Category Archives: News

Life here in the UC is much better than anything they got out there!

Members of the Drubin/Barnes Lab and others collaborated this month to create musical magic (or madness?) in the form a parody of the musical number “Under the Sea” from Disney’s The Little Mermaid. The video was a submission for UC-Berkeley Department of Molecular and Cell Biology‘s annual funny movie event MCB Follies.

We hope you enjoy it!

CONCEPT: Akemi Kunibe

LYRICS: Eric Lewellyn

VOCALS: Nathaniel Krefman

BACKING VOCALS: Sun Hae Hong & Akemi Kunibe

CINEMATOGRAPHY: Akemi Kunibe, Jeff Woodruff, & Eric Lewellyn

EDITING: Jasper Weinberg & Akemi Kunibe

STARRING: Eric Lewellyn, Rebecca Lu, & Jasper Weinberg

CAST (in order of appearance): Rebecca Lu, Jasper Weinberg, Eric Lewellyn, Jeff Woodruff, Akemi Kunibe, Kathryn Sievert, Adrienne Greene, Sun Hae hong, Benjamin Gowen, Wendy Ingram, Kevin Barry, Caitlin DeJong, aileen Kelly, Caitlin Shartner, Christopher Alvaro, Jennifer Cisson, Nathaniel Krefman, Colin Cerretani, Thomas Burke, Julia Durack, Christina Glazier, & Michelle Reniere

________________________________________________

LYRICS:

Private industry, it’s a mess. Life here in the UC Berkeley is much better than anything they got out there.

The money is always greener,
In some private company.
You quit you could be a tech there,
But you would be sad you’ll see.
Just look at the world around you,
Right here through the lab room door.
Such wonderful things surround you.
What more is you lookin’ for?

In the UC!
In the UC!
Darling it’s better,
Grab your pipetter,
Come follow me!
Here you can surf for half the day.
With a real job you’ll slave away.
Ya we be chillin’.
Time we be killin’.
In the UC!

Right here all the postdoc happy.
They follow where research go.
The industry doc ain’t happy —
They feel like they sold their soul.
But doc with a job is lucky —
They in for a worser fate:
One day when the boss sell company,
Guess who eatin’ ramen plate!
Uh Oh!

In the UC!
In The UC!
We doin’ science.
We not some appliance,
for makin’ money.
They got a team of robots manned.
We got the Zen of workin’ by hand.
We got no worries,
Troubles or hurries,
In the UC!
In the UC!
Each protein gel here,
Runnin’ so well here,
Bands are so clean.
Even though takin’ lots of class,
Can be a real pain in the ass,
While we be learnin’,
money be earning,
In the UC!

The tub is the bass,
the drum is the flask,
the beakers are good,
for most any task.
Our science is play.
We do every day,
Like Nate, who’s the Duke of Clone.
Yeah!
He put DNA,
In cells on the plate.
The sequence is good.
There ain’t no debate.
Right here where it’s at,
Our microscope phat.
An’ oh that protein glow!

In the UC!
In the UC!
No scientist here,
Like to get pissed here,
You will agree.
We got a campus full a perks.
They got a boardroom full of rich jerks.
Each undergrad here,
Learning like mad here.
In the UC!
None of our tech here,
is pain in the neck here.
In the UC!
Each PI swell here.
Get the Nobel here.
Publish in Science,
Nature, and Cell here.
Stay academic.
The fun is pandemic!
In the UC!

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!

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.

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

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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 Monday, July 09

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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.

A model for signals that link mitotic entry to membrane growth.

An Interview with David Drubin in Biowire

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The May 2012 edition of Biowire, a publication of Sigma-Aldrich, includes an interview with David Drubin about the projects in our lab looking at clathrin-mediated endocytosis (CME) in mammalian cells using zing finger nuclease (ZFN) technology to undertake targeted genome modification. Traditionally, CME has been studied in cells in which fluorescently-tagged components of endocytic machinery are overexpressed using exogenous constructs. Data obtained in many labs using these methods suggested that CME was highly variable. Using ZFN technology, in collaboration with Sangamo Biosciences, our lab recently showed that CME is robust and efficient in mammalian cells. The new results highlight the technical advantages of tagging genes at their endogenous loci, an approach that has been historically limited to genetically tractable organisms, such as the Drubin/Barnes Lab favorite Saccharomyces cerevisiae (budding yeast). Emerging technologies, such as ZFNs and TALENs, however, are now making this sort of precise genomic manipulation possible in animal cells, including human cells, giving us new and powerful ways of studying cellular biology.

Cellular processes should be studied as close to their natural states as possible. I suspect that, as we see more uses of zinc finger nucleases [for tagging endogenous genes], people will find that they have been inadvertently perturbing the processes that they have been studying.

David Drubin (Biowire, May 2012)

Prof. David Drubin, for Biowire

Congratulations to Yidi Sun on her new paper!

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

Orm protein phosphoregulation mediates transient sphingolipid biosynthesis response to heat stress via the Pkh-Ypk and Cdc55-PP2A pathways. Sun Y, Miao Y, Yamane Y, Zhang C, Shokat KM, Takematsu H, Kozutsumi Y, Drubin DG. Mol Biol Cell. 2012 Apr 25. PMID: 22535525.

Abstract

Sphingoid intermediates accumulate in response to a variety of stresses, including heat, and trigger cellular responses. However, the mechanism by which stress affects sphingolipid biosynthesis has yet to be identified. Recent studies in yeast suggested that sphingolipid biosynthesis is regulated through phosphorylation of the Orm proteins, which in humans are potential risk factors for childhood asthma. Here, we demonstrate that Orm phosphorylation status is highly responsive to sphingoid bases. We also demonstrate by monitoring temporal changes in Orm phosphorylation and sphingoid base production in cells inhibited for Ypk1 protein kinase activity, that Ypk1 transmits heat stress signals to the sphingolipid biosynthesis pathway via Orm phosphorylation. Our data indicate that heat-induced sphingolipid biosynthesis in turn triggers Orm protein dephosphorylation, making the induction transient. We identified Cdc55-PP2A (protein phosphatase 2A) as a key phosphatase that counteracts Ypk1 activity in Orm mediated sphingolipid biosynthesis regulation. In total, our study reveals a mechanism through which the conserved Pkh-Ypk kinase cascade and Cdc55-PP2A facilitate rapid, transient sphingolipid production in response to heat stress through Orm protein phosphoregulation. We propose that this mechanism serves as the basis for how Orm phosphoregulation controls sphingolipid biosynthesis in response to stress in a kinetically coupled manner.

A feedback regulation pathway in which Orm protein phosphorylation dynamics rapidly and precisely regulate sphingolipid biosynthesis in response to heat stress. See the text for a description.

Lillie joined the Drubin/Barnes Lab!

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The Drubin/Barnes Yeast and HeLa Cell Manufacturing Company is excited to welcome Lillie Cohn as a new graduate student in the lab! Lillie is a first year in the Molecular and Cell Biology program at UC-Berkeley. Her proposed thesis project is “The Meaning of Life.” On this occasion, let us pause to consider these wise words of the sage Philosoraptor:

Philosoraptor asks “what if finding the meaning of life is the meaning of life?”

Rebecca Lu is qualified!

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The Drubin/Barnes Lab would like to congratulate Rebecca Lu who passed her qualifying exam on Wednesday, April 18!

Our note to Rebecca reads: “Congrats! We used to like you! We still do! But we used to, too!”

Here we recount the epic saga of Rebecca’s Ph.D qualification:

After she wrote her proposal, her chair asked her to rewrite it. Rebecca is smarter than Randy Schekman though. She just made a copy.

Rebecca brought food for her committee, and Doug Koshland said, ‘I’m gonna have a donut. Does anyone want one?’ That’s when Rebecca realized that a Qualifying Exam is like some weird quiz where your committee reveals the answers before asking their questions.

During Rebecca’s exam, her committee didn’t ask her a question for 30 minutes. That would have been a REALLY long question, after all.

Rebecca closed her eyes a lot during her Qual. She wasn’t sleeping. She just drew a picture of Randy handing her the Nobel Prize on the back of her eyelids.

You can’t please all the people all the time. Fortunately, all those people weren’t at Rebecca’s Qualifying Exam.

When her exam was over, Randy said, “Guess what. You passed.” Rebecca told Randy, “Dude, you gotta give me time to guess. If you’re gonna quiz me, you must insert a pause in there.”

Akemi Kunibe was the last grad student in the Drubin/Barnes Lab to pass her Qual. She’s smart. She was a tough act to follow. Rebecca will be an especially hard act to follow, cuz when she finished her Qual, she took all of the dry-erase markers with her.

Rebecca doesn’t know the meaning of the word “fail.” And that is kinda worse than not passing in a way, if you think about it. She’s a Ph.D candidate, but she still doesn’t understand simple words.

Congratulations Rebecca Lu! And thank you Mitch Hedberg for the jokes!

2012 “Lab Comedy of the Year”

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Two weeks ago, we announced that the blog of BioTechniques Journal had selected “Grad School, I Love You (But You’re Bringing Me Down)” as the 2012 “Science Parody of the Year.”

Now I’m excited to announce that the “Lab Comedy of the Year” for 2012 is Vol I: How to Run a DNA Gel (Molecular and Cell Biology Training Video Series). The video stars Nate Krefman (a graduate student in the Drubin/Barnes Lab) and Aaron Welch (a graduate student in Doug Koshland’s lab). The video was filmed and directed by graduate students Brock Roberts (Henk Roelink’s lab) and Robbie Calderon (Krishna Niyogi lab, Plant and Microbial Biology). The video was conceived and produced by Nate. The scientific journal BioTechniques put the “Science Parody of the Year” to a readers’ vote this week on their blog.

The winning video is actually the first in two part series. The second video, Vol II: How do Do a DNA Mini-Prep (Molecular and Cell Biology Training Video Series), stars Robbie and Brock, and was directed and produced by Nate.

All of the videos were produced for an annual funny movie event called MCB Follies held by graduate students in UC-Berkeley’s Department of Molecular and Cell Biology. Look for more of these sort of videos from Nate and other graduate students in the Drubin/Barnes lab in the future.

2012 “Lab Comedy of the Year”: