New PhotosynQ Related Publication

Check out the new publication in Photosynthesis Research, using the MultispeQ and PhotosynQ Platform (10.1007/s11120-017-0449-9)

Faster photosynthetic induction in tobacco by expressing cyanobacterial flavodiiron proteins in chloroplasts

Rodrigo GómezNéstor Carrillo, María P. Morelli, Suresh Tula, Fahimeh Shahinnia, Mohammad-Reza Hajirezaei, Anabella F. Lodeyro

Plants grown in the field experience sharp changes in irradiation due to shading effects caused by clouds, other leaves, etc. The excess of absorbed light energy is dissipated by a number of mechanisms including cyclic electron transport, photorespiration, and Mehler-type reactions. This protection is essential for survival but decreases photosynthetic efficiency. All phototrophs except angiosperms harbor flavodiiron proteins (Flvs) which relieve the excess of excitation energy on the photosynthetic electron transport chain by reducing oxygen directly to water. Introduction of cyanobacterial Flv1/Flv3 in tobacco chloroplasts resulted in transgenic plants that showed similar photosynthetic performance under steady-state illumination, but displayed faster recovery of various photosynthetic parameters, including electron transport and non-photochemical quenching during dark–light transitions. They also kept the electron transport chain in a more oxidized state and enhanced the proton motive force of dark-adapted leaves. The results indicate that, by acting as electron sinks during light transitions, Flvs contribute to increase photosynthesis protection and efficiency under changing environmental conditions as those found by plants in the field.


More PhotosynQ related publications are available here

Intelligent Information Technologies in Education and Science – Ukraine

 

On October 18, 2017, the Interdisciplinary Workshop on the dissemination of knowledge on “Intellectual Information Technologies in Education and Science” took place at the Faculty of Chemistry and Biology of the Ternopil National Pedagogical University (TNPU).

The co-organizers of this event were Andriy and Natalia Hertz, employees of the Department of General Biology and Methodology of Natural Sciences Teaching and the Department of Botany and Zoology (Faculty of Chemistry and Biology of TNPU).

According to the program, a demonstration of the possibilities of IT solutions in biological, educational and pedagogical research took place. 

In particular, the on-line PhotosynQ platform was presented as a web tool for an integrated assessment of the physiological state of plants. 

Information was disseminated on how the MultispeQ can measure, collect and analyze photosynthesis data in field and laboratory conditions.

The focus was on the openness and flexibility of the PhotosynQ platform and the development of educational tools through it, and more.

The students and faculty all wished to have the opportunity to work with MultispeQ and PhotosynQ and to evaluate the condition of plants for themselves.

More Info [English] | More Info [Original]

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

PhotosynQ co-founder highlighted at MSU

The PhotosynQ project started in David Kramers lab at Michigan State University, but it is by far not the only project, that is devoted to gain a deeper understanding into how plants do photosynthesis and how it is regulated. See what else is developed in this lab to study plant photosynthesis, all with the ultimate […]

Landing page header

Goodbye Flot, Hello Plotly | Other Website Updates

Our most recent website update probably got lost in the excitement about the news that we had started shipping the new MultispeQ v1.0. We have continued to work on the tutorials and data analysis and are happy to announce another update to https://photosynq.org. There are several libraries out there to graph data in the browser and when we started the platform, we decided to use Flot, a great, performance library, which is unfortunately no longer actively developed. Implementing new methods of plotting would have required us to build certain features from scratch. Instead we are now using Plot.ly which opened up its libraries to the public. It not only provides the library, but also its own platform to create and manipulate plots, as well as libraries for popular languages like Python or R. We would like to give you a quick update on what has changed and improved.

New and Improved Tutorials

While some people really like using YouTube videos to learn new technologies, others don’t find them very helpful. So, we updated the tutorials (available in the learn more menu from the top of the page) to include text pages that include step by step directions, pictures and screen caps to get you started with PhotosynQ. Also, you can now download a Getting Started manual in pdf form if you need to refer to the tutorials while working offline! We kept the the video’s for those you like them, you can find them in their own videos tab on the tutorials page.

New Plot Options

Scatter plots are a great way of looking at data down to individual measurements. At the same time it can be hard to see trends in a big cloud of points. We hope these new plotting options will help analyzing your data.

Contour Plots

Contour plot with additional histograms.
Contour plot with additional histograms.

The 2D contour plot allows you to do exactly that. With additional histograms they are a great way to visualize populations within a big data set.

Histograms

2D histogram using the Jet color gradient
2D histogram using the Jet color gradient

In addition to the already existing histograms, you can now plot two parameters as a 2D histogram.

Box Plots

Box plots with all data points.
Box plots with all data points.

Box plots are available now. Like the bar charts, you can use a category as well.

New Parameter – Time of Day

We added the parameter Time of Day, showing the time, when the measurement was recorded as a number (e.g. 1:30 pm = 13.5). This will be helpful to plot time dependent trends, which could not be visualized using a regular timescale, which could be the case when measurements were recorded over multiple days.

New Data Selection and Plot Capturing

With the new ways to plot data comes the ability to select a set of data points in a scatter plot using the box or lasso selection. It can be used to generate a selection based Series, or the data can be saved with the measurement identifiers as well as the meta data including time and the project questions and answers. The little camera icon enables you to save the current graph as an image (png or jpeg), including the graphs’ legend.

Selecting data points using the lasso tool.
Selecting data points using the lasso tool.

Using Python and R

Analyzing big datasets using the data viewer inside the browser might be difficult. Or you might want to do your own statistical analysis or plot the data in a way that is not available. For this reason we made packages for Python and R to help you get the most out of your data.

Go to https://photosynq.org/software to find the links to the packages and how to use them.
The tutorial section (https://photosynq.org/tutorials) has some examples for Python and R on how to get your data analysis started.

And There is more to Discover…

  • On your user page, you can now see your Network. Your Network includes people who collaborate with you and have joined one or more of your Projects, as well as all Project Leads of projects you have joined.
  • Tags and Project Categories are now displayed on your user page.
  • Tags are now links and can be searched. Just click on a tab or type your tag into the search field (e.g. #beans).

What’s No Longer Available

  1. Plots – We said goodbye to a few features, because there was no good way of adding it to the new plotting library or the available options didn’t turn out to be all that useful.
    • The options of plotting spline lines and area charts.
    • “Time (normalized)” is no longer available. It got replaced by the parameter “Time of Day”
  2. Dashboard – To make the dashboard a little easier we decided to remove the following options.
    • The Panel with a pie chart of total submitted and flagged. The totals are added to the other data quality panels.

We hope that these new features will help you to analyze your collected data.

~ Sebastian

MultispeQs on track to ship

Hi everyone – we’ve had 3 days of production with a pace of 24 finished, boxed, ready to ship units per day!  We should be able to fill the first 200 units over the course of the next 2 – 3 weeks.  With a few exceptions, we will be shipping MultispeQs in the order they were received.

Thank you all for your immense patience as we have worked through this long process.

On a personal note, this is my last week as part of the PhotosynQ project.  My hope is that the project continues to strive for the values of open software, hardware, and data in science, and to create tools which are broadly useful to the both the scientific and non-scientific communities.  I know that these ideals are sometimes hard to hit, but if not us then who, and if not now then when?

Thanks to everyone that I’ve interacted with over the years for your patience, enthusiasm, support, and collaboration.  In the future I’ll be on google plus +GregAustic and twitter @GregAustic.   Hope to see you in my next project!

– Greg