Today marked the third day of our Carleton externship! We started out early in the lab, cleaning echinacea heads with some admirable longstanding volunteers. Then we started rechecking the 2020 cleaned batches instead, and I felt like I had moved up in life.
Funnily enough, a couple of days ago I was timid to touch anything in the lab that I could possibly mess up, but now I just dive in and a few hours pass by like nothing. After we finished the 2020 rechecking (yay!), Wanying and Cassie started reordering the 2020 envelopes, which were assigned random labels in order to remove biases during analysis.
I, on the other hand, started rechecking the 2021 batch. I definitely realized how much I loved having the others’ help, as after today I am still left with this 2021 mountain of a box:
In addition to learning more about the research process, I enjoyed our meeting with Jared today, who prompted us to start thinking about what projects we want to pursue during the externship. Some ideas came up about working with the data at different stages, meeting with other employees at the garden, and proposing hypotheses that can be answered with the team’s available lab data.
The day ended with some great banana bread from Alex and a plan of more project group brainstorming the next day. My goals for tomorrow include both the project focus and the 2021 box. Tomorrow we also move along the process and start scanning the ordered achenes.
Overall, today gave me an appreciation for the people contributing to this project as well as excitement for how I can explore my curiosities using the research and guidance of this incredible team.
Today, the Lake Forest College students returned for their second day at the lab. After cleaning heads last week, they moved on to the next steps of the ACE process today: quality control and scanning. They worked in teams of two, so one group rechecked cleaned heads from rem2020 and rem2021 while the other group scanned the achenes that had passed the quality control step. The students will have a dataset of 40 echinacea heads from 2021, 20 burned and 20 unburned, as well as 40 heads from 2020. They wondered whether the drought this summer affected seed production in echinacea or whether controlled burns influence achene count, and they developed hypotheses to test these questions.
Alondra and Marina do quality control while Maeve and Connor scan achenes
The new x-ray machine also arrived this week! It showed up in an enormous wooden crate, but fortunately the machine itself is not that large. Today, the company representatives gave us a tutorial of how to operate the x-ray. We will need to do some trials to find the best settings and adjust our protocol to the new machine. For example, we will need smaller sheets of paper to fit in the x-ray. Based on today’s test run, it seems that the x-ray can only hold 15 bags of achenes (3 rows of 5) at a time instead of 20 bags (4 rows of 5). However, each image takes only 45 seconds, so hopefully it won’t slow down the process too much. According to the Kubtec website, this model is also good at x-raying explosives, art, and gems, so I guess that might come in handy, too.
Today, we welcomed four undergraduate students from Lake Forest College: Alondra, Connor, Maeve, and Marina. As part of their plant biology class, they will conduct a project related to fire’s effect on echinacea reproduction. At the lab, they will gain hands-on experience for three Wednesday afternoons, and their project will culminate with a poster presentation. Today, everyone learned how to clean heads from the rem 2021 harvest. Next week, they will develop their hypotheses and hopefully practice scanning and counting achenes from remnant echinacea populations.
Jared gives a crash course in echinacea reproduction
Lake Forest College students clean rem 2021 heads
Mosaic cube
This evening after dark, several of us attended the Chicago Botanic Garden’s annual lightshow, called Lightscape. At night, the garden was completely transformed by holiday music, elaborate sculptures, a laser show, and even a glowing ball of yarn. It was quite impressive!
What sort of radioactive fertilizer have they been using?
Visiting Minnesota to plant seeds last week was a welcome break from sitting at a desk all day. However, we were glad to be back in the lab this week. On Thursday, I finished the inventory of the remnant 2021 heads, so they are now ready to be cleaned by volunteers.
We have a great crew of volunteers this fall. Suzanne wins the award for the longest volunteer record; she has been helping the Echinacea Project since 1999! In contrast, Elif joined the lab in 2019 and is our newest volunteer. So far, all of the volunteers have been cleaning seed heads, an important early step in the ACE workflow. However, many of them specialize in other steps of the process such as quality control, scanning, randomization, weighing, x-raying, counting, or classifying. Once we have made a dent in the backlog of seed heads, the volunteers will be able to diversify and find the steps that they enjoy most.
Marty is an expert at the scanner and x-ray machine
Elif started in 2019 has only cleaned heads so far
Mike has pinned all the bees for the Yellow Pan Trap project
We have yet to discover Luk’s favorite job!
Suzanne specializes at inventory and randomization
Allen is a pro at counting and classifying achenes
Our other project this week was to clean out the freezer in the lab. The freezer mainly contained coolers of empty vials that were used to collect bees for the Yellow Pan Trap (YPT) project. As Mia and I sorted through the vials, we also discovered one cooler that still contained bees! Why were these bees collected? To what project do they belong? Why haven’t they been pinned like all the other bees? According to Detective Stuart, “We have a mystery to solve. First stage is to gather evidence. (Don’t disturb the scene of the crime.)” I followed Stuart’s instructions and returned the cooler to the freezer. After doing some sleuthing, I now suspect that vial GQ-9417 contains YPT specimens that were collected on 31 July 2019. The other vials, however, remain a mystery. If anyone can identify the suspects or has information about the day of the crime, 16 July 2019, please let me know.
For the seed addition experiment, we used achenes from p2 in 2016, which were selected for the batch’s particularly high seed set. The achenes were originally in 160 envelopes sorted by flowering head so that we knew which maternal plants were contributing to the experiment. The envelopes were selected mostly randomly, though some that appeared upon visual inspection to have non-viable achenes were excluded to ensure maximum viability in the achenes used for the experiment.
We combined the achenes from all 160 envelopes into one pile in order to make a homogenized mixture. Using a column blower set to 5/8″, we segregated the “rich” achenes (containing a seed) from the “thin” achenes (seedless). Achenes were considered rich if their mass was above 2 mg. We measured a sample of achenes from the final rich batch to ensure exclusion of thin achenes, finding that only about 1/30 achenes was <2 mg, and acceptable margin of error.
This collection of isolated rich achenes would became our source of seeds for the seed addition experiment. In order to divide achenes equally for use along different transects, we counted by hand achenes from the rich pile and placed them into envelopes, with each envelope containing 50 achenes. During this process, we removed achenes that appeared to be visually severely damaged to ensure that only viable achenes will be used for the experiment.
The end result of the achene selection process was 250 envelopes each containing 50 achenes, all of which were taken from a homogenized mixture of achenes whose maternal plants flowered in p2 in 2016.
Mia, Marty, Allen, and Stuart hard at work in the lab
On Monday, we welcomed back our second volunteer of the season, Marty. Marty is an expert on the scanner and x-ray, but since the new x-ray machine hasn’t arrived yet, she and Allen have been our rockstar head cleaners. So far, it has taken 22 person hours to clean 85 echinacea heads. Based on these numbers, it will take an additional 56 hours to finish cleaning the 216 remaining heads in the 2020 burn rem batch that we’re currently working on. If the volunteers continue to work at this rate, cleaning this batch would be completed by next Tuesday, October 26. In preparation for future head cleaning, we emptied out the seed dryer and refilled it with gbags from the 2021 harvest.
To celebrate several birthdays this month, Mia baked cupcakes for us! They were very chocolatey and delicious. We even made some new friends in the Plant Conservation Science Building by offering them cupcakes.
I’m still here! In Chicago, that is. Hilary, the volunteers, and I have been quietly and methodically catching up on lab work for the last month. An update on our progress:
Earlier this week, Art completed counting the last achenes from 2014! Now we have estimates of seed set for every plant harvested in 2014. He and Aldo will now count achenes from one of the inbreeding experiments, before moving on to P2, which Lois has been working on since March.
Anne has finished scanning qGen_a in 2015. These have been uploaded and are ready to be counted.
Thanks to Char, Susie, Suzanne, Shelley and Laura, we are almost done randomizing qGen_a in 2015. These guys finished randomizing the massive P2 experiment last month. I think they are randomizing so quickly I am going to have to ask some of them to switch to cleaning soon.
Speaking of cleaning, there are only 31 heads left from 2015 to clean. Wow! That is less than 1% of that year’s massive harvest of over 3200 heads. Soon, they will start the much smaller and more manageable harvest of 2016, which had only 1060 heads. Naomi, Allen and Susie have done a lot of the cleaning recently.
Leslie and Kathryn have been rechecking very efficiently and providing good, clean achene packets for scanning. They are currently rechecking qGen_b from 2015.
Art and Anne have picked up in assembling sheets for x-raying in the Fall. All of 2013 and 2014’s sheets have been assembled, so they are assembling sheets from P2 in 2015. Today Anne assembled over 10 sheets! In her words it was, “kinda meditative”.
Echinacea is only starting to flower in Minnesota, but it has been flowering here at the Botanic Garden for a few weeks now. I’ve taken some pictures of some of the pollinators I’ve seen!
Just a reminder that it’s not just bees that feed on pollen! Here is a fly I saw sitting directly on an anther . Interestingly, I didn’t see it move around the head — I wonder how much pollen it was actually transferring.
This bumblebee was going to down on this Echinacea pallida outside the Rice building! This surprised me because Stuart said he has only once ever seen any type of bumblebee pollinating angustifolia.
In other exciting news, today we had a power outage at CBG due to construction! This meant that I worked for part of the day in the dark. Anne and Shelley came in later to keep me company and we moved to a room with big windows to enjoy the ambient light. We were so inspired by this day without electricity that Shelley took me to Stuart and Gretel’s house, where I harvested some of the lettuce from their garden. I was happy for the lettuce, but sad because today was my last day of working with both Shelley and Anne. Hopefully I will see them again some day.
Me living off of that rich Highland Park soil! Thanks Stuart and Gretel!
We had a great time at our annual lab potluck on Tuesday. We celebrated all the people in the lab, including all of the undergraduate interns. Scott told us about the smoke experiment. Then Amy explained the pollinator study from 2016. Lea talked about her projects on flowering phenology. We reviewed some of our many accomplishments in the lab, including: 1) cleaning and randomizing all 1233 heads from exPt2 in 2015, 2) counting 478,069 achenes from 3078 heads, 3) scanning 1710 images, 4) assembling 198 xray sheets. This year Lois, our reigning “achene queen,” counted her 800,000th achene and Sam counted his 250,000th! This summer we have ambitious plans for the field and lab. It was a lot of fun and the food was great–an incredibly diverse spread of tasty dishes.
We took a group photo:
First row (L to R): Lois, Art, Leslie, Amy, Laura; Second row: Susie, Char, Gretel, Anne, Stuart, Allen, Mike, Ivy, Lea, Scott, Shelley. Not pictured: Aldo, Susan, Michele, Marty, Naomi, Sam, Kathryn, Lou, Suzanne, Nicolette, Sarah.
Instead of posting from Kensington, I’m posting today from the lab computer at the Plant Conservation Science Center at the Chicago Botanic Garden. This morning, I met up with Lea (who devoted flog readers will remember from the summer) and Sam, an undergraduate Biology student at Northwestern who will be working at the Garden this Fall. Sam and I were able to bond over how the bike ride from Evanston was longer than we both expected. I also got to meet Chris and several of our excellent and expert volunteers for the first time. They taught me how to dissect heads and separate the achenes from other flower-parts (the “chaff”) and gave some helpful advice from years of their own experiences. After that, Sam and Stuart brainstormed some cool projects that Sam could get involved with. I then looked at some materials for counting and classifying achenes as full, empty, or partially-full in x-ray images using an informative tutorial that Danny wrote last year. These classifications are used to estimate seed-set size, an important part of quantifying Darwinian fitness, as well as assessing the amount (or quality) of pollen these flowers are receiving.
Volunteers show Sam, Lea and me how to dissect heads and count achenes. From left, Suzanne, Bill (in back), Char, me, Art, Aldo, Sam, Lea, Susie.
We had a great turnout for our annual lab potluck yesterday. Good times were had by all as we heard updates about what the lab accomplished this past year. Here are some highlights:
This year, Bob and Aldo counted their 250,000th achenes. Anne counted her 400,000th, and Bill counted his 500,000th. Just yesterday morning, Lois, our reigning “achene queen,” counted her 700,000th!
We finished doing all the hands-on work for 2014 and have already made great progress on cleaning and randomizing heads from the 2015 harvest.
Stuart summarized progress and preliminary analyses of the qGen_a experiment, which tests for the heritability of fitness traits in Echinacea.
The lab interns, Rachael, Gordon, Danny, and I, talked about our independent projects, all of which push the frontiers of science!
We talked about plans for this summer. While Stuart, Gretel, and I head back to Minnesota, Danny and our citizen scientists will be busy in the lab cleaning last year’s (huge) harvest from Experimental Plot 2 and counting experiments from 2015. They’ll be joined by Chris, a MS student at Northwestern who will help get our (many) achenes organized for storage in the seed bank.
There were too many tasty dishes to name all of the ones I enjoyed here. However, as a sampling, there was homemade spinach dip, mashed sweet potatoes, several broccoli dishes, iced tea, and a rhubarb crisp, which we polished off.
We took a group photo:
First row (L to R): Aldo, Gretel, Lois, Shelley, Char, Stuart; Second row: Art, Amy, Susie; Third row: Danny, Sarah, Kathryn, Susan; Fourth row: Rachael, Gordon, Bill, Suzanne; Not pictured: Anne, Bob, Laura, Leslie, Marty, Sam, and interns Mackenzie, Keke, and Nina
Thanks for coming, those of you who could make it, and for a great year!
