Browsing by Author "Wang, Baojun"

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    CRISPR-enabled genetic logic circuits for biosensing
    (Elsevier, 2025-09-01) Wang, Xiyan; Gao, Yuanli; Zhou, Nan; Yang, Zhugen; Cooper, Jonathan M.; Wang, Baojun
    Synthetic biology aims to engineer genetic circuits for custom-designed behaviors in living systems, including sophisticated biosensing applications. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system has gained attention for its potential in genetic circuit design due to its modularity, programmability, precision, and orthogonality. Here we highlight the current CRISPR-based tools for gene regulation at both transcriptional and translational levels. We discuss how these CRISPR technologies facilitate the design and construction of complex genetic circuits that can perform customized logic computations within living systems. Furthermore, we summarize the applications of CRISPR-based genetic logic circuits in biosensing, emphasizing their potential for detecting diverse biological and environmental signals. Finally, we highlight the key challenges facing the development and application of CRISPR-enabled genetic logic circuits and propose directions for future research to overcome these bottlenecks.
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    CRISPR-enabled sensors for rapid monitoring of environmental contaminants
    (Elsevier, 2025-03-01) Wang, Yiting; Pan, Yuwei; Han, Wenchao; Rossi, Carla Spatola; Hui, Qingxin; Guo, Ying; Owoseni, Mojisola Christiana; McAdam, Ewan; Yong, Yang-Chun; Wang, Baojun; Yang, Zhugen
    There is increasing attention on the impacts of contaminants on environmental and human health. To better understand the potential threat to ecosystems and human health, biosensing has played an important role in monitoring contaminants and biomarkers. In the past decade, the integration of CRISPR-Cas systems with technologies like microfluidic devices and isothermal amplification methods has paved the way for developing advanced sensors for environmental surveillance. Here we discuss the recent progress of various CRISPR-Cas systems to develop new biosensing devices, ranging from the fundamental mechanisms to their practical applications. We present a comprehensive and critical overview on the current state-of-the-art of CRISPR-Cas-based sensing platforms, including for both nucleic acid and non-nucleic acid contaminants, as well as portable engineered systems for on-site detection. We also provide the prospects of CRISPR-Cas systems for next-generation environmental surveillance, together with emerging technologies such as data science and artificial intelligence.
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    Paper microfluidic sentinel sensors enable rapid and on-site wastewater surveillance in community settings
    (Elsevier, 2024-10-16) Pan, Yuwei; Wang, Baojun; Cooper, Jonathan M.; Yang, Zhugen
    Tracking genomic sequences as microbial biomarkers in wastewater has been used to determine community prevalence of infectious diseases, contributing to public health surveillance programs worldwide. Here, we report upon a low-cost, rapid, and user-friendly paper microfluidic platform for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza detection, using loop-mediated isothermal amplification, with signal read using a mobile phone camera. Sample-to-answer results were collected in less than 1.5 h, providing rapid multiplexed detection of viruses in wastewater, with a detection limit of <20 copies mL−1. The device was subsequently used for on-site testing of SARS-CoV-2 in wastewater samples from four quarantine hotels at London Heathrow Airport, showing comparable results to those obtained using polymerase chain reaction. This sensing platform, which enables rapid and localized testing without requiring samples to be sent to centralized laboratories, provides a potentially important public health tool for pandemic preparedness, with a variety of future wastewater surveillance applications in community settings.
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    Paper-based devices for rapid diagnosis and wastewater surveillance
    (Elsevier, 2022-09-06) Pan, Yuwei; Mao, Kang; Hui, Qinxin; Wang, Baojun; Cooper, Jonathan; Yang, Zhugen
    Infectious diseases are a global concern for public health resulting in high rates of infection with subsequent health and socio-economic impacts through resulting morbidity and mortality. The emergence of such diseases has motivated researchers to develop cost-effective, rapid and sensitive analytical methods and devices to better understand the transmission routes of infections within populations. To this end, rapid and low-cost diagnosis and testing devices for infectious diseases are attracting increasing amounts of attention, e.g., through using paper-based analytical devices (PADs). In this paper, the recent development of PADs is critically reviewed both for the diagnosis of inviduals and population health, by using devices for testing wastewater. Finally, the review also focuses on PADs for the analysis of bacteria and viruses in wastewater, together with a discussion on thee future development of PADs for rapid diagnosis and wastewater surveillance.
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    Rapid enzymatic assays for fecal contamination in aquatic environment: challenges, advances and prospects
    (Elsevier, 2024-07-01) Yuan, Xiaofei; Glidle, Andrew; Yang, Zhugen; Wang, Baojun
    Routine monitoring of sanitation and hygiene to identify fecal contamination in aquatic environments is an effective means to prevent threatening disease transmission. Compared to immunological or genetic methods performed in a central lab, enzymatic assays are considered simple, quick, cost-effective and thus promising for in-field (near) real-time detection. However, the long detection time for mildly polluted samples is a major obstacle to its deployment as an early warning system. Here, the challenges faced by the assays in real environmental sample measurements are summarized, followed by the current status of their field applications. Furthermore, the likelihood and ways are discussed for significant assay improvements using state-of-the-art synthetic biology technologies. Rapid advances in synthetic biology such as various new enabling tools for precise biomolecular manipulation and cell-free expression systems have great potential to address the present bottlenecks of the enzymatic assays, paving the way for better early warning strategies and performance.
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    Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors
    (Nature Publishing Group, 2022-04-11) Liu, Yang; Pinto, Filipe; Wan, Xinyi; Yang, Zhugen; Peng, Shuguang; Li, Mengxi; Cooper, Jonathan M.; Xie, Zhen; French, Christopher E.; Wang, Baojun
    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.