Publications
The publications listed here, written by Life Sciences faculty and lab members, were published in January through June 2009.

  • Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JM, Orwig SD, Kozakov D, Brenke R, Chuang GY, Beglov D, Vajda S, Petsko GA, Ringe D. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput Aided Mol Des. 2009 Jun 12.

  • de Almeida L, Idiart M, Lisman JE. The input-output transformation of the hippocampal granule cells: from grid cells to place fields. J Neurosci. 2009 Jun 10;29(23):7504-12.

  • de Almeida L, Idiart M, Lisman JE. A second function of gamma frequency oscillations: an e%-max winner-take-all mechanism selects which cells fire. J Neurosci. 2009 Jun 10;29(23):7497-503.

  • Ma M, Szabo TM, Jia C, Marder E, Li L. Mass Spectrometric Characterization and Physiological Actions of Novel Crustacean C-type Allatostatins. Peptides. 2009 Jun 5.

  • Chen JZ, Settembre EC, Aoki ST, Zhang X, Bellamy AR, Dormitzer PR, Harrison SC, Grigorieff N. Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Proc Natl Acad Sci U S A. 2009 Jun 1.

  • Maryott J, Sekuler R. Age-related changes in imitating sequences of observed movements. Psychol Aging. 2009 Jun;24(2):476-86.

  • Hedstrom L. IMP Dehydrogenase: Structure, Mechanism, and Inhibition. Chem Rev. 2009 May 29.

  • Okaty BW, Miller MN, Sugino K, Hempel CM, Nelson SB. Transcriptional and electrophysiological maturation of neocortical fast-spiking GABAergic interneurons. J Neurosci. 2009 May 27;29(21):7040-52.

  • Sigala PA, Caaveiro JM, Ringe D, Petsko GA, Herschlag D. Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site. Biochemistry. 2009 May 26.

  • Osborne A, Reis AH, Bach L, Wangh LJ. Single-molecule LATE-PCR analysis of human mitochondrial genomic sequence variations. PLoS ONE. 2009 May 20;4(5):e5636.

  • Gainey MA, Hurvitz-Wolff JR, Lambo ME, Turrigiano GG. Synaptic scaling requires the GluR2 subunit of the AMPA receptor. J Neurosci. 2009 May 20;29(20):6479-89.

  • Hage R, Tung L, Du H, Stands L, Rosbash M, Chang TH. A Targeted Bypass Screen Identifies Ynl187p, Prp42p, Snu71p, and Cbp80p for Stable U1 snRNP/Pre-mRNA Interaction. Mol Cell Biol. 2009 May 18.

  • Handa N, Morimatsu K, Lovett ST, Kowalczykowski SC. Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli. Genes Dev. 2009 May 15;23(10):1234-45.

  • Gandhi M, Achard V, Blanchoin L, Goode BL. Coronin switches roles in actin disassembly depending on the nucleotide state of actin. Mol Cell. 2009 May 15;34(3):364-74.

  • Petsko GA. Guilt by association. Genome Biol. 2009;10(4):104. Epub 2009 Apr 29.

  • D'Aquino JA, Denninger AR, Moulin AG, D'Aquino KE, Ringe D. Decreased Sensitivity to Changes in the Concentration of Metal Ions as the Basis for the Hyperactivity of DtxR(E175K). J Mol Biol. 2009 May 8.

  • Taylor AL, Goaillard JM, Marder E. How multiple conductances determine electrophysiological properties in a multicompartment model. J Neurosci. 2009 Apr 29;29(17):5573-86.

  • Luther JA, Birren SJ. p75 and TrkA signaling regulates sympathetic neuronal firing patterns via differential modulation of voltage-gated currents. J Neurosci. 2009 Apr 29;29(17):5411-24.

  • Slawson JB, Kim EZ, Griffith LC. High-resolution video tracking of locomotion in adult Drosophila melanogaster. J Vis Exp. 2009 Feb 20;(24).

  • Lackner JR, DiZio P. Angular displacement perception modulated by force background. Exp Brain Res. 2009 May;195(2):335-43.

  • Fiser J. Perceptual learning and representational learning in humans and animals. Learn Behav. 2009 May;37(2):141-53.

  • Lieberman RL, D'aquino JA, Ringe D, Petsko GA. Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry. 2009 Jun 9;48(22):4816-27.

  • Doksani Y, Bermejo R, Fiorani S, Haber JE, Foiani M. Replicon dynamics, dormant origin firing, and terminal fork integrity after double-strand break formation. Cell. 2009 Apr 17;137(2):247-58.

  • Dementieva IS, Tereshko V, McCrossan ZA, Solomaha E, Araki D, Xu C, Grigorieff N, Goldstein SA. Pentameric assembly of potassium channel tetramerization domain-containing protein 5. J Mol Biol. 2009 Mar 20;387(1):175-91.

  • Petsko GA. Too big to succeed? Genome Biol. 2009;10(3):103. Epub 2009 Mar 30.

  • Pulver SR, Pashkovski SL, Hornstein NJ, Garrity PA, Griffith LC. Temporal Dynamics of Neuronal Activation by Channelrhodopsin-2 and TRPA1 Determine Behavioral Output in Drosophila Larvae. J Neurophysiol. 2009 Jun;101(6):3075-88.

  • Petsko GA. The greatest book you never read. EMBO Rep. 2009 Apr;10(4):298.

  • Pomeranz Krummel DA, Oubridge C, Leung AK, Li J, Nagai K. Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature. 2009 Mar 26;458(7237):475-80.

  • Dore JJ, Dewitt JC, Setty N, Donald MD, Joo E, Chesarone MA, Birren SJ. Multiple Signaling Pathways Converge to Regulate Bone-Morphogenetic-Protein-Dependent Glial Gene Expression. Dev Neurosci. 2009 Mar 27.

  • Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry. 2009 Apr 21;48(15):3247-57.

  • Rosbash M. The implications of multiple circadian clock origins. PLoS Biol. 2009 Mar 17;7(3):e62. Review.

  • Petsko GA. Many happy returns. Genome Biol. 2009 Feb 27;10(2):102.

  • Hornstein NJ, Pulver SR, Griffith LC. Channelrhodopsin2 mediated stimulation of synaptic potentials at Drosophila neuromuscular junctions. J Vis Exp. 2009 Mar 16;(25).

  • Novak WR, Moulin AG, Blakeley MP, Schlichting I, Petsko GA, Ringe D. A preliminary neutron diffraction study of gamma-chymotrypsin. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Mar 1;65(Pt 3):317-20.

  • Ferullo DJ, Cooper DL, Moore HR, Lovett ST. Cell cycle synchronization of Escherichia coli using the stringent response, with fluorescence labeling assays for DNA content and replication. Methods. 2009 May;48(1):8-13.

  • Fontanini A, Grossman SE, Figueroa JA, Katz DB. Distinct subtypes of basolateral amygdala taste neurons reflect palatability and reward. J Neurosci. 2009 Feb 25;29(8):2486-95.

  • Lackner JR, DiZio P. Control and calibration of multi-segment reaching movements. Adv Exp Med Biol. 2009;629:681-98. Review.  

  • Petsko GA. Life is a Ponzi scheme. Genome Biol. 2009;10(1):101. Epub 2009 Jan 27.

  • Bracken BK, Turrigiano GG. Experience-dependent regulation of TrkB isoforms in rodent visual cortex. Dev Neurobiol. 2009 Apr;69(5):267-78.

  • Kadener S, Rodriguez J, Abruzzi KC, Khodor YL, Sugino K, Marr MT 2nd, Nelson S, Rosbash M. Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. RNA. 2009 Apr;15(4):537-45. Epub 2009 Feb 17.

  • Chesarone M, Gould CJ, Moseley JB, Goode BL. Displacement of formins from growing barbed ends by bud14 is critical for actin cable architecture and function. Dev Cell. 2009 Feb;16(2):292-302.

  • Visscher KM, Kahana MJ, Sekuler R. Trial-to-trial carryover in auditory short-term memory. J Exp Psychol Learn Mem Cogn. 2009 Jan;35(1):46-56.

  • Jain S, Sugawara N, Lydeard J, Vaze M, Tanguy Le Gac N, Haber JE. A recombination execution checkpoint regulates the choice of homologous recombination pathway during DNA double-strand break repair. Genes Dev. 2009 Feb 1;23(3):291-303.

  • Quintero-Monzon O, Jonasson EM, Bertling E, Talarico L, Chaudhry F, Sihvo M, Lappalainen P, Goode BL. Reconstitution and dissection of the 600-kDa Srv2/CAP complex: roles for oligomerization and cofilin-actin binding in driving actin turnover. J Biol Chem. 2009 Apr 17;284(16):10923-34.

  • Marr MT 2nd. TAF4 takes flight. Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1295-6. Epub 2009 Jan 27.

  • Hoyte KJ, Brownell H, Wingfield A. Components of speech prosody and their use in detection of syntactic structure by older adults. Exp Aging Res. 2009 Jan-Mar;35(1):129-51.

  • Chesarone MA, Goode BL. Actin nucleation and elongation factors: mechanisms and interplay. Curr Opin Cell Biol. 2009 Feb;21(1):28-37.

  • Kim JA, Haber JE. Chromatin assembly factors Asf1 and CAF-1 have overlapping roles in deactivating the DNA damage checkpoint when DNA repair is complete. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1151-6.

  • Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry. 2009 Feb 0;48(5):981-94.

  • Lim HH, Miller C. Intracellular proton-transfer mutants in a CLC Cl-/H+ exchanger. J Gen Physiol. 2009 Feb;133(2):131-8. Epub 2009 Jan 12.

  • Marder E. Electrical synapses: rectification demystified. Curr Biol. 2009 Jan 13;19(1):R34-5. Review.

  • Prakash R, Satory D, Dray E, Papusha A, Scheller J, Kramer W, Krejci L, Klein H, Haber JE, Sung P, Ira G. Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination. Genes Dev. 2009 Jan 1;23(1):67-79.

  • Sun XX, Bostrom SL, Griffith LC. Alternative splicing of the eag potassium channel gene in Drosophila generates a novel signal transduction scaffolding protein. Mol Cell Neurosci. 2009 Mar;40(3):338-43.

  • Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST. A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS. Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):611-6.

  • Stroupe ME, Xu C, Goode BL, Grigorieff N. Actin filament labels for localizing protein components in large complexes viewed by electron microscopy. RNA. 2009 Feb;15(2):244-8.

  • Karabacak NM, Li L, Tiwari A, Hayward LJ, Hong P, Easterling ML, Agar JN. Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Mol Cell Proteomics. 2009 Apr;8(4):846-56.

  • Meinhardt J, Sachse C, Hortschansky P, Grigorieff N, Fändrich M. Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils. J Mol Biol. 2009 Feb 27;386(3):869-77.

  • Grissom PM, Fiedler T, Grishchuk EL, Nicastro D, West RR, McIntosh JR. Kinesin-8 from fission yeast: a heterodimeric, plus-end-directed motor that can couple microtubule depolymerization to cargo movement. Mol Biol Cell. 2009 Feb;20(3):963-72.

  • Miller C, Nguitragool W. A provisional transport mechanism for a chloride channel-type Cl-/H+ exchanger. Philos Trans R Soc Lond B Biol Sci. 2009 Jan 27;364(1514):175-80.

  • Mortimer SE, Xu D, McGrew D, Hamaguchi N, Lim HC, Bowne SJ, Daiger SP, Hedstrom L. IMP dehydrogenase type 1 associates with polyribosomes translating rhodopsin mRNA. J Biol Chem. 2008 Dec 26;283(52):36354-60.

  • Agam Y, Hyun JS, Danker JF, Zhou F, Kahana MJ, Sekuler R. Early neural signatures of visual short-term memory. Neuroimage. 2009 Jan 5;44(2):531-6.

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