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Kovacs CJ, Antonacci A, Graham A, Jessup F, Rankin W, Brasko B, Maguire F, Washington MA, Kua SC, Burpo FJ, Barnhill JC. Comparing Methods to Genetically Engineer Bacteriophage and Increase Host Range. Mil Med 2024; 189:e1488-e1496. [PMID: 38780999 DOI: 10.1093/milmed/usae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION Antibacterial resistance is an emerging problem in military medicine. Disruptions to the health care systems in war-torn countries that result from ongoing conflict can potentially exacerbate this problem and increase the risk to U.S. forces in the deployed environment. Therefore, novel therapies are needed to mitigate the impact of these potentially devastating infections on military operations. Bacteriophages are viruses that infect and kill bacteria. They can be delivered as therapeutic agents and offer a promising alternative to traditional antibiotic chemotherapy. There are several potential benefits to their use, including high specificity and comparative ease of use in the field setting. However, the process of engineering phages for military medical applications can be a laborious and time-consuming endeavor. This review examines available techniques and compares their efficacy. MATERIALS AND METHODS This review evaluates the scientific literature on the development and application of four methods of bacteriophage genome engineering and their consideration in the context of military applications. Preffered Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for a systematic review of available literature that met criteria for analysis and inclusion. The research completed for this review article originated from the United States Military Academy's library "Scout" search engine, which compiles results from 254 available databases (including PubMed, Google Scholar, and SciFinder). Particular attention was focused on identifying useful mechanistic insight into the nature of the engineering technique, the ease of use, and the applicability of the technique to countering the problem of antimicrobial resistance in the military setting. RESULTS A total of 52 studies were identified that met inclusion criteria following PRISMA guidelines. The bioengineering techniques analyzed included homologous recombination (12 articles), in vivo recombineering (9 articles), bacteriophage recombineering of electroporated DNA (7 articles), and the CRISPR-Cas system (10 articles). Rates of success and fidelity varied across each platform, and comparative benefits and drawbacks are considered. CONCLUSIONS Each of the phage engineering techniques addressed herein varies in amount of effort and overall success rate. CRISPR-Cas-facilitated modification of phage genomes presents a highly efficient method that does not require a lengthy purification and screening process. It therefore appears to be the method best suited for military medical applications.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Alessia Antonacci
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Abigail Graham
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Faye Jessup
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - William Rankin
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Brianna Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Fiona Maguire
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael A Washington
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - Siang C Kua
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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2
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Beyazit F, Arica MY, Acikgoz-Erkaya I, Ozalp C, Bayramoglu G. Quartz crystal microbalance-based aptasensor integrated with magnetic pre-concentration system for detection of Listeria monocytogenes in food samples. Mikrochim Acta 2024; 191:235. [PMID: 38570380 PMCID: PMC10990998 DOI: 10.1007/s00604-024-06307-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
A fast and accurate identification of Listeria monocytogenes. A new quartz crystal microbalance (QCM) aptasensor was designed for the specific and rapid detection of L. monocytogenes. Before detection of the target bacterium from samples in the QCM aptasensor, a magnetic pre-enrichment system was used to eliminate any contaminant in the samples. The prepared magnetic system was characterized using ATR-FTIR, SEM, VSM, BET, and analytical methods. The saturation magnetization values of the Fe3O4, Fe3O4@PDA, and Fe3O4@PDA@DAPEG particles were 57.2, 40.8, and 36.4 emu/g, respectively. The same aptamer was also immobilized on the QCM crystal integrated into QCM flow cell and utilized to quantitatively detect L. monocytogenes cells from the samples. It was found that a specific aptamer-magnetic pre-concentration system efficiently captured L. monocytogenes cells in a short time (approximately 10 min). The Fe3O4@PDA@DA-PEG-Apt particles provided selective isolation of L. monocytogenes from the bacteria-spiked media up to 91.8%. The immobilized aptamer content of the magnetic particles was 5834 µg/g using 500 ng Apt/mL. The QCM aptasensor showed a very high range of analytical performance to the target bacterium from 1.0 × 102 and 1.0 × 107 CFU/mL. The limit of detection (LOD) and limit of quantitation (LOQ) were 148 and 448 CFU/mL, respectively, from the feeding of the QCM aptasensor flow cell with the eluent of the magnetic pre-concentration system. The reproducibility of the aptasensor was more than 95%. The aptasensor was very specific to L. monocytogenes compared to the other Listeria species (i.e., L. ivanovii, L. innocua, and L. seeligeri) or other tested bacteria such as Staphylococcus aureus, Escherichia coli, and Bacillus subtilis. The QCM aptasensor was regenerated with NaOH solution, and the system was reused many times.
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Affiliation(s)
- Fatma Beyazit
- Department of Obstetrics and Gynecology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Mehmet Yakup Arica
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500, Teknikokullar, Ankara, Turkey
| | - Ilkay Acikgoz-Erkaya
- Department of Environmental Science, Faculty of Engineering and Architecture, Ahi Evran University, Kırsehir, Turkey
| | - Cengiz Ozalp
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, Turkey
| | - Gulay Bayramoglu
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500, Teknikokullar, Ankara, Turkey.
- Department of Chemistry, Faculty of Sciences, Gazi University, 06500, Teknikokullar, Ankara, Turkey.
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Costa AR, Azeredo J, Pires DP. Synthetic Biology to Engineer Bacteriophage Genomes. Methods Mol Biol 2024; 2734:261-277. [PMID: 38066375 DOI: 10.1007/978-1-0716-3523-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered toward a wide range of applications, including pathogen control and detection, targeted drug delivery, or even assembly of new materials.In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes will be addressed: the bacteriophage recombineering of electroporated DNA (BRED) and the yeast-based phage-engineering platform.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Diana Priscila Pires
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
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4
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Kumar A, Yadav A. Synthetic phage and its application in phage therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:61-89. [PMID: 37739560 DOI: 10.1016/bs.pmbts.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Synthetic phage analysis has been implemented in progressive various areas of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been altered for developing gene circuits to program biological systems. Due to their extremely potent potency, phages also provide greater medical availability against bacterial agents and bacterial diagnostic agents. Its host specificity and our growing ability to manipulate, them further expand its possibility. New Phages also genetically redesign programmable biomaterials with highly tunable properties. Moreover, new phages are central to powerful directed evolution platforms. It is used to enhance existing biological, functions to create new phages. In other sites, the mining of antibiotics, and the emergence and dissemination of more than one type of drug-resistant microbe, a human health concerns. The major point in controlling and treating microbial infections. At present, genetic modifications and biochemical treatments are used to modify phages. Among these, genetic engineering involves the identification of defective proteins, modification of host bodies, recognized receptors, and disruption of bacterial phage resistance signaling gateways.
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Affiliation(s)
- Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
| | - Anuj Yadav
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
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5
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Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development. Signal Transduct Target Ther 2023; 8:112. [PMID: 36906608 PMCID: PMC10007681 DOI: 10.1038/s41392-023-01375-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023] Open
Abstract
The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.
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Sun Q, Shen L, Zhang BL, Yu J, Wei F, Sun Y, Chen W, Wang S. Advance on Engineering of Bacteriophages by Synthetic Biology. Infect Drug Resist 2023; 16:1941-1953. [PMID: 37025193 PMCID: PMC10072152 DOI: 10.2147/idr.s402962] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Since bacteriophages (phages) were firstly reported at the beginning of the 20th century, the study on them experiences booming-fading-emerging with discovery and overuse of antibiotics. Although they are the hotspots for therapy of antibiotic-resistant strains nowadays, natural phage applications encounter some challenges such as limited host range and bacterial resistance to phages. Synthetic biology, one of the most dramatic directions in the recent 20-years study of microbiology, has generated numerous methods and tools and has contributed a lot to understanding phage evolution, engineering modification, and controlling phage-bacteria interactions. In order to better modify and apply phages by using synthetic biology techniques in the future, in this review, we comprehensively introduce various strategies on engineering or modification of phage genome and rebooting of recombinant phages, summarize the recent researches and potential directions of phage synthetic biology, and outline the current application of engineered phages in practice.
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Affiliation(s)
- Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Lixin Shen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Bai-Ling Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People’s Republic of China
| | - Jiaoyang Yu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
| | - Fu Wei
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
- The Clinical Infectious Disease Center of Nanjing, Nanjing, 210003, People’s Republic of China
- Correspondence: Wei Chen; Shiwei Wang, Email ;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
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7
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Genome characterization of the novel lytic genome sequence of the phage YUEEL01 of the Myoviridae family. Virus Res 2021; 309:198670. [PMID: 34971703 DOI: 10.1016/j.virusres.2021.198670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 12/24/2022]
Abstract
Antimicrobial resistance is a global concern because of its rapid emergence in the environment and the associated high risk to human and animal health. Municipal wastewater, including urban, hospital, and pharmaceutical effluent, is the primary source of contamination by antibiotics and antibiotic-resistant bacteria (ARB). Biological processes are commonly used for wastewater treatment. Biologically based strategies are a promising approach to effective integrated ARB control because they focus on antibiotic resistance. An effective bacteriophage against multi-drug resistance (MDR) microbes in municipal wastewater was.
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8
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He J, Nissim L, Soleimany AP, Binder-Nissim A, Fleming HE, Lu TK, Bhatia SN. Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection. ACS Synth Biol 2021; 10:2231-2242. [PMID: 34464083 DOI: 10.1021/acssynbio.1c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The integration of nanotechnology and synthetic biology could lay the framework for new classes of engineered biosensors that produce amplified readouts of disease states. As a proof-of-concept demonstration of this vision, here we present an engineered gene circuit that, in response to cancer-associated transcriptional deregulation, expresses heterologous enzyme biomarkers whose activity can be measured by nanoparticle sensors that generate amplified detection readouts. Specifically, we designed an AND-gate gene circuit that integrates the activity of two ovarian cancer-specific synthetic promoters to drive the expression of a heterologous protein output, secreted Tobacco Etch Virus (TEV) protease, exclusively from within tumor cells. Nanoparticle probes were engineered to carry a TEV-specific peptide substrate in order to measure the activity of the circuit-generated enzyme to yield amplified detection signals measurable in the urine or blood. We applied our integrated sense-and-respond system in a mouse model of disseminated ovarian cancer, where we demonstrated measurement of circuit-specific TEV protease activity both in vivo using exogenously administered nanoparticle sensors and ex vivo using quenched fluorescent probes. We envision that this work will lay the foundation for how synthetic biology and nanotechnology can be meaningfully integrated to achieve next-generation engineered biosensors.
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Affiliation(s)
- Jiang He
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lior Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ava P. Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Graduate Program in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft Research New England, Cambridge, Massachusetts 02142, United States
| | - Adina Binder-Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Family Medicine, Meuhedet Health Maintenance Organization, Tel Aviv 62038, Israel
| | - Heather E. Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
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9
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MacDonald IC, Seamons TR, Emmons JC, Javdan SB, Deans TL. Enhanced regulation of prokaryotic gene expression by a eukaryotic transcriptional activator. Nat Commun 2021; 12:4109. [PMID: 34226549 PMCID: PMC8257575 DOI: 10.1038/s41467-021-24434-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/17/2021] [Indexed: 11/23/2022] Open
Abstract
Expanding the genetic toolbox for prokaryotic synthetic biology is a promising strategy for enhancing the dynamic range of gene expression and enabling new engineered applications for research and biomedicine. Here, we reverse the current trend of moving genetic parts from prokaryotes to eukaryotes and demonstrate that the activating eukaryotic transcription factor QF and its corresponding DNA-binding sequence can be moved to E. coli to introduce transcriptional activation, in addition to tight off states. We further demonstrate that the QF transcription factor can be used in genetic devices that respond to low input levels with robust and sustained output signals. Collectively, we show that eukaryotic gene regulator elements are functional in prokaryotes and establish a versatile and broadly applicable approach for constructing genetic circuits with complex functions. These genetic tools hold the potential to improve biotechnology applications for medical science and research. Expanded toolkits for prokaryotic synthetic biology can enhance the dynamic range of gene expression. Here the authors move the eukaryotic transcription factor QF into E. coli and integrate it into genetic devices.
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Affiliation(s)
- I Cody MacDonald
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Travis R Seamons
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Jonathan C Emmons
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Shwan B Javdan
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Tara L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA.
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10
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Marucci L, Barberis M, Karr J, Ray O, Race PR, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt J, Seabrook R, Shaw W, Woods C. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Front Bioeng Biotechnol 2020; 8:942. [PMID: 32850764 PMCID: PMC7426639 DOI: 10.3389/fbioe.2020.00942] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023] Open
Abstract
Computer-aided design (CAD) for synthetic biology promises to accelerate the rational and robust engineering of biological systems. It requires both detailed and quantitative mathematical and experimental models of the processes to (re)design biology, and software and tools for genetic engineering and DNA assembly. Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity. CAD strategies require quantitative models of cells that can capture multiscale processes and link genotypes to phenotypes. Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology. We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems. We also discuss several challenges for the realization of our vision. The possibility to describe and build whole-cells in silico offers an opportunity to develop increasingly automatized, precise and accessible CAD tools and strategies.
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Affiliation(s)
- Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jonathan Karr
- Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Oliver Ray
- Department of Computer Science, University of Bristol, Bristol, United Kingdom
| | - Paul R Race
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Miguel de Souza Andrade
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil.,Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Claire Grierson
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Stefan Andreas Hoffmann
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sophie Landon
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Elibio Rech
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil
| | - Joshua Rees-Garbutt
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Richard Seabrook
- Elizabeth Blackwell Institute for Health Research (EBI), University of Bristol, Bristol, United Kingdom
| | - William Shaw
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Christopher Woods
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Chemistry, University of Bristol, Bristol, United Kingdom
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11
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Cameron JM, Butler HJ, Smith BR, Hegarty MG, Jenkinson MD, Syed K, Brennan PM, Ashton K, Dawson T, Palmer DS, Baker MJ. Developing infrared spectroscopic detection for stratifying brain tumour patients: glioblastoma multiforme vs. lymphoma. Analyst 2020; 144:6736-6750. [PMID: 31612875 DOI: 10.1039/c9an01731c] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over a third of brain tumour patients visit their general practitioner more than five times prior to diagnosis in the UK, leading to 62% of patients being diagnosed as emergency presentations. Unfortunately, symptoms are non-specific to brain tumours, and the majority of these patients complain of headaches on multiple occasions before being referred to a neurologist. As there are currently no methods in place for the early detection of brain cancer, the affected patients' average life expectancy is reduced by 20 years. These statistics indicate that the current pathway is ineffective, and there is a vast need for a rapid diagnostic test. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy is sensitive to the hallmarks of cancer, as it analyses the full range of macromolecular classes. The combination of serum spectroscopy and advanced data analysis has previously been shown to rapidly and objectively distinguish brain tumour severity. Recently, a novel high-throughput ATR accessory has been developed, which could be cost-effective to the National Health Service in the UK, and valuable for clinical translation. In this study, 765 blood serum samples have been collected from healthy controls and patients diagnosed with various types of brain cancer, contributing to one of the largest spectroscopic studies to date. Three robust machine learning techniques - random forest, partial least squares-discriminant analysis and support vector machine - have all provided promising results. The novel high-throughput technology has been validated by separating brain cancer and non-cancer with balanced accuracies of 90% which is comparable to the traditional fixed diamond crystal methodology. Furthermore, the differentiation of brain tumour type could be useful for neurologists, as some are difficult to distinguish through medical imaging alone. For example, the highly aggressive glioblastoma multiforme and primary cerebral lymphoma can appear similar on magnetic resonance imaging (MRI) scans, thus are often misdiagnosed. Here, we report the ability of infrared spectroscopy to distinguish between glioblastoma and lymphoma patients, at a sensitivity and specificity of 90.1% and 86.3%, respectively. A reliable serum diagnostic test could avoid the need for surgery and speed up time to definitive chemotherapy and radiotherapy.
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Affiliation(s)
- James M Cameron
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George St, Glasgow, G1 1RD, UK.
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12
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Soleimany AP, Bhatia SN. Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring. Trends Mol Med 2020; 26:450-468. [PMID: 32359477 DOI: 10.1016/j.molmed.2020.01.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022]
Abstract
Diagnostics to accurately detect disease and monitor therapeutic response are essential for effective clinical management. Bioengineering, chemical biology, molecular biology, and computer science tools are converging to guide the design of diagnostics that leverage enzymatic activity to measure or produce biomarkers of disease. We review recent advances in the development of these 'activity-based diagnostics' (ABDx) and their application in infectious and noncommunicable diseases. We highlight efforts towards both molecular probes that respond to disease-specific catalytic activity to produce a diagnostic readout, as well as diagnostics that use enzymes as an engineered component of their sense-and-respond cascade. These technologies exemplify how integrating techniques from multiple disciplines with preclinical validation has enabled ABDx that may realize the goals of precision medicine.
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Affiliation(s)
- Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Wyss Institute at Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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13
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Bonilla-Rosso G, Steiner T, Wichmann F, Bexkens E, Engel P. Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota. Proc Natl Acad Sci U S A 2020; 117:7355-7362. [PMID: 32179689 PMCID: PMC7132132 DOI: 10.1073/pnas.2000228117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.
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Affiliation(s)
- Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Théodora Steiner
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Fabienne Wichmann
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Evan Bexkens
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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14
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Xu J, Li X, Kang G, Bai L, Wang P, Huang H. Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules. Viruses 2020; 12:v12020205. [PMID: 32059512 PMCID: PMC7077233 DOI: 10.3390/v12020205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/29/2022] Open
Abstract
A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.
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Affiliation(s)
- Jingzhi Xu
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xiaobo Li
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin 300392, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Liang Bai
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ping Wang
- Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin 300392, China
- Correspondence: (P.W.); (H.H.); Tel.: +86-22-6031-8081 (P.W.); +86-22-2740-3389 (H.H.)
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Correspondence: (P.W.); (H.H.); Tel.: +86-22-6031-8081 (P.W.); +86-22-2740-3389 (H.H.)
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15
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Synthetic biology: Recent progress, biosafety and biosecurity concerns, and possible solutions. JOURNAL OF BIOSAFETY AND BIOSECURITY 2019. [DOI: 10.1016/j.jobb.2018.12.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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16
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Brownell D, King J, Caliando B, Sycheva L, Koeris M. Engineering Bacteriophage-Based Biosensors. Methods Mol Biol 2019; 1898:37-50. [PMID: 30570721 DOI: 10.1007/978-1-4939-8940-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacteriophages have been used for diagnostic purposes in the past, but a lack of parallelizable engineering methods had limited their applicability to a narrow subset of diagnostic settings. More recently, however, advances in DNA sequencing and the introduction of more sensitive reporter systems have enabled novel engineering methods, which in turn have broadened the scope of modern phage diagnostics. Here we describe advanced methods to engineer the genomes of bacteriophages in a modular and rapid fashion.
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Affiliation(s)
- Daniel Brownell
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - John King
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - Brian Caliando
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - Lada Sycheva
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - Michael Koeris
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA.
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17
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Farooq U, Yang Q, Ullah MW, Wang S. Bacterial biosensing: Recent advances in phage-based bioassays and biosensors. Biosens Bioelectron 2018; 118:204-216. [PMID: 30081260 DOI: 10.1016/j.bios.2018.07.058] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
Abstract
In nature, different types of bacteria including pathogenic and beneficial ones exist in different habitats including environment, plants, animals, and humans. Among these, the pathogenic bacteria should be detected at earlier stages of infection; however, the conventional bacterial detection procedures are complex and time-consuming. In contrast, the advanced molecular approaches such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) have significantly reduced the detection time; nevertheless, such approaches are not acceptable to a large extent and are mostly laborious and expensive. Therefore, the development of fast, inexpensive, sensitive, and specific approaches for pathogen detection is essential for different applications in food industry, clinical diagnosis, biological defense and counter-terrorism. To this end, the novel sensing approaches involving bacteriophages as recognition elements are receiving immense consideration owing to their high degree of specificity, accuracy, and reduced assay times. Besides, the phages are easily produced and are tolerant to extreme pH, temperature, and organic solvents as compared to antibodies. To date, several phage-based assays and sensors have been developed involving different systems such as quartz crystal microbalance, magnetoelastic platform, surface plasmon resonance, and electrochemical methods. This review highlights different taxonomic species and genera of phages infecting eight common disease-causing bacterial genera. It further overviews the most recent advancements in phage-based sensing assays and sensors. Likewise, it elaborates various whole-phage and phage components-based assays. Overall, this review emphasizes the importance of electrochemical biosensors as simple, reliable, cost-effective, and accurate tools for bacterial detection.
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Affiliation(s)
- Umer Farooq
- Advanced Biomaterials & Tissue Engineering Centre, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Qiaoli Yang
- Advanced Biomaterials & Tissue Engineering Centre, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Muhammad Wajid Ullah
- Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Shenqi Wang
- Advanced Biomaterials & Tissue Engineering Centre, Huazhong University of Science and Technology, Wuhan 430074, PR China.
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18
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Cameron JM, Butler HJ, Palmer DS, Baker MJ. Biofluid spectroscopic disease diagnostics: A review on the processes and spectral impact of drying. JOURNAL OF BIOPHOTONICS 2018; 11:e201700299. [PMID: 29377638 DOI: 10.1002/jbio.201700299] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/18/2018] [Indexed: 06/07/2023]
Abstract
The complex patterns observed from evaporated liquid drops have been examined extensively over the last 20 years. Complete understanding of drop deposition is vital in many medical processes, and one which is essential to the translation of biofluid spectroscopic disease diagnostics. The promising use of spectroscopy in disease diagnosis has been hindered by the complicated patterns left by dried biological fluids which may inhibit the clinical translation of this technology. Coffee-ring formation, cracking and gelation patterns have all been observed in biofluid drops, and with surface homogeneity being a key element to many spectroscopic techniques, experimental issues have been found to arise. A better understanding of the fundamental processes involved in a drying droplet could allow efficient progression in this research field, and ultimately benefit the population with the development of a reliable cancer diagnostic.
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Affiliation(s)
- James M Cameron
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Holly J Butler
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - David S Palmer
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
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19
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Optimizing Propagation of Staphylococcus aureus Infecting Bacteriophage vB_SauM-phiIPLA-RODI on Staphylococcus xylosus Using Response Surface Methodology. Viruses 2018; 10:v10040153. [PMID: 29584701 PMCID: PMC5923447 DOI: 10.3390/v10040153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/19/2018] [Accepted: 03/26/2018] [Indexed: 01/13/2023] Open
Abstract
The use of bacteriophages for killing pathogenic bacteria is a feasible alternative to antibiotics and disinfectants. To obtain the large quantities of phages required for this application, large-scale production of bacteriophages must be optimized. This study aims to define conditions that maximize the phage yield of the virulent and polyvalent staphylococcal bacteriophage vB_SauM-phiIPLA-RODI in broth culture, using the food-grade species Staphylococcus xylosus as the host strain to reduce the risk of growing massive quantities of pathogenic bacteria and therefore, to ensure the safety of the final phage stock. The effect of four variables, namely initial bacterial concentration (5.66–8.40 log10 colony-forming unit (CFU)/mL), initial phage concentration (5–8 log10 plaque-forming unit (PFU)/mL), temperature (21–40 °C) and agitation (20–250 rpm), on phage yield (response) was studied by using response surface methodology (RSM). Successive experimental designs showed that agitation did not significantly impact phage yield, while temperature did have a significant effect, with 38 °C being the optimum for phage propagation. The results allowed the design of a model to describe phage yield as a function of the initial bacterial and phage concentrations at fixed agitation (135 rpm), and optimum temperature (38 °C). The maximum experimental phage yield obtained was 9.3 log10 PFU/mL, while that predicted by the model under the optimized conditions (7.07 log10 CFU/mL initial bacterial population and 6.00 log10 PFU/mL initial phage titer) was 9.25 ± 0.30 log10 PFU/mL, with the desirability of 0.96. This yield is comparable to that obtained when the phage was propagated on the original host, Staphylococcus aureus. Bacteriophage phiIPLA-RODI showed the same host range and very similar biofilm removal ability regardless of the staphylococcal species used for its propagation. The results presented in this study show the suitability of using a food-grade strain of S. xylosus for the propagation of S. aureus infecting phages and the application of RSM to define the optimal propagation conditions.
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20
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Rita Costa A, Milho C, Azeredo J, Pires DP. Synthetic Biology to Engineer Bacteriophage Genomes. Methods Mol Biol 2018; 1693:285-300. [PMID: 29119447 DOI: 10.1007/978-1-4939-7395-8_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered towards a wide range of applications including pathogen control and detection, targeted drug delivery, or even assembly of new materials.In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes are addressed: a yeast-based platform and bacteriophage recombineering of electroporated DNA.
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Affiliation(s)
- Ana Rita Costa
- LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal
| | - Catarina Milho
- LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal
| | - Joana Azeredo
- LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal
| | - Diana Priscila Pires
- LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal.
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21
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22
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Xin Y, Guo T, Mu Y, Kong J. Identification and functional analysis of potential prophage-derived recombinases for genome editing in Lactobacillus casei. FEMS Microbiol Lett 2017; 364:4628040. [DOI: 10.1093/femsle/fnx243] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Yingli Mu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
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23
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Sum R, Swaminathan M, Rastogi SK, Piloto O, Cheong I. Beta-Hemolytic Bacteria Selectively Trigger Liposome Lysis, Enabling Rapid and Accurate Pathogen Detection. ACS Sens 2017; 2:1441-1451. [PMID: 28929742 DOI: 10.1021/acssensors.7b00333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For more than a century, blood agar plates have been the only test for beta-hemolysis. Although blood agar cultures are highly predictive for bacterial pathogens, they are too slow to yield actionable information. Here, we show that beta-hemolytic pathogens are able to lyse and release fluorophores encapsulated in sterically stabilized liposomes whereas alpha and gamma-hemolytic bacteria have no effect. By analyzing fluorescence kinetics, beta-hemolytic colonies cultured on agar could be distinguished in real time with 100% accuracy within 6 h. Additionally, end point analysis based on fluorescence intensity and machine-extracted textural features could discriminate between beta-hemolytic and cocultured control colonies with 99% accuracy. In broth cultures, beta-hemolytic bacteria were detectable in under an hour while control bacteria remained negative even the next day. This strategy, called beta-hemolysis triggered-release assay (BETA) has the potential to enable the same-day detection of beta-hemolysis with single-cell sensitivity and high accuracy.
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Affiliation(s)
- Rongji Sum
- Department
of Molecular Pathogenesis, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Muthukaruppan Swaminathan
- Department
of Molecular Pathogenesis, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
- Department
of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Sahil Kumar Rastogi
- Department
of Molecular Pathogenesis, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Ian Cheong
- Department
of Molecular Pathogenesis, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
- Department
of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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24
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Choi J, Seong TW, Jeun M, Lee KH. Field-Effect Biosensors for On-Site Detection: Recent Advances and Promising Targets. Adv Healthc Mater 2017; 6. [PMID: 28885777 DOI: 10.1002/adhm.201700796] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Indexed: 12/21/2022]
Abstract
There is an explosive interest in the immediate and cost-effective analysis of field-collected biological samples, as many advanced biodetection tools are highly sensitive, yet immobile. On-site biosensors are portable and convenient sensors that provide detection results at the point of care. They are designed to secure precision in highly ionic and heterogeneous solutions with minimal hardware. Among various methods that are capable of such analysis, field-effect biosensors are promising candidates due to their unique sensitivity, manufacturing scalability, and integrability with computational circuitry. Recent developments in nanotechnological surface modification show promising results in sensing from blood, serum, and urine. This report gives a particular emphasis on the on-site efficacy of recently published field-effect biosensors, specifically, detection limits in physiological solutions, response times, and scalability. The survey of the properties and existing detection methods of four promising biotargets, exosomes, bacteria, viruses, and metabolites, aims at providing a roadmap for future field-effect and other on-site biosensors.
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Affiliation(s)
- Jaebin Choi
- Sensor System Research Center; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
| | - Tae Wha Seong
- Center for Biomaterials; Biomedical Research Institute; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
| | - Minhong Jeun
- Center for Biomaterials; Biomedical Research Institute; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
| | - Kwan Hyi Lee
- Center for Biomaterials; Biomedical Research Institute; Korea Institute of Science and Technology (KIST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
- Department of Biomedical Engineering; Korea University of Science and Technology (UST); 5 Hwarang-ro 14-gil Seongbuk-gu Seoul 02792 Republic of Korea
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25
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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26
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Anany H, Chou Y, Cucic S, Derda R, Evoy S, Griffiths M. From Bits and Pieces to Whole Phage to Nanomachines: Pathogen Detection Using Bacteriophages. Annu Rev Food Sci Technol 2017; 8:305-329. [DOI: 10.1146/annurev-food-041715-033235] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- H. Anany
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt 11566
| | - Y. Chou
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - S. Cucic
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
| | - R. Derda
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - S. Evoy
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - M.W. Griffiths
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
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27
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Hurwitz AM, Huang W, Estes MK, Atmar RL, Palzkill T. Deep sequencing of phage-displayed peptide libraries reveals sequence motif that detects norovirus. Protein Eng Des Sel 2017; 30:129-139. [PMID: 28035012 PMCID: PMC5241761 DOI: 10.1093/protein/gzw074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 10/12/2016] [Accepted: 12/14/2016] [Indexed: 01/10/2023] Open
Abstract
Norovirus infections are the leading cause of non-bacterial gastroenteritis and result in about 21 million new cases and $2 billion in costs per year in the United States. Existing diagnostics have limited feasibility for point-of-care applications, so there is a clear need for more reliable, rapid, and simple-to-use diagnostic tools in order to contain outbreaks and prevent inappropriate treatments. In this study, a combination of phage display technology, deep sequencing and computational analysis was used to identify 12-mer peptides with specific binding to norovirus genotype GI.1 virus-like particles (VLPs). After biopanning, phage populations were sequenced and analyzed to identify a consensus peptide motif-YRSWXP. Two 12-mer peptides containing this sequence, NV-O-R5-3 and NV-O-R5-6, were further characterized to evaluate the motif's functional ability to detect VLPs and virus. Results indicated that these peptides effectively detect GI.1 VLPs in solid-phase peptide arrays, ELISAs and dot blots. Further, their specificity for the S-domain of the major capsid protein enables them to detect a wide range of GI and GII norovirus genotypes. Both peptides were able to detect virus in norovirus-positive clinical stool samples. Overall, the work reported here demonstrates the application of phage display coupled with next generation sequencing and computational analysis to uncover peptides with specific binding ability to a target protein for diagnostic applications. Further, the reagents characterized here can be integrated into existing diagnostic formats to detect clinically relevant genotypes of norovirus in stool.
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Affiliation(s)
- Amy M Hurwitz
- Interdepartmental Program in Translational Biology & Molecular Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Wanzhi Huang
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
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Krishnamurthy M, Moore RT, Rajamani S, Panchal RG. Bacterial genome engineering and synthetic biology: combating pathogens. BMC Microbiol 2016; 16:258. [PMID: 27814687 PMCID: PMC5097395 DOI: 10.1186/s12866-016-0876-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. RESEARCH The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. CONCLUSIONS The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.
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Affiliation(s)
- Malathy Krishnamurthy
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Richard T. Moore
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Sathish Rajamani
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Rekha G. Panchal
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
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Braff D, Shis D, Collins JJ. Synthetic biology platform technologies for antimicrobial applications. Adv Drug Deliv Rev 2016; 105:35-43. [PMID: 27089812 DOI: 10.1016/j.addr.2016.04.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/08/2016] [Accepted: 04/06/2016] [Indexed: 12/11/2022]
Abstract
The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels.
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Affiliation(s)
- Dana Braff
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - David Shis
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Pires DP, Cleto S, Sillankorva S, Azeredo J, Lu TK. Genetically Engineered Phages: a Review of Advances over the Last Decade. Microbiol Mol Biol Rev 2016; 80:523-43. [PMID: 27250768 PMCID: PMC4981678 DOI: 10.1128/mmbr.00069-15] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.
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Affiliation(s)
- Diana P Pires
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sara Cleto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sanna Sillankorva
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B. Bacteriophages and phage-derived proteins--application approaches. Curr Med Chem 2016; 22:1757-73. [PMID: 25666799 PMCID: PMC4468916 DOI: 10.2174/0929867322666150209152851] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Currently, the bacterial resistance, especially to most commonly used antibiotics has proved to be a severe therapeutic problem. Nosocomial and community-acquired infections are usually caused by multidrug resistant strains. Therefore, we are forced to develop an alternative or supportive treatment for successful cure of life-threatening infections. The idea of using natural bacterial pathogens such as bacteriophages is already well known. Many papers have been published proving the high antibacterial efficacy of lytic phages tested in animal models as well as in the clinic. Researchers have also investigated the application of non-lytic phages and temperate phages, with promising results. Moreover, the development of molecular biology and novel generation methods of sequencing has opened up new possibilities in the design of engineered phages and recombinant phage-derived proteins. Encouraging performances were noted especially for phage enzymes involved in the first step of viral infection responsible for bacterial envelope degradation, named depolymerases. There are at least five major groups of such enzymes – peptidoglycan hydrolases, endosialidases, endorhamnosidases, alginate lyases and hyaluronate lyases – that have application potential. There is also much interest in proteins encoded by lysis cassette genes (holins, endolysins, spanins) responsible for progeny release during the phage lytic cycle. In this review, we discuss several issues of phage and phage-derived protein application approaches in therapy, diagnostics and biotechnology in general.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 2016; 165:1255-1266. [PMID: 27160350 DOI: 10.1016/j.cell.2016.04.059] [Citation(s) in RCA: 836] [Impact Index Per Article: 104.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/19/2016] [Accepted: 04/24/2016] [Indexed: 01/22/2023]
Abstract
The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP.
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Affiliation(s)
- Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ 85287, USA
| | - Melissa K Takahashi
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dana Braff
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Guillaume Lambert
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Jeong Wook Lee
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Tom Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ 85287, USA
| | - Nina Donghia
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Nichole M Daringer
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Irene Bosch
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dawn M Dudley
- Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA
| | - Lee Gehrke
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Courbet A, Endy D, Renard E, Molina F, Bonnet J. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Sci Transl Med 2016; 7:289ra83. [PMID: 26019219 DOI: 10.1126/scitranslmed.aaa3601] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Whole-cell biosensors have several advantages for the detection of biological substances and have proven to be useful analytical tools. However, several hurdles have limited whole-cell biosensor application in the clinic, primarily their unreliable operation in complex media and low signal-to-noise ratio. We report that bacterial biosensors with genetically encoded digital amplifying genetic switches can detect clinically relevant biomarkers in human urine and serum. These bactosensors perform signal digitization and amplification, multiplexed signal processing with the use of Boolean logic gates, and data storage. In addition, we provide a framework with which to quantify whole-cell biosensor robustness in clinical samples together with a method for easily reprogramming the sensor module for distinct medical detection agendas. Last, we demonstrate that bactosensors can be used to detect pathological glycosuria in urine from diabetic patients. These next-generation whole-cell biosensors with improved computing and amplification capacity could meet clinical requirements and should enable new approaches for medical diagnosis.
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Affiliation(s)
- Alexis Courbet
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France
| | - Drew Endy
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Eric Renard
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Department of Endocrinology, Diabetes, Nutrition, Montpellier University Hospital; INSERM 1411 Clinical Investigation Center; Institute of Functional Genomics, CNRS UMR 5203, INSERM U661, University of Montpellier, 34090 Montpellier, France. Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Franck Molina
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France.
| | - Jérôme Bonnet
- Sys2Diag FRE3690-CNRS/ALCEDIAG, Cap Delta, 34090 Montpellier, France. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Department of Endocrinology, Diabetes, Nutrition, Montpellier University Hospital; INSERM 1411 Clinical Investigation Center; Institute of Functional Genomics, CNRS UMR 5203, INSERM U661, University of Montpellier, 34090 Montpellier, France. Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France.
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Abstract
There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.
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35
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Guliy OI, Zaitsev BD, Kuznetsova IE, Shikhabudinov AM, Dykman LA, Staroverov SA, Karavaeva OA, Pavliy SA, Ignatov OV. Determination of the spectrum of lytic activity of bacteriophages by the method of acoustic analysis. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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36
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Välimaa AL, Tilsala-Timisjärvi A, Virtanen E. Rapid detection and identification methods for Listeria monocytogenes in the food chain – A review. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.02.037] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors. Biosens Bioelectron 2015; 74:1076-86. [PMID: 26277908 DOI: 10.1016/j.bios.2015.07.078] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 01/05/2023]
Abstract
Biosensors are powerful tunable systems able to switch between an ON/OFF status in response to an external stimulus. This extraordinary property could be engineered by adopting synthetic biology or biomimetic chemistry to obtain tailor-made biosensors having the desired requirements of robustness, sensitivity and detection range. Recent advances in both disciplines, in fact, allow to re-design the configuration of the sensing elements - either by modifying toggle switches and gene networks, or by producing synthetic entities mimicking key properties of natural molecules. The present review considered the role of synthetic biology in sustaining biosensor technology, reporting examples from the literature and reflecting on the features that make it a useful tool for designing and constructing engineered biological systems for sensing application. Besides, a section dedicated to bioinspired synthetic molecules as powerful tools to enhance biosensor potential is reported, and treated as an extension of the concept of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules. Thus, the design of synthetic molecules, such as aptamers, biomimetics, molecular imprinting polymers, peptide nucleic acids, and ribozymes were encompassed as "products" of biomimetic chemistry.
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Tawil N, Sacher E, Mandeville R, Meunier M. Bacteriophages: biosensing tools for multi-drug resistant pathogens. Analyst 2015; 139:1224-36. [PMID: 24434867 DOI: 10.1039/c3an01989f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pathogen detection is of utmost importance in many sectors, such as in the food industry, environmental quality control, clinical diagnostics, bio-defence and counter-terrorism. Failure to appropriately, and specifically, detect pathogenic bacteria can lead to serious consequences, and may ultimately be lethal. Public safety, new legislation, recent outbreaks in food contamination, and the ever-increasing prevalence of multidrug-resistant infections have fostered a worldwide research effort targeting novel biosensing strategies. This review concerns phage-based analytical and biosensing methods targeted towards theranostic applications. We discuss and review phage-based assays, notably phage amplification, reporter phage, phage lysis, and bioluminescence assays for the detection of bacterial species, as well as phage-based biosensors, including optical (comprising SPR sensors and fiber optic assays), electrochemical (comprising amperometric, potentiometric, and impedimetric sensors), acoustic wave and magnetoelastic sensors.
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Affiliation(s)
- N Tawil
- Regroupement Québécois de Matériaux de Pointe, Department of Engineering Physics, École Polytechnique de Montréal, Case Postale 6079, succursale Centre-ville, Montréal, Québec H3C 3A7, Canada.
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Citorik RJ, Mimee M, Lu TK. Bacteriophage-based synthetic biology for the study of infectious diseases. Curr Opin Microbiol 2014; 19:59-69. [PMID: 24997401 PMCID: PMC4125527 DOI: 10.1016/j.mib.2014.05.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/14/2014] [Accepted: 05/28/2014] [Indexed: 01/01/2023]
Abstract
Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the microbiome.
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Affiliation(s)
- Robert J. Citorik
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
| | - Mark Mimee
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
| | - Timothy K. Lu
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Schmelcher M, Loessner MJ. Application of bacteriophages for detection of foodborne pathogens. BACTERIOPHAGE 2014; 4:e28137. [PMID: 24533229 PMCID: PMC3919822 DOI: 10.4161/bact.28137] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/22/2022]
Abstract
Bacterial contamination of food products presents a challenge for the food industry and poses a high risk for the consumer. Despite increasing awareness and improved hygiene measures, foodborne pathogens remain a threat for public health, and novel methods for detection of these organisms are needed. Bacteriophages represent ideal tools for diagnostic assays because of their high target cell specificity, inherent signal-amplifying properties, easy and inexpensive production, and robustness. Every stage of the phage lytic multiplication cycle, from the initial recognition of the host cell to the final lysis event, may be harnessed in several ways for the purpose of bacterial detection. Besides intact phage particles, phage-derived affinity molecules such as cell wall binding domains and receptor binding proteins can serve for this purpose. This review provides an overview of existing phage-based technologies for detection of foodborne pathogens, and highlights the most recent developments in this field, with particular emphasis on phage-based biosensors.
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Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition and Health; ETH Zurich; Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health; ETH Zurich; Zurich, Switzerland
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Denes T, Wiedmann M. Environmental responses and phage susceptibility in foodborne pathogens: implications for improving applications in food safety. Curr Opin Biotechnol 2013; 26:45-9. [PMID: 24679257 DOI: 10.1016/j.copbio.2013.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/26/2013] [Accepted: 09/02/2013] [Indexed: 01/02/2023]
Abstract
Bacterial foodborne pathogens can rapidly respond to changes in their environment, granting them the ability to survive under a broad range of conditions. In doing so, they undergo physiological alterations that can influence the efficacy of detection and interventions used in the food industry. As bacteriophage-based applications in food safety are gaining traction, it is crucial that we consider the effect the environment can have on phage-host interactions. This review aims to bridge knowledge of the responses of bacterial foodborne pathogens to changing environmental conditions with our understanding of phage-host interactions. An improved understanding of these intersections will aid in the development of bacteriophage-based products for the detection, biocontrol and biosanitation of foodborne pathogens.
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Affiliation(s)
- Thomas Denes
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
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