Research update: May 2017

May is over and summer is officially here! In the past, this has meant that it’s time for me to get up on the green roofs and start collecting data again. But not this year.

ksiazek mikenas penstemon hirsutus green roof summer blooming pollination diversity

Penstemon hirsutus or “hairy beardtongue,” is one of the species that I am studying for my dissertation. It started blooming on a green roof by the end of May. My research found that although the genetic diversity of this population is not very high, the flowers still get visited by a lot of pollinators. Pollinator visits can help keep genetic diversity from becoming too low – this is a good sign for the Penstemon.

This past May, my research schedule was a bit different because I have been busy trying to finish analyzing my data and writing up my results. I’m in the processes of finishing my Ph.D. and wanted to defend my dissertation by the end of the month. So instead of collecting new data, I looked at what I had already gathered and worked hard on uncovering the story that the data had to tell. I’m happy to say that by the end of the month I had written a story of how green roofs could be used for conservation of native plants. I then presented the nearly 200 pages of information to my defense committee in a 30-minute oral presentation and they asked me questions about my research for about 3 hours. All in all, it was a long process, but it was also very exciting to be able to look back at all the research that I’ve done over the past 6 years and finally be able to say that I have some conclusions and recommendations. The committee decided that I passed this test, which was excellent news! I still have some revisions that I need to incorporate into my overall dissertation and then I’ll continue working on getting my research published in peer-reviewed journals. This will take some time. But I’ll have all the revisions done so I get to be called “Dr.” this year, which was my goal.

Defense Cover ksiazek mikenas green roof habitat

The first slide of my dissertation defense. Can green roofs provide habitat for native plant species? In a word, YES! (But the other thousands of words in my dissertation also say that “It’s complicated” …)

As I transition from research for my dissertation to a new career path, there is no new research or data collection. In fact, I’ll be taking some time off this summer from both the research and the blog posts. I’m sure it will be strange not visiting some of the green roofs that I’ve been going to year after year. But I’m also sure that I’ll enjoy some of the cooler temperatures on the ground when the sun is really beating down on the hot, hot rooftops. After tending to some of my sites for 4 years now, it’s time to see what they do on their own.

Happy summer to all! Go visit a green roof this season. I’ll talk to you again in September!

green roof prairie summer ksiazek mikenas chicago botanic

My green roof plots at the Chicago Botanic Garden continue to grow and are looking good to start their fifth summer season. Without monitoring or data collection this year, it will be interesting to see how they do. Good luck my little plants!

Research update: March/April 2017

ksiazek mikenas green roof prairie smoke Chicago

Prairie smoke (Geum triflorum) is one of the first plants that blooms in the spring. It was flowering on this green roof in Chicago among the short leaves of other native plants. This rooftop will look like a fully-functioning prairie in a couple months!

Welcome spring! It’s time for the plants on the green roof to wake up from their dormancy and start growing once again. It’s wonderful to see that some of the native prairie species that I planted back in 2012-2014 are still alive and doing well on the green roofs around Chicago. Though most of them are still tiny, I think they’ve been enjoying the milder temperatures and lots of rain. By mid-summer, things will look quite different!

ksiazek mikenas green roof prairie plants spring

Even though I’m not collecting data this year, my experimental prairies are still going strong on the green roofs. You can see the plants starting to emerge in the strip along the lower right corner of the photo.

allium cernuum green roof experiment mikenas ksiazek cactus

The native nodding onions (Allium cernuum) have survived another winter and are emerging in the green roof trays, along with some prickly pear cactus (Opuntia humifusa)

I’m finished collecting data on the green roofs for now and these past months I’ve mostly been analyzing my data to see what patterns emerge and writing about my results. I’ll be finishing my graduate program this year and I’ve got enough data to write about for my dissertation. It already feels a bit strange not to go back to some of the same green roof sites that I’ve been visiting year after year, but I’m sure that my post-graduation plans will involve green roofs in some way so I know I won’t be away for too long. It’s also kind of nice to just go to the green roofs and appreciate their beauty without all the strenuous data collection!

ksiazek mikenas growing up in the city book children

For part of a virtual conference, I filmed myself talking about my children’s activity book “Growing UP in the City: A Book About Green Roofs.” The video was featured during the month of April.

Other than data analysis and writing, I was also involved in a conference this spring. Not a typical conference this time, but a “virtual summit” which is a type of conference that is 100% online. It’s the first time I’ve ever been a presenter at a virtual conference and it was quite a different experience. I was invited by greenroofs.com to speak about the children’s activity book I wrote for their 2017 Green Roofs and Wall of the World 2017 Virtual Summit. Being a speaker involved writing a script, videotaping myself, and collecting video clips and photos of people using the book. Thankfully, the organizers of the conference helped produce a nice video. Now people who are registered for the summit can watch it online to learn all about how and why my coauthor and I designed this fun book. There was also a live question and answer session about the book, which is similar to the Q&A sessions at the end of regular presentations in live conferences. All in all, this virtual presentation was a neat way to talk about some of my work with people from around the world. And I didn’t even have to leave my house!

ksiazek mikenas film WTTW green roof Notebaert urban nature

Back in August, I was filmed for the video series, Urban Nature. In March 2017, the video was released. Check it out!

Speaking of videos, in March WTTW Chicago put out the video series for which I was filmed back in August. The series of videos are all about urban nature and they include a lot of really interesting stories! The one I’m in is called Rooftop Refuges and you can watch it by clicking here. It starts off in New York where researchers are looking at how birds use green roofs. My part about native plants ended up being pretty short, considering the hours of filming (and extreme sweating in over 100 degrees F heat), but I think it came out very well. Be sure to take a look – I’m sure you’ll learn something new! There is also a short article about the video series that you can read by clicking here. Enjoy!

Research update: February 2017

 

Just a quick update here for February. Although we got no snow cover (no February snow in Chicago – can you believe it? I wonder how the green roof plants will do after this unusually warm winter!) it was still a good time to get some indoor work done. This past month, that meant more writing and lab work.

 

2017-03-03-14-14-32

Which offspring do I have enough genetic data for? Color-coded charts help me figure out which samples I need to run next in the lab. 

 

My February writing mostly focused on a manuscript I’m writing about the different types of plants that survive on green roofs over long periods of time. I used some long-term plant surveys of 6 green roofs in Germany and included a plant survey I conducted on 13 green roofs in the same region when I was there back in 2013. While I was writing, I was also analyzing the collected data to see if the types of plants that arrive on green roofs right after their planted are different than those that end up staying there for a long time. I did find some differences. It turns out that weedy plants able to spread seeds and easily use resources like water and soil nutrients are common on green roofs for a few years after they are built. But later, only the species that have traits that make them tough enough to withstand the heat and drought on green roofs will remain. It took a long time to figure this out and write up the manuscript. I now have a draft. I’ll keep working on this manuscript and will hopefully be able to submit it to a journal for publication review sometime this spring.

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More little test tubes of DNA and more genetic sequencing in the lab. I’m getting more data every month but still have more to collect.

In between writing, I also got in a little bit of work in the genetics lab. I’m still trying to figure out how much genetic diversity the plants on the green roofs have. When I have some more data, I’ll figure out if this is similar to plants that have been living on the ground for a long time. I’m hypothesizing that the plants on the green roofs don’t have as much genetic diversity because there are fewer pollinators there so the plants that can breed with themselves, do. I’ve been collecting the data for this experiment for a while now. I think I’m getting closer but will still be spending more time over the next month or two working with machines in the lab that help me make copies of my plants’ DNA and then determine their genetic sequences.

Other than the writing and lab work, I did get to present some of my work at a local conference in February. The Chicagoland conference was called WildThings and brought together over 1,000 people from the area who are interested in conserving the wild plants, animals, and other critters that we share our space with. The presentation went well and the presentations that I got to see were very interesting too. I especially liked learning more about conservation efforts that are happening in the corner of the world that I call home.

Next month: more writing and lab work!

Research update: January 2017

Happy New Year and welcome to year #6 of my research blog. I think it’s going to be an interesting but different year as I transition from conducting research as a graduate student scientist to… well, a regular scientist! For one thing, I won’t have any of the typical field work during the summer that I’ve always had in the past. I’m sure I’ll still get out on the green roofs now and then but just without all the data collection. Instead, I’ll be doing a lot more data analysis to determine what all of my past data mean and I’ll be writing a lot about my conclusions. That, and applying for a new job where I can continue to do even more research in the future!

 

A new year means it's time to clean out old samples from the freezer and make way for the new ones. Say goodbye to thousands and thousands of little bits of now useless DNA.

A new year means it’s time to clean out old samples from the freezer and make way for the new ones. Say goodbye to thousands and thousands of little bits of now useless DNA.

 

In January, although the plants on the green roofs weren’t covered in snow for even a single day (in Chicago – can you believe it?), I still spent all my research time indoors. I spent most of my time writing. Specifically, I worked on manuscript revisions for an article I’m writing about the data I collected on the green roofs in Germany back in 2013. After writing this article last summer and submitting it to a journal for review, I received comments back from the scientist reviewers. I needed to make a lot of little changes and a few big ones before the journal would consider publishing it in a special issue about green roof ecology. It was a lot of work to complete all the changes and defend some of my methods to the reviewers, but I’m happy to say that all the effort was worth it and the manuscript has been accepted for publication! Now I wait for the editorial process to continue. I hope the special issue of the journal is complete and published by this spring. It seems like these things can sometimes take a very long time.

Aside from the manuscript revisions, I’ve also been writing little sections of four other manuscripts that I have yet to finish and submit. Each of these papers is a chapter of my dissertation. They are all in various stages of completeness. When I decided to become a botanist I didn’t realize just how much writing was involved. Now I have to set reminders on my watch just to remember to get up from my desk and take writing breaks every couple hours. It’s a different kind of work from the data collection but it really helps me solidify my thoughts and explain the results of my experiments. I’m looking forward to meeting my weekly writing goals and completing more manuscripts in the future.

I was one of the keynote speakers at the dinner for the Presidential Fellows at Northwestern University in January.

I was one of the keynote speakers at the dinner for the Presidential Fellows at Northwestern University in January.

In the middle of the month, I took a break from writing to prepare and give a presentation at a dinner held for the Presidential Fellows at Northwestern University. This group of scholars comes from all of the departments in the graduate school so the audience has a wide variety of backgrounds; both science and non-science. It’s a different kind of presentation to give because I needed to talk about the merits of my research but in a way that anyone could understand. It was a little nerve-wracking but it went very well and I’m glad it’s over!

It worked! I look at the height of some blue peaks on the computer screen that help me determine the genetic makeup of all my plant samples. It feels so good when all the machines work and I actually get some data.

It worked! I look at the height of some blue peaks on the computer screen that help me determine the genetic makeup of all my plant samples. It feels so good when all the machines work and I actually get some data.

And finally, January was also filled with some lab work. (No surprise there!) I’ve been having some troubles getting some of the equipment to work so in January, I re-ran a lot of my samples through the genetic sequencing machine. I never have 100% success but I was able to collect a little more data for some of my samples. Over the next couple months, I’ll keep trying to get a little bit more and a little bit more but by the end of March I think I’ll just have to make do with what I have. Hopefully next month I’ll have some good news to report on this part of my research. Fingers crossed!

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: August 2016

August is over and the summer field work is slowly coming to an end. Back-to-school for teachers and students means back-to-lab-and-writing for me.

Some of the plants in my green roof experiments are providing nectar and pollen for local bees. The bumble bees are especially loving the Allium cernuum (nodding onion).

Some of the plants in my green roof experiments are providing nectar and pollen for local bees. The bumble bees are especially loving the Allium cernuum (nodding onion).

I spent a lot of time this past month at my computer, looking at data I collected back in 2013 and writing about my results. I’ve been working on a written report or “manuscript” for a scientific journal. I finally improved things to the point where I felt pretty good about the way that everything looked and sounded so I submitted the manuscript to an urban ecology journal. Next, other scientists who have similar research interests will carefully review my work and let me know if they think I’ve missed something or performed any analyses incorrectly. When I receive their comments in about a month, I hope I will be able to make all the necessary changes and then re-submit my manuscript to be published. As soon as I submitted this first manuscript for review, I immediately started working on another manuscript looking at a different part of the data (the first manuscript is about how plant and insect diversity change on green roofs over time and the second manuscript is about how certain types of plants are better at surviving on green roofs than others). After I’ve spent more time on this second manuscript, I will submit it to a different journal and the whole review and re-writing process will be repeated. If you’re a scientist, there’s always more writing to be done.

As far as the outdoor work, I’ve finally finished the water-holding and evaporation experiment that I was running with my experimental green roof trays. I say “finally” because I had to add an extra trial due to some July rains and because this experiment is not one of my favorites to perform. It involves weighing the trays when they’re filled with soil, plants, and water, which can add up to about 40 pounds per tray. And there are 40 trays that each get measured 6 times in a 24-hour period. If you’re doing the math, that’s lifting trays 240 times. So yes, that experiment is FINALLY over and I’m pretty happy about it (so is my sore back). The next step will be to analyze the data and see what all those measurements mean. I’m excited to be able to use the results of that experiment to tell a story about which types of plants can absorb rainwater on green roofs.

It was strange to be fake-running my experiments on the green roofs as a film crew captured every move.

It was strange to be fake-running my experiments on the green roofs as a film crew captured every move.

One day this past month, I even got to “fake-run” this water-holding experiment as I was followed by a film crew. A local TV station is putting together a series on urban wildlife and asked me to participate by talking about biodiversity on green roofs and demonstrating some of my experimental techniques. It was fun to be hooked up to a microphone and followed around by a camera crew but they picked a VERY hot day for filming and it ended up being over 100 degrees (F) on the roofs! I think I’m going to look very sweaty in my first TV appearance but at least they captured the real-life work conditions that are present on green roofs. The episode will be in production for a while and I hope to put a link to the show on my blog this spring when it airs.

Every move was caught on camera as the film crew followed me on the green roofs. This is one of the few pictures where I'm not wiping away sweat in the 100+ degree heat.

Every move was caught on camera as the film crew followed me on the green roofs. This is one of the few pictures where I’m not wiping away sweat in the 100+ degree heat.

I think that really hot day with the TV crew will be the last one for a while. As the fall begins, I’ll get back to lab work, finish gathering the temperature data from all my research sites, start analyzing the data that I finished collecting this summer, and start writing more manuscripts for my dissertation. I’ll also be mentoring high school students through the PlantingScience program I participated in this summer and will begin the all-important search for a job. It should be an exciting time!

This fall, I'll be mentoring high school students through an online program. I got to learn all about the experiments they'll be doing at a hands-on summer workshop this past June.

This fall, I’ll be mentoring high school students through an online program. I got to learn all about the experiments they’ll be doing at a hands-on summer workshop this past June.

In the meantime, check out this article about how green roofs can help prevent urban flooding. Click here. Toward the end, there are even a few quotes from a familiar green roof ecologist! 😉 It’s fun to be able to be an expert on green roofs and biodiversity!

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.