We went for a nice lunch gathering at the Heirloom Cafe. Without the usual student crowd, the place is warm and cozy. Great food and company!
Left, from front to the back: Hanxi Tang (master), Eric Anderson (rotation student), Varsh Saravanakumar (RA), Chris Youngstrom (Postdoc)
Right, from front to the back: Jinye Liang (doctoral), Baylee Bruce (rotation student), Lindsey Snyder (doctoral), Emily O'Brien (RA)
Bin took the picture (hence not in it).
The GRE lab had a good summer, with several new undergraduate students joining us, including Sarai, who came to us from U of Texas at Permian Basin and is here for the Interdisciplinary Evolutionary Biology REU program. Also here is Sierra, who is a high school senior and with us as an intern. We also had a nice ice-cream social, where we welcomed our new rotation graduate students, Lucretia and Chase.
In the group picture (left to right): Bin He, Sarai Badillo, Jessica Miller, Emily O'Brien, Lindsey Snyder, Jinye Liang, Cole Belcher.
In the ice-cream social (left to right): Annika, Hanxi, Sierra, Jinye, Lindsey, Lucretia, Emily (in the front) and Chase.
Bin was invited to give a talk on our recent adhesin paper at the SMBE satellite meeting on the Evolution of Fungal Pathogens. The talk went well and attracted many interests. The conference was held in the old Quebec City, which is a great place to visit!
Congratulations to Jinye for being awarded the Graduate College's Summer Fellowship. Jinye is planning to use this award to finish up her first manuscript on the exciting acquired stress resistance project. Stay tuned!
GRE lab's first preprint is online! Read it here or a synopsis in this twitter thread. This work started as a student project for the 2019 Bioinformatics course I co-taught with Dr. Jan Fassler (who is co-corresponding author on this manuscript). In this course we ask the students to apply the tools they learned to conduct new research on a protein family from a species whose genome was recently released. In the 2019 course, the theme genome is that of C. auris. Two of the star students in that class, Rachel Smoak from the Civil and Environmental Engineering program and Lindsey Snyder from our lab bravely delved into the unknown world of fungal adhesins. Their discoveries were exciting enough that we decided to spend another year and half to develop it further. And this is our product! Thanks to this fortuitous encounter with fungal adhesins, we are now actively looking into connections between stress in the host and cell wall alterations in both C. auris and our favorite species C. glabrata.
After a busy semester is finally over, we decided to have a small get-together at Bread Garden, both to celebrate the end of the semester and the isolation imposed by the pandemic, and also to send off some of our lab members with a mixture of pride and sadness: Jia has graduated with honor and distinction from the university and will start her graduate school in MIT Biology this fall. Also graduating from the college are Emily and Diandian. Emily will stay in the lab as a research assistant (Yah!) and Diandian will also continue to work in the lab in the summer. In the meantime, our wonderful high school interns, Ananya and Peter, have both graduated from their high schools and will go off to their dream schools this fall -- Oxford in UK for Ananya and UCSD in California for Peter. We will surely miss all of you, best wishes and good luck!
In the picture (left to right): Ananya, Peter, Bin, Vivek, Lindsey, Emily, Jinye, Diandian, Jia (Erin missed the gathering).
Delayed welcome to Peter Chen, who joined us back in January of 2021 as a high school intern. He has been learning and applying Python skills to look at amino acid composition differences between orthologous TFs. Also warm welcome to Vivek Kumar Srivastava, who joined us from his home country of India as a postdoctoral researcher. Vivek has got his Ph.D. in the lab of Dr. Rupinder Kaur, whose work on C. glabrata has been inspiring for me. Vivek will be working on a few projects including the evolution of oxidative stress response between related yeast species with different pathogenic potentials.
Congratulations to Jinye for being awarded the Graduate College's Post-Comprehensive Fellowship. The competition for this fellowship is especially strong this year, with many more applications than normal. Jinye was nominated by the Integrated Biology Graduate Program housed in the Biology Department and we are proud for her winning the fellowship! (picture credit: snack bought by the awardee herself)
Congratulations to Jia for her successful graduate school application this year! Among the many top programs that she got the offer from, she has decided to accept and join the MIT Biology Graduate Program. We are so proud of you!
A postdoc position is availabe in the GRE lab. Come and join us to discover how stress response networks evolved between free-living and commensal yeasts using a combination of biochemistry, molecular and functional genomics! See here for details. Update 2020-11-14 This position is now filled.
As a response to the pandemic-forced lab shut-down, we organized a programming bootcamp over the summer, where half the lab followed the CodeHS's Python course, and the other half followed Udacity's Data Analysis with R course (thanks to the recommendation by Pleuni Pennings). We also had a new member -- Ananya, who joined us as a high school intern and has been amazing! After finishing the courses, I assigned real research problems to both groups. In the past two weeks, both teams reported their results at the lab meeting. Moreove, to make our research accessible and reproducible, both teams' results are on github. Team 1 (Erin, Jia); Team 2 (Amanda, Ananya). Proud of our students!
Excited to announce that we were awarded our first NIH grant, an R35 (Maximizing Investigator's Research Award) titled "Evolution of Stress Response Gene Regulatory Networks in a Commensal and Opportunistic Yeast Pathogen"! To be honest, my feeling is more relief than excitement, because, I can finally focus on my research now! Will be recruiting a postdoc soon.
The past four months have been surreal, with labs closed and classes moved online. However, even amidst this pandemic, we do have some exciting achievements to celebrate. Let's put them in order! First, our undergraduate researcher Jia won both the College of Liberal Arts and Sciences Kenneth J. and Sharon L. (Reisch) Erickson Scholarship and (!) the Biology Department Clifford W. Hesseltine Award for Academic Excellence. Next, both Erin and Jia again, were awarded the 2020 Summer Fellowship by the Iowa Center for Undergraduate Research, for which they are deeply buried in a computational project (which was not our original plan, but it is working really well!). Amanda put in a strong application for the 2020 academic year research fellowship by the same center, whose result will be announced later. Erin also won the Latham Science Engagement Fellowship, for which she will engage in science communication through a course and an independent project. We need more science communicators like you, Erin! Now to the graduate students side: Jinye was awarded the Biology Department summer graduate research fellowship. Meanwhile, Lindsey put in a really strong application for her renewal of the T32 grant. Although it was not selected in the end, I'm really proud of her work and I'm sure she is going to do great in the coming years! Oh, what a lab!
We are welcoming three new members joining the lab, Amanda Caraballo, Daniel Ikobar and Erin Smith.
Tom started as a senior RA in our lab after plenty of research experience from the Prahlad lab. We were lucky to have him and he has helped jump start the BioLayer Interferometry experiments. Now he is on to his dream trip -- a solo drive through Canada to Alaska -- before he starts his medical school here at UIowa. Good luck, Tom! We always welcome you come back to visit!
The GRE lab has had a great semester. Now it's time to relax and enjoy the summer (finally)! Here we are in the City Park shelter #11. In the picture are: (front) Abhi, Jinye, Jia; (back) Yann (special guest), Lindsey, Zoheb, Kyle, Tom, Bin; (top) Agnes (special guest).
Welcome Lindsey Snyder to join our lab. Lindsey is a first year Interdisciplinary Graduate Programs in Genetics student. During her undergraduate research in the University of Idaho, she has got a solid training in microbiology and molecular biology. She rotated in our lab last fall and we are thrilled to have her officially join the lab. She will work on Pho4 protein evolution, taking advantage of the additional skills in CRISPR and computational biochemistry she gained during her other two rotations. Welcome Lindsey!
Congratulations to Jia Zhao for winning two prestigeous awards from the Biology Department. The first one is the Clifford W. Hesseltine Scholarship in Biology, which recognizes one Biology or Biomedical Sciences student of sophomore or junior undertaking laboratory research and have a strong academic record (GPA > 3.5). She was also accepted into the Iowa Biosciences Academy (IBA),an NIH-funded program that supports the academic and personal success of University of Iowa students interested in pursuing a Ph.D. Well done Jia, proud of your achievement!
Everytime I read a paper or listen to a talk that includes plethora of gels, and each time I see other people play with the HPLC and columns, I thought I would never do those things -- I'm an evolutionary geneticist after all, or so I believed, until... now we are officially purifying protein from E. coli. I know it's trivial for many people, but I'm really proud of what we achieved. Kudos to the heros, Tom Cassier and Kyle Malcolm.
Welcome Tom Cassier to join our lab. Tom came to us with a solid research background in Veena Prahlad's lab from our department. He will stay with us until the end of May, during which time he will work on recombinant TF purification, BioLayer Interferometry, and will help with a number of lab maintenance tasks. After that, he will go on a solo trip and then, start his medical school at the University of Iowa.
Warm welcome to the newest members of the lab: Abhishiktha Godthi is a first year iBio graduate student and Diandian Tang is a junior UI undergrad. Check out their profiles in the Team/Join page. We are sad to say goodbye to Joe Wisniewski, who has been one of the earliest members of the lab and has helped the lab in many ways, including being the safety and MSDS tzar and working on the Pho4 target validation project. Good luck Joe, you will be an awesome doctor!
This is probably the peak size of the GRE lab, as we luckily have two rotation students joining us in addition to our summer crew. From left to right: Weilong (Jesse) Liu (undergrad assistant), Abhi Godthi (iBio rotation student), Jinye Liang (iBio graduate student), Lindsey Snyder (Genetics rotation student), Jia Zhao (sophomore), Carl Skoog (junior), Bin He, Zoheb Khan (senior), Joe Wisniewski (senior), Kyle Malcolm (senior). Thanks again to our awesome photographer, Steve Kehoe at the admin office of Biology Department!
These are the awesome students who were brave enough to join a new PI's lab. From left to right: Ian Wallace(rising sophomore from U of Minn), Jinye Liang (1st year iBio graduate student), Kyle Malcolm (rising senior of UI), Jia Zhao (rising sophomore of UI), Bin He (yup, that dude), Carl Skoog (rising junior of UI), Zoheb Khan (rising senior of UI). Joe Wisniewski, who is also a rising senior of UI, couldn't join us because he is back home in Illinois. Lastly, big thanks to our awesome photographer, Steve Kehoe at the admin office of Biology Department!
Carl (right) and Kyle (middle) from Team 1 presented their latest understanding about transcription factor cooperativity at the Summer Undergraduate Research Conference. We had a lot of fun explaining our ideas to the audience, which include both fellow undergrad researchers as well as cool faculties from our own department!
I'm excited to have six talented undergrad students and a high school intern to join me for the first summer of research. Gabi Mumm, Joe Wisniewski, Kyle Malcolm, Carl Skoog and Zoheb Khan are from U of Iowa and Ian Wallace is from U of Minnesota. Noah Bullwinkle is from the Iowa City's City High. We are going to form two teams: Team 1 is the TF protein evolution task force, while Team 2 will investigate the target genes of the TF (C. glabrata Pho4). Stay tuned for our first batch of results!
Today is my first day on the job. Excited to join a great group of faculty, students, staff!