Tag Archives: molecular biology

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).

An Interview with David Drubin in Biowire

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

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

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 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.

Journal Club on Monday, April 16

For our next Journal Club, Christa Cortesio will present the following paper:

Distinct and separable activities of the endocytic clathrin-coat components Fcho1/2 and AP-2 in developmental patterning.  Umasankar PK, Sanker S, Thieman JR, Chakraborty S, Wendland B, Tsang M, Traub LM.  Nat Cell Biol. 2012 Apr 8. doi: 10.1038/ncb2473. PMID: 22484487.

Interaction diagram for FCHO1/2 and select endocytic pioneer coat components. Presumptive contacts are indicated with dotted lines.

Journal Club on Monday, March 05

For our last Journal Club, Itziar Benitez-Ibarlucea presented the following paper:

Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains. DeWitt MA, Chang AY, Combs PA, Yildiz A. Science. 2012 Jan 13;335(6065):221-5. PMID: 22157083