Research update: September/October 2016

The prairie grasses are in flower on the green roofs - it must be fall!

The prairie grasses are in flower on the green roofs – it must be fall!

Fall is here once again and the plants on the green roofs are getting ready to face another tough winter. I, on the other hand, am getting ready to face a winter of lab work, data analysis, and writing. I’m happy to say that over the past couple months I’ve finished collecting all my data from my outdoor green roof experiments. After carrying out some experiments for 4 years, it was kind of bitter-sweet to see this step come to an end.

The nodding onion plants that had pollinators on them last month are now bursting with seeds. I can't wait to see if there are lots of new seedlings next year!

The nodding onion plants that had pollinators on them last month are now bursting with seeds. I can’t wait to see if there are lots of new seedlings next year!

I finished collecting all of my temperature probes in September.

I finished collecting all of my temperature probes in September.

I've collected a lot of temperature data from the green roofs over the past 2 years. Now I'm trying to make sense of the trends that I've found.

I’ve collected a lot of temperature data from the green roofs over the past 2 years. Now I’m trying to make sense of the trends that I’ve found.

 

 

 

 

 

 

 

 

 

 

In September, I collected all of the remaining temperature probes from my plots. This was a little tricky in some plots where the vegetation is now almost 5 feet tall! I compiled all the data, which was actually a big task – I’ve been recording temperature every 3 hours for over 2 years on over 60 probes.I’ve started to look at trends in these data and so far it looks like there is little difference between my different treatments in the winter but larger differences between the native prairie plants and the non-native succulent sedum plants during the summer. As you might expect, the succulent plants provide more cover and shade, so they tend to keep the soil cooler than the soil that’s exposed to the full-sun conditions. I’ll spend more time analyzing these data over the winter and will be writing my conclusions in my dissertation this spring.

Finding the temperature probes - only about the size of a dime - was a little tough in some of my plots where the vegetation was so tall. Eventually, I found them all!

Finding the temperature probes – only about the size of a dime – was a little tough in some of my plots where the vegetation was so tall. Eventually, I found them all!

I'm growing quite a collection of name tags from guest lectures and speaker events. It's always fun to talk to people about my research.

I’m growing quite a collection of name tags from guest lectures and speaker events. It’s always fun to talk to people about my research.

I was also invited to give a couple guest-lectures in October, including at an Economic Botany class at the Morton Arboretum and during a tour of the Chicago Botanic Garden by the Northwestern University Women’s Board. It’s always fun to teach people about green roofs, urban ecology, and the unique opportunities I have as a graduate researcher in a joint program between two remarkable institutions.

The prickly pear cactus is one of the only native species that survived two harsh years in the green roof trays.

The prickly pear cactus is one of the only native species that survived two harsh years in the green roof trays.

Fall has arrived on the green roofs! I'm happy that my research plots are really starting to look like prairies.

Fall has arrived on the green roofs! I’m happy that my research plots are really starting to look like prairies.

Other than finishing field work and guest lectures, I’ve mostly been organizing and analyzing data, mentoring students in an online program called Planting Science, preparing job applications, and getting lab work done (when all the equipment has been working… which seems to be a rare event). I finished extracting the DNA from all of my samples and have very slowly been making progress with my paternity study. I’m hoping that next month will be a big one for lab work success. I’ve got my fingers crossed!

 

The green roof trays are ready for another winter as the colors of fall creep in.

The green roof trays are ready for another winter as the colors of fall creep in.

Big bluestem is flowering in my green roof plots. See you next spring, prairie plants!

Big bluestem grass is flowering in my green roof plots. See you next spring, prairie plants!

Finally, I’ve been working on writing a short article about a unique plant that found its way to a green roof in London. The story should be published next month – stay tuned!

 

Research update: April 2016

Data have been recorded from the temperature probes. They've been cleaned and are waiting to be reburied once again. They'll keep recording data until next fall.

Data have been recorded from the temperature probes. They’ve been cleaned and are waiting to be reburied once again. They’ll keep recording data until next fall.

In April, I started to transition some of my work outdoors once again. Not much yet, but I’ve been to 3 of my sites so far to recover data from the temperature probes that have been buried all winter long. From the data I can see so far, I can tell you that it was a pretty cold winter on the green roofs! I’m glad I wasn’t a rooftop plant all winter long. Next month I’ll get the temperature data from the rest of my sites. Then I’ll try and figure out how to interpret over 10,000 data points representing the temperature readings taken every 3 hours for almost 2 years now. It’s a little overwhelming but I hope I’ll be able to tell an interesting story about how different green roof plants help insulate buildings.

The lab got a new fancy machine that shakes up plant tissue so fast that the test tubes just appear as a blur. It kind of looks like some alien pod to me but it does its job beautifully!

The lab got a new fancy machine that shakes up plant tissue so fast that the test tubes just appear as a blur. It kind of looks like some alien pod to me but it does its job beautifully!

 

 

So that was it for the outdoor work. Back in the lab, things have been humming along. I just finished extracting the DNA from the second round of 2015 seedlings that I germinated over the winter. I’m almost finished with the DNA copying step for my 2014 seedlings (47/50 reactions – so close!). And I’m working away on genotyping the 2014 seedlings. The genotyping will tell me which types of genes my seedlings have for nine different sections of their DNA. When I’m finished, I’ll be able to match up the seedlings’ genotypes with their mothers’ genotypes. If it’s a perfect match, then I’ll know that the seedling was made by a process called “selfing” where a plant pollinates itself and is basically both mother and father. If the genotypes are not a perfect match, then I know the pollen for the seedling came from another plant. Then the search will begin to identify which plant is the pollen donor, or father. But I’m getting ahead of myself. Hopefully, I’ll be doing all those “paternity tests” by the summer, but with the outdoor research ramping up in May, well… we’ll just have to see.

Half green, half brown, the plants in my green roof trays are slowly starting to come alive after winter.

Half green, half brown, the plants in my green roof trays are slowly starting to come alive after winter.

This past month I also started taking a course about science writing. Taught by journalism professors, the class is helping me gain some experience presenting complex ideas in ways that a non-scientist could understand. While this is something I’m already very interested in (hence, this blog!) it’s great to learn some new techniques. By the end of the course, I hope to be able to write an editorial article for a major newspaper. If it gets published, I’ll surely write about it here.

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!

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: December 2015

Protected from the cold by a thick glove, I dip my test tubes into liquid nitrogen to freeze the plant tissue.

Protected from the cold by a thick glove, I dip my test tubes into liquid nitrogen to freeze the plant tissue.

As 2015 came to a close, my winter research got quite cold! But I wasn’t outside like you might think. I was actually in the lab trying out a new protocol using liquid nitrogen. Liquid nitrogen can be used to flash freeze things extremely quickly. In my case, I used this liquid to freeze my tiny little plant seedlings before I crushed the tissue in order to extract DNA. I thought that that extreme freezing would help so that more of the cells in the plant seedlings would get shattered when the tubes were shaken a very high speeds. I think this technique is helping me to get as much DNA from my seedlings as possible. This is important because the seedlings are so small so they don’t have a lot of DNA to begin with. In December I used this technique several times to extract DNA from the offspring of the plants I was working with last summer. The next steps are to see if I can use another procedure to make many copies of the small amount of DNA that I was able to extract and then to see if I can determine where the pollen came from for each seedling. I still have a great deal of work to do for this project but winter is a good time to be inside the laboratory in Chicago.

I added small metal beads to my test tubes with the tiny seedlings to help break up the cells and extract the DNA.

I added small metal beads to my test tubes with the tiny seedlings to help break up the cells and extract the DNA.

This past month, I also did a lot of writing and continued to read work from other scientists and think about how their work relates to what I am finding from my own green roof data. In a study I conducted in Germany in 2013, I hypothesized that green roofs would have similar types of plants that grow during different stages. For example, maybe plants that were very good at spreading their seeds would arrive at green roofs shortly after they were built and then plants that were more competitive and better than others at using resources like water and nutrients would be more common later on. But what I actually found was that each green roof seems to play by its own rules with different groups coming and going at different times. So now I’m working on making figures, finding more resources and using the other similar studies to write up an official report that will be reviewed by a small group of scientists, edited and then submitted to a scientific journal for publication. I’m learning that this is actually a very long and involved process. But when it’s complete, my hope is that many scientists and other interested people from around the world will be able to learn something from my research. I’ll keep working on this writing throughout the winter.

Research update: September 2015

It’s fall once again in Chicago and you can really begin to tell on the green roofs. They’re still looking good, but most of the plants are starting to turn brown, shed their seeds and get ready for their long, cold winter up on the rooftops. It almost getting too chilly for this roof top botanist to enjoy collecting data outdoors so it’s a good thing that the work is starting to gradually move indoors.

It's fall on the green roofs. The plants aren't dead, they're just beginning to go dormant for the winter.

It’s fall on the green roofs. The plants aren’t dead, they’re just beginning to go dormant for the winter.

To start off the month, I spent a weekend in Michigan with the other Northwestern University Presidential Fellows. This group of outstanding grad students from a wide variety of departments in the graduate school is doing some amazing research! As one of the fellows, I got to share my research with the others in a relatively informal presentation. I really liked learning about what other graduate researchers are doing and I loved getting to answer some difficult questions about the motivations behind my own work. I’m looking forward to more presentations with this group in the future during my next 2 years as a fellow.

In a more formal setting, I also shared some aspect of my ecological research through a new course I’m teaching. Twice a week, 45 undergraduate students at Loyola University and I learn together about the environmental issues that impact us and the world we live in. As a former high school teacher and undergraduate instructor, this is something that I really enjoy doing! I get to teach the students a little bit about the ecological benefits of green roofs but also learn about some of the bigger picture concepts, like the importance of water conservation, right along with them. With a motivated and enthusiastic group of students, it’s looking to be a pretty good semester!

As I take a last look at my green roof plots this fall, I make a note of any new growth. This little native cactus started off with just one pad (the one on the left) and now it has two. Good luck over the winter little guy!

As I take a last look at my green roof plots this fall, I make a note of any new growth. This little native cactus started off with just one pad (the one on the left) and now it has two. Good luck over the winter little guy!

In terms of research, I started to conduct my last “checkups” on the green roofs. These checkups involve collecting data from the temperature probes that I have buried there and resetting the probes to collect data all throughout the winter. I also collect all remaining weeds from the green roof trays so I can clean, dry, and weigh them back at the lab over the winter. I fix anything that’s broken and make any final notes about the plants. After the final checkups at my 5 research sites, I won’t be back until April or May. So I cross my fingers that all the plants and probes are still there when I come back in the spring.

As the outdoor work winds down, the indoor lab work and writing start to take up more of my time. I’m now working on figuring out a new procedure for getting as much DNA as possible out of the tiny little seedlings that I was growing in the spring. In September I tried two new procedures and unfortunately neither of them really worked. So now it’s time to try procedure #3 – hopefully I’ll have some good successes to report in next month’s research update. Wish me (and the little seedlings) luck!

Small tubes full of plant tissue heat up as I try to develop new methods for getting DNA out of tiny little seedlings.

Small tubes full of plant tissue heat up as I try to develop new methods for getting DNA out of tiny little seedlings.

Research Update: November 2014

It’s the end of November, and it’s time to give thanks. This year, I’m thankful that I’m continuing to make progress on my research! It can be really slow-going at times, but it’s always nice to look back at the end of the month and know that some of the tasks have been crossed off the list.

At the Chicago Botanic Garden, I gave a presentation about the importance of pollinators.

At the Chicago Botanic Garden, I gave a presentation about the importance of pollinators.

Early in the month, I was invited to give a presentation about why pollinators are important to people (they give us a lot of our food, for one thing!) and what I’ve learned about their relationship to plants on green roofs. It was fun to get to talk to a new audience of local gardeners and share some of my findings and stories with them. I hope I inspired at least a couple to include a larger variety of local native plants in their gardens to help both plants and pollinators thrive in the future.

This month, I continued to weigh fruits and count seeds, as I discussed last month. I have hundreds of fruits and need to be very careful to count all the seeds so it’s probably going to take a while to get this job done.

 

The little tubes that each contain a small piece of leaf from one of my parent plants are lined up and ready for the extraction procedure to begin.

The little tubes that each contain a small piece of leaf from one of my parent plants are lined up and ready for the extraction procedure to begin.

Other indoor lab work that I started in November included some of the first steps to a plant paternity test that I’ll be doing. Back in June, I told you about an experiment I set up to determine if pollinators were moving wildflower pollen between green roofs. My goal is to be able to determine the “father plant” of the seeds that I’ve been removing from fruits.  To do this, I need to get the DNA from all the mother plants and the DNA from all the possible father plants. The plant I’m working with has flowers with both male and female parts so all my plants can be both moms and dads (I know, reproduction is a little complicated in the plant world sometimes!)

I place a tiny drop of liquid + DNA liquid on the  Nano-drop machine. I use this machine to see if my DNA extractions worked. They did! (Well, they did after I tried the procedure for a second time)

I place a tiny drop of liquid + DNA liquid on the Nano-drop machine. I use this machine to see if my DNA extractions worked. They did! (Well, they did after I tried the procedure for a second time)

There are a lot of steps involved to match up the mom & dad DNA with the seed’s DNA. To start, I have to get the DNA out of the parents’ leaves through a process called “extraction.” Then I have to use a special machine called a “Nano-drop” to make sure that the extraction worked. I place a tiny drop of liquid with the DNA on the Nano-drop and a press a button to run a type of laser through the liquid. If the laser hits DNA, it sends a signal to my computer and I get happy that the extraction worked! Next, I have to be able to look at certain parts of the plant DNA for tiny differences between each individual. Because each individual gets half of their DNA from their dad and the other half from their mom, I can match up these differences. THEN… OK, well there are many more steps but this is where I’m at right now so I’ll leave the next steps for future research updates!