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Selected Recent Publications by MCB Students

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Papers published by MCB graduate students in Neuro labs:

Ford KJ, Félix AL, Feller MB. (2012) Cellular mechanisms underlying spatiotemporal features of cholinergic retinal waves. J Neurosci. 32(3):850-63.

Caporale N*, Kolstad KD*, Lee T, Tochitsky I, Dalkara D, Trauner D, Kramer R, Dan Y, Isacoff EY, Flannery JG. (2011) LiGluR restores visual responses in rodent models of inherited blindness. Mol Ther. 19(7):1212-9. *co-first authors

Wilson SR, Gerhold KA, Bifolck-Fisher A, Liu Q, Patel K, Dong X, Bautista DM. (2011) TRPA1 is required for histamine-independent, Mas-related G- protein coupled receptor-mediated itch. Nature Neuroscience. 14(5):595-602.

Lee H, Dean, C, Isacoff EY. (2010) Alternative splicing of neuroligin regulates the rate of presynaptic differentiation. J Neurosci. 30(34):11435-46.

*Shelly M, *Lim BK, Cancedda L, Heilshorn SC, Gao H, Poo M-m. (2010) Local and long-range reciprocal regulation of cAMP and cGMP in axon/dendrite formation. Science. 327(5965):547-52. * equal contribution

Klimczak RR, Koerber JT, Dalkara D, Flannery JG, Schaffer DV. (2009) A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Müller cells. PLoS One. 4(10):e7467.

Scolnick JA, Cui K, Xuan S, Duggan CD, Yuan XB, Efstratiadis A, Ngai J. (2008) Role of IGF signaling in olfactory sensory map formation and axon guidance. Neuron. 57(6):847-57.

Papers published by MCB graduate students in IMP labs:

Lee B, Moon J, Shu J, Lin Y, Newman Z, Schekman R, Barton GM. (2013) UNC93B1 mediates differential trafficking of endosomal TLRs. eLife. 19(2):e00291.

Jung H, Hsiung B, Pestal K, Procyk E, Raulet DH. (2012) RAE-1 ligands for the NKG2D receptor are regulated by E2F transcription factors, which control cell cycle entry. J Exp Med. 209(13):2409-2422.

Von Moltke J, Trinidad NJ, Moayeri M, Kintzer AF, Wang SB, von Rooijen N, Brown CR, Krantz BQ, Leppla SH, Gronert K, Vance RE. (2012) Rapid induction of inflammatory lipid mediators by the inflammasome in vivo. Nature. 490(7418):107-111.

Arpaia N, Godec J, Lau L, Sivick KE, MLaughlin LM, Jones MB, Dracheva T, Peterson SN, Monack DM, Barton GM. (2011) TLR signaling is required for Salmonella typhimurium virulence. Cell. 144(5): 675-688.

Kofoed EM, Vance RE. (2011) Innate immune recognition of bacterial ligands by NAIPs determines inflammasome specificity. Nature. 477(7366):592-5.

Mouchess ML, Arpaia N, Souza G, Barbalat R, Ewald SE, Lau L, Barton GM. (2011) Transmembrane mutations in Toll-like Receptor 9 bypass the requirement for ectodomain proteolysis and induce fatal inflammation. Immunity. 35(5): 721-32.

Tokuyama M, Lorin C, Delebecque F, Jung H, Raulet DH, Coscoy L. (2011) Expression of the RAE-1 family of the stimulatory NK-cell ligands requires activation of the PI3K pathway during viral infection and transformation. PLoS Pathog. 7(9):e31002265.

Osborn SL, Diehl G, Han SJ, Xue L, Kurd N, Hsieh K, Cado D, Robey EA, Winoto A. (2010) Fas-associated death domain (FADD) is a negative regulator of T-cell receptor-mediated necroptosisProc Natl Acad Sci U S A. 107(29):13034-9.

Nice TJ, Coscoy L, Raulet DH. (2009) Posttranslational regulation of the NKG2D ligand Mult1 in response to cell stress. J Exp Med. 206(2):287-98.

Crimmins GT, Herskovits AA, Rehder K, Sivick KE, Lauer P, Dubensky TW Jr, Portnoy DA. (2008) Listeria monocytogenes multidrug resistance transporters activate a cytosolic surveillance pathway of innate immunityProc Natl Acad Sci U S A. 105(29):10191-6.

Ewald SE, Lee BL, Lau L, Wickliffe KE, Shi GP, Chapman HA, Barton GM. (2008)  The ectodomain of Toll-like receptor 9 is cleaved to generate a functional receptorNature. 456(7222):658-62.

Papers published by MCB graduate students in GGD labs:

Abitua PB, Wagner E, Navarrete IA, Levine M. (2012) Identification of a rudimentary neural crest in a non-vetebrate chordate. Nature. 492(7427):104-7.

Thistle R, Cameron P, Ghorayshi A, Dennison L, Scott K. (2012) Contact Chemoreceptors Mediate Male-Male Repulsion and Male-Female Attraction during Drosophila Courtship. Cell 149(5):1140-1151.

Liu Z, Scannell DR, Eisen MB, Tjian R. (2011) Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell. 146:720-731.

Taliaferro JM, Alvarez N, Green RE, Blanchette M, Rio DC (2011) Evolution of a tissue-specific splicing network. Genes Dev 25(6): 608-20.

Young JJ, Cherone JM, Doyon Y, Ankoudinova I, Faraji FM, Lee AH, Ngo C, Guschin DY, Paschon DE, Miller JC, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Harland RM, Zeitler B. (2011)  Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases. Proc Natl Acad Sci USA. 108:7052-7057.

Cameron P, Hiroi M, Ngai J, Scott K. (2010) The molecular basis for water taste in Drosophila. Nature 465, 91-96.

Lusk RW, Eisen MB. (2010) Evolutionary mirages: selection of binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet 6(1): e1000829.

Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC. (2010) THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor groovesNat Struct Mol Biol. 17(1):117-23.

Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L. (2010)  Early chordate origins of the vertebrate second heart field. Science. 329(5991):565-8.

Mets DG, Meyer BJ. (2009) Condensins regulate meiotic DNA break distribution, thus crossover frequency, by controlling chromosome structure. Cell. 139(1):73-86.

Osborne EA, Dudoit S, Rine J. (2009) The establishment of gene silencing at single-cell resolution. Nat Genet. 41(7):800-6.

Abedin M, King N. (2008) The premetazoan ancestry of cadherins. Science. 319(5865):946-8.

Papers published by MCB graduate students in BBS labs

Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ, Zhou Q, Alber T. (2013) HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold. Proc Natl Acad Sci U S A. 110(2):E123-31.

*Lander GC, *Estrin E, Matyskiela ME, Bashore C, Nogales E, Martin A. (2012) Complete subunit architecture of the proteasome regulatory particle. Nature 482(7384):186-91. *co-first author

Chao LH, Stratton MM, Lee IH, Rosenberg OS, Levitz J, Mandell DJ, Kortemme T, Groves JT, Schulman H, Kuriyan J. (2011) A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme. Cell. 146(5):732-45.

Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JHD. (2011) Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science. 332(6032):981-4.

Garcia G. III, Bertin A, Li Z, McMurray M, Thorner J, Nogales E. (2011) Subunit-dependent modulation of septin assembly: budding yeast septin Shs1 promotes ring and gauze formation. J.Cell Biol. 195(6):993-1004.

He N, Chan C, Sobhian B, Chou S, Xue Y, Liu M, Alber T, Benkirane M, Zhou Q. (2011) Human Polymerase-associated factor complex (PAFc) connects the super Elongation complex (SEC) to RNA polymerase II on chromatin. PNAS. 108(36):E636-45.

Wickliffe KE, Lorenz S, Wemmer DE, Kuriyan J, Rape M. (2011) The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2. Cell. 144(5):769-81.

Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 329(5997):1355-8

He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan N, Alber T, Zhou Q. (2010) HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol Cell 38(3): 428-438.

Patterson JC, Klimenko ES, Thorner J. (2010) Single-cell analysis reveals that insulation maintains signaling specificity between two yeast MAPK pathways with common components. Science Signaling 3(144):ra75.

Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM. (2010) A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature. 465(7298):641-4

Shank EA, Cecconi C, Dill JW, Marqusee S, Bustamante C. (2010) The folding cooperativity of a protein is controlled by its chain topology. Nature. 465(7298):637-40.

Thomsen ND, Berger JM. (2009) Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell. 139(3):523-34.

Papers published by MCB graduate students in CDB labs

Mannowetz N, Naidoo N, Choo S, Smith J, Lishoko P. (2013) Slo1 is the principal potassium channel of human spermatozoa. eLife, 2:e01009.

Wilson SR, Thé L, Batia LM, Beattie K, Katibah G, McClain S, Pellegrino M, Estandian D, Bautista D. (2013) The epithelial cell-derived atopic dermatitis cytokine TSLP activates neurons to induce itch. Cell. 155(2):285-95.

Worley M, Setiawan L, Hariharan I. (2013) TIE-DYE: a combinatorial marking system to visualize and genetically manipulate clones during development in Drosophila melanogaster. Development. 140(15): 3275-3284.

Hafezi Y, Bosch JA, Hariharan IK. (2012) Differences in levels of the transmembrane protein Crumbs can influence cell survival at clonal boundaries. Dev. Biol. 368(2): 358-69.

Jin L, Pahuja KB, Wickliffe KE, Gorur A, Baumgärtel C, Schekman R, Rape M. (2012) Ubiquitin-dependent regulation of COPII coat size and function. Nature 482(7386): 495-500.

Carroll JS, Munchel SE, Weis K. (2011) The DExD/H box ATPase Dhh1 functions in translational repression, mRNA decay, and processing body dynamics. J Cell Biol. 194(4):527-37.

Haigo SL, Bilder D. (2011) Global tissue revolutions in a morphogenetic movement controlling elongation. Science. 331(6020):1071-4.

Harper NC, Rillo R, Jover-Gil S, Assa ZJ, Bhalla N, Dernburg AF. (2011) Paining centers recruit a Polo-like kinase to orchestrate meiotic chromosome dynamics in C. elegans. Developmental Cell. 21(5):934-47.

Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC. (2010) The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell. 140(5):631-42.

Haglund CM, Choe JE, Skau CT, Kovar DR, Welch MD. (2010) Rickettsia Sca2 is a bacterial formin-like mediator of actin-based motility. Nat Cell Biol. 12(11):1057-63.

Merte J*, Jensen D*, Wright K, Sarsfield S, Wang Y, Schekman R, Ginty DD. (2009) Sec24b selectively sorts Vang12 to regulate planar cell polarity during neural tube closure. Nature Cell Biol.12(1):41-6; sup pp 1-8.

Olive V, Bennett MJ, Walker JC, Ma C, Jiang I, Cordon-Cardo C, Li QJ, Lowe SW, Hannon GJ, He L. (2009) miR-19 is a key oncogenic component of mir-17-92. Genes Dev. 23(24):2839-49.

Phillips CM, Meng X, Zhang L, Chretien JH, Urnov FD, Dernburg AF. (2009) Identification of chromosome sequence motifs that mediate meiotic pairing and synapsis in C. elegans. Nat Cell Biol. 11(8):934-42.