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.

 

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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: 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: 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.