New Article Published: When you’re strange: Unusual features of the MUTYH glycosylase and implications in cancer.
New Article Published: When you’re strange: Unusual features of the MUTYH glycosylase and implications in cancer.
Think MUTYH is a simple adenine glycosylase? Think again. Explore the dizzying diversity of MUTYH interactions to DNA damage response proteins and their implications in cancer in our lab’s newest review by Alan Raetz and Sheila David.
Click here or on the image to link to the article!
Raetz, A.G.; David, S.S. When you’re strange: Unusual features of the MUTYH glycosylase and implications in cancer. DNA Repair. 2019, 80, 16-25.
#DavidLab #MUTYH #Muty #DNArepair #glycosylase #DDR #cancer #ucdavis #chemistry #chemicalbiology #AlanRaetz #SheilaDavid
The David Laboratory attends CBBA 2019 at UCSF
Members of Sheila David’s Laboratory at UC Davis attended the Chemical Biology in the Bay Area (CBBA) Day on June 1st, 2019, which was hosted by UCSF in San Francisco. This event brought in graduate student presenters from UC Davis, UC Santa Cruz, UC Berkeley, and UCSF. The keynote speaker was Anthony Ogawa from Merck. Merve Demir from our lab presented a research poster titled, “Elucidating Additional Features of 8-Oxo-guanine Recognition and Adenine Excision Mechanism by the DNA Glycosylase MutY.” The speakers were consistently excellent throughout the day, touching on a broad range of topics within the wide world of chemical biology. We all had a great time. Cheers to all of the presenters and volunteers that helped run the conference!
Undergraduate Student Spotlight: Madeline Bright
Meet UC Davis Undergraduate Researcher Madeline Bright in our lab’s new Undergraduate Student Spotlight Video! Hear about how she got into undergraduate research and how it will help her career. Undergrads – there is solid advice included on how to join a research lab if you have been thinking about it. Madeline wants to enter into an M.D.-Ph.D. program after her undergraduate work, and is very well on her way towards that goal.
Madeline is a 2nd year Biological Sciences student working in the David Laboratory in the Chemistry Department at UC Davis, and has been with us for over one year. Madeline recently won the 2019 Francesca Miller Undergraduate Research Award at the 2019 Miller Symposium at UC Davis.
Here’s to a Bright future!
Beal Lab: There is an Easter Egg in this video for you! Enjoy!
#research #UCDavis #DavidLab #chemistry #dnarepair #undergraduateresearch #millersymposium #biologicalsciences #MadelineBright
The David Lab attends the 2019 Miller Symposium at UC Davis
The Annual R. Bryan Miller Symposium at UC Davis brings top speakers from the field of chemical biology to share cutting edge research results and perspectives on the future of chemical biology research. Dr. Sheila David is the Miller Symposium Committee Chair, and directs the event with the support of faculty, staff, and students. The David Lab attended the 2019 Miller Symposium at UC Davis in full force.
This year’s theme of the Miller Symposium was “Chemistry and Biology of Pain,” and included speakers such as Justin DuBois of Stanford, Alanna Schepartz of Yale, Jon Sack of UC Davis, Ann Weber of Kallyope & Merck, and more.
Chandrima Majumdar of the David Lab played a significant role in supporting and organizing the event, and received recognition for her contribution at the awards ceremony.
The Miller Symposium also includes a poster session where researchers present their latest findings. Liz Lotsof and Savannah Conlon of the David Lab shared their work at the poster session, which involves DNA glycosylases NEIL1 and NEIL3 and their ability to recognize and excise oxidative damage located in G-quadruplexes.
Undergraduate Researcher Madeline Bright of the David Lab won the 2019 Francesca Miller Undergraduate Research Award for her work involving the synthesis and duplex stability analysis of previously unreported and rationally designed modified oligonucleotides developed to act as substrates for DNA repair protein MutY in enzyme assays utilized by the David Lab. The modified oligonucleotides synthesized in this project will help elucidate the target recognition mechanism of MutY. Madeline has been a member of the David Lab since January 2018 and works with 3rd year PhD student Robert Van Ostrand. Congratulations Maddy!
The David Lab @ Miller 2019
Thank you to Jackson Zhu for taking the photos.
Keywords:
#MillerSymposium #UCDavis #ChemicalBiology #DNARepair #DavidLab #SheilaDavid #UCDavisChemistry
New Manuscript Published: The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair.
New Manuscript Published: The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair.
A recent publication from the David, Siegel and Lim (Academia Sinica, Taiwan) labs (Nuñez et al., JACS, 2018) provides insight into the coordination sphere and critical role of a Zn2+ metal binding site in the DNA repair glycosylase MUTYH. Genome database mining and sequence alignment of MUTYH orthologs, along with computational modeling, identified and supported Zn2+ ligation by four Cys residues. Three of the Cys residues lie in an interdomain connector region unique to mammalian MutY enzymes, while the 4th Cys is located in close proximity to the Fe-S cluster DNA binding domain. The functional consequences of reduced Zn2+ chelation on MUTYH-mediated DNA repair activity evaluated using a battery of in vitro and cell-based assays revealed the importance of Zn-coordination in recognition of the damaged DNA substrate. The critical nature of the “Zinc Linchpin Motif” suggests additional functions unique to higher organisms in damage signaling and crosstalk with other DNA repair pathways.
More information at https://pubs.acs.org/doi/10.1021/jacs.8b06923.
Source:
J. Am. Chem. Soc. 2018, 140, 13260-13271.
Keywords: #Muty #Mutyh #BER #DNA #DNARepair #ZincLinchpinMotif #Zn2+ #8OG #DavidLab #UCDavis
We bid you adieu, Holly Vickery!
David Lab researcher Holly Vickery is off to graduate school, and the David Lab wishes her farewell. Holly worked on multiple projects as a research scientist in the David Lab. One project was focused on measuring the cellular repair efficiency of MutY variants, while another project revolved around optimizing a purification technique of MUTYH for higher yields and purity. Holly is moving on to graduate school as part of the Chemistry and Chemical Biology Program at the University of California San Francisco. We’ll miss you here at the David Lab, Holly, but we’re glad to see you move forward. Good luck at UCSF!
[slideshow_deploy id=’936′]
New Manuscript Published: Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC.
New Manuscript Published: Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC.
The preservation of genomic integrity performed by DNA repair machinery is crucial for living organisms, and malfunctions in DNA repair machinery can have far-reaching and devastating effects on a cell’s ability to attain precise DNA replication, properly regulate cell differentiation and self-renewal, and to regulate cell growth and apoptosis, among other important cellular functions. Mutations of critical residues in DNA repair proteins can drastically reduce DNA repair capability in cells, allowing for a build-up of genomic mutations. Inherited variants in DNA repair proteins such as glycosylase MUTYH have been linked to a predisposition to tumors in patients with disease MUTYH Associated Polyposis (MAP). The David Lab is interested in delineating DNA repair mechanisms to help shed light on the etiology of cancer and other diseases, providing mechanistic and structural information that may be used, for example, to design drug molecules targeting DNA repair proteins.
New work from the David Lab examined the selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC, which primarily targets alkylated-DNA damage product N3-methyladenine (3mA). This work details how AlkC selects for and excises 3mA with its non-base-flipping mechanism. The authors carried out a comprehensive phylogenetic, biochemical, and structural comparison of AlkC and AlkD proteins for comparison, which shows, notably, characteristics important for substrate specificity and why bulkier substrates are not preferred. Interestingly, AlkC’s excision mechanism involves using HEAT-like repeat domains and in most cases Ig-like domains to introduce a kink in the target DNA, helping to expose the target nucleobase, allowing for subsequent insertion of the enzyme active site to excise its target.
Click here to read more about AlkC’s non-base-flipping mechanism.
Source:
David Lab Graduate Student Spotlight: Nicole N. Nuñez
8/28/2017
Presenting the David Lab Graduate Student Spotlight, featuring Nicole Nuñez. We discuss with Nicole how she found her way onto the STEM pathway she is currently traveling as she is completing her Ph.D, and Nicole details the powerful motivation behind her passion for investigating the mechanisms of cancer, and how her path helped lead her to the David Lab. Members of the David Lab chime in with what they like about Nicole, and how she has helped them. Additionally, Nicole gives advice for the next generation of graduate students, and as this was an interview about graduate school, the topic of pizza was eventually brought to the forefront. Nicole has been a vital member of the David Lab for some time now, and we are proud to see her moving onward. Enjoy the show!
[youtube https://www.youtube.com/watch?v=MKDooqfjsWA&w=853&h=480]
Direct Link to YouTube Video:
Best Wishes to David Lab researchers Taylor, Jazmin, and Beili!
8/11/2017
As summer continues to roll on, and summer REU’s are approaching their completion, we have to say goodbye to our summer REU researchers Jazmin and Beili, and to recently graduated David Lab researchers like Taylor who are moving on to graduate school.
→Taylor McCart, who recently graduated from UC Davis with a B.S. in Pharmaceutical Chemistry, is moving on to seek her M.S. in Biochemistry at California State University, Northridge. Taylor worked with graduate student mentor Brittany Anderson-Steele, and spent a total of two years conducting research in the David Lab. We will miss Taylor here at the David Lab, but we are proud she is moving forward to graduate school, and we know she is ready to succeed at the next level.
→Jazmin Stenson spent the summer as an undergraduate researcher in the David Lab working with postdoctoral researcher Alan Raetz via the Chemistry and Chemical Biology Graduate Admissions Pathways Program (CCBGAP) from Xavier University of Louisiana. Jazmin is completing her B.S. in Biochemistry at Xavier University of Louisiana next year.
Chemistry and Chemical Biology Graduate Admissions Pathways Program:
→Beili Huang participated in summer research at the David Lab via the ACS Project SEED Program. Beili worked with graduate student mentor Kori Lay, and is starting on her B.S. in Chemical Engineering at UC Davis this fall.
ACS Project SEED Program:
https://www.acs.org/content/acs/en/education/students/highschool/seed.html
Good luck Taylor, Jazmin, and Beili! Thank you for your hard work in the David Lab!
Farewell Young Scholar Garrett Ma!
8/4/2017
Garrett has spent the summer in the David Lab conducting advanced research alongside graduate student lab members Nicole and Cindy as part of the UC Davis Young Scholars Program. Even good things come to an end, and in following with David Lab tradition, Garrett leaves his mark before saying goodbye. We wish Garrett the best of luck in the future!
UC Davis Young Scholars Program
Science Daily News
- First evidence of human occupation in lava tube cave in Saudi Arabia April 17, 2024New research has highlighted an area in Arabia that once acted as a key point for cultural exchanges and trades amongst ancient people -- and it all took place in vast caves and lava tubes that have remained largely untapped reservoirs of archaeological abundance in Arabia. Through meticulous excavation and analysis, the international team uncovered […]
- Paleontologists unearth what may be the largest known marine reptile April 17, 2024The fossilized remains of a second gigantic jawbone measuring more than two meters long has been found on a beach in Somerset, UK.
- 38 trillion dollars in damages each year: World economy already committed to income reduction of 19 % due to climate change April 17, 2024Even if CO2 emissions were to be drastically cut down starting today, the world economy is already committed to an income reduction of 19% until 2050 due to climate change, a new study finds. These damages are six times larger than the mitigation costs needed to limit global warming to two degrees. Based on empirical […]
- Understanding climate warming impacts on carbon release from the tundra April 17, 2024The warming climate shifts the dynamics of tundra environments and makes them release trapped carbon, according to a new study published in Nature. These changes could transform tundras from carbon sinks into a carbon source, exacerbating the effects of climate change.
- Workings of working memory detailed April 17, 2024Investigators have discovered how brain cells responsible for working memory--the type required to remember a phone number long enough to dial it--coordinate intentional focus and short-term storage of information.