June 2023: Lennice’s review on evolution of CARD8 and NLRP1 tripwires is now published in Current Opinion in Immunology! This is a fast moving field, and Lennice nicely summarizes what we know, and all of the interesting potential directions this might go. Congrats Lennice!
June 2023: Brian Tsu’s CARD8 paper is now published in PLoS Biology! We describe another innate immune ‘tripwire’ for viral proteases (as in Tsu et al., 2021), this time with the inflammasome sensor protein CARD8. We found CARD8 has evolved to sense protease activity from coronaviruses (CoVs), and results in inflammasome activation and cell death upon infection with pandemic (SARS-CoV-2) and seasonal (hCoV-229E) viruses. CARD8, not surprisingly, is fast evolving and we found that the bat CARD8 inflammasome is inhibited rather than activated by CoV proteases. Even wilder, we found a SNP in humans that switches the specificity of CARD8 from sensing CoVs to sensing enterovirus (e.g. rhinovirus) infection. Huge thanks to many other labs involved, especially (former baymate) Patrick Mitchell’s lab at UW. And huge congratulations to first author Brian Tsu! Original bioRxiv post from October 2022 is here.
May 2023: Sofia Delgado-Rodriguez’s macrodomain evolution paper is now published in Pathogens for their special edition on ADP-ribosylation in host-pathogen interactions! For a while now, we’ve been thinking about macrodomains, the enzymatic domain that can remove ADP-ribosylation from proteins, since they are found in rapidly evolving PARP proteins and in the non-structural proteins of alphaviruses and coronaviruses. Interestingly, many macrodomains can’t actually catalyze the removal of ADP-ribose. So we decided to see which PARP macrodomains and viral macrodomains are enzymatically active. Surprisingly, we found within mammals and within alphaviruses that this catalytic activity has been lost several independent times. Very strange, but also further evidence for the host-virus battle over ADP-ribosylation! Congrats to Sofia and Andy for getting this out there!
April 2023: Chinmay Kalluraya’s IRBP evolution paper is now published in PNAS! We found that a key protein involved in the vertebrate eye originated as a horizontal gene transfer (HGT) event from bacteria. Another striking example of how microbial genes have shaped our evolution. Congratulations to first author Chinmay Kalluraya, who discovered this and several other interesting cases of bacteria->metazoan HGT still to be published. This has also garnered some nice press since evolution of the eye has been such a longstanding mystery (even to Charles Darwin), including a nice write-up at Science by Elizabeth Pennisi here.
March 2023: Isabel Mejia joins the lab as a new PhD student! Welcome to the lab Isabel!
February 2023: Two papers are published with our contributions. The first is a Journal of Virology paper on IFIT-mediated antiviral activity against a methyltransferase-mutant SARS-CoV-2 from Vineet Menachery’s lab. Paper is here. The second is a many-PI review/comment on the importance of continuing to fund and support virology research. This was published in Journal of Virology, mBio, and mSphere. J. Virology version is here.
January 2023: Andy Ryan graduates! He’s the third PhD student to graduate from the Daugherty lab and led our efforts to study ADP-ribosylation in host-virus conflicts. As one of the first grad students to join the lab, he also set up most of the viral systems we have going in the lab, and established so many other protocols we still use. Congratulations Andy!
November 2022: New paper now published in Current Biology! This paper was a collaboration with Dengke Ma’s lab at UCSF. Our second foray into nematode evolution (I definitely know how to spell Caenorhabditis now!), this time describing the horizontal gene transfer of a gene from green algae into the nematode lineage that gave rise to a genetic circuit that allows nematodes to detoxify cyanide-producing compounds. Original bioRxiv post from July 2022 is here.
October 2022: Alex Stevens and Chris Beierschmitt’s NINL paper is now published in eLife! This paper describes our evolution-guided discovery of a novel antiviral role for a cytoplasmic transport protein, ninein-like (NINL), while at the same time discovering how viruses are antagonizing NINL! This has been a fantastic collaboration with Sam Reck-Peterson’s lab at UCSD. Lots of amazing work delving into some unknown host-virus biology and innate immunology by members past and present of the Daugherty and Reck-Peterson labs. Special congratulations to co-first authors Chris Beierschmitt (Daugherty lab) and Alex Stevens (Reck-Peterson lab)! Original bioRxiv post from July 2022 is here.
August 2022: Chris Beierschmitt graduates! He’s the second PhD student to graduate from the Daugherty lab and led our charge into viral conflicts with cytoplasmic transport with Sam Reck-Peterson’s lab (see NINL paper in November 2022). Congratulations Chris!
July 2022: Lennice does it again! She is awarded an HHMI Gilliam Fellowship for all of her fantastic outreach/DEI efforts as well as her fantastic science! Congrats Lennice!
July 2022: Matt gets tenure. Looks like we’ll be here a while longer!
June 2022: Congrats to recently graduated undergraduates Miles Corley and Katelyn Nguyen and to Rimjhim Agarwal for starting a PhD program! Miles is off to University of Washington to start his PhD, Bindhu will continue in the lab as a master’s degree student, and Rimjhim is starting her PhD in the UCSD Biomedical Sciences program. Congrats to you all!
March 2022: Lennice Castro is awarded a Ford Foundation Predoctoral Fellowship! Such a huge honor! Congrats Lennice!
March 2022: Two new undergrads join the lab. Welcome to Rose Cascio and Charlie Rezanka!
March 2022: Shivani Khosla joins the lab as a new PhD student! Shivani adds to our ranks of UC Berkeley grads (we have a whole bay full now) where she did undergrad research in Britt Glaunsinger’s lab. Shivani comes to us with a Curci Foundation Predoctoral Fellowship. Congrats and welcome Shivani!
November 2021: Our review on evolutionary arms races between viral proteases and host proteins (“Running with scissors”) is published! This was a huge effort by lead authors Brian Tsu and Liz Fay and a great group of undergrads who took the pandemic shutdown as a chance to do a deep dive on viral protease literature. Congrats to all authors! Article is here.
August 2021: Brian Tsu graduates! He’s the first PhD student to graduate from the Daugherty lab and has had an amazing graduate career here. Congratulations Brian!
August 2021: Congrats to recently graduated undergraduates Bindhu Hosuru! Bindhu will continue in the lab as a master’s degree student.
June 2021: Three new undergraduates join the lab now that things are somewhat returning to normal. Welcome to Nidhi Pareddy, Lance Freiman, and Kolya Isterabadi!
May 2021: Lennice Castro joins the lab as a PhD student and is also awarded a position on the PiBS T32 training grant. Welcome and congratulations Lennice!
April 2021: Paper with Eric Bennett’s lab describing the role that ribosome quality control plays in vaccinia virus replication is published in J. Cell Science! This has been a great collaboration (hopefully the first of many) with the Bennett lab to understand how viruses manipulate and hijack protein translation control mechanisms. Congrats Andy! Article is here.
March 2021: Dustin Glasner joins the lab as a postdoc. Dustin did his PhD in Eva Harris’s lab at UC Berkeley and then a short computational postdoc in Charles Chui’s lab at UCSF. Welcome Dustin!
January 2021: Our paper on viral proteases cleaving human NLRP1 and activating the inflammasome (previously posted 10/2020 on bioRxiv) is now published in eLife! It has all sorts of cool aspects: rapid evolution, mimicry, viral proteases, effector-triggered immunity, and more! Congrats to Brian, Chris, Andy and our UC Berkeley collaborators, especially for getting this out in COVID times! Article is here.
October 2020: Our paper showing the first example of a viral-encoded activator of the NLRP1 inflammasome is posted on bioRxiv! It has all sorts of cool aspects: rapid evolution, mimicry, viral proteases, effector-triggered immunity, and more! Congrats to Brian, Chris, Andy and our UC Berkeley collaborators, especially for getting this out in COVID times! Article is here.
September 2020: Paper with Nan Hao’s lab (UCSD) describing a feedback loop that controls desensitization to type I interferon is published in eLife! This was a fun collaboration with the Hao and Zhang labs at UCSD, including nice virology by Andy Ryan. Congrats Andy! Article is here.
September 2020: Congratulations to Brian Tsu and Chris Beierschmitt for receiving two of this year’s prestigious Goeddel Fellowships! Brian received the Goeddel Chancellor’s Fellowship and Chris received the Goeddel Endowed Fellowship out of the six total fellowships awarded to PhD students this year. Congrats!
June 2020: Liz Fay joins the lab as a postdoc. Liz comes to us from Ryan Langlois’s lab at UMN (https://www.langloislab.umn.edu/), where she did really great work on the host response to flu infection and viral evolution during intra- and inter-species transmission. Welcome Liz!
March-May 2020: These are strange times. The lab and university has mostly shut down due to COVID-19. Huge kudos to Andy Ryan, Brian Tsu and Chris Beierschmitt for quickly pivoting some coronavirus work we were doing to getting some SARS-CoV-2 work off the ground. Also, check out some UCTV videos that Matt was involved in with several other UCSD faculty describing how evolution shapes hosts and viruses like SARS-CoV-2 here and here.
February 2020: Chinmay does it again! He is awarded the Selma and Robert Silagi Award for Undergraduate Excellence, one of the top prizes for undergrads at UCSD. This caps an amazing undergrad career for Chinmay! Congrats!
January 2020: Bindhu Hosuru and Viviana Dominguez join the lab as undergrad researchers. Welcome to you both!
December 2019: Paper with Amy Pasquinelli’s lab (UCSD) describing how transposable elements have ‘re-wired’ the heat shock response in Caenorhabditis species is published in eLife! Great contribution by Brian Tsu to this very nice story. Article is here.
November 2019: Our collaborative paper with Ram Savan’s lab (University of Washington) on the different functions of PARP13 isoforms is out in Nature Immunology! This was a really nice synergy between our (i.e. Andy Ryan’s) work on the antiviral functions of the long isoform of PARP13 and the Savan lab’s discovery that the short isoform of PARP13 negatively regulates the interferon response. Explains a lot of prior data in the literature and may be an interesting strategy to avoid being antagonized by viruses. Article is here. Also, a nice write-up as an “Editor’s Choice” in Science Signaling here.
August 2019: Matt’s review with SaraH Zanders (Stowers Institute) on the role that gene conversion plays in genetic conflicts is out. This is an idea that Matt and SaraH talked about when they were postdocs together where Matt kept running into gene conversion in immunity genes and SaraH kept running into it with meiotic drive genes. Article is here.
July 2019: The lab gets its first NIH grant from NIGMS!
May 2019: Chris is awarded a National Science Foundation Graduate Research Fellowship. Katelyn Nguyen, Miles Corley, and Jaxon Wagner start as undergrads in the lab. Welcome, undergrads and congrats, Chris!
March 2019: Chinmay is awarded a Triton Research and Experiential Learning Scholarship and a Halıcıoğlu Data Science Institute Undergraduate Scholarship for his work on HGT. Congrats Chinmay!
Fall 2018: Bryant Cao, Xaver Audhya and Priscilla Pan start as undergrads in the lab. Welcome!
June 2018: Matt is named a Pew Biomedical Scholar. Press release is here.
June 2018: Congrats to Roxanne, our first graduating MS student! Roxanne is off to UCLA for a Masters in Public Health in the fall! And congrats to Preethi and Cade for graduating with their bachelors degrees. Preethi is off to medical school at California Northstate University College of Medicine and Cade will start optometry school at the Souther California College of Optometry. Bittersweet to have such great people leave the lab, but they are all off to bright futures!
April 2018: Chris joins the lab as a new PhD student. Exciting to have another student in the lab! And then Chris gets a CMG training grant. Congrats Chris!
January 2018: Elena and Ian join as undergrads (soon to be masters students). Welcome Elena and Ian!
September 2017: Agustina joins the lab as a postdoc. Agustina comes to us from Jason Brickner's lab at Northwestern University where she did amazing work on the molecular basis for epigenetic memory. Welcome Agu!
June 2017: New Polyomavirus taxonomy for the ICTV is now online. Summary paper is here: [Pubmed]. Matt's interest in Polyomavirus evolution started with a study on the de novo birth of a new viral gene in a clade of oncogenic Polyomaviruses in collaboration with Denise Galloway's lab at Fred Hutch [Pubmed].
May 2017: Matt gives a Major Symposium talk at Immunology 2017, the annual meeting of the American Association of Immunologists.
April 2017: Derek joins as an undergrad (and soon to be masters) student. Welcome Derek!
February 2017: Preethi and Chinmay join the lab as undergrads. Welcome Preethi and Chinmay!
December 2016: PLOS Pathogens paper in collaboration with Russell Vance's lab is now online: [PLoS Pathogens}. This paper, a continuation of an ongoing collaboration with the Vance lab, is an interesting report about the evolution of host 'tripwire' sensors of bacterial proteases.
September 2016: Roxanne joins as an undergrad student. She'll continue on to do her masters degree in the lab in 2017-2018.
July 2016: Candace joins the lab as our lab manager. Welcome Candace!
June 2016: Brian and Andy join the lab as PhD students ... and then both get training grants! Welcome and congrats to Andy and Brian!
May 2016: Andy starts as a rotation student. This place is starting to look like a lab now.
April 2016: Brooke and Brian start as rotation students. No real lab equipment yet, but we have computers.
March 2016: Cade and Hashi join as undergrads in the lab. They're the first people in the lab (and have the fantastic job of unpacking a bunch of boxes). Welcome Cade and Hashi!
