Whole-cell biocomputing

SemiSynBio: A new era for neuromorphic computing

Neuromorphic computing has the potential to achieve the requirements of the next-generation artificial intelligence (AI) systems, due to its advantages of adaptive learning and parallel computing. Meanwhile, biocomputing has seen ongoing development with the rise of synthetic biology, becoming the driving force for new generation semiconductor synthetic biology (SemiSynBio) technologies. DNA-based biomolecules could potentially perform the functions of Boolean operators as logic gates and be used to construct artificial neural networks (ANNs), providing the possibility of executing neuromorphic computing at the molecular level. Herein, we briefly outline the principles of neuromorphic computing, describe the advances in DNA computing with a focus on synthetic neuromorphic computing, and summarize the major challenges and prospects for synthetic neuromorphic computing. We believe that constructing such synthetic neuromorphic circuits will be an important step toward realizing neuromorphic computing, which would be of widespread use in biocomputing, DNA storage, information security, and national defense.

Harnessing split fluorescent proteins in modular protein logic for advanced whole-cell detection

Whole-cell biosensors have demonstrated promising capabilities in detecting target molecules. However, their limited selectivity and precision can be attributed to the broad substrate tolerance of natural proteins. In this study, we aim to enhance the performance of whole-cell biosensors by incorporating of logic AND gates. Specifically, we utilize the HrpR/S system, a widely employed hetero-regulation module from Pseudomonas syringae in synthetic biology, to construct an orthogonal AND gate in Escherichia coli. To accomplish this, we compare the HrpR/S system with self-associating split fluorescent proteins using the Spy Tag/Spy Catcher system. Our objective is to selectively activate a reporter gene in the presence of both IPTG and Hg(II) ions. Through systematic genetic engineering and evaluation of various biological parts under diverse working conditions, our research demonstrates the utility of self-associating split fluorescent proteins in developing high-performance whole-cell biosensors. This approach offers advantages such as engineering simplicity, reduced basal activity, and improved selectivity. Furthermore, the comparison with the HrpR/S system serves as a valuable control model, providing insights into the relative advantages and limitations of each approach. These findings present a systematic and adaptable strategy to overcome the substrate tolerance challenge faced by whole-cell biosensors.

Recent progress in nanomaterial-based bioelectronic devices for biocomputing system

Bioelectronic devices have received the massive attention because of their huge potential to develop the core electronic components for biocomputing system. Up to now, numerous bioelectronic devices have been reported such as biomemory and biologic gate by employment of biomolecules including metalloproteins and nucleic acids. However, the intrinsic limitations of biomolecules such as instability and low signal production hinder the development of novel bioelectronic devices capable of performing various novel computing functions. As a way to overcome these limitations, nanomaterials have the great potential and wide applicability to grant and extend the electronic functions, and improve the inherent properties from biomolecules. Accordingly, lots of nanomaterials including the conductive metal, graphene, and transition metal dichalcogenide nanomaterials are being used to develop the remarkable functional bioelectronic devices like the multi-bit biomemory and resistive random-access biomemory. This review discusses the nanomaterial-based superb bioelectronic devices including the biomemory, biologic gates, and bioprocessors. In conclusion, this review will provide the interdisciplinary information about utilization of various novel nanomaterials applicable for biocomputing system.

Synthetic Biology Goes Cell-Free

Cell-free systems (CFS) have recently evolved into key platforms for synthetic biology applications. Many synthetic biology tools have traditionally relied on cell-based systems, and while their adoption has shown great progress, the constraints inherent to the use of cellular hosts have limited their reach and scope. Cell-free systems, which can be thought of as programmable liquids, have removed many of these complexities and have brought about exciting opportunities for rational design and manipulation of biological systems. Here we review how these simple and accessible enzymatic systems are poised to accelerate the rate of advancement in synthetic biology and, more broadly, biotechnology.

Characterization of Pseudomonas aeruginosa Films on Different Inorganic Surfaces before and after UV Light Exposure

The changes of the surface properties of Au, GaN, and SiO _x after UV light irradiation were used to actively influence the process of formation of Pseudomonas aeruginosa films. The interfacial properties of the substrates were characterized by X-ray photoelectron spectroscopy and atomic force microscopy. The changes in the P. aeruginosa film properties were accessed by analyzing adhesion force maps and quantifying the intracellular Ca²⁺ concentration. The collected analysis indicates that the alteration of the inorganic materials' surface chemistry can lead to differences in biofilm formation and variable response from P. aeruginosa cells.

Muscle-Cell-Based "Living Diodes"

A new type of diode that is made entirely of electrically excitable muscle cells and nonexcitable fibroblast cells is designed, fabricated, and characterized. These two cell types in a rectangular pattern allow the signal initiated on the excitable side to pass to the nonexcitable side, and not in the opposite direction.

Computational Biosensors: Molecules, Algorithms, and Detection Platforms

Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.

Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit

The promise of adapting biology to information processing will not be realized until engineered gene circuits, operating in different cell populations, can be wired together to express a predictable function. Here, elementary biological integrated circuits (BICs), consisting of two sets of transmitter and receiver gene circuit modules with embedded memory placed in separate cell populations, were meticulously assembled using live cell lithography and wired together by the mass transport of quorum-sensing (QS) signal molecules to form two isolated communication links (comlinks). The comlink dynamics were tested by broadcasting "clock" pulses of inducers into the networks and measuring the responses of functionally linked fluorescent reporters, and then modeled through simulations that realistically captured the protein production and molecular transport. These results show that the comlinks were isolated and each mimicked aspects of the synchronous, sequential networks used in digital computing. The observations about the flow conditions, derived from numerical simulations, and the biofilm architectures that foster or silence cell-to-cell communications have implications for everything from decontamination of drinking water to bacterial virulence.

Sealable femtoliter chamber arrays for cell-free biology

Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g., global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) device contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Here we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques used in cellular systems to characterize CFPS gene circuits and their interactions with the cell-free environment.

Programming the quorum sensing-based AND gate in Shewanella oneidensis for logic gated-microbial fuel cells

A modularly structured, flexible, and reprogrammable AND logic gate gene circuit-controlled microbial fuel cell.

How to make a synthetic multicellular computer

Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.

Multi-input regulation and logic with T7 promoters in cells and cell-free systems

Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in an E. coli cell-free protein expression system. Our results expand the utility of T7 promoters in cell based as well as cell-free synthetic biology applications.

Molecular AND logic gate based on bacterial anaerobic respiration

Enzyme coding genes that integrate information for anaerobic respiration in Shewanella oneidensis MR-1 were used as input for constructing an AND logic gate. The absence of one or both genes inhibited electrochemically-controlled anaerobic respiration, while wild type bacteria were capable of accepting electrons from an electrode for DMSO reduction.

Enzyme-based D-flip-flop memory system

The enzyme system was used to mimic the D-flip-flop memory unit. The reversible conversion of NAD(+) and NADH cofactors was used to encode the states of the memory unit, while a mixture of inhibitors was used as the Clock input and the substrates were used as the Data input.

Fluctuations and correlations in physical and biological nanosystems: the tale is in the tails

The inherently small system sizes involved imply that, in the absence of large applied fields designed to overwhelm them, fluctuations will play a major role in determining the response and functionality of nanoscale systems. Theoretical advances over the past two decades have provided fresh insight into fluctuations and their role at the nanoscale, even in the presence of arbitrarily large applied external fields. In contrast to traditional engineered systems, Nature's approach to nanotechnology is to embrace and to exploit fluctuations and noise to create adaptable, persistent, optimized functional architectures. We describe some of the mechanisms by which Nature exploits noise, with the goal of applying these lessons to engineered physical and chemical nanosystems. In particular, we emphasize the critical role of the tails of distributions of properties in both physical and biological nanosystems and their impact on system behavior.

An IMP-Reset gate-based reusable and self-powered "smart" logic aptasensor on a microfluidic biofuel cell

The development of microfluidic devices has been spurred by the desire to produce low-cost point-of-care diagnostics and environmental monitoring devices. By combining the adaptive behavior of microfluidic biofuel cells (micro-BFCs) self-regulating the power release with aptamer IMP logic, we constructed a novel IMP-Reset gate-based reusable and self-powered on-chip aptasensor, which can be used to logically determine the presence of one specific target in the absence of another target in complex physiological samples (such as human serum) in a single test.

Assembly of Anionic Conjugated Polymer with 6-O-Modified PNP-β-Galactoside for Fluorescence Logic-signal-based Multiplex Detections of Enzymes

Anionic conjugated polymer (PFP-SO 3-) was assembled with a novel enzymatic substrate 6-O-modified PNP-β-galactoside (1) for sensitive multiplex enzyme detections. The PFP-SO 3-/1/lipase/β-galactosidase system has two chemical input signals which are Input 1 (lipase) and Input 2 (β-galactosidase), and output optical signals such as fluorescence emission at 416 nm or 450 nm. Four types of logic gates, including YES, INH, NAND and AND, were successfully constructed and utilized for multiplex detections of lipase and β-galactosidase in one tube.

Addition of glutamate to serum-free culture promotes recovery of electrical activity in adult hippocampal neurons in vitro

A long-term cell culture system utilizing normal adult hippocampal neurons would represent an important tool that could be useful in research on the mature brain, neurological disorders and age-related neurological diseases. Historically, in vitro neuronal systems are derived from embryonic rather than mature brain tissue, a practice predicated upon difficulties in supporting regeneration, functional recovery and long-term survival of adult neurons in vitro. A few studies have shown that neurons derived from the hippocampal tissue of adult rats can survive and regenerate in vitro under serum-free conditions. However, while the adult neurons regenerated morphologically under these conditions, both the electrical activity characteristic of in vivo neurons as well as long-term neuronal survival was not consistently recovered in vitro. In this study, we report on the development of a defined culture system with the ability to support functional recovery and long-term survival of adult rat hippocampal neurons. In this system, the cell-adhesive substrate, N-1 [3-(trimethoxysilyl) propyl]-diethylenetriamine, supported neuronal attachment, regeneration, and long-term survival of adult neurons for more than 80 days in vitro. Additionally, the excitatory neurotransmitter glutamate, applied at 25muM for 1-7 days after morphological neuronal regeneration in vitro, enabled full recovery of neuronal electrical activity. This low concentration of glutamate promoted the recovery of neuronal electrical activity but with minimal excitotoxicity. These improvements allowed electrically active adult neurons to survive in vitro for several months, providing a stable test-bed for the long-term study of regeneration in adult-derived neuronal systems, especially for traumatic brain injury (TBI).

Enzyme logic gate associated with a single responsive microparticle: scaling biocomputing to microsize systems

A microsize biocomputing system based on enzyme logic processing biochemical signals was developed. Optical transduction of pH signals generated in situ by the enzyme OR logic gate was achieved with the use of a single optode microparticle.

A synthetic mammalian electro-genetic transcription circuit

Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electro-genetic implants assembled from electronic and genetic parts.

Biomedical implications of information processing in chemical systems: Non-classical approach to photochemistry of coordination compounds

Analogies between photoactive nitric oxide generators and various electronic devices: logic gates and operational amplifiers are presented. These analogies have important biological consequences: application of control parameters allows for better targeting and control of nitric oxide drugs. The same methodology may be applied in the future for other therapeutic strategies and at the same time helps to understand natural regulatory and signaling processes in biological systems.

Nano-enabled synthetic biology

Biological systems display a functional diversity, density and efficiency that make them a paradigm for synthetic systems. In natural systems, the cell is the elemental unit and efforts to emulate cells, their components, and organization have relied primarily on the use of bioorganic materials. Impressive advances have been made towards assembling simple genetic systems within cellular scale containers. These biological system assembly efforts are particularly instructive, as we gain command over the directed synthesis and assembly of synthetic nanoscale structures. Advances in nanoscale fabrication, assembly, and characterization are providing the tools and materials for characterizing and emulating the smallest scale features of biology. Further, they are revealing unique physical properties that emerge at the nanoscale. Realizing these properties in useful ways will require attention to the assembly of these nanoscale components. Attention to systems biology principles can lead to the practical development of nanoscale technologies with possible realization of synthetic systems with cell-like complexity. In turn, useful tools for interpreting biological complexity and for interfacing to biological processes will result.

A synthetic biology challenge: making cells compute

Advances in biology and engineering have enabled the reprogramming of cells with well-defined functions, leading to the emergence of synthetic biology. Early successes in this nascent field suggest its potential to impact diverse areas. Here, we examine the feasibility of engineering circuits for cell-based computation. We illustrate the basic concepts by describing the mapping of several computational problems to engineered gene circuits. Revolving around these examples and past studies, we discuss technologies and computational methods available to design, test, and optimize gene circuits. We conclude with discussion of challenges involved in a typical design cycle, as well as those specific to cellular computation.