New PhotosynQ Related Publication

Check out the new publication in the journal Crop Science, using the MultispeQ and PhotosynQ Platform (10.2135/cropsci2018.04.0275)

Screening for Heat Tolerance in Phaseolus spp. Using Multiple Methods.

Jesse Traub, Timothy Porch, Muhammad Naeem, Carlos A. Urrea, Greg Austic, James D. Kelly and Wayne Loescher

Common bean (Phaseolus vulgaris L.) is a nutritious crop grown around the world, a staple that provides high levels of protein and iron in the diets of Central and South Americans and East Africans. Heat stress negatively affects common bean seed yields and prevents cultivation in certain areas. Furthermore, under field conditions, heat stress often coincides with and exacerbates drought stress effects. Breeding more heat-tolerant cultivars would stabilize seed yield and open new regions to field production. To support these efforts, we examined a variety of methods for screening large numbers of bean germplasm exposed to heat stress at the vegetative growth stage as opposed to the reproductive stage, which would prolong the screening process. Tepary bean (P. acutifolius A. Gray), a closely related species to common bean, was used as a heat-stress-tolerant check. Plants exposed to day/night temperatures of 45/36°C for 2 d showed measurable signs of heat stress, but tepary bean outperformed the common beans on all stress tolerance measures. Gas exchange, chlorophyll fluorescence, and oxidative stress were only affected by this high temperature and not by temperatures below 45/36°C. Heat stress measurements also correlated well with visual signs of leaf tissue damage. Gradually raising temperatures was useful for screening large number of entries for heat tolerance, but this heat tolerance was only partially related to drought tolerance in the field. Plant breeders can use some of these methods to supplement field data and to further characterize the stress tolerance of bean lines.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the journal Planta, using the MultispeQ and PhotosynQ Platform (10.1007/s00425-018-3014-7)

DOTAP, a lipidic transfection reagent, triggers Arabidopsis plant defense responses

Carolina Grandellis, Betiana S. Garavaglia, Natalia Gottig, Caroline Lonez, Jean-Marie Ruysschaert, Jorgelina Ottado

DOTAP is a cationic lipid widely used as a liposomal transfection reagent and it has recently been identified as a strong activator of the innate immune system in animal cells. Plants are sessile organisms and unlike mammals, that have innate and acquired immunity, plants possess only innate immunity. A key feature of plant immunity is the ability to sense potentially dangerous signals, as it is the case for microbe-associated, pathogen-associated or damage-associated molecular patterns and by doing so, trigger an active defense response to cope with the perturbing stimulus. Here, we evaluated the effect of DOTAP in plant basal innate immunity. An initial plant defense response was induced by the cationic lipid DOTAP in the model plant Arabidopsis thaliana, assessed by callose deposition, reactive oxygen species production, and plant cell death. In addition, a proteomic analysis revealed that these responses are mirrored by changes in the plant proteome, such as up-regulation of proteins related to defense responses, including proteins involved in photorespiration, cysteine and oxylipin synthesis, and oxidative stress response; and down-regulation of enzymes related to photosynthesis. Furthermore, DOTAP was able to prime the defense response for later pathogenic challenges as in the case of the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Disease outcome was diminished in DOTAP-pre-treated leaves and bacterial growth was reduced 100 times compared to mock leaves. Therefore, DOTAP may be considered a good candidate as an elicitor for the study of plant immunity.


More PhotosynQ related publications are available here

New Desktop App

A New Desktop App Is Coming

We are releasing a new version of the Desktop App which will replace the current one for the Google Chrome Browser (Chrome App). The reason is a discontinued support for Chrome Apps on Windows and MacOS (see below). So please go to https://photosynq.org/software to check out the new Desktop App. If you have any issues, please let us know and write to support@photosynq.org.

What’s New

First and foremost we tried to make the new app work in the same way as the old one, so you can immediately feel comfortable using it. Further, we have fixed issues, improved the workflow, added compatibility and better support with the latest Firmware and added some new features.

The new Desktop App on Windows and MacOS
The new Desktop App on Windows (right) and MacOS (left)

General

  • QR codes and barcodes can now be scanned with a webcam to answer questions
  • More and better keyboard shortcut support
  • Drag ‘n drop for images
  • Images can be previewed inside the app
  • More native look and feel depending on the OS you are using
  • Faster search inside the app
  • Instrument Settings available through the app
  • The instrument console has been moved to a separate window
  • Instead of tags, measurements in the notebook are now sorted by name and experiment

Protocol Editor

  • Ctrl/Cmd+Space will bring up Commands and Hardware configurations in the Protocol Editor (advanced view)
  • Code folding and code can be displayed more compact
  • Hover over commands to get a description of their function
  • Search and replace, search hits are highlighted along the scrollbar

Macro Editor

  • The Macro Editor supports protocol sets introduced with the last firmware update (1.23 or later)
  • Code folding
  • Non linear fit for exponential decay
  • New functions to access parameters in protocol sets
  • Search and replace, search hits are highlighted along the scrollbar

Installation & Updates

  • An executable one click installer for Windows
  • Drag ‘n drop installation from a disk image on MacOS
  • Updates will be automatically downloaded and installed

What will Change

There are only minor changes for you as a user. Instead of the Chrome Store, now you have to download the new Desktop App from our website (https://photosynq.org/software). Updates are downloaded automatically and you only have to confirm installing the update.

Making the Transition

The transition to the new app will be easy. After you installed the app, just sign in with your PhotosynQ account and all your Projects, Protocols and Macros will be synchronized. No need to do anything else. In case you have measurements saved in your Notebook, you can transfer them following these steps:

  1. Open your old app and select the Notebook from the side bar.
  2. Select all the measurements you want to keep and select Export from the Action menu.
  3. Open the new app and select File->Import Notebook… from the menu.
  4. Select the file you just exported and click on open to import all measurements.
  5. And… you are done!

Windows, Mac and Linux Support

Windows

If you are using Windows, you just download the app and execute the installer. It will automatically install the app and add a shortcut to your desktop. Updates will be automatically downloaded and installed. If you are using Windows 7 or 8, you have to download and run the Windows serial installer to connect an instrument, if you haven’t already done it.

Mac

If you are using a Mac, just download the app, open the disk image and drag ‘n drop the app into your applications folder. Updates will be automatically downloaded and installed.

Linux

The Linux version is currently at an early developing stage. If you are interested in helping us by testing the app, please drop us a line (support@photosynq.org). Due to the framework we are only providing installers for Debian based distributions like Ubuntu.

TL;DR

The great features of Chrome Apps were amongst others, their small size (about 3mb), the easy way of installing them, the sandbox they were running in and the automatic updates and push notifications.

So, why exactly do we abandon the existing app?

A while ago, Google announced, that Chrome Apps in their current form will be discontinued by mid 2018 for Windows, MacOS and Linux and will only kept for ChromeOS. Nevertheless, Chrome extensions will remain available. Those are pretty similar to apps, yet they have one big issue, they don’t have all the APIs available that we need and as a consequence don’t allow communication with serial devices. This means, that we will no longer be able to use Google Chrome apps / extensions to take measurements with PhotosynQ instruments like the MultispeQ.
As a consequence, we started to build a new app that is not depending on the Google Chrome Browser infrastructure any more. We are using the popular Electron Framework that is used by apps like Atom, Slack, WordPress, Skype or Visual Studio Code and allows to build cross platform applications using HTML and JavaScript as well as Node.js packages.

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

In memory of Prof. Ruth Gates

Prof. Ruth Gates, one of the prominent coral scientists in the world, the director of Hawai’i Institute of Marine Biology, and the president of the International Society for Reef Studies (ISRS), passed away on October 25 after a battle with cancer (In Memory of Ruth Gates – The Atlantic).

Her recent works include breeding heat tolerant corals or “super corals”, for the effort to save the coral reefs from severe bleaching, and holding the public forums to make the communities aware the benefit of saving the reefs and what kind of actions the normal citizens can take. She was one of the PhotosynQ/CoralspeQ collaborators. You could find her detailed scientific works, news articles and contributions elsewhere. Here, I would like to write about brief but memorable interactions with her.

It started in summer of 2015. Prof. Peter Ralph at University of Technology, Sydney, visited us in Michigan, telling us about the upcoming monstrous El Nino… officially called Godzilla El Nino. Peter, our long time collaborator and early adopter of PhotosynQ, proposed us if we could make a field deployable instrument like MultispeQ (it was Beta type back then) to monitor corals. It was a challenge, because it has to work under water. Thus, CoralspeQ was born. Peter strongly suggested Ruth Gates as a collaborator, because not only she was a respected coral expert, but also she constantly touted the importance of collaboration and data sharing. We had also contacted several other scientists who are marine biologists and spectroscopists, and received a positive response.

When we finally built a prototype in November when the damages from El Nino had already started, we needed a field test instead of the lab test. It was Ruth who emailed me directly and said, “What can I do for you?” I flew to her Institute in Coconut Island with 2 instruments in December, 2015 (CoralspeQ Prototype 1.5 Update – Ready to go for the field test!), and took measurements with captive corals with a help from Jennifer Davidson, and in the reef with a help from Elizabeth Lenz. This field test was crucial to see what we could tell about the coral conditions in the real environment.

In the following summer, at the 13th International Coral Reef Symposium in Honolulu, I finally had an opportunity to talk to her in person (CoralspeQ Debut at International Coral Reef Symposium). Being the president of the ISRS and one of the Symposium organizers, she had people lined up to have a brief private conversation. I was fortunate to have an interaction, and was totally flattered by her saying “Thank you for doing this!” She meant that making inexpensive instrument and sharing the data through the cloud-connected scientific platform would benefit everybody. Her closing plenary talk was about the need of scientists and communities working together and coming up with the solutions to save the reef ecosystem. I think she had been inspiring many people with her optimistic open-minded attitude. Now she has passed a baton to the next generation. CoralspeQ is a difficult long-term project, but equipped with Ruth’s optimism, we will get there.

One Million Measurements!

 

We are excited to announce that the PhotosynQ Community has collected over one million measurements, since the first one was taken and saved to the cloud in April 2014.

The PhotosynQ community has been busy over the last 4 years, producing not only an amazing amount of projects and measurements, but has also published data in several peer-reviewed journals (find a list here) already.

It all started here at Michigan State University, but we can now truly say, that this project has grown into a global community.

We are so proud of the community, their contributions and we are truly excited about the future!

Your PhotosynQ Team

Sessions, Sharing and Downloads

Sessions, Sharing and Downloads | Website Update

Now you can save and share your analysis as sessions or download your data as a spreadsheet.

The data viewer on PhotosynQ is the tool to analyze your collected data. You can filter the data set and create sub-sets (Series), you can Plot parameters in various ways, view the data on a map based of the geo-location attached to each measurement, do simple statistics, or dive into every value using the spreadsheet. We are introducing a few new functions, we hope you will give you a better experience.

Sessions

Now you can save your results as sessions when analyzing the data. Every session will save your current dashboard, plot, map, filter settings/series and thresholds. They are a great way of saving interesting observations, compare different filters, thresholds, without having to repeat all the steps to get there.

Sharing a Session

When you save a session, you will notice a checkbox labeled shareable, making the session available to others when checked. After you saved your session, just click on the copy button in the list of available sessions, to save the link to your clipboard. Use the link, to share your findings with collaborators, in the forums or for presenting them in the Project results section. You can also un-share the session at any time. The link will still be pointing to the Project’s data, but your session is no longer available. In case you make up your mind, just re-share it and the link works again.

Auto-Save

When you have been been analyzing your data, you might have noticed, that the filters and thresholds you were applying got saved and re-applied the next time you opened the dataset. This was only saved locally, so opening your project on a different computer, would mean you have to start all over again. Now it gets saved to the cloud, so you can continue working where you have left off, even when you are using different computer.


Downloads

We developed the Data Viewer so you can analyze the measurements you have collected for a project, online. But we do understand, that downloading the data and using it in spreadsheets like Excel, Origin or others can be necessary. To this point, we have offered libraries for Python and R to get data from PhotosynQ into an easy to use format to work with. Now we also offer a download* of the data in a spreadsheet (xlsx) or in the JSON format right from the project page.

Yet, we strongly recommend you view your data using the data viewer, since there you can flag measurements that were not taken correctly, you can look at raw traces, etc. That way you can ensure the best data quality, when it comes to your final analysis.

*The downloads are only available for the project lead and project collaborators


Statistics – Summary

The data viewer is offering simple statistic functions as well as a summery for a selected parameter. The histogram in the summary has been extended and is showing now the normal distribution for the sample as well.

Please be aware, that all functions are currently at a beta stadium, so you might experience some issues and the functionality might be different in the final version.

New PhotosynQ Related Publication

Check out the new publication in the journal Front. Plant Sci., using the MultispeQ and PhotosynQ Platform (10.3389/fpls.2018.00767)

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)

Soltani A, MafiMoghaddam S, Oladzad-Abbasabadi A, Walter K, Kearns PJ, Vasquez-Guzman J, Mamidi S, Lee R, Shade AL, Jacobs JL, Chilivers MI, Lowry DB, McClean P and Osorno JM

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.


More PhotosynQ related publications are available here