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!

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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: May 2016

May is over already? Where does the time go? It seems to just fly by in the spring and there’s a lot of research to be done.

In May, I started measuring the plants from the green roof trays again. Despite a lot of rain, many of the plants were gone!

In May, I started measuring the plants from the green roof trays again. Despite a lot of rain, many of the plants were gone!

Now that my experimental plots look a little more like prairies, the temperature probes are more difficult to find.

Now that my experimental plots look a little more like prairies, the temperature probes are more difficult to find.

At the risk of sounding like a broken record, yes, there was a lot to do in the lab in May. I’m still trying to complete a paternity test of about 600 baby plants and, wouldn’t you know, things that were working just fine a few months ago have stopped working and I can’t seem to figure out why. My advisor says, “welcome to the lab,” meaning, that sometimes this is just the ways things go. One day, things work and the next they don’t. So I’ve been spending a lot of time troubleshooting, collecting little bits of data and troubleshooting again. I am making tiny baby steps of progress in the lab but had hoped to be flying through the data collection process by now so it’s a little frustrating. In any case, it’s almost time for a break in the lab because summer means lots to do on the green roofs.

This little prickly-pear cactus has some new growth. Those "baby cacti" are so cute, right?

This little prickly-pear cactus has some new growth. Those “baby cacti” are so cute, right?

Some of my native primrose plants were pollinated and seeds germinated. These new babies weren't planted by me!

Some of my native primrose plants were pollinated and seeds germinated. These new babies weren’t planted by me!

In May, I also finished collecting the temperature data from the green roofs and at the end of the month, I started measuring some of the plants again. There is some good news and bad news here. The good news is that many of the plants are still alive – for some species, this means that they’ve made it for almost 4 years now. Other plants are reproducing and there are new little seedlings popping up, so that’s exciting. The bad news is that it looks like many of the plants from my green roof trays that were doing so well last summer haven’t returned. I’m not sure if they were still dormant when I checked in on them or if they’re dead. I’ll return each month over the summer so I should know for sure in a couple weeks.

 

 

My strip of experimental prairie is slowly starting to come back. The plants are still pretty short. Let's see how this looks by the end of summer.

My strip of experimental prairie is slowly starting to come back. The plants are still pretty short. Let’s see how this looks by the end of summer.

As things started heating up on the roofs, my science communication schedule seemed to be getting hot too. I gave a presentation at the beautiful Lurie Garden in Millennium Park in Chicago. I was also the curator of a Twitter account called BioTweeps – this is where a different biologist interacts with followers and discusses their science. It was a bit overwhelming since BioTweeps has thousands of followers, but it was fun too! This past month I also continued taking a science writing class about communicating complex topics to non-scientists through newspaper and magazine articles (online versions too). I got to meet the editors of Discover Magazine and Audubon Magazine, which was a really great experience. I’m hoping that one of the articles I started writing during the course will be published and the editor of Audubon said she’s interested, so I’m keeping my fingers crossed and trying to keep my editing fingers typing. If it gets published somewhere, I’ll definitely include an update here.

Next month looks like lots more work on the green roofs (June is the best month for measuring the plants!) and a couple interesting science communication workshops. See you then!

In between spring thunderstorms, I collect my temperature probes from the green roofs and see how cold things got over the winter.

In between spring thunderstorms, I collect my temperature probes from the green roofs and see how cold things got over the winter.

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: January 2015

This is the cover of the children's activity book I just published about my green roof research.

This is the cover of the children’s activity book I just published about my green roof research.

This month’s research update is starting with something quite different! I am very proud to share that I am now the coauthor of a published book! It may not be a very long one (24 pages) but it’s on sale on Amazon.com, so I figure that’s pretty official. As part of an outreach project to share my plant research with people other than scientists, my friend and fellow botanist/educator Olyssa Starry and I wrote a children’s activity book about the benefits of green roofs in cities. The book was beautifully illustrated by Ryan Patterson, who did a fantastic job bringing our ideas to life. Now children everywhere (and grown-ups kids too) can learn about green roofs while completing activities like a word search, coloring, reading temperatures, stepping-stone game, roof design, and bug hunt, just to name a few. There is even a part at the end that guides the reader through designing and carrying out a green roof research project, so if you’re interested, you too can bring botany to action in your city. Olyssa and I have been talking about this idea for years now and it’s really exciting to have come this far. Our goal is to be able to provide books to environmental education programs wherever there are green roofs – which is pretty much all over the world! I added a new page to this blog site with more information on how to get a free digital copy if you’d like.

Winter weather means lots of lab work for botanists like me!

Winter weather means lots of lab work for botanists like me!

This plate with nearly 100 little wells is filled with liquid and then used to help me separate my parental plants according to their unique DNA.

This plate with nearly 100 little wells is filled with liquid and then used to help me separate my parental plants according to their unique DNA.

As far as my research progress goes, I’ve been spending a lot of my time in the laboratory, working on my genetic paternity experiment. I’m making sure that my plant seeds are all “hibernating” in their winter-temperature incubator, and I’ve been performing a lot of tests to try and figure out how to sort out all of my individuals according to their DNA. Unfortunately, most of the plants I used in the experiment have very similar DNA because they all came from the same plant nursery. I’ll only be able to find a unique DNA “fingerprint” or DNA sequence for each individual if I keep looking at more sections in each plant… so I’ll keep looking.

In addition to writing and lab work in January, I also started taking a class about “population genetics” – this is the study of how organisms spread their genes or DNA over time. It’s a really tough class, but it will be useful when it’s time for me to explain how pollinators move pollen (which has plants’ DNA) between the rooftop populations of my test plants. I’m also helping to teach a class about statistics, which is the fancy math that plant biologists use to describe the relationships that we see between plants and their environment. Together, the population genetics information and the statistics will help me find the trends in my data once I’ve collected them all. So as the winter continues to move on, I’m continuing to gather little pieces to help solve my plant research puzzles.

I've loaded tiny little wells in this gel with my DNA samples and a blue dye. I'll run electric current through the submerged gel to see if my experiments worked.

I’ve loaded tiny little wells in this gel with my DNA samples and a blue dye. I’ll run electric current through the submerged gel to see if my experiments worked.