PhotosynQ Focus : Osamu Watanabe

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Osamu Watanabe, a researcher at the Agriculture Facility at Shinshu University studying invasive weed species and their effect on rice.

 

When Osamu Watanabe was first introduced to PhotosynQ by Dr. Kenji.Takizawa, a coworker at his laboratory at Shinshu University in Japan, he thought not only would this platform be great for him, but also his students!  Osamu graduated from and works in the Agricultural Facility at Shinshu University in the Nagano prefecture in central Japan. Nagano was the site of the 1998 Winter Olympics as the surrounding terrain is very mountainous, which is not only great for skiing, but also for high altitude terraced rice farming!

 

Dr. Watanabe’s research focuses on invasive weed species in Japan and how they effect both the natural environment and agriculture. In Japan, rice is the most important food crop grown, and Dr. Watanabe uses his MultispeQ to measure the photosynthesis of both the rice and common weed species such as Ambrosia trifida (Giant Ragweed) and Oryza sativa (Weedy Red Rice). In these cases, Dr. Watanabe will “measure the photosynthesis characteristics of the plants in different density communities using MultispeQ”. This data can help them determine the weed density where the weeds outcompete the crop, causing a drop in crop photosynthesis. Measurements are also made after herbicides have been applied to evaluate how herbicide application rate impacts the photosynthetic rate of both the crop and weed.

 

In addition to research, Dr. Watanabe also teaches multiple classes at the university where he has integrated the PhotosynQ platform into his curriculum. He teaches students in their 3rd year of undergrad, about 50 in the class, all the way up to Master’s students, and they all get out there with MultispeQs, take measurements and learn more about invasive weed species. I was nervous that this might be difficult for his students since Dr. Watanabe says none of them speak English and the platform, app and other aspects are in English. However Dr. Watanabe said that when they pick up devices and create projects they “operate intuitively” and that  as “students teach the other students, [their] skills rise, so I only have to watch” He added that “PhotsynQ’s website is very easy to use, simple analysis of the collected data is also available in the tool, so it is very handy!”

 

It was great to hear the Dr. Watanabe is getting along great with the PhotosynQ platform. He is learning more and more about the weed species he hopes to curtail along with teaching the next generation of plant scientists about PhotosynQ.

 

JapanGroup

 

 

 

PhotosynQ Focus: Rodrigo Gomez

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Rodrigo Gomez, a researcher at the Institute of Molecular and Cellular Biology of Rosario in Argentina who leads the way in macro and protocol creation on the PhotosynQ platform.

 

Dr. Rodrigo Gomez is one of the earliest adopters of PhotosynQ, becoming involved during the MultispeQ beta days. Beyond being an early adopter, Dr. Gomez has taken full advantage of PhotosynQ’s flexibility. Not satisfied with the default measurement protocols offered for the MultispeQ, Dr. Gomez would teach himself Javascript and become one of the most prolific creators of protocols and macro’s on the PhotosynQ platform.

 

Dr. Gomez first became interested in plant biology while attending high school in Argentina’s third largest city, Rosario, when his teacher assigned him a project on photosynthesis, and from there his interest would grow. This interest led to his earning his Ph.D in Biological Science in the Centre of Studies on Photosynthesis and Biochemistry at the National University of Rosario.

 

Eventually Dr. Gomez found himself working for the Institute of Molecular and Cellular Biology of Rosario (IBR) under the direction of Dr.  Néstor Carrillo, who just so happened to be his Molecular Biology professor during college. Dr. Carrillo’s lab is focused on the study of stress biology in plants and the creation of biotechnology tools to make plants more resistance to such stress. Dr. Gomez’s role in the lab is to construct transgenic tobacco plants that express flavodiiron proteins (Flvs) from cyanobacteria. The aim of the project is to increase plant stress tolerance to high and fluctuating light, and other sources of abiotic stress.

 

Dr. Gomez first heard about PhotosynQ from a colleague of his. They were discussing the difficulty they were having measuring chlorophyll fluorescence with their old and outdated equipment. His colleague, another early PhotosynQ’er Alavaro Quijano, told Dr. Gomez that he had read about a very affordable fluorometer, recently released, and that he bought it; it was the MultispeQ beta. As soon as Alavaro got it, Rodrigo started using it, but he wanted to conduct very specific types of measurements, beyond what we offered at the time.  Dr. Gomez explains, “I started creating my own protocols using the PhotosynQ tutorials and basically copying and editing staff protocols. But I couldn’t do it without the great help that Greg Austic gave me.”  After that, he started learning how to code using Javascript so that he could create his own protocol’s and macro’s. Dr. Gomez would go on to be PhotosynQ’s number one creator of protocols and macros.

 

Since Dr. Gomez became involved with the PhotosynQ project early he has seen “all the changes of the devices and the platform over the years.” Dr. Gomez says that he came a big fan of PhotosynQ. In his most recently published manuscript all of the measurements were taken using PhotosynQ. More importantly, having access to PhotosynQ’s open, affordable and flexible tools has helped him find his research field in science. He explained to us that “now I certainly know that I want to continue working in photosynthesis, so I can say that the discovery of MultispeQ/PhotosynQ was decisive for me”.

 

 

 

Flagging Data to Improve Data Quality

Improve your PhotosynQ projects by getting rid of low quality measurements with the flagging data feature.

 

Whether you are taking measurements in the field or in the lab, it is not uncommon for a handful of measurements to be returned to you with an issue warning. There are a variety of warnings you might receive, red issue warnings suggest that a measurement might be bad, while yellow and blue issue messages simply provide information about the measurement. You may find it is necessary to remove the measurements with red issue warnings from a project before you can properly analyze your data.

WHY

Bad measures can happen for many reasons, maybe someone had shaky hands or the leaf was dead. Or maybe the leaf was not totally covering the light guide, many  of these things can be attended to and fixed if you follow our Best Measurement Practices. It could be our fault, your fault, or maybe natures. All of these will return issue warnings that something went wrong during your measurement. You always have the choice to discard and redo the measurement in the field, however this can be easy to overlook. If you go through your experiment, accept everything and later realize you may have made some mistakes, we allow you to flag this data later in the Data Explorer. Flagging data DOES NOT delete the measurements from the website, but rather hides them. Flagged data can always be viewed by clicking the “Include flagged datasets” box in the Add Series tab, so don’t worry!

FlagDataBlogpic2Including flagged data in your data series

HOW

Flagging your data could not be any easier in the Data Viewer at photosynq.org. All you will have to do is select a single suspect point (1), either from a scatter plot or the table. Look at the data point in the single data view, and see if there were any issue warnings (2). If you determine this point is no good and you’d like to flag it, under the name of the person who submitted the data point, you will see a tab for Issues. Click here, write up your issue in the Reason for Flagging dialog box and click Submit to quickly flag a data point (3). It is important to remember that when you flag a data point you are hiding it from your analysis, NOT deleting it entirely, don’t worry, we never delete your data.

CIRCLEBADBADBAD(1) This measurement’s SPAD (relative chlorophyll content) is very low, we can take a closer look at it by clicking on the data point

BADTRACE

(2) Here we can see that the macro output an issue warning when the measurement was taken. Even if there is no issue warning, you may spot a problem with the measurement by examining the measurement trace. In this case it appears that someone failed to completely cover their entire light guide!

GOODTRACE

For reference, this is a good, average trace for the Leaf Photosynthesis MultispeQ V1.0

owowoww

(3)Flagging data requires a reason, this helps everyone involved be on the same page

The Difference Flagging Makes

When you a flag a data point, you are essentially putting them aside, not to be considered when you run analysis, so it is easy to see how your outcomes might be different depending on if you flagged your data or not.

phi2AVGwflag.png

First, let’s look at data for a project that includes every data point. This is what you might see in your project after a day in the field and no work done to your data yet. You can see for the Phi2 parameter that the standard error is very large, even reaching into the negatives. Since plants can’t have a negative Phi2, it indicates some work on the data needs to be done before we can be confident in the results. If you went through and flagged bad measurements, you will end up with a better graph like the one below.

phi2AVGnoflag

After flagging all of the measurements that either had issue warnings or had obvious problems, by looking at the measurement traces, we get a very different graph. Even after flagging the poor quality measurements we still see large standard error bars. Remember, photosynthetic parameters are highly dependent on ambient conditions such as light intensity, time of day and temperature. We recommend using multivariate analysis to account for these factors, for more tips on data analysis, check out our tutorials here.

Issue warnings can occur on exceptional leaves, such as ones with a very dark deep green colour, and still be fine, so it is important to examine them, rather than just flag whole chunks. Flagging your data where appropriate will make your data tighter and more true to what was observed in your experiment. This is useful when interpreting your results because you are not being bogged down by faulty measurements, which in turn should make statistical analysis of your results much better!

Read More »

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.

gif

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!

 

PhotosynQ Focus

Now that the MultispeQ v1.0 instruments are released, we want to share some stories of how the community is using PhotosynQ technolgies. Today we want to focus on Isaac Osei-Bonsu from Ghana, currently a PhD student in the Kramer Lab at Michigan State University.

 

OB_Isaac

Isaac Osei-Bonsu has been a PhotosynQ user since the early beta days in 2015. Over that time, he has collected over 13,000 measurements and created 46 PhotosynQ projects. As we worked towards releasing the new instruments, Isaac was often tasked with testing out new MultispeQ prototypes, and some iterations did not work so well! At the end of the day, Isaac collected over 3,000 measurements with MultispeQ v1.0 prototypes and his feedback helped us to modify and improve the MultispeQ throughout the design and manufacturing process.

Isaac’s background

Isaac hails from the west African nation of Ghana, where he was a research scientist for the Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI). In Isaac’s own words, “The company is a National Agricultural Research institution which focuses on research on different crop species with the aim to improve agriculture in Ghana.” He studied a wide variety of crops including cowpea, peanut, pepper, eggplants, citrus, mangoes, avocado, pear, papaya and watermelon.

Ghana, like many countries in sub-Saharan Africa, is struggling to achieve food security and develop a robust economy. This means that the government wants farmers to produce more high value crops, like cocoa, for international markets. However, this comes at the expense of land for growing food crops, which is why it is so important to improve the productivity and efficiency of important food crops.

What Isaac is doing now

Isaac arrived at MSU with the help of a Legume Scholars Award which he received from the Consultative Group on International Agricultural Research (CGIAR) in 2015. The Legume Scholars Program supports the graduate study of young scientists from developing countries so they can pursue research careers involving grain legumes  (http://legumelab.msu.edu/training/legume_scholars).

Isaac’s is studying the photosynthetic response of  grain legumes to abiotic stress in order to improve grain legume production. His interest with automatic plant phenotyping was piqued “by the simple yet powerful nature of the MultispeQ device, connected to the PhotosynQ platform, and its possible use for rapid phenotyping in the field.” Manual phenotyping can be extremely slow and not entirely accurate. The MultispeQ instrument and the PhotosynQ platform make it easy and quick. He now uses the MultispeQ in most of his experiments. He doesn’t just use PhotosynQ because it is easier, but also because it allows him to develop a deeper understanding of abiotic stress responses in grain legumes.

Thank you to Isaac for taking some time out of your busy days to answer all of our questions. Having Isaac around our lab is a pleasure and his input into the PhotosynQ platform and MultispeQ instruments have been invaluable. We hope our instruments can help him as much as he has helped us and wish him luck in his continued research.