Graduate MCO

Student Publications

2017 Publications

46 publications listed for 2017

  1. Piechura, JR, Amarnath, K, and O’Shea, EK. (2017) Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria. Elife, 6.
    http://www.ncbi.nlm.nih.gov/pubmed/29239721
  2. Freifeld, L, Odstrcil, I, Frster, D, Ramirez, A, Gagnon, JA, Randlett, O, Costa, EK, Asano, S, Celiker, OT, Gao, R, Martin-Alarcon, DA, Reginato, P, Dick, C, Chen, L, Schoppik, D, Engert, F, Baier, H, and Boyden, ES. (2017) Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proc Natl Acad Sci U S A, 114(50):E10799-E10808.
    http://www.ncbi.nlm.nih.gov/pubmed/29162696
  3. May, JM, Owens, TW, Mandler, MD, Simpson, BW, Lazarus, MB, Sherman, DJ, Davis, RM, Okuda, S, Massefski, W, Ruiz, N, and Kahne, D. (2017) The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport. J Am Chem Soc, 139(48):17221-17224.
    http://www.ncbi.nlm.nih.gov/pubmed/29135241
  4. Stirling, F, Bitzan, L, O’Keefe, S, Redfield, E, Oliver, JWK, Way, J, and Silver, PA. (2017) Rational Design of Evolutionarily Stable Microbial Kill Switches. Mol Cell, 68(4):686-697.e3.
    http://www.ncbi.nlm.nih.gov/pubmed/29149596
  5. Montague, TG, and Schier, AF. (2017) Vg1-Nodal heterodimers are the endogenous inducers of mesendoderm. Elife, 6.
    http://www.ncbi.nlm.nih.gov/pubmed/29140251
  6. Barber, F, Ho, PY, Murray, AW, and Amir, A. (2017) Details Matter: Noise and Model Structure Set the Relationship between Cell Size and Cell Cycle Timing. Front Cell Dev Biol, 5:92.
    http://www.ncbi.nlm.nih.gov/pubmed/29164112
  7. Wallace, JL, Wienisch, M, and Murthy, VN. (2017) Development and Refinement of Functional Properties of Adult-Born Neurons. Neuron, .
    http://www.ncbi.nlm.nih.gov/pubmed/29056299
  8. Kuo, J, Stirling, F, Lau, YH, Shulgina, Y, Way, JC, and Silver, PA. (2017) Synthetic genome recoding: new genetic codes for new features. Curr Genet, .
    http://www.ncbi.nlm.nih.gov/pubmed/28983660
  9. Russell, JR, Cabeen, MT, Wiggins, PA, Paulsson, J, and Losick, R. (2017) Noise in a phosphorelay drives stochastic entry into sporulation in Bacillus subtilis. EMBO J, 36(19):2856-2869.
    http://www.ncbi.nlm.nih.gov/pubmed/28838935
  10. Menegas, W, Uchida, N, and Watabe-Uchida, M. (2017) A Self-Killing Rabies Virus That Leaves a Trace on the DNA. Trends Neurosci, 40(10):589-591.
    http://www.ncbi.nlm.nih.gov/pubmed/28890212
  11. Wang, E, and Hunter, CP. (2017) SID-1 Functions in Multiple Roles To Support Parental RNAi in Caenorhabditis elegans. Genetics, 207(2):547-557.
    http://www.ncbi.nlm.nih.gov/pubmed/28751423
  12. Saak, CC, Zepeda-Rivera, MA, and Gibbs, KA. (2017) A single point mutation in a TssB/VipA homolog disrupts sheath formation in the type VI secretion system of Proteus mirabilis. PLoS One, 12(9):e0184797.
    http://www.ncbi.nlm.nih.gov/pubmed/28949977
  13. Stoddard, PR, Williams, TA, Garner, E, and Baum, B. (2017) Evolution of polymer formation within the actin superfamily. Mol Biol Cell, 28(19):2461-2469.
    http://www.ncbi.nlm.nih.gov/pubmed/28904122
  14. Weir, NR, Kamber, RA, Martenson, JS, and Denic, V. (2017) The AAA protein Msp1 mediates clearance of excess tail-anchored proteins from the peroxisomal membrane. Elife, 6.
    http://www.ncbi.nlm.nih.gov/pubmed/28906250
  15. Diallo, A, Foster, HR, Gromek, KA, Perry, TN, Dujeancourt, A, Krasteva, PV, Gubellini, F, Falbel, TG, Burton, BM, and Fronzes, R. (2017) Bacterial transformation: ComFA is a DNA-dependent ATPase that forms complexes with ComFC and DprA. Mol Microbiol, 105(5):741-754.
    http://www.ncbi.nlm.nih.gov/pubmed/28618091
  16. Mazo, C, Grimaud, J, Shima, Y, Murthy, VN, and Lau, CG. (2017) Distinct projection patterns of different classes of layer 2 principal neurons in the olfactory cortex. Sci Rep, 7(1):8282.
    http://www.ncbi.nlm.nih.gov/pubmed/28811534
  17. Smolentseva, O, Gusarov, I, Gautier, L, Shamovsky, I, DeFrancesco, AS, Losick, R, and Nudler, E. (2017) Mechanism of biofilm-mediated stress resistance and lifespan extension in C. elegans. Sci Rep, 7(1):7137.
    http://www.ncbi.nlm.nih.gov/pubmed/28769037
  18. Krieger, B, Qiao, M, Rousso, DL, Sanes, JR, and Meister, M. (2017) Four alpha ganglion cell types in mouse retina: Function, structure, and molecular signatures. PLoS One, 12(7):e0180091.
    http://www.ncbi.nlm.nih.gov/pubmed/28753612
  19. Oteiza, P, Odstrcil, I, Lauder, G, Portugues, R, and Engert, F. (2017) A novel mechanism for mechanosensory-based rheotaxis in larval zebrafish. Nature, 547(7664):445-448.
    http://www.ncbi.nlm.nih.gov/pubmed/28700578
  20. Cabeen, MT, Russell, JR, Paulsson, J, and Losick, R. (2017) Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis. PLoS Genet, 13(7):e1006901.
    http://www.ncbi.nlm.nih.gov/pubmed/28727759
  21. Kauke, MJ, Traxlmayr, MW, Parker, JA, Kiefer, JD, Knihtila, R, McGee, J, Verdine, G, Mattos, C, and Wittrup, KD. (2017) An engineered protein antagonist of K-Ras/B-Raf interaction. Sci Rep, 7(1):5831.
    http://www.ncbi.nlm.nih.gov/pubmed/28724936
  22. DeFrancesco, AS, Masloboeva, N, Syed, AK, DeLoughery, A, Bradshaw, N, Li, GW, Gilmore, MS, Walker, S, and Losick, R. (2017) Genome-wide screen for genes involved in eDNA release during biofilm formation by Staphylococcus aureus. Proc Natl Acad Sci U S A, 114(29):E5969-E5978.
    http://www.ncbi.nlm.nih.gov/pubmed/28674000
  23. Koppel, N, Maini, V, and Balskus, EP. (2017) Chemical transformation of xenobiotics by the human gut microbiota. Science, 356(6344).
    http://www.ncbi.nlm.nih.gov/pubmed/28642381
  24. Levinson, AM, McGee, JH, Roberts, AG, Creech, GS, Wang, T, Peterson, MT, Hendrickson, RC, Verdine, GL, and Danishefsky, SJ. (2017) Total Chemical Synthesis and Folding of All-l and All-d Variants of Oncogenic KRas(G12V). J Am Chem Soc, 139(22):7632-7639.
    http://www.ncbi.nlm.nih.gov/pubmed/28448128
  25. Lee, KB, Wang, J, Palme, J, Escalante-Chong, R, Hua, B, and Springer, M. (2017) Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes. PLoS Genet, 13(5):e1006766.
    http://www.ncbi.nlm.nih.gov/pubmed/28542190
  26. Daniele, JR, Chu, T, and Kunes, S. (2017) A novel proteolytic event controls Hedgehog intracellular sorting and distribution to receptive fields. Biol Open, 6(5):540-550.
    http://www.ncbi.nlm.nih.gov/pubmed/28298318
  27. Daniele, JR, Baqri, RM, and Kunes, S. (2017) Analysis of axonal trafficking via a novel live-imaging technique reveals distinct hedgehog transport kinetics. Biol Open, 6(5):714-721.
    http://www.ncbi.nlm.nih.gov/pubmed/28298319
  28. Douglas, SM, Chubiz, LM, Harcombe, WR, and Marx, CJ. (2017) Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation. PLoS One, 12(5):e0174345.
    http://www.ncbi.nlm.nih.gov/pubmed/28493869
  29. Vong, M, Ludington, JG, Ward, HD, and Nibert, ML. (2017) Complete cryspovirus genome sequences from Cryptosporidium parvum isolate Iowa. Arch Virol, .
    http://www.ncbi.nlm.nih.gov/pubmed/28477174
  30. Bendesky, A, Kwon, YM, Lassance, JM, Lewarch, CL, Yao, S, Peterson, BK, He, MX, Dulac, C, and Hoekstra, HE. (2017) The genetic basis of parental care evolution in monogamous mice. Nature, 544(7651):434-439.
    http://www.ncbi.nlm.nih.gov/pubmed/28424518
  31. Puszynska, AM, and O’Shea, EK. (2017) Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway. Elife, 6.
    http://www.ncbi.nlm.nih.gov/pubmed/28430105
  32. Tilburgs, T, Meissner, TB, Ferreira, LMR, Mulder, A, Musunuru, K, Ye, J, and Strominger, JL. (2017) NLRP2 is a suppressor of NF-B signaling and HLA-C expression in human trophoblasts,. Biol Reprod, 96(4):831-842.
    http://www.ncbi.nlm.nih.gov/pubmed/28340094
  33. Ferreira, LM, Meissner, TB, Tilburgs, T, and Strominger, JL. (2017) HLA-G: At the Interface of Maternal-Fetal Tolerance. Trends Immunol, 38(4):272-286.
    http://www.ncbi.nlm.nih.gov/pubmed/28279591
  34. Cai, W, Sakaguchi, M, Kleinridders, A, Gonzalez-Del, G, Dreyfuss, JM, O’Neill, BT, Ramirez, AK, Pan, H, Winnay, JN, Boucher, J, Eck, MJ, and Kahn, CR. (2017) Domain-dependent effects of insulin and IGF-1 receptors on signalling and gene expression. Nat Commun, 8:14892.
    http://www.ncbi.nlm.nih.gov/pubmed/28345670
  35. Mathis, MW, Mathis, A, and Uchida, N. (2017) Somatosensory Cortex Plays an Essential Role in Forelimb Motor Adaptation in Mice. Neuron, 93(6):1493-1503.e6.
    http://www.ncbi.nlm.nih.gov/pubmed/28334611
  36. Jang, S, Choubey, S, Furchtgott, L, Zou, LN, Doyle, A, Menon, V, Loew, EB, Krostag, AR, Martinez, RA, Madisen, L, Levi, BP, and Ramanathan, S. (2017) Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. Elife, 6.
    http://www.ncbi.nlm.nih.gov/pubmed/28296635
  37. Wzorek, JS, Lee, J, Tomasek, D, Hagan, CL, and Kahne, DE. (2017) Membrane integration of an essential -barrel protein prerequires burial of an extracellular loop. Proc Natl Acad Sci U S A, 114(10):2598-2603.
    http://www.ncbi.nlm.nih.gov/pubmed/28223520
  38. Fame, RM, Dehay, C, Kennedy, H, and Macklis, JD. (2017) Subtype-Specific Genes that Characterize Subpopulations of Callosal Projection Neurons in Mouse Identify Molecularly Homologous Populations in Macaque Cortex. Cereb Cortex, 27(3):1817-1830.
    http://www.ncbi.nlm.nih.gov/pubmed/26874185
  39. Bisson-Filho, AW, Hsu, YP, Squyres, GR, Kuru, E, Wu, F, Jukes, C, Sun, Y, Dekker, C, Holden, S, VanNieuwenhze, MS, Brun, YV, and Garner, EC. (2017) Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division. Science, 355(6326):739-743.
    http://www.ncbi.nlm.nih.gov/pubmed/28209898
  40. Minkina, O, and Hunter, CP. (2017) Stable Heritable Germline Silencing Directs Somatic Silencing at an Endogenous Locus. Mol Cell, 65(4):659-670.e5.
    http://www.ncbi.nlm.nih.gov/pubmed/28212751
  41. McElroy, KA, Jung, YL, Zee, BM, Wang, CI, Park, PJ, and Kuroda, MI. (2017) upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks. G3 (Bethesda), 7(2):625-635.
    http://www.ncbi.nlm.nih.gov/pubmed/28064188
  42. Scholes, C, DePace, AH. (2017) Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle. Cell Syst, 4(1):97-108.e9.
    http://www.ncbi.nlm.nih.gov/pubmed/28041762
  43. Menegas, W, Babayan, BM, Uchida, N, and Watabe-Uchida, M. (2017) Opposite initialization to novel cues in dopamine signaling in ventral and posterior striatum in mice. Elife, 6.
    http://www.ncbi.nlm.nih.gov/pubmed/28054919
  44. Nasr, ML, Baptista, D, Strauss, M, Sun, ZJ, Grigoriu, S, Huser, S, Plckthun, A, Hagn, F, Walz, T, Hogle, JM, and Wagner, G. (2017) Covalently circularized nanodiscs for studying membrane proteins and viral entry. Nat Methods, 14(1):49-52.
    http://www.ncbi.nlm.nih.gov/pubmed/27869813
  45. Ter-Ovanesyan, D, Kowal, EJK, Regev, A, Church, GM, and Cocucci, E. (2017) Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy. Methods Mol Biol, 1660:233-241.
    http://www.ncbi.nlm.nih.gov/pubmed/28828661
  46. Kowal, EJK, Ter-Ovanesyan, D, Regev, A, and Church, GM. (2017) Extracellular Vesicle Isolation and Analysis by Western Blotting. Methods Mol Biol, 1660:143-152.
    http://www.ncbi.nlm.nih.gov/pubmed/28828654