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: 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: April 2015

Welcome spring – I think it’s finally here to stay!

April was a good month and things are finally starting to look a little more exciting up on the green roofs. For a botanist, “exciting” means that the plants are back!

The experimental seeds in the incubator are getting bigger!

The experimental seeds in the incubator are getting bigger!

My little germinating seeds in the incubator are beginning to grow up a bit. But even more exciting is that after a long winter (well, a typical winter – but in Chicago this always tends to feel a bit long), I am happy to report that many of the prairie plants that I planted on the green roofs last year or the year before are coming back. A lot of the species seemed to have made it through the winter and are starting to pop up through the surface of the rocky green roof soil. Among the dried leaves from last year are little bits of green – exciting to see!

The prairie plants are starting to grow again on the green roofs!

The prairie plants are starting to grow again on the green roofs!

Blades of a grass called "little bluestem" are starting to emerge around last year's dried up leaves.

Blades of a grass called “little bluestem” are starting to emerge around last year’s dried up leaves.

 

The winter data from the temperature probes has been recorded and they're ready to record data all summer long.

The winter data from the temperature probes has been recorded and they’re ready to record data all summer long.

It’s still a bit too early in the year to start taking measurements of the plants (that task will start next month) but I was able to find all the temperature probes that I buried in the fall. I dug them up, downloaded their data onto my computer, and re-buried them so that they keep recording temperature data all year long. It was interesting to see that it got pretty cold up on the roofs over the winter. Sometimes my probes were even encased in blocks of ice and continued to record 0 degrees Celsius (that’s 32 degrees Fahrenheit, or the freezing point of water) for many days and nights in a row. These green roof plants are a lot tougher than I am – no way I would have survived all winter up on the roofs!

 

The honey bees are buzzing on the green roofs again.

The honey bees are buzzing on the green roofs again.

In addition to the plants coming back to the roofs, some of the animals are back too. Although they are not part of my research, it’s still fun for me to see honey bees buzzing around their hives, geese nesting and little killdeer laying eggs on the roofs. Sometimes the green roofs where I work are not accessible to other people and I’m collecting data by myself so it’s nice to know that I’ve got a couple green roof buddies… even if they’re all of the flying variety.

 

 

A killdeer nest on a green roof. I can't wait to see the cute little baby killdeer!

A killdeer nest on a green roof. I can’t wait to see the cute little baby killdeer!

A mother goose keeps her eggs warm on one of the green roofs where I have my experiments.

A mother goose keeps her eggs warm on one of the green roofs where I have my experiments.

Dr. Kevin Rice visits from California and talks about his plant science research.

Dr. Kevin Rice visits from California and talks about his plant science research.

As the outdoor data collection season starts to ramp up, I’ve also been doing some indoor work, especially giving and organizing presentations. I had the privilege of helping to organize a visit from Dr. Kevin Rice, a plant scientist from the University of California in Davis. Along with some smaller meetings and social events, Dr. Rice gave a presentation about his research. It was really interesting to learn from a more experienced scientist, especially hearing about how he and his research team have been saving blue oak trees from severe drought in California.

"Design your own green roof" worksheets from my new activity book, Growing UP in the City, are ready to bring to a group of 5-8 graders.

“Design your own green roof” worksheets from my new activity book, Growing UP in the City, are ready to bring to a group of 5-8 graders.

I also gave four presentations myself this month, three of them in Pittsburgh through the Phipps Conservatory and Botanical Gardens as a current Botany in Action Fellow. During my trip to Pittsburgh, I talked to about 120 students at an all-girls school, a group of interested community members, and various Phipps staff members.

 

 

I bring a variety of resources and some of my research tools to my presentations so people can get a better visual of what I discuss in my presentations.

I bring a variety of resources and some of my research tools to my presentations so people can get a better visual of what I discuss in my presentations.

Back in the Chicago area, I gave a presentation to a local group of beekeepers who were interested in learning more about native pollinators and native plants. It was a pleasure to be able to talk about my research to such a diverse group of people and I look forward to doing a lot more of this type of science communication in the future.

I had a great time talking with a group of 5th-8th graders in Pittsburgh about my life as a botanist.

I had a great time talking with a group of 5th-8th graders in Pittsburgh about my life as a botanist.

Research update: March 2015

Could it be? Has spring finally sprung in Chicago? In the beginning of March it seemed like winter might hang on forever, but as the month went on, the weather started to turn and there are now even a few little flowers in bloom around Chicago. This is an exciting time for any botanist because it means that very soon, there will be all kinds of leaves, stems, flowers and fruits for us to enjoy.

I'm continuing to work on my DNA paternity analyses. This is still going to take many more months before I have collected all the data I need.

I’m continuing to work on my DNA paternity analyses. This is still going to take many more months before I have collected all the data I need.

There were signs of life for my indoor work too. I’ve been continuing my lab work for the paternity tests that I’m doing, which is tedious but moving along. The seeds that I’ve had in the incubator all winter are starting to germinate, or wake up from their winter dormant period and grow. You can see from my picture that they’re not very big yet, but over the next couple of weeks they’ll gradually get bigger and bigger until they have enough tissue for me to extract their DNA and hopefully determine which plant was each seed’s father. This will involve a lot more time in the lab (months and months) but it’s nice to know that at least this part of my experiment is heading in the right direction.

My seeds have germinated and are starting to grow now that they're in the warmer incubator.

My seeds have germinated and are starting to grow now that they’re in the warmer incubator.

It was exciting to attend the Climate Change Conference at Loyola University

It was exciting to attend the Climate Change Conference at Loyola University

In March, my research also took me in a couple unique directions. The class I was helping to teach came to an end and I completed the course in population genetics that I was taking, so I had a little time to get away from my home campus. This allowed me to attend the Climate Change Conference that was held at the Institute for Environmental Sustainability at Loyola University. The speakers were very interesting and my favorite part was learning about how some universities are choosing not to invest their money in companies (for example oil companies) that harm the environment. As a botanist and someone who cares about plants and the environment, this “divestment” (taking money out of an investment and putting it somewhere else) seems like a good idea although it can be tricky.

In March I traveled to Guatemala to talk to tenth grade students about the environmental benefits of green roofs.

In March I traveled to Guatemala to talk to tenth grade students about the environmental benefits of green roofs.

In addition to this local conference, my research took me far away to Guatemala, where I gave a presentation to 10th grade students about the environmental benefits of plants on green roofs. As a culminating activity, all the students had to design their own green roof. I can tell you, there were some very unique designs that included potato plants, compost, sunbathing areas and even hen houses. It makes me excited that young students are so creative and are able to think outside the box when it comes to making cities greener, more environmentally-friendly places that incorporate more plants. I think there may have been some future botanists in the group!

And as the month closes, I’m now on my way to Pittsburgh for some more presentations, so be sure to come back and read my April update.

Research update: February 2015

Perhaps it’s fitting that in the month of groundhog day, I felt a little like I was a character in the movie Groundhog Day, where a single day keeps repeating over and over again. A lot of the lab work that I was working on in February involved repeating procedures that I carried out in January. Several steps of the technique I’m using to looks at the DNA of my experimental plants haven’t been perfected for my specific species yet, so I re-run treatments to try and determine the best techniques. In the botany labs we call it “troubleshooting” but it’s really just doing things over and over again, each time with a slight variation in the procedure to try and find the exact right formula for success. I have a feeling the lab work I’m conducting to find unique DNA sequences for some of my plants is going to involve a lot more rounds of this repeating and trouble shooting, so at least I’m getting more comfortable with some of the methods that were new to me at the beginning of the year.

Grasses and dried up wildflowers peek out through snow drifts on a green roof. Every season is beautiful up here on the roof.

Grasses and dried up wildflowers peek out through snow drifts on a green roof. Every season is beautiful up here on the roof.

 

The green roofs are closed for the winter - the plants get the roofs all to themselves.

The green roofs are closed for the winter – the plants get the roofs all to themselves.

As you might expect, my outdoor work is pretty much on hold for now. I’m hoping that the record cold days that Chicago experienced in February haven’t harmed the plants that I’ve been monitoring on the green roofs in various locations throughout the city. But I think they should be OK. These species are prairie plants, native to the Chicago region and they should be able to withstand the harsh cold and heat that this area sometimes experiences. I like to look at the snowdrifts that I see on some of the green roofs and know that my little plants are safely underneath the blanket of snow, just waiting for spring – like me!

 

 

My experimental seeds are still just "chilling out" in the cold incubators. In a few weeks, I'll turn up the temperature and it will feel like spring to the seeds.

My experimental seeds are still just “chilling out” in the cold incubators. In a few weeks, I’ll turn up the temperature and it will feel like spring to the seeds.

The seeds that I put in the incubator back in December are still dormant, just waiting for me to turn up the temperature and create an artificial spring time for them. They don’t have too much longer to wait – it will only be a couple more weeks before I move them on to the next part of the experiment and start growing them up into little seedlings.

 

As I look into March, I can feel that spring is right around the corner and the busy data collection time is about to get even busier. There is a sense of excitement as the days start to get longer and the temperatures start to get warmer. The three main research projects that make up my dissertation are starting to come into focus. I am also excited looking forward, as this past month I was awarded a Northwestern University Presidential Fellowship, which will allow me to interact with other researchers at my university and at the same time focus on my research without the additional time commitment of performing departmental duties. I am thrilled to represent the botanists of world in this amazing group of scholars and look forward to learning many things from them over the next 2 years.

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.