JournalClub

In 2009, the journal club will be folded into the lab meeting.

Calendar

(Also shows lab meeting)

%CALENDAR% Edit this list to add date, name and paper:

Past papers (2008):

• 17 Oct 2008 - Lars - 18833279
• 24 Oct 2008 - Oscar - 18687880
• 31 Oct 2008 - Ian - 14978301
• 21 Nov 2008 - Mitch - 18929678
• 5 Dec 2008 - Oscar - 14633391

Proposed papers

General theme for fall 2008: evolutionary origins & reconstruction.

= already done

• JournalClub
  • Calendar
  • Proposed papers
    • Algorithms
    • The oldest genes
    • Disease & biomedical applications
      • Viruses
      • Other pathogens
      • Repetitive sequence
      • Pharmacognosy
    • Cell biology
    • Transposons
    • Experimental Validation of Reconstruction
  • See also...

Algorithms

• Haussler reconstruction papers
  • Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D.  The infinite sites model of genome evolution.  Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14254-61. doi: 10.1073/pnas.0805217105. Epub 2008 Sep 11.
  • Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D.  DUPCAR: reconstructing contiguous ancestral regions with duplications.  J Comput Biol. 2008 Oct;15(8):1007-27. doi: 10.1089/cmb.2008.0069.

• Theoretical limits of reconstruction accuracy
  • Li G, Steel M, Zhang L.  More taxa are not necessarily better for the reconstruction of ancestral character states.  Syst Biol. 2008 Aug;57(4):647-53. doi: 10.1080/10635150802203898.
  • Mossel E.  On the impossibility of reconstructing ancestral data and phylogenies.  J Comput Biol. 2003;10(5):669-76.
  • http://front.math.ucdavis.edu/0406.5447
  • http://www.stat.berkeley.edu/~mossel/publications/second.pdf

The oldest genes

• Gutell, Smith et al -- origins of the ribosome
  • Smith TF, Lee JC, Gutell RR, Hartman H.  The origin and evolution of the ribosome.  Biol Direct. 2008 Apr 22;3:16. doi: 10.1186/1745-6150-3-16.
• Primordial genes
  • Isenbarger TA, Carr CE, Johnson SS, Finney M, Church GM, Gilbert W, Zuber MT, Ruvkun G.  The most conserved genome segments for life detection on Earth and other planets.  Orig Life Evol Biosph. 2008 Dec;38(6):517-33. doi: 10.1007/s11084-008-9148-z. Epub 2008 Oct 14.

Disease & biomedical applications

Viruses

• Worobey et al -- origins of HIV
  • Worobey M et al.  Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.  Nature. 2008 Oct 2;455(7213):661-4. doi: 10.1038/nature07390.

• Quasispecies & error thresholds
  • Bull JJ, Meyers LA, Lachmann M.  Quasispecies made simple.  PLoS Comput Biol. 2005 Nov;1(6):e61.
  • http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010061

• Selection in viruses
  • de Groot S, Mailund T, Lunter G, Hein J.  Investigating selection on viruses: a statistical alignment approach.  BMC Bioinformatics. 2008 Jul 10;9:304. doi: 10.1186/1471-2105-9-304.
• Rate variation in HIV
  • Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N, Pupko T.  Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.  PLoS Comput Biol. 2008 Nov;4(11):e1000214. doi: 10.1371/journal.pcbi.1000214. Epub 2008 Nov 7.

Other pathogens

• Origin and evolution of M. tuberculosis
  • 9000 year old M. tuberculosis DNA?!
  • Article

Repetitive sequence

• Microsatellite dynamics
  • Bacolla A, Larson JE, Collins JR, Li J, Milosavljevic A, Stenson PD, Cooper DN, Wells RD.  Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties.  Genome Res. 2008 Oct;18(10):1545-53. doi: 10.1101/gr.078303.108. Epub 2008 Aug 7.
  • Tanay A, Siggia ED.  Sequence context affects the rate of short insertions and deletions in flies and primates.  Genome Biol. 2008;9(2):R37. doi: 10.1186/gb-2008-9-2-r37. Epub 2008 Feb 21.
• Prions
  • Ahn I, Son HS.  Comparative bioinformatics analysis of prion proteins isolated from reptile, rodent, ruminant, and human species.  Exp Mol Med. 2007 Dec 31;39(6):769-77.
  • Lupi O, Dadalti P, Cruz E, Goodheart C.  Did the first virus self-assemble from self-replicating prion proteins and RNA?  Med Hypotheses. 2007;69(4):724-30. Epub 2007 May 18.
  • Lupi O, Dadalti P, Cruz E, Sanberg PR.  Are prions related to the emergence of early life?  Med Hypotheses. 2006;67(5):1027-33. Epub 2006 Jun 30.

Pharmacognosy

• Antimicrobial peptides
  • Zhu S, Gao B.  A fossil antibacterial peptide gives clues to structural diversity of cathelicidin-derived host defense peptides.  FASEB J. 2009 Jan;23(1):13-20. doi: 10.1096/fj.08-114579. Epub 2008 Sep 16.

Background reading:

• Wikipedia:Pharmacognosy
• First example of pharmacognosy: discovery of penicillin

Cell biology

• Evolution of phospholipid signaling
  • Phosphatidylinositols form an important membrane-based signaling code and inositol-based probes are an emerging area at the interface of proteomics & chemical biology. This review outlines a very interesting evolutionary connection to Wikipedia:Symbiogenesis
  • Michell RH.  Inositol derivatives: evolution and functions.  Nat Rev Mol Cell Biol. 2008 Feb;9(2):151-61. doi: 10.1038/nrm2334.
• Denker et al -- horizontal gene transfer and the evolution of cnidarian stinging cells
  • only two pages, but looks like there's a lot of fun stuff to dig in to in the supplemental
  • Denker E, Bapteste E, Le Guyader H, Manuel M, Rabet N.  Horizontal gene transfer and the evolution of cnidarian stinging cells.  Curr Biol. 2008 Sep 23;18(18):R858-9. doi: 10.1016/j.cub.2008.07.031.

Transposons

See also TransposonPapers.

• horizontal transfer of DNA transposons in mammals
  • simultaneous transposon transfers in multiple distinct lineages, presumably the result of a virus
  • article

• Selfish elements & the evolution of genome architecture
  • Koonin EV.  Evolution of genome architecture.  Int J Biochem Cell Biol. 2009 Feb;41(2):298-306. doi: 10.1016/j.biocel.2008.09.015. Epub 2008 Sep 26.

Experimental Validation of Reconstruction

• Resurrecting ancestral alcohol dehydrogenases from yeast

See also...

See also

• LabMeeting
• ReconstructionTargets
• OldJournalClubInfo

Lab meeting events (included from LabMeeting page):

• 17 Sep - joint BBOP/HL meeting - 381 Stanley
• 29 Oct - Le Petit Cheval
• 5 Nov - Chris Nasrallah - 421 Stanley