Project Proposal: Environmental sensor networks based on plant electrical signalling
Nervous systems of animals use electrical signalling to enable fast responses to environmental stimuli. In higher plant, similar electrical signalling in phloems regulate a wide-range of physiological functions including stress responses to drought, light condition and wounding. Tools for sensing and recording plant electrical signals could open up promising applications in agriculture and environmental engineering. Nonetheless, existing setups for monitoring plant electrophysiology often require the uses of cumbersome, expensive and specialised equipment on only small areas of plants in well-controlled laboratory environment. In practice, one would prefer to have a network of low-cost measurement tools that can function robustly in the field, capture overall electrical activities of multiple plants.
Previously, our team have prototyped a plant electrical signal amplifier coupled with a radio module. We demonstrated that this prototype can sense and transmit signals from Venus flytrap action potential (pulse width ~ 1400 ms; amplitude ~ 5 mV) responding to tactile inputs. We showed that it is possible to distinguish action potential from other disturbance using post-transmission signals. The estimated cost of each of our current amplifier – radio module is approximately £40.
Here we plan to improve upon our first prototypes, specifically, to expand detection bandwidth, to increase sampling rates and to further reduce the cost. The design of the device should be simple and cheap enough to be mass produced for whole plant / whole field measurement. Additionally, we plan to test our device performance in wider range of plant species especially non-sensitive and woody plants. An ability to reduce cost, lower down barrier of entry and scale up plant electrophysiological research would bring us closer to realising the full application potential of this field.
Who We Are
Pakpoom Subsoontorn (firstname.lastname@example.org) received his B.S. degree in Biology and Computer science from California Institute of Technology. He finished his Ph.D. in Bioengineering from Stanford university and currently works as a postdoctoral researcher at department of plant science, University of Cambridge. His previous research projects cover diverse topics in synthetic biology ranging from in vitro DNA nanotechnology, biophysics of gene expression and synthetic gene networks. His current research focuses on cell-cell communication and emergent properties of multicellular systems.
Sakonwan Kuhaudomlarp (Sakonwan.Kuhaudomlarp@jic.ac.uk) received her B.A. and M.Sci. degree in Biochemistry from University of Cambridge. She has research experiences in plant cell wall synthesis under guidance of professor Paul Dupree and microfluidics platform as diagnostic tools under the supervision of professor Florian Hollfelder. She currently pursues her Ph.D. in Plant Sciences and Microbiology at the John Innes Centre, under the supervision of professor Robert A. Field, investigating beta glucan metabolism in Euglena gracilis.
Kyle Lopin (email@example.com) received his B.S. and M.S. degree in Electrical and Computer Engineering from the University of California at Santa Barbara. He received a Ph.D. in Physiology and Biophysics from Case Western Reserve University for working on research of electrophysiology and computer modeling of ion channel permeation and gating. He worked as a Research Fellow at the Cleveland Clinic Foundation in the BioMedical Engineering department developing an electrical device to measure physiological properties of organs-on-a-chip as part of the microphysiology research program by the United States Defense Advanced Research Projects Agency (DARPA). He is currently a faculty member at Naresuan University, Thailand, working on computational biology, and biomedical device development.
Settha Tangkawanit (firstname.lastname@example.org) received the B.Eng. degree in Computer Engineering and M.Eng. degree in Electrical Engineering from Naresuan University. He currently works at the Department of Electrical and Computer Engineering, Faculty of Engineering, Naresuan University, Thailand. His research interests are in the area of embedded system, computer vision and wireless sensor network. He is also the founder and the owner of Settzer Lab, a school of electronic engineering for kids.
1. To design and build a robust, portable, low cost, and open source device for measuring and recording plant electrical potential. Our primary goal is to focus on extracellular electrical potential recording from woody plants. Built upon our existing prototypes (see our previous prototype outline, prototype demonstration and result), we would like to improve plant-device interface and powering systems to enable more robust connection and long-term operation. The device should be able to stably operate in open environment, collecting and storing data for several days without human intervention. The device should be modular enough to be scaled up for collecting data from multiple locations on plant simultaneously without the need for major hardware changes.
2. To create a platform for community engagement in plant electrophysiology research. The platform will consist of self-contained tutorial for operating the device, standard protocols for depositing data and open forum for sharing problems and application ideas. This platform would not only expand our workforce for exploring plant electrophysiology in natural environment, but also serve as educational tools for students who are interested the interface between biology and engineering.
1. Possible sensor/controller improvement. A Programmable System on a Chip (PSoC) from Cypress Semiconductor will be used for analog-digital conversion. We plan to use the CY8KIT-059 PSoC 5LP Prototyping Kit by Cypress semiconductor. The use of such prototyping kits manufactured in large batches would allow us to lower the cost (~ £7.5 total cost per kit as oppose to £20 for Arduino) and better analog to digital conversion (20 bit as oppose to 10 bit for Arduino). The PSoC is a novel programmable electrical chip that has both programmable analog and digital components. This will allow the use of just one integrated circuit to make the device. Devices used in previous plant electrophysiology studies usually have separate digital and analog boards, resulting in higher cost and complexity. This is especially true for the analog part where equipments in previous studies need to be custom-made, an expensive and difficult undertaking for researchers who are not experts in electrical engineering. The proposed device will make it easier for biologist to study plant electrophysiology. To verify this device, we will compare the results of our device and a device that uses a higher-end instrumentation amplifier. It could be a problem that the electrical potentials of the plants need an amplifier with a lower input bias current and higher gain than that can be provided by the PSoC 5LP. Compared to other devices in the literature, the PSoC 5LP has better current and gain characteristics. To confirm that the PSoC is adequate, an external instrumentation amplifier with lower input current and higher gain will be used for comparison. If it is found that an instrumentation amplifier is needed to adequately record plant electrical activity, it will be incorporated into our design.
2. Possible wireless network implementation. We have successfully developed a wireless network for our prototyping device, which allow signal transmission between the remote and receiver units. We will expand our current work by developing an internet data logging system which will allow us to deposit processed data directly onto an online interface. To achieve this, we will incorporate an XBee wifi module into our current receiver unit design. The wifi module will enable the Internet access and allow data transmission from the microcontroller onto the online interface. We will also look for an alternative of XBee module in order to further reducing the cost of the prototype such as XRF module by Ciseco.
3.Reference plants and test conditions. To test whether our device function as expected, we will use a selection of plants of which electrophysiology have been well-characterised as references. Here are some tentative examples:
a. Venus Fly trap (respond to touch) is available for ordering online. For reference, we will use measurement data from Backyard Brain.
b.Mimosa pudica (respond to touch) is available for ordering online. For reference, we will use measurement data from Volkov et al 2010
c. Arabidopsis thaliana (respond to wounding) is available at Plant Science Department, University of Cambridge, for example, from Alex Web’s lab and can be readily ordered from Horticultural service at JIC. We can use measurement from Mousavi et al 2013 as a reference.
d. Poplar trees (daily cyclical variation) We can use measurement result from Gilbert et al 2006 as a reference
1.Deliverable hardware prototype for outdoor, portable, and wireless plant electrophysiology together with publishable research article describing the work.
2. Online database collection for electrical response in plants. We will create an online website for database deposition in a similar fashion to PhysioBank, which is an archive of well-characterized digital recordings of human cardiopulmonary, neural and other biomedical signals, which can be freely downloaded for use by the biomedical research.
Who will be involved
1. Pakpoom/Kyle have leading roles in electrophysiology and hardware engineering.
2. Sakonwan will be responsible for developing data logging system, wireless communication and online interface design.
3. Settha will be a design advisor on microcontroller and wireless communication devices.
Fromm, J., and Spanswick, R. (1993). Characteristics of action potentials in willow (Salix-viminalis L). J. Exp. Bot. 44, 1119–1125.
Gibert, D., Le Mouël, J.L., Lambs, L., Nicollin, F., and Perrier, F. (2006). Sap flow and daily electric potential variations in a tree trunk. Plant Sci. 171, 572–584.
Gurovich, L. a., and Hermosilla, P. (2009). Electric signalling in fruit trees in response to water applications and light-darkness conditions. J. Plant Physiol. 166, 290–300
Mousavi, S. a R., Chauvin, A., Pascaud, F., Kellenberger, S., and Farmer, E.E. (2013). GLUTAMATE RECEPTOR-LIKE genes mediate leaf-to-leaf wound signalling. Nature 500, 422–426.
Mousavi, S.A.R., Nguyen, C.T., Farmer, E.E., and Kellenberger, S. (2014). Measuring surface potential changes on leaves. Nat. Protoc. 9, 1997–2004.
Pombert, J.-F., James, E.R., Janouškovec, J., and Keeling, P.J. (2012). Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome. PLoS One 7, e53433.
Ríos-Rojas, L., Tapia, F., and Gurovich, L. a. (2014). Electrophysiological assessment of water stress in fruit-bearing woody plants. J. Plant Physiol. 171, 799–806.
Ríos-Rojas, L., Morales-Moraga, D., Alcalde, J.A., and Gurovich, L.A. (2015). Use of plant woody species electrical potential for irrigation scheduling. Plant Signal. Behav. 10, e976487.
Transactions, E.C.S., and Society, T.E. (2014). Citrus Greening (Huanglongbing): Fast Electrochemical Detection and Phytomonitoring of the Trees Diseases Alexander G. Volkov. 58, 9–17.
Benefits and outcomes
1. The project involves the collaborative efforts of researchers from the John Innes Centre (JIC), the department of Plant Sciences, University of Cambridge and Naresuan University, Thailand. Not only will it complement the existing collaboration between JIC and Cambridge, but also expand the work into international setting, which could substantially enhance the progression of the project.
2. The protocol for device construction and data interpretation will be published via an online interface, which will be easily accessible by plant research communities for scientific research purposes and also available for non-scientific communities for public engagement and outreach opportunities. The online platform will also be used for information sharing between plant researchers, technical support for instrument set-up, and article collections providing background to plant electrophysiology and neurobiology fields. So far, we have introduced our project through social media platforms such as Facebook and Twitter under the name “TEPARAC” and has received a good feedback from the audience.
3. The portability and user-friendly design of the device will enable the collection of plant electrical signals from various plant species, both in well-controlled and natural environments. The data collection process could be easily adopted by plant research communities and non-scientist citizen, which will aid data acquisition and creation of an unprecedented “plant electrical signal database” that could be shared on our online platform. The database could provide a stepping stone for addressing further biological questions related to plant electrophysiology.
If our OpenPlant fund application is successful, there will be a match funding provided by Naresuan University, Thailand, as aforementioned in the previous section.