A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

Collaborative light-off and light-on bacterial luciferase biosensors: Innovative approach for rapid contaminant detection

Bioluminescence-based light-off and light-on biosensors are widely used in environmental monitoring due to their rapid, cost-effective, real-time, and easy operation. However, stability and sensitivity issues in detecting real samples remain challenging. This study introduces a novel approach utilizing combined light-off and light-on biosensors for rapid and sensitive contaminants detection within 45 min in real samples. First, a recombinase-based state machine (RSM) was used to construct light-off RSM biosensors (light-off RSMs) for continuously strong light emission and overexpressing of outer membrane porins OmpC and OmpF enhanced their sensitivity to toxic contaminants. Additionally, a new experimental protocol containing the cell culture, collection, preparation, and the contaminant measurement was established for bioluminescent light-on whole-cell biosensors (light-on WCBs) in contaminant detection, initially developed using cadmium (Cd) and later applied to lead (Pb) and mercury (Hg). For Cd light-on WCBs, overexpressing OmpC and knocking out the contaminant exporter ZntA enhanced the accumulation of intracellular Cd in WCB cells, resulting in increased sensitivity to low concentrations of contaminants. Further, metabolic modifications in light-on WCBs significantly boosted luminescence. These genetic modified bacterial strains, whether freshly harvested or as freeze-dried powders, showed rapid luminescent responses to contaminants in the picomolar (pM) to nanomolar (nM) range within 45 min. Finally, the combined use of light-off RSMs and light-on WCBs successfully assessed toxicity and detected specific contaminants in real environmental and food samples. These strategies could be applied to developing other bacterial luciferase-based biosensors and even other types such as colorimetric biosensors.

Paving the way for bacteria-based drug delivery: biohybrid microrobots emerging from microrobotics and synthetic biology

Advances in microrobotics and synthetic biology are paving the way for innovative solutions to long-standing challenges in drug delivery. Both fields have independently worked on engineering bacteria as a therapeutic system, focusing on enhancing propulsion, cargo delivery, detection, and biocompatibility. Bacteria, with their inherent adaptability and functional versatility, serve as an ideal foundation for these efforts, enabling them to navigate complex biological environments such as the human body. This review explores the convergence of microrobotics and synthetic biology, which has catalysed the development of biohybrid bacterial microrobots that integrate the strengths of both disciplines. By incorporating external control modalities - such as light, ultrasound, and magnetic fields - these hybrid systems address the limitations of purely microrobotic or biological approaches, offering new opportunities to enhance precision and efficacy in targeted therapies. However, realising the full potential of biohybrid bacterial microrobots requires overcoming critical challenges, such as ensuring compatibility between biological and synthetic components, scaling manufacturing processes, and defining regulatory pathways tailored to living therapeutics. Addressing these hurdles through joint, interdisciplinary research efforts, can unlock the transformative possibilities of these systems in modern medicine.

Innovative applications and research advances of bacterial biosensors in medicine

The demand for early disease detection, treatment monitoring, and personalized medicine is increasing, making it more imperative than ever to create effective, accurate, portable, intelligent, multifunctional diagnostic equipment. Bacteria possess a remarkable perception of their surroundings and have the capacity to adapt by altering the expression of specific genes. Bacteria interact with target substances and produce detectable signals in response to their presence or concentration. This unique property has been harnessed in the development of bacterial biosensors. Due to groundbreaking advancements in synthetic biology, genetic engineering now enables the creation of bacteria tailored with exceptional detecting traits. In addition to meeting a wide range of application needs, this allows quick and precise detection in intricate settings and offers a strong technological basis for early disease diagnosis and treatment monitoring. This article reviews the applications and recent advancements of bacterial biosensors in the medical field and discusses the challenges and obstacles that remain in their research and application.

Challenges of Using Whole-Cell Bioreporter for Assessment of Heavy Metal Bioavailability in Soil/Sediment

Soil and sediment contamination with heavy metals (HMs) is a critical environmental issue, posing significant risks to both ecosystems and human health. Whole-cell bioreporter (WCB) technology offers a promising alternative to traditional detection techniques due to its ability to rapidly assess the bioavailability of pollutants. Specifically, lights-on WCBs quantify pollutant bioavailability by measuring bioluminescence or fluorescence in response to pollutant exposure, demonstrating comparable accuracy to traditional methods for quantitative pollutant detection. However, when applied to soil and sediment, the signal intensity directly measured by WCBs is often attenuated due to interference from solid particles, leading to the underestimation of bioavailability. Currently, no standardized method exists to correct for this signal attenuation. This review provides a critical analysis of the benefits and limitations of traditional detection methods and WCB technology in assessing HM bioavailability in soil and sediment. Based on the approaches used to address WCB signal attenuation, correction methods are categorized into four types: the assumed negligible method, the non-inducible luminescent control method, the addition of a standard to a reference soil, and a pre-exposure bioreporter. We provide a comprehensive analysis of each method's applicability, benefits, and limitations. Lastly, potential future directions for advancing WCB technology are proposed. This review seeks to establish a theoretical foundation for researchers and environmental professionals utilizing WCB technology for pollutant bioavailability assessment in soil and sediment.

Engineering intercellular communication using M13 phagemid and CRISPR-based gene regulation for multicellular computing in Escherichia coli

Engineering multicellular consortia, where information processing is distributed across specialized cell types, offers a promising strategy for implementing sophisticated biocomputing systems. However, a major challenge remains in establishing orthogonal intercellular communication, or "wires," within synthetic bacterial consortia. In this study, we address this bottleneck by integrating phagemid-mediated intercellular communication with CRISPR-based gene regulation for multicellular computing in synthetic E. coli consortia. We achieve intercellular communication with high sensitivity by regulating the transfer of single guide RNAs (sgRNAs) encoded on M13 phagemids from sender to receiver cells. Once inside the receiver cells, the transferred sgRNAs mediate gene regulation via CRISPR interference. Leveraging this approach, we successfully constructed one-, two-, and four-input logic gates. Our work expands the toolkit for intercellular communication and paves the way for complex information processing in synthetic microbial consortia, with diverse potential applications, including biocomputing, biosensing, and biomanufacturing.

Enhancement of Sensitivity in Aggregation-Based Whole-Cell Arsenite Sensor Utilizing Arsenic Metabolism Regulation

Arsenite [As(III)] is a toxic substance widely present on Earth, and the development of low-cost and simple microbial-based As(III) sensors has been attracting attention. Recently, we discovered that the protein LuxR, which contains multiple cysteine residues with high affinity for As(III), forms an insoluble structure upon binding to As(III) and exhibits OFF-switching properties as a quorum sensing transcriptional activator. Based on this property, the LuxR sensor operates on a new principle distinct from conventional whole-cell As(III) sensors; however, its sensitivity remains a challenge. In this study, we aimed to improve the sensitivity of the whole-cell OFF-type As(III) sensor by increasing the frequency of intracellular interactions between the sensor protein and As(III). We utilized the super-repressor properties of ArsR, a transcriptional repressor of the As(III)-metabolizing ars operon, achieved by replacing C34 in its As(III)-binding domain with Y. By linking ArsRC34Y with the OFF-type As(III) sensor protein LuxR, we constructed a single plasmid to create a portable ArsRC34Y-LuxR sensor protein. By suppressing the expression of ArsB, an As(III) efflux transporter encoded in the ars operon, using ArsRC34Y, we successfully enhanced the sensitivity of the OFF-type As(III) response.

A sensitive PnpR-based biosensor for p-nitrophenol detection

A common aromatic and phenolic pollutant, p-nitrophenol (PNP), is widely used in various industry and has serious risk to the environmental health. Biosensors have been extensively employed as an alternative technology for pollutants monitoring. By mining the new sensing elements, more specific biosensors could be characterized for highly sensitive detection. Herein, the PnpR transcription factor was identified to activate the transcription of pnpC1 by binding to PpnpC1 promoter region in P. putida DLL-E4, and PNP was recognized as its specific inducer. The PnpR-based biosensor for detection of PNP was developed, demonstrating adequate sensitivity in a liquid solution with satisfactory specificity. The biosensor was optimized by adopting a transcriptional amplifier, which increased the maximum output by 149-fold, and improved the detection limit by 100-fold, from 1 mg/L to 10 μg/L. These biosensors had a linear range of 5-80 mg/L and 0.01-1.0 mg/L for PNP determination, respectively. Then, the agarose gel entrapment-based biosensor was constructed and allowed a good of PNP detection in the range of 5-60 mg/L in M9 solid agar within 70 min, and a detection sensitive of 16.8 mg/kg in soil. The good performance of the biosensor suggested its potential application of high-efficient and on-site detection in environmental matrices.

Genetically engineered bacteria as inflammatory bowel disease therapeutics

Inflammatory bowel disease (IBD) is a chronic and recurrent disease caused by immune response disorders that disrupt the intestinal lumen symbiotic ecosystem and dysregulate mucosal immune functions. Current therapies available for IBD primarily focus on symptom management, making early diagnosis and prompt intervention challenging. The development of genetically engineered bacteria using synthetic biology presents a new strategy for addressing these challenges. In this review, we present recent breakthroughs in the field of engineered bacteria for the treatment and detection of IBD and describe how bacteria can be genetically modified to produce therapeutic molecules or execute diagnostic functions. In particular, we discuss the challenges faced in translating live bacterial therapeutics from bacterial design to delivery strategies for further clinical applications.

Development of CadR-based cadmium whole cell biosensor for visual detection of environmental Cd2

BACKGROUND

As a threat to human health and public health, cadmium (Cd) pollution has received widespread social concern. Our previously constructed CadR-based bacterial whole cell biosensor (WCB) epCadR5 showed high sensitivity and specificity in cadmium detection. However, the application of the sensor is still hindered by the need for laboratory equipment to read the fluorescence signal output. In this study, we aimed to optimizing the sensor to make it available for visual detection of environmental cadmium and simplify the detection process to advance practical application of the sensor.

RESULTS

By replacing the constitutive promoter with J110, the fluorescence signal output of the sensor was significantly increased and the fluorescence leakage was decreased. In addition, the fluorescence signal output of green fluorescence protein (GFP) was enhanced by the addition of a 5' untranslated region (5'-UTR) mlcR10. The fluorescence signal output of the WCB is sufficiently robust to be visible and distinguishable to the naked eye, which is of paramount importance for visual detection. The sensor readout can be conveniently recorded by mobile phone camera and quantified. For ease of on-site application, the WCB's visual detection procedures and conditions were further optimized and simplified. The WCB demonstrated good linearity and detection limit (1.81 μg/L) for visual detection of Cd2+ without the assistance of bulky laboratory equipment. For the detection of real environmental samples, the WCB visual detection results were close to those of WCB-flow cytometry (FACS) and graphite furnace atomic absorption spectroscopy (GFAAS).

SIGNIFICANCE

In this work, we developed an easy-to-use, on-site and visual detection biosensor for monitoring environmental Cd2+. It will advance the utilization of cadmium WCBs in practical settings. The optimization and simplification strategy in the study also provide new insights into the visualization of other bacterial biosensors, and will advance the practical application of WCBs.

Development of a two component system based biosensor with high sensitivity for the detection of copper ions

Recent advancements in bacterial two-component systems (TCS) have spurred research into TCS-based biosensors, notably for their signal amplification and broad input responsiveness. The CusRS system in Escherichia coli (E. coli), comprising cusS and cusR genes, is a copper-sensing module in E. coli. However, due to insufficient sensing performance, CusRS-based biosensors often cannot meet practical requirements. To address this issue, we made improvements and innovation from several aspects. CusR and CusS expression were adjusted to enhance the Cu(II) biosensor's performance. A copy-number inducible plasmid was used for signal amplification, while removing copper detox genes cueO and cusCFBA improved sensitivity and lowered detection limits. Ultimately, in the optimized biosensor of Cu26, the fold-change (I/I0) increased from 1.5-fold to 18-fold at 1 μM, rising to 100-fold after optimizing the cell culture procedure. The biosensor's high fluorescence enabled rapid, instrument-free detection and an improved analysis strategy reduced the detection limit to 0.01 μM, surpassing traditional methods.

Genetically programmed synthetic cells for thermo-responsive protein synthesis and cargo release

Synthetic cells containing genetic programs and protein expression machinery are increasingly recognized as powerful counterparts to engineered living cells in the context of biotechnology, therapeutics and cellular modelling. So far, genetic regulation of synthetic cell activity has been largely confined to chemical stimuli; to unlock their potential in applied settings, engineering stimuli-responsive synthetic cells under genetic regulation is imperative. Here we report the development of temperature-sensitive synthetic cells that control protein production by exploiting heat-responsive mRNA elements. This is achieved by combining RNA thermometer technology, cell-free protein expression and vesicle-based synthetic cell design to create cell-sized capsules able to initiate synthesis of both soluble proteins and membrane proteins at defined temperatures. We show that the latter allows for temperature-controlled cargo release phenomena with potential implications for biomedicine. Platforms like the one presented here can pave the way for customizable, genetically programmed synthetic cells under thermal control to be used in biotechnology.

Engineered Bacteria as Living Biosensors in Dermal Tattoos

Dermal tattoo biosensors are promising platforms for real-time monitoring of biomarkers, with skin used as a diagnostic interface. Traditional tattoo sensors have utilized small molecules as biosensing elements. However, the rise of synthetic biology has enabled the potential employment of engineered bacteria as living analytical tools. Exploiting engineered bacterial sensors will allow for potentially more sensitive detection across a broad biomarker range, with advanced processing and sense/response functionalities using genetic circuits. Here, the interfacing of bacterial biosensors as living analytics in tattoos is shown. Engineered bacteria are encapsulated into micron-scale hydrogel beads prepared through scalable microfluidics. These biosensors can sense both biochemical cues (model biomarkers) and biophysical cues (temperature changes, using RNA thermometers), with fluorescent readouts. By tattooing beads into skin models and confirming sensor activity post-tattooing, our study establishes a foundation for integrating bacteria as living biosensing entities in tattoos.

Controllable detection threshold achieved through the toehold switch system in a mercury ion whole-cell biosensor

Due to the toxicity of mercury and its harmful effects on human health, it is essential to establish a low-cost, highly sensitive and highly specific monitoring method with a wide detection range, ideally with a simple visual readout. In this study, a whole-cell biosensor with adjustable detection limits was developed for the detection of mercury ions in water samples, allowing controllable threshold detection with an expanded detection range. Gene circuits were constructed by combining the toehold switch system with lactose operon, mercury-ion-specific operon, and inducible red fluorescent protein gene. Using MATLAB for design and selection, a total of eleven dual-input single-output sensing logic circuits were obtained based on the basic logic of gene circuit construction. Then, biosensor DTS-3 was selected based on its fluorescence response at different isopropyl β-D-Thiogalactoside (IPTG) concentrations, exhibiting the controllable detection threshold. At 5-20 μM IPTG, DTS-3 can achieve variable threshold detection in the range of 0.005-0.0075, 0.06-0.08, 1-2, and 4-6 μM mercury ion concentrations, respectively. Specificity experiments demonstrated that DTS-3 exhibits good specificity, not showing fluorescence response changes compared with other metal ions. Furthermore spiked sample experiments demonstrated its good resistance to interference, allowing it to distinguish mercury ion concentrations as low as 7.5 nM by the naked eye and 5 nM using a microplate reader. This study confirms the feasibility and performance of biosensor with controllable detection threshold, providing a new detection method and new ideas for expanding the detection range of biosensors while ensuring rapid and convenient measurements without compromising sensitivity.

Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology

Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.

An insight on the plausible biological and non-biological detoxification of heavy metals in tannery waste: A comprehensive review

A key challenge for the tannery industries is the volume of tannery waste water (TWW) generated during the processing of leather, releasing various forms of toxic heavy metals resulting in uncontrolled discharge of tannery waste (TW) into the environment leading to pollution. The pollutants in TW includes heavy metals such as chromium (Cr), cadmium (Cd), lead (Pb) etc, when discharged above the permissible limit causes ill effects on humans. Therefore, several researchers have reported the application of biological and non-biological methods for the removal of pollutants in TW. This review provides insights on the global scenario of tannery industries and the harmful effects of heavy metal generated by tannery industry on micro and macroorganisms of the various ecological niches. It also provides information on the process, advantages and disadvantages of non-biological methods such as electrochemical oxidation, advanced oxidation processes, photon assisted catalytic remediation, adsorption and membrane technology. The various biological methods emphasised includes strategies such as constructed wetland, vermitechnology, phytoremediation, bioaugmentation, quorum sensing and biofilm in the remediation of heavy metals from tannery wastewater (TWW) with special emphasize on chromium.

Progress in Identification of UDP-Glycosyltransferases for Ginsenoside Biosynthesis

Ginsenosides, the primary pharmacologically active constituents of the Panax genus, have demonstrated a variety of medicinal properties, including anticardiovascular disease, cytotoxic, antiaging, and antidiabetes effects. However, the low concentration of ginsenosides in plants and the challenges associated with their extraction impede the advancement and application of ginsenosides. Heterologous biosynthesis represents a promising strategy for the targeted production of these natural active compounds. As representative triterpenoids, the biosynthetic pathway of the aglycone skeletons of ginsenosides has been successfully decoded. While the sugar moiety is vital for the structural diversity and pharmacological activity of ginsenosides, the mining of uridine diphosphate-dependent glycosyltransferases (UGTs) involved in ginsenoside biosynthesis has attracted a lot of attention and made great progress in recent years. In this paper, we summarize the identification and functional study of UGTs responsible for ginsenoside synthesis in both plants, such as Panax ginseng and Gynostemma pentaphyllum, and microorganisms including Bacillus subtilis and Saccharomyces cerevisiae. The UGT-related microbial cell factories for large-scale ginsenoside production are also mentioned. Additionally, we delve into strategies for UGT mining, particularly potential rapid screening or identification methods, providing insights and prospects. This review provides insights into the study of other unknown glycosyltransferases as candidate genetic elements for the heterologous biosynthesis of rare ginsenosides.

Cascaded amplifying circuit enables sensitive detection of fungal pathogens

The rapid and accurate detection of fungal pathogens is of utmost importance in the fields of healthcare, food safety, and environmental monitoring. In this study, we implemented a cascaded amplifying circuit in Saccharomyces cerevisiae to improve the G protein-coupled receptor (GPCR) mediated fungal detection. The GPCR signaling pathway was coupled with the galactose-regulated (GAL) system and a positive feedback loop was implemented to enhance the performance of yeast biosensor. We systematically compared four generations of biosensors for detecting the mating pheromone of Candida albicans, and the best biosensor exhibited the limit of detection (LOD) as low as 0.25 pM and the limit of quantification (LOQ) of 1 pM after 2 h incubation. Subsequently, we developed a betaxanthin-based colorimetric module for the easy visualization of signal outputs, and the resulting biosensors can give reliable naked-eye readouts. In summary, we demonstrated that cascaded amplifying circuits could substantially improve the engineered yeast biosensors with a better sensitivity and signal output magnitude, which will pave the way for their real-world applications in public health.

Genetic Parts and Enabling Tools for Biocircuit Design

Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.

Design and Model-Driven Analysis of Synthetic Circuits with the Staphylococcus aureus Dead-Cas9 (sadCas9) as a Programmable Transcriptional Regulator in Bacteria

Synthetic circuit design is crucial for engineering microbes that process environmental cues and provide biologically relevant outputs. To reliably scale-up circuit complexity, the availability of parts toolkits is central. Streptococcus pyogenes (sp)-derived CRISPR interference/dead-Cas9 (CRISPRi/spdCas9) is widely adopted for implementing programmable regulations in synthetic circuits, and alternative CRISPRi systems will further expand our toolkits of orthogonal components. Here, we showcase the potential of CRISPRi using the engineered dCas9 from Staphylococcus aureus (sadCas9), not previously used in bacterial circuits, that is attractive for its low size and high specificity. We designed a collection of ∼20 increasingly complex circuits and variants in Escherichia coli, including circuits with static function like one-/two-input logic gates (NOT, NAND), circuits with dynamic behavior like incoherent feedforward loops (iFFLs), and applied sadCas9 to fix a T7 polymerase-based cascade. Data demonstrated specific and efficient target repression (100-fold) and qualitatively successful functioning for all circuits. Other advantageous features included low sadCas9-borne cell load and orthogonality with spdCas9. However, different circuit variants showed quantitatively unexpected and previously unreported steady-state responses: the dynamic range, switch point, and slope of NOT/NAND gates changed for different output promoters, and a multiphasic behavior was observed in iFFLs, differing from the expected bell-shaped or sigmoidal curves. Model analysis explained the observed curves by complex interplays among components, due to reporter gene-borne cell load and regulator competition. Overall, CRISPRi/sadCas9 successfully expanded the available toolkit for bacterial engineering. Analysis of our circuit collection depicted the impact of generally neglected effects modulating the shape of component dose-response curves, to avoid drawing wrong conclusions on circuit functioning.

Tailored bacteria tackling with environmental mercury: Inspired by natural mercuric detoxification operons

Mercury (Hg) and its inorganic and organic compounds significantly threaten the ecosystem and human health. However, the natural and anthropogenic Hg environmental inputs exceed 5000 metric tons annually. Hg is usually discharged in elemental or ionic forms, accumulating in surface water and sediments where Hg-methylating microbes-mediated biotransformation occurs. Microbial genetic factors such as the mer operon play a significant role in the complex Hg biogeochemical cycle. Previous reviews summarize the fate of environmental Hg, its biogeochemistry, and the mechanism of bacterial Hg resistance. This review mainly focuses on the mer operon and its components in detecting, absorbing, bioaccumulating, and detoxifying environmental Hg. Four components of the mer operon, including the MerR regulator, divergent mer promoter, and detoxification factors MerA and MerB, are rare bio-parts for assembling synthetic bacteria, which tackle pollutant Hg. Bacteria are designed to integrate synthetic biology, protein engineering, and metabolic engineering. In summary, this review highlights that designed bacteria based on the mer operon can potentially sense and bioremediate pollutant Hg in a green and low-cost manner.

Recent Developments and Applications of Microbial Electrochemical Biosensors

This chapter provides a comprehensive overview of microbial electrochemical biosensors, which are a unique class of biosensors that utilize the metabolic activity of microorganisms to convert chemical signals into electrical signals. The principles and mechanisms of these biosensors are discussed, including the different types of microorganisms that can be used. The various applications of microbial electrochemical biosensors in fields such as environmental monitoring, medical diagnostics, and food safety are also explored. The chapter concludes with a discussion of future research directions and potential advancements in the field of microbial electrochemical biosensors.

A Genetic Circuit Design for Targeted Viral RNA Degradation

Advances in synthetic biology have led to the design of biological parts that can be assembled in different ways to perform specific functions. For example, genetic circuits can be designed to execute specific therapeutic functions, including gene therapy or targeted detection and the destruction of invading viruses. Viral infections are difficult to manage through drug treatment. Due to their high mutation rates and their ability to hijack the host's ribosomes to make viral proteins, very few therapeutic options are available. One approach to addressing this problem is to disrupt the process of converting viral RNA into proteins, thereby disrupting the mechanism for assembling new viral particles that could infect other cells. This can be done by ensuring precise control over the abundance of viral RNA (vRNA) inside host cells by designing biological circuits to target vRNA for degradation. RNA-binding proteins (RBPs) have become important biological devices in regulating RNA processing. Incorporating naturally upregulated RBPs into a gene circuit could be advantageous because such a circuit could mimic the natural pathway for RNA degradation. This review highlights the process of viral RNA degradation and different approaches to designing genetic circuits. We also provide a customizable template for designing genetic circuits that utilize RBPs as transcription activators for viral RNA degradation, with the overall goal of taking advantage of the natural functions of RBPs in host cells to activate targeted viral RNA degradation.

Customizing cellular signal processing by synthetic multi-level regulatory circuits

As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.

Establishing Tunable Genetic Logic Gates with Versatile Dynamic Performance by Varying Regulatory Parameters

Genetic logic gates can be employed in metabolic engineering and synthetic biology to regulate gene expression based on diverse inputs. Design of tunable genetic logic gates with versatile dynamic performance is essential for expanding the usability of these toolsets. Here, using the p-coumaric acid biosensor system as a proof-of-concept, we initially investigated the parameters influencing the buffer (BUF) genetic logic gates. Subsequently, integrating binding sequences from the p-coumaric acid biosensor system and tetR or lacI regulation systems into a constitutive promoter yielded AND genetic logic gates. Additionally, characterized antisense RNAs (asRNAs) or single guide RNAs (sgRNAs) with various repression efficiencies were combined with BUF gates to construct a suite of p-coumaric acid-triggered NOT genetic logic gates. Finally, the designed BUF and NOT gates were combined to construct bifunctional genetic circuits that were subjected to orthogonality evaluation. The genetic logic gates established in this study can serve as valuable tools in future applications of metabolic engineering and synthetic biology.

Validation and calibration of a novel GEM biosensor for specific detection of Cd2+, Zn2+, and Pb2

BACKGROUND

In this study, we designed a novel genetic circuit sensitive to Cd2+, Zn2+ and Pb2+ by mimicking the CadA/CadR operon system mediated heavy metal homeostasis mechanism of Pseudomonas aeruginosa. The regular DNA motifs on natural operon were reconfigured and coupled with the enhanced Green Fluorescent Protein (eGFP) reporter to develop a novel basic NOT type logic gate CadA/CadR-eGFP to respond metal ions mentioned above. A Genetically Engineered Microbial (GEM)-based biosensor (E.coli-BL21:pJET1.2-CadA/CadR-eGFP) was developed by cloning the chemically synthesised CadA/CadR-eGFP gene circuit into pJET1.2-plasmid and transforming into Escherichia coli (E. coli)-BL21 bacterial cells.

RESULTS

The GEM-based biosensor cells indicated the reporter gene expression in the presence of Cd2+, Zn2+ and Pb2+ either singly or in combination. Further, the same biosensor cells calibrated for fluorescent intensity against heavy metal concentration generated linear graphs for Cd2+, Zn2+ and Pb2+ with the R2 values of 0.9809, 0.9761 and 0.9758, respectively as compared to non-specific metals, Fe3+ (0.0373), AsO43- (0.3825) and Ni2+ (0.8498) making our biosensor suitable for the detection of low concentration of the former metal ions in the range of 1-6 ppb. Furthermore, the GEM based biosensor cells were growing naturally within the concentration range of heavy metals, at 37 °C and optimum pH = 7.0 in the medium, resembling the characteristics of wildtype E.coli.

CONCLUSION

Finally, the novel GEM based biosensor cells developed in this study can be applied for detection of targeted heavy metals in low concentration ranges (1-6 ppb) at normal bacterial physiological conditions.

Natural Microbial Reactor-Based Sensing Platform for Highly Sensitive Detection of Inorganic Arsenic in Rice Grains

Rice is a major dietary source of inorganic arsenic (iAs), a highly toxic arsenical that accumulates in rice and poses health risks to rice-based populations. However, the availability of detection methods for iAs in rice grains is limited. In this study, we developed a novel approach utilizing a natural bacterial biosensor, Escherichia coli AW3110 (pBB-ArarsR-mCherry), in conjunction with amylase hydrolysis for efficient extraction, enabling high-throughput and quantitative detection of iAs in rice grains. The biosensor exhibits high specificity for arsenic and distinguishes between arsenite [As(III)] and arsenate [As(V)] by modulating the concentration of PO43- in the detection system. We determined the iAs concentrations in 19 rice grain samples with varying total As concentrations and compared our method with the standard technique of microwave digestion coupled with HPLC-ICP-MS. Both methods exhibited comparable results, without no significant bias in the concentrations of As(III) and As(V). The whole-cell biosensor demonstrated excellent reproducibility and a high signal-to-noise ratio, achieving a limit of detection of 16 μg kg-1 [As(III)] and 29 μg kg-1 [As(V)]. These values are considerably lower than the maximum allowable level (100 μg kg-1) for infant rice supplements established by the European Union. Our straightforward sensing strategy presents a promising tool for detecting iAs in other food samples.

Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics

A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters. This provides a set of biomarkers that act as a proxy for the transcriptional state referred to as cell state. We construct low-dimensional models of gene expression dynamics and rank genes by their ability to capture the perturbation-specific cell state using a novel observability analysis. Using this ranking, we extract 15 analyte-responsive promoters for the organophosphate malathion in the underutilized host organism Pseudomonas fluorescens SBW25. We develop synthetic genetic reporters from each analyte-responsive promoter and characterize their response to malathion. Furthermore, we enhance malathion reporting through the aggregation of the response of individual reporters with a synthetic consortium approach, and we exemplify the library's ability to be useful outside the lab by detecting malathion in the environment. The engineered host cell, a living malathion sensor, can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover perturbation-inducible gene expression systems in the compendium of host organisms.

A logical way to reprogram plants

Living cells constantly monitor their external and internal environments for changing conditions, stresses or developmental cues. Networks of genetically encoded components sense and process these signals following pre-defined rules in such a way that specific combinations of the presence or absence of certain signals activate suitable responses. Many biological signal integration mechanisms approximate Boolean logic operations, whereby presence or absence of signals are computed as variables with values described as either true or false, respectively. Boolean logic gates are commonly used in algebra and in computer sciences, and have long been recognized as useful information processing devices in electronic circuits. In these circuits, logic gates integrate multiple input values and produce an output signal according to pre-defined Boolean logic operations. Recent implementation of these logic operations using genetic components to process information in living cells has allowed genetic circuits to enable novel traits with decision-making capabilities. Although several literature reports describe the design and use of these logic gates to introduce new functions in bacterial, yeast and mammalian cells, similar approaches in plants remain scarce, likely due to challenges posed by the complexity of plants and the lack of some technological advances, e.g., species-independent genetic transformation. In this mini review, we have surveyed recent reports describing synthetic genetic Boolean logic operators in plants and the different gate architectures used. We also briefly discuss the potential of deploying these genetic devices in plants to bring to fruition a new generation of resilient crops and improved biomanufacturing platforms.

Advances in Synthetic-Biology-Based Whole-Cell Biosensors: Principles, Genetic Modules, and Applications in Food Safety

A whole-cell biosensor based on synthetic biology provides a promising new method for the on-site detection of food contaminants. The basic components of whole-cell biosensors include the sensing elements, such as transcription factors and riboswitches, and reporting elements, such as fluorescence, gas, etc. The sensing and reporting elements are coupled through gene expression regulation to form a simple gene circuit for the detection of target substances. Additionally, a more complex gene circuit can involve other functional elements or modules such as signal amplification, multiple detection, and delay reporting. With the help of synthetic biology, whole-cell biosensors are becoming more versatile and integrated, that is, integrating pre-detection sample processing, detection processes, and post-detection signal calculation and storage processes into cells. Due to the relative stability of the intracellular environment, whole-cell biosensors are highly resistant to interference without the need of complex sample preprocessing. Due to the reproduction of chassis cells, whole-cell biosensors replicate all elements automatically without the need for purification processing. Therefore, whole-cell biosensors are easy to operate and simple to produce. Based on the above advantages, whole-cell biosensors are more suitable for on-site detection than other rapid detection methods. Whole-cell biosensors have been applied in various forms such as test strips and kits, with the latest reported forms being wearable devices such as masks, hand rings, and clothing. This paper examines the composition, construction methods, and types of the fundamental components of synthetic biological whole-cell biosensors. We also introduce the prospect and development trend of whole-cell biosensors in commercial applications.

Genetic circuits in microbial biosensors for heavy metal detection in soil and water

With the rapid population growth, the world is witnessing an ever-increasing demand for energy and natural resources. Consequently, soil, air, and water are polluted with diverse pollutants, including heavy metals (HM). The detection of heavy metals is necessary to remediate them, which is achieved with biosensors. Initially, these HM were detected using atomic absorption spectroscopy (AAS), emission spectroscopy, mass spectrometry, gas chromatography etc., but these were costly and time consuming which further paved a way for microbe-based biosensors. The development of genetic circuits for microbe-based biosensors has become more popular in recent years for heavy metal detection. In this review, we have especially discussed the various types of genetic circuits such as toggle switches, logic gates, and amplification modules used in these biosensors as they are used to enhance sensitivity and specificity. Genetic circuits also allow for rapid and multiple analyte detection at the same time. The use of microbial biosensors for the detection of HM in the soil as well as the water is also described below. Although with a higher success rate than classical biosensors, these microbial biosensors still have some drawbacks like bioavailability and size of the analyte which are needed to be addressed.

Synthetic bacteria for the detection and bioremediation of heavy metals

Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.

Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis

Whole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control, and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be nonfunctional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse species Bacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular "AND gate" logic system based on the B. subtilis two-subunit σ-factor, SigO-RsoA, designed to maximize future use for synthetic biology applications in B. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potentially wider applicability of the approach to other systems and genetic backgrounds.

Engineering Modular and Highly Sensitive Cell-Based Biosensors for Aromatic Contaminant Monitoring and High-Throughput Enzyme Screening

Although a variety of whole-cell-based biosensors have been developed for different applications in recent years, most cannot meet practical requirements due to insufficient sensing performance. Here, we constructed two sets of modular genetic circuits by serial and parallel modes capable of significantly amplifying the input/output signal in Escherichia coli. The biosensors are engineered using σ54-dependent phenol-responsive regulator DmpR as a sensor and enhanced green fluorescent protein as a reporter. Cells harboring serial and parallel genetic circuits displayed nearly 9- and 16-fold higher sensitivity than the general circuit. The genetic circuits enabled rapid detection of six phenolic contaminants in 12 h and showed the low limit of detection of 2.5 and 2.2 ppb for benzopyrene (BaP) and tetracycline (Tet), with a broad detection range of 0.01-1 and 0.005-5 μM, respectively. Furthermore, the positive rate was as high as 73% when the biosensor was applied to screen intracellular enzymes with ester-hydrolysis activity from soil metagenomic libraries using phenyl acetate as a phenolic substrate. Several novel enzymes were isolated, identified, and biochemically characterized, including serine peptidases and alkaline phosphatase family protein/metalloenzyme. Consequently, this study provides a new signal amplification method for cell-based biosensors that can be widely applied to environmental contaminant assessment and screening of intracellular enzymes.

Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.

Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs

Synthetic control of gene expression, whether simply promoter selection or higher-order Boolean-style logic, is an important tool for metabolic engineering and synthetic biology. This work develops a suite of orthogonal T7 RNA polymerase systems capable of exerting AND/OR switchlike control over transcription in the yeastSaccharomyces cerevisiae. When linked with CRISPR dCas9-based regulation systems, more complex circuitry is possible including AND/OR/NAND/NOR style control in response to combinations of extracellular copper and galactose. Additionally, we demonstrate that these T7 system designs are modular and can accommodate alternative stimuli sensing as demonstrated through blue light induction. These designs should greatly reduce the time and labor necessary for developing Boolean gene circuits in yeast with novel applications including metabolic pathway control in the future.

Prebiotics-Controlled Disposable Engineered Bacteria for Intestinal Diseases

As a new method of diagnosis and treatment for intestinal diseases, intelligent engineered bacteria based on synthetic biology have been developed vigorously in recent years. However, how to deal with the engineered bacteria in vivo after completing the tasks is an urgent problem to be resolved. In this study, we constructed a thiosulfate (a biomarker of inflammatory bowel disease)-responsive engineered bacteria to generate two signals, sfGFP (monitoring) and gain-of-function (translation activation) mutation (ACG to ATG), in the initiation codon of lysisE (recording) via the CRISPR/Cas9-mediated base editing system. Once these two signals were detected, xylose could be added to induce lysis E expression, resulting in the destruction of the edited bacteria and the release of AvCystain simultaneously. Overall, our innovative engineered bacteria can record instant and historical information of the disease, and especially, the edited bacteria can be artificially attenuated and release drug in situ when needed, ultimately serving as a disposable and recyclable candidate for more types of diseases.

Bacterial degrons in synthetic circuits

Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.

Engineering microbial consortia with rationally designed cellular interactions

Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. We then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.

Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants

Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg²⁺, Zn²⁺, Pb²⁺, Au³⁺, Cd²⁺, As³⁺, Ni²⁺, Cu²⁺, and UO₂²⁺) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.

Mercury bioremediation by engineered Pseudomonas putida KT2440 with adaptationally optimized biosecurity circuit

Hazardous materials, such as heavy metals, are the major sources of health risk. Using genetically modified organisms (GMOs) to dispose heavy metals has the advantages of strong environmental compatibility and high efficiency. However, the biosecurity of GMOs used in the environment is a major concern. In this study, a self-controlled genetic circuit was designed and carefully fine-tuned for programmable expression in Pseudomonas putida KT2440, which is a widely used strain for environmental bioremediation. The cell behaviours were controlled by automatically sensing the variation of Hg²⁺ concentration without any inducer requirement or manual interventions. More than 98% Hg²⁺ was adsorbed by the engineered strain with a high cell recovery rate of 96% from waterbody. The remaining cells were killed by the suicide module after the mission was accomplished. The escape frequency of the engineered P. putida strain was lower than 10^-9 , which meets the recommendation of US NIH guideline for GMOs release (<10^-8 ). The same performance was achieved in a model experiment by using natural lake water with addition of Hg²⁺ . The microbial diversity analysis further confirmed that the remediation process made little impact on the indigenous ecosystem. Thus, this study provides a practical method for environmental remediation by using GMOs.

Synthetic biology and bioelectrochemical tools for electrogenetic system engineering

Synthetic biology research and its industrial applications rely on deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and electrodes), allowing for the direct integration of electronics with biological processes. However, the use of electrogenetic systems is limited by poor activity, tunability, and standardization. In this work, we developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Last, we demonstrated electrochemical activation of gene expression under aerobic conditions using a novel, modular bioelectrochemical device. These genetic and electrochemical tools facilitate the design and improve the performance of electrogenetic systems. Furthermore, the genetic design strategies used can be applied to other redox-responsive promoters to further expand the available tools for electrogenetics.

Detection of environmental pollutant cadmium in water using a visual bacterial biosensor

Cadmium (Cd) contamination in water and soil is considered an environmental pollutant. Food crops can absorb and accumulate bioavailable Cd. Continuous monitoring of Cd levels in the environment can minimize exposure and harm to humans. Visual pigments have been demonstrated to have great potential in the development of minimal-equipment biosensors. In the present study, a metabolically engineered bacterium was employed to produce blue-purple pigment violacein responsive to toxic Cd(II). The high stability of the bisindole pigment contributed to determining the violacein at wavelengths of 578 nm. Visual and quantifiable signals could be captured after a 1.5-h Cd(II) exposure. This novel biosensor showed significantly stronger responses to Cd(II) than to other heavy metals including Pb(II), Zn(II), and Hg(II). A significant increase in pigment signal was found to respond to as low as 0.049 μM Cd(II). The naked eye can detect the color change when violacein-based biosensor is exposed to 25 μM Cd(II). A high-throughput method for rapid determination of soluble Cd(II) in environmental water was developed using a colorimetric microplate.

Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors

In type II CRISPR systems, the guide RNA (gRNA) comprises a CRISPR RNA (crRNA) and a hybridized trans-acting CRISPR RNA (tracrRNA), both being essential in guided DNA targeting functions. Although tracrRNAs are diverse in sequence and structure across type II CRISPR systems, the programmability of crRNA-tracrRNA hybridization for Cas9 is not fully understood. Here, we reveal the programmability of crRNA-tracrRNA hybridization for Streptococcus pyogenes Cas9, and in doing so, redefine the capabilities of Cas9 proteins and the sources of crRNAs, providing new biosensing applications for type II CRISPR systems. By reprogramming the crRNA-tracrRNA hybridized sequence, we show that engineered crRNA-tracrRNA interactions can not only enable the design of orthogonal cellular computing devices but also facilitate the hijacking of endogenous small RNAs/mRNAs as crRNAs. We subsequently describe how these re-engineered gRNA pairings can be implemented as RNA sensors, capable of monitoring the transcriptional activity of various environment-responsive genomic genes, or detecting SARS-CoV-2 RNA in vitro, as an Atypical gRNA-activated Transcription Halting Alarm (AGATHA) biosensor.

A Recombinase-Based Genetic Circuit for Heavy Metal Monitoring

Rapid progress in the genetic circuit design enabled whole-cell biosensors (WCBs) to become prominent in detecting an extensive range of analytes with promise in many fields, from medical diagnostics to environmental toxicity assessment. However, several drawbacks, such as high background signal or low precision, limit WCBs to transfer from proof-of-concept studies to real-world applications, particularly for heavy metal toxicity monitoring. For an alternative WCB module design, we utilized Bxb1 recombinase that provides tight control as a switch to increase dose-response behavior concerning leakiness. The modularity of Bxb1 recombinase recognition elements allowed us to combine an engineered semi-specific heat shock response (HSR) promoter, sensitive to stress conditions including toxic ions such as cadmium, with cadmium resistance regulatory elements; a cadmium-responsive transcription factor and its cognitive promoter. We optimized the conditions for the recombinase-based cadmium biosensor to obtain increased fold change and shorter response time. This system can be expanded for various heavy metals to make an all-in-one type of WCB, even using semi-specific parts of a sensing system.

CRISPR Interference Modules as Low-Burden Logic Inverters in Synthetic Circuits

CRISPR and CRISPRi systems have revolutionized our biological engineering capabilities by enabling the editing and regulation of virtually any gene, via customization of single guide RNA (sgRNA) sequences. CRISPRi modules can work as programmable logic inverters, in which the dCas9-sgRNA complex represses a target transcriptional unit. They have been successfully used in bacterial synthetic biology to engineer information processing tasks, as an alternative to the traditionally adopted transcriptional regulators. In this work, we investigated and modulated the transfer function of several model systems with specific focus on the cell load caused by the CRISPRi logic inverters. First, an optimal expression cassette for dCas9 was rationally designed to meet the low-burden high-repression trade-off. Then, a circuit collection was studied at varying levels of dCas9 and sgRNAs targeting three different promoters from the popular tet, lac and lux systems, placed at different DNA copy numbers. The CRISPRi NOT gates showed low-burden properties that were exploited to fix a high resource-consuming circuit previously exhibiting a non-functional input-output characteristic, and were also adopted to upgrade a transcriptional regulator-based NOT gate into a 2-input NOR gate. The obtained data demonstrate that CRISPRi-based modules can effectively act as low-burden components in different synthetic circuits for information processing.

New approach in SARS-CoV-2 surveillance using biosensor technology: a review

Biosensors are analytical tools that transform the bio-signal into an observable response. Biosensors are effective for early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection because they target viral antigens to assess clinical development and provide information on the severity and critical trends of infection. The biosensors are capable of being on-site, fast, and extremely sensitive to the target viral antigen, opening the door for early detection of SARS-CoV-2. They can screen individuals in hospitals, airports, and other crowded locations. Microfluidics and nanotechnology are promising cornerstones for the development of biosensor-based techniques. Recently, due to high selectivity, simplicity, low cost, and reliability, the production of biosensor instruments have attracted considerable interest. This review article precisely provides the extensive scientific advancement and intensive look of basic principles and implementation of biosensors in SARS-CoV-2 surveillance, especially for human health. In this review, the importance of biosensors including Optical, Electrochemical, Piezoelectric, Microfluidic, Paper-based biosensors, Immunosensors, and Nano-Biosensors in the detection of SARS-CoV-2 has been underscored. Smartphone biosensors and calorimetric strips that target antibodies or antigens should be developed immediately to combat the rapidly spreading SARS-CoV-2. Wearable biosensors can constantly monitor patients, which is a highly desired feature of biosensors. Finally, we summarized the literature, outlined new approaches and future directions in diagnosing SARS-CoV-2 by biosensor-based techniques.