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Information contained herein is as of July 1, 2014. To find our latest papers, please click "PubMed Search."
Reprint and Material Request
Reprints and/or materials (plasmids, strains etc.) will be mailed on request. Request should be addressed to:

Carl Johnson
Department of Biological Sciences
Vanderbilt University
VU Station B 35-1634
Nashville, TN 37235-1634, USA
Phone: +1 (615) 322-2384
Fax: +1 (615) 936-0205

* Research in our laboratory is supported by grants from NIH. We strictly follow the NIH Guidelines for sharing of biomedical research resources. Please feel free to ask us for our published biological materials.

Listed in reverse chronological order.

Johnson lab personnel are underlined.

2020 | 2019   2018 | 2017 | 2016 |2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 | 1989 | 1988 | 1987 | 1986 | 1985 | 1984 | 1983 | 1982 | 1981




  • Cumberbatch D*, Mori T*, Yang J*, Mi D, Vinson P, Weaver D,Johnson CH. A BRET Ca2+ sensor enables high-throughput screening in the presence of background fluorescence. Science Signaling, in press.
  • Shi SQ,Mahoney CE, Houdek P, Zhao W, Anderson MP, Zhuo X, Beaudet A, Sumova A, Scammell TE, Johnson CH. Circadian rhythms and sleep are dependent upon expression levels of key ubiquitin ligase Ube3a. Frontiers in Neurobiology 16: 837523.
  • Jabbur ML, and Johnson CH. Spectres of clock evolution: Past, Present, and Yet to Come. Frontiers in Physiology 12: 815847. PMCID: PMC8874327 
  • Kelly KP*, Borsetti H*,Wenzler ME, Ustione A, Kim K, Christov PP, Ramirez B, Bauer JA, Piston DW, Johnson CH**,Sulikowski GA**. Screen for Small-Molecule Modulators of Circadian Rhythms Reveals Phenazine as Redox-State Modifying Clockwork Tuner. ACS Chemical Biology 17: 1658-1664. **co-corresponding authors. PMID: 35679588 Note that the initial screen data for all the positive (but mostly unverified) hits may be downloaded from (using password VanderbiltU8211):


  • McNaughton CD, Adams NM, Johnson CH, Ward MJ, Schmitz JE, Lasko TA. Diurnal variation in SARS-CoV-2 PCR test results: Test accuracy may vary by time of day. J. Biological Rhythms 36: 595-601. PMCID: PMC8599649
  • Kelly KP, Ellacott KJ, Chen H, McGuinness OP, and Johnson CH. Time-Optimized Feeding is Beneficial Without Enforced Fasting. Open Biology 11: 210183. PMCID: PMC8492177
  • Ralph MR, Shi SQ, Johnson CH, Houdek P, Shrestha TC, Crosby P, O’Neill JS, Sládek M, Stinchcombe AR, Sumová A. Targeted modification of the Per2 clock gene alters circadian function in mPer2luciferase (mPer2Luc) mice. PLOS Computational Biology 17(5): e1008987. PMCID: PMC8191895
  • Wang B, Xu Y, Wang X, Yuan JS, Johnson CH, Young JD, Yu J. A guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria. Nature Communications 12: 5150. PMCID: PMC8390497
  • Amaral DT, Johnson CH, and Viviani VR. RNA-Seq analyses of the blue-light emitting Orfelia fultoni (Diptera: Keroplatidae) suggest photoecological adaptations at the molecular level. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, 39:100840. PMID: 34022525
  • Ellis BM, Babele P, May JC, Johnson CH, Pfleger BF, Young JD, McLean JA. Accelerating Strain Phenotyping with Desorption Electrospray Ionization-Imaging Mass Spectrometry and Untargeted Molecular Analysis of Intact Microbial Colonies. Proc. Natl. Acad. Sci. USA 118: e2109633118 PMCID: PMC8670462
  • Yang J, and Johnson CH. Bioluminescent sensors for Ca++ flux imaging and the introduction of a new intensity-based Ca++ sensor. Frontiers in Bioengineering and Biotechnology 9: 773353. PMCID: PMC8578923
  • Circadian Rhythms in Bacteria and Microbiomes, C.H. Johnson and M. Rust, eds. (Springer Nature), 415 pages. Publication date: July 28, 2021.
  • Johnson CH and Rust MJ. The Bacterial Perspective on Circadian Clocks. Chapter 1 in: Circadian Rhythms in Bacteria and Microbiomes, C.H. Johnson and M. Rust, eds. (Springer), pp. 1-17.
  • Jabbur ML, Zhao C, and Johnson CH. Insights into the Evolution of Circadian Clocks Gleaned from Bacteria. Chapter 7 in: Circadian Rhythms in Bacteria and Microbiomes, C.H. Johnson and M. Rust, eds. (Springer), pp. 111-135.


  • Kelly, K.P., O.P. McGuinness, M. Buchowski, J.J. Hughey, H. Chen, J. Powers, T. Page, C.H. Johnson. Eating breakfast and avoiding late-evening snacking sustains lipid oxidation. PLoS Biology 18: e3000622. PMCID: PMC7046182
  • Kim, P., B. Porr, T. Mori, Y-S Kim, C.H. Johnson, C. Diekman, Y-I Kim. CikA, an input pathway component, senses the oxidized quinone signal to generate phase delays in the cyanobacterial circadian clock. J. Biological Rhythms 35: 227-234. PMCID: PMC7269861
  • Fustin, J.-M., S. Ye, C. Rakers, K. Kaneko, K. Fukumoto, M. Yamano, M. Versteven, E. Grünewald, S.J. Cargill, T.K. Tamai, Y. Xu, M.L. Jabbur, R. Kojima, M.L. Lamberti, K. Yoshioka-Kobayashi, D. Whitmore, S. Tammam, L. Howell, R. Kageyama, T. Matsuo, R. Stanewsky, D.A. Golombek, C.H. Johnson, H. Kakeya, G. van Ooijen, H. Okamura. Methylation deficiency disrupts biological rhythms from bacteria to humans. Communications Biology 3: 211. PMCID: PMC7203018
  • Hellweger, F., M.L. Jabbur, C.H. Johnson, E. van Sebille, H. Sasaki. Circadian clock helps cyanobacteria manage energy in coastal and high latitude ocean. ISME Journal 14: 560–568. PMCID: PMC6976579
  • Cheah, Y.E., Y. Xu, S.A. Sacco, P.K. Babele, A.O. Zheng, C.H. Johnson, J.D. Young. Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942. Metabolic Engineering 60: 56-65. PMCID: PMC7217728
  • Viviani, V.R. J.R. Silva, D.T. Amaral, V.R. Bevilaqua, F.C. Abdall, B.R. Branchini, C.H. Johnson. A new brilliantly blue-emitting luciferin-luciferase system from Orfelia fultoni and Keroplatinae (Diptera). Scientific Reports 10: 9608. PMCID: PMC7295969
  • Davis, C.R., C.H. Johnson, J.B. Robertson. A bioluminescent reporter for the halophilic archaeon Haloferax volcanii. Extremophiles 24: 773–785. PMCID: PMC7462420

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  • Shi, S. , and C.H. Johnson . Circadian biology and sleep in monogenic neurological disorders and its potential application in drug discovery. Current Opinion in Behavioral Sciences 25: 23–30. PMCID: PMC6615557 [PubMed]
  • Guo, G., K. Wang, S-S. Hu, T. Tian, P. Liu, T. Mori , P. Chen, C. H. Johnson , X. Qin. Auto-kinase activity of Casein Kinase 1 δ/ε Governs the Period of Mammalian Circadian Rhythms. J. Biological Rhythms 34: 482–496. PMID: 31392916 [ PubMed ]

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  • Mori, T ., S. Sugiyama, M. Byrne, C.H. Johnson , T. Uchihashi, T. Ando. Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time. Nature Commun. 9: 3245. [PubMed]

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  • Johnson, C.H. C. Zhao Y. Xu , and  T. Mori . Timing the day: what makes bacterial clocks tick? Nature Reviews Microbiology 15: 232-242. [ PubMed ]
  • Jazmin, L.J., Y. Xu , Y.E. Cheah, A.O. Adebiyi, C.H. Johnson , and J.D. Young. Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production. Metabolic Engineering 42: 9-18. [PubMed]
  • Tackenberg, M.C., C.H. Johnson , T.L. Page, and S. Daan. Revealing oft-cited but unpublished papers of Colin Pittendrigh and co-workers. J. Biol. Rhythms 32: 291-294. [PubMed]
  • Hughes, M.E. . . . C.H. Johnson . . . J.B. Hogenesch (93 authors). Guidelines for genome-scale analysis of biological rhythms. J. Biol. Rhythms 32: 380-393. [PubMed]

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  • Shi, S.-Q, M.J. White, H.M. Borsetti, J.S. Pendergast, A. Hida, C.M. Ciarleglio, P.A. de Verteuil, A.G. Cadar, C. Cala, D.G. McMahon, R.C. Shelton, S.M. Williams, C.H. Johnson . (2016) Molecular Analyses of Circadian Gene Variants Reveal Sex-dependent Links Between Depression and Clocks. Translational Psychiatry 6: e748. [Pubmed]
  • Ma, P., T. Mori, C. Zhao , T. Thiel, C.H. Johnson . (2016) Evolution of KaiC-dependent timekeepers: a proto-circadian timing mechanism confers adaptive fitness in the purple bacterium Rhodopseudomonas palustris. PLoS Genetics 12: e1005922. [Pubmed]
  • Yang, J., D. Cumberbatch , S. Centanni, S.Q. Shi , D. Winder, D. Webb, C.H. Johnson. (2016) Coupling Optogenetic Stimulation with NanoLuc-based Luminescence (BRET) Ca++ Sensing. Nature Communications 7: 13268. [Pubmed]
  • Zhang, Y., J.B. Robertson, Q. Xie, C.H. Johnson . (2016) Monitoring Intracellular pH change with a Genetically Encoded and Ratiometric Luminescence Sensor in Yeast and Mammalian Cells. Chapter 9 in: Bioluminescence: Methods and Protocols, Third Edition, S.-B. Kim, ed. (Methods in Molecular Biology Series, Humana Press), pp. 117-130.

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  • Shi, S. , T.J. Bichell, R.A. Ihrie, C.H. Johnson . (2015) Ube3a Imprinting Impairs Circadian Robustness in Angelman Syndrome Models. Current Biology 25: 537-545. [PubMed]
  • Qin, X., T. Mori, Y. Zhang, and C.H. Johnson . (2015) PER2 Differentially Regulates Clock Phosphorylation versus Transcription by Reciprocal Switching of CK1µ Activity. J. Biological Rhythms 30: 206-216. [PubMed]
  • Egli, M. and C.H. Johnson . (2015) Biochemistry that Times the Day. Biochemistry 54: 104-109. [PubMed]
  • Veatch, O.J., J.S. Pendergast, M.J. Allen, R.M. Leu, C.H. Johnson , S.H. Elsea, and B.A. Malow. (2015) Genetic Variation in Melatonin Pathway Enzymes in Children with Autism Spectrum Disorder and Comorbid Sleep Onset Delay. J. Autism & Developmental Disorders 45: 100-10. [PubMed]
  • Mori, T., H. Mchaourab, and C.H. Johnson. (2015) Circadian Clocks: Unexpected Biochemical Cogs. Current Biology 25: R842-4. [Pubmed]

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  • Johnson, C. H ., and M. Egli. (2014) Metabolic compensation and circadian resilience in prokaryotic cyanobacteria. Annu. Rev. Biochem. 83: 221-47. [PubMed]
  • Johnson, C.H . (2014) Carl Hirschie Johnson (Current Biology feature Q&A). Current Biology 24: 100-102.
  • Pattanayek, R., Y. Xu , A. Lamichhane, C.H. Johnson , and M. Egli. (2014) An arginine tetrad as mediator of input-dependent and -independent ATPases in the clock protein KaiC. Acta Crystallographica Section D, Biological Crystallography 70(Pt 5): 1375-90. [PubMed]
  • Yan Y, Jiang L, Aufderheide KJ, Wright GA, Terekhov A, Costa L, Qin K, McCleery WT, Fellenstein JJ, Ustione A, Robertson JB, Johnson CH , Piston DW, Hutson MS, Wikswo JP, Hofmeister W, Janetopoulos C. (2014) A Microfluidic-Enabled Mechanical Microcompressor for the Immobilization of Live Single- and Multi-Cellular Specimens. Microsc Microanal. 20: 141-51. [PubMed]

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  • Xu Y, Ma P, Shah P, Rokas A, Liu Y, Johnson CH (2013) Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature 495: 116-20. [PubMed]
  • Shi S, Ansari T, McGuinness OP, Wasserman DH, Johnson CH (2013) Circadian disruption leads to insulin resistance and obesity. Current Biology 23: 372-81. [PubMed]
  • Xu, Y. , P.D. Weyman, M. Umetani, J. Xiong, X. Qin, Q. Xu, H. Iwasaki, and C. H. Johnson. (2013) Circadian Yin-Yang regulation and its manipulation to globally reprogram gene expression. Current Biology 23: 2365-2374. [PubMed]
  • Egli, M., and C.H. Johnson . (2013) A circadian clock nanomachine that runs without transcription or translation. Current Opinion Neurobiology 23:732-740. [PubMed]
  • Egli M, Pattanayek R, Sheehan J, Xu Y, Mori T, Smith J, Johnson CH (2013) Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock. Biochemistry 52: 1208-1220. [PubMed]
  • Villarreal, S.A., R. Pattanayek, D.R. Williams, T. Mori, X. Qin, C.H. Johnson , M. Egli, and P.L. Stewart. CryoEM and Molecular Dynamics of the Circadian KaiB-KaiC Complex Indicates KaiB Monomers Interact with KaiC and Block ATP Binding Clefts. (2013) J. Molecular Biology 425: 3311-3324. [PubMed]
  • Robertson, J.B., C. R. Davis, and C. H. Johnson. (2013) Visible light alters yeast metabolic rhythms by inhibiting respiration. PNAS 110: 21130-21135. [PubMed]
  • Ma P, Woelfle MA, and Johnson CH . (2013) An Evolutionary Fitness Enhancement Conferred by the Circadian System in Cyanobacteria. Special issue on “Functionality and Dynamics in Biological Systems." Chaos, Solitons & Fractals 50: 65-74. [PubMed]
  • de la Iglesia, H.O. and C.H. Johnson . (2013) Biological Clocks: Riding the tides. Current Biology 23: R921-R923. [PubMed]
  • Bittman EL, Johnson CH. (2013) Animal care practices in research on biological rhythms and sleep. J Biol Rhythms 28: 303-4. [PubMed]
  • Gamble, K.L., D. Resuehr, and C.H. Johnson . (2013) Shift work and circadian dysregulation of reproduction. Frontiers in Systems and Translational Endocrinology 4:92. [PubMed]

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  • Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, Johnson CH, Kyriacou CP, O'Neill JS, Reddy AB. (2012) Peroxiredoxins are conserved markers of circadian rhythms. Nature 485: 459-64. [PubMed]
  • Zhang Y, Xie Q, Robertson JB, and Johnson CH . (2012) pHlash: A New Genetically Encoded and Ratiometric Luminescence Sensor of Intracellular pH. PLoS ONE 7: e43072. [PubMed]
  • Egli M, Mori T, Pattanayek R, Xu Y, Qin X, and Johnson CH. (2012) Dephosphorylation of the Core Clock Protein KaiC in the Cyanobacterial KaiABC Circadian Oscillator Proceeds via an ATP Synthase Mechanism. Biochemistry 51: 1547-1558. [PubMed]

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  • Gamble KL, Motsinger-Reif AA, Hida A, Borsetti HM, Servick SV, Ciarleglio CM, Robbins S, Hicks J, Carver K, Hamilton N, Wells N, Summar ML, McMahon DG, Johnson CH (2011) Shift work in nurses: contribution of phenotypes and genotypes to adaptation. PLoS ONE 6, e18395. [PubMed]
  • Robertson JB, and Johnson CH (2011) Luminescence as a Continuous Real-Time Reporter of Promoter Activity in Yeast Undergoing Respiratory Oscillations or Cell Division Rhythms. Methods Mol Biol. 734:63-79. [PubMed]
  • Johnson CH, Stewart PL, Egli M (2011) The cyanobacterial circadian system: from biophysics to bioevolution. Annu. Rev. Biophys. 40:143-167. [PubMed]
  • Xie Q, Soutto M, Xu X, Zhang Y, Johnson CH (2011) Bioluminescence resonance energy transfer (BRET) imaging in plant seedlings and mammalian cells. Methods Mol. Biol. 680, 3-28. [PubMed]

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  • Johnson CH (2010) Circadian clocks and cell division: What's the pacemaker? Cell Cycle 9, 3864-3873. (Review) [PubMed]
  • Qin X, Byrne M, Mori T, Zou P, Williams DR, McHaourab H, Johnson CH (2010) Intermolecular associations determine the dynamics of the circadian KaiABC oscillator. Proc. Natl. Acad. Sci. USA 107, 14805-14810. [PubMed] [PDF (5.5 MB)]
  • Qin X, Byrne M, Xu Y, Mori T, Johnson CH (2010) Coupling of a core post-translational pacemaker to a slave transcription/translation feedback loop in a circadian system. PLoS Biol. 8, e1000394. [PubMed] [PLoS Biol] [PDF (4.1 MB)]
  • Shi S, Hida A, McGuinness OP, Wasserman DH, Yamazaki S, Johnson CH (2010) Circadian clock gene Bmal1 is not essential; Functional replacement with its paralog, Bmal2. Curr. Biol. 20, 316-21. [PubMed]

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  • Pattanayek R, Mori T, Xu Y, Pattanayek S, Johnson CH, Egli M (2009) Structures of KaiC circadian clock mutant proteins: a new phosphorylation site at T426 and mechanisms of kinase, ATPase and phosphatase. PLoS One 4, e7529. [PubMed]
  • Xu Y, Mori T, Qin X, Yan H, Egli M, Johnson CH (2009) Intramolecular regulation of phosphorylation status of the circadian clock protein KaiC. PLoS One 4, e7509. [PubMed]
  • Wang Y, Ji J, Bu H, Zhao Y, Xu Y, Johnson CH, Kolar J (2009) Genetic transformation of Nicotiana tabacum L. by Agrobacterium tumefaciens carrying genes in the melatonin biosynthesis pathway and the enhancement of antioxidative capability in transgenic plants. (in Chinese) Sheng Wu Gong Cheng Xue Bao 25, 1014-1021. [PubMed]
  • Xu X, Graeff R, Xie Q, Gamble KL, Mori T, Johnson CH (2009) Comment on "The Arabidopsis circadian clock incorporates a cADPR-based feedback loop." Science 326, 230. (Comment) [PubMed]
  • Robertson JB, Zhang Y, Johnson CH (2009) Light-emitting diode flashlights as effective and inexpensive light sources for fluorescence microscopy. J. Microsc. 236, 1-4. [PubMed]
  • Ditty JL, Mackey SR, Johnson CH , eds. (2009) Bacterial Circadian Systems. Springer, Berlin [Springer] [WorldCat] [Google Book Search]

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  • Robertson JB, Stowers CC, Boczko E, Johnson CH (2008) Real-time luminescence monitoring of cell-cycle and respiratory oscillations in yeast. Proc. Natl. Acad. Sci. U.S.A 105, 17988-17993. [PubMed]
  • Johnson CH, Egli M, Stewart PL (2008) Structural insights into a circadian oscillator. Science 322, 697-701. (Review) [PubMed] [Abstract] [Full Text]
  • Vougogiannopoulou K, Ferandin Y, Bettayeb K, Myrianthopoulos V, Lozach O, Fan Y, Johnson CH, Magiatis P, Skaltsounis AL, Mikros E, Meijer L (2008) Soluble 3',6-substituted indirubins with enhanced selectivity toward glycogen synthase kinase -3 alter circadian period. J. Med. Chem. 51, 6421-6431. [PubMed]
  • Johnson CH, Mori T, Xu Y (2008) A cyanobacterial circadian clockwork. Curr. Biol. 18, R816-R825. (Review) [PubMed]
  • Ciarleglio CM, Ryckman KK, Servick SV, Hida A, Robbins S, Wells N, Hicks J, Larson SA, Wiedermann JP, Carver K, Hamilton N, Kidd KK, Kidd JR, Smith JR, Friedlaender J, McMahon DG, Williams SM, Summar ML, Johnson CH (2008) Genetic differences in human circadian clock genes among worldwide populations. J. Biol. Rhythms 23, 330-340. [PubMed]
  • Pattanayek R, Williams DR, Pattanayek S, Mori T, Johnson CH, Stewart PL, Egli M (2008) Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation. EMBO J. 27, 1767-1778. [PubMed]

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  • Johnson CH (2007) Bacterial circadian programs. Cold Spring Harb. Symp. Quant. Biol. 72, 395-404. [PubMed]
  • Xu X, Hotta CT, Dodd AN, Love J, Sharrock R, Lee YW, Xie Q, Johnson CH, Webb AAR (2007) Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis. Plant Cell 19, 3474-3490. [PubMed]
  • Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS (2007) A predictive model for transcriptional control of physiology in a free living cell. Cell 131, 1354-1365. [PubMed]
  • Woelfle MA, Xu Y, Qin X, Johnson CH (2007) Circadian rhythms of superhelical status of DNA in cyanobacteria. Proc. Natl. Acad. Sci. U.S.A 104: 18819-18824. [PubMed]
  • Fan Y, Hida A, Anderson DA, Izumo M, Johnson CH (2007) Cycling of CRYPTOCHROME proteins is not necessary for circadian-clock function in mammalian fibroblasts. Curr. Biol. 17, 1091-11009. [PubMed] [PDF (1.45 MB)]
  • Xu X, Soutto M, Xie Q, Servick S, Subramanian C, von Arnim AG, Johnson CH (2007) Imaging protein interactions with bioluminescence resonance energy transfer (BRET) in plant and mammalian cells and tissues. Proc. Natl. Acad. Sci. U.S.A 104, 10264-10269. [PNAS] [PubMed] [PDF (1.51 MB)]
  • Mori T, Williams DR, Byrne MO, Qin X, Mchaourab HS, Egli M, Stewart PL, Johnson CH (2007) Elucidating the ticking of an in vitro circadian clockwork. PLoS Biol. 5, e93. [PubMed] [PLoS Biol] [PDF (4.42 MB)]

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  • Woelfle MA, Johnson CH (2006) No promoter left behind: global orchestration of circadian gene expression in cyanobacteria. J. Biol. Rhythms 21, 419-431. (Review) [PubMed]
  • Izumo M, Sato TR, Straume M, Johnson CH (2006) Quantitative analyses of circadian gene expression in mammalian cell cultures. PLoS Comput Biol 2, e136. [PubMed] [PLoS Comput Biol]
  • Subramanian C, Woo JC, Cai X, Xu X, Servick S, Johnson CH, Nebenfuhr A, von Arnim A (2006) A suite of tools and application notes for in vivo protein interaction assays using Bioluminescence Resonance Energy Transfer (BRET). Plant J 48, 138-152. [PubMed]
  • Pattanayek R, Williams DR, Pattanayek S, Xu Y, Mori T, Johnson CH, Stewart PL, Egli M (2006) Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J. 25, 2017-2028. [EMBO J] [PubMed]
  • Johnson CH (2006) Reminiscences from Pittendrigh's last Ph.D. student. Resonance 11, 22-31.
  • Johnson CH, Shingles R, Ettinger WF (2006) Regulation and role of Ca++ fluxes in the chloroplast. In: R.R. Wise and J.K. Hoober (eds). Chapter 20 in The Structure and Function of Plastids. Vol. 23. In Govindjee (series ed) Advances in Photosynthesis and Respiration, Kluwer Academic Press, pp. 403-416. (Review)
  • Johnson CH, Golden SS (2006) Circadian Rhythms in Cyanobacteria. In: Nature Encyclopedia of Life Sciences, Nature Publishing Group, London:

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  • Johnson CH (2005) Testing the adaptive value of circadian systems. Methods Enzymol. 393, 818-837. [Methods Enzymol.] [PubMed]
  • Soutto M, Xu Y, Johnson CH (2005) Bioluminescence RET (BRET): techniques and potential. In: Molecular Imaging: FRET Microscopy and Spectroscopy. A. Periasamy and R.N. Day, eds. (Oxford University Press, NY), pp. 260-271. (Review)
  • Johnson CH, Kyriacou CP (2005) Clock evolution and adaptation: whence and whither? Chapter 10 in Endogenous Plant Rhythms (eds. A.J.W. Hall and H. McWatters), Blackwell Publishing Ltd, Oxford, pp. 237-260. (Review)
  • Mittag M, Kiaulehn S, Johnson CH (2005) The circadian clock in Chlamydomonas reinhardtii. What is it for? What is it similar to? Plant Physiol. 137, 399-409. (Review) [Plant Physiol] [PubMed]

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  • Woelfle MA, Ouyang Y, Phanvijhitsiri K, Johnson CH (2004) The adaptive value of circadian clocks: an experimental assessment in cyanobacteria. Curr. Biol. 14, 1481-1486. [PubMed]
  • Xu Y, Mori T, Pattanayek R, Pattanayek S, Egli M, Johnson CH (2004) Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses. Proc. Natl. Acad. Sci. U.S.A 101, 13933-13938. [PNAS] [PubMed]
  • Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M (2004) Visualizing a circadian clock protein: crystal structure of KaiC and functional insights. Mol. Cell 15, 375-388. [Mol. Cell] [RCSB/PDB] [PubMed] [PDF (1.3 MB)]
  • Johnson CH (2004) Circadian rhythms: as time glows by in bacteria. Nature 430, 23-24. (Comment) [Nature] [PubMed]
  • Johnson CH, Egli M (2004) Visualizing a biological clockwork's cogs. Nature Struct. Mol. Biol. 11, 584-585. (Comment) [PubMed]
  • Subramanian C, Xu Y, Johnson CH, von Arnim AG (2004) In vivo detection of protein-protein interaction in plant cells using BRET. Methods Mol. Biol. 284, 271-286. (Review) [PubMed]
  • Subramanian C, Kim BH, Lyssenko NN, Xu X, Johnson CH, von Arnim AG (2004) The Arabidopsis repressor of light signaling, COP1, is regulated by nuclear exclusion: mutational analysis by bioluminescence resonance energy transfer. Proc. Natl. Acad. Sci. U.S.A 101, 6798-6802. [PNAS] [PubMed]
  • Johnson CH (2004) Precise circadian clocks in prokaryotic cyanobacteria. Curr. Issues Mol. Biol. 6, 103-110. (Review) [PubMed]
  • Johnson CH (2004) Global orchestration of gene expression by the biological clock of cyanobacteria. Genome Biol. 5, 217. (Review) [Genome Biol.] [PubMed] [PDF (148 KB)]
  • Min H, Liu Y, Johnson CH, Golden SS (2004) Phase determination of circadian gene expression in Synechococcus elongatus PCC 7942. J. Biol. Rhythms 19, 103-112. [PubMed]

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  • Izumo M, Johnson CH, Yamazaki S (2003) Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: Temperature compensation and damping. Proc. Natl. Acad. Sci. U.S.A 100, 16089-16094. [PNAS] [PubMed] [PDF (860 KB)] [Supporting Information]
  • Johnson CH, Elliott JA, Foster R (2003) Entrainment of circadian programs. Chronobiol. Int. 20, 741-774. (Review) [] [PubMed] [PDF (464 KB)]
  • Johnson CH, Elliott J, Foster R, Honma K, Kronauer R (2003) Fundamental properties of circadian rhythms. (Chapter 3). In Chronobiology: biological timekeeping (J. C. Dunlap, J. J Loros, P. J. DeCoursey, eds.) pp. 67-105, Sinauer Associates, Sanderland, MA. (Book Chapter) [Sinauer] [] []
  • Kolar J, Johnson CH, Machackova I (2003) Exogenously applied melatonin (N-acetyl-5-methoxytryptamine) affects flowering of the short-day plant Chenopodium rubrum. Physiol. Plantarum 118, 605-612. [Blackwell Synergy]
  • Schoenhard JA, Smith LH, Painter CA, Eren M, Johnson CH, Vaughan DE (2003) Regulation of the PAI-1 promoter by circadian clock components: differential activation by BMAL1 and BMAL2. J. Mol. Cell Cardiol. 35, 473-481. [PubMed]
  • Xu Y, Mori T, Johnson CH (2003) The cyanobacterial circadian clockwork: roles of KaiA, KaiB, and the kaiBC promoter in KaiC expression, phosphorylation, and degradation. EMBO J. 22, 2117-2126. [EMBO J.] [PubMed] [PDF (428 KB)]
  • Xu Y, Kanauchi A, von Arnim AG, Piston DW, Johnson CH (2003) Bioluminescence resonance energy transfer: monitoring protein-protein interactions in living cells. Methods Enzymol. 360, 289-301. [PubMed] [] [Academic Press]
  • Hastings JW, Johnson CH (2003) Bioluminescence and chemiluminescence. Methods Enzymol. 360, 75-104. [PubMed] [] [Academic Press]

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  • Mori T, Saveliev SV, Xu Y, Stafford WF, Cox MM, Inman RB, Johnson CH (2002) Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. Proc. Natl. Acad. Sci. U.S.A 99, 17203-17208. [PNAS] [PubMed] [GenBank] [PDF (452 KB)]
  • Xu Y, Johnson CH, Piston DW (2002) Bioluminescence resonance energy transfer: Assays for protein-protein interactions in living cells. In Methods in Molecular Biology, vol. 183: Green Fluorescent Protein: Applications and Protocols (B. W. Hicks ed.) pp.121-133, Humana Press, Totowa, NJ. (Book Chapter) [Humana Press] [] [] [PubMed]
  • Schoenhard JA, Eren M, Johnson CH, Vaughan DE (2002) Alternative splicing yields novel BMAL2 variants: tissue distribution and functional characterization. Am. J. Physiol. Cell Physiol. 283, C103-C114. [AJP] [PubMed]
  • Sai J, Johnson CH (2002) Dark-stimulated calcium ion fluxes in the chloroplast stroma and cytosol. Plant Cell 14, 1279-1291. DOI 10.1105/tpc.000653 [DOI] [Plant Cell] [PubMed] [PDF (300 KB)]
  • Suzuki L, Johnson CH (2002) Photoperiodic control of germination in the unicell Chlamydomonas. Naturwissenschaften 89, 214-220. DOI 10.1007/s00114-002-0302-6. [DOI] [PubMed] [Springer-Verlag] [PDF (142 KB)]
  • Xu Y, Kanauchi A, Piston DW, Johnson CH (2002) Resonance energy transfer as an emerging technique for monitoring protein-protein interactions in Vivo: BRET vs. FRET. In Luminescence Biotechnology: Instruments and Applications (K. V. Dyke, C. V. Dyke and K. Woodfork, eds) pp. 529-538, CRC Press, Boca Raton. (Book Chapter) [] []

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  • Johnson CH, Kondo T (2001) Circadian rhythms in unicellular organisms (Chapter 3). In Handbook of Behavioral Neurobiology, Volume 12: Circadian Clocks (J. S. Takahashi, F. W. Turek, R. Y. Moore, eds.) pp. 61-77, Kluwer Academic/Plenum Publishers. (Book Chapter) [Kluwer] [] []
  • Suzuki L, Johnson CH (2001) Algae know the time of day: circadian and photoperiodic programs. J. Phycol. 37, 933-942. (Review) [J. Phycol.] [PDF]
  • DasSarma S, Kennedy SP, Berquist B, Ng BWV, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L (2001) Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth. Res. 70, 3-17. [Kluwer]
  • Mori T, Johnson CH (2001) Circadian programming in cyanobacteria. Semin. Cell Dev. Biol. 12, 271-278. (Review) [IDEAL] [PubMed] [PDF (1,840KB)]
  • Xu Y, Johnson CH (2001) A clock- and light-regulated gene that links the circadian oscillator to LHCB gene expression. Plant Cell 13, 1411-1426. [Plant Cell] [PubMed] [GenBank] [PDF]
  • Johnson CH, Golden SS, Kondo T (2001) Circadian Programs in Cyanobacteria. In Encyclopedia of Life Sciences. Nature Publishing Group, London: (Review) [PDF (120 KB)]
  • Mori T, Johnson CH (2001) Independence of circadian timing from cell division in cyanobacteria. J. Bacteriol. 183, 2439-2444. [J. Bacteriol.] [PubMed] [GenBank] [PDF]
  • Johnson CH (2001) Endogenous timekeepers in photosynthetic organisms. Annu. Rev. Physiol. 63, 695-728. (Review) [Annu. Rev.] [PubMed]
  • Wood NT, Haley A, Viry-Moussaid M, Johnson CH, van Der Luit AH, Trewavas AJ (2001) The calcium rhythms of different cell types oscillate with different circadian phases. Plant Physiol. 125, 787-796. [Plant Physiol.] [PubMed]

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  • Xu Y, Mori T, Johnson CH (2000) Circadian clock-protein expression in cyanobacteria: rhythms and phase-setting. EMBO J. 19, 3349-3357. [EMBO J.] [PubMed] [PDF]
  • Nikaido SS, Johnson CH (2000) Daily and circadian variation in survival from ultraviolet radiation in Chlamydomonas reinhardtii. Photochem. Photobiol. 71, 758-765. [Photochem. Photobiol.] [PubMed] [PDF]
  • Mori T, Johnson CH (2000) Circadian control of cell division in unicellular organisms. Prog. Cell Cycle Res. 4, 185-192. (Review) [PubMed] [PDF (668 KB)]

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  • Kolar J, Johnson CH, Machackova I (1999) Presence and possible role of melatonin in a short-day flowering plant, Chenopodium rubrum. Adv. Exp. Med. Biol. 460, 391-393. [PubMed]
  • Xu Y, Piston DW, Johnson CH (1999) Resonance energy transfer as an emerging strategy for monitoring protein-protein interaction in vitro: BRET vs. FRET. Spectrum 12, 9-14. (Review) [Spectrum] [PDF]
  • Johnson CH (1999) Forty years of PRCs--what have we learned? Chronobiol. Int. 16, 711-743. (Review) [PubMed] [PDF (1.9 MB)]
  • Lakin-Thomas PL, Johnson CH (1999) Commentary: molecular and cellular models of circadian systems. J. Biol. Rhythms 14, 486-489. (Comment) [PubMed]
  • Minko I, Holloway SP, Nikaido S, Carter M, Odom OW, Johnson CH, Herrin DL (1999) Renilla luciferase as a vital reporter for chloroplast gene expression in Chlamydomonas. Mol. Gen. Genet. 262, 421-425. [Mol. Gen. Genet.] [PubMed]
  • Johnson CH, Golden SS (1999) Circadian programs in cyanobacteria: adaptiveness and mechanism. Annu. Rev. Microbiol. 53, 389-409. (Review) [Annu. Rev.] [PubMed]
  • Sai J, Johnson CH (1999) Different circadian oscillators control Ca2+ fluxes and Lhcb gene expression. Proc. Natl. Acad. Sci. U.S.A 96, 11659-11663. [PNAS] [PubMed] [PDF]
  • Xu Y, Piston DW, Johnson CH (1999) A bioluminescence resonance energy transfer (BRET) system: Application to interacting circadian clock proteins. Proc. Natl. Acad. Sci. U.S.A 96, 151-156. [PNAS] [PubMed] [PDF]

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  • Golden SS, Johnson CH, Kondo T (1998) The cyanobacterial circadian system: a clock apart. Curr. Opin. Microbiol. 1, 669-673. (Review) [PubMed]
  • Johnson CH, Golden SS, Kondo T (1998) Adaptive significance of circadian programs in cyanobacteria. Trends Microbiol. 6, 407-410. (Review) [PubMed]
  • Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, Kondo T (1998) Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281, 1519-1523. [Science] [PubMed] [GenBank]
  • Johnson CH, Knight M, Trewavas A, Kondo T (1998) A clockwork green: circadian programs in photosynthetic organisms. Chapter 1 in Biological Rhythms and Photoperiodism in Plants (P. Lumsden and A. Millar, eds.) pp. 1-34, BIOS Scientific Publishers, Oxford. (Book Chapter)
  • Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH (1998) Resonating circadian clocks enhance fitness in cyanobacteria. Proc. Natl. Acad. Sci. U.S.A 95, 8660-8664. [PNAS] [PubMed] [PDF]

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  • Golden SS, Ishiura M, Johnson CH, Kondo T (1997) Cyanobacterial circadian rhythms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48, 327-354. (Review) [Annu. Rev.]

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  • Jacobshagen S, Kindle KL, Johnson CH (1996) Transcription of cabII is regulated by the biological colock in Chlamydomonas reinhardtii. Plant Mol. Biol. 31, 1173-1184. [PubMed]
  • Mori T, Binder B, Johnson CH (1996) Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours. Proc. Natl. Acad. Sci. U.S.A 93, 10183-10188. [PNAS] [PubMed] [PDF]
  • Johnson CH, Golden SS, Ishiura M, Kondo T (1996) Circadian clocks in prokaryotes. Mol. Microbiol. 21, 5-11. (Review) [PubMed]
  • Liu Y, Tsinoremas NF (1996) An unusual gene arrangement for the putative chromosome replication origin and circadian expression of dnaN in Synechococcus sp. strain PCC 7942. Gene 172, 105-109. [PubMed] [GenBank]
  • Liu Y, Tsinoremas NF, Golden SS, Kondo T, Johnson CH (1996) Circadian expression of genes involved in the purine biosynthetic pathway of the cyanobacterium Synechococcus sp. strain PCC 7942. Mol. Microbiol. 20, 1071-1081. [PubMed] [GenBank]
  • Tsinoremas NF, Ishiura M, Kondo T, Andersson CR, Tanaka K, Takahashi H, Johnson CH, Golden SS (1996) A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria. EMBO J. 15, 2488-2495. [EMBO J.] [PubMed]

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  • Johnson CH, Knight MR, Kondo T, Masson P, Sedbrook J, Haley A, Trewavas A (1995) Circadian oscillations of cytosolic and chloroplastic free calcium in plants. Science 269, 1863-1865. [PubMed] [PDF (764 KB)]
  • Liu Y, Tsinoremas NF, Johnson CH, Lebedeva NV, Golden SS, Ishiura M, Kondo K (1995) Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 9, 1469-1478. [Genes Dev.] [PubMed]
  • Johnson CH (1995) Photobiology of circadian rhythms. In CRC Handbook of Organic Photochemistry and Photobiology (W.M. Horspool and S.P. Song, eds.) pp. 1602-1610, CRC Press, Boca Raton. (Book Chapter)
  • Goto K, Johnson CH (1995) Is the cell division cycle gated by a circadian clock? The case of Chlamydomonas reinhardtii. J. Cell Biol. 129, 1061-1069. [JCB] [PubMed]
  • Liu Y, Golden SS, Kondo T, Ishiura M, Johnson CH (1995) Bacterial luciferase as a reporter of circadian gene expression in cyanobacteria. J. Bacteriol. 177, 2080-2086. [PubMed] [PDF]

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  • Johnson CH (1994) Illuminating the clock: Circadian photobiology. Semin. Cell Biol. 5, 355-362. (Review) [PubMed]
  • Johnson CH, Nakaoka Y, Miwa I (1994) The effects of altering extracellular potassium ion concentration on the membrane potential and circadian clock of Paramecium bursaria. J. Expt. Biol. 197, 295-308. [PubMed]
  • Kondo T, Ishiura M, Golden SS, Johnson CH (1994) Circadian rhythms of cyanobacteria expressed from a luciferase reporter gene. In Evolution of Circadian Clock. (T. Hiroshige and K. Honma, eds.) pp. 59-73, Hokkaido Univ. Press, Sapporo. (Book Chapter)
  • Kondo T, Tsinoremas NF, Golden SS, Johnson CH, Kutsuna S, Ishiura M (1994) Circadian clock mutants of cyanobacteria. Science 266, 1233-1236. [PubMed] [JSTOR]
  • Jacobshagen S, Johnson CH (1994) Circadian rhythms of gene expression in Chlamydomonas reinhardtii: Circadiancycling of mRNA abundances of cab II, and possibly of beta-tubulin and cytochrome c. Eur. J. Cell Biol. 64, 142-152. [PubMed]

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  • Kondo T, Strayer CA, Kulkarni RD, Taylor T, Ishiura M, Golden SS, Johnson CH (1993) Circadian rhythms in prokaryotes Luciferase as a reporter of circadian gene expression in cyanobacteria. Proc. Natl. Acad. Sci. U.S.A 90, 5672-5676. [PubMed] [JSTOR]

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  • Johnson CH, Kondo T (1992) Light pulses induce "singular" behavior and shorten the period of the circadian phototaxis rhythm in the CW15 strain of Chlamydomonas. J. Biol. Rhythms 7, 313-327. [PubMed]
  • Byrne TE, Wells MR, Johnson CH (1992) Circadian rhythms of chemotaxis to ammonium and of methylammonium uptake in Chlamydomonas. Plant Physiol. 93, 879-886.
  • Johnson CH (1992) Phase response curves: What can they tell us about circadian clocks? In Circadian Clocks from Cell to Human (T. Hiroshige and K. Honma, eds.) pp. 209-249, Hokkaido Univ. Press, Sapporo. (Book Chapter) [Full Text] [PDF (1.9MB)]
  • Johnson CH, Kondo K, Goto K (1992) Circadian rhythms in Chlamydomonas. In Circadian Clocks from Cell to Human (T. Hiroshige and K. Honma, eds.) pp. 139-155, Hokkaido Univ. Press, Sapporo. (Book Chapter)

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  • Johnson CH, Kondo T, Hastings JW (1991) Action spectrum for resetting the circadian phototaxis rhythm in the CW15 strain of Chlamydomonas. II. Illuminated cells. Plant Physiol. 97, 1122-1129.
  • Kondo T, Johnson CH, Hastings JW (1991) Action spectrum for resetting the circadian phototaxis rhythm in the CW15 strain of Chlamydomanas. I. Cells in darkness. Plant Physiol. 97, 197-205.

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  • Johnson CH, Nakashima N (1990) Cycloheximide inhibits light-induced phase shifting of the circadian clock in Neurospora. J. Biol. Rhythms 5, 159-167. [PubMed]
  • Johnson CH (1990) An Atlas of Phase Responses Curves for Circadian and Circatidal Rhythym., 715 Pages, Department of Biology, Vanderbilt University, Nashville. Macintosh HyperCard and MS-Excel versions are available here (courtesy of Drs. V. Gooch, T. Kondo and M. Stokes).

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  • Johnson CH, Hastings JW (1989) Circadian phototransduction: phase-resetting and frequency of the circadian clock of Gonyaulax cells in red light. J. Biol. Rhythms 4, 417-437. [PubMed]
  • Johnson CH, Miwa I, Kondo K, Hastings JW (1989) Circadian rhythm of photoaccumulation in Paramecium bursaria. J. Biol. Rhythms 4, 405-415. [PubMed]
  • Broda H, Johnson CH, Taylor W, Hastings JW (1989) Temperature dependence of phase response curves for drug-induced phase shifts. J. Biol. Rhythms 4, 327-333. [PubMed]

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  • No publicaion in 1988

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  • Olesiak W, Ungar A, Johnson CH, Hastings JW (1987) Are protein synthesis inhibition and phase-shifting of the circadian clock in Gonyaulax correlated? J. Biol. Rhythms 2, 121-138. [PubMed]
  • Nicolas MT, Nicolas G, Johnson CH, Bassot JM, Hastings JW (1987) Characterization of the bioluminescent organelles in Gonyaulax after fast-freeze fixation and antiluciferase immunogold staining. J. Cell Biol. 105, 723-735.

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  • Johnson CH, Hastings JW (1986) The elusive mechanism of circadian clocks. American Scientist 74, 29-36. (Review)

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  • Dube F, Schmidt T, Johnson CH, Epel D (1985) The hierarchy of requirements for an elevated intracellular pH during early development of sea urchin embryos. Cell 40, 657-666.
  • Nicolas MT, Johnson CH, Bassot JM, Hastings JW (1985) Immunogold labelling of organelles in the bioluminescent dinoflagellate Gonyaulax with anti-luciferase antibody. Cell Biol. Int. Reports 9, 797-802.
  • Johnson CH, Inoue S, Flint A, Hastings JW (1985) Compartmentalization of algal bioluminescence: autofluorescence of bioluminescent particles in the dinoflagellate Gonyaulax as studied with image-intensified video microscopy and flow cytometry. J. Cell Biol. 100, 1435-1446. [PubMed]
  • Hastings JW, Broda H, Johnson CH (1985) Phase and period effects of physical and chemical factors. Do cells communicate? In Temporal Order (L. Rensing and N. I. Jaeger, eds.) pp. 213-221, Springer-Verlag. (Review)
  • Johnson CH, Hastings JW (1985) Bioluminescence and Chronobiology. In Photobiology 1984 (Longworth, Jaffer, and Shropshire, eds.) pp. 189-193, Praeger, New York. (Review)

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  • Johnson CH, Roeber JF, Hastings JW (1984) Circadian changes of enzyme concentration account for rhythm of enzyme activity in Gonyaulax. Science 223, 1428-1430. [PDF (888 KB)]

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  • Johnson CH (1983) Changes of intracellular pH are not correlated with the circadian rhythm of Neurospora. Plant Physiol. 72, 129-133.
  • Johnson CH, Clapper DL, Winkler MW, Lee HC, Epel D (1983) A volatile inhibitor immobilizes sea urchin sperm in semen by depressing the intracellular pH. Devel. Biol. 98, 493-501.
  • Johnson CH, Epel D (1983) Heavy metal chelators prolong motility and viability of sea urchin sperm by inhibiting spontaneous acrosome reactions. J. Exp. Zool. 226, 431-440.
  • Lee HC, Johnson CH, Epel D (1983) Changes in internal pH associated with initiation of motility and acrosome reaction of sea urchin sperm. Devel. Biol. 95, 31-45.

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  • Johnson CH, Epel D (1982) Starfish oocyte maturation and fertilization: intracellular pH is not involved in activation. Devel. Biol. 92, 461-469.

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  • Johnson CH, Epel D (1981) Intracellular pH of sea urchin eggs measured by the dimethyloxazolidinedione (DMO) method. J. Cell Biol. 89, 284-291.

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