PhotosynQ Website Update and New Features

We’ve updated the PhotosynQ website and added many new features to improve your user experience!

Some of the new features include: expanded plotting, mapping and graphing data options, improving the user page to help users better track their PhotosynQ projects, protocols and macros, and adding more content to the tutorials and help center.

We will be detailing these new features in blog posts over the next two weeks, but let me briefly explain a couple of the updates:

Tutorials

Two area’s where new PhotosynQ users seem to struggle are with creating robust projects and cleaning up their data prior to data analysis.

Project Creation

Since we began shipping the MultispeQ v1.0’s over 9 months ago we have seen a drastic increase in the number of PhotosynQ projects that are being created. Which is really exciting! Occasionally, we’ll check out new projects to figure out how people are doing with the platform and try to come up with ways to improve the PhotosynQ experience. We have noticed that setting up projects has been a problem for many users. The most common problems are choosing the wrong measurement protocol or not asking good project questions, which then makes filtering, analyzing and interpreting data difficult.

So we have added a Project creation tutorial to better guide users through the process.

Data Quality

Recently we published a blog post about how to Flag data to improve data quality. This is an important step in getting the most out of your PhotosynQ project. In our default Leaf Photosynthesis MultispeQ v1.0 and Photosynthesis RIDES protocols we add issue warnings that help identify measurements that may have technical issues, but many people are unfamiliar with what these mean. So we have also added a Data Quality tutorial to explain issue warnings and data flagging.

Help Center

If you have ever visited the help center you may have noticed a little poll at the bottom of each post asking if the article was helpful or not. Well, believe it or not, clicking those buttons actually matters! We have updated a number of help articles to be more helpful and have added numerous articles.

That’s it for today, but stay tuned! More details about new features will be coming soon!

 

Building Strong Research Collaborations

If you have ever visited the PhotosynQ webpage (you’re reading the PhotosynQ blog, so I’ll assume you have), you know that the banner across our homepage reads “Truly Collaborative Plant Research.”

We have always aspired to making PhotosynQ a flexible platform to accommodate many forms of collaboration. For example, we hope the open nature of PhotosynQ data combined with built-in discussion tools will foster communication and collaboration between researchers across the globe.

I recently returned from Uganda, where I conducted some training workshops and (hopefully) established a long-term collaboration between PhotosynQ and the Makerere University Regional Centre for Crop Improvement (MaRCCI). Before my trip, MaRCCI had a few MultispeQ devices, a few students had used PhotosynQ, and they have even published a few papers. However, until now, there has been little direct communication between MaRCCI and PhotosynQ.

After spending 2 days together, learning how to create robust projects and collect, analyze and interpret quality photosynthesis data, we hope to develop a much stronger collaboration.

MaRCCI pic for blog

What does ‘stronger’ collaboration mean?

MaRCCI already has access to PhotosynQ’s low-cost, cutting edge phenotyping technologies and platform for data storage, visualization and management. Building a stronger collaboration means giving MaRCCI students and faculty the opportunity to work directly with the PhotosynQ team to analyze the links between complex photosynthesis phenotypes and crop outcomes (this requires sharing of outcome data such as yield, disease resistance, etc). It also brings MaRCCI into the PhotosynQ development workflow. So, as we continue to work on automating advanced analytical tools like multivariate analysis, prediction and QTL mapping we will work closely with MaRCCI students and faculty to make sure that what we are developing will solve their problems.

On the flip side, collaboration with MaRCCI offers PhotosynQ some great benefits. MaRCCI recently received support from the World Bank as an “African Higher Education Centre of Excellence” in plant breeding and related activities. This means that they are positioned to be a hub of plant breeding training for breeding programs throughout sub-Saharan Africa. They receive Masters and PhD students from 20 different countries, and while I was there I met students from Benin, Burundi and Tanzania, just to name a few. Such a diverse group of students allows us to disseminate PhotosynQ technology over a wide geographical area, and have much greater impact.

The end result, we hope, will be a long-term partnership that improves the education and capacity of young plant breeders across Africa and helps PhotosynQ continue to evolve as an advanced phenotyping platform.

Personally, I look forward to continuing the work with a great institution with enthusiastic students and faculty.

 

 

PhotosynQ measures more than just plants: A history of our forays into measuring soils

Over the past several years there has been quite a bit of interest in measuring soil properties, which makes sense given that most of the plants we care about grow in soil. In response to that interest, we have developed numerous PhotosynQ prototypes, protocols and macros to measure soils over the past two years.

We started by using the MultispeQ to measure soil active C using potassium permanganate. This method used a cuvette to measure a color change in solution. The problem with using colorimetry, however, is that it requires users to do wet chemistry in the field. We would rather avoid that.

Another approach was to measure in situ C mineralization as an indicator of soil health. We have built multiple iterations of in situ soil C chambers (below). In general, the results from these chambers were positive, but there were a few drawbacks. One is that the results were highly dependent on soil moisture content and temperature. Therefore, we would need to collect a lot of data at different moisture and temperature conditions to account for these variations, much like we need to collect photosynthesis data at multiple light intensities to account for the effect of light on Phi2, PhiNPQ and PhiNO. The second problem is that the prototypes were quite clunky, and generated a lot of funny looks around campus when they were half-buried with random wires hanging out. If enough people were interested in using the in situ chambers, we could make a few mechanical changes to make them look less like an IED.

Soil chambers

Going back to the drawing board, we brainstormed different ideas to simply assess soil health without having to take a lot of measurements or have multiple devices. This led us to develop a simple tool for measuring soil C mineralized from a sealed container. Using a “24-hour C mineralization burst” we can control for different temperature and moisture conditions by first air-drying, and then rewetting soil samples in quart jars. Then we use a syringe to sample headspace in the jar and inject it into a pass-through CO2 sensor.

C min

The technology is pretty simple, just a CO2 sensor connected to a microcontroller, loaded with PhotosynQ firmware. To demonstrate our new SoilspeQ, we worked with a professor at MSU and took soil samples from a field where she was testing the effect of cover cropping on soil quality and maize productivity.  We took many samples from different areas including soil that had mixed cover crops, soils without cover crops and some soil from the bare ground bordering the field plots. We also collected the soil from 1-5 cm and 5-10 cm deep, so we could see if there were differences between them. Check out the results here.

Our final approach to measuring soils is still in its early stages, but we are looking forward to see where it goes. We have teamed up with a professor at Colorado State University to develop microfluidics cards. The goal is to use reagent embedded cards to reduce in field wet chemistry and accurately measure key soil properties. We then use the MultispeQ or a version of the CoralspeQ to measure the color change. Our initial test, using Al3+ in solution at different concentrations is shown below.  

Al Fig

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, I headed over to North Kedzie Hall to check out the research posters being displayed by BS 172 students. 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.

 

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