Racing to measure photosynthesis: why fast gas exchange measurements matter

One of the grand challenges of the 21st century is to meet global food demand. The circumstances that lead to this issue are: 1) population growth, 2) climate change, and 3) limited genetic variability. Let’s focus on issues 2 and 3, since these are issues that photosynthesis research can help solve.

Climate change is changing precipitation patterns, increasing temperatures, and increasing the frequency of extreme weather events. Generally, crops will face drier and hotter conditions, and more frequent extreme heat events.

Photosynthesis research can help by allowing us to find plants and crop varieties that are capable of maintaining carbon-fixation (required for growth) while minimizing water use in the face of these climate change-induced stresses. Different crop varieties have different traits, and given that there can be thousands of varieties of a given crop, it can be very time consuming to measure traits of interest (such as water use efficiency) in all varieties.

This is where rapid gas exchange techniques can help. In collaboration with Dr. David T. Hanson at the University of New Mexico and LI-COR Biosciences, we developed a method for rapidly measuring the response of photosynthesis to CO2. Measuring such a response allows us to understand the underlying biochemistry. Our method is up to 12 times faster than the traditional approach.

This is fast enough to be able to measure these CO2 responses in thousands of varieties within a reasonable time frame, which could allow a researcher to correlate the data-rich gas exchange measurements with the underlying genetic variation among plant varieties. In turn, this could enhance crop breeding efforts to improve crop yields, stress tolerance, and yield sustainability.

If you’re interested in learning more about the rapid gas exchange method, you can read the article for free (it is open access) here.

Stay safe and stay informed,
-Joe

Fulbright Travels, January 2017

Fulbright Travels, January 2017

There are some secrets about science that are kept hidden until you are actually practising it, and the importance of writing is one of those secrets. As a scientist, you have to think, design experiments, run the experiments, analyze the data, and at the end of all that, you need to compile everything that you learned from your experiments into a cohesive story. Written communication is one of the most important parts of being a scientist – if you don’t communicate your research, few people will know about it.

Crafting a scientific article can be difficult by itself, but complex data analysis can make it even more difficult. However, sometimes it is straight-forward, and I have two contrasting examples. This past week, I have had two papers accepted into the same scientific journal: one is my first thesis chapter, and the other is from research I’ve carried out on my Fulbright exchange here at the University of New Mexico. My thesis chapter is the product of a multi-year experiment, with data from multiple levels of biological organization, and more statistics than you can shake a stick at. It took months to put together into a cohesive story and to make sense of the data; sometimes you think that you’ve analyzed everything that you could, but then you find a different, creative way to analyze the data that leads to a different conclusion, and then you’re back at square one with the story. My Fulbright research, on the other hand, is the product of less than a month of experimentation, and only took a few weeks to put the story together and submit the article. Writing these articles were completely different experiences in both time and difficulty. But now the research is available (or will be soon once it’s posted to the journal website).

This brings me to an important point: writing is a key skill of a scientist, and one that is largely ignored until graduate school. Anyone aspiring to be a scientist should be encouraged to learn to write well and often, as writing up research is often the rate-limiting step, and a barrier that can be reduced by teaching scientists-to-be to write well before graduate school.

In other news, the first paper from my Fulbright research as been accepted into the journal, Plant, Cell and Environment. As soon as it’s available online, I will be posting a link!

I also went to the Albuquerque aquarium – it’s the first time I’ve ever been to an aquarium, and it was fantastic. They have all sorts of fish, corals, jellyfish, and even a baby ray petting area. If you’ve never touched a ray, it is quite a strange feeling!

 

img_20170107_140128
Baby rays at the Albuquerque aquarium.

 

Stay safe and stay informed,
-Joe

Fulbright Travels, Weeks Eleven and Twelve

The past couple weeks in Albuquerque covered American Thanksgiving and the Albuquerque Twinkle Lights Parade.

American Thanksgiving made for a particularly short work week. In Canada, we celebrate Thanksgiving in October instead of November. This year I had the chance to attend my first American Thanksgiving celebration, and I was not disappointed. The most notable food item is definitely sweet potato pie/casserole, which is mashed sweet potatoes mixed with butter and brown sugar, and a layer of marshmallows roasted on the top. If you ever get a chance to make it or try it, I highly recommend it.

This past weekend I made it out to see the Twinkle Lights Parade, which is more or less Albuquerque’s version of the Santa Claus parade. There were spectacular marching band and dance routines from the local schools and hundreds of floats. Definitely an event to check out if you’re in Albuquerque this time next year.

img_20161203_185743
One of the many well-decorated floats at the Twinkle Lights parade.

In regards to my science, I managed to get my first paper from my Fulbright exchange submitted this past week! It’s currently undergoing review, so it will be a little while before I get a decision. In the meantime, I am waiting for some rather super-heat tolerant plants to grow.

img_20161127_142953
Heat tolerant plants from the genus Boechera.

Until next time,
Stay safe and stay informed,
-Joe

Fulbright Travels, Week Ten

Fulbright Travels, Week Ten

This week we had the opportunity to see a rare phenomenon: the super moon. The moon appears much larger than usual because it is at the closest point to Earth in its orbit, and this one was special because it was the closest the moon has been since 1948. While I didn’t get to see the moon rise over the horizon, where it appears biggest, I did get to see it rise over the Sandias from a vantage point in west Albuquerque. It was quite spectacular, and made all the lights in the city appear dark as the intense moonlight bathed the city.

As for my science this week, I learned how to extract the cuticle from leaves. The cuticle on leaves is a waxy layer that protects the plant from losing too much water. This waxy layer could affect the way that (or the way we perceive that) plants uptake carbon dioxide as well, which is why I am studying how the cuticle and its thickness affect measurements of photosynthesis. You can see a couple part of the extraction process below.

And on Saturday, I went to Gatos y Galletas, a cat café in Albuquerque. All of the cats are up for adoption, and it is an excellent place to go hangout with some cats and get to know them. The whole concept around the place is really cool, because it lets you see how the cats interact with other people (and cats), which is very important to know before adopting an animal.

wp-1479665616209.jpg
A puddle of kittens at Gatos y Galletas.

Every week I discover just how much Albuquerque has to offer!

Stay safe and stay informed,
-Joe

Fulbright Travels, Week Nine

Fulbright Travels, Week Nine

Surprise. That definitely encompasses the mood in Albuquerque this past week.

Of course I am talking about the United States Presidential Election. The US has a rather strange election process – it starts over a year in advance of the actual election, and involves endless campaigning, bargaining, and media stunts. This most recent election was going to be historic regardless of who got elected: either the first female president or the first president without previous political experience.

The surprise in the election results comes from the ‘expected’ outcomes based on polls in the weeks leading up to the election. In short, the pollsters were very wrong. There is a science to polling, however whenever the behaviour of people is involved in a science, things can get more complicated. In the case of the polls leading up to the US election, there is widespread speculation as to why the polls were wrong.

One thing that I consider frequently in my science is the timescale of the processes that I study: if I am looking at the growth of a tree, I may look at a weekly- or monthly- timescale; if I am looking at photosynthesis in a leaf, I may look at it on a second- or minute- timescale. I choose these timescales based on how fast I expected to observe a response, and in any science, it is important to choose the proper timescale. This can be difficult in practice if your system in question maintains itself in a steady state as long as possible, and ‘flips’ to a new state when environmental conditions change. In this case, the precise moment of the flip would need to be captured to fully appreciate the mechanism that led to the change in state, and that requires good, old fashioned, luck.

Now in the case of the polls leading up to the US election, given the volatility of the candidates, their behaviours, and their respective scandals, a poll one month or even one week in advance was likely to be misleading, and given the actual outcome, it’s entirely possible that the American public, on a population level, changed states on election day, explaining why the polls were consistently wrong.

In any case, as with every democratic election on the planet, there are people who are upset, and people who are happy. It was saddening to see comments from people lambasting the American public on their decision. No one, and no people deserve to be treated that way. A divided world is a world prone to war, and given the challenges that face humanity this century, including food security, climate change, over-population, and poverty, we need now, more than ever, to unite as a species and solve these problems on a global scale.

So please support, rather than deride, the American people for their recent choice – they need it more than ever: it was unbelievably quiet and sombre in Albuquerque on Wednesday morning.

And to my fellow Canadians, let’s remind Americans that they are good people, that we appreciate the role they play in our world, and that we will love and support them through these (potentially) turbulent times.

Stay safe and stay informed,
-Joe

Fulbright Travels, Week Eight

Fulbright Travels, Week Eight

Dia de los Muertos. Day of the dead.

This week I celebrated the day of the dead in New Mexico. It’s a tradition that celebrates, rather than grieves, dead friends and loved ones. A typical activity is to decorate sugar skulls, construct a shrine, and offer the sugar skulls to the dead, while others will bring them to where their loved ones are buried.

On Tuesday, I decorated sugar skulls – of course, without a mold, we had to improvise.

14915537_10154872324093814_3120952199739916644_n.jpg
Handmade sugar skulls with icing

In Albuquerque, there’s a big parade on the Sunday following the day of the dead. There are many activities and crafts to participate in, including decorating sugar skulls, face painting, and watching the parade.

The parade this year was full of political statements and encouragement to vote in the upcoming US election. There were classic low-riders and people operating large skeletons!

Overall, the parade was quite exciting with lots of cheering and singing! A must-see if you’re ever in Albuquerque at this time of year.

Stay safe and stay informed,
-Joe

Fulbright Travels, Week Seven

Fulbright Travels, Week Seven

Learning by trial and error.

I’ve heard people call this bad form when learning, but I have to disagree. Yes, sometimes it’s better to spend a rather long time learning a set of concepts to solve a problem or ask someone for help. But sometimes, it’s better (and faster) to learn through trial and error. This is a strategy that I’m taking with custom gas exchange setup.

Any custom gas exchange system runs into the same issues as designing an HVAC system for a building: pressure drops, flow issues, temperature control, etc. And as I’ve learned over the past week, the system is not only sensitive to the materials used to make the system, but also the order of the components. If you put a condenser in the wrong spot, humidity could get too high in another part of the system, or the temperature fluctuations could adversely affect your measurements. If you are pressurizing the system, the elasticity of the component tubes can affect whether you can actually pressurize the system. And lastly, where you put the impeller or fan can cause large problems with pressure fluctuations. Luckily I have a limited number of components in the system, and this is a case where trial and error can work quite well – it didn’t take long to rearrange the components and test whether the setup worked. However, I only recommend this when the problem is sufficiently small, or when there is no evidence or theory to use as a starting point.

Moving on from science, this past week I explored the climbing available in the Albuquerque area. Stone Age Climbing Gym is the largest climbing gym that I’ve seen, with  two large bouldering areas and roped climbing throughout. The routes range from being easy introductory problems for newcomers to advanced technical problems for the experienced climbing. There is a very supportive atmosphere, and if you enjoy climbing indoors, it is definitely worth checking out!

On the weekend, I went out to the Sandia foothills to explore the bouldering there. The rock is very much like concrete – unfortunately this means that it is not very pleasant to climb (which explained the complete lack of other climbers). However, the views from atop the boulders are spectacular.

I also went to the Kasha-Katuwe Tent Rocks National Monument, which is about an hour’s drive north of Albuquerque. Tent Rocks is a place that is sacred to a local aboriginal group, and was formed through a combination of flooding, volcanic activity, sedimentation, and erosion. The rock formations are absolutely beautiful. The hike takes about an hour to get to the top, and is of moderate difficulty for most people, but the views are worth it. At the top, it is very easy to understand why Tent Rocks is considered a sacred place.

If you are ever in northern New Mexico, the Kasha-Katuwe Tent Rocks National Monument is worth the trek. The pictures capture but a fraction of the beauty and the experience.

Stay safe and stay informed,
-Joe