Welcome Gabriella and Sybrina

Excited to announce that Gabriella Perez Lopez has decided to join the lab for her Ph.D. studies. Gabriella is working to understand ribosome biogenesis, with a specific interest in how these complexes are built in non-model organisms, including human pathogens. Armed with this knowledge, we hope to develop novel classes of antibiotics specifically targeted to assembling ribosomes.

Additionally, we are thrilled to welcome Sybrina Kerr who will be working in the lab as a summer MSRP undergraduate researcher. Sybrina joins us from Clafin University, and will be working on an exciting new autophagosome assembly project.

NSF CAREER AWARD

Many thanks to the National Science Foundation for awarding the lab a 5-year CAREER Grant. These funds will support our ongoing work to untangle ribosome biogenesis, as well as some of our mass spectrometry and cryo-EM methods development efforts.

Equally importantly, we have allocated funds from this grant to form better collaborations with Historically Black Colleges and Universities, including Howard University, North Carolina A&T State University, and Spellman College, and to recruit talented Black scientists to MIT for our summer MSRP program. I am incredibly grateful to professors Kimberly Jackson, Misty Thomas, Bertina Telusma, and Mandana Sassanfar for their help in putting this program together.

Where did the time go?

It’s hard to believe it’s been ~2 years since I last posted here, but I guess that’s a sign that we’ve been keeping busy. Also, the last time I posted, my son wasn’t born, and now he’s teasing our dog…that might also explain the lapse. Anyways, in no particular order, here’s some of the latest lab updates:

  • Laurel, April, and Barrett joined the lab for their PhDs…ahh…how is this “news”. Anyways, despite the pandemic, they are making amazing progress to help us understand autophagosome assembly in yeast (Laurel and Barrett) and how ferritin is targeted for autophagy (April) in mammalian cells.

  • The lab joined The Borg, sorry, I meant The Broad as an affiliate member lab. I guess they were right, resistance was futile - there’s just way too many amazing scientists and fancy toys over there to not assimilate.

  • Danica decides to join the lab as a post-doc and is awarded a Life Science Research Fellowship - congrats!!!

  • We were selected for funding from the James H. Ferry Fund, the Whitehead Family, the Alfred P. Sloan Foundation, and the National Science Foundation. Thank you, thank you, thank you!

  • Jen and Gabriella join the lab to work on their PhD’s to work on exciting projects in autophagy and ribosome biogenesis.

  • Ellen gives a ton of talks about cryoDRGN…the oohhhss and aahhha are palatable :)

  • We published cryoDRGN and started a bunch of collaborations to apply the tool to interesting biological problems.

  • In collaboration with Alan Brown’s group, we published a nice story in Nature Structural and Molecular Biology applying cryoDRGN to ciliary complexes.

  • Joey gave talks at the American Crystallographic Association and the New York Academy of Sciences. The embarrassing press convinces him to mute the labs twitter bot ;)

  • My wife and I had a baby, and there was a pandemic, but let’s focus on the baby.

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We’re incredible grateful for new research funding from the MIT J-Clinic, which will support our ongoing work to apply machine learning approaches to understand protein structure and function.

In related news, I’m also thrilled to announce that Dr. Andrew Grasstti’s work to find novel autophagy components in human cells was selected for funding by the John W. Jarve (1978) Seed Fund for Science Innovation.

Thank you again to all of our research sponsors!

Off we go!

It’s been an absolutely incredible year, and I can’t begin to express how happy I am with the team we’ve built. Someone in the shuffle, I neglected to highlight that we’ve grown (by 2-fold) and are excited to welcome our first class of Ph.D. students - Ellen Zhong, Bertina Telusma, and Samantha Webster. Also, Dr. Andrew Grassetti joined the lab this summer…welcome welcome welcome!

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 joey@jhdavislab.rocks 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 :)