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Zuo S, Jiang G, Zheng Y, Zhang X, Qin Z, Chen L, Ren T, Zhang XB, Yuan L. Family of hNQO1 Activatable Near-Infrared Fluoro-Photoacoustic Probes for Diagnosis of Wound Infection and Ulcerative Colitis. Anal Chem 2023; 95:898-906. [PMID: 36604944 DOI: 10.1021/acs.analchem.2c03436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial infections can easily occur when patients mishandle wounds or eat moldy food. The prompt diagnosis of a bacterial infection could effectively reduce the risk of possible anatomical damage. However, non-invasive early detection of bacterial infections is difficult to achieve due to the lack of favorable tools. Here, we designed two hNQO1 fluorescent probes (RX2 and RX3) to visualize bacterial infection after deep learning on the pathogenesis of bacterial infection. RX2 and RX3 enable early detection of bacterial infection and are verified to be, respectively, suitable for fluorescence imaging (FLI) and photoacoustic imaging (PAI) by comparing the signal-to-background ratio of both probes in a mouse model of myositis caused by Escherichia coli infection. In view of the difference in penetration depth between the two imaging modalities, we further applied RX2 for FLI of E. coli-infected wounds and RX3 for PAI of E. coli-infected inflammatory bowel disease, suggesting the great potential of both probes for early diagnosis of bacterial infections.
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Affiliation(s)
- Shan Zuo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Gangwei Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Yingxin Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xingxing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Zuojia Qin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Tianbing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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Engineering Protein-Based Parts for Genetic Devices in Mammalian Cells. Methods Mol Biol 2021. [PMID: 33405230 DOI: 10.1007/978-1-0716-1032-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Synthetic biology has been advancing cellular and molecular biology studies through the design of synthetic circuits capable to examine diverse endogenously or exogenously driven regulatory pathways. While early genetic devices were engineered to be insulated from intracellular crosstalk, more recently the need of achieving dynamic control of cellular behavior has led to the development of smart interfaces that connect signal information (sensor) to desired output activation (actuator). Sensor-actuator circuits can respond to diverse inputs, including small molecules, exogenous and endogenous mRNA, noncoding RNA (i.e., miRNA), and proteins to regulate downstream events, transcriptionally, posttranscriptionally, and translationally. These devices require attentive engineering to either create complex chimeric proteins or modify protein structures to be amenable to the specific circuits' architecture and/or purpose.In this chapter, we describe how to implement two different protein-based devices in mammalian cells: (1) a modular platform that sense and respond to disease-associated proteins and (2) a protein-based system that allows simultaneous regulation of RNA translation and protein activity, via RNA-protein and newly engineered protein-protein interactions.
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Khan N, Yeung E, Farris Y, Fansler SJ, Bernstein HC. A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species. Synth Biol (Oxf) 2020. [DOI: 10.1093/synbio/ysaa002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractModern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli. It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads—Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.
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Affiliation(s)
- Nymul Khan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Enoch Yeung
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hans C Bernstein
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT - The Arctic University of Norway, Tromsø, Norway
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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