Hello is there a doctor in the building?

Well, probably not the kind you need but we do have four new ones in the lab! Congratulations to Cyna, Yui, and Max on becoming doctors*!!! We had an amazing couple days of exit talks, commencement, partying, and family/friend time.

* none of us have actually filed yet, but we promise we will real soon

The graduates!!! Dr. Shirazinejad, Torvi, Iwamoto, and Ferrin! Congrats!!!!

Congratulations to Max and Emily on their new reconstitution paper in PNAS!

The culmination of work from Emily Stoops’ postdoc and Max Ferrin’s PhD was just published as David Drubin’s inaugural article as a new member of the National Academy of Sciences! In the paper they combine time-lapse volumetric confocal fluorescence microscopy with correlative light and electron microscopy to demonstrate the capacity of endocytic proteins to assemble on synthetic membranes and drive vesiculation in a cell-free system. This work was made possible by the excellent shared resources and expertise available to our lab on campus. Most of the fluorescence microscopy was performed on equipment managed by the Molecular Imaging Center, while much of the design and execution of electron microscopy experiments were carried out by Danielle Jorgens in the Electron Microscope Lab. Check out the paper here!

Reconstitution of endocytic actin networks on supported lipid bilayers.

Congratulations to Zane and Jonathan on their new Kar3 paper!

The dynamic duo is at it again, “taking our dynamics reconstitution assay a step further to dissect the differences between the two heterodimers of Kar3, the yeast kinesin-14”! In a heroic effort, Zane and Jonathan have looked at Kar3, Cik1, and Vik1 across the cell cycle in both cells and in our microtubule reconstitution assay. Seriously, it’s a majorly epic undertaking because they don’t just look at these three proteins localization and dynamics, but also their affects on microtubules! I’m so happy for them and their wonderful paper. Check it out here!

A glimpse at the creative process behind our posts.

Goodbye to Zane & Meiyan

One of the saddest parts of being in a lab, is we become family, but yet people do have to move on with their lives. On one hand, it’s great we end up with friends sprinkled all around the world, but sometimes you just really miss them. And since the last website update, both Zane and Meiyan have moved on to new adventures. Truly, I am so happy for them. Zane and his family have moved down to San Diego were he now is a staff scientist in the Oegema/Desai lab. Finally, his kids can wear shorts all year and have it not being weird and cold! Meiyan and her family are also in warmer climates as they have moved down to Florida, specifically the University of Florida, where her and her husband will continue their research! We all wish them luck, happiness, and success in their new adventures.

The lab gives a farewell toast to Zane.

David says goodbye to Meiyan.

 

Congratulations to Julia and Jonathan for their paper reconstitution kinetochore dynamics in yeast lysate

Major congratulations to them both, but because I (Julia) am writing this, I mainly want to heavily emphasize and thank Jonathan for all his hard work, kindness, patience, and perseverance in working with me. I couldn’t have imaged having a better mentor throughout grad school and I feel like our paper together is something I am truly proud of. It’s our friendship in publication form! Just kidding reader, it’s very much a normal science paper. BUT it is very cool. Check it out if you love microtubule dynamics, kinetochores, reconstitution, motors and especially THE COMBO OF ALL 4! Also I love talking about this data so feel free to reach out anytime if you have a question!

peekaboo kinetochore that didn’t make publication but I loved

Congratulations to Meiyan and Cyna on their paper regarding asymmetric force production during CME

Congratulations again to Meiyan and Cyna on their beautiful publication and all their hard work. A wonderful collaboration to witness in the lab, Meiyan a stem cell CRISPR editing cell biology wizard and Cyna the statistics quantitative imaging master. Combine the two of them together? Well, read the paper and find out. But, to spoil it a bit, they do beautiful imaging and very thorough quantification to show asymmetrical force production in CME.

“An updated schematic model of actin-negative and actin-positive clathrin-coated pits in human cells.”

Congratulations to Bob on his paper that discovers a function for clathrin in membrane curvature stabilization in CME

During clathrin-mediated endocytosis (CME), flat plasma membrane is remodeled to produce nanometer-scale vesicles. The mechanisms underlying this remodeling are not completely understood. The ability of clathrin to bind membranes of distinct geometries casts uncertainty on its specific role in curvature generation/stabilization. Here, we used nanopatterning to produce substrates for live-cell imaging, with U-shaped features that bend the ventral plasma membrane of a cell into shapes resembling energetically unfavorable CME intermediates. This induced membrane curvature recruits CME proteins, promoting endocytosis. Upon AP2, FCHo1/2, or clathrin knockdown, CME on flat substrates is severely diminished. However, induced membrane curvature recruits CME proteins in the absence of FCHo1/2 or clathrin and rescues CME dynamics/cargo uptake after clathrin (but not AP2 or FCHo1/2) knockdown. Induced membrane curvature enhances CME protein recruitment upon branched actin assembly inhibition under elevated membrane tension. These data establish that membrane curvature assists in CME nucleation and that the essential function of clathrin during CME is to facilitate curvature evolution, rather than scaffold protein recruitment.

Congratulations to Daniel and co-authors on their cryo-ET study of actin-based force generation in CME!

“How does actin filament assembly generate pulling forces during endocytosis?”

Actin assembly provides force for a multitude of cellular processes. Compared to actin-assembly-based force production during cell migration, relatively little is understood about how actin assembly generates pulling forces for vesicle formation. Here, cryo-electron tomography identified actin filament number, organization, and orientation during clathrin-mediated endocytosis in human SK-MEL-2 cells, showing that force generation is robust despite variance in network organization. Actin dynamics simulations incorporating a measured branch angle indicate that sufficient force to drive membrane internalization is generated through polymerization and that assembly is triggered from ∼4 founding “mother” filaments, consistent with tomography data. Hip1R actin filament anchoring points are present along the entire endocytic invagination, where simulations show that it is key to pulling force generation, and along the neck, where it targets filament growth and makes internalization more robust. Actin organization described here allowed direct translation of structure to mechanism with broad implications for other actin-driven processes.

Congratulations to Matt for starting his lab at the University of Washington in the summer of 2022!

We gathered for a picnic in beautiful North Berkeley to celebrate Matt’s time in the lab. We wish Matt the best in his new adventure and look forward to hearing about his lab’s accomplishments!

Cheers to Matt!

Matt catches up with his graduate school advisor, Tom Pollard, who happens to be one of our newest lab members.