Tag Archives: Journal Club

Journal Club on Thursday, April 18

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.

Journal Club on Monday, March 17

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).

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.

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.

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.

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).

Journal Club on Monday, October 15

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

Journal Club on Monday, October 1

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

Journal Club on Thursday, July 26

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.

Centromeres (CB-mCherry) and chromosomes (YFP emission) for a single time point. (bottom) Color-coded YFP/CFP emission ratio at different time points. The timestamp (minutes and seconds) is relative to ZM washout at t = 0. Bar, 5 µm.

Journal Club on Monday, July 09

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.

Journal Club on Monday, June 25

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.

Scatter plot of correlation coefficients comparing GI profiles for Sp versus Sc. Highlighted examples of pairwise relationships that are correlated in Sp but not Sc are listed below the scatter plot. Bold indicates functional relationships explored in this study. See Table S1 for additional examples of correlated pairwise relationships conserved between Sp and Sc (green), and pairwise relationships that are correlated in Sc but not Sp (cyan) or Sp but not Sc (red).

Journal Club on Monday, June 11

For our next Journal Club, Lillie Cohn will present the following paper:

Reconstitution of clathrin-coated bud and vesicle formation with minimal components.  Dannhauser PN, Ungewickell EJ.  Nat Cell Biol. 2012 Apr 22;14(6):634-9.  PMID: 22522172.

Ultrathin section of H6-ΔANTH-AP180328–896-coated liposomes that were incubated with clathrin at 4 °C (c) or 37 °C