Introducing Carson Ingold
Contributed by Carson Ingold
Hello all, my name is Carson and I am currently a second-year medical microbiology student. I joined the Lee Lab last spring and have been working in the lab ever since! I found my way into the Lee Lab via BIOL 455 – General Microbiology, specifically, the required lab component of the course. I had previously become interested in research through some work in a psychology laboratory but found myself looking for a way to mesh the goal-oriented mindset and laboratory setting I fell in love with at the psychology lab, with the interactions of the bacteria I had become fascinated with.
Early in the course, my lab TA, Tanner Richie, gave a short biography, as usual. She mentioned how her research was focused around how changes in the population densities of the human gut microbiome affect health, a topic I remembered being mentioned at Bio Bonanza, and I was most definitely intrigued. After class that day, I asked Tanner for more details on her project. At the time, she was forceps deep collecting mouse fecal samples, for a project investigating the effect of fecal microbiota transplants on two groups of cefoperozone-induced mouse models of inflammatory bowel disorders, one of which was interleukin-10 gene-deficient. I was not too keen on the idea of working with mice again. But the in vivo studies showed that the change in microbial membership in the gene-deficient group was associated with alterations in the nitrogen metabolism of the microbiome. From this finding, Tanner began moving toward modeling the human gut in vitro for a series of nitrate assays and would be culturing HeLa and Caco-2 cell lines for those models. Tanner told me I would be likely be working on the in vitro study. This caught my attention, as I had never worked with cell or bacterial culture.
By the end of my freshman year, I had transitioned from the psychology lab to The Lee Lab, working with Tanner, and cell culture was in full swing. We began the summer culturing both HeLa and Caco-2 cells. The HeLa cells grew as expected and we ran proof-of-concept nitrate assays on a co-culture of HeLa cells and Escherichia Coli. After we proved the co-culture assay would work, the next step is to complete similar assays on the Caco-2 cells, as a truer model of the human gut. Our Caco-2 cultures over the summer had issues with contamination, but after obtaining a new starting culture, we are now closer than ever to being ready for Caco-2 co-cultures.
Needless to say, I found what I was looking for in a lab!
contributed by Leah Heeren
contributed by Sophia Pogranichniy
My name is Sophia Pogranichniy and I am a second year student studying Animal Biology in hopes of becoming a veterinarian one day. Currently, I am in the Early Admission Program for KSU’s veterinary school, contingent on keeping up with classes, extracurricular activities, and animal experience hours. I joined the Lee Lab in the spring semester of my first year at K-State and over the summer I got the amazing opportunity to lead my own independent research project thanks to the Mark Chapman Scholarship. I learned so much throughout this experience and I cannot wait to continue learning new things as I examine the results of this project during the school year.
The goal of this microbiology project was to examine how a swine farm impacts the microbial environment surrounding it. My team and I went out to a swine farm every other week to collect water, soil, and swine fecal samples. We ended up going to the farm five times before the end of the summer, and I was able to collect many samples for my data analysis.
After processing all the samples, the next step was extracting microbial DNA from them. The gut microbes help with digestion, fighting infection, and play a crucial role in the environment they are in. There are microbes in the swine gut as well as in the soil and the water, and my project is looking at how many of these microbes are the same and how many are different. The extraction process takes about 4 hours for each type of sample (fecal, soil, water) and I did molecular microbial DNA extractions every day of the week that I did not go to the farm. It was a very long, tedious process but it is gratifying to see all my hard work pay off when I quantify my extractions and find high values of microbial DNA!
After describing all that I did this summer, you may be wondering- what happens next? I was able to send off the DNA exudates for 16S (bacterial) sequencing. Although I do not have the results back yet, when I do they will tell me what microbes were found in the swines’ gut and what microbes were found in the environment, and how many are similar and how many are different. This project has a very open-ended research question so I am excited about what I will find. I hope to find an association between the swine host and the environment. The significance of these findings may impact how scientists, engineers, farmers, and policy makers develop approaches to sustain food production systems while preserving important biodiversity and ecosystem health. I also collected samples in a linear direction from the swine barn towards the retention pond, so another hypothesis is that perhaps as the samples get further away from the farm the microbial environment will deviate more from what is found in the host. These are some of the research questions I am considering right now but I am excited to start the next step in this project and learn even more as I go!
contributed by Kourtney Rumback
During the summer before my sophomore year, I was taking a microbiology course and learned how the gut microbiome can impact mental health. Using this knowledge, I proposed to add a microbiome analysis to the rats in my psychology lab, the RTD lab, that was examining how high-fat diets impacted impulsive choice. To propose a project like this required much work and convincing of the graduate students and my PI. I found a research article by Dr. Alexandria Vaughn examining a similar concept, but I was confused about the analytical aspects that goes into microbiome sequencing. From here, I reached out to one of my old professors that I knew quite well, Dr. Ari Jumpponen, who guided me through the process of 16S sequencing and gave me some direction on how to proceed with the project further. At this point I was becoming discouraged due to the cost it would take my psychology lab to be able to extract the DNA independently and to send off the DNA for sequencing. This is when I learned about Dr. Sonny Lee and I reached out to him for collaboration.
After talking to Sonny, I was able to get this project approved by my psychology lab and was able to apply for an Arts & Sciences Undergraduate Research Award, and later, an OURCI award. Due to Covid, I had to postpone this project until my junior year, but this allowed me to work closer with Sonny and was offered a position in his lab. Once the project was up and rolling, I extracted the DNA from 48 rat samples I collected pre-Covid. This was a great opportunity for me to practice my lab techniques and gain more skills with new equipment. The DNA was then prepared and sent to the K-State Genomics lab.
Before I continue more, I want to share about the core project that this analysis stemmed from. In the RTD lab, we wanted to examine how high-fat vs low-fat diets effected impulsive choice. We had 48 rats split into four groups of 12. Group one received a normal chow only, group two received normal chow with Crisco, group 3 received a low-lard commercially produced chow, and group four received a high-lard commercially produced chow. Groups three and four were enriched with vitamins and minerals. We were also curious as to whether fat type can impact impulsivity, hence the Crisco and lard diets. The overall results of this core study were that the rats consuming low fat diets (groups one and three) made more self-controlled choices overall and the high-fat diets (groups two and four) were more impulsive. We also did not see a difference between the two fat types.
The fun part now, after two years of preparation, is finally here: Data! The data analysis portion of this project was by far the most overwhelming and intimidating. It required programs that I was not used to and data sets that were not compatible with Excel. Sonny and Brandi were both great about helping me through this process and making sure I knew exactly what each graph entailed. I received two graphs that were used for this analysis. The PCA clustering plot which places points on a graph to represent each subject’s microbiome composition relative to one another. Within this plot, I was able to see that there was a separation between the two fat types (Crisco vs lard). There was also some evidence of the groups that received high-fat diets being closer together which suggests that their microbiome compositions were more similar. The second graph represented the relative abundance of individual phyla in each sample. Overall, we did not see a significant difference between any of the phyla between groups. This could be due to the high variability of abundance of phyla. Another point to mention is although the relative abundance of phyla was not significant, this does not mean that the phyla have the same identity in each group. Due to this, I would like to further cultivate the remaining samples to see if there is a similarity when examining the specific phyla of interest.
Written by Kourtney Rumback
During my three years of undergrad, I have learned much about taking exams, studying, and how to manage stress. Although these are all important for college success, I was missing a foundational mindset that I finally learned a week before taking my MCAT.
For those who do not know me as well, I am Kourtney, a senior majoring in Biology & Psychology. I have been accepted to KU School of Medicine in the Scholars in Rural Health Program. With this program, I am required to meet a certain score on the MCAT and complete other requirements to ensure my position in the school. I took my MCAT on Friday, July 30th for the first time, and will receive my score in a month.
I began studying full time for the MCAT in May and ran into multiple obstacles along the way. After months of studying and content review, my score was actually going down and I was far from my needed score for medical school. I experienced self doubt and postponed my test date to later in the summer as I was originally supposed to take it in June. I actually postponed my test twice during this time.
To overcome this imposter syndrome I was experiencing, I began to reduce my studying time from 12 hours a day to about 8. I also cut back on my work responsibilities so I had more time to focus on myself and my mental health. At this time, my score started to quickly improve and provided me with hope! Although my score was improving, I still had not crossed the threshold needed to meet the minimum score requirement. This was very difficult for me as I have always received good grades and graduated top of my class in high school. Struggling with academics was not a familiar concept to me.
One week before my exam, I was still stuck on this score plateau and had considered pushing my date back again. I was frustrated with my lack of improvement and questioned where I would be using some of this information and it’s relevance to medical school. This mindset quickly changed when one of my psychology professors walked past my office in Bluemont and asked how I was doing. When I expressed my disdain for organic chemistry and the importance of amino acid structures, she changed my outlook of my education. She stated “although you may not directly need this information to be a doctor, being able to know how chemicals react and their structure may make it easier to prescribe medications and know drug interactions, which will overall make you a better doctor.”
Having no comment on this, I realized that she was right and that my mindset during my first three years of undergrad was completely wrong. I attended lectures and learned information just for exams and only retained information that I deemed important. This thinking has hindered my ability to succeed on the MCAT and I realized that if I worked harder in my past classes, and cared more about the connection to medicine, the MCAT would have been much easier for me and I wouldn’t have had to work as hard as I did.
With this newfound mentality, I came to another conclusion that was critical to my future. I realized that it is okay to fail sometimes. If I do not get the score I need, it is okay, and I can take the test again. If I have to take the test again, it will provide me with another opportunity to learn more about the information I pushed aside the past few years and will ultimately make me a more well-rounded student. This change in attitude made my actual test day much less stressful. It was less of a task to overcome and more of a challenge for me to face.
For all of the undergraduate students wondering why some classes are necessary and why we are taught this “unrelated” information, I dare you to find a connection to your desired career. I dare you to look beyond the textbook and find a way to make the information useful for you. If you are able to do this, your college experience will be much more meaningful and worthwhile.
Written by Brandi Feehan
Hey all you posh pigs and piglets! Even with social distancing, stay at home orders and travel restrictions, The Lee Lab has been keeping busy, and I’m excited to introduce myself and share an update on my work. I joined The Lee Lab in January after rotating in the fall 2019 semester to find a good fit for my genetics PhD. I’m no stranger to KSU: I’ll be a triple crown K-State wildcat after my PhD! My passion for pigs and animal health research started in my undergraduate when I interned with Merck Animal Health. During my time at the research facility, I loved working with the pigs, and the experience fueled my enthusiasm to learn and support these animals.
Although I’m new to our lab, we already have some great news: Global Food Systems awarded The Lee Lab a grant to support my swine microbiome studies! So I’ve been lucky enough to be keeping busy collecting fecal samples. I know that doesn’t sound glamorous, but the pigs are adorable, and we are going to make some great investigations to support science surrounding swine production, digestive microbiomes and nutrient utilization. Going to see the pigs is the highlight of my weeks now that we’re home-bound (but let’s be honest the pigs are fun and cute so it’d probably be the highlight anyways). My 10 piggies are very rambunctious and curious; they love distracting me by chewing on my boots or randomly taking off running. Just writing about them has me grinning from ear to ear. Soon I’ll be done with collecting samples and onto lab work, but for now I’m counting down till I get to see my pigs again.
Stay safe everyone!
Written by Abigail Kamke
This January, I was selected to attend the 2020 Undergraduate Research Day at the Capitol. I and four other Kansas State University students were chosen by the Office of Undergraduate Research & Creative Inquiry for this honor. In the couple months prior to the event, I was able to finish extracting the microbial DNA of the Colby site, Andropogon gerardii root samples. With the aid of the K-State Integrated Genomics Facility, we were able to get quick DNA sequencing results. Finally, with help from my wonderful Lee Lab team, I was able to put together a detailed research poster to present.
On March 4th, I headed to the Capitol Building in Topeka, KS. We were directed to the beautiful 2nd floor of the Capitol Rotunda for setting up our posters. Pictures were taken with my fellow KSU students, and then certificates were awarded to the student presenters from each of the Kansas Board of Regents (KBOR) public four-year universities. After a short break to view the other students’ research posters, the poster session began. I was able to speak to lobbyists, senators, and house representatives involved in our Kansas legislature. Dan Kerschen, the senator from my home district whom I had sent a personal invitation to, went out of his way to meet with me and hear about my research. It was a very rewarding experience to present my research about a vital prairie grass facing the effects of climate change to our legislature. Without this grass, we would lose a main soil erosion combatant and a major livestock food source. It was wonderful to be given a chance to speak out about the necessary research the Lee Lab is undergoing to preserve our Kansas prairies.
Abby's rehearsal talk
Written by Lauren Anderson.
The main project our lab has been focusing on especially our undergraduate students is the topic of plant-soil microbiome specifically the rhizosphere and phyllosphere microbial composition in relation to the microbiome function for climate variation across the Great Plains grassland. Our team has collected many samples across Kansas and southern Illinois. We have been extracting DNA from those samples and have sent them to be sequenced for further analysis. The goal of this research project is to understand the host-microbial interactions in relation to the functions of the plant corresponding to different climate conditions and how it may enhance its drought resistance.
Abigail Kamke, pictured above, is one of our undergraduate research students that is involved with her part focusing on the rhizobiome diversity and its impact on drought resistant in Andropogon geradii. She personally worked on the rhizosphere portion specifically the samples that were collected from Colby, Kansas. Due to her exceptional work, she was selected as one of the five undergraduate research students from Kansas State University to go to the undergraduate research day the Capital in Topeka. In Topeka, she will present them with her findings and results from her research project along with many other undergraduate students across the state of Kansas.
Plant microbiome research is going on!
Since August 2019, Shiva has been hard at work! He has since then collected all his plant samples for the first growing season - these included roots, leaves and soil samples from 4 different sites across the state of Kansas and Illinois. At the end of the season, he had collected a total of 480 roots, 480 leaves and 40 bulk soil samples. However, that is only the start :)
Now, Shiva is busy in the molecular lab extracting microbial DNA from these samples. It is has been a long semester for him as he juggles between course work, teaching as well as research, and of course play! Life as a graduate student is not easy, and it takes a lot of discipline, hard work and determination to forge ahead. Shiva definitely hits all the right notes, and we are eagerly looking forward to his success in the near future.
The Lee Lab
Welcome to The Lee Lab adventures and updates