Lilium Project Update

         The lilium project is almost wrapping up as I am approaching the end of my semester long internship. I am almost finished with processing my seed data. All the scans and x-rays of lilium ovules have been done. The only steps left are to finish counting and classifying the ovules. Counting is done to quantify the total number of ovules in the each lilium pod. Classifying is using the x-ray image to determine the number of fertilized ovules in each pod. Once I have the data for the total and full counts of each lilium pod, I will be able to obtain the seed set for each individual lilium philadelphicum. Then, I will analyze the relationship between variation in seed set and proximity in nearest neighboring plants. Jared showed me the FNN package in R which, like its name, will find the nearest neighbor between x and y coordinates. The knn.dist function is a handy tool that allows you to compare distances of a point and its nth neighbors. In order to further analyze the data, my first step is to conduct data management and organize the different variables into a data frame. This process is very useful for researchers that use R for data analysis and data visualization. Next week, I will have a data frame that includes the information necessary for the analysis and visualization of the lilium data. 

Orchids Untamed:

Here is a recap of the Orchid Show if you missed it this year! The annual orchid show at the Chicago Botanic Garden displays a wide collection of orchids. This event celebrates the beginning of spring with the unique and vibrant colors that orchids have to offer. After hearing great reviews from friends that visited the exhibition, I knew I couldn’t miss the opportunity to be mesmerized by orchids myself. Roaming through rooms filled with orchids was a magical experience. Your environment is transformed into a tropical paradise of thousands of blooming orchids. Some of them hang from the ceiling and others grow from patches of moss positioned on a man made tree. Every turn of the corner and you will see a unique combination of colors. The variation amongst different species is incredible. One of my favorites reminded me of a sunset, she had the perfect gradient of yellow, peach and pink. I was surprised to find an orchid that happen to match my hair color, which is an aqua mint green. The beauty of orchids will truly take your breath away. The orchids had my undivided attention and I enjoyed spending time to appreciate their beauty. Sometimes we all need an afternoon to look at nothing but pretty flowers 😉 If you missed the orchid show this time, be sure to come back next year for a mesmerizing experience!

Week 7: X-ray Time

This week I continued to make progress on cleaning and scanning for the lilium project (Figure 2). All the pods have been cleaned and we have established a scanning protocol for lilium pods. These protocols allow for others to replicate our methods in future projects with lilies.

Jared and I conducted a couple trials with x-raying the lilium seeds. We will experiment with adjusting the settings on the x-ray and after effects for the images. Further experimentation is necessary to generate high quality x-ray scans in order to classify the seeds. In the x-ray images, the seeds that contain fertilized embryos will appear bright white (Figure 1). We use this to classify which seeds contain fertilized embryos and which ones are empty. The contrast of appearance in the x-ray is due to the increase in density of the fertilized embryos.

Week 6: Scanning Wood Lily

This week I was able to clearly define the research question for the L. philadelphicum project. My research question is focused on investigating pollination and reproduction success in wood lily. Specifically, does seed set increase with the proximity of neighboring flowers. If lilies have closer proximity to neighboring flowers, then the proportion of fertilized seeds will increase as well. We will be able to test our hypothesis with the collected seed data and recorded GPS location of each individual plant. Additionally, I made progress on cleaning lilium seeds and started writing the scanning protocol. We found that using an ionizing bar will help prevent static which causes the seeds to be difficult to handle (See Fig 1). 

Furthermore, I was able to create a graph representing the progress of the lilium project with the help of Alex (Fig 3). Similarly, to echinacea, the lilium project will also go through the main steps of cleaning, scanning, counting and x-raying. This graph allows us to visualize the progress being made in the ACE protocol for L. philadelphicum. Stay tuned for next week while we experiment with methods in counting and x-raying lilium seeds!

Week 3: All About Wood Lily

This week, I have decided on my independent project for the rest of my internship! I will be working with Lilium philadelphicum, wood lily and investigating questions surrounding its pollination and reproduction. I felt more informed on the past research by the Echinacea Project after hearing presentations from Stuart and Jared. Jared further taught me the benefits of fire on prairie ecosystems. Prairie plants are fire dependent and thrive after burns. This is due to the natural landscape and indigenous traditions. It was very interesting to learn about the natural history of our region and how plants grew before impacts of modernization. Results from past research in the lab has shown benefits from prescribed burns on the reproduction of echinacea. This applied conservation method could potentially benefit other fire dependent prairie plants as well! I hope to observe patterns and variation of pollination success in L. philadelphicum. I am currently developing a hypothesis for this project. Later on I will analyze the data set collected by Jared over the summer. 

We have already completed inventory of the data set and started on the cleaning process of L. philadelphicum. The fruits of L. philadelphicum can be seen in the picture below. It contains many seeds, some of which are large and dark, others small and lighter in color. We hope to find interesting information through the variation of these seeds. Stay tuned for next week, as I will be working on developing the protocol for cleaning, scanning and counting these seeds.

Week 2 Flog: Introduction to the ACE protocol

In the first two weeks of being at the Echinacea Project Lab, I have become well acquainted with parts of the ACE protocol. I have done counting, cleaning, re-checking, randomizing, and scanning. In my first week, Alex showed me how to clean echinacea heads. During the cleaning process, we press the dried echinacea head into a glass pyrex tray. Usually, the achenes will fall out. However, i’ve gotten some really tough flower heads where the achenes were firmly attached to the bracts and other parts of the head. Alex taught me a good method to gently grab onto the achene with tweezers and wiggle them out of the head. After adapting that hack, things went much smoother. The contents of each head get separated into two envelopes. The achenes are stored in the achene folder and the bracts and dust are stored in the chaff folder. The achenes are ready to be scanned after a round of rechecking to ensure all achenes are accounted for!

I found it fascinating that there is so much variation in achenes between different echinacea heads. On the other hand, there are many similarities between achenes from the same flowering head. I also realized that handling achenes is a very delicate process because they have a tendency to fly away. I was very impressed with the organization system of all the achenes going through the ACE protocol. Different boxes and labels indicate which stage the achenes are currently at in a certain box.

Next week, I will be developing some questions for my own research project. I am excited to start my journey to uncover the secrets of echinacea!

Sophia Chen

Echinacea Project 2022

I am a biology major and environmental studies minor at Lake Forest College. After I graduate in Fall’23, I hope to continue working in research labs before I embark on my grad school journey. 
I have a wide range of academic interests including, experimental philosophy, neuroscience, environmental justice and conservation. I am an aspiring research scientist and hope to attend grad school for cognitive neuroscience in the future. 

I am from Shanghai, China. While growing up, I’ve lived between Shanghai and Chicago. Besides academics, I love nature adventures! This summer I am hoping to learn more about foraging and identifying fungus. I also enjoy swimming, biking and watching theater productions.