Better than a lump of coal

Festivus came early to the Davis lab this year! New toys include large shaking incubators, an expanded cell culture facility and the installation of our new Bio-Rad FPLC.

Using these instruments, we will purify a series of autophagy-related proteins. Using these purified components, we can perform experiments to understand individual proteins fold, how they assemble into enormous molecular machines, and, eventually, how these assembled complexes enable autophagy. Exciting days ahead!

We're looking to hire a UROP...Bueller...Bueller...

The Davis lab is currently looking for an enthusiastic undergraduate with to join the team and work on a computational project in the lab - see the posting below and feel free to contact me directly at if you're interested:

Project Title: Accelerating proteomics data analysis using highly parallel GPU-based processing

Project Description: High resolution mass analysis of proteins and peptides reveals complex spectra that must be accurately fit to determine the relative abundance of analytes. This fitting process is computationally intensive, but is readily amenable to parallelization using modern graphic processing units (GPUs). In this project, we will implement a least-squares Fourier transform convolution algorithm in CUDA and apply this algorithm to the analysis of a variety of mass spectra generated in our laboratory. The project includes the following aspects: 

  1. Implementation of a fitting algorithm on GPU hardware
  2. Use of a top-of-the-line mass spectrometer to generate reference mass spectra for analysis
  3. Application of this fitting algorithm to the quantitation of spectra generated above
  4. Analysis of the benefits of GPU-based processing over traditional CPU-based implementations.

This UROP is offered in the Biology department, however highly motivated applicants from departments such as Electrical Engineering & Computer Science, Mathematics, and Biological Engineering are encouraged to apply. While this UROP is primarily computational, students interested in learning more about mass spectrometry will have significant opportunities to work in the wet laboratory. This UROP project will be directly supervised by Prof. Joey Davis.

Prerequisites: Candidates of all experience levels will be considered. However, preference is given to candidates with experience with CUDA and/or python who can commit to working at least 20 hours per week during IAP and summer and 9 hours per week during the academic year. I am offering academic credit for new UROPs.

This project is expected to require IAP/Spring terms for completion, however the UROP can be expanded to include additional projects in the coming years.

Welcome welcome!!

Super excited to announce the arrivals of new lab members Gina Lee and Osvaldo Cruz this week. Osvaldo recently completed his Ph.D. in John Tessmer's group at the University of Michigan and will use his protein and lipid biochemistry expertise to investigate the early stages of autophagosome formation. Gina will be keeping the lab running smoothly and efficiently with her administrative awesomeness. The days of talking to myself in an empty office are over (I hope :)

What the HEK293t?

More progress on the Davis lab renovations! Reps from Thermo just installed a stack of new incubators (pretty, right?), which we will use to culture mammalian cell lines including HEK293t. These studies are aimed at determining both the identity of, and the rate at which cellular substrates are degraded via autophagy. With this assay in hand, we hope to eventually measure how mutations, environmental stress, or other perturbations affect the cell's ability to perform autophagy. See our research page for more info.


Huge congratulations to Joachim Frank, Richard Henderson, and Jacques Dubochet

Today the Royal Swedish Academy of Sciences announced that the 2017 prize in Chemistry was awarded to Joachim Frank, Richard Henderson, and Jacques Dubochet for "developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." CryoEM is a truly transformative technology perfectly suited to study macromolecular machines. The Davis lab uses this technique regularly and we're excited to take advantage of MIT's recent investments in the space.

Check out this lovely flowchart of Joachim Frank's widely used approach to generate 3D electron density maps from 2D micrographs.


New mass spectrometer installed

Our new Thermo Q-Exactive HF-X mass spectrometer is installed and operational!

This instrument is the most advanced mass spectrometer in the Q-exactive line released to date and features an improved high capacity transfer tube allowing for exquisite sensitivity as well as an ultra-high field orbitrap analyzer, which doubles the speed (up to 40 Hz) and resolution (up to 240,000 resolving power) of the instrument. 


Marvel at the glowing lights :)