Research update: November/December 2016

The fall sun sets over the dormant plants on a green roof. See you next spring, plants!

The fall sun sets over the dormant plants on a green roof. See you next spring, plants!

In my previous post, I started by saying that I was gearing up for a winter of lab work, data analysis, and writing. In between holiday gatherings and celebrations (GO CUBS!), my work predictions for November and December were pretty accurate.

I remove the sealed top from my tray of samples after the DNA has been copied. It may not look like a lot of liquid in there, but there are thousands of copies of DNA!

I remove the sealed top from my tray of samples after the DNA has been copied. It may not look like a lot of liquid in there, but there are thousands of copies of DNA!

I drop oil on top of my samples in the little wells before running the final step of my paternity experiment. Then I cross my fingers that everything works this time.

I drop oil on top of my samples in the little wells before running the final step of my paternity experiment. Then I cross my fingers that everything works this time.

A renewed focus on lab work was my biggest priority over the past two months. I’ve been having a difficult time collecting all the data I need for this portion of my research due to a variety of factors including bad reagents (chemicals), low DNA quantities, low genetic diversity in my samples, faulty equipment, running out of supplies, dwindling research funding, possibly some unknown errors on my part and maybe even just some bad luck. (The lab manager also suggested that gremlins might be coming into the lab at night to mess with my experiments… at this point, is anything possible? Who knows!) So I’ve been fighting the good fight and filling in the missing data a little bit at a time. Sometimes it feels like I’m putting together a 1000 piece puzzle one piece at a time. It’s very arduous and I don’t know what the finished product will look like but I’m getting there and can’t wait to see the final results! In the meantime, I’ll keep on extracting more DNA, amplifying or making copies of the DNA, conducting the paternity tests, and looking for patterns of genetic diversity in the plant populations on my green roofs. You’ll no doubt hear more about these tasks during the next update.

I use this helpful pipette to transfer multiple samples at a time as I load the next yellow plate for DNA copying. Lots of the lab procedures are repeated over and over again.

I use this helpful pipette to transfer multiple samples at a time as I load the next yellow plate for DNA copying. Lots of the lab procedures are repeated over and over again.

This is what it looks like when you wait too long to collect your soil samples from your green roof experiment and have to do it when it's really cold outside!

This is what it looks like when you wait too long to collect your soil samples from your green roof experiment and have to do it when it’s really cold outside!

When I needed a mental break from the lab work, I mostly kept busy indoors. There was one chilly day that I spent on a green roof collecting some soil samples for a later analysis in the lab. I could have collected the soil back in October when temperatures were still balmy but this task slipped my mind and I ended up getting the job done on a very windy cold November day when the wind chill was about 20 degrees F (that’s about -7 degrees C). At least it wasn’t snowing yet! Other than that, I spent a lot of time analyzing the data that I’ve been collecting from the green roofs over the past few years and starting to interpret the patterns that I’m seeing. After having some initial data interpretations, I spent two weeks in December in a dissertation boot camp. This boot camp is a quiet place for doctoral candidates like me to really focus on writing about their research. It’s a great way to get some encouragement from peers to accomplish some writing before taking a little holiday break.

Another set of 96 samples is loaded up and ready to be processed in the DNA sequencing machine. This is the step in the paternity test where I determine each sample's genetic fingerprint... if it works correctly.

Another set of 96 samples is loaded up and ready to be processed in the DNA sequencing machine. This is the step in the paternity test where I determine each sample’s genetic fingerprint… if it works correctly.

As the year came to an end, so did my mentoring with the PlantingScience project. This program matches up thousands of students with plant science mentors from all around the country. As a liaison and scientist mentor for the project, I helped high school students and their teachers learn about “The Power of Sunlight,” or how plants perform photosynthesis. As a previous high school teacher myself, it was great to get to interact with this group of students and see how the teachers were using technology to introduce students to a diverse group of scientists. Who knows, maybe some of these students are now budding plant scientists!

Dried leaves rest among the last sprigs of green on top of a green roof at the Chicago Botanic Garden. Snow is coming soon!

Dried leaves rest among the last sprigs of green on top of a green roof at the Chicago Botanic Garden. Snow is coming soon!

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: 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: 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.