Evolutionary Cell Biology
Journal Club
Meetings are currently held on Mondays, 1:30-2:30pm in the Lieber Room.
October 28, 2010: What is evolutionary cell biology? See Mike's talk at KITP here.
Reading: Elde, Long, and Turkewitz, 2007. A role for convergent evolution in the secretory life of cells.
November 4, 2010: The nuclear envelope and nuclear pores.
Readings: Strambio-De-Castillia, Niepel, and Rout, 2010. The nuclear pore complex: bridging nuclear transport and gene regulation.
Devos, Dokudovskaya, Alber, Williams, Chait, Sali, and Rout, 2004. Components of coated vesicles and nuclear pore complexes share a common molecular architecture.
November 11, 2010: Origins of the nuclear envelope and nuclear pores.
Readings: Neumann, Lundin, and Poole, 2010. Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor.
Mans, Anantharaman, Aravind, and Koonin, 2004. Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.
November 18, 2010 : Nuclear pores and transposable elements.
Readings: Irwin, Aye, Baldi, et al. 2005. Retroviruses and yeast retrotransposons use overlapping sets of host genes.
Varadarajan, Mahalingam, Liu, et al. 2005. The functionally conserved nucleoporins Nup124p from fission yeast and the human Nup153 mediate nuclear import and activity of the Tf1 retrotransposon and HIV-1 Vpr
.
December 2, 2010: The nucleus and the evolution of genome size.
Reading: Cavalier-Smith, 2005. Economy, Speed and Size Matter: Evolutionary Forces Driving Nuclear Genome Miniaturization and Expansion.
January 28, 2011 : Postponed
February 4, 2011 : Evolution of complex traits. Mike Lynch will present.
February 11, 2011: Conflict and the pore complex.
Readings: Presgraves, 2007. Does genetic conflict drive rapid molecular evolution of nuclear transport genes in Drosophila?
Presgraves and Stephan, 2007. Pervasive Adaptive Evolution among Interactors of the Drosophila Hybrid Inviability Gene, Nup96.
February 18, 2011 : Introduction to cytoskeleton.
Reading: Lowe and Amos, 2009. Evolution of cytomotive filaments: The cytoskeleton from prokaryotes to eukaryotes.
March 5, 2011: Protein folds
Readings: Tokuriki and Tawfik, 2009. Protein Dynamism and Evolvability.
Wang, et al., 2011. A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation.
March 11, 2011: Chaperones
Readings: Macario, et al., 2006. Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three lineages of the archaeal hsp70(dnaK) gene.
Hartl and Hayer-Hartl, 2009. Converging concepts of protein folding in vitro and in vivo.
March 24, 2011: Tubulin protein modifications
Readings: Hammond, et al., 2008. Tubulin modifications and their cellular functions.
Janke and Kneussel, 2010. Tubulin post-translational modifications: encoding functions on the neuronal microtubule cytoskeleton.
April 1, 2011: Protein modifications and disease
Readings: Lundin, et al., 2009. Quality control of cytoskeletal proteins and human disease.
April 11, 2011: Protein promiscuity and evolvability
Readings: Patrick, et al., 2007. Multicopy Suppression Underpins Metabolic Evolvability.
Khersonsky, et al., 2006. Enzyme promiscuity: evolutionary and mechanistic aspects.
April 18, 2011: Protein promiscuity and protein folding
Readings: Anderson, 2011. Evolving promiscuously.
Soo, et al., 2011. Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli.
Pena, et al., 2010. Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection.
April 22, 2011: Gene duplication
Innan and Kondrashov, 2010. The evolution of gene duplications: classifying and distinguishing between models.
October 3, 2011:
Readings: Stoltzfus, 1999. On the Possibility of Constructive Neutral Evolution.
Optional: Short Science perspectives piece explaining some context and significance: http://www.sciencemag.org/content/330/6006/920.full
A longer more recent review, but less theoretically comprehensive than Stoltzfus 1999: http://onlinelibrary.wiley.com/doi/10.1002/iub.489/full
October 10, 2011:
Readings:
Richter, et al., 2007. Functional diversification of closely related ARF-GEFs in protein secretion and recycling.
Supplemental background review: Donaldson JG, Jackson CL. Nat Rev Mol Cell Biol. 2011 Jun: 12(6):362-375.
October 17, 2011:
Readings: Hirst, et al., 2011. The fifth adaptor protein complex.
October 24, 2011:
Readings: Iwamoto, et al., 2009. Two distinct repeat sequences of Nup98 nucleoporins characterize dual nuclei in the binucleated ciliate Tetrahymena.
Goldfarb and Gorovsky, 2009. Nuclear dimorphism: two peas in a pod.
October 31, 2011:
Gurkan, et al., 2005. Large-scale profiling of Rab GTPase trafficking networks: the membrome.