9/6/24
We published a new preprint from Ginny and Michael showing that nicking by Cas9 can be sufficient to provide protection against phage! Ginny tested four Cas9 variants, including two nickases, to determine which cleavage activities are necessary to provide phage protection. It turns out that cleavage by the RuvC domain can be dispensable for protection, although cleavage by the HNH domain is required. We find that this cleavage pattern correlates with nicking that occurs in vitro under physiological conditions, in which the RuvC domain can be readily outcompeted for binding to metal ions by other cellular biomolecules like ATP. Thus, our results suggest that Cas9 may achieve anti-phage defense through nicking by the HNH domain, especially under conditions where free metal ions are limited due to binding by other biomolecules. Congrats to Ginny on her cool findings and thanks to Michael for continuing the project since Ginny moved on back in May!
9/5/24
Liz presented her “Pi-minute thesis” at the annual BSRP showcase today! Way to go Liz!
8/1/24
Jasmine, Courtney and Sharon presented posters at the Iowa State Summer Undergraduate Research Symposium! Thanks to all three for their hard work this summer!
7/18/24
Our paper on the metal-dependence of Cas12a specificity was published at NAR! We are excited that the paper was selected as a Breakthrough Article! Congrats to Ginny, Michael, and the rest of the authors!
7/1/24
Dipa was officially promoted to full professor! Thanks to everyone in the lab for all the amazing work you have done throughout the 10 years since we started!
6/17/24
Jasmine Lopez, a high school student from Boone, IA, is joining our lab for a 6-week summer internship. Welcome Jasmine!
5/11/24
Ginny and Avani graduated! Avani was the Student Marshal for the College of Liberal Arts and Sciences and got to give a speech at the LAS Convocation. Avani will be attending medical school at the Long School of Medicine - UT Health San Antonio this fall. Congrats to both of the graduates! We will miss you both!
4/30/24
Dipa won a few awards! She has been named a Suresh Faculty Fellow and was awarded the Margaret Ellen White Graduate Faculty! The second award is especially meaningful because she was nominated by several former graduate students from the lab, spearheaded by Yukti. Thanks everyone!
4/9/24
Ginny successfully defended her thesis today! Ginny will be moving on at the end of May to a Scientist position in the Shengdar Tsai lab at St. Jude’s Research. Congrats Dr. Nguyen!
4/4/24
The annual Stupka Undergraduate Research symposium took place today, and several lab members presented their work. Avani gave a talk on her work on retron msDNA degradation. It was amazing! Liz and Sharon both presented posters, and Liz won a poster prize! Way to go everyone!
2/29/24
Ginny gave her “exit seminar” during the BBMB seminar series today! She will defend her thesis in April. Congrats Ginny!
1/17/24
Two new undergraduate students, Sharon Tsimese and Courtney Schmidt, have joined the lab. Welcome!
1/1/24
A new graduate student, Akshara Raju, officially joins the lab today! Akshara is a first-year Ph.D. student in the MCDB program and will work on the metal-dependence of Cas effector specificity. Welcome Akshara!
12/15/23
Yukti officially graduated today and is off to her postdoc in NYC. Best of luck Yukti, we will miss you!
11/30/23
We posted a preprint! Ginny and Michael explored the importance of metal ions for the specificity of Cas12a cleavage. We previously observed that phages escape Cas12a by accumulating mutations in the PAM-distal region of the target, instead of in the PAM or seed. When Ginny performed cleavage assays, she found that while seed mutants are more deleterious than PAM-distal mutants a high Mg2+ concentrations, seed mutants are cleaved faster than PAM-distal mutants at low Mg2+. To test this further, Ginny and Michael performed plasmid library cleavage assays at a variety of Mg2+ concentrations. Our results reveal a striking specificity switch at low, physiologically relevant metal ion concentrations. We are very excited about this finding and its implications!
11/19/23
Yukti and Dipa wrote a Preview article on a cool paper from the Sternberg lab describing the mechanism of sequence non-specific integration by type V-K CAST systems and how to improve specificity. Check it out here!
10/30/23
Meric passed his prelim! Congrats Meric!
10/24/23
Russell passed his ORPE! Congrats Russell!
10/6/23
Yukti successfully defended her Ph.D. thesis today! Yukti has spent much of this year away from our lab doing an internship at Moderna. We have been excited to have her back to finish up her thesis. Yukti plans to move on to a postdoctoral position in the labs of Elizabeth Campbell and Seth Darst at Rockefeller University in January. Congrats Dr. Dhingra!
8/23/23
The final version of Yukti’s Cas4/1 paper is now out in JBC. Congrats!
6/5/23
We posted a preprint describing Yukti’s work on a type I-G Cas4/1 fusion protein! Yukti discovered that the protein has two separate nuclease functions, in both the Cas4 and Cas1 domains. The Cas1 nuclease activity is sequence independent, but cleaves single-stranded overhangs a fixed distance away from the end of a duplex. On the other hand, Cas4’s nuclease activity requires a PAM in a single-stranded overhang. Together, these two nuclease domains allow for prespacer selection, ordered processing, and integration without the requirement of other host factors. Check it out here!
5/12/23
Two undergrads from our lab, Aline and Dinitha, graduated! Aline will be attending graduate school at Caltech in the Chemical Engineering Ph.D. program. Dinitha will be joining our neighbors, the Stone Chen lab, as a lab technician. Congrats to both the graduates!
4/14/23
Michael and Ginny’s paper on phage escape from Cas12a was published in PLOS Biology! Congrats!
3/30/24
The annual Stupka Undergraduate Symposium took place today, and Avani won the poster prize competition! Congrats Avani!
1/27/23
Two new undergraduate students, Liz Dougherty and Megan Friederich, have joined the lab. Welcome Liz and Megan!
1/1/23
A new year brings several changes to our lab! Yukti left for a six month internship at Moderna, where she will work with the structural biology team. Dinitha left for a co-op at Corteva that will encompass his last semester as an Iowa State undergrad. Good luck to both Yukti and Dinitha! We will miss you both!
We also have a new addition to the lab! Russell Greene, a first year graduate student in the Biochemistry Ph.D. program, has joined the lab and will be taking over aspects of Yukti’s project in her absence. Welcome Russell!
12/12/22
Michael successfully defended his Ph.D. thesis! Michael has done outstanding work using phage to learn more about the specificity of Cas effectors, while also contributing to our understanding of how phages escape from CRISPR-mediated defense. We are excited to see what he does next! Congrats Michael!
10/21/22
Our paper reporting the cryo-EM structure of the Cas4-Cas1-Cas2 complex was published in Molecular Cell! Check it out here.
10/18/22
Meric passed his ORPE! Congratulations Meric!
9/16/22
It has again been a while since we updated the lab website, and many many things have again happened in the last year. Here are some of the highlights!
On May 30, we posted two preprints! The first was from Michael and Ginny, who collaborated to look at the impact of Cas12a specificity on phage escape. In this work, we examined the effects of pre-existing mismatches across the crRNA on the ability of Cas12a to provide phage defense. We found that even conservative, non-deleterious mismatches greatly decreased the length of time that Cas12a could defend against phage due to emergence of phage mutations. By sequencing the emerged phages, we found that the location of the initial mismatch had a strong effect on the locations of mutations within the phage genome, with mutations emerging outside of the PAM or seed region. Check this work out here!
The second preprint was from Yukti and Shravanti, along with Puneet Juneja. We reported the first cryo-EM structures solved at the Iowa State Cryo-EM Facility and the first cryo-EM structures of the type I-C Cas4-Cas1-Cas2 complex! The structures reveal how Cas4 recognizes PAM sequences, how Cas4 is activated as a nuclease through interactions with Cas1 and Cas2, and how the CRISPR repeat interacts with the overall complex. We also found through biochemical experiments that Cas4 has an additional role in the complex in increasing the efficiency of spacer integration. Check out the preprint here!
Shravanti successfully defended her Ph.D. thesis in June, 2022! Shravanti has moved on to a position as a Scientist at Mammoth Biosciences in South San Francisco, where she will be applying her expertise on Cas protein characterization. We are very excited to see her move into an exciting are of biotech, although we miss her!
Ginny passed her preliminary exam in November, 2021! Congrats Ginny!
Tulika and Kathryn, two amazing undergrads, both graduated in May, 2022 and have both begun graduate programs (coincidentally at two alma maters of Dipa). Tulika joined the Integrated Program in Biochemistry (IPiB) at the University of Wisconsin, Madison, while Kathryn joined the Molecular & Integrative Physiology division of the Program in Biological Sciences (PIBS) at the University of Michigan, Ann Arbor. We miss both Tulika and Kathryn a lot but are excited to see what they both do in their graduate careers and beyond!
We had several new members join the lab! Meric Ozturk joined the lab in January, 2022 as a new Ph.D. student in Biochemistry. Avani Laharia, Aline Milach Teixeira and Caroline Meis joined the lab as undergraduate researchers. We have really enjoyed all these new members!
Some news from our alum: Chaoyou’s lab at Tianjin Institute of Industrial Biotechnology is going strong and has set up their first TIRF microscope! Hayun published her first paper as a corresponding author, a review on adaptation mechanisms in Trends in Biochemical Sciences! Karthik is doing well at IDT and got to spend time hanging out with our lab at the CRISPR meeting in the summer of 2022! Phong has several semesters of teaching under his belt now, and is almost certainly now the most popular professor at the American University of Vietnam!
7/16/21
It has been a while since we updated the lab website, and many many things have happened in the last year. The COVID-19 pandemic kept us apart and away from lab for much of that time, but the lab has slowly returned to some level of normalcy. And in the meantime there have been many lab milestones and much news that was missed! Here is a summary:
We published two papers and two preview articles! Karthik’s first paper, on Cas12a specificity, was published in Journal of Biological Chemistry in April, 2020. In the paper, Karthik showed that Cas12a has several additional cleavage activities that can lead to nicking of mismatched and non-specific targets. The paper was chosen as an Editor’s Pick! Karthik also published preprint and in April, 2021 a Nucleic Acids Research paper of his Cas9 specificity paper. In this work, Karthik profiled five different Cas9 variants to compare their specificity. In 2020, Michael and Yukti also published preview articles on work from the Marraffini lab (in eLife) and the Brouns and Joo lab (in CRISPRj).
We had two successful Ph.D. thesis defenses! Karthik defended his thesis in July, 2020 on Zoom. His seminar was well attended, even by several former Sashital lab members who live in other countries! Shortly after defending, Karthik began an internship at Integrated DNA Technologies in Coralville, IA. This internship was funded through an INTERN supplement to our NSF grant. Karthik’s internship was so successful that IDT hired him on as a Research Scientist III position. Phong also defended his thesis in July, 2021. Phong has an exciting position lined up at The American University in Vietnam, where he will be an assistant professor teaching molecular biology in the new Biology program that the university is establishing. We miss Karthik a lot and will soon miss Phong as well, but we are so excited to see them in great new positions!
Yukti passed her preliminary exam in June, 2020! This was several months early, but Yukti decided to try to get the prelim done while our lab was closed due to the pandemic. Along with the preview article she wrote, this was a very successful work from home period. Well done Yukti!
Ginny passed her ORPE in November, 2020! Ginny wrote a great outside proposal on determining the mechanisms of phage defense by retrons. Congrats Ginny!
Emma and Spydel, two outstanding undergraduates, both graduated in May, 2020 and moved on to graduate programs! Emma is thriving at the Vanderbilt University Interdisciplinary Graduate Program, where she has joined the Dewar lab. Spydel joined the Department of Biochemistry at University of Iowa, where he is in the same program as another Sashital lab alum, Justin Ling. We miss both Emma and Spydel and are looking forward to following their careers!
Tulika was selected as a 2021-22 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. Tulika will follow up her win by being the co-chair of the organizing committee for the 2022 Stupka Undergraduate Research Symposium. Congrats Tulika!
The Iowa State Cryo-EM Facility opened! The Glacios cryo-TEM was installed in June-July, 2020 and the K3 detector was installed in July-October, 2020. Puneet Juneja joined as the facility manager. We are enjoying our first forays into cryo-EM!
Some news from our lab alumni: Both Chaoyou and Hayun, the first two graduate students in the lab, have begun positions as assistant professors! After finishing his very successful postdoc in Eric Greene’s lab, Chaoyou has started his lab at Tianjin Institute of Industrial Biotechnology, part of the Chinese Academy of Sciences. Hayun spent two years at CJ Cheiljedang in Seoul before moving on to an assistant professor position at Dongyang Mirae University. Congrats to both of you!
1/13/20
A new year brings new lab members. Graduate student Giang (Ginny) Nguyen and undergraduate student Dinitha Caldera have joined the lab! Ginny is a first year Ph.D. candidate in the Biochemistry program and Dinitha is a freshman Biochemistry major. Welcome!
12/14/19
We had a great year, see a recap in pictures here!
12/2/19
Phong passed his preliminary exam! Congrats Phong!
11/15/19
Michael passed his preliminary exam! Congrats Michael!
10/31/19
It was a happy Halloween this year, as Yukti passed her ORPE! Congrats Yukti!
6/30/19
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!
6/19/19
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!
6/2/19
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!
5/8/19
Tulika has been awarded a Linder Fellowship to pursue her research in the lab this upcoming fall. Congratulations Tulika!
5/3/19
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!
4/25/19
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!
4/5/19
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!
4/1/19
Shravanti, Karthik and Dipa wrote a News & Views article on enzymatic anti-CRISPR proteins discovered by the Doudna and Huang labs! Check it out!
3/5/19
Shravanti passed her preliminary exam! Congrats Shravanti!
2/6/19
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!
1/14/19
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!
1/2/19
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!
12/21/18
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!
12/5/18
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!
11/29/18
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!
11/28/18
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!
11/15/18
Michael passed his ORPE! Way to go Michael!
11/12/18
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!
9/5/18
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!
6/22/18
Dipa contributed a short piece on her CRISPR inspirations for a Cell Voices article. Check it out!
5/31/18
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!
5/18/18
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!
5/3/18
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!
4/24/18
Dipa wrote a preview article on new nucleic acid detection technologies using CRISPR-Cas12 and Cas13. Check it out!
4/5/18
Justin won a best undergraduate poster prize at the 13th annual Stupka Undergraduate Research Symposium. Way to go Justin!
3/27/18
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!
3/8/18
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!
1/8/18
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!
1/2/17
The lab's work was featured in a news item on the ISU LAS website. Check it out!
1/2/17
It's official, Michael Schelling has joined our lab! Michael is a graduate student in the Biochemistry Ph.D. program. Welcome Michael!
12/26/17
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!
12/15/17
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!
11/15/17
Shravanti successfully defended her ORPE! Congratulations Shravanti!
11/9/17
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!
10/10/17
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!
10/5/17
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.
7/10/17
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!
5/10/17
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!
5/8/17
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!
3/20/17
Karthik successfully completed his preliminary exam! Congrats Karthik!
3/16/17
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.
2/15/17
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.
12/13/16
Two new graduate students, Shravanti Suresh and Phong Phan, have joined the lab! They are both students in the Biochemistry PhD program. Welcome aboard!
10/27/16
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!
7/26/16
Our lab has moved to 3232 MBB. Check out pictures of the move here.
6/22/16
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!
4/27/16
Hayun successfully completed her preliminary exam! Congratulations Hayun!
4/7/16
Our lab was well represented at the 11th Annual Stupka Symposium held in the ISU BBMB department. Natalie gave an outstanding talk and is a 2016 Stupka Scholar! Earlier this week, she presented her work at the 2016 ASBMB meeting in San Diego. Chaoyou and Karthik presented posters on their work, and Chaoyou won the Best Graduate Student poster prize! Check out photos of their presentations here . Congratulations to all!
3/15/16
Our website is officially on-line! Stay tuned for more updates from our lab.