provides a more complete inhibition of NRAS signaling and a more effective antitumor effect in vivo.

Transcription factor Foxp3 is essential for the development and function of regulatory T cells, but it does not act in isolation. Benoist and colleagues identify a quintet of factors that facilitate transcriptional regulation by Foxp3.

Skamagki et al. show that pluripotency factor ZSCAN10 is poorly expressed in iPSCs derived from aged donors, and its addition during reprogramming restores the DNA damage response and genomic stability through normalization of ROS–glutathione levels.

Synthetic biology approaches to characterize gene regulation have largely used transcription factor circuits in bacteria. However, the multilayered regulation of genes by chromatin in eukaryotes provides opportunities for more sophisticated control of gene expression. This Review describes diverse approaches for engineering eukaryotic chromatin states, the insights gained into physiological gene regulation principles, and the broad potential applications throughout biomedical research and industry.

The concept of Six Degrees of Separation has been formalized in so-called ‘small-world networks’. The principles involved could be of use in settings as diverse as improving networks of cellular phones and understanding the spread of infections.

Stochastic resonance increases the ability of some nonlinear systems to detect weak signals. Paddlefish are now shown to use stochastic resonance to locate and capture prey, implicating this phenomenon in animal behaviour.

This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets.

Ligand-responsive riboregulators enable extracellular control of post-transcriptional gene expression.

Noise is inherent in gene expression, and can lead to sizeable fluctuations in the concentrations of expressed RNA and proteins. But many biological processes, such as circadian rhythms, are predictable and must be robust to internal noise. New simulations and studies of synthetic gene networks indicate that negative feedback may counteract noise.

A large-scale study of the protein network in yeast cells demonstrates the merit of taking an integrated approach to cellular dynamics, and shows the value of databases.

A systematic exploration of noise in gene expression demonstrates the value of integrating novel experiments with computational modeling.

The length of a single guide RNA (gRNA) determines the function of Cas9. In this study 20-nt gRNAs allowed nuclease activity and genome editing, whereas 14-nt gRNAs mediated transcriptional activation or repression.

A comparison of seven dCas9-based transcriptional activators shows that VPR, SAM, and Suntag perform best in cell lines from a variety of organisms.

The fusion of three transcriptional activation domains to a nuclease-deficient Cas9 achieves robust induction of gene expression and can induce differentiation of hiPSCs.