Browsing by Author "Cooper, Jonathan M."

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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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    Low sample volume origami-paper-based graphene-modified aptasensors for label-free electrochemical detection of cancer biomarker-EGFR
    (Nature Publishing Group, 2020-05-18) Wang, Yang; Sun, Shuai; Luo, Jinping; Xiong, Ying; Ming, Tao; Liu, Juntao; Ma, Yuanyuan; Yan, Shi; Yang, Yue; Yang, Zhugen; Reboud, Julien; Yin, Huabing; Cooper, Jonathan M.; Cai, Xinxia
    In this work, an electrochemical paper-based aptasensor was fabricated for label-free and ultrasensitive detection of epidermal growth factor receptor (EGFR) by employing anti-EGFR aptamers as the bio-recognition element. The device used the concept of paper-folding, or origami, to serve as a valve between sample introduction and detection, so reducing sampling volumes and improving operation convenience. Amino-functionalized graphene (NH2-GO)/thionine (THI)/gold particle (AuNP) nanocomposites were used to modify the working electrode not only to generate the electrochemical signals, but also to provide an environment conducive to aptamer immobilization. Electrochemical characterization revealed that the formation of an insulating aptamer–antigen immunocomplex would hinder electron transfer from the sample medium to the working electrode, thus resulting in a lower signal. The experimental results showed that the proposed aptasensor exhibited a linear range from 0.05 to 200 ngmL−1 (R2 = 0.989) and a detection limit of 5 pgmL−1 for EGFR. The analytical reliability of the proposed paper-based aptasensor was further investigated by analyzing serum samples, showing good agreement with the gold-standard enzyme-linked immunosorbent assay
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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 nanosensors to evaluate community-wide illicit drug use for wastewater-based epidemiology
    (Elsevier, 2020-10-23) Mao, Kang; Yang, Zhugen; Zhang, Hua; Li, Xiqing; Cooper, Jonathan M.
    Wastewater-based epidemiology (WBE) is a powerful technique for monitoring illicit drugs of abuse in the community. Here, we report on a surface-enhanced Raman scattering/spectroscopy (SERS) sensor for the sensitive and selective detection of methamphetamine based on the assembly of noble metal core-shell nanoparticles on a bespoke glassy nanofibrous electrospun paper matrix. The hierarchical structure of the fibrous paper, modified with the synthesized Au@Ag core-shell nanoparticles (Au@Ag) possessing good SERS efficiency, enables us to evaluate the community-wide prevalence of methamphetamine in wastewater treatment plants around Beijing. We show that when normalized for the daily flow of the wastewater treatment plants, higher mass loads of drugs are found in sewage influent from urban areas, implying greater local methamphetamine usage than that in less populated areas. These user-friendly and disposable paper devices demonstrate the applicability of rapid on-site illicit drug detection, illustrating the application to wastewater-based epidemiology, which has the potential to inform government agencies regarding societal interventions.
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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.