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As an absolute quantification method at the single-molecule level, digital PCR (dPCR) offers the highest accuracy. In this work, we developed a 3D scalable chamber-array chip that multiplied the number of partitions by stacking chamber-array layers and realized digital loop-mediated isothermal amplification to quantify DNA molecules. It greatly increases the number of partitions to improve the performance of dPCR without increasing the chip size, the operation workflow complicity, and operation time. For the three-chamber-array-layer chip which contains 200,000 reactors of a 0.125 nL volume, it has been proved that the reagent filling and partition were finished within 3 min, and the whole detection could be finished within 1 h. The method demonstrated that it could be scalable to a six-chamber-array layer, which contains 400,000 reactors without increasing the size of the chip and the complication of filling/partition workflow but only takes an additional hour for scanning. Due to its potential for high throughput, low cost, and simple operation, our device may significantly expand the clinical application range of dPCR.

Microfluidic systems have advantages such as a high throughput, small reaction volume, and precise control of the cellular position and environment. These advantages have allowed microfluidics to be widely used in several fields of synthetic biology in recent years. In this article, we reviewed the microfluidic‐based methods for synthetic biology from two aspects: the construction of synthetic gene circuits and the analysis of synthetic gene systems. We used some examples to illuminate the progresses and challenges in the steps of synthetic gene circuits construction and approaches of gene expression analysis with microfluidic systems. Comparing to traditional methods, microfluidic tools promise great advantages in the synthetic genetic circuit building and analysis process. Moreover, new microfluidic systems together with the mathematical modeling of synthetic circuits or consortiums are desirable to perform complex genetic circuit construction and understand the natural gene regulation in cells and population interactions better. Author summary:Microfluidics‐based methods for synthetic biology include the construction of synthetic gene circuits and the analysis of synthetic gene systems. In the former, the high‐throughput, automated control of reaction media and the mini reaction systems of microfluidic systems for gene circuit synthesis can substantially improve efficiency, which leads to a significant cost reduction. In the latter, the precise control of cellular growth directions and environments combined with time‐lapse microscopy makes the description of cell behavior or gene expression easier and more accurate. Accordingly, there is a great opportunity for microfluidics to be applied in synthetic biology research in the future.

As a reaction-diffusion system strongly affected by temperature, early fly embryos surprisingly show highly reproducible and accurate developmental patterns during embryogenesis under temperature perturbations. To reveal the underlying temperature compensation mechanism, it is important to overcome the challenge in quantitative imaging on fly embryos under temperature perturbations. Inspired by microfluidics generating temperature steps on fly embryos, here we design a microfluidic device capable of ensuring the normal development of multiple fly embryos as well as achieving real-time temperature control and fast temperature switches for quantitative live imaging with a home-built two-photon microscope. We apply this system to quantify the temperature compensation of the morphogen Bicoid (Bcd) gradient in fly embryos. The length constant of the exponential Bcd gradient reaches the maximum at 25°C within the measured temperatures of 18–29°C and gradually adapts to the corresponding value at new temperatures upon a fast temperature switch. The relaxation time of such an adaptation becomes longer if the temperature is switched in a later developmental stage. This age-dependent temperature compensation could be explained if the traditional synthesis-diffusion-degradation model is extended to incorporate the dynamic change of the parameters controlling the formation of Bcd gradients.

Label-free plasmonic sensors based on localized surface plasmon resonances of nanostructured noble metal materials usually transduce optical refractive index changes occurring in the vicinity of the nanostructures by optical scattering or by extinction. We demonstrate in experiments that the photoluminescence of plasmonic nanoparticles can also be employed to detect biological molecule binding events efficiently. Photoluminescence probably due to plasmon emission of a single gold nanorod presents a similar resonance peak and resembles the response to a refractive index change observed by scattering. The well-known biotin–streptavidin binding assay was detected successfully using the photoluminescence of an individual isolated nanorod. The localized surface plasmon resonances’ responses by scattering in situwith the same nanorod and control experiments were also performed to verify the sensing process. The results evidence that a nanoscale plasmonic sensor can also be archived effectively through the photoluminescence of a single plasmonic nanostructure. Furthermore, key parameters to optimize the photoluminescence based label-free plasmonic sensing are discussed in detail. The photoluminescence provides an alternative way for label-free plasmonic sensing. And it is believed that further exploration of this concept could lead to a whole new class of efficient plasmonic sensors with diverse and novel functionalities.

A simple but highly specific immunoassay system for goat anti-human IgG has been developed using gold nanoparticles and microfluidic techniques. The assay is based on the deposition of gold nanoparticles that are coated with protein antigens in the presence of their corresponding antibodies to microfluidic channel surface. The effects of time accumulation, the flow velocity, and the concentration of antibodies to the red light absorption percentage RAP of deposition were investigated with an ordinary optical microscope. By controlling the reaction time and flow velocity, a dynamic range of 3 orders of magnitude and a detection sensitivity of 10 ng ml−1of goat anti-human IgG were achieved. Because of its simplicity and flexibility, this new technique should be useful for fast, highthroughput screening of antibodies in clinical diagnostic applications.

ABSTRACTPseudomonas aeruginosais an opportunistic human pathogen that has long been known to chemotax. More recently, it has been established that chemotaxis is an important factor in the ability of P. aeruginosato make biofilms. Genes that allow P. aeruginosato chemotax are homologous with genes in the paradigmatic model organism for chemotaxis, Escherichia coli. However, P. aeruginosais singly flagellated and E. colihas multiple flagella. Therefore, the regulation of counterclockwise/clockwise flagellar motor bias that allows E. colito efficiently chemotax by runs and tumbles would lead to inefficient chemotaxis by P. aeruginosa, as half of a randomly oriented population would respond to a chemoattractant gradient in the wrong sense. How P. aeruginosaregulates flagellar rotation to achieve chemotaxis is not known. Here, we analyze the swimming trajectories of single cells in microfluidic channels and the rotations of cells tethered by their flagella to the surface of a variable-environment flow cell. We show that P. aeruginosachemotaxes by symmetrically increasing the durations of both counterclockwise and clockwise flagellar rotations when swimming up the chemoattractant gradient and symmetrically decreasing rotation durations when swimming down the chemoattractant gradient. Unlike the case for E. coli, the counterclockwise/clockwise bias stays constant for P. aeruginosa. We describe P. aeruginosa’s chemotaxis using an analytical model for symmetric motor regulation. We use this model to do simulations that show that, given P. aeruginosa’s physiological constraints on motility, its distinct, symmetric regulation of motor switching optimizes chemotaxis.IMPORTANCEChemotaxis has long been known to strongly affect biofilm formation by the opportunistic human pathogen P. aeruginosa, whose essential chemotaxis genes have homologues in E. coli, which achieves chemotaxis by biasing the relative probability of counterclockwise and clockwise flagellar rotation. However, the physiological difference between multiflagellated E. coliand singly flagellated P. aeruginosaimplies that biased motor regulation should prevent P. aeruginosapopulations from chemotaxing efficiently. Here, we used experiments, analytical modeling, and simulations to demonstrate that P. aeruginosauses unbiased, symmetric regulation of the flagellar motor to maximize its chemotaxis efficiency. This mode of chemotaxis was not previously known and demonstrates a new variant of a paradigmatic signaling system in an important human pathogen.

ABSTRACTHeteroresistance refers to phenotypic heterogeneity of microbial clonal populations under antibiotic stress, and it has been thought to be an allocation of a subset of “resistant” cells for surviving in higher concentrations of antibiotic. The assumption fits the so-called bet-hedging strategy, where a bacterial population “hedges” its “bet” on different phenotypes to be selected by unpredicted environment stresses. To test this hypothesis, we constructed a heteroresistance model by introducing a blaCTX-M-14gene (coding for a cephalosporin hydrolase) into a sensitive Escherichia colistrain. We confirmed heteroresistance in this clone and that a subset of the cells expressed more hydrolase and formed more colonies in the presence of ceftriaxone (exhibited stronger “resistance”). However, subsequent single-cell-level investigation by using a microfluidic device showed that a subset of cells with a distinguishable phenotype of slowed growth and intensified hydrolase expression emerged, and they were not positively selected but increased their proportion in the population with ascending antibiotic concentrations. Therefore, heteroresistance—the gradually decreased colony-forming capability in the presence of antibiotic—was a result of a decreased growth rate rather than of selection for resistant cells. Using a mock strain without the resistance gene, we further demonstrated the existence of two nested growth-centric feedback loops that control the expression of the hydrolase and maximize population growth in various antibiotic concentrations. In conclusion, phenotypic heterogeneity is a population-based strategy beneficial for bacterial survival and propagation through task allocation and interphenotypic collaboration, and the growth rate provides a critical control for the expression of stress-related genes and an essential mechanism in responding to environmental stresses.IMPORTANCEHeteroresistance is essentially phenotypic heterogeneity, where a population-based strategy is thought to be at work, being assumed to be variable cell-to-cell resistance to be selected under antibiotic stress. Exact mechanisms of heteroresistance and its roles in adaptation to antibiotic stress have yet to be fully understood at the molecular and single-cell levels. In our study, we have not been able to detect any apparent subset of “resistant” cells selected by antibiotics; on the contrary, cell populations differentiate into phenotypic subsets with variable growth statuses and hydrolase expression. The growth rate appears to be sensitive to stress intensity and plays a key role in controlling hydrolase expression at both the bulk population and single-cell levels. We have shown here, for the first time, that phenotypic heterogeneity can be beneficial to a growing bacterial population through task allocation and interphenotypic collaboration other than partitioning cells into different categories of selective advantage.