For our Journal Club on April 18, Akemi Kunibe presented the following paper:
Endoplasmic reticulum-associated mitochondria-cortex tether functions in the distribution and inheritance of mitochondria. Lackner LL, Ping H, Graef M, Murley A, Nunnari J. Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):E458-67. PMID: 23341591.
The ER is a component of the Num1 mitochondria–cell cortex tether.
For our Journal Club on March 17, Rebecca Lu will present the following paper:
Robust polarity establishment occurs via an endocytosis-based cortical corralling mechanism. Jose M, Tollis S, Nair D, Sibarita JB, McCusker D. J Cell Biol. 2013 Feb 18;200(4):407-18. PMID: 23401000
Schematics illustrating the mathematical model. Shown are the Cdc42 autoamplification module (A), the complete endocytosis module (B), the exocytosis module (C), and a legend for graphics (D).
Synthetic boy band 37 Degrees made a surprise live performance at MCB Follies this year. Before a screaming hoard of desperate graduate students, 37 Degrees performed their new single “I Want to Graduate.” You may recognize the song as a parody of the Backstreet Boys single “I Want it That Way.”
You may also recognize one of the members of 37 Degrees as Nate Krefman, a graduate student in the Drubin/Barnes Lab! The other participants in this transient complex are fellow MCB graduate students Phil Cleves and Andrew Glazer from Craig Miller’s Lab (also from “I’m Bringin’ Stickleback”), Alec Sexton from Cathy Collins’ Lab (also from “Grad School Pressure”), and Brock Roberts from Henk Roelink’s Lab (also from “Vol II: How to Do a DNA Mini-Prep (Molecular and Cell Biology Training Video Series”).
37 DEGREES is Nate Krefman, Phil Cleves, Andrew Glazer, Alec Sexton, & Brock Roberts
CONCEPT: Meru S.
LYRICS: Meru S. & Nate Krefman
PRE-RECORDED VOCALS: Nate Krefman
LIVE VOCALS: 37 Degrees
CAMERA: David McCleary
SLIDESHOW & VIDEO EDITING: Nate Krefman
________________________________________________
LYRICS:
Nate:
It is my fire —
my one desire.
Believe when I say:
I want to graduate.
Phil:
But we are two worlds apart,
Just years from the start.
It’s your fate:
You’ll never graduate.
All:
Tell me when…
I’m begging my committee.
Tell me when…
Be in grad school till I’m fifty.
Tell me when…
You never wanna hear me say:
I want to graduate
Andrew:
It will be so wrong,
If this just goes on.
Please don’t come too late.
Cuz I want to graduate.
All:
Tell me when…
All my friends are wearing Polo.
Tell me when…
But I’m still dressing like a hobo.
Tell me when…
You never wanna hear me say:
I want to graduate.
Phil:
Now I can see that you wanna depart —
But not if it’s up to me. Yeah.
No matter your progress,
I want you to know,
There’s no way you’ll ever leave.
Alec:
It is my fire —
My one desire.
Nate:
Ph.D…
Andrew:
Ph.D…
Alec:
Ph.D…
Brock:
Ph.D…
Phil:
You never hear me!
All:
I’m ready for my thesis.
I could even do a defense.
I never wanna hear you say:
You’ll never graduate.
All:
Tell me when…
This stipend ain’t a salary.
Tell me when…
I wanna get better pay.
Tell me when…
You never wanna hear me say:
I want to graduate.
Nate:
Cuz I want to graduate…
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!
For our Journal Club on February 7, Yansong Miao will present the following paper:
Rocket launcher mechanism of collaborative actin assembly defined by single-molecule imaging. Breitsprecher D, Jaiswal R, Bombardier JP, Gould CJ, Gelles J, Goode BL. Science. 2012 Jun 1;336(6085):1164-8. doi: 10.1126/science.1218062. PMID: 22654058
Proposed ‘rocket launcher’ model for mDia1-APC collaboration during actin filament assembly
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.
PtdIns(4,5)P2-positive intracellular vesicles, visualized with GFP- or RFP-PHPLCδ, colocalize with endocytic clathrin machinery components (endogenous AP-2, epsin 1, and dynamin 2–GFP) but not with markers of endosomes (endogenous EEA1, GFP-Rab5, and GFP-Rab9), the endosomal phosphoinositide PtdIns3P (GFP-2×FYVEHrs), and Golgi-localized PtdIns4P (GFP-PHOSBP). For clarity, PHPLCδ is false colored green, and the second marker is false colored red in all images.
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.
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.
Maps of entry clone pE-GFP, expression cloning vector pX-lacZ and expression construct pX-GFP. Black arrows show the position of the restriction sites for the enzymes BseRI and HindIII, and the numbers next to these indicate the sizes of the restriction fragments obtained. The grey triangle represents a Streptomyces phage C31 attB recombination site (this site is not used for the cloning procedure described here). Z, LacZ alpha fragment; N, Viral 3′ Non-translated region; T, Nos terminator; RB/LB, T-DNA right/left borders; S1–S2, selectable markers 1 and 2 (resistance to carbenicillin and kanamycin, respectively).
For our Journal Club on October 15, Jay Ryoo presented the following paper:
The first five seconds in the life of a clathrin-coated pit. Cocucci E, Aguet F, Boulant S, Kirchhausen T. Cell. 2012 Aug 3;150(3):495-507. PMID: 22863004.
Schematic representation of the experimental setup and computational analysis
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
Phase transition correlates to biochemical activity transition in the nephrin/Nck/N-WASP system