Introducing PhotosynQ to Scientists in West Africa

On August 11 – 12, the PhotosynQ team conducted a workshop with researchers from across West Africa in Ouagadougou, Burkina Faso

The Kramer Lab has a cross-cutting grant from the McKnight Foundations Collaborative Crop Research Program, which provides resources for training and supporting local McKnight grantee’s throughout Western, Eastern, and Southern Africa. Using these resources, we were able to bring together members of the PhotosynQ team and 13 researchers from Niger, Mali and Burkina Faso for an intense, 2-day workshop. During the workshop, participants learned how to take MultispeQ measurements, create their own projects and interpret photosynthesis data. Additionally, and again with McKnight support, a number of participants were able to take MultispeQ instruments home from the conference, so that they can start their own PhotosynQ pilot projects.

It was one of the most challenging and fun workshops that I have participated in. On the one hand, the local researchers were very enthusiastic and ready to learn. There was a great mix of plant breeders, crop physiologists, and agronomists. This led to some lively discussion about how photosynthesis measurements, the MultispeQ and the PhotosynQ platform could all be integrated into local research projects, ultimately to the benefit of local smallholder farmers. Hopefully we can find ways to put some of the ideas generated into practice and see what happens!

On the other hand, internet connectivity was very poor, an obvious challenge for a web-based platform. Also, with all of the local researchers hailing from francophone countries, and with my French not extending beyond “bonjour,” the language barrier was a real hurdle. We did have translators who helped fill in the communication gaps, but they were not well versed in plant science lingo. They got a workout!

We look forward to long and productive collaborations with our new friends from West Africa!

 

My leaves are too small, my project is too big and other special cases

We have developed a number of special features that can improve your PhotosynQ experience.

We have tried to build PhotosynQ to be flexible for a variety of different users, projects, goals, etc. Sometimes we have succeeded, sometimes we have not, and sometimes we have succeeded but failed to clearly explain the features that made it successful (which is not very helpful!). In fact, while writing this blog post I was reminded of a feature that we built, but then forgot about!

What kind of flexibility am I talking about?

  • Want to measure leaves that are too small to cover the light guides? You can do that!
  • Want to measure a lot of different plant populations without spending all day scrolling through long lists of multiple choice answers in the field? You can do that!
  • Want to read Barcodes and QR codes with the PhotosynQ apps? You can do that!
  • Want to upload custom data to the PhotosynQ database so you can compare it to your MultispeQ data? You guessed it, you can do that!

To find out how, check out our new special features page.

We hope these features improve your PhotosynQ experiment!

PhotosynQ Focus – Andriy and Nataliia Herts are introducing PhotosynQ in Ukraine

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Andriy and Nataliia Herts, biologists and beta-testers from Ukraine.

Andriy and Nataliia Herts began beta testing the PhotosynQ platform and MultispeQ instrument at the Ternopil Volodymyr Hnatiuk National Pedagogical University in Ternopil, Ukraine in 2015. Andriy and Nataliia have contributed over 4,400 data points on 13 projects since then, with the help of some of their students (below). Their research investigates the influence light-related parameters on the development, growth, productivity, and biochemical composition of plants in autonomous agroecosystems, like greenhouses, in order to understand the influence of artificial lights (LED lights for example) and ultimately improve growth strategies based on that knowledge. Some other area’s of study include the assessment of seasonal and daily dynamics parameters of the photosynthetic apparatus of Magnolia kobus L., the effect of low temperatures on the primary processes of photosynthesis in Yucca filamentosa and how heavy metals, molybdenum ions, water stress and pest invasion change particular physiological parameters in Phaseolus vulgaris.

Now, they have initiated work on a new project entitled: “Physiological, genetic basis of multi-stepping biotechnology in vitro-ex vitro-in situ to stabilise the populations of rare species.” The studies aim is to better understand the physiological and genetic characteristics of cultured in vitro rare plant species using the MultispeQ instrument and PhotosynQ platform for phenotyping. The goal is to develop multi-stage biotechnology plant adaptation to ex vitro conditions that will further transfer them in natural conditions to stabilize populations and to preserve the gene pool. Andriy and Nataliia plan to conduct multivariate analysis to identify the link between the plants photosynthetic efficiency and pigment concentrations and growth parameters of plants in vitro, their genetic stability / variability and conditions of cultivation. Based on the results, they plan to develop a system of criteria for selection of plants for carrying in ex vitro.

Herts image 2

 

The NPQ(T) Parameter

Measuring non-photochemical quenching in a few seconds without an initial long dark acclimation.

Over the past 3 years, many MultispeQ users have noticed that the NPQ(T) parameter (and ΦNPQ) can be a powerful predictor of plant stress, either biotic or abiotic. The NPQ(T) parameter has also correlated with crop yields in some PhotosynQ projects, like this project from Malawi.

Indeed, one of the big breakthroughs with the MultispeQ is the ability to estimate NPQ (Non-Photochemical Quenching) without a long dark acclimation period, which allows us to develop robust protocols that take less than 20 seconds. So how is the NPQ(T) parameter derived and how does it compare to the established NPQ parameter?

Tietz et al. out of the Kramer Lab have just published a paper in Plant, Cell and Environment describing the parameter and its derivation. Congratulations!

Read the peer reviewed publication or the story on the Michigan State University’s Plant Research Laboratories Website, Protecting plants from the power of sunlight.

Tietz, S., Hall, C. C., Cruz, J. A., Kramer, D. M. (2017) NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem-II-associated antenna complexes Plant. Cell Environ. 40(8), 1243–1255. doi:10.1111/pce.12924

The MultispeQ beta’s Future

The first version of the MultispeQ, the MultispeQ beta has been a great instrument, workhorse and proof of concept for the PhotosynQ platform and its utility in phenotyping plants outside the lab in large sample sizes. There are still MultispeQ beta instruments out there which are in use. We have decided with a heavy heart to stop the active development for them, since they have already exceeded their anticipated lifespan and focus our limited resources on the new MultispeQ v1.0.

The MultispeQ beta - Our proof of concept instrument that worked longer and produced more results than we expected.
The MultispeQ beta – Our proof of concept instrument that worked longer and produced more results than we ever expected.

So, what does it mean?

You will still be able to use the instruments and use the existing protocols, as well as create your own new ones. If there will be a change that breaks the compatibility with the Platform, we will give you enough of a heads up, so you can finish your experiments before we release the update. Since all the informations about the instrument is open, we hope that fixes or improvements might be made by the community to extend the instrument’s lifetime.

The Hardware

We are no longer supporting hardware fixes, mainly, because we don’t have parts in stock any more. Pieces like the light guides were custom made and can’t be ordered. Electronic parts can be ordered and we are more than happy to point you to where to source the needed parts. Just let us know and write to support@photosynq.org. Otherwise, we advice you to get the new MultispeQ v1.0 for your future data collection.

The Software

There are no more measurement protocols developed for the old MultispeQ beta. The structure and some of the commands have changed when we introduced the new MultispeQ v1.0 and some of the new features would need a complete re-write of the instruments software (firmware).

We are no longer updating the firmware since we want to focus our limited resources on the current instruments and make sure they receive updates and improvements on a regular bases. As long as the communication protocol doesn’t change, the instruments can be used with the apps and submit data to the PhotosynQ platform.

Thank You!

We would like to say thank you again to all the beta testers not only for testing the MultipseQ beta, but the PhotosynQ platform as a whole. We learned a lot and the new MultispeQ v 1.0 has benefitted from those experiences a lot.

~ The PhotosynQ Team

Working with PhotosynQ: Open/Close Start Feature

Does it seem like your MultispeQ measurements are taking too long? You heard each measurement should take 15 seconds but you feel like it is taking almost a minute? There is a simple and easy solution!

One of the most common issues that users of the MultispeQ v1.0 are reporting is that their measurement time has dramatically increased when using the “Leaf Photosynthesis MultispeQ v1.0” protocol, taking up a minute to finish. What the heck is going on here, are all these devices lagging or broken? No! In fact this issue is due to a new command we introduced into the protocol.

Before, when you wanted to take a measurement in the field, you would probably answer project questions on your phone, clamp the leaf using your MultispeQ, and then hit measure in the app. It would take 15 seconds, and everything was great, so why did we change this order of operations? Well, there was always a delay from when you hit measure to when the actinic lights turned on, during which time the leaf begins to dark adapt.

Now, we have added an open/close start command that it is really cool and will hopefully make your measurements easier. The open/Close start is now at the beginning of the protocol code, because it happens before anything else. Utilizing the magnet in the MultispeQ, we are able to detect when the devices clamp is fully open, and when it closes. Using this, users are now able to fill out their project questions, hit measure, find their leaf, and then clamp the leaf just like you normally would. The difference? Now the actinic light turns on, and the measurement starts as soon as the MultispeQ senses that the clamp is fully closed.

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Another advantage of this feature is that it provides you with the option to hit measure, set the phone down, and use two hands to make sure you properly clamp the leaf. This can be especially useful when it is difficult to properly clamp the leaf, such as with small leaves.

If the device does not detect that the clamp fully opened and then closed, it will wait for 30 seconds and then automatically start the measurement. This means that if you clamp the leaf and then hit measure, the measurement will seem to take 45 seconds. Also, if you are hitting measure first, then clamping the leaf, and it is still taking 45 seconds to complete a measurement, take care to make sure that the clamp is closing completely.

Hopefully this clears up some confusion about best measurement practices and will help you get out there and up your data production. We here at PhotosynQ are cooking up bigger and better things for the next round of firmware and protocol updates. We are hoping we can mimic the ambient light through the PAR sensor and shine that from the device before we clamp so the leaf will never begin to dark adapt, pretty neat! Stick around for these updates.

PhotosynQ Focus

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Matthew Daniel, an Arborist from Australia and one of PhotosynQ’s most active users.

matthew

Matthew is the director of Tree Preservation Australia and CEO of Global Urban Forest Pty Ltd, a company dedicated to the relationship between soil and tree health and the science of urban forestry. He travels to many cities in Australia and abroad collecting data on tree and soil health and prescribing proper health care programs to ensure that cities have happy, healthy trees. These prescriptions include compost tea’s, deep root soil injections, and vascular stem injections of specially formulated microbial plant and soil health inoculants and organic stimulants. However, his job was limited by the lack of affordable tools and the ability to share data and results with others.

How Matthew Connected with PhotosynQ

Matthew Daniel was born and raised in Tasmania, where he first developed his interest in trees and the outdoors in general. We asked him what his first memories with trees were and he told us “When I was 5 years old my uncle found me 40 feet up a tree, freaked my mum out”, no doubt this guy was destined to climb trees for a living! He would eventually receive training and certifications for arboriculture, working near high voltage power lines and in confined spaces, become a partner in Tree Preservation Australia and eventually founded Global Urban Forest Pty Ltd.

From the moment he first heard about PhotosynQ he knew “it was exactly what I needed to understand the tree health response to soil health intervention.” He has now completely integrated the PhotosynQ platform into his workflow saying “I use PhotosynQ before, during and after all the trees I work with.” That is a lot of trees!

He successfully applied to be a PhotosynQ beta tester and created his main project tree health calculator – Beta/Experts Program – 2015-2017, which has over 8,000 data points. Matthew recently received the new MultispeQ v1.0 and is working hard to build collaborations with community groups across Australia.

Now What?

Ultimately, Matthew wants to use PhotosynQ as “an international collaborative platform to be a major part in quantifying and mitigating climate change.” Matthew believes that a global arborist community that shares data on a common, open platform can do more than improve the health of individual urban trees. It can also help to mitigate one of the causative factors of the Urban Heat Island Effect, namely a lack of vegetation in cities. Lack of vegetation in cities decreases levels of both evapotranspiration and carbon dioxide removal. It has been observed over the last century that cities are significantly warmer than the rural areas that surround them. The UHI effect affects many areas of life, such as the weather, health and the environment. It will increase the production of rain clouds and thunder over your city, make you more prone to violence during heat waves, increase your electricity bill, and even kill off fish in lakes and streams just outside your city if mitigation processes are not undertaken. By going around Australian cities and learning about the trees that are present, Matthew and a global arborist community can learn which trees are most effective at mitigating the UHI effect and make your city a more enjoyable environment.

He knows this will not be easy, but it’s the potential that is driving Matthew. The potential to build a global arborist community that can collect data for cities that they can then utilize to manage their urban tree population, the potential to reduce the urban heat island effect, and finally, the potential to mitigate the effects of climate change.

Thank you to Matthew Daniel for allowing us to write about him and taking the time to answer all our questions. Hope to see you back in the US soon!