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Cleaning 2018 is done!

On Friday, volunteers Marty and Mike finished cleaning the last batch of heads from the 2018 common garden experiment. Huzzah! The volunteers had been working on the 2018 heads back before the pandemic started, and after a long break, 2018 is finally done. Many thanks to all the volunteers who made this possible, especially the 2021-2022 crew: Allen, Char, Elif, Laura, Luk, Marty, Mike, and Suzanne! Now, we have a lot of rechecking to do.

ACE progress update

So far this year, we have sadly not been able to have volunteers in the lab due to the continuing threat of COVID-19. However, over the last few months, we made quite a bit of progress on the remnant Echinacea harvests from 2020 and 2021. In the fall, we had help from volunteers, students from Lake Forest College, and externs from Carleton College. Thanks for your help! In January, Sophia finished cleaning the last head from 2021, which was an exciting accomplishment.

To track our progress in the lab, I created an R script to visualize the various steps of the ACE process for each batch of Echinacea. The figures for rem2020 and rem2021 are included here. Hopefully, this method will work for the cg harvests as well.

The ACE stages are listed along the x-axis, and the number of Echinacea heads are on the y-axis. The light blue shows how much we have completed, and the dark blue shows what remains to be done. The small numbers on each bar indicate the corresponding number of heads, and the width of the bars is roughly proportional to the amount of time each step takes. Along the top, the dates indicate the last day that the totals for each stage were updated.

The script to create these graphs can be found here: echinaceasandbox/oop/trackAceProgressTest.R

QC, scanning, and a new x-ray machine!

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.

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.

Volunteers and mystery bees

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.

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.

Cupcakes and cleaning

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.

Meet Tate!

Tate is interning with us in November with his classmates from Lake Forest College. We’re excited to have his help around lab!

Tate, happy to see a scan with barely any chaff! Nice work, cleaners!

Hi FLOG!

I’m Tate Rosenhagen, a junior biology major at Lake Forest College doing a four week mini internship at the Chicago Botanical Garden for a Plant Biology course. It’s my second week in the Echinacea lab, coming in once a week for four hours, and this week I’m learning how to count achenes and randomize samples! Last week I learned a lot of the background of the Echinacea project; what an achene is, how to remove the achenes from the flower head, and a little bit about Echinacea and their pollinators. One of the questions I hope to answer while I’m here is if there is a relationship between seed number and average seed weight in Echinacea. I hypothesized that in heads with fewer seeds, the average seed weight should be higher as all of the plants are in the same experimental plot and thus are subject to the same conditions and nutrients. If the plants have roughly the same amount of nutrients and conditions, theoretically plants should use the same amount of energy as their neighbors. Therefore, I hypothesized that if one plant has created fewer achenes than another plant, their achenes may have more nutrients in their endosperm thus leading to a higher weight. However, a number of factors could cause plants to use their energy in places other than their seeds, such as damage repair on the plant itself or stem growth. I hope that some of the data I find while I’m here will begin to answer this question, however, only being here once a week for four weeks limits how much data I am able to collect.

Best,
Tate Rosenhagen

Tate searches for the answer!

The big five-oh-oh-oh-oh-oh!

Today we’re celebrating a huge milestone– Allen Wagner has counted half a million achenes!

Great going, Allen! We’re looking forward to the next 500,000!

Busy time in the lab at CBG!

Since Stuart and Team Echinacea have started summer field work in Minnesota, you might guess the lab at CBG slowed down- but you would be wrong! Last week we finished cleaning another bag of Echinacea heads, and this week we’ve gone through over half of the next bag! People counting achenes and classifying x-rays have also been super productive, and some of the newer volunteers finally got their official CBG badges. So even though there’s a lot going on in Minnesota, we’re still busy back in Chicago. Stay tuned for more lab updates throughout the summer.

From right to left, Char is cleaning, Aldo and Alan are counting, Tessa is cleaning, and Art is chatting because he was actually working outside this morning!

New year, new x-rays

Hello flog!

For those of you who read all of my flog posts (I know there’s a solid number of you out there!) you’ve probably figured out by now that I love posting about numbers. So what’s today’s number?

Why, it’s 1948 of course!

Now this is the point that you might furtively look at wikipedia and say “I don’t understand what 1948 has to do with Echinacea. Everyone already knows that 1948 was a leap year starting on Thursday of the Gregorian calendar, the 1948th year of the Common Era (CE) and Anno Domini (AD) designations, the 948th year of the 2nd millennium, the 48th year of the 20th century, and the 9th year of the 1940s decade.” To which I would say that we are dealing with the number 1948, not the year.

No, 1948 is the number of seed packets of echinacea we x-rayed at the garden this week: and it’s only Wednesday! Through the combined efforts of many volunteers we are making some headway into the daunting task of figuring out which achenes have seeds in them and which do not. Look for updates soon about these number for our pollen limitation heads!

Michael

p.s., here’s a small sampler of what the xrays look like

A look at our qGen_a xrays from 2013. There’s almost 900 images total in this folder (not nearly that many are shown here)

Counting like the Achene Queen

Counting the total number of achenes provides important information regarding seed set to access the female fitness.

Before you start to count achenes you may want to get adjusted to looking at them. Under the tab “Useful Links” on the echinaceaproject.org/lab page you will find “Developing Your Echinacea Eyes” click on it to get familiar with the different types of achenes you may see. Achenes range from rays to tiny achenes so it’s important to make sure you know what to count( Figure 1).

Figure 1. Familiarize yourself with what different achenes look like

The “counters” (people who count achenes) use the scanned image of the achenes to count how many achenes come from a single head. This is done by logging on to the echinaceaproject.org/lab website to access the page to count seeds; a detailed protocol is available in lab.  All volunteers and staff will need a username and password for this website to be set up in advance. Once logged on to the website, click the link under the side Menu entitled “Count Seeds” (Figure 2). 

Figure 2. Lois (the Achene Queen) has counted 862,912 achenes and counting…

This will then lead you to another screen where you will have information on the progress of the project you are working on as well as the number of seeds you have counted. The example shows our Achene Queen Lois’ stats, she has counted well over 800,000 achenes! Start counting seeds by clicking on the green button aptly titled “Click here to start counting seeds!” (Figure 2). The next page will provide you with a set of questions to answer regarding the head from which you will count seeds. The letno (Letter/Number combination) of the head will be provided and you should open the image in a separate tab. Once you see the image is of good quality you will be shown the envelope that should have the same letno combination (Figure 3). 

Figure 3. Make sure you are counting achenes from the correct Echinacea head!

At times there is nothing in the image in question four but if the envelope in the scan you opened matches the letno the question asks about then you should mark “yes” they do match (Figure 4).

Figure 4. Full image of achenes with the envelope and LetNo in lower left corner

 

In the tab with the scanned image you will see a floating counter. When you click on an achene you will see a cyan dot appear and the number of dots, i.e. achenes, will be recorded (Figure 5). You can get rid of dots by double clicking on them and the counter will adjust to a new total.

Figure 5. Circled achenes that have been counted. Red arrow points to a cyan dot that the floating counter in upper left corner tracks.

Once you have counted all the achenes the total should be recorded in question five (Figure 6). Once you are done with that head you can submit the information and you will be asked if you want to count another head.

Figure 6. Return to the other tab and fill in the count information

Now you can start counting like the Achene Queen Lois!