PhotosynQ Focus: Sonya Lawrence

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Sonya Lawrence, an Instructor in the Biological Sciences Program at MSU who has been incorporating PhotosynQ into her courses since 2014

As the first summer term came to an end, the hallways of North Kedzie Hall were crowded with BS 172 students displaying their research posters. This year marks three years that Sonya Michaud Lawrence, an instructor in Michigan State University’s Biological Sciences Program, has been using PhotosynQ as an educational tool in her lab classes.

Sonya was one of the first MultispeQ beta testers, beginning way back in the fall of 2014. Sonya uses PhotosynQ has a tool to help students learn the scientific method. Groups of students develop a hypothesis, design an experiment, use PhotosynQ to collect data and then use that data to test their hypothesis and learn statistical methods. Common research questions for her students include comparing how different species, canopy density, cardinal direction, time of day or proximity to fruit affects the photosynthetic efficiency of leaves.

Since Sonya’s first class project, her students have created more than 50 PhotosynQ projects and contributed tens of thousands of measurements. If you want to check out her students work, go the Discover tab on www.photosynq.org, scroll down to the Education section and select see all. Chances are those project were created by her students.

Sonya blog image2

BS 172 student collecting PhotosynQ data on campus with the MultispeQ beta (left). Luke Weaver, Megan Campbell, and teammates present their findings at the BS 172 poster session (right).

As I meandered from poster to poster, talking to the students, a couple of themes kept popping up. Quite a few students mentioned that their results did not match their hypothesis. That’s ok! Happens in science all the time! Other students were impressed by how PhotosynQ made data collection easy, and by the amount of data they could collect in a short period of time. There were a few technical issues–with a couple old beta MultispeQ’s not working properly and measurements with the new MultispeQ’s taking too long because students were not familiar with the open-close start function. But overall, these students had a very different experience from those first brave students, back in the early beta testing days, when the software was still being developed and bugs frequently caused frustrations.

If you are wandering across MSU’s campus in the summer or fall and see students armed with MultispeQ’s and android phones, chances are they are Sonya’s students.

 

PhotosynQ at Feed the Future Legume Innovation Lab (LIL) Conference in Burkina Faso August 13-18, 2017

Following the PhotosynQ Workshop (see Dan’s post), we had moved to the LIL conference site at Laico Ouaga 2000, a high security hotel/conference venue outside of Ouagadougou city.  “Feed the Future” is a program funded by USAID under the US government’s Global Hunger and Food Security Initiative.  This program has been engaging many universities, institutions and private organizations in the US, Africa and Central/South America to improve the quality and management of legume, and contributing to the well-beings of local people. Michigan State University (http://legumelab.msu.edu/) is one of the leading institutions contributing researches and new technologies to the world.

One of the designated official languages being French, we had a simultaneous translation through headphone at this conference. The last time when I had to use French in daily basis was almost 20 years ago. Listening to the scientific talks was manageable, but my speaking ability was quite embarrassing. Another challenge was internet connectivity. As Dan mentioned, we had to manage the workshop with almost no internet connection. We were hoping to have a better connection at this best hotel in Burkina Faso, but unfortunately, it seemed the system could not handle a large traffic at once. The conference participants expressed that they had never experienced this in the past anywhere in Africa. It seems it was an isolated incidence, but we came up with some better solutions for the future.

  PhotosynQ booth (From right: Dan, Frank and Atsuko)

 Presentation by Dr. Irvin Widders, Director of Legume Innovation Lab, MSU. PhotosynQ was mentioned as one of the highlights of the ‘Feed the Future’ program.

At the last LIL conference held at Livingston, Zambia, Dave Kramer and Dan TerAvest presented the PhotosynQ project using MultispeQ Beta. This year in Burkina Faso, not only the people from Kramer Lab (Dave, Dan, Donghee Hoh, Isaac Osei-Bonsu and me), but also our PhotosynQ collaborators (Dr. Isaac Dramadri in Uganda, Dr. James Kelly with Dr. Jesse Traub and Dr. Wayne Loescher of MSU, and Dr. Kelvin Kamfwa of U of Zambia) presented more detailed and sophisticated data showing the correlations among photosynthesis, plant responses and gene expressions. It was very encouraging for us to see more people started thinking that the PhotosynQ platform and hand-held devices are useful and practical to the broad applications.

We are very excited about the new challenges, collaborations and long-lasting friendships. And we all hope to see you again!

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