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Editorial overview: Environmental biotechnology
Available online at www.sciencedirect.com
ScienceDirect Editorial overview: Environmental biotechnology Jan Roelof van der Meer and Man Bock Gu Current Opinion in Biotechnology 2017, 45:ix–xi For a complete overview see the Issue Available online 17th May 2017 http://dx.doi.org/10.1016/j.copbio.2017.05.001 0958-1669/ã 2017 Published by Elsevier Ltd.
Jan Roelof van der Meer
Department of Fundamental Microbiology, University of Lausanne, Baˆtiment Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland e-mail: [email protected] Jan Roelof van der Meer is Professor in Environmental Microbiology at the Department of Fundamental Microbiology of the University of Lausanne, Switzerland. The primary interest of Prof. van der Meer’s research is environmental microbiology. His research focuses on genetic adaptation processes in bacteria, the mechanisms by which they deal with toxic substances and how microbial processes can be applied in a useful way. His group was one of the pioneers in design and applications of bacterial bioreporters.
Man Bock Gu
Hana Science Hall A-603, Department of Biotechnology, Korea University, Anamdong, Seongbuk-Gu, Seoul 136-713, Republic of Korea e-mail: [email protected]
This issue of Current Opinion in Biotechnology on Environmental Biotechnology focuses specifically on new developments in biosensing. The design and development of biosensors is traditionally one of the key areas in environmental biotechnology. Biosensors are analytical devices composed of a biological ‘core’ that forms the essential sensing element embedded in or on reaction chambers or surfaces, and integrated with detectors to read out the signal coming from the sensor in response to a sample. Typical biological sensing elements consist of antibodies or aptamers (immobilized on surfaces or other), or living cells. Much research is devoted to the question of designing the biological sensing element as closely as possible to the desired chemical target molecule, obtaining high selectivity and specificity, enabling low limits of target detection ideally in a label-free mode. Along these lines Lechuga and co-workers in this issue describe the latest developments to produce antibody-based biosensors for environmental monitoring. This includes the successes and pitfalls to obtain appropriate antibodies and reagents for environmentally relevant molecules, and different strategies to bind the immunoreagents to surfaces in order to enable nanophotonic label-free detection. In particular new types of nanophotonic detection such as bimodal or asymmetric waveguide platforms are promising for miniaturization of immunoassays while achieving excellent limits of detection in the nanogram per liter range. Gu and co-workers then discuss the usage of aptamers as biologically active molecules for target chemical detection in biosensors. Aptamers have the advantage of antibodies in being more easily amenable to in vitro evolution and selection procedures, which allows easy screening of large aptamer libraries and optimization of the appropriate aptamer for binding the chemical target. Lu and co-workers along similar lines discuss developments in DNAzymes as biosensors for metals. Much interest exists also in the use of living cells for biosensing. Living cells can be used as such, but this makes it difficult to record their reactions to environmental samples. Lu and Schirmer, however, describe recent successes in using eukaryotic cell lines for label-free detection of toxic effects. This can be achieved by seeding and growing cell monolayers on electrodes. The cell–cell contacts are particularly sensitive to toxicant stress, which results in changes of impedance upon sample exposure. Instead of using non-labeled cells, several contributions in this issue focus on engineered ‘reporter’ cells. These are eukaryotic or prokaryotic cell lines/ strains, which express easily measurable reporter proteins upon contact to
www.sciencedirect.com
Current Opinion in Biotechnology 2017, 45:ix–xi
x Environmental biotechnology
Man Bock Gu is a professor, the department chair, and the director of BK21 PLUS School of Life Sciences and Biotechnology in the Department of Biotechnology at Korea University, Seoul, Republic of Korea. He received his Ph.D. in Chemical Engineering from the University of Colorado at Boulder, Colorado, USA in 1994. Prof. Gu was a president of Korean Biochip Society in 2014 and a regular member of Korean Association of Science and Technology (KAST) since 2015.
target chemicals or conditions in the sample. Roggo and van der Meer discuss these principles and give examples where reporter strains were used in field measurements or were embedded in automated instruments. Belkin and co-workers describe the specific application of bacterial bioreporters to remotely detect explosives from land mines in a procedure whereby the (immobilized) cells are sprayed on the site. Cells reacting to the volatile explosives produce the fluorescent reporter, which can be remotely assayed by laser illumination and telescope detection. Despite their ease of engineering and application, bioreporters have the disadvantage of being genetically modified organisms restricting their deployment in the field. In order to potentially overcome this issue, recent efforts have focused on using in vitro transcription-translation systems to reproduce the complete chain of reporter protein induction. This cell-free synthetic biology application is discussed by David Karig. Finally, several groups are looking into possibilities to extend the spectrum of possible compound or molecular pathway detection beyond what was easily reachable using bioreporters. Krell and Matilla in this issue discuss the characteristics of bacterial chemoreceptors and their mode of target detection. Chemoreceptors typically lead to changes in bacterial motility but a large variety of natural chemoreceptors exists, which could perhaps be exploited for chemosensing in biosensors. Pelet and Wosika discuss recent efforts to interrogate cellular pathways by reporter proteins that change their subcellular location. Classical bioreporter strains rely on de novo gene induction to visualize the reporter protein irrespective of its localisation. The new idea discussed by Pelet is that detecting the change in subcellular location of the reporter protein potentially is much faster than de novo expression, plus follows more directly the cellular pathway. One could thus imagine having faster reporter strains and interrogating different cell pathways for, for example, toxicity measurements. Yoon and co-workers, finally, go a step beyond just using single cell reporters, and describe how recreated organs-on-chip can be deployed to detect toxic compounds in environmental samples. Although sensing of chemical assaults is important for environmental monitoring, there is also increasing risk of biological assaults in the water. Particularly algal blooms can lead to the release of extremely toxic molecules; therefore, it is important to be able to assess rapidly the presence of particular algal species in the water. This is the topic of the opinion article by O’Kennedy and co-workers, who discuss recent developments in detection of algal blooms by focusing not so much on the toxic compounds as well as on the algal species. Also the contribution by McQuillan and Robidart focuses on rapid automated detection of algal and bacterial species in marine systems by DNA-based sensor technologies. To complete this issue on environmental biosensing, we felt it would be important to present the analytical challenges for biosensors in comparison to regular high-end chemical analytics. This task has been expertly taken up by Sanchis and colleagues, who discuss environmental analytical practice, in particular with respect to preconcentration and sample purification methods. Their discussion highlights the importance for future biosensor applications to focus on biocompatible preconcentration methods, because only in that way will biosensors be able to achieve detection limits competitive with high-end analytics.
Current Opinion in Biotechnology 2017, 45:ix–xi
www.sciencedirect.com
Editorial overview van der Meer and Gu xi
Finally, don’t we all dream of being able to implant biosensors in automated or robotic devices, that would go around and report wherever is the contamination? Bayat and colleagues in this issue present recent developments on environmental surveying using automated vehicles. Automated surveying poses specific challenges that go much beyond the biosensing itself. Data from the biosensors is only one input for the robots, which
www.sciencedirect.com
simultaneously have to deal with self-localization, data integration, data transmission and guidance algorithms. We sincerely thank all authors for their excellent contributions. We hope you as readers will like this overview of ongoing developments in environmental biosensing, and may find it inspiring for further new studies and ideas of your own.
Current Opinion in Biotechnology 2017, 45:ix–xi
ScienceDirect Editorial overview: Environmental biotechnology Jan Roelof van der Meer and Man Bock Gu Current Opinion in Biotechnology 2017, 45:ix–xi For a complete overview see the Issue Available online 17th May 2017 http://dx.doi.org/10.1016/j.copbio.2017.05.001 0958-1669/ã 2017 Published by Elsevier Ltd.
Jan Roelof van der Meer
Department of Fundamental Microbiology, University of Lausanne, Baˆtiment Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland e-mail: [email protected] Jan Roelof van der Meer is Professor in Environmental Microbiology at the Department of Fundamental Microbiology of the University of Lausanne, Switzerland. The primary interest of Prof. van der Meer’s research is environmental microbiology. His research focuses on genetic adaptation processes in bacteria, the mechanisms by which they deal with toxic substances and how microbial processes can be applied in a useful way. His group was one of the pioneers in design and applications of bacterial bioreporters.
Man Bock Gu
Hana Science Hall A-603, Department of Biotechnology, Korea University, Anamdong, Seongbuk-Gu, Seoul 136-713, Republic of Korea e-mail: [email protected]
This issue of Current Opinion in Biotechnology on Environmental Biotechnology focuses specifically on new developments in biosensing. The design and development of biosensors is traditionally one of the key areas in environmental biotechnology. Biosensors are analytical devices composed of a biological ‘core’ that forms the essential sensing element embedded in or on reaction chambers or surfaces, and integrated with detectors to read out the signal coming from the sensor in response to a sample. Typical biological sensing elements consist of antibodies or aptamers (immobilized on surfaces or other), or living cells. Much research is devoted to the question of designing the biological sensing element as closely as possible to the desired chemical target molecule, obtaining high selectivity and specificity, enabling low limits of target detection ideally in a label-free mode. Along these lines Lechuga and co-workers in this issue describe the latest developments to produce antibody-based biosensors for environmental monitoring. This includes the successes and pitfalls to obtain appropriate antibodies and reagents for environmentally relevant molecules, and different strategies to bind the immunoreagents to surfaces in order to enable nanophotonic label-free detection. In particular new types of nanophotonic detection such as bimodal or asymmetric waveguide platforms are promising for miniaturization of immunoassays while achieving excellent limits of detection in the nanogram per liter range. Gu and co-workers then discuss the usage of aptamers as biologically active molecules for target chemical detection in biosensors. Aptamers have the advantage of antibodies in being more easily amenable to in vitro evolution and selection procedures, which allows easy screening of large aptamer libraries and optimization of the appropriate aptamer for binding the chemical target. Lu and co-workers along similar lines discuss developments in DNAzymes as biosensors for metals. Much interest exists also in the use of living cells for biosensing. Living cells can be used as such, but this makes it difficult to record their reactions to environmental samples. Lu and Schirmer, however, describe recent successes in using eukaryotic cell lines for label-free detection of toxic effects. This can be achieved by seeding and growing cell monolayers on electrodes. The cell–cell contacts are particularly sensitive to toxicant stress, which results in changes of impedance upon sample exposure. Instead of using non-labeled cells, several contributions in this issue focus on engineered ‘reporter’ cells. These are eukaryotic or prokaryotic cell lines/ strains, which express easily measurable reporter proteins upon contact to
www.sciencedirect.com
Current Opinion in Biotechnology 2017, 45:ix–xi
x Environmental biotechnology
Man Bock Gu is a professor, the department chair, and the director of BK21 PLUS School of Life Sciences and Biotechnology in the Department of Biotechnology at Korea University, Seoul, Republic of Korea. He received his Ph.D. in Chemical Engineering from the University of Colorado at Boulder, Colorado, USA in 1994. Prof. Gu was a president of Korean Biochip Society in 2014 and a regular member of Korean Association of Science and Technology (KAST) since 2015.
target chemicals or conditions in the sample. Roggo and van der Meer discuss these principles and give examples where reporter strains were used in field measurements or were embedded in automated instruments. Belkin and co-workers describe the specific application of bacterial bioreporters to remotely detect explosives from land mines in a procedure whereby the (immobilized) cells are sprayed on the site. Cells reacting to the volatile explosives produce the fluorescent reporter, which can be remotely assayed by laser illumination and telescope detection. Despite their ease of engineering and application, bioreporters have the disadvantage of being genetically modified organisms restricting their deployment in the field. In order to potentially overcome this issue, recent efforts have focused on using in vitro transcription-translation systems to reproduce the complete chain of reporter protein induction. This cell-free synthetic biology application is discussed by David Karig. Finally, several groups are looking into possibilities to extend the spectrum of possible compound or molecular pathway detection beyond what was easily reachable using bioreporters. Krell and Matilla in this issue discuss the characteristics of bacterial chemoreceptors and their mode of target detection. Chemoreceptors typically lead to changes in bacterial motility but a large variety of natural chemoreceptors exists, which could perhaps be exploited for chemosensing in biosensors. Pelet and Wosika discuss recent efforts to interrogate cellular pathways by reporter proteins that change their subcellular location. Classical bioreporter strains rely on de novo gene induction to visualize the reporter protein irrespective of its localisation. The new idea discussed by Pelet is that detecting the change in subcellular location of the reporter protein potentially is much faster than de novo expression, plus follows more directly the cellular pathway. One could thus imagine having faster reporter strains and interrogating different cell pathways for, for example, toxicity measurements. Yoon and co-workers, finally, go a step beyond just using single cell reporters, and describe how recreated organs-on-chip can be deployed to detect toxic compounds in environmental samples. Although sensing of chemical assaults is important for environmental monitoring, there is also increasing risk of biological assaults in the water. Particularly algal blooms can lead to the release of extremely toxic molecules; therefore, it is important to be able to assess rapidly the presence of particular algal species in the water. This is the topic of the opinion article by O’Kennedy and co-workers, who discuss recent developments in detection of algal blooms by focusing not so much on the toxic compounds as well as on the algal species. Also the contribution by McQuillan and Robidart focuses on rapid automated detection of algal and bacterial species in marine systems by DNA-based sensor technologies. To complete this issue on environmental biosensing, we felt it would be important to present the analytical challenges for biosensors in comparison to regular high-end chemical analytics. This task has been expertly taken up by Sanchis and colleagues, who discuss environmental analytical practice, in particular with respect to preconcentration and sample purification methods. Their discussion highlights the importance for future biosensor applications to focus on biocompatible preconcentration methods, because only in that way will biosensors be able to achieve detection limits competitive with high-end analytics.
Current Opinion in Biotechnology 2017, 45:ix–xi
www.sciencedirect.com
Editorial overview van der Meer and Gu xi
Finally, don’t we all dream of being able to implant biosensors in automated or robotic devices, that would go around and report wherever is the contamination? Bayat and colleagues in this issue present recent developments on environmental surveying using automated vehicles. Automated surveying poses specific challenges that go much beyond the biosensing itself. Data from the biosensors is only one input for the robots, which
www.sciencedirect.com
simultaneously have to deal with self-localization, data integration, data transmission and guidance algorithms. We sincerely thank all authors for their excellent contributions. We hope you as readers will like this overview of ongoing developments in environmental biosensing, and may find it inspiring for further new studies and ideas of your own.
Current Opinion in Biotechnology 2017, 45:ix–xi