MultispeQ v1.0 cometh!

Hey everyone, I know it’s been radio silence from the PhotosynQ team for a while. We’ve been working our tails off learning lessons from the beta test, designing the v1.0 MultispeQ, and beta testing the CoralspeQ device. But it’s time to reconnect…

New MultispeQ v1.0 pre-orders will start sometime in 2015 ( !!!! ), and I wanted to show you what we’ve been up to. Our goal is to hit an April 1 deadline for shipping devices, so that you can be ready to collect data in the Northern Hemisphere’s growing season. If you missed out on the MultispeQ beta test which occurred this summer (which I know a lot of people did) don’t worry, a new and much improved MultispeQ is coming.

Let’s dive in to pics and specs, but please note — these are preliminary and this is all a work in progress, so things may change slightly as we get to manufacturing. We’ve got Hardware / Design updates this time, but we’ll be following in a few days with updates about new applications and some interesting scientific outcomes from MultispeQ projects, and the some information about CoralspeQ, a device to measure coral bleaching (still in beta testing phase, not part of the April 1 release).

Enjoy!

 

v1.0 Hardware / Design

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Redesigned exterior for MultispeQ v1.0 from Barry Hutzel at Bazza Designs.
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Recent evolution of the MultispeQ. The current beta device is on the far side of the desk, while the new design provided by Barry is on the near side. The other components were 3D printed or milled ABS used to test hand fit, as well as mechanical action of the clamp.
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MultispeQ v1.0 early mechanical design. The initial case design needs to define all of the hard requirements relating to the clamp mechanism, location of components (PAR sensor, batteries, circuit boards, etc.). Once this is complete, then Barry can build a beautiful exterior around it. You can see that the new design can measure very thick items like cuvette’s by default (no need to take apart the unit to measure algae!). This is just one of many improved features.

 

We learned a lot from this summer’s beta test, both by using the device ourselves and from the feedback of our many amazing beta testers. Here’s a partial list of improvements in v1.0 for the April 1st launch.

CASE

  • 3x bigger internal battery – Recharges via USB just like your phone, no more replacing AAA batteries!
  • Improved PAR sensor – Achieves an r-squared linear fit of .98 with same light conditions using a LiCOR PAR sensor. Light conditions tested were highly varied (full sun, in canopy, LED, fluorescent)
  • Thinner design – easier to measure very small leaves (like arabidopsis) and get into tight spaces
  • Form fits hand, right or left handed
  • Measure cuvette or leaf without modification – changed the clamp mechanism so you can measure anything from .1mm to 13mm thick – no need to unscrew or add anything (or mess up the calibration) to measure leaves or cuvettes!
  • White case heats up less, more accurate ambient temperature and relative humidity – Your hand and the black case make the current temp and rh kind of useless… in the new version, these measurements should be significantly more accurate.

SENSORS

  • Contactless leaf temperature – using IR sensor, accuracy of .1 degrees C
  • Leaf thickness sensor – no guarantee but we’re trying to include this. Measures leaf thickness to an accuracy of 10 microns
  • Leaf angle and cardinal direction – gives you leaf wilt angle, and what direction the leaf is facing
  • Reduced noise by 5 – 10x – we’re still verifying, but based on some improvements in the circuit we’re expect to see a big jump here. We’re hoping this will allow you to measure proton motive force (ECS) quickly and effectively in the field, and improve fluorescence measurements with weak signals (like dilute algae).
  • 10 LEDs instead of 8 – more options for spectroscopic measurements
  • External sensor connector – we’ll have a connector so you can plug in any sort of sensor with analog or digital outputs to read using the MultispeQ (soil moisture sensors, pH probes, etc.). Connector includes power, ground, and 16 bit analog pins. This is a developer option right now – so you’ll have to do some hacking to make it work but we really hope you do!

USABILITY

  • Automatic firmware updates – firmware will update automatically over USB or bluetooth from the PhotosynQ apps – no more following complicated directions, and it means you’re always up to date!
  • Bluetooth 4.0 – fewer dropped measurements, simpler to connect

SOFTWARE

  • Fixed annoying bugs! – we (and our lovely, patient, hard working beta testers) identified lots of bugs with the Android and Chrome apps, especially dropped connections and aggravating user experiences – these are being fixed. Beta testers know what I’m talking about here :
  • Clearer selection of measurements – we know that not everyone is a photosynthesis researcher – v1.0 will be much clearer about what the measurements do (or do not do), and try to provide reference projects which can help you identify what measurements are most useful for your project.
  • More flexible project creation – now change anything (questions, protocols, their order, whatever) in a project whenever you want without losing data.
  • Shorter loading times when viewing your data on the website
  • iPhone app – it’s on our to do list, but can’t guarantee we’ll have it done by April – but we’re sure going to try.

That’s it for this time – next time we’ll walk through some of the advances we and the community have made on the science and applied end of things – some exciting stuff going on there too.

Oh – and I want to congratulate Veronica Greeve – she just broke the 10,000 measurement mark. Congratulations Veronica… you’ve contributed about 5% of all data to the platform… pretty amazing!!!

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Updates: CoralspeQ/ AquaspeQ to measure coral bleaching

Shrink-wrapped devices
Shrink-wrapped devices

coral picture

We have been working on the modification of MultispeQ for the under-water use.

In order to establish the connection between an Android phone and a MultispeQ, they have to be very close, meaning they have to be in the same enclosure—a plastic bag. However, phone’s touch-screen does not work in salt water. Venny (Vanessa) found out that placing a thin plastic bag, containing baby oil, on the screen solved this problem.

Kathryn and Geoff R. tested the inductive charging set (5V kit from Adafruit), and yes, it can charge the phone. This way, we do not need a USB cable hanging out from the phone. We could seal the instruments completely inside of e.g. a plastic bag. So the next step is modifying the MultispeQ charging system.

We also tried different plastic bags/ tubes to encase the entire device. The best material we found so far is the polyethylene heat-sealable shrink film. We still need to perfect the sealing, but the initial test showed being water-tight, and minimal air space (=minimal buoyancy).

I will post more updates when available!

 

Updates: Devices available and progress during Beta

Devices Available!

10 devices without CO2 sensors (so no soil respiration measurements) are available on publiclab.org (http://store.publiclab.org/products/multispeq-handheld-fluorometer).  We have quite a few more in the works, so if you miss this batch you can catch the next.

New ways to get a MultispeQ

 

PhotosynQ Share

We’ve learned two important things so far in the Beta: 1) We suck at making MultispeQ devices quickly and 2) Most people just need a device for a short time (a month or so).  So we decided to make a lending library for MultispeQs.  Just click on this link, fill out the form, and we’ll let you know if and when we can get you a device.

Mobile Phenotyping Group

Also, we started a crew of fearless data collectors to work with partners here at Michigan State University.  We call these guys the Mobile Phenotyping Group.  We’re working with folks like Marty Chilvers on pest management in corn, soybeans, and wheat, Jim Kelly on selection of the common bean, and a whole bunch of other folks on everything from photosynthesis research to forest management.  If you are at Michigan State and you’d like our help designing, implementing, and analyzing data collected using the MultispeQ please go apply here.

Project highlights

We realize that the site is a bit messy, and sometimes it’s hard to find really interesting projects, so I thought I’d list a few to check out.  Click on ‘dashboard’ to see the raw data and play with it, or the discussion button to see what people have been saying about the project.

Nitrogen Management in CA systems in Malawi (Plant) 11. – This was data collected in Malawi comparing 5 different crop rotation systems with some surprising results (farmer recommendations on which treatment is optimal would NOT be the same for each location!) .  If you click on ‘dashboard’ and map you can see the 3 site’s where the data were collected from.

Testing Parents for Genetic Variation -Jared Crain from Kansas State University was able to identify very small (<3%) differences in photosynthetic efficiency of photosystem 2 between two elite wheat lines.

MSU’s Sonya Lawrence is having her summer biology students create projects – here’s a few:

BS 172 US15 Photosynthetic Activity – [Beta]
Tree Age influence on Photosynthetic rates. – [Beta]
Sugar Tyme Efficiency Sum 15 – [Beta]
I’m going to improve the quality of the projects and the results pages, so keep an eye out for more highlighted projects in the future.

Improvements to Forum

The website forum has been updated, and many problems are now fixed.  You can communicate with other collaborators within your project using the forum, get tech support (we trawl the tech support forum so you’ll get an answer as fast or faster than emailing me directly!) or find others with similar interests.  You can adjust your forum settings in the “Manage Subscriptions” part of your user profile page (see image below).

 

 

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Go to your user profile and click Manage Subscriptions to join a forum. Any projects you join or create you are automatically included in the forum.
Screenshot from 2015-06-08 08:12:35
Forums are located in the Forums tab.

v1.0 update

We are furiously working on the next version of the MultispeQ, v1.0.  We’re getting the first test PCBs out soon, and the case is being redesigned with some important improvements like integrated cuvette measurements (so no separate cuvette holder to install) and integrated leaf thickness sensor and leaf temperature.  At some point in the next 3 months, we’ll give a more significant update on the features of this next version, so stay tuned.

 

What you can measure with your MultispeQ

Production line, located in the Plant Research Lab Dungeon!
PhotosynQ production line, located in the Plant Research Lab dungeon!

Production of the MultispeQ has begun in earnest!  We have all the parts (except the circuit boards which are coming next week) to build 250 beta MultispeQ devices, and we’ve got Geoff full time on production to make it happen.  The hardware version is locked, device calibrations are known, the software platform is stable and works in the lab and in the field,  and we have a suite of high quality methods for measuring plant and soil health.  It’s been a long journey, but we feel good that we’re finally ready to let go 🙂

I’d like to take this post to give more detail about just what the heck you’re going to be able to do with your MultispeQ device once you get it.  Next to each measurement you’ll see a comparable commercial device, though it’s important to note in some cases the MultispeQ is more accurate, and in some cases less accurate.  Combined, the commercial cost of devices which measure everything described below is 10s of thousands of dollars so we think we’re doing pretty good!

Measurements

The machinery of photosynthesis! The red circled items are areas which can be measured using the MultispeQ.
The machinery of photosynthesis! The red circled items are areas which can be measured in some way using the MultispeQ.

Light Levels

LiCOR PAR meter

Photosynthetically Active Radiation (PAR)

PAR is the range of wavelengths of light which are actually absorbed by plants to do photosynthesis.  This range is 400nm (purple) to 700nm (dark red).  Standard light meters are influenced by infra-red and UV, which are not used in photosynthesis.  We use PAR, combined with the other measurements below, the figure out the flow of energy via electrons and H+ ions which ultimately produce sugar and plant tissues.

Chlorophyll content

spad 502 plus
Minolta SPAD meter

SPAD

Chlorophyll content in the leaf has been shown to relate to overall plant health, and NDVI (a similar measurement taken using reflectance instead of transmittance) is used commercially to determine the timing of nitrogen application in corn and other crops.  This measurement is very short (about 1/2 a second) and can be calibrated easily in a few seconds in the field.  SPAD measurement was initially popularized by Minolta and they continue to produce most of these types of handheld devices.

Efficiency of Photosynthesis

Pulse modulated chlorophyll fluorometer

Photosystem II and Photosystem I efficiency

Photosystem II (PSII) is where most the energy gets captured from the sun which is used by plant to make food.  Tracking it’s activity, efficiency, and regulation tells us a lot about the condition of the plant.  For example, PSII efficiency changes based on stresses (like drought or lack of nutrients) quite quickly – in fact it is possible to spot a under-watered plant using PSII efficiency before the change is noticeable by eye.  We can calculate PSII efficiency by measuring infra-red chlorophyll fluorescence under various conditions – here’s a cool infra-red filtered time-lapse showing fluorescing plants in a growth chamber!

Photosystem I (PSI) also captures energy from the sun, but it’s role is a bit more complex and not worth diving into here.  But, knowing both PSII and PSI together can tell us linear and cyclic electron flow (the flow rate of the very electrons which ultimately produce ATP and sugars)… that’s kind of like measuring the pulse of a human being.  The faster our pulse, the harder we’re working or more stressed we are.

There are lots more details about these measurements and the mechanisms linked below:

http://www.advancedaquarist.com/2004/7/aafeature
http://en.wikipedia.org/wiki/Photosynthetic_efficiency
http://jxb.oxfordjournals.org/content/51/345/659.full.pdf
http://blog.our-sci.net/wp-content/uploads/2013/03/photosynthesis-state-of-the-art-2007.pdf (warning – very in depth but lots of good information!)
See page 1112 in this article “PSI Electron Flux” for a description of PSI measurement using 850nm

ATP production

Benchtop spectrometer

Proton Motive Force (PMF)

We are quite proud of this measurement, because we are the only handheld device that we know of capable of taking it!  The Proton Motive Force (PMF) is the energy produced by the flow of H+ ions out of the thylakoid membrane (see picture above).  What does that mean?  If we imagine that photosynthesis is like a hydro-electric dam then PMF is the energy produced by the water flowing through the turbines.   But for plants, instead of turbines producing electricity, it’s the ATP synthase producing ATP.  We can estimate PMF by measuring something called electrochromic shift (ECS).

This is a very new measurement so we don’t have a lot of clear applications in the field as of yet, but we hope the PhotosynQ community will help us find more!

Photosynthetic regulation

Non Photochemical Quenching (NPQ)

Plants spend a lot of time dissipating energy from the sun because too much light can damage plant tissue.  Chlorophyll fluorescence is one way to dissipate that energy (fancy term for this is photochemical quenching), but the plant can also turn excess light into heat.  This dissipation as heat is called non-photochemical quenching, or NPQ for short.  Normally, it takes about 10 minutes or more to accurately measure NPQ, but Dave and Stefi have been working on a new measurement called NPQt which cuts that time down to about 10 seconds… which means plant breeders, ag extension agents, and others can take this measurement in the field, in real time!

Combining photosynthesis measurements

One measurement to rule them all!

We’re working on combining PSI, PSII, and NPQ described above into a single measurement which takes 10 – 15 seconds to complete.  This is possible because these measurements all share similar components, like a saturating light, a measuring light, far red, etc.  In fact, combining them is potentially better than performing them separately because the measurements themselves disturb the plant – so the fewer times you flash lights at the plant, the more accurate your readings will be.  Expect to see a blog post detailing this measurement soon.

Soil biological activity

Solvita CO2- Burst Soil
Soil biological activity by CO2 accumulation

Soil CO2 production

Soil health is hard to measure because there are so many different components – nitrogen, phosphorus, potassium (NPK), micro-nutrients, the presence or absence of toxic chemicals, and other factors.  So measuring overall biological activity in a soil can give us a general indication of the soil health by measuring the CO2 produced by micro-organisms in the soil.  The rate of this CO2 production tells us the amount of biological activity.  Here’s an graph of some recent measurements we took showing the CO2 production of swamp, forest, and grassland soils taken in the field – swamp was the most active (fastest increase in CO2), as expected.

Soil organic carbon (humus)

Product image for Colorimeter
Standard small colorimeter

Permangenate oxidizable carbon

Organic carbon in the soil helps maintain pH, reduces leeching of nutrients, and increases water holding capacity.  It can be measured by using a potassium permangenate solution according to this protocol.  We have done initial successful testing but can’t wait to get more feedback from the community on this method!

Soil moisture and ion concentration

Soil EC meter and display

Electrical Conductivity (EC)

While the MultispeQ itself doesn’t have a conductivity meter attached, you can purchase a conductivity meter and hook it into the MultispeQSoil conductivity, i.e. passing an electrical current through the soil and measuring it’s resistance, is influenced by the presence of ions like nitrates, potassium, sodium, sulfate, and ammonia as well as the presence of water.  It’s a tricky measurement, because it’s influenced by soil type and moisture levels.  However, we’re particularly excited about this because if we can collect global soil EC data, and correlate it with soil type and weather information, we think we could eventually predict soil ion concentrations.

 

Other ideas

Polyphenol concentration in grapes, relates to taste for wine makingBrix (sugar concentration), relates to taste and readiness for picking

Anthocyanin content in leaves, a measure of stress

Pulse oxymetry, not plants, but hey why not

Seed mold, seed storability by measuring temperature, CO2, and relative humidity

We can’t wait to get these devices out into the field, and see what you guys come up with… expect more updates soon!

World Tour

We’ve been on a PhotosynQ world tour of sorts in the last month, starting with Mozfest in London, PhenoDays in France, TechCon in Berkeley, and now Public Lab’s Barnraising in Louisiana!  And, of course, we’ve been doing more method development and Geoff and Robert even managed to whip out a few more units on our march towards 100 to ship to beta testers.  Our media stream from these events are on our g+ page

Explore our data!

Where do I find the data for all these projects? Click here! Expect some nice tutorial videos on how to explore the data soon!
Where do I find the data for all these projects? Go to the project’s main page and click on the dashboard button. Expect some nice tutorial videos on how to explore the data soon!

We recently reskinned our website (www.photosynq.org) and made our initial alpha and beta testing data available to all!

A lot of it is old, performed on old instruments which we’ll clean up before we send out new devices.  Be gentle – we know there’s lots of bad data points, and that the data itself isn’t well documented – we’re working on that!  Also, expect a full video tutorial on this in the next few weeks.  But given all those caveats, here’s some cool ones to check out:

North Dakota State Bean Variety Trials: We measured 150 different crosses of the common bean this summer with Juan Osorno’s lab at NDSU.  You can see clear differences in photosystem 2 efficiency and SPAD.  Definitely some error in the data also – one of the devices was way out of range for PAR light intensity!

MSU North Campus Tree Phenology Research Project: about 20 students from Michigan State University tracked the color and photosynthetic efficiency of 6 different trees on campus over the course of 2 months.  Are red leaves still doing photosynthesis?  What about yellow leaves?  You’ll have to check the data to find out!

Malawi Bean Variety Trials: These were several different fields of different management methods on beans over the course of about 7 weeks.

Assaying Sampling Techniques using Beans: This is an ongoing project where we’re trying to figure out how each leaf on a common bean stalk is responding to light.  We’re measuring every leaf (about 11 or so in these 5 week old beans) for photosystem 2 efficiency, SPAD (greenness), and ECS (measures proton motive force).  We may switch the project as we change and adjust the protocols and user questions, but the data is quite interesting!

World Tour!

MozFest logo copy

 

MozFest in London.

Met folks from Zooniverse, Open Knowledge Foundation, and got Professor Grey from CERN excited about the idea of making a open scientific hardware conference (hope to post more about that later – if you’re interested in helping to organize please contact me!).  Hooked up with some awesome guys from Chicago Hive who will make great educational partners, and had a long and very educational talk with a gaggle of 14 year old British girls in a workshop about teens and citizen science.  Coolest of all – a DIY atomic force microscope for ~100 bucks… holy mackrel.

Also learned about some really neat tools Mozilla have developed to help the next generation be creators in the open web (instead of consumers in the ‘shopping mall’ web, as they describe it).   Check it out.

 

https://i0.wp.com/www.phenodays.com/fileadmin/templates/images/top-banner.jpg

PhenoDays in Beaune, France.

PhenoDays is a conference put on by LemnaTec, a company which makes very large scale plant phenotyping systems, focused mainly on imaging technologies for estimating biomass, though it also does chlorophyll fluorescence and even (as we saw in a nearby facility) measures root growth (see picture).

I met lots of great folks here, including a contingent from the Danforth Center, the Australian Phenotyping Center and the UK one (in Wales, the land of no vowels),

I wasn’t sure how we would be received, given that we are kind of the opposite of everyone else there (open data/software/hardware, low cost, measure the field not the greenhouse, uncontrolled conditions).  But actually, everyone loved the concept of an public database of plant health measurements in the field, and in fact we complement (not compete) with the existing plant phenotyping platforms like Lemnatec and Phenospex, because the data we collect can feed interesting ideas, phenotypes, outcomes, and questions into the more controlled chamber-type systems.

Also, we were thoroughly wined and dined. One night we had dinner here… in a ‘chateau’… pretty much a 1000 year old castle.

 

 

USAID’s TechCon in Berkeley CA.

TechCon is intended to bring together non-profits (including USAID), universities, for profits, and venture capital to help solve the toughest problems in the developing world.  The venture capital is there to help successful small projects to take it to the next level, as scale up is a big problem in development.

We met more interesting folks than I could mention, though the coolest thing I saw was Planet Labs, who want to take an image of the entire earth once per day.

Chris giving his pitch in the Innovation Marketplace
Chris Zatzke (of pick and place troubleshooting fame) presented the PhotosynQ project in the Innovation Marketplace, a competition among 49 teams funded through USAID. We won the Audience Choice award and we were chosen to take part in Venturewell’s development process (which leads to further funding and possible investment down the road). Basically, Chris rocked it!

 

Public Lab

Publiclab.org ‘s barnraising in Cocodrie Louisiana.

Actually, this is happening as we speak – Robert and Geoff are there learning and teaching and having fun.  We’ll be presenting the PhotosynQ platform to the Public Lab community, and hopefully we can get some interest in folks using, forking, or otherwise contributing to our pretty robust data collection, sharing, and analysis backend.

We’re also talking with Public Lab as a distribution partner through their Kits Initiative.  That saves us time in packing/shipping/fulfillment and gets us access to the amazing community that is Public Lab.

Other News

While we spent a lot of time on the road, we have also managed to develop some new and interesting methods.  The next blog post will have lots more detail, but we have successfully implemented the soil biological activity measurement using our CO2 sensor, and a spectroscopic measurement of proton motive force (using ECS).  This is actually kind of a big deal – no other handheld device IN THE WORLD can measure proton motive force, in part because of the accuracy required (an example measurement is shown below).  Our goal is to make sure short enough that people can take the measurement in the field.  More detail in the future, but we’re really excited about this.

measuring proton motive force using electrochromic shift caused by chlorophyll absorbption at 520ishnm
measuring proton motive force using electrochromic shift caused by chlorophyll absorbption at 520ishnm

 

We’ve also managed to make another 3 units, and we will STOP AT NOTHING until we have 100 units in hand!  Nothing is holding us up except all this traveling (which ends this weekend) and hand wringing so we will get it done!

Fun with PhotosynQ: Cuvette Holder

So while I had some down time (we are going through a slight board re-design to decrease noise and cross-talk) I worked on the ability of the PhotosynQ platform to gather non-plant data. I present to in all its glory, the MultispeQ cuvette holder attachment!

Here is the obligatory “action shot”. In reality the light pulses are so fast/short you can’t see anything.

IMG_1522   IMG_1520

 

Since a cuvette holder is basically useless without established methods that use it, I decided to adapt an assay designed to measure active soil carbon (carbon that is readily available for use by microbes) to the PhotosynQ platform. This assay is already in use by the USDA & many Universities ( Ohio, Missouri, etc).

The cuvette holder and PhotosynQ platform can (with a little work) be used for any of your standard absorbance assays that use wavelengths close to what the MultispeQ has available. For example, you could do Bradfords assay, or OD590 (the MultispeQ’s version of OD600). I am also working on a right angle cuvette holder for turbidity and fluorescence measurements.

The method is described here http://lter.kbs.msu.edu/protocols/133 (it is pretty close to what I did) and I’ve got my own procedure that I will put out shortly (once I make a how to guide).

The MultispeQ in its natural habitat (the MSU Horticulture Gardens http://www.hrt.msu.edu/our-gardens/).

IMG_1533

The basic idea is that you can go outside, collect a soil sample, oxidize it with permanganate for 10 minutes, find the absorbance of the sample, compare it to a standard curve/plug some numbers into a formula, and then get a mg/kg amount of active carbon in your soil.

Here is a picture of my standard solutions (in the falcon tubes) and my soil sample (in the cuvette). Don’t worry, even though it looks like my soil sample will fall outside of the standard curve it doesn’t.

IMG_1532

So after some troubleshooting I developed a protocol that works pretty well with the MultispeQ as it is now (once the new boards are in I might have to redo it, but its only going to get better).

Sadly as of now you have to calculate the absorbance manually (we are working on fixing that).

As you can see the standard deviation for the MultispeQ is higher than the labs spectrophotometer, but we expect that to go down significantly with the new boards.

Screen Shot 2014-10-06 at 2.10.31 PMScreen Shot 2014-10-06 at 2.10.40 PM

This is a graph of the stand curve as done on the MultispeQ and the standard curve produced by the labs spectrophotometer.

Screen Shot 2014-10-06 at 2.08.10 PM

 

Once the new boards are in I will work on optimizing this protocol so that the MultispeQ reports values that are closer to the labs spectrophotometer. I also have grand plans to integrate this assay into the PhotosynQ app, so you won’t need to plug anything into formulas or excel. As shown above, the deviation between the two becomes greater as adsorption rises. This will cause the MultispeQ to report values that can be ~30% greater than our control spectrophotometer. However, absorbances this large only occur in very poor soils, and as soil quality increases the error between the MultispeQ and the control spectrophotometer goes down considerably (in laymans terms we are able to very accurately calculate the absorbance of dilute solutions, even with the cross-talk and noise problems that we are correcting).

 

Hello Fargo, I’ve come for your beans!

Project: Bean Variety Trials at North Dakota State University
Project Leads: Juan Osorno and Ali Soltani, North Dakota State University
Goal: Collect photosynthesis and plant health data on 150 varieties of common bean for eventual QTL (genetic) mapping.

Project Page
View and analyze the data (create a login if necessary)
Juan Osorno’s NDSU page

 

Hello Fargo!
Hello Fargo!

This week I went to Fargo, North Dakota to meet with Professor Juan Osorno and post-doc Ali Soltani, bean breeders at North Dakota State University. I bet you didn’t know that NDSU has one of the premier bean breeding programs in the US – well they do!

On my flight in, I told the guy next to me I’d never been to North Dakota before, and his response was “You’re going to love it”… Love it? North Dakota? Well, yes, I did love it. People were nice, and it appeared that everyone was there because they wanted to be, which makes sense, you don’t end up in North Dakota for no reason. Agriculture is booming, and the the fields are gigantic (at least in comparison to the ones I was used to growing up in central New York). So, what were we doing there? I’ll let Ali give a recap:

So our goal is to show that you can correlate photosynthetic outcomes to actual genes or groups of genes.   This has so far proven difficult and slow to achieve for breeders especially in comparison with the dizzying pace of mapping the genome, which has been automated and has come down in cost many orders of magnitude over the last 15 years. We took measurements of 150 different varieties with 6 replicates each (900 measurements total).  Each measurement included two protocols: SPAD (a measure of leaf greenness which correlates to Nitrogen content) and Phi2 (a measure of photosynthetic efficiency).

Stephan collecting data using the Android app
Stephan collecting data using the Android app

It took us some time to get ready to collect data.  We had to go to a coffee shop to get internet to make sure everyone had an account at PhotosynQ.org and their cell phones had the PhotosynQ android app installed correctly.  But once we got to the field (a full 1.5 hours away!), taking measurements was a snap.  The only technical problems we had were swapping batteries as they needed to be recharged – that was a big success for us, and shows we’re ready to do real work with this thing!

MultispeQs charging their batteries after a hard days work.
MultispeQs charging their batteries after a hard days work.

So let’s look at some preliminary results using the online analysis tool (so you can view and play with the data too!  Note that you may have to create a login first). This tool is intended to be a Swiss Army knife of sorts – it can do lots of quick analysis, but none of them too deeply.  If you need to do multiple regression analysis… you’ll probably have to just download the data 🙂  We might to see more data in this project this week, as Ali and Stephan go back to a second field, we’ll see.  Also, Ali is working on more in depth device comparisons, to try to use statistics to parse out the variation coming from the device versus that coming from the varieties themselves.

 

We can also compare two variables on the X and Y axis. Here we have LEF (linear electron flow) a measure of energy from photosynthesis compared to light intensity. Each device has a separate series. These differences may be due to calibration, or differences in plants, hard to know yet.
We can also compare two variables on the X and Y axis. Here we have fluorescence in the steady state (normal light) versus that from a saturated state (very high light).  These differences may be due to calibration, or differences in plants, hard to know yet.
SPAD (a measure of greenness) was fairly consistent across devices as you can see. Some variation is due to the fact that each device only measured 60 of the 150 varieties, so there's not perfect overlap there.
SPAD (a measure of greenness) was fairly consistent across devices as you can see. Some variation is due to the fact that each device only measured 60 of the 150 varieties, so there’s not perfect overlap there.
The most important outcome from this trial was to determine if 6 devices could produce consistent results. As you can see here, device 43 was reading too high on light intensity PAR - we'll have to investigate that!
The most important outcome from this trial was to determine if 6 devices could produce consistent results. As you can see here, device 43 was reading too high on light intensity PAR – we’ll have to investigate that!
This is a simple average of Phi2 for 15 varieties. The black bars are 1 standard deviation.
This is a simple average of Phi2 for 15 varieties. The black bars are 1 standard deviation.  Anything statistically significant here?… mmm… not quite yet.
Histogram showing Phi2 (photosynthetic efficiency) for the entire sample - distribution isn't too bad!
Histogram showing Phi2 (photosynthetic efficiency) for the entire sample – distribution isn’t too bad!  Not a lot of outliers which means the MultispeQs worked ok.
temperature by time
This graph doesn’t show much from a plant health perspective, but it does show how temperature in the device varied over time. In general we’ve found that people’s hands heat up the device the longer they hold it. You can see that effect here for each device (each series snakes upwards), and you can see how long it took us to take all our measurements. This is something else we need to address in the next version.
Here's a map of the field colored by device ID. The entire field is offset to the left by about 10 meters. However, you can see that each user measured from left to right over only a few rows, which was correct - cool!
Here’s a map of the field colored by device ID. The entire field is offset to the left by about 10 meters. However, you can see that each user measured from left to right over only a few rows, which was correct – cool!