Author Archives: NateKrefman

The Drubin/Barnes Lab Has a New Theme Song!

We now present to you a brand new theme song to introduce the world to all of the awesome people in the Drubin/Barnes Lab!

The Drubin-Barnes Lab!
(Parody of The Brady Bunch Theme Song)

Submission for UC-Berkeley MCB Follies 2012-2013
(UC-Berkeley, Dept. of Molecular and Cell Biology)

LYRICS, VOCALS, CAMERA, EDITING:  Nathaniel Krefman

ADDITIONAL VOCALS:  Akemi Kunibe

STARRING:  The Drubin/Barnes Lab at UC-Berkeley (Fall 2012)!

PIs:  Profs. David Drubin and Georjana Barnes

1st GROUP (microtubules, spindles, kinetochores, & mitosis in budding yeast):  Adrianne Pigula (top left), Nathaniel Krefman (center left), Itziar Ibarlucea-Benitez (bottom left), Prof. Georjana Barnes (center), Anthony Cormier (center right)

2nd GROUP (actin cytoskeleton and endocytosis in mammalian cells and budding yeast):  Aaron Cheng (top left square, left), Jasper Weinberg (top left square, right), Rebecca Lu (center left square, left), Lillie Cohn (center left square, center), Akemi Kunibe (center left square, right), Yansong Miao (bottom left square), Prof. David Drubin (center square), Sun Hae Hong (top right square, left), Yidi Sun (top right square, right), Alex Grassart (center right square, left), Daphne Dambournet (center right square, right), Christa Cortesio (bottom right square, left), Eric Lewellyn (bottom right square, right).

________________________________________________

LYRICS:

Here’s the story of a lovely lady.
Who studied what a microtubule’s for.
All her group loves mitosis, like Georjana,
And kinetochores.

Here’s the story of a PI named David,
Who was interested in actin in live cells,
And his group mapped endocytosis dynamics,
Yet they were by themselves.

After their post-docs, where the lady met this fellow,
And named a protein complex DAM instead of DARN,
They knew their groups must form one laboratory.
That’s the way our lab became the Drubin/Barnes!
The Drubin/Barnes!

That’s the way our lab became the Drubin/Barnes!

Journal Club on Monday, January 7

For our Journal Club on January 7, Yidi Sun presented the following paper:

PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity.  Nakatsu F, Baskin JM, Chung J, Tanner LB, Shui G, Lee SY, Pirruccello M, Hao M, Ingolia NT, Wenk MR, De Camilli P.  J Cell Biol. 2012 Dec 10;199(6):1003-16.  PMID:  23229899.

Congratulations to Yidi Sun on her new paper!

Yidi Sun‘s new paper is out now as an electronic publication ahead of print in the Journal of Cell Science.  Congratulations to Yidi on her great work!  The abstract is below.  The PDF can be downloaded from JCS here.

The functions of anionic phospholipids during clathrin-mediated endocytosis site initiation and vesicle formation. Sun Y, Drubin DG. J Cell Sci. 2012 Oct 24. PMID: 23097040.

Abstract

Anionic phospholipids PI(4,5)P(2) and phosphatidylserine (PS) are enriched in the cytosolic leaflet of the plasma membrane where endocytic sites form. In this study, we investigated the roles of PI(4,5)P(2) and PS in clathrin-mediated endocytosis (CME) site initiation and vesicle formation in Saccharomyces cerevisiae. Live-cell imaging of endocytic protein dynamics in an mss4(ts) mutant, which has severely reduced PI(4,5)P(2) levels, revealed that PI(4,5)P(2) is required for endocytic membrane invagination but is less important for endocytic site initiation. We also demonstrated that in various deletion mutants of genes encoding components of the Rcy1-Ypt31/32 GTPase pathway, endocytic proteins dynamically assemble not only on the plasma membrane but also on intracellular membrane compartments, which are likely derived from early endosomes. In rcy1Δ cells, fluorescent biosensors indicated that PI(4,5)P(2) only localized to the plasma membrane while PS localized to both the plasma membrane and intracellular membranes. Furthermore, we found that polarized endocytic patch establishment is defective in the PS-deficient cho1Δ mutant. We propose that PS is important for directing endocytic proteins to the plasma membrane and that PI(4,5)P(2) is required to facilitate endocytic membrane invagination.

Journal Club on Monday, November 5

For Journal Club on November 5, Nate Krefman presented the following papers on Golden Gate Cloning:

A one pot, one step, precision cloning method with high throughput capability. Engler C, Kandzia R, Marillonnet S. PLoS One. 2008;3(11):e3647. PMID: 18985154.

Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. Engler C, Gruetzner R, Kandzia R, Marillonnet S. PLoS One. 2009;4(5):e5553. PMID: 19436741.

A modular cloning system for standardized assembly of multigene constructs. Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. PLoS One. 2011 Feb 18;6(2):e16765. PMID: 21364738.

Journal Club on Monday, October 1

Leave a reply

For our next Journal Club, Padmini Rangamani will present the following paper:

Phase transitions in the assembly of multivalent signalling proteins. Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, Russo PS, Jiang QX, Nixon BT, Rosen MK. Nature. 2012. PMID: 22398450

Lighting Up Live Cells with Fluorescence (Genetic Engineering & Biotechnology News)

Leave a reply

Genetic Engineering & Biotechnology News is out with a Feature Article this week including some comments from David Drubin about targeted genome modification in mammalian cells for fluorescence microscopy studies.

Lighting Up Live Cells with Fluorescence. Christine Herman. GEN. Sep 1, 2012 (Vol. 15, No. 32)

“The difference between taking snapshots of the process and watching a movie is just night and day,” says David Drubin, Ph.D., professor of cell and developmental biology at the University of California, Berkeley, whose lab uses fluorescence to understand the intricate details underlying clathrin-mediated endocytosis.

 

Researchers in David Drubin’s lab at the University of California, Berkeley genetically engineered a human cell line to express endogenous levels of RFP-tagged clathrin light chain A (red) and GFP-tagged dynamin 2 (green) for studying clathrin-mediated endocytosis. The above 3D kymograph of the cell surface, with the time dimension in the z-axis, shows the full lifetime of hundreds of clathrin patches on the membrane, which terminate upon recruitment of dynamin. [Aaron T. Cheng]

Journal Club on Thursday, July 26

Leave a reply

For our next Journal Club, our summer undergraduate researcher Josh Johnson will present the following paper:

Aurora B dynamics at centromeres create a diffusion-based phosphorylation gradient.  Wang E, Ballister ER, Lampson MA.  J Cell Biol. 2011 Aug 22;194(4):539-49.  PMID: 21844210.

Journal Club on Monday, July 09

Leave a reply

For our next Journal Club, Adrianne Pigula will present the following paper:

A link between mitotic entry and membrane growth suggests a novel model for cell size control.  Anastasia SD, Nguyen DL, Thai V, Meloy M, MacDonough T, Kellogg DR.  J Cell Biol. 2012 Apr 2;197(1):89-104. Epub 2012 Mar 26.  PMID: 22451696.

Journal Club on Monday, June 25

Leave a reply

For Journal Club on Monday, June 25, Connie Peng presented the following paper:

Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions.  Frost A, Elgort MG, Brandman O, Ives C, Collins SR, Miller-Vedam L, Weibezahn J, Hein MY, Poser I, Mann M, Hyman AA, Weissman JS.  Cell. 2012 Jun 8;149(6):1339-52.  PMID: 22682253.