Research update: February/March 2016

Could it be? Is spring on its way? After a lot of working in the last this past February and March, it sure sounds nice to be able to work outside again in the near future!

A kildeer has built its nest on the green roof at the Chicago Botanic Garden. This has happened every year and it's nice to see a sign that spring is here!

A killdeer has built its nest on the green roof at the Chicago Botanic Garden. This has happened every year and it’s nice to see a sign that spring is here once again!

Just a few of the many test tubes filled with plant DNA that I've been working with the past two months.

Just a few of the many test tubes filled with plant DNA that I’ve been working with the past two months.

The winter to spring transition months included a lot of test tubes! I’m happy to report that I finally finished extracting the DNA from all of my little seedlings. That’s almost 550 samples. Phew! It took a lot longer than I expected just to perfect the technique of getting DNA out of such little bits of plant tissue but I was able to get the procedure streamlined enough and finally finished. The next step was to start the DNA amplification – a process called PCR that makes many copies of the DNA so I can work with it in the future. I need to amplify 9 sections of DNA in each of my 550 samples. If you’re doing the math at home, that’s nearly 5,000 reactions. Luckily, there is a machine that helps me out with making temperature changes so the reactions can occur without my constant guidance but I still have the fun task of loading the test tubes with the correct materials – yep, all 5000 combinations. So that’s been most of my March and the project will continue into the future. By the end of the month I was able to test some of the PCR samples and see if they worked. I’m happy to say that I’ve got mostly positive results so far. There are still a few kinks to be worked out but at least I know that things are moving forward in the right direction.

The 2015 seeds have germinated. The seedlings are in these small tubes and are kept frozen until I can find the time to extract their DNA this spring.

The 2015 seeds have germinated. The seedlings are in these small tubes and are kept frozen until I can find the time to extract their DNA this spring.

Moving in the right direction is a good thing, especially in light of the fact that I’ve got another round of DNA extraction and amplification to go. I’ve just completed these steps with the seeds I collected at the end of the 2014 season. In March, I also collected the germinated seedlings from all of the 2015 seeds. The new little seedlings (only about half as many this time, thank goodness!) had finished getting as big as they were going to get in the incubators so I collected them in small test tubes and put them in a very cold freezer. In April or May I’ll start the DNA extraction procedure all over again with these new samples. Then more amplification…

Things are looking pretty dormant in my green roof plots. But I know my plants are there. Just wait a few months!

Things are looking pretty dormant in my green roof plots. But I know my plants are there. Just wait a few months!

As March came to a close, I ventured out to a couple of my roofs just to see if there were any signs of life. It was a pretty mild winter but it still looks too early for most of my little plants to start growing yet. I guess I was just getting a little hopeful – wishful thinking! I’m looking forward to getting out to all of my green roof sights again this spring and summer. It’s hard to believe (but kind of exciting too) that this will be the last summer of data collection for my dissertation research. In the future, I’m not sure what will happen to these plots that I’ve established, but I think at least some of them will be left alone and the plants will just do what plants do; grow, reproduce… hopefully survive for many generations. We’ll have to see. One thing I do know is that it’s going to be a busy summer.

 

By the end of March, a few signs of life started to appear in my green roof plots.

By the end of March, a few signs of life started to appear in my green roof plots.

My temperature probes have been recording data all winter long (hopefully). I'll collect them again this spring to see what happened on the roofs while I was inside staying warm.

My temperature probes (like this one taped to the roof) have been recording data all winter long (hopefully). I’ll collect them again this spring to see what happened on the roofs while I was inside staying warm.

In other fun news, my green roof children’s activity book has been featured, both on an industry website and in a non-profit magazine. My coauthor Olyssa and I were asked to write a little piece describing the unique features of our book for the international website greenroofs.com. Check out that story by clicking here. I was also interviewed by a reporter a couple months back (remember that photo shoot in December that I wrote about in my last post?) about the environmental education benefits of our book and a short piece was included in the Chicago Botanic Garden’s member magazine, Keep Growing. Check out that article by clicking here and going to page 74. We continue to have people download our free book and have recently even been asked to translate it into Dutch for a wider international audience. It’s great to know that people are enjoying the book and that our hard work is helping teach people about the benefits of green roofs!

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Research update: January 2016

Winter = writing & lab work. After a few years as a botanical researcher I’m beginning to really understand this seasonal work pattern. So that’s what my January looked like. I spent time making revisions to a research report that I’ve been working on for a while now. This particular report keeps getting better little by little but it is quite a process to take years’ worth of work and write a technical yet brief summary of what it all means and why it all matters. It’s getting there!

Tiny seeds on agar plates experience simulated spring in an incubator.

Tiny seeds on agar plates experience simulated spring in an incubator.

I spin the small tubes filled with DNA and chemicals in a centrifuge to separate the layers and help purify the DNA

I spin the small tubes filled with DNA and chemicals in a centrifuge to separate the layers and help purify the DNA

Lab work has also taken on some different forms and was in full swing in January. In one part of the lab, I washed soil off of the roots of weeds collected from my green roof plots. The clean weeds were then dried in an oven and weighed to compare how much weedy plant tissue (called “biomass”) grows in traditional succulent green roofs compared to my prairie-style green roofs. In another part of the lab, I continued to extract DNA from some tiny plant seedlings for a different experiment. This DNA will later be used to measure how pollen moves between green roofs.

I use this computer hooked up to a fancy machine to determine if my DNA primers are working to make lots of copies of the DNA from my plant seedlings.

I use this computer hooked up to a fancy machine to determine if my DNA primers are working to make lots of copies of the DNA from my plant seedlings.

In a different part of the lab, I took some of my seeds already set out on agar plates from a refrigerator where they were experiencing simulated winter and moved them to an incubator where they are now experiencing simulated spring. I’ll later get all of their DNA too. And in still another part of the lab, I continued to work with something called “primers” which are used to help make many copies of small quantities of DNA. I know what you must be thinking: “Just how big is this lab?” Luckily, pretty big!

I weigh the dried plant tissue to determine how "weedy" my different treatments are.

I weigh the dried plant tissue to determine how “weedy” my different treatments are.

Aside from the writing and lab work, this month I also got to be in a research-related mini photoshoot of sorts. Remember that children’s activity book about green roofs that I wrote and published last year? Well, the Chicago Botanic Garden is going to be featuring the book in a small article published in their quarterly magazine. I got to feel like a celebrity for a few minutes while I got my picture taken for the article. Of course I’ll share the article on the blog when it comes out – maybe as soon as next month!

Smile! I had fun participating in a mini photo-shoot related to my green roof activity book.

Smile! I had fun participating in a mini photo-shoot related to my green roof activity book.

And finally, in case you’re interested in the more technical side of some of the research I’ve worked on in the past, my “Publications” page has been updated with downloadable full text versions of many of my research papers.

Happy New Year!

Research update: October/November 2015

Fall was a time of big changes out on the Chicago green roofs. From summer temperatures to snow and beautiful blooming flowers to brown, dried grass, the plants changed almost daily on the roofs. Now they’re pretty much dormant and ready to face another cold winter.

The last of the fall flowers bloom on the green roofs in early October.

The last of the fall flowers bloom on the green roofs in early October.

The last of the wildflowers and grasses bloom on the green roofs in Chicago

The last of the wildflowers and grasses bloom on the green roofs in Chicago

As in previous years, this season was also a transition for me from outdoor data collection to indoor writing and lab work. I finished collecting the last of the temperature probes and finished the “checkups” on the green roofs. I recorded the temperatures and packed the probes back into their small water-tight bags and wished them good luck until I dig them up again in the spring. I made sure that all signs and little sticks I use for marking my sites were in the right place. I recorded all final observations and closed my notebook… for now.

 

 

 

All the fruits that I collected are carefully weighed on an electronic balance in the lab

All the fruits that I collected are carefully weighed on an electronic balance in the lab

In the lab, I cleaned and weighed the fruits that I had collected from the green roof and ground-level plants in one of my experiments. I then opened the fruits and carefully counted each little seed that was contained inside. These seeds are very tiny and have to be counted under a microscope. After the seeds were counted, I rinsed them off in a weak bleach solution to kill any fungus and put them on these little agar plates. The agar is a substance with the same texture as Jello that is able to hold moisture that the seeds can use later when they start to grow. I sealed up these agar plates with the seeds and put them in a dark refrigerator where they’ll stay for at least a couple months. Later, I hope I’ll get these seeds to grow so I can take a closer look at their DNA and see if there is pollen moving between plants on the green roof and plants on the ground.

As the season changed, it was also time to work on more writing. Yes, it turns out that scientists write a lot! I am currently working on writing the results of the experiment I completed when I was in Germany 2 years ago. It has taken a long time to look at all the data I collected very carefully. After some long days in the library reading, writing, reading, and writing some more, I am beginning to explain some of the patterns that I see in my data. This is a long process and I still have more writing to do this winter but I hope that soon I’ll be able to publish these results and share them with my fellow botanists and other scientists that are also interested in the ecology of green roofs.

I spend long hours in the library reading and writing about the results of my experiments.

I spend long hours in the library reading and writing about the results of my experiments.

Research update: May 2015

It’s hard to believe that spring has already come and gone. Yep, May is over and summer is officially here. It’s been a good past month for research with a lot of chances for me to collect more data on the green roofs and spread the word about the importance of native plants in cities.

The experimental green roof trays at Loyola University are looking good!

The experimental green roof trays at Loyola University are looking good!

Early in the month, I wrote a blog post of a different kind for the main blog at the Chicago Botanic Garden, describing different ways in which botanists like me can share their research with a wide variety of people. About a week later I was also able to “walk the walk” as they say, and give a presentation to the Will County Audubon Society about how native pollinators can be supported by using native plants in urban gardens like the green roofs I study. The audience was very attentive and had some great questions – they even built their own “bee condos” which are homes for native mason bees. Later in the month, I was an audience member myself at an event hosted by the West Cook County chapter of WildOnes, an organization that promotes awareness of native plants and animals. At their annual Native Plant Conference, I was able to hear Dr. Doug Tallamy speak – he is a real champion of native plants and both his presentation and his book, Bringing Nature Home, were really inspiring!

 

The temperature probes have all been read and are now buried in the green roof soil again. A little lady bug was also interested in my data!

The temperature probes have all been read and are now buried in the green roof soil again. A little lady bug was also interested in my data!

The native plants on the green roofs are still small but looking pretty good!

The native plants on the green roofs are still small but looking pretty good!

Out on the roofs, my research plants are looking good. For the most part. Of the 5 locations where I planted prairie plants, 4 of them are going strong and the other one… well… about 90% of the plants are dead. It’s a bit disappointing but that’s science for you. Not to worry though, I still have plenty of projects to keep me busy. In May, I finished collecting all of the temperature probes from the green roofs so I now know just how cold it got on all the roofs this past winter (very cold, in case you’re wondering!). I started recording data on all the plants that survived the winter and how much they’re grown since last summer. I’ll continue to gather these data for the rest of the summer, so stay tuned.

 

To record all the temperature data, I bring a computer up to the roofs. And then I cross my fingers that it doesn't rain.

To record all the temperature data, I bring a computer up to the roofs. And then I cross my fingers that it doesn’t rain.

I collected some interesting data about the evaporation rates in the green roof trays.

I collected some interesting data about the evaporation rates in the green roof trays.

This past month, I also started a new experiment, where I’m measuring the rate of water capture and evaporation from my experimental trays. I think that the trays with native prairie plants and the ones with the non-native succulent plants will be able to capture rainwater at the same rate. It is important for all green roofs to keep rainwater on the roof so it doesn’t run into already-stressed stormwater/sewer systems in the city. It’s also important for the green roofs to be able to release this water slowly in warm weather because this evaporation helps keep buildings cool. I measure evaporation rate by weighing wet trays every few hours. This was a great way to collect data but I learned that it’s also very physically demanding! Each time, you bend down to pick up a heavy (about 25-30 pounds) tray,  bend down to put it on the scale, bend down to pick it up, and bend down again to put it back in its place. Multiply that by 40 trays and 6 rounds of measurements in 24 hours… well you do the math on that. Let’s just say that there’s no need to go to the gym on these evaporation measurement days!

I carefully took about 600 tiny seedlings out of their petri dishes and put them into small test tube. I'll extract the seedlings' DNA soon.

I carefully took about 600 tiny seedlings out of their petri dishes and put them into small test tube. I’ll extract the seedlings’ DNA soon.

To get a break from the outdoor work, I also finished the task of germinating the seeds for my paternity experiment. I was hoping that the seedlings would get a bit bigger but they were just growing in this jello-like substance and they didn’t have the nutrients they needed to grow anymore. So I took about 600 of the seedlings, put them in tiny test tubes, and put them in a very cold freezer. I’m hoping that on rainy days this summer I’ll be able to start extracting their DNA and determine if pollen is moving between green roof to produce seedlings with parents from more than one green roof. There will be a lot more work involved with this experiment in the future.

And finally, this month I was officially inducted as a Northwestern University Presidential Fellow! I am honored to be part of an incredibly amazing group of graduate students and am really looking forward to learning from them as well as sharing my research with this talented group of fellows.

Research update: December 2014

Well, December really flew by. It was a busy month with traveling, holidays, family gatherings, and, of course, botany research!

At the beginning of the month, I finished teaching a university course about the relationship between plants and people. It’s been really interesting to incorporate what I’ve been learning through my research into a class. I hope my students enjoyed it and I hope I’ll have the chance to teach it or another class like it sometime soon. Next month, I’ll be a teaching assistant for a different course about how to interpret ecological and botanical data. I’m looking forward to sharing my research skills with a new group of students!

Writing bootcamp helped me think about the story that some of my data tell. Writing about your research is a big part of the whole process.

Writing bootcamp helped me think about the story that some of my data tell. Writing about your research is a big part of the whole process.

Earlier this past month, I also started to write a publication about my research. If you read my blog posts from 2013, you know I was collecting plant and insect data from green roofs in Germany. Now it’s time to take a close look at all the data and figure out what story they tell. To help me begin to write the story, I went to a writing “bootcamp” where other graduate students and I helped each other stay motivated to write about our research for 10 days. I was able to make a good start at writing but the bootcamp also helped me realize just how much MORE work I still need to do. Collecting the data is just one part of the whole research process!

Collecting the temperature data in December - it was pretty chilly on the rooftops!

Collecting the temperature data in December – it was pretty chilly on the rooftops!

Undergraduate student Sussana helps to remove the temperature probes on a green roof.

Undergraduate student Sussana helps to remove the temperature probes on a green roof.

It was a cold month and luckily I did most of my work in a heated office or lab. But there were a couple days when an undergraduate student and I had to finish collecting temperature probe data from the green roofs. The soil in the roof trays was a little frozen, but (with the help of some strong metal spoons and a trusty hair-dryer) we were eventually able to remove all the probes, record the data, and rebury the probes, where they are now safely collecting data until the spring.

Little agar plates are prepared and ready for me to put the cleaned seeds inside. The agar plates with seeds will stay in a cold incubator for the rest of winter.

Little agar plates are prepared and ready for me to put the cleaned seeds inside. The agar plates with seeds will stay in a cold incubator for the rest of winter.

And I am happy to report that I finally finished weighing fruits, extracting the seeds, and cleaning and counting them all. Would you believe there were more than 40,000 seeds!?! I’m sure glad that the seed counting portion of my research is over for now! After I finished this part, I was able to move on to the next part of the experiment, which involved cleaning the seeds in a weak bleach solution to remove any contaminating fungi, rinsing the seeds, and putting them into small petri dishes filled with a liquid jello-like substance called agar. The agar holds water so when the seeds begin to grow, they will have a water source. All the petri dishes are now in an incubator that is set at a very cold temperature to mimic winter in Chicago. In the spring, after the seeds have experienced a simulated winter in the incubator, I’ll remove them and help them grow into little seedlings so I can get DNA from their leaves for the next part of my experiment.

I'm using a computer program to help me determine the DNA fingerprint of each plant that I used in my experiment this summer.

I’m using a computer program to help me determine the DNA fingerprint of each plant that I used in my experiment this summer.

In the meantime, I’ll keep doing the lab work I’ve started, where I am trying to get a DNA fingerprint for all the parent plants in one of my experiments. The DNA fingerprints will help me differentiate between all 50 plants that I had out on 10 green roofs this past summer. Over the next few months, I’ll keep using some fancy expensive tools to help me learn about the small differences in the plants’ DNA that makes each one unique, just like you and me.