Our website is officially on-line! Stay tuned for more updates from our lab.
With sadness, we wished farewell to John Brogie, the first postdoc in the lab. John will soon be joining the Army as a biochemist in the Army Medical Corp, fulfilling a lifelong dream to serve in the armed forces. Best of luck with your new position, we will miss you!
Iowa State has officially ordered cryo-EM instrumentation! Thanks to a very generous gift from the Roy J. Carver Trust, Iowa State will soon have a Thermo Fisher Glacios equipped with K3 detector. The whole lab eagerly awaits the delivery and installation of this new state-of-the-art equipment to help further our structural studies!
We posted a preprint on Karthik’s study of Cas12a specificity (link). Karthik used a high-throughput in vitro cleavage assay to determine the native specificity of three Cas12a orthologs. Surprisingly, he found that Cas12a can cleave targets with several mismatches, although these cleavage events often result in nicks rather than double-strand breaks. Moreover, Cas12a can nick non-specific dsDNA once activated by target binding, similar to ssDNA degradation that has been previously observed. These activities could help to explain how Cas12a overcomes its apparent high specificity to provide broad immunity against phages. Special thanks to Arun Seetharam and Andrew Severin for their help with HTS data analysis! Great work!
Tulika has been awarded a Linder Fellowship to pursue her research in the lab this upcoming fall. Congratulations Tulika!
Lots of good news this week! Dipa has received notice that she will be promoted to associate professor with tenure on July 1! We also learned that Dipa has been selected for two awards: the Camille Dreyfus Teacher-Scholar award and an LAS Mid-Career research award. Thanks to the foundation, college and nominators! All of these things would not have been possible without the hard work and contributions of everyone in the lab. Thanks!
Our latest research was published in eLife! Hayun discovered that Cas4 forms a ternary complex with Cas1-Cas2. We were able to determine the architecture of this complex by negative stain EM (first structures from our lab!). Hayun also showed that Cas4 is activated as a single-stranded endonuclease within this complex, and that it cleaves precisely upstream of PAM sequences. Yukti performed important follow-up experiments during revision to show that Cas4 can only cleave when the PAM is located well into a single-stranded overhang in a duplex substrate, but that the position of the PAM does not matter once sufficient space is present. Together, their work reveals the mechanism of substrate processing and handoff within this adaptation complex. Great work!
Emma gave an excellent talk at the annual Stupka Undergraduate Research Symposium! The talk was on her researcher to produce new tools using CRISPR-Cas6 systems. Great job Emma!
Shravanti, Karthik and Dipa wrote a News & Views article on enzymatic anti-CRISPR proteins discovered by the Doudna and Huang labs! Check it out!
Shravanti passed her preliminary exam! Congrats Shravanti!
Chaoyou and Dipa wrote a review article on CRISPR-Cas systems in enterobacteria for the journal EcoSal Plus. We took a deep dive into the mechanisms of type I-E and I-F systems, which are prevalent in these types of bacteria. Check it out!
More new students have joined the lab! Tulika Sharan and Kathryn Butterfield are both freshmen in our biochemistry major. They will be joining the lab as undergraduate researchers this semester. Welcome Tulika and Kathryn!
Exciting news to start the new year: graduate student Yukti Dhingra has officially joined our lab! Yukti is a graduate student in the Biochemistry Ph.D. program. Welcome Yukti!
Our lab contributed to two chapters in an upcoming Methods in Enzymology volume on CRISPR techniques. Karthik contributed to a chapter on using molecular beacons to measure Cas endonuclease activity from our collaborators Vladimir Mekler and Konstantin Severinov (check it out here!). Phong and Michael wrote a chapter on our fluorescence-based reporter assay for measuring CRISPR interference that was originally developed by Chaoyou (check it out here!). Great job to all!
We had our final lab lunch with Hayun this afternoon. She is off to her new job as a Senior Researcher at CJ CheilJedang in South Korea. We will miss her very much!
Dipa gave a Sigma Xi lecture on CRISPR technology at the Memorial Union. The talk was open to the public, and was well attended. The talk was covered by the Iowa State Daily, check out the story!
Spydel was named as a 2019-2020 Stupka Scholar! This is the most prestigious award available to BBMB undergraduate students, recognizing excellence in research, academics and contributions/leadership in BBMB activities. Read more about the award here. Congrats Spydel!
Michael passed his ORPE! Way to go Michael!
Hayun successfully defended her Ph.D. thesis! Her defense went great, and we are excited to have our third Ph.D. from the lab. Congratulations Dr. Lee!
Courtney’s paper identifying the core RNAi machinery of three insect pests was published in PLOS One! Using transcriptome data, Courtney identified the core RNAi genes of western corn rootworm, southern green stinkbug and fall armyworm. She examined the expression of these genes over the life stages of each insect. This is a first important step in understanding the RNAi pathways in these non-model, economically important insects. Great work Courtney!
Dipa contributed a short piece on her CRISPR inspirations for a Cell Voices article. Check it out!
Hayun and Dipa attended the 23rd Annual RNA Society Meeting in Berkeley! Hayun was the first student from the lab to give a talk at an international conference. She presented her work on Cas4 to an audience of nearly 1,000 people! Great job Hayun!
Courtney's paper on the effects of knockdown of the core RNAi machinery on Western Corn Rootworm (WCR) fitness was published today in Scientific Reports! Courtney addressed a potential mechanism for the development of resistance to environmental RNAi (eRNAi), a new form of pest control against WCR. Through a huge months-long effort, Courtney monitored the effects of knocking down eight core genes from the RNAi pathway on the fitness of WCR throughout their life cycle. Her work shows that changes in the expression level of these core genes is an unlikely path to resistance against eRNAi. Awesome work Courtney!
Courtney and Justin graduated! Courtney received her Ph.D. in biochemistry and Justin received his B.S. in Biochemistry and Genetics. The lab celebrated (along with the Underbakke lab) their success at a going-away party in June. Check out pictures of Courtney's graduation and the celebration here! Courtney will continue her work at Corteva Agriscience (formerly Dupont Pioneer) and Justin will attend the Department of Biochemistry Graduate Program at the University of Iowa. We will miss them both, but hopefully see them often!
Dipa wrote a preview article on new nucleic acid detection technologies using CRISPR-Cas12 and Cas13. Check it out!
Justin won a best undergraduate poster prize at the 13th annual Stupka Undergraduate Research Symposium. Way to go Justin!
Hayun's paper on the Cas4 was published today in Molecular Cell! She showed that Cas4 is a Cas1-Cas2-dependent endonuclease that is required for efficient prespacer processing during CRISPR adaptation. We also collaborated with David Taylor's lab to solve the structure of the Cas4-Cas1 complex. This study helps to answer long-standing questions about the role of Cas4, a core Cas protein family, in CRISPR–Cas immunity. Awesome work Hayun!
Courtney successfully defended her PhD thesis! The defense went very well, and her committee was very impressed with the amount of work and the quality of her dissertation. Even more impressive, Courtney completed all that work while continuing her full-time job at DuPont Pioneer! She will now continue working at Pioneer, with plans to never work on the weekend again. Congratulations Dr. Davis-Vogel!
With the start of the new semester we welcome three new undergraduate students to our lab! Spydel Nardy is a sophomore biochemistry major, and Grace Trembath and Jacob Schmieder are freshmen biochemistry majors joining us through the Freshman Honors Program. Welcome to all three new students!
The lab's work was featured in a news item on the ISU LAS website. Check it out!
It's official, Michael Schelling has joined our lab! Michael is a graduate student in the Biochemistry Ph.D. program. Welcome Michael!
Our paper on how Cascade searches DNA for PAMs and targets was published in Cell Reports. Chaoyou collaborated with Yeon-Kyun Shin's lab to use single-molecule FRET to visualize how Cascade samples DNA. Awesome work Chaoyou!
Chaoyou officially graduated with his Ph.D. in Biochemistry at the Fall Graduate College Commencement ceremony. Check out pictures here. He left for his postdoc at Columbia University in Eric Greene's lab two days later, and started in the lab on December 18th! Best of luck to Chaoyou, we will miss him!
Shravanti successfully defended her ORPE! Congratulations Shravanti!
Lots of news today! Phong successfully defended his Outside Research Proposition Exam, the first step toward qualifying to be a full dissertator in the BBMB graduate program. Just after he finished, Chaoyou presented his exit talk at the BBMB departmental seminar. They both did an awesome job! Congrats Phong and Chaoyou!
Chaoyou successfully defended his PhD thesis! The defense went very well, and he passed with flying colors. Check out pictures from our celebration here. Congratulations Dr. Xue!
Karthik and Dipa collaborated with Rakhi Rajan's lab at University of Oklahoma to write a review article on newly discovered Class 2 effectors in Type V and VI CRISPR-Cas systems. It was published today in Molecular Cell.
John Brogie, a new postdoctoral associate, has joined our lab! John completed his PhD at the University of Iowa in the lab of David Price. We are excited to welcome him as the first postdoc in our lab!
Two of our outstanding undergrads, Natalie Whitis and Stephanie Le, graduated last weekend. We held a graduation/going-away party in their honor, joint with the Underbakke lab and their graduating seniors (check out the Photos page for some pictures). Both Natalie and Stephanie are on to exciting new adventures. Natalie will be starting graduate school in the Tetrad program at UCSF this fall. Stephanie will be doing an internship with the Sakaguchi lab in Ames Lab this summer, and then moving to Italy for an internship in the Lancrin lab at EMBL Monterotondo in August. Congrats to the graduates, we will miss them!
A new undergraduate student, Emma Vontalge, has joined the lab! Emma just completed her freshman year at ISU. She is majoring in biochemistry with a minor in Spanish. Welcome Emma!
Karthik successfully completed his preliminary exam! Congrats Karthik!
Dipa previewed a new article from the Wang, Joo and van der Oost labs in the latest issue of Molecular Cell. The new study reveals the mechanism of guide DNA generation and loading by prokaryotic Argonaute proteins during host defense.
The lab has received a new NSF grant! The NSF CAREER award will fund research to investigate the importance of Cas endonuclease specificity for CRISPR immunity, which will also inform our understanding of off-target effects for CRISPR-Cas biotechnology.
Two new graduate students, Shravanti Suresh and Phong Phan, have joined the lab! They are both students in the Biochemistry PhD program. Welcome aboard!
Our paper investigating how Cascade conformation influences CRISPR immune response was published online at Molecular Cell! Congrats to Chaoyou and Natalie who did this awesome work!
Our lab has moved to 3232 MBB. Check out pictures of the move here.
Our lab has been awarded its first R01 grant! We plan to study how broad-range sequence specificity of CRISPR immune systems allows bacteria to minimize viral escape and to rapidly adapt upon initial infection. We are very excited to get to work!
Hayun successfully completed her preliminary exam! Congratulations Hayun!
Our website is officially on-line! Stay tuned for more updates from our lab.