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Light-regulated promoters for tunable, temporal, and affordable control of fungal gene expression.

Fuller KK, Dunlap JC, Loros JJ.

Appl Microbiol Biotechnol. 2018 May;102(9):3849-3863. doi: 10.1007/s00253-018-8887-7. Epub 2018 Mar 22. Review.


A HAD family phosphatase CSP-6 regulates the circadian output pathway in Neurospora crassa.

Zhou X, Wang B, Emerson JM, Ringelberg CS, Gerber SA, Loros JJ, Dunlap JC.

PLoS Genet. 2018 Jan 19;14(1):e1007192. doi: 10.1371/journal.pgen.1007192. eCollection 2018 Jan.


Circadian Clearance of a Fungal Pathogen from the Lung Is Not Based on Cell-intrinsic Macrophage Rhythms.

Chen S, Fuller KK, Dunlap JC, Loros JJ.

J Biol Rhythms. 2018 Feb;33(1):99-105. doi: 10.1177/0748730417745178. Epub 2017 Dec 27.


Just-So Stories and Origin Myths: Phosphorylation and Structural Disorder in Circadian Clock Proteins.

Dunlap JC, Loros JJ.

Mol Cell. 2018 Jan 18;69(2):165-168. doi: 10.1016/j.molcel.2017.11.028. Epub 2017 Dec 21.


Light sensing by opsins and fungal ecology: NOP-1 modulates entry into sexual reproduction in response to environmental cues.

Wang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP.

Mol Ecol. 2018 Jan;27(1):216-232. doi: 10.1111/mec.14425. Epub 2017 Dec 12.


Guidelines for Genome-Scale Analysis of Biological Rhythms.

Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB.

J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3.


Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity.

Ivanov IP, Wei J, Caster SZ, Smith KM, Michel AM, Zhang Y, Firth AE, Freitag M, Dunlap JC, Bell-Pedersen D, Atkins JF, Sachs MS.

MBio. 2017 Jun 27;8(3). pii: e00844-17. doi: 10.1128/mBio.00844-17.


Making Time: Conservation of Biological Clocks from Fungi to Animals.

Dunlap JC, Loros JJ.

Microbiol Spectr. 2017 May;5(3). doi: 10.1128/microbiolspec.FUNK-0039-2016. Review.


Fungal Light Sensing at the Bench and Beyond.

Fuller KK, Dunlap JC, Loros JJ.

Adv Genet. 2016;96:1-51. doi: 10.1016/bs.adgen.2016.08.002. Epub 2016 Sep 23. Review.


The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion.

Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D.

G3 (Bethesda). 2017 Jan 5;7(1):129-142. doi: 10.1534/g3.116.034298.


Aspergillus fumigatus Photobiology Illuminates the Marked Heterogeneity between Isolates.

Fuller KK, Cramer RA, Zegans ME, Dunlap JC, Loros JJ.

MBio. 2016 Sep 20;7(5). pii: e01517-16. doi: 10.1128/mBio.01517-16.


Circadian Oscillators: Around the Transcription-Translation Feedback Loop and on to Output.

Hurley JM, Loros JJ, Dunlap JC.

Trends Biochem Sci. 2016 Oct;41(10):834-846. doi: 10.1016/j.tibs.2016.07.009. Epub 2016 Aug 3. Review.


Modulation of Circadian Gene Expression and Metabolic Compensation by the RCO-1 Corepressor of Neurospora crassa.

Olivares-Yañez C, Emerson J, Kettenbach A, Loros JJ, Dunlap JC, Larrondo LF.

Genetics. 2016 Sep;204(1):163-76. doi: 10.1534/genetics.116.191064. Epub 2016 Jul 22.


Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock.

Conrad KS, Hurley JM, Widom J, Ringelberg CS, Loros JJ, Dunlap JC, Crane BR.

EMBO J. 2016 Aug 1;35(15):1707-19. doi: 10.15252/embj.201694327. Epub 2016 Jun 23.


Yes, circadian rhythms actually do affect almost everything.

Dunlap JC, Loros JJ.

Cell Res. 2016 Jul;26(7):759-60. doi: 10.1038/cr.2016.65. Epub 2016 May 31.


The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa.

Wang Z, Li N, Li J, Dunlap JC, Trail F, Townsend JP.

MBio. 2016 Mar 8;7(2):e02148. doi: 10.1128/mBio.02148-15.


Alternative Use of DNA Binding Domains by the Neurospora White Collar Complex Dictates Circadian Regulation and Light Responses.

Wang B, Zhou X, Loros JJ, Dunlap JC.

Mol Cell Biol. 2015 Dec 28;36(5):781-93. doi: 10.1128/MCB.00841-15.


period-1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of the Neurospora circadian clock.

Emerson JM, Bartholomai BM, Ringelberg CS, Baker SE, Loros JJ, Dunlap JC.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):15707-12. doi: 10.1073/pnas.1521918112. Epub 2015 Dec 8.


The circadian system as an organizer of metabolism.

Hurley JM, Loros JJ, Dunlap JC.

Fungal Genet Biol. 2016 May;90:39-43. doi: 10.1016/j.fgb.2015.10.002. Epub 2015 Oct 20. Review.


Seeing the world differently: variability in the photosensory mechanisms of two model fungi.

Dasgupta A, Fuller KK, Dunlap JC, Loros JJ.

Environ Microbiol. 2016 Jan;18(1):5-20. doi: 10.1111/1462-2920.13055. Epub 2015 Oct 26. Review.


Development of the CRISPR/Cas9 System for Targeted Gene Disruption in Aspergillus fumigatus.

Fuller KK, Chen S, Loros JJ, Dunlap JC.

Eukaryot Cell. 2015 Nov;14(11):1073-80. doi: 10.1128/EC.00107-15. Epub 2015 Aug 28.


A Tool Set for the Genome-Wide Analysis of Neurospora crassa by RT-PCR.

Hurley JH, Dasgupta A, Andrews P, Crowell AM, Ringelberg C, Loros JJ, Dunlap JC.

G3 (Bethesda). 2015 Aug 6;5(10):2043-9. doi: 10.1534/g3.115.019141.


Biological Significance of Photoreceptor Photocycle Length: VIVID Photocycle Governs the Dynamic VIVID-White Collar Complex Pool Mediating Photo-adaptation and Response to Changes in Light Intensity.

Dasgupta A, Chen CH, Lee C, Gladfelter AS, Dunlap JC, Loros JJ.

PLoS Genet. 2015 May 15;11(5):e1005215. doi: 10.1371/journal.pgen.1005215. eCollection 2015 May.


Circadian control sheds light on fungal bioluminescence.

Oliveira AG, Stevani CV, Waldenmaier HE, Viviani V, Emerson JM, Loros JJ, Dunlap JC.

Curr Biol. 2015 Mar 30;25(7):964-8. doi: 10.1016/j.cub.2015.02.021. Epub 2015 Mar 19.


Dissecting the mechanisms of the clock in Neurospora.

Hurley J, Loros JJ, Dunlap JC.

Methods Enzymol. 2015;551:29-52. doi: 10.1016/bs.mie.2014.10.009. Epub 2014 Dec 26. Review.


Circadian rhythms. Decoupling circadian clock protein turnover from circadian period determination.

Larrondo LF, Olivares-Yañez C, Baker CL, Loros JJ, Dunlap JC.

Science. 2015 Jan 30;347(6221):1257277. doi: 10.1126/science.1257277.


Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16995-7002. doi: 10.1073/pnas.1418963111. Epub 2014 Oct 31.


Fungal photobiology: visible light as a signal for stress, space and time.

Fuller KK, Loros JJ, Dunlap JC.

Curr Genet. 2015 Aug;61(3):275-88. doi: 10.1007/s00294-014-0451-0. Epub 2014 Oct 17. Review.


Neurospora WC-1 recruits SWI/SNF to remodel frequency and initiate a circadian cycle.

Wang B, Kettenbach AN, Gerber SA, Loros JJ, Dunlap JC.

PLoS Genet. 2014 Sep 25;10(9):e1004599. doi: 10.1371/journal.pgen.1004599. eCollection 2014 Sep.


Editorial overview: Host-microbe interactions: fungi.

Dunlap JC, Latgé JP.

Curr Opin Microbiol. 2014 Aug;20:v-vi. doi: 10.1016/j.mib.2014.07.004. Epub 2014 Jul 25. No abstract available.


Genome-wide characterization of light-regulated genes in Neurospora crassa.

Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS.

G3 (Bethesda). 2014 Jul 21;4(9):1731-45. doi: 10.1534/g3.114.012617.


Bright to dim oscillatory response of the Neurospora circadian oscillator.

Gooch VD, Johnson AE, Larrondo LF, Loros JJ, Dunlap JC.

J Biol Rhythms. 2014 Feb;29(1):49-59. doi: 10.1177/0748730413517983.


A kinetic study of the effects of light on circadian rhythmicity of the frq promoter of Neurospora crassa.

Gooch VD, Johnson AE, Bourne BJ, Nix BT, Maas JA, Fox JA, Loros JJ, Larrondo LF, Dunlap JC.

J Biol Rhythms. 2014 Feb;29(1):38-48. doi: 10.1177/0748730413517981.


Conserved RNA helicase FRH acts nonenzymatically to support the intrinsically disordered neurospora clock protein FRQ.

Hurley JM, Larrondo LF, Loros JJ, Dunlap JC.

Mol Cell. 2013 Dec 26;52(6):832-43. doi: 10.1016/j.molcel.2013.11.005. Epub 2013 Dec 5.


Aging well with a little wine and a good clock.

Belden WJ, Dunlap JC.

Cell. 2013 Jun 20;153(7):1421-2. doi: 10.1016/j.cell.2013.05.055.


Developing and assessing curriculum on the physics of medical instruments.

Christensen W, Johnson JK, Van Ness GR, Mylott E, Dunlap JC, Anderson EA, Widenhorn R.

CBE Life Sci Educ. 2013 Jun 1;12(2):250-61. doi: 10.1187/cbe.12-09-0142.


The circadian Per1 and Per2 genes influence alcohol intake, reinforcement, and blood alcohol levels.

Gamsby JJ, Templeton EL, Bonvini LA, Wang W, Loros JJ, Dunlap JC, Green AI, Gulick D.

Behav Brain Res. 2013 Jul 15;249:15-21. doi: 10.1016/j.bbr.2013.04.016. Epub 2013 Apr 20.


The fungal pathogen Aspergillus fumigatus regulates growth, metabolism, and stress resistance in response to light.

Fuller KK, Ringelberg CS, Loros JJ, Dunlap JC.

MBio. 2013 Mar 26;4(2). pii: e00142-13. doi: 10.1128/mBio.00142-13.


Functional analysis of the Aspergillus nidulans kinome.

De Souza CP, Hashmi SB, Osmani AH, Andrews P, Ringelberg CS, Dunlap JC, Osmani SA.

PLoS One. 2013;8(3):e58008. doi: 10.1371/journal.pone.0058008. Epub 2013 Mar 7.


Cell biology: A fable of too much too fast.

Hurley JM, Dunlap JC.

Nature. 2013 Mar 7;495(7439):57-8. doi: 10.1038/nature11952. Epub 2013 Feb 17. No abstract available.


Light-inducible system for tunable protein expression in Neurospora crassa.

Hurley JM, Chen CH, Loros JJ, Dunlap JC.

G3 (Bethesda). 2012 Oct;2(10):1207-12. doi: 10.1534/g3.112.003939. Epub 2012 Oct 1.


Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control.

Grant GD, Gamsby J, Martyanov V, Brooks L 3rd, George LK, Mahoney JM, Loros JJ, Dunlap JC, Whitfield ML.

Mol Biol Cell. 2012 Aug;23(16):3079-93. doi: 10.1091/mbc.E11-02-0170. Epub 2012 Jun 27.


Global analysis of serine-threonine protein kinase genes in Neurospora crassa.

Park G, Servin JA, Turner GE, Altamirano L, Colot HV, Collopy P, Litvinkova L, Li L, Jones CA, Diala FG, Dunlap JC, Borkovich KA.

Eukaryot Cell. 2011 Nov;10(11):1553-64. doi: 10.1128/EC.05140-11. Epub 2011 Sep 30.


Structure of a light-activated LOV protein dimer that regulates transcription.

Vaidya AT, Chen CH, Dunlap JC, Loros JJ, Crane BR.

Sci Signal. 2011 Aug 2;4(184):ra50. doi: 10.1126/scisignal.2001945.


CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency.

Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC.

PLoS Genet. 2011 Jul;7(7):e1002166. doi: 10.1371/journal.pgen.1002166. Epub 2011 Jul 21.


The circadian clock of Neurospora crassa.

Baker CL, Loros JJ, Dunlap JC.

FEMS Microbiol Rev. 2012 Jan;36(1):95-110. doi: 10.1111/j.1574-6976.2011.00288.x. Epub 2011 Aug 1. Review.


Modulation of clock gene expression by the transcriptional coregulator receptor interacting protein 140 (RIP140).

Poliandri AH, Gamsby JJ, Christian M, Spinella MJ, Loros JJ, Dunlap JC, Parker MG.

J Biol Rhythms. 2011 Jun;26(3):187-99. doi: 10.1177/0748730411401579.


High-throughput production of gene replacement mutants in Neurospora crassa.

Park G, Colot HV, Collopy PD, Krystofova S, Crew C, Ringelberg C, Litvinkova L, Altamirano L, Li L, Curilla S, Wang W, Gorrochotegui-Escalante N, Dunlap JC, Borkovich KA.

Methods Mol Biol. 2011;722:179-89. doi: 10.1007/978-1-61779-040-9_13.


Physical interaction between VIVID and white collar complex regulates photoadaptation in Neurospora.

Chen CH, DeMay BS, Gladfelter AS, Dunlap JC, Loros JJ.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16715-20. doi: 10.1073/pnas.1011190107. Epub 2010 Aug 23.

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