The Potential for Convergence between Synthetic Biology and Bioelectronics

Improving the Biocompatibility and Functionality of Neural Interface Devices with Silica Nanoparticles

ConspectusNeural interface technologies enable bidirectional communication between the nervous system and external instrumentation. Advancements in neural interface devices not only open new frontiers for neuroscience research, but also hold great promise for clinical diagnosis, therapy, and rehabilitation for various neurological disorders. However, the performance of current neural electrode devices, often termed neural probes, is far from satisfactory. Glial scarring, neuronal degeneration, and electrode degradation eventually cause the devices to lose their connection with the brain. To improve the chronic performance of neural probes, efforts need to be made on two fronts: enhancing the physiochemical properties of the electrode materials and mitigating the undesired host tissue response.In this Account, we discuss our efforts in developing silica-nanoparticle-based (SiNP) coatings aimed at enhancing neural probe electrochemical properties and promoting device-tissue integration. Our work focuses on three approaches:(1) SiNPs' surface texturization to enhance biomimetic protein coatings for promoting neural integration. Through covalent immobilization, SiNP introduces biologically relevant nanotopography to neural probe surfaces, enhancing neuronal cell attachments and inhibiting microglia. The SiNP base coating further increases the binding density and stability of bioactive molecules such as L1CAM and facilitates the widespread dissemination of biomimetic coatings. (2) Doping SiNPs into conductive polymer electrode coatings improves the electrochemical properties and stability. As neural interface devices are moving to subcellular sizes to escape the immune response and high electrode site density to increase spatial resolution, the electrode sites need to be very small. The smaller electrode size comes at the cost of a high electrode impedance, elevated thermal noise, and insufficient charge injection capacity. Electrochemically deposited conductive polymer films reduce electrode impedance but do not endure prolonged electrical cycling. When incorporated into conductive polymer coatings as a dopant, the SiNP provides structural support for the polymer thin films, significantly increasing their stability and durability. Low interfacial impedance maintained by the conducting polymer/SiNP composite is critical for extended electrode longevity and effective charge injection in chronic neural stimulation applications. (3) Porous nanoparticles are used as drug carriers in conductive polymer coatings for local drug/neurochemical delivery. When triggered by external electrical stimuli, drug molecules and neurochemicals can be released in a controlled manner. Such precise focal manipulation of cellular and vascular behavior enables us to probe brain circuitry and develop therapeutic applications.We foresee tremendous opportunities for further advancing the functionality of SiNP coatings by incorporating new nanoscale components and integrating the coating with other design strategies. With an enriched nanoscale toolbox and optimized design strategies, we can create customizable multifunctional and multimodal neural interfaces that can operate at multiple spatial levels and seamlessly integrate with the host tissue for extended applications.

A pro-reparative bioelectronic device for controlled delivery of ions and biomolecules

Wound healing is a complex physiological process that requires precise control and modulation of many parameters. Therapeutic ion and biomolecule delivery has the capability to regulate the wound healing process beneficially. However, achieving controlled delivery through a compact device with the ability to deliver multiple therapeutic species can be a challenge. Bioelectronic devices have emerged as a promising approach for therapeutic delivery. Here, we present a pro-reparative bioelectronic device designed to deliver ions and biomolecules for wound healing applications. The device incorporates ion pumps for the targeted delivery of H+ and zolmitriptan to the wound site. In vivo studies using a mouse model further validated the device's potential for modulating the wound environment via H+ delivery that decreased M1/M2 macrophage ratios. Overall, this bioelectronic ion pump demonstrates potential for accelerating wound healing via targeted and controlled delivery of therapeutic agents to wounds. Continued optimization and development of this device could not only lead to significant advancements in tissue repair and wound healing strategies but also reveal new physiological information about the dynamic wound environment.

Electroceuticals: emerging applications beyond the nervous system and excitable tissues

Electroceuticals have evolved beyond devices manipulating neuronal signaling for symptomatic treatment, becoming more precise and disease modulating and expanding beyond the nervous system. These advancements promise transformative applications in arthritis, cancer treatment, tissue regeneration, and more. Here, we discuss these recent advances and offer insights for future research.

Living electrochemical biosensing: Engineered electroactive bacteria for biosensor development and the emerging trends

Bioelectrical interfaces made of living electroactive bacteria (EAB) provide a unique opportunity to bridge biotic and abiotic systems, enabling the reprogramming of electrochemical biosensing. To develop these biosensors, principles from synthetic biology and electrode materials are being combined to engineer EAB as dynamic and responsive transducers with emerging, programmable functionalities. This review discusses the bioengineering of EAB to design active sensing parts and electrically connective interfaces on electrodes, which can be applied to construct smart electrochemical biosensors. In detail, by revisiting the electron transfer mechanism of electroactive microorganisms, engineering strategies of EAB cells for biotargets recognition, sensing circuit construction, and electrical signal routing, engineered EAB have demonstrated impressive capabilities in designing active sensing elements and developing electrically conductive interfaces on electrodes. Thus, integration of engineered EAB into electrochemical biosensors presents a promising avenue for advancing bioelectronics research. These hybridized systems equipped with engineered EAB can promote the field of electrochemical biosensing, with applications in environmental monitoring, health monitoring, green manufacturing, and other analytical fields. Finally, this review considers the prospects and challenges of the development of EAB-based electrochemical biosensors, identifying potential future applications.

Modeling control and transduction of electrochemical gradients in acid-stressed bacteria

Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.

Parallel transmission in a synthetic nerve

Bioelectronic devices that are tetherless and soft are promising developments in medicine, robotics and chemical computing. Here, we describe bioinspired synthetic neurons, composed entirely of soft, flexible biomaterials, capable of rapid electrochemical signal transmission over centimetre distances. Like natural cells, our synthetic neurons release neurotransmitters from their terminals, which initiate downstream reactions. The components of the neurons are nanolitre aqueous droplets and hydrogel fibres, connected through lipid bilayers. Transmission is powered at these interfaces by light-driven proton pumps and mediated by ion-conducting protein pores. By bundling multiple neurons into a synthetic nerve, we have shown that distinct signals can propagate simultaneously along parallel axons, thereby transmitting spatiotemporal information. Synthetic nerves might play roles in next-generation implants, soft machines and computing devices.

Biology-guided engineering of bioelectrical interfaces

Bioelectrical interfaces that bridge biotic and abiotic systems have heightened the ability to monitor, understand, and manipulate biological systems and are catalyzing profound progress in neuroscience research, treatments for heart failure, and microbial energy systems. With advances in nanotechnology, bifunctional and high-density devices with tailored structural designs are being developed to enable multiplexed recording or stimulation across multiple spatial and temporal scales with resolution down to millisecond-nanometer interfaces, enabling efficient and effective communication with intracellular electrical activities in a relatively noninvasive and biocompatible manner. This review provides an overview of how biological systems guide the design, engineering, and implementation of bioelectrical interfaces for biomedical applications. We investigate recent advances in bioelectrical interfaces for applications in nervous, cardiac, and microbial systems, and we also discuss the outlook of state-of-the-art biology-guided bioelectrical interfaces with high biocompatibility, extended long-term stability, and integrated system functionality for potential clinical usage.

Mediated electrochemistry for redox-based biological targeting: entangling sensing and actuation for maximizing information transfer

Biology and electronics are both expert at receiving, analyzing, and responding to information, yet they use entirely different information processing paradigms. Biology processes information using networks that are intrinsically molecular while electronics process information through circuits that control the flow of electrons. There is great interest in coupling the molecular logic of biology with the electronic logic of technology, and we suggest that redox (reduction-oxidation) is a uniquely suited modality for interfacing biology with electronics. Specifically, redox is a native biological modality and is accessible to electronics through electrodes. We summarize recent advances in mediated electrochemistry to direct information transfer into biological systems intentionally altering function, exposing it for more advanced interpretation, which can dramatically expand the biotechnological toolbox.

Mediated Electrochemical Probing: A Systems-Level Tool for Redox Biology

Biology uses well-known redox mechanisms for energy harvesting (e.g., respiration), biosynthesis, and immune defense (e.g., oxidative burst), and now we know biology uses redox for systems-level communication. Currently, we have limited abilities to "eavesdrop" on this redox modality, which can be contrasted with our abilities to observe and actuate biology through its more familiar ionic electrical modality. In this Perspective, we argue that the coupling of electrochemistry with diffusible mediators (electron shuttles) provides a unique opportunity to access the redox communication modality through its electrical features. We highlight previous studies showing that mediated electrochemical probing (MEP) can "communicate" with biology to acquire information and even to actuate specific biological responses (i.e., targeted gene expression). We suggest that MEP may reveal an extent of redox-based communication that has remained underappreciated in nature and that MEP could provide new technological approaches for redox biology, bioelectronics, clinical care, and environmental sciences.

Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology

The construction of artificial cells from inanimate molecular building blocks is one of the grand challenges of our time. In addition to being used as simplified cell models to decipher the rules of life, artificial cells have the potential to be designed as micromachines deployed in a host of clinical and industrial applications. The attractions of engineering artificial cells from scratch, as opposed to re-engineering living biological cells, are varied. However, it is clear that artificial cells cannot currently match the power and behavioural sophistication of their biological counterparts. Given this, many in the synthetic biology community have started to ask: is it possible to interface biological and artificial cells together to create hybrid living/synthetic systems that leverage the advantages of both? This article will discuss the motivation behind this cellular bionics approach, in which the boundaries between living and non-living matter are blurred by bridging top-down and bottom-up synthetic biology. It details the state of play of this nascent field and introduces three generalised hybridisation modes that have emerged.

Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology

The construction of artificial cells from inanimate molecular building blocks is one of the grand challenges of our time. In addition to being used as simplified cell models to decipher the rules of life, artificial cells have the potential to be designed as micromachines deployed in a host of clinical and industrial applications. The attractions of engineering artificial cells from scratch, as opposed to re-engineering living biological cells, are varied. However, it is clear that artificial cells cannot currently match the power and behavioural sophistication of their biological counterparts. Given this, many in the synthetic biology community have started to ask: is it possible to interface biological and artificial cells together to create hybrid living/synthetic systems that leverage the advantages of both? This article will discuss the motivation behind this cellular bionics approach, in which the boundaries between living and non-living matter are blurred by bridging top-down and bottom-up synthetic biology. It details the state of play of this nascent field and introduces three generalised hybridisation modes that have emerged.

Clinical Potential of Nerve Input to Tumors: A Bioelectricity Perspective

We support the notion that the neural connections of the tumor microenvironment (TME) and the associated 'bioelectricity' play significant role in the pathophysiology of cancer. In several cancers, the nerve input promotes the cancer process. While straightforward surgical denervation of tumors, therefore, could improve prognosis, resulting side effects of such a procedure would be unpredictable and irreversible. On the other hand, tumor innervation can be manipulated effectively for therapeutic purposes by alternative novel approaches broadly termed "electroceuticals." In this perspective, we evaluate the clinical potential of targeting the TME first through manipulation of the nerve input itself and second by application of electric fields directly to the tumor. The former encompasses several different biophysical and biochemical approaches. These include implantable devices, nanoparticles, and electroactive polymers, as well as optogenetics and chemogenetics. As regard bioelectrical manipulation of the tumor itself, the "tumor-treating field" technique, applied to gliomas commonly in combination with chemotherapy, is evaluated. Also, as electroceuticals, drugs acting on ion channels and neurotransmitter receptors are highlighted for completeness. It is concluded, first, that electroceuticals comprise a broad range of biomedical tools. Second, such electroceuticals present significant clinical potential for exploiting the neural component of the TME as a strategy against cancer. Finally, the inherent bioelectric characteristics of tumors themselves are also amenable to complementary approaches. Collectively, these represent an evolving, dynamic field and further progress and applications can be expected to follow both conceptually and technically.

Sensing the future of bio-informational engineering

The practices of synthetic biology are being integrated into 'multiscale' designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of 'bio-informational' engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.

Functional roles of microbial cell-to-cell heterogeneity and emerging technologies for analysis and control

Clonal cell populations often display significant cell-to-cell phenotypic heterogeneity, even when maintained under constant external conditions. This variability can result from the inherently stochastic nature of transcription and translation processes, which leads to varying numbers of transcripts and proteins per cell. Here, we showcase studies that reveal links between stochastic cellular events and biological functions in isogenic microbial populations. Then, we highlight emerging tools from engineering, computation, and synthetic and molecular biology that enable precise measurement, control, and analysis of gene expression noise in microorganisms. The capabilities offered by this sophisticated toolbox will shape future directions in the field and generate insight into the behavior of living systems at the single-cell level.

Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology

Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.

A Microfluidic Ion Sensor Array

A balanced concentration of ions is essential for biological processes to occur. For example, [H⁺ ] gradients power adenosine triphosphate synthesis, dynamic changes in [K⁺ ] and [Na⁺ ] create action potentials in neuronal communication, and [Cl^- ] contributes to maintaining appropriate cell membrane voltage. Sensing ionic concentration is thus important for monitoring and regulating many biological processes. This work demonstrates an ion-selective microelectrode array that simultaneously and independently senses [K⁺ ], [Na⁺ ], and [Cl^- ] in electrolyte solutions. To obtain ion specificity, the required ion-selective membranes are patterned using microfluidics. As a proof of concept, the change in ionic concentration is monitored during cell proliferation in a cell culture medium. This microelectrode array can easily be integrated in lab-on-a-chip approaches to physiology and biological research and applications.

Endogenous Bioelectrics in Development, Cancer, and Regeneration: Drugs and Bioelectronic Devices as Electroceuticals for Regenerative Medicine

A major frontier in the post-genomic era is the investigation of the control of coordinated growth and three-dimensional form. Dynamic remodeling of complex organs in regulative embryogenesis, regeneration, and cancer reveals that cells and tissues make decisions that implement complex anatomical outcomes. It is now essential to understand not only the genetics that specifies cellular hardware but also the physiological software that implements tissue-level plasticity and robust morphogenesis. Here, we review recent discoveries about the endogenous mechanisms of bioelectrical communication among non-neural cells that enables them to cooperate in vivo. We discuss important advances in bioelectronics, as well as computational and pharmacological tools that are enabling the taming of biophysical controls toward applications in regenerative medicine and synthetic bioengineering.

Metabolic perceptrons for neural computing in biological systems

Synthetic biological circuits are promising tools for developing sophisticated systems for medical, industrial, and environmental applications. So far, circuit implementations commonly rely on gene expression regulation for information processing using digital logic. Here, we present a different approach for biological computation through metabolic circuits designed by computer-aided tools, implemented in both whole-cell and cell-free systems. We first combine metabolic transducers to build an analog adder, a device that sums up the concentrations of multiple input metabolites. Next, we build a weighted adder where the contributions of the different metabolites to the sum can be adjusted. Using a computational model fitted on experimental data, we finally implement two four-input perceptrons for desired binary classification of metabolite combinations by applying model-predicted weights to the metabolic perceptron. The perceptron-mediated neural computing introduced here lays the groundwork for more advanced metabolic circuits for rapid and scalable multiplex sensing.

So far, synthetic genetic circuits have relied on digital logic for information processing. Here the authors present metabolic perceptrons that use analog weighted adders to vary the contributions of multiple inputs, resulting in different classification functions.

An atlas of nano-enabled neural interfaces

Advances in microscopy and molecular strategies have allowed researchers to gain insight into the intricate organization of the mammalian brain and the roles that neurons play in processing information. Despite vast progress, therapeutic strategies for neurological disorders remain limited, owing to a lack of biomaterials for sensing and modulating neuronal signalling in vivo. Therefore, there is a pressing need for developing material-based tools that can form seamless biointerfaces and interrogate the brain with unprecedented resolution. In this Review, we discuss important considerations in material design and implementation, highlight recent breakthroughs in neural sensing and modulation, and propose future directions in neurotechnology research. Our goal is to create an atlas for nano-enabled neural interfaces and to demonstrate how emerging nanotechnologies can interrogate neural systems spanning multiple biological length scales.

Synthetic Biology of Yeast

With the rapid development of DNA synthesis and next-generation sequencing, synthetic biology that aims to standardize, modularize, and innovate cellular functions, has achieved vast progress. Here we review key advances in synthetic biology of the yeast Saccharomyces cerevisiae, which serves as an important eukaryal model organism and widely applied cell factory. This covers the development of new building blocks, i.e., promoters, terminators and enzymes, pathway engineering, tools developments, and gene circuits utilization. We will also summarize impacts of synthetic biology on both basic and applied biology, and end with further directions for advancing synthetic biology in yeast.

Is Research on "Synthetic Cells" Moving to the Next Level?

"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?