Constructing Smartphone-Controlled Optogenetic Switches in Mammalian Cells.

With the increasing indispensable role of smartphones in our daily lives, the mobile health care system coupled with embedded physical sensors and modern communication technologies make it an attractive technology for enabling the remote monitoring of an individual's health. Using a multidisciplinary design principle coupled with smart electronics, software, and optogenetics, the investigators constructed smartphone-controlled optogenetic switches to enable the ultraremote-control transgene expression. A custom-designed SmartController system was programmed to process wireless signals from smartphones, enabling the regulation of therapeutic outputs production by optically engineered cells via a far-red light (FRL)-responsive optogenetic interface. In the present study, the investigators describe the details of the protocols for constructing smartphone-controlled optogenetic switches, including the rational design of an FRL-triggered transgene expression circuit, the procedure for cell culture and transfection, the implementation of the smartphone-controlled far-red light-emitting diode (LED) module, and the reporter detection assay.

Characterizing Genetic Parts and Devices Using RNA Sequencing.

Synthetic genetic circuits are composed of many parts that must interact and function together to produce a desired pattern of gene expression. A challenge when assembling circuits is that genetic parts often behave differently within a circuit, potentially impacting the desired functionality. Existing debugging methods based on fluorescent reporter proteins allow for only a few internal states to be monitored simultaneously, making diagnosis of the root cause impossible for large systems. Here, we present a tool called the Genetic Analyzer which uses RNA sequencing data to simultaneously characterize all transcriptional parts (e.g., promoters and terminators) and devices (e.g., sensors and logic gates) in complex genetic circuits. This provides a complete picture of the inner workings of a genetic circuit enabling faults to be easily identified and fixed. We construct a complete workflow to coordinate the execution of the various data processing and analysis steps and explain the options available when adapting these for the characterization of new systems.

Type II anti-CRISPR proteins as a new tool for synthetic biology.

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) system represents, in prokaryotes, an adaptive and inheritable immune response against invading DNA. The discovery of anti-CRISPR proteins (Acrs), which are inhibitors of CRISPR-Cas, mainly encoded by phages and prophages, showed a co-evolution history between prokaryotes and phages. In the past decade, the CRISPR-Cas systems together with the corresponding Acrs have been turned into a genetic-engineering tool. Among the six types of CRISPR-Cas characterized so far, type II CRISPR-Cas system is the most popular in biotechnology. Here, we discuss about the discovery, the reported inhibitory mechanisms, and the applications in both gene editing and gene transcriptional regulation of type II Acrs. Moreover, we provide insights into future potential research and feasible applications.

Programming Escherichia coli to function as a digital display.

Synthetic genetic circuits offer the potential to wield computational control over biology, but their complexity is limited by the accuracy of mathematical models. Here, we present advances that enable the complete encoding of an electronic chip in the DNA carried by Escherichia coli (E. coli). The chip is a binary-coded digit (BCD) to 7-segment decoder, associated with clocks and calculators, to turn on segments to visualize 0-9. Design automation is used to build seven strains, each of which contains a circuit with up to 12 repressors and two activators (totaling 63 regulators and 76,000 bp DNA). The inputs to each circuit represent the digit to be displayed (encoded in binary by four molecules), and output is the segment state, reported as fluorescence. Implementation requires an advanced gate model that captures dynamics, promoter interference, and a measure of total power usage (RNAP flux). This project is an exemplar of design automation pushing engineering beyond that achievable "by hand", essential for realizing the potential of biology.

Ultracompact 3D microfluidics for time-resolved structural biology.

To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s-1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.

Cytomorphic Electronics With Memristors for Modeling Fundamental Genetic Circuits.

Cytomorphic engineering attempts to study the cellular behavior of biological systems using electronics. As such, it can be considered analogous to the study of neurobiological concepts for neuromorphic engineering applications. To date, digital and analog translinear electronics have commonly been used in the design of cytomorphic circuits; Such circuits could greatly benefit from lowering the area of the digital memory via memristive circuits. In this article, we propose a novel approach that utilizes the Boltzmann-exponential stochastic transport of ionic species through insulators to naturally model the nonlinear and stochastic behavior of biochemical reactions. We first show that two-terminal memristive devices can capture the non-linear and stochastic behavior of biochemical reactions. Then, we present the design of several building blocks based on analog memristive circuits that inherently model the biophysical mechanisms of gene expression. The circuits model induction by small molecules, activation and repression by transcription factors, biological promoters, cooperative binding, and transcriptional and translational regulation of gene expression. Finally, we utilize the building blocks to form complex mixed-signal networks that can simulate the delay-induced oscillator and the p53-mdm2 interaction in the cancer signaling pathway. Our approach can provide a fast and simple emulative framework for studying genetic circuits and arbitrary large-scale biological networks in systems and synthetic biology. Some challenges may be that memristive devices with frequent learning and programming do not have the same longevity as traditional transistor-based electron-transport devices, and operate with significantly slower time constants, which can limit emulation speed.

Programmed assembly of long DNA synthons: design, mechanism, and online monitoring.

Synthesis of custom de novo DNA sequences is highly demanded by fast-growing field of synthetic biology. Usually DNA sequences with length more than 1 kb are assembled from smaller synthetic DNA fragments (synthons) obtained by PCR assembly. The ability to synthesize longer synthons sufficiently reduces efforts and time for DNA synthesis. We developed a novel rational oligonucleotide design and programmed approach for the assembly of synthetic DNA synthons up to 1550 bp. The developed procedure was thoroughly investigated by synthesis of cholesterol oxidase gene from Streptomyces lavendulae (1544 bp). Our approach is based on combined design, oligonucleotide concentration gradient, and specialized assembly program that directs assembly reaction to full-length gene in a stepwise manner. The process includes conventional thermodynamically balanced assembly, thermodynamically balanced inside-out elongation, and further amplification. The ability of DNA polymerase to perform programmed assembly is highly influenced by the presence of 5' → 3'-exonuclease activity. Oligonucleotide probing of PCR assembly products allowed us to shed light on the nature of high molecular weight spurious by-products and to understand the mechanism of their formation. For the first time, we applied light scattering techniques for tracking of oligonucleotide annealing, analysis of gene assembly products, and even for real-time monitoring of gene assembly process.

A Makerspace for Life Support Systems in Space.

Human space exploration and settlement will require leaps forward in life support for environmental management and healthcare. Life support systems must efficiently use nonrenewable resources packed from Earth while increasingly relying on resources available locally in space. On-demand production of components and materials (e.g., 3D printing and synthetic biology) holds promise to satisfy the evolving set of supplies necessary to outfit human missions to space. We consider here life support systems for missions planned in the 2020s, and discuss how the maker and 'do-it-yourself' (DIY) biology communities can develop rapid, on-demand manufacturing techniques and platforms to address these needs. This Opinion invites the diverse maker community into building the next generation of flight hardware for near-term space exploration.

Microfluidic Synchronizer Using a Synthetic Nanoparticle-Capped Bacterium.

Conventional techniques to synchronize bacterial cells often require manual manipulations and lengthy incubation lacking precise temporal control. An automated microfluidic device was recently developed to overcome these limitations. However, it exploits the stalk property of Caulobacter crescentus that undergoes asymmetric stalked and swarmer cell cycle stages and is therefore restricted to this species. To address this shortcoming, we have engineered Escherichia coli cells to adhere to microchannel walls via a synthetic and inducible "stalk". The pole of E. coli is capped by magnetic fluorescent nanoparticles via a polar-localized outer membrane protein. A mass of cells is immobilized in a microfluidic chamber by an externally applied magnetic field. Daughter cells are formed without the induced stalk and hence are flushed out, yielding a synchronous population of "baby" cells. The stalks can be tracked by GFP and nanoparticle fluorescence; no fluorescence signal is detected in the eluted cell population, indicating that it consists solely of daughters. The collected daughter cells display superb synchrony. The results demonstrate a new on-chip method to synchronize the model bacterium E. coli and likely other bacterial species, and also foster the application of synthetic biology to the study of the bacterial cell cycle.

More from less - bottom-up reconstitution of cell biology.

The ultimate goal of bottom-up synthetic biology is recreating life in its simplest form. However, in its quest to find the minimal functional units of life, this field contributes more than its main aim by also offering a range of tools for asking, and experimentally approaching, biological questions. This Review focusses on how bottom-up reconstitution has furthered our understanding of cell biology. Studying cell biological processes in vitro has a long tradition, but only recent technological advances have enabled researchers to reconstitute increasingly complex biomolecular systems by controlling their multi-component composition and their spatiotemporal arrangements. We illustrate this progress using the example of cytoskeletal processes. Our understanding of these has been greatly enhanced by reconstitution experiments, from the first in vitro experiments 70 years ago to recent work on minimal cytoskeleton systems (including this Special Issue of Journal of Cell Science). Importantly, reconstitution approaches are not limited to the cytoskeleton field. Thus, we also discuss progress in other areas, such as the shaping of biomembranes and cellular signalling, and prompt the reader to add their subfield of cell biology to this list in the future.

The Use of an Automated Platform to Assemble Multigenic Constructs for Plant Transformation.

Compared to traditional means, modern DNA assembly methods allow cloning of large, multigenic vectors for plant transformation in rapid fashion. These methods are often robust and efficient and can assemble multiple DNA fragments into a single vector in one reaction. Here we describe the use of an automated DNA assembly platform for the generation of complex, multigenic T-DNA binary vectors using a hierarchical Golden Gate cloning strategy. These DNA constructs contained diverse DNA elements for the expression of multiple genes for trait stacking in the crop of interest. This platform streamlines the DNA assembly and validation process through high-efficiency cloning methods, integrated automation equipment, and increased throughput. The implementation of this platform removes bottlenecks for routine molecular biology and opens new possibilities for downstream experimental idea testing.

Time to Get Serious about Measurement in Synthetic Biology.

For synthetic biology to mature, composition of devices into functional systems must become routine. This requires widespread adoption of comparable and replicable units of measurement. Interlaboratory studies organized through the International Genetically Engineered Machine (iGEM) competition show that fluorescence can be calibrated with simple, low-cost protocols, so fluorescence should no longer be published without units.

Mastering Complexity: Towards Bottom-up Construction of Multifunctional Eukaryotic Synthetic Cells.

With the ultimate aim to construct a living cell, bottom-up synthetic biology strives to reconstitute cellular phenomena in vitro - disentangled from the complex environment of a cell. Recent work towards this ambitious goal has provided new insights into the mechanisms governing life. With the fast-growing library of functional modules for synthetic cells, their classification and integration become increasingly important. We discuss strategies to reverse-engineer and recombine functional parts for synthetic eukaryotes, mimicking the characteristics of nature's own prototype. Particularly, we focus on large outer compartments, complex endomembrane systems with organelles, and versatile cytoskeletons as hallmarks of eukaryotic life. Moreover, we identify microfluidics and DNA nanotechnology as two technologies that can integrate these functional modules into sophisticated multifunctional synthetic cells.

Concurrent In Vitro Synthesis and Functional Detection of Nascent Activity of the KcsA Channel under a Membrane Potential.

Processes involved in the functional formation of prokaryotic membrane proteins have remained elusive. Here, we developed a new in vitro membrane protein expression system to detect nascent activities of the KcsA potassium channel in lipid bilayers under an applied membrane potential. The channel was synthesized using a reconstituted Escherichia coli-based in vitro transcription/translation system (IVTT) in a water-in-oil droplet lined by a membrane. The synthesized channels spontaneously incorporated into the membrane even without the translocon machinery (unassisted pathway) and formed functional channels with the correct orientation. The single-channel current of the first appearing nascent channel was captured, followed by the subsequent appearance of multiple channels. Notably, the first appearance time shortened substantially as the membrane potential was hyperpolarized. Under a steadily applied membrane potential, this system serves as a production line of membrane proteins via the unassisted pathway, mimicking the bacterial synthetic membrane.

Construction of synthetic T7 RNA polymerase expression systems.

T7 RNA polymerase (T7 RNAP) is one of the preferred workhorses for recombinant gene expression, owing in part to its high transcriptional activity and the fact that it has a small (17 base-pair), easily manipulated promoter. Furthermore, the fact that T7 RNAP is largely orthogonal to most hosts enables its use in a wide variety of contexts. However, the high activity of the enzyme also often leads to an increased fitness burden on the host, limiting the predictability of its interactions and impact on host physiology, and potentially leading to mutations in the constructs. Here we use a synthetic biology approach to design and characterize a panel of T7 RNAP expression circuits with different modes of regulation that enable the reliable expression of downstream targets under a variety of conditions. First, we describe the construction of a minimal T7 RNAP expression system that is inducible by a small molecule anhydrotetracycline (aTc), and then characterize a self-limiting T7 RNAP expression circuit that provides better control over the amount of T7 RNAP produced upon induction. Finally, we characterize a so-called T7 RNAP homeostasis circuit that leads to constitutive, continuous, and sub-toxic levels of T7 RNAP. Coupled with previously characterized mutant T7 RNAP promoters in vitro, we demonstrate that this modular framework can be used to achieve precise and predictable levels of output (sfGFP) in vivo. This new framework should now allow modeling and construction of T7 RNAP expression constructs that expand the utility of this enzyme for driving a variety of synthetic circuits and constructs.

Programmed hierarchical patterning of bacterial populations.

Modern genetic tools allow the dissection and emulation of fundamental mechanisms shaping morphogenesis in multicellular organisms. Several synthetic genetic circuits for control of multicellular patterning have been reported to date. However, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its importance in biological self-organization. Here we report a synthetic genetic system implementing population-based AND-logic for programmed autonomous induction of bacterial gene expression domains. We develop a ratiometric assay for bacteriophage T7 RNA polymerase activity and use it to systematically characterize different intact and split enzyme variants. We then utilize the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. We validate the AND gate-like behavior of this system both in cell suspension and in surface culture. Finally, we use the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations.