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”.

 

 

 

Recording interesting observations in the field with PhotosynQ

The field data collection season is just getting started here in the USA. I thought this would be a good opportunity to highlight a feature in the app that may be useful when you are out collecting data: adding notes and photo’s to PhotosynQ measurements.

You never know what you are going to encounter in the field, so when you encounter something worth noting, you need a space to do so. For example, maybe you notice disease symptoms or insect damage on a leaf that you want to record. Or maybe you want to note that the plant you measured appears to be dying.

Adding notes and photo’s in the mobile app

There are two ways to add notes and pictures to measurements: 1) add a picture or note question to your project using the project creation tool or 2) add a note or picture to a completed measurement, before uploading the measurement to the website.

The first option requires that you take a picture or add a note for EVERY measurement. If you take a lot of measurements with photo’s attached, you may notice that your data loads slower in the data viewer. You may also notice that all of your photo’s look quite similar, and may not add much value to your project. Who wants to slow down their PhotosynQ project with 500 nearly identical pictures of soybean leaves?

Another option is to only take notes and pictures when there is an interesting observation you want to record, and you want to limit these pictures or notes to JUST interesting observations.

In the mobile app, you can add notes to any completed measurement as long as the measurement is not submitted. Here’s how:

  1. Navigate to the Measurements tab in the app. After you Accept a measurement you are automatically directly to this screen.
  2. Select the measurement that you want to add a note or picture to.
  3. Once you have selected the measurement of interest, a new top menu will provide you with options to add a note, delete the measurement, upload the measurement or take a picture (from left to right, below).
  4. Complete your note or image and select Save note or OK for a picture.
  5. Upload your measurement.

Notes image

Viewing notes and photo’s in the data viewer

You can view your notes from the data viewer in the individual datum view or through the spreadsheet tab. In order to view notes or pictures in the spreadsheet view, click on the More menu at the top of the spreadsheet and check the boxes for what you want to see in your spreadsheet.

view notes post

*You can also add notes and photo’s to the desktop app, see the help article here

PhotosynQ Focus: Isaac Dramadri

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Isaac Dramadri, who just completed a PhD program in Plant Breeding and Genetics here at Michigan State University.

Isaac Dramadri was another of our early adopters, who started experimenting with PhotosynQ way back in the fall of 2014 (not to be confused with Isaac Osei-Bonsu, who we profiled here).

Not only was Isaac one of our earliest adopters, he has also been one of our most active users. Since he began experimenting with PhotosynQ, he has collected over 38,000 measurements. That accounts for 5% of all measurements on the PhotosynQ platform!

Isaac came to MSU from Uganda in 2013 to pursue his PhD, which he recently completed. Congratulations Dr. Dramadri!

He began in the greenhouse at MSU, attempting to identify drought tolerant lines in a common bean breeding population. In 2016, he took some MultispeQ Beta’s on the road, introducing PhotosynQ to scientists at the Makerere University Regional Centre for Crop Improvement (MaRCCI) and national agricultural research services. In 2016 and 2017, he conducted field trials at multiple sites in Uganda, collecting photosynthesis phenotypes from hundreds of common bean lines.

The PhotosynQ platform generated a lot of interest in Uganda, where inexpensive options for high throughout in-field phenotyping technologies are limited. This eventually led to a broader collaboration between the Kramer Lab and MaRCCI.

The overarching goal of Isaac’s 3 years of MultispeQ use was to link photosynthetic traits to other agronomic traits and drought recovery in common bean. His preliminary results have shown that it is possible to use PhotosynQ parameters to identify quantitative trait loci related to drought tolerance. This is exciting and we can’t wait to see more of his results as he publishes them in the near future.

Isaac has now returned to Uganda as a cowpea breeder, and we are sure we will continue to work with him. Good luck Isaac!

Connecting the PhotosynQ Community

We have built numerous tools to facilitate discussion among the PhotosynQ community. In this post I am going to give a brief rundown of these options. All of these options have been present on the platform for a while. However, we have recently updated some of these features and have not actively promoted other features. So, here is the tour…

Forums

We have recently updated the forums, making two significant changes. First, we changed the forums homepage. Now you can see all of the available forums (left) as well as the most recent activity on the forums (right). Second, we added a new “Measurements, Protocols & Macros” forum. Those of you who posted on the forums may notice that we moved some of your forum posts into this new category.

Have a question? Looking for tips or support from the PhotosynQ community? Please visit our forums!

Forums

Project Discussions

You can have discussions within a PhotosynQ project. This is a great way for all of the project collaborators to communicate with each other. It can also be a good way for people who are interested in your project to reach out to you. Project discussions are accessible from your project page on PhotosynQ.

Discussion

Protocol and Macro discussions

The ability to comment on protocols and macro’s gives you an opportunity to interact with the creator of that protocol or macro. Each protocol and macro on the PhotosynQ platform has its own page where you can comment (below left) or you can post comments from the desktop app (below right).

Protocol discussion

Update for Photosynthesis RIDES users

We have identified an error in the Photosynthesis RIDES macro, which is used to process the data from the Photosynthesis RIDES protocol. If you were using this protocol you may have noticed that your NPQt values were a bit higher than expected, or your PhiNO values were a bit lower than expected. This was due to an error in how we determined Foprime, which is key in calculating these parameters.

The good news is that the PhotosynQ platform is built to allow users to correct issues like this, and apply it to data that you have already collected!

We have now changed the macro to correct the error. So, the next time you go to one of your Photosynthesis RIDES projects, you will see the prompt below asking if you want to recalculate your parameters based on updates to the macro. If you choose yes, the updates will be applied to your data. If you choose no, your data will remain in its present form.project updates

User Page | PhotosynQ Website

User Page | Website Update

We are working on making your user page the central hub for all the information regarding your work with PhotosynQ.

We have found that one of the most useful features for any PhotosynQ project is the Dashboard, which allows you to quickly view important project results on one page.

We are currently using the same approach to allow users to have a personal dashboard that makes all of their PhotosynQ information (e.g. projects, protocols, macro’s etc) available in one place.

If you haven’t visited your user page recently, you should try it now, we think you’ll be pleasantly surprised! To get there, click on your name in the top right hand corner of the PhotosynQ webpage, this leads to your user page.

Over the past couple of months we have made a number of changes to this page that should really help you navigate through your PhotosynQ projects and collaborations.

user page image

Recent Activity

This change has been around for a while, but if you haven’t been checking in you may have missed it. We have now added your most recent projects, collaborations and comments to your user homepage. This should help you navigate quickly to your most active projects, instead of always going through the PhotosynQ search bar.

Side Menu

The side menu now contains a link to the instrument page (see below), your invitations, and the last two updates posted on PhotosynQ.

About – Contributions

We replaced the bar chart showing your contributions over the past year and doughnut chart with a calendar histogram. This view will provide more details about when and how many contributions you made over the last year.

Contributions over the last 12 months, shown as a calendar heat map.
Contributions over the last 12 months, shown as a calendar heat map.

Protocols & Macros

Do you make any of your own protocols and macros? If you do, now you can see all of your protocols and macros, sorted alphabetically and by their category, right from your user page.

Instruments

Now you can see all the instruments you have used in the past. It will show some basic information, based on the last measurement, including the firmware version, the total number of contributions (you and others, if you borrowed/lent the instrument) and the last time the instrument was seen (based on the latest submitted measurement).

Basic information panel for an instrument
Basic information panel for an instrument

If you have questions or need support, please check our forum or send us an email to support@photosynq.org.