Fall 2010 Journal Club (Graduate Research Seminar)-Department of Biological Sciences - Carnegie Mellon University

Fall 2010 Journal Club

(Graduate Research Seminar)

Journal club is held in the Conference Room of the Mellon Institute at 12:30 p.m. on Wednesdays unless otherwise indicated.




8/25 Paul Barton
Interfering with RNAi: Evasion of Antiviral Activity

Michael Gamalinda HOTAIR Just Got Hotter: lincRNAS Could Actually Link
9/1 Nathan Hsu
Circadian and Social Cues Regulate Ion Channel Trafficking

James Hughes

DNA Zip Codes Control an Ancient Mechanism for Gene Targeting to the Nuclear Periphery

Ahmed, S. et al. DNA Zip Codes Control an Ancient Mechanism for Gene Targeting to the Nuclear Periphery. Nature Cell Biology 2, 111-118, 2010.

9/8 Stephanie Hughes

Evolutionary Mirages: Illusions of Conserved Structures in Enhancers

Lusk RW, Eisen MB. Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. PLoS Genet 6(1): e1000829, 2010.

Andrew Kehr

A Complex(in) Switch Mechanism for SNARE-Mediated Fusion

Giraudo, et. al. Alternative Zippering as an On-Off Switch for SNARE-Mediated Fusion. Science 323: 512-6, 2009.


Andrew Markham

mRNA Quality Control: Evidence for a Novel De-capping Enzyme

Jiao X, Xiang S, Oh C, Martin C, Tong L, Kiledjian M. Identification of a quality-control mechanism for mRNA 5'-end capping. Nature:1-5, 2010.

Ashita Magal
NADPH: The Gatekeeper for Drosophila Apoptosis

Yang et. al. Metabolic regulation of Drosophila apoptosis through inhibitory phosphorylation of Dronc. The Embo Journal, 2010.

Deborah Makin Dissecting the CTD Code of RNA Polymerase II: Phosphorylation of Ser7 Across Protein-coding Genes
Tietjen JR, et al. Chemical-genomic dissection of the CTD code. Nat. Struct. Mol. Biol. 17: 1154-1161, 2010.

Ezgi Kunttas-Tatli

Testing Interactions between APC2 and Armadillo in Wnt Signaling

Sailatha Ravi

DNA Packaging Role of phi-29 Homomeric Ring ATPase
Moffitt et al., Intersubunit coordination in a homomeric ring ATPase, Nature, 2009.

Suchitra Ramachandran Information is Wealth: Midbrain Dopamine Neurons Signal Preference for Advance Information about Upcoming Rewards
Bromberg-Martin E and Hikosaka O. Midbrain Dopamine Neurons Signal Preference for Advance Information about Upcoming Rewards. Neuron, 63(1):119-126, 2009 July 16.
10/6 Simran Saini Staph vs. Staph: A New Way to Attack Staphylococcus aureus
Iwase et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 2010.

Gregory Smith
Codon Pair Bias: A Powerful Tool in Rational Influenza Vaccine Design
Mueller, S. et al. Live attenuated influenza virus vaccines by computer-aided rational design. Nature Biotechnology 28, 723-726, 2010.
Amanda Soohoo With Curves like Those, I'll Go Inside: How Membrane Curvature Proteins Nucleate Endocytosis
Henne et. al. FCHo Proteins Are Nucleators of Clathrin-Mediated Endocytosis. Science 328, June 2010.

Ritika Tewari Early to Late Endosome Transition
Dmitry Poteryaev,Sunando Datta,Karin Ackema, Marino Zerial and Anne Spang.Identification of the Switch in Early-to-Late Endosome Transition. Cell 141, 497–508, 30 Apr 2010.
Idil Ulengin To be or not to be Translocated: A Quality Control Pathway that Regulates Translocation during ER Stress Leads to Neurodegeneration
Rane NS et al. Reduced translocation of Nascent Prion protein during Er stress contributes to Neurodegeneration. Developmental Cell, 15:359-370, 2008.

Phu Van
Targeted Proteomics with Selected Reaction Monitoring
Picotti P, Bodenmiller B, Mueller L, Domon B, Aebersold R.Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell, 138(4)795-806, 2009.
10/27 Rachel Vistein
Hanging in the Balance: CDK5 and Calcineurin Regulate the Exocytosis of Presynaptic Vesicles
Kim SH and Ryan TA. CDK5 Serves as a Major Control Point in Neurotransmitter Release. August 2010.

Mingrui Zhang
Rescuing Vision in Retinitis Pigmentosa Patients
Busskamp et al. Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa. Science (329), 413-417, 2010.
11/3 Shantanu Bhattacharyya NMR Structure of Single Chain Antibody Fragment M8

Russell Schwartz, Ph.D.
How a Few Years of Work Can Save You a Millisecond
Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-Level Characterization of the Structural Dynamics of Proteins. Science:341-346, 15 October 2010.
11/10 (12:30 - 1:40 p.m.)
Rotation 1 Presentations

Shanna Bowersox
Effects of Chronic Morphine on Trafficking of the mu Opioid Receptor
Advisor: Puthenveedu

Ting Liu
Two Small GTPases & One Big Question- Recycling Study of β2 Adrenergic Receptors
Advisor: Puthenveedu

Zhongling Sun
Characterizing Neuronal Diversity in the Neocortex
Advisor: Barth

Madhumitha Ramesh
Correlations in Intrinsic Properties between Sister and Non-sister Mitral Cells
Advisor: Urban

John Pettersson
Osmotic Suppression of Giant Genome Phage λ Ejection
Advisor: Evilevitch

Han Lai
Human Papillomavirus (HPV) Capsid Formation
Advisor: Schwartz

Sahil Sangani
NMR Structure of Single-chain Antibody (ScFv) K7
Advisor: Rule

11/11 (12:30 - 1:40 p.m., Mellon Institute Social Room)
Rotation 1 Presentations

Yi Wang
Altering Dye Binding with Directed Mutagenesis of a Fluorogen Activating Peptide
Advisor: Bruchez

Elizabeth Ransey
Progress in Detection of 5HTR2A Internalization in Live Cells Using FAP-based Biosensor Technology
Advisor: Jarvik

Salini Konikkat
The Role of DNA Replication and Cell Division in Re-wiring Developmental Gene Regulatory Networks
Advisor: Ettensohn

Jigarkumar Desai
Adenomatous Polyposis Coli(APC): Understanding the Mode of Regulation of its Activity in a Cell-cycle Dependent Manner in the Drosophila Syncytial Blastoderm
Advisor: McCartney

Eugenio Gallo
A Rapid and Systematic Approach for Detecting Protein-protein Interactions in Candida Albicans
Advisor: Mitchell

Olivia Molinar
RNA Recognition by DNA Nanotags: A New Approach to Fluorescent Labeling of RNA
Advisor: Armitage

Karen Kormuth
Expression and Purification of RNA Debranching Enzyme
Advisor: Macbeth

11/17 Shantanu Ganguly
Quorum Sensing in Candida albicans Biofilms

John Holleran
Cell Surface Detection of Proteins Implicated in Cystic Fibrosis
No Journal Club - Thanksgiving Week
12/1 Elmer Ker
Toward Spatial Control of Complex Tissues using Growth Factor Patterns and Fiber Alignment

Aaron Mitchell, Ph.D.
Septins Skore