Home » Uncategorized (Page 2)

Category Archives: Uncategorized

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:

The EMBO Journal 

 

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:

https://youtu.be/MKDooqfjsWA

 



 

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.

Taylor, Brittany, and Sheila say goodbye. Good luck at CSUN, Taylor!

 

Taylor marks her permanent spot in the David Lab.

 

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:

http://ccbgap.ucdavis.edu/

 

Jazmin says goodbye to Alan and Sheila as she gets ready to finish her degree at Xavier.

 

Jazmin leaves her fingerprint on the David Lab wall.

 

 

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

 

Beili is ready to start her Chemical Engineering degree at UC Davis as she leaves her fingerprint in the David Lab with her summer research graduate student mentor Kori.

 

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

Garrett’s Goodbye Ceremony: Nicole, Garrett, Cindy, and Sheila

Garrett leaving his mark on the wall in the David Lab with Nicole and Cindy.

Garrett signs his name above his fingerprint.

 

Just Accepted Manuscript: Structure Activity Relationships Reveal Key Features of 8-Oxoguanine:Adenine Mismatch Detection by the MutY DNA Glycosylase


7/20/2017

The recently accepted manuscript, Structure Activity Relationships Reveal Key Features of 8-Oxoguanine:Adenine Mismatch Detection by the MutY DNA Glycosylase, was accepted for publication in ACS Chemical Biology.

MutY, remarkably, is able to specifically recognize and initiate repair of target OG:A mismatches from among a vast sea of natural DNA. To help reveal molecular features of OG that are critical for MutY recognition, this work explored the effects of systematic OG:A substrate alterations on MutY recognition in a cellular context. OG analogs were synthesized, assembled into OG:A modified oligonucleotides, and structure activity relationships were investigated using binding and cellular repair assays. Read the article to find out more about how specific OG modifications effect MutY glycosylase activity. Click here for the article: http://pubs.acs.org/doi/abs/10.1021/acschembio.7b00389.

 

Keywords: #Muty #DNA #DNARepair #BER #ModifiedNucleosides #Enzymes #8OG #DavidLab #UCDavis #glycosylase

Just Accepted Manuscript: S K-edge XAS Studies of the Effect of DNA Binding on the [Fe4S4] Site in EndoIII and MutY


7/18/2017

Check out the latest manuscript from the David Lab and collaborators: S K-edge XAS Studies of the Effect of DNA Binding on the [Fe4S4] Site in EndoIII and MutY, which was recently accepted for publication in JACS. In this work, the iron-sulfur clusters of DNA repair glycosylases Endonuclease III and MutY were examined using S K-edge X-ray Absorption Spectroscopy (XAS) in order to investigate DNA binding and solvation effects on Fe-S bond covalencies.

Click below to view the manuscript:

http://pubs.acs.org/doi/abs/10.1021/jacs.7b03966


 

Dare to Repair with Nicole Nuñez

6/6/2017

Take a walk with Nicole Nuñez as she illustrates how the David Lab investigates DNA repair.

RSS Science Daily News

  • Artificial reef designed by MIT engineers could protect marine life, reduce storm damage March 27, 2024
    Engineers designed an 'architected' reef that can mimic the wave-buffering effects of natural reefs while providing pockets for marine life. The sustainable and cost-saving structure could dissipate more than 95 percent of incoming wave energy using a small fraction of the material normally needed.
  • Persistent hiccups in a far-off galaxy draw astronomers to new black hole behavior March 27, 2024
    Astronomers have found that a previously quiet black hole, which sits at the center of a galaxy about 800 million light years away, has suddenly erupted, giving off plumes of gas every 8.5 days before settling back to its normal, quiet state.
  • Robot, can you say 'cheese'? March 27, 2024
    What would you do if you walked up to a robot with a human-like head and it smiled at you first? You'd likely smile back and perhaps feel the two of you were genuinely interacting. But how does a robot know how to do this? Or a better question, how does it know to get […]
  • Researchers turn back the clock on cancer cells to offer new treatment paradigm March 27, 2024
    Scientists reversed an aggressive cancer, reverting malignant cells towards a more normal state. Rhabdoid tumors are an aggressive cancer which is missing a key tumor suppressor protein. Scientists discovered that removing a second protein from cancer cells already experiencing tumor suppressor loss can reverse cancer cell identity.
  • Making long-term memories requires nerve-cell damage March 27, 2024
    Just as you can't make an omelet without breaking eggs, scientists have found that you can't make long-term memories without DNA damage and brain inflammation.

Contact:

Dr. Sheila S. David
ssdavid@ucdavis.edu
(530)-752-4280

Department of Chemistry
One Shields Ave.
Davis, CA 95616