A team of plant scientists at the Sainsbury Laboratory Cambridge University (SLCU) would like to turn this science fiction into reality using light-based messaging to ‘talk’ to plants.

Early lab experiments with tobacco (Nicotiana benthamiana) have demonstrated that they can activate the plant’s natural defence mechanism (immune response) using light as a stimulus (messenger).

Light serves as a universal means of daily human communication, for example the signalling at traffic lights, pedestrian crossings, or the open-closed status of a shop.

Alexander Jones’ research team is using light as a messenger in the development of tools that enable plants to communicate with humans and humans to communicate with plants.

The University of Cambridge team previously engineered a series of biosensors using fluorescent light to visually communicate in real-time what is happening at the cellular level in plants, revealing the dynamics of critical plant hormones. These biosensors can tell us how plants are reacting to environmental stresses — plants ‘talking’ to humans.

Their latest research published in PLOS Biology, describes a new tool called Highlighter, which uses specific light conditions to activate the expression of a target gene in plants, for example to trigger their defence mechanisms — humans ‘talking’ to plants.

The concept of humans being able to communicate with plants on a meaningful level has long captured the imagination of people. If such a capability was possible, it could revolutionise agriculture and our relationship with plants.

“If we could warn plants of an impending disease outbreak or pest attack, plants could then activate their natural defence mechanisms to prevent widespread damage,” Dr Jones said. “We could also inform plants about approaching extreme weather events, such as heatwaves or drought, allowing them to adjust their growth patterns or conserve water. This could lead to more efficient and sustainable farming practices and reduce the need for chemicals.”

Bo Larsen, who engineered Highlighter while at SLCU, has taken us a major step closer to this goal of ‘talking’ to plants by engineering a light-controlled gene expression system (optogenetics system) from a prokaryotic system into a eukaryotic system that is tailored for plants.

Optogenetics can bring light to biomolecular processes in plants

To understand cellular activity biologists need to be able to control biomolecular processes at the cellular level. Optogenetics is a scientific technique that uses a light stimulus to activate or deactivate a specific process. “Light stimuli are cheap, reversible, non-toxic and can be delivered with high-resolution,” Dr Jones said.

To do this, scientists engineer light-sensitive proteins (photoreceptors) to control a target process and then deliver these optogenetic ‘actuators’ to the cells they want to control.

Optogenetics has revolutionised many fields including neuroscience where biologists can isolate functions of individual neurons.

However, optogenetics has been difficult to apply to plants. This is because plants already contain lots of photoreceptors and need a wide spectrum of light to grow. Switching from dark to light also activates native plant photoreceptors and a myriad of cellular systems.

Exacerbating this problem is the fact that many of the best performing optogenetic actuators use genetic parts from plants, meaning they could cross-talk with native photoreceptors if used in plants.

The story behind the research

Dr Jones, looking for an optogenetic gene expression switch that could be applied under normal horticultural light conditions without impacting on endogenous plant physiology and development, sought advice from J. Clark Lagarias, from UC Davis, who is an expert in phytochrome and cyanobacteriochrome light-switches.

He suggested repurposing the prokaryotic CcaS-CcaR optogenetic system, which was originally sourced from photosynthetic microbes and uses the ratio of green (on) — red (off) light signals. By modulating the spectrum of white light plants need to grow, genes could be turned on or off using a minimally invasive stimulus.

But when developing Highlighter into a eukaryotic optogenetic system, Dr Larsen detected an unexpected blue-off behaviour. Could the conversion have altered the green-red spectral properties of the CcaS photoreceptor?

Working together with Alex Jones, Ines Camacho and Richard Clarke from the National Physical Laboratory (NPL), they detected that the new system was still able to use green and red light just like the original system. But the spectroscopic analysis at NPL also showed evidence of an independent blue-light sensing. Co-author Roberto Hofmann noticed that, in addition to the red-green sensing domain, CcaS had a domain with homology to blue-light photosensors called phototropins. It seems the engineering efforts had inadvertently unlocked a latent CcaS blue sensing behaviour, providing an alternate way to control CcaS-CcaR activity.

Highlighter is an optogenetic tool for plants

When deployed in plants, Highlighter uses minimally invasive light signals for activation and inactivation, and is unaffected by the light-dark cycling in growth chambers.

The current Highlighter system is inactive under blue light conditions and active in the dark and under white light, green light and, mysteriously, red light conditions. Further work is planned to progress development of Highlighter, but the team has already demonstrated optogenetic control over plant immunity, pigment production and a yellow fluorescent protein, the latter at cellular resolution.

“Highlighter is an important step forward in the development of optogenetics tools in plants and its high-resolution gene control could be applied to study a large range of fundamental plant biology questions,” Dr Jones added. “A growing toolbox for plants, with diverse optical properties, also opens exciting opportunities for crop improvement. For example, in the future we could use one light condition to trigger an immune response, and then a different light condition to precisely time a particular trait, such as flowering or ripening.”

In a study in the Journal of Cataracts & Refractive Surgery, researchers from the University of Rochester created computational eye models that included the corneas of post-LASIK surgery patients and studied how standard intraocular lenses and lenses designed to increase depth of focus performed in operated eyes. Susana Marcos, the David R. Williams Director of the Center for Visual Science and the Nicholas George Professor of Optics and of Ophthalmology at Rochester, says the computational models that use anatomical information of the patient’s eye provide surgeons with important guidance on the expected optical quality post-operatively.

“Currently the only pre-operative data used to select the lens is essentially the length and curvature of the cornea,” says Marcos, a coauthor of the study. “This new technology allows us to reconstruct the eye in three dimensions, providing us the entire topography of the cornea and crystalline lens, where the intraocular lens is implanted. When you have all this three-dimensional information, you’re in a much better position to select the lens that will produce the best image at the retinal plane.”

The future of optical coherence tomography

Marcos and her collaborators from the Center for Visual Science, as well as Rochester’s Flaum Eye Institute and Goergen Institute for Data Science, are conducting a larger study to quantify in three dimensions the eye images using the optical coherence tomography quantification tools they’ve developed to find broader trends. They are using machine-learning algorithms to find relationships between pre- and post-operation data, providing parameters that can inform the best outcomes.

Additionally, they have developed technology that can help patients see for themselves what different lens options will look like.

“What we see is not strictly the image that is project on the retina,” says Marcos. “There is all the visual processing and perception that comes in. When surgeons are planning the surgery, it is very difficult for them to convey to the patients how they are going to see. A computational, personalized eye model tells which lens is the best fit for the patient’s eye anatomy, but patients want to see for themselves.”

With an optical bench, the researchers use technology originally developed for astronomy, such as adaptive optics mirrors and spatial light modulators, to manipulate the optics of the eye as an intraocular lens would. The approach allows Marcos and her collaborators to perform fundamental experiments and collaborate with industry partners to test new products. Marcos also helped develop a commercial headset version of the instrumentation called SimVis Gekko that allows patients to see the world around them as if they had had the surgery.

In addition to studying techniques to help treat cataracts, the researchers are applying their methods to study other major eye conditions, including presbyopia and myopia.

The authors argue that we could transform arid ecosystems into efficient carbon-capture systems with improved soil health, enhanced photosynthetic efficiency, and larger root biomass by engineering ideal combinations of plants, soil microbes, and soil type to facilitate a naturally occurring biogeochemical process called the oxalate-carbonate pathway to create below-ground carbon sinks.

“Re-greening deserts by restoration of ecosystem functions, including carbon sequestration, should be the preferential approach,” writes the research team, led by senior author and plant scientist Heribert Hirt of King Abdullah University of Science and Technology. “The advantage of reclaiming arid regions for re-greening and carbon sequestration is that they do not compete with lands used in agriculture and food production.”

The method takes advantage of arid-adapted plants that produce oxalates — ions containing carbon and oxygen that might ring a bell if you’re unlucky enough to suffer from kidney stones or gout. Some soil microbes use oxalates as their sole carbon source, and in doing so, they excrete carbonate molecules into the soil. Carbonate usually breaks down quickly, but if these plant-microbe systems are grown in alkaline- and calcium-rich soils, the carbonate reacts with calcium to form stable deposits of calcium carbonate.

Carbon naturally cycles between the atmosphere, oceans, and terrestrial ecosystems, but human actions have resulted in the accumulation of excess CO₂ in the atmosphere. Even if we can reduce CO₂ emissions, the researchers write that the .” ..climate effects of elevated CO₂ will remain irreversible for at least 1,000 years unless CO₂ can be sequestered from the atmosphere.”

Trees are considered an ideal system for carbon capture, but reforestation competes directly with agriculture for arable land. In contrast, arid lands, which constitute approximately one-third of terrestrial surfaces, are not utilized for agriculture.

Currently, arid ecosystems support very little plant life, with the lack of water being the biggest limiting factor. However, some plants have adapted to arid life by evolving different mechanisms for coping with the lack of water and extreme temperatures. Some arid-adapted plants have special root systems for reaching deep into the soil to tap hidden water sources while others use different forms of photosynthesis that allow them to minimize water loss during the hottest parts of the day. Yet others, so-called “oxalogenic” plants, produce large amounts of oxalates that they can convert into water during times of drought. Some of the carbon from these oxalates is deposited below-ground as carbon deposits when oxalogenic plants are grown under certain conditions, and it’s this mechanism that the authors want to exploit for carbon sequestration.

“Overall, in this form of carbon sequestration, one out of every sixteen photosynthetically fixed carbon atoms might be sequestered into carbonates,” the authors write.

Amplifying this naturally occurring biogeochemical process in arid lands could convert these currently unproductive and degraded ecosystems into carbon sinks with healthier soil and plants, the authors say. They suggest beginning with “fertility islands” — small pockets of re-greened habitat from which the plants and microbes can spread to form a carpet of vegetation.

The authors estimate that these approaches could result in significant increases in both plant and soil carbon sequestration in less than ten years. However, they note that the success and speed of the proposed method will depend on the rate of plant growth (which tends to be slow under water-scarce conditions) and .” ..will also depend on the financial and political means to apply this technology in various arid countries.”

This work was supported by grants from the King Abdullah University of Science and Technology.

Dr. Lang and colleagues found that the presence of an enzyme isoform called α-tryptase, which is encoded by the TPSAB1 gene, correlates with increased prevalence of anaphylaxis or severe reaction to food as compared to subjects without any α-tryptase.

“Determining whether or not a patient with food allergies has α-tryptase can easily be done in clinical practice using a commercially available test to perform genetic sequencing from cheek swabs,” said lead author Abigail Lang, MD, MSc, attending physician and researcher at Lurie Children’s and Assistant Professor of Pediatrics at Northwestern University Feinberg School of Medicine. “If the biomarker is detected, this may help us understand that the child is at a higher risk for a severe reaction or anaphylaxis from their food allergy and should use their epinephrine auto-injector if exposed to the allergen. Our findings also open the door to developing an entirely new treatment strategy for food allergies that would target or block α-tryptase. This is an exciting first step and more research is needed.”

Tryptase is found mainly in mast cells, which are white blood cells that are part of the immune system. Mast cells become activated during allergic reactions. Increased TPSAB1 copy number which leads to increased α-tryptase is already known to be associated with severe reactions in adults with Hymenoptera venom allergy (or anaphylaxis following a bee sting).

Dr. Lang’s study included 119 participants who underwent TPSAB1 genotyping, 82 from an observational food allergy cohort at the National Institute of Allergy and Infectious Diseases (NIAID) and 37 from a cohort of children who reacted to peanut oral food challenge at Lurie Children’s.

“We need to validate our preliminary findings in a much larger study, but these initial results are promising,” says Dr. Lang. “We also still need a better understanding of why and how α-tryptase makes food allergy reactions more severe in order to pursue this avenue for potential treatment.”

Rajesh Kumar, MD, MSc, from Lurie Children’s is the co-senior author on the study. Dr. Kumar is the Interim Division Head of Allergy and Immunology and Professor of Pediatrics at Northwestern University Feinberg School of Medicine.

This work was supported in part by the Midwest Allergy Research Institute (MARI) Food Allergy Pilot Research Award and NIAID-sponsored T32 grant AI083216. This project was funded in part with federal funds from the Division of Intramural Research of the National Institute of Allergy and Infectious Diseases, NIH. This project has also been funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024.