Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif

Cellular interactions are subject to random fluctuations (noise) in quantities of interacting molecules. Noise presents a major challenge for the robust function of natural and engineered cellular networks. Past studies have analyzed how noise is regulated at the intracellular level. Cell–cell communication, however, may provide a complementary strategy to achieve robust gene expression by enabling the coupling of a cell with its environment and other cells. To gain insight into this issue, we have examined noise regulation by quorum sensing (QS), a mechanism by which many bacteria communicate through production and sensing of small diffusible signals. Using a stochastic model, we analyze a minimal QS motif in Gram-negative bacteria. Our analysis shows that diffusion of the QS signal, together with fast turnover of its transcriptional regulator, attenuates low-frequency components of extrinsic noise. We term this unique mechanism “diffusional dissipation” to emphasize the importance of fast signal turnover (or dissipation) by diffusion. We further show that this noise attenuation is a property of a more generic regulatory motif, of which QS is an implementation. Our results suggest that, in a QS system, an unstable transcriptional regulator may be favored for regulating expression of costly proteins that generate public goods

Development of a Modular Biosensor System for Rapid Pathogen Detection

Progress in the field of pathogen detection relies on at least one of the following three qualities: selectivity, speed, and cost-effectiveness. Here, we demonstrate a proof of concept for an optical biosensing system for the detection of the opportunistic human pathogen Pseudomonas aeruginosa while addressing the abovementioned traits through a modular design. The biosensor detects pathogen-specific quorum sensing molecules and generates a fluorescence signal via an intracellular amplifier. Using a tailored measurement device built from low-cost components, the image analysis software detected the presence of P. aeruginosa in 42 min of incubation. Due to its modular design, individual components can be optimized or modified to specifically detect a variety of different pathogens. This biosensor system represents a successful integration of synthetic biology with software and hardware engineering

Trade-offs and Noise Tolerance in Signal Detection by Genetic Circuits

Genetic circuits can implement elaborated tasks of amplitude or frequency signal detection. What type of constraints could circuits experience in the performance of these tasks, and how are they affected by molecular noise? Here, we consider a simple detection process–a signal acting on a two-component module–to analyze these issues. We show that the presence of a feedback interaction in the detection module imposes a trade-off on amplitude and frequency detection, whose intensity depends on feedback strength. A direct interaction between the signal and the output species, in a type of feed-forward loop architecture, greatly modifies these trade-offs. Indeed, we observe that coherent feed-forward loops can act simultaneously as good frequency and amplitude noise-tolerant detectors. Alternatively, incoherent feed-forward loop structures can work as high-pass filters improving high frequency detection, and reaching noise tolerance by means of noise filtering. Analysis of experimental data from several specific coherent and incoherent feed-forward loops shows that these properties can be realized in a natural context. Overall, our results emphasize the limits imposed by circuit structure on its characteristic stimulus response, the functional plasticity of coherent feed-forward loops, and the seemingly paradoxical advantage of improving signal detection with noisy circuit components

Biological hydrogels as selective diffusion barriers

The controlled exchange of molecules between organelles, cells, or organisms and their environment is crucial for life. Biological gels such as mucus, the extracellular matrix (ECM), and the biopolymer barrier within the nuclear pore are well suited to achieve such a selective exchange, allowing passage of particular molecules while rejecting many others. Although hydrogel-based filters are integral parts of biology, clear concepts of how their barrier function is controlled at a microscopic level are still missing. We summarize here our current understanding of how selective filtering is established by different biopolymer-based hydrogels. We ask if the modulation of microscopic particle transport in biological hydrogels is based on a generic filtering principle which employs biochemical/biophysical interactions with the filtered molecules rather than size-exclusion effects.National Institutes of Health (U.S.) (Grant P50GM068763)MIT Start-up FundsGerman Academic Exchange Service (Postdoctoral Fellowship

Performance of SW-ARQ in bacterial quorum communications

Bacteria communicate with one another by exchanging specific chemical signals called autoinducers. This process, also called quorum sensing, enables a cluster of bacteria to regulate their gene expression and behaviour collectively and synchronously, such as bioluminescence, virulence, sporulation and conjugation. Bacteria assess their population density by detecting the concentration of autoinducers. In Vibrio fischeri, which is a heterotrophic Gram-negative marine bacterium, quorum sensing relies on the synthesis, accumulation and subsequent sensing of a signalling molecule (3-oxo-C6-HSL, an N-acyl homoserine lactone or AHL). In this work, a data link layer protocol for a bacterial communication paradigm based on diffusion is introduced, considering two populations of bacteria as the transmitter node and the receiver node, instead of employing two individual bacteria. Moreover, some initial results are provided, which concern the application of the Stop-N-Wait Automatic Repeat reQuest (SW-ARQ) schemes to the proposed model. The performances of the system are later evaluated, in terms of the transmission time, frame error rate, energy consumption and transmission efficiency