Bhaya Lab Publications


Chau R, Bhaya D, Huang K C. (2017) Emergent phototactic responses of cyanobacteria under complex light regimes. Mbio;8(2). pii: e02330-16. (featured in Commentary section: Kim).

Govindjee, Bhaya D, Grossman AR. (2016) Gordon research conference on the dynamics and regulation of photosynthesis: from the origin of bio-catalysis to innovative solar conversion. Photosyn Res. 127:379-89. doi: 10.1007/s11120-015-0187-9. PMID: 26338068.

Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR,Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ. (2017) On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires. MBio. 2017 Jul 11;8(4). pii: e00897-17.

Yu FB, Willis L, Chau RM, Zambon A, Horowitz M, Bhaya D, Huang KC, Quake SR. (2017) Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing. BMC Biol.; 15 (1):11.

Silas S, Mohr G, Sidote DJ, Markham LM, Sanchez- Amat A, Bhaya D, Lambowitz AM, Fire AZ (2016) Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein Science 351(6276): 351(6276):aad4234. doi:10.1126/science.aad4234.

Bhaya D. (2016) In the Limelight: Photoreceptors in Cyanobacteria. MBio.7(3). pii: e00741-16. (Invited Commentary)

Rosen M, Davison M,  Bhaya D, Fisher D. (2015) A quasi-sexual bacterial population occupying a broad niche Science. 348(6238):1019-23. PMID: 26023139   PDF  Supporting information  see Comment ('Flexible Gene Pools' by Desai MM and AM Walczak)

Chau RM,,Ursell T, Wang S, Huang KC , Bhaya D. (2015) Rapid motility bias adaptation during cyanobacterial phototaxis Biophys J. 108(7):1623-32. PMID: 25863054   PDF  Supporting information

Davison M, Bhaya D. (2015) Creation and Analysis of a Virome: Using CRISPR Spacers. Methods Mol Biol. CRISPR methods and Protocols 1311:307-16. PMID: 25981482  PDF

Davison M, Hall E, Zare RN, Bhaya D (2014) Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. Photosyn Res Dec 17 ePub PMID: 25515769  PDF

Gomez R, Fazeli F,  Bhaya D. (2013) The role of polyphosphate accumulation in Synechococcus sp. J. Bact 195(15):3309-19 PMID: 23687278  PDF  Supporting information

Ursell T, Chau R, Wisen S, Bhaya, D, Huang KC. (2013) Motiltiy enhancement through surface modification is sufficient for cyanobacetrail community organization during phototaxis PLoS Comp Biol. (9):e1003205 PMID: 24039562  PDF 

Galante A, Wisen S, Bhaya D, Levy D. (2012) Modeling local interactions during the motion of cyanobacteria. J Theor Biol. 309:147-58.   PMID: 22713858    PDF

Nelson WC, Bhaya D, Heidelberg JF. (2012) Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population. J Bacteriol. 194(14):3636-42.    PMID: 22563047    PDF    Supporting information

Bhaya D, Davison M, Barrangou R.Bhaya D, Davison M, Barrangou R. (2011) CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Ann Rev Genet  45:273-97.  PMID: 22060043   PDF

Klatt CG, Wood JM, Rusch DB, Bateson MM, Hamamura N, Heidelberg JF, Grossman AR, Bhaya D, Cohan FM, Kühl M, Bryant DA, Ward DM. (2011) Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J. 5(8):1262-78.   PMID: 21697961  PDF    Supporting information

Chueh BH, Li CW, Wu H, Davison M, Wei H, Bhaya D, Zare RN. (2011) Whole gene amplification and protein separation from a few cells. Anal Biochem. 411(1):64-70. PMID: 21185803   PDF

Jensen SI, Steunou AS, Bhaya D, Kühl M, Grossman AR. (2011) In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS. ISME J.  5(2):317-28.   PMID: 20740024     PDF      Supporting information

Nelson WC, Wollerman L, Bhaya D, Heidelberg JF. (2011) Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance. Appl Environ Microbiol. 77(15):5458-66.  PMID: 21666019   PDF    Supporting information

Gomez-Garcia MR, Davison M, Hartnung MB, Grossman AR, D Bhaya (2011) Alternative Pathways for Phosphonate Metabolism in Thermophilic Cyanobacteria from Microbial Mats  ISME J.  5(1):141-9  PMID:20631809     PDF    Supporting information

Jensen S., Steunou, A-S, Bhaya, D, Kühl M. and A.R. Grossman (2011) In situ Dynamics of O2, pH and Cyanobacterial Transcripts Associated with Inorganic Carbon Concentration, Photosynthesis and Detoxification of Reactive Oxygen Species in Hot Spring Microbial Mats ISME J  5(2):317-28    PMID:20740024    PDF   Supporting information

Heidelberg J.F., W.C. Nelson, T. Schoenfeld and D. Bhaya (2009) Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PloS ONE  4(1):e4169.  PMID:19132092    PDF     Supporting information   Commentary in Faculty of 1000 Biology

Adams M, Gomez, R. Grossman A.R. and D. Bhaya (2008) Responses of thermophilic Synechococcus sp. to phosphate deprivation and growth on phosphonate. J Bacteriol. 190 (24):8171-84. Oct 17  PMID: 18931115    PDF    Supporting information

Ulijasz, AT. G. Cornilescu, D. von Stetten, S. Kaminsky, M.A. Mroginski, J. Zhang, D. Bhaya, P. Hildebrandt, and R. D. Vierstra (2008) Characterization of two thermostable cyanobacterial phytochromes reveal global movements in the chromophore–binding domain during photoconversion. J. Biol. Chem. 283(30):21251-66 PMID:18480055   PDF

Burriesci M. and Bhaya D. (2008) Tracking phototactic responses and modeling motility of Synechocystis sp. strain PCC6803 J. Photochem. Photobiol. 91(2-3):77-86. Feb 13 PMID: 18343151  PDF  Supporting information 

Steunou A-S, Jensen S, Brecht E., Becraft E.D., Bateson, Kilian O, Bhaya D. , Ward D.M., Peters J.W., Grossman A.R., Kühl M. (2008) Regulation of nif Gene Expression and the Energetics of N2 Fixation over the Diel Cycle in a Hot Spring Microbial Mat ISME J., 2(4):364-78. PMID: 18323780    PDF    Supporting information 

Kilian O, Steunou A-S., Grossman A.R., Bhaya D. A novel two domain-fusion protein in cyanobacteria with similarity to the CAB/ELIP/HLIP superfamily: Evolutionary implications and regulation (2008) Molecular Plant 1;155-166 PMID: 20031922   PDF

Bhaya D., Grossman, A.R., Steunou A.S., N.Khuri, F.M. Cohan, N. Hamamura, M. C. Melendrez, M. M. Bateson, D. M. Ward, J.F. Heidelberg (2007) Genomic, metagenomic and functional analyses of cyanobacteria from hot-spring microbial mats reveal an unexpected diversity in nutrient utilization strategies  ISME J: 1(8):703-13 PMID:18059494   PDF    Supporting information   Commentary in Faculty of 1000 Biology

Kilian O, A-S Steunou, F. Fazeli, S. Bailey, D. Bhaya, A R. Grossman: Light Responses of Thermophilic Synechococcus isolates from the Microbial Mats of Octopus Spring (2007) Appl. Environ. Microbiol. 73: 4268-4278 PMID:17483258   PDF

Ward D.M., Cohan, F.M., Bhaya D., Heidelberg J.F., Kühl, M., and Grossman A.R. (2007) Genomics, Environmental Genomics and the Issue of Microbial Species. Nature Heredity 100(2):207-19 PMID: 17551524    PDF

Huang, B., Wu H., Bhaya D., Grossman A. R., Granier, S., Kobilka B.K. and Zare R. N.(2007) Counting low-copy number proteins in a single cell. Science 315: 81-84  PMID: 17204646  PDF  Supporting information      Faculty of 1000 Biology

Labiosa, R.G., Arrigo, K.R. Tu C.J., Bhaya D, Bay S, Grossman A.R., and J Shrager (2006) Examination of diel changes in global transcript accumulation in Synechocystis sp. Strain PCC6803: A study in photoacclimation. J Phycol. 42:622-636 PDF

Kapell A.D., Bhaya D., van Waasbergen L.G. (2006) Negative control of the high light-inducible hliA gene and implications for the activities of the NblS sensor kinase in the cyanobacterium Synechococcus elongatus strain PCC 7942. Arch. Microbiol 186:403-413 PMID: 16897032   PDF

Bhaya, D., Fazeli F, Nakasugi K.N., and Burriesci M., (2006) Phototaxis and impaired motility in adenylyl cyclase and cyclase receptor protein mutants of Synechocystis sp. Strain PCC6803 J. Bacteriol 188: 7306-7610 PMID:17015670   PDF

Steunou, A.S., Bhaya, D., Bateson, M., Melendrez, M., Ward, D., Brecht, E., Peters, J.W., Kühl, K, Grossman, A.R. (2006) In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting a hot-spring microbial mat Proc. Natl. Acad. Sci. U.S.A.103:2398-2407 PMID: 16467157   PDF   Supporting information  Commentary in Faculty of 1000 Biology

Bhaya, D., (2004) Light matters: Phototaxis and signal transduction in unicellular cyanobacteria Mol. Microbiol. 53:745-754 PMID: 15255889    PDF

Ng, W-O, Grossman A.R. and D. Bhaya (2003) Multiple light inputs control phototaxis in Synechocystis sp. Strain PCC6803. J.Bacteriol 185:1599-607 PMID: 12591877    PDF

Bhaya, D., Dufresne A., Vaulot D. and A.R.Grossman (2002):  Analysis of the hli gene family in marine and freshwater cyanobacteria. FEMS Microbiol Letters. 215:209-219 PMID: 12399037   PDF

Bhaya D, Takahashi A, Shahi P., and A R. Grossman (2001) Novel motility mutants from Synechocystis PCC6803 generated by in vitro transposon mutagenesis. J. Bacteriol. 183:6140-6143 PMID:11567015   PDF

Bhaya D, Takahashi, A and A R. Grossman (2001) Light regulation of TypeIV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC 6803. Proc. Natl. Acad. Sci. U.S.A.,98:7540-7545 PMID:11404477   PDF

Grossman, A. R., D. Bhaya and Q. He (2001) Tracking the light environment by cyanobacteria and the dynamic nature of light harvesting. Journal of Biological Chemistry. 276:11449-52 PMID: 11279225   PDF

Mrázek, J., D. Bhaya, A. R. Grossman and S. Karlin (2001) Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29:1590-601 PMID: 11266562   PDF

Huala, E, et al. The Arabidopsis Information Resource (TAIR) (2001): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29:102-105 PMID: 11125061   PDF

Bhaya, D, N. R. Bianco, D. Bryant and A. R. Grossman (2000) Type IV pilus biogenesis and motility in the cyanobacterium Synechocystis sp. PCC6803. Mol. Microbiol. 37: 941-951 PMID: 10972813   PDF

Bhaya, D., D.Vaulot, P.Amin, A.W. Takahashi and A.R. Grossman (2000)  Isolation of regulated genes of the unicellular cyanobacterium Synechocystis sp.strain PCC6803 by differential display. J. Bacteriol. 182:5692-5699 PMID: 10077659   PDF

Bhaya, D. and A.R. Grossman (1999) The role of an alternative sigma factor in motility and pilus formation in the cyanobacterium Synechocystis sp. strain PCC6803.  Proc. Natl. Acad. Sci. U.S.A., 96: 3188-3193 PMID: 10077659   PDF

Bhaya, D (1996) Molecular responses of cyanobacteria to nutrient stress. Journal of Industrial Research 55: 630-637

Grossman, A.R., D. Bhaya, K.E. Apt and D.M. Kehoe (1995) Light harvesting in photosynthetic organisms: Regulation and evolution. Annu. Rev. Genet. 29: 231-288 PMID: 9512353  PDF

Dolganov, N., D. Bhaya and A.R. Grossman (1995) Cyanobacterial protein with homology to the chlorophyll a/b binding proteins of plants: Evolution and regulation. Proc. Natl. Acad. Sci. U.S.A., 92: 636-640 PMID: 7831342   PDF

Srivastava, M., D. Bhaya, P. Mohanty and S. Bose (1994) Changes in the antenna size of photosystem I and photosystem II in Synechococcus PCC 7942 in the presence of Sandoz 9785, a photosystem II inhibitor. Photosyn. Res., 41: 303-313

Apt, K.E., D. Bhaya and A.R. Grossman (1994) Characterization of the genes encoding the light-harvesting proteins in diatoms: the biogenesis of the fucoxanthin-chlorophyll a/c protein complex. Journal of Applied Phycol. 6:225-230

Bhaya, D. and A.R. Grossman (1993) Characterization of gene clusters encoding the fucoxanthin chlorophyll protein of the diatom Phaeodactylum tricornutum. Nucleic Acids Res. 21: 4458-4466 PMID: 8233779   PDF

Bhaya, D. and A.R. Grossman (1991) A new route for targeting proteins into plastids: evidence from diatoms. Molec. Gen. Genet. 229: 400-404.

Ray, J., Bhaya, D., M. Block and A.R. Grossman (1991) An atypical alkaline phosphatase from Synechococcus sp. strain PCC 7942; gene isolation, transcription and inactivation. J. Bacteriol. 173: 4297-4309

Bhaya, D. and P.A. Castelfranco (1986) Regulation of chlorophyll and cytochrome in isolated developing plastids. Plant Physiol. 82: 960-964 PDF

Bhaya, D. and P.A. Castelfranco (1986) In vitro synthesis of chlorophyll and assembly of chlorophyll protein complexes in developing plastids of cucumber and peas. Proc. Natl. Acad Sci. U.S.A. 82: 5370-5374 PDF

Bhaya, D. and A.T. Jagendorf (1985) Alpha and beta subunits of CF1 are synthesized on the thylakoid-bound ribosomes of pea chloroplasts. Arch. Biochim. Biophys. 234: 273-278

Bhaya, D. and A.T. Jagendorf (1984) Synthesis of subunit III of the CFo on thylakoid-bound polysomes from pea chloroplasts. Plant Molec. Biol. 3:273-280

Bhaya, D and A.T. Jagendorf (1984) Optimal conditions for the translation of thylakoid-bound ribosomes from pea chloroplasts. Plant Physiol. 75: 832-838


Bhaya D and Brahamsha B (2014) “Motility and the regulation of phototaxis in cyanobacteria” in "The Cell Biology of Cyanobacteria"  pp 233-262 Eds : E. Flores & A. Herrero, Caister Academic Press. PDF

Held N, Childs L M, Davison M, Weitz, J S, Whitaker R J and  Bhaya, D. (2013) “CRISPR-cas systems to probe ecological diversity and host-viral interactions” in CRISPR-Cas systems RNA-Mediated Adaptive immuinty in Bacteria and Archaea Eds R. Barrangou and J. van der Oost , Springer. PDF

Bhaya D. (2012) “Meta- and functional genomic analysis of oxygenic phototrophy in the hot springs” In “Functional Genomics and Evolution of Photosynthetic Systems”, ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION Series on Photosynthesis, Springer PDF

Bhaya D. (2011)“Approaches to understanding population level functional diversity in a microbial community” Invited chapter in “Handbook of Molecular Microbial Ecology, Vol II: Metagenomics in Different Habitats”,  Ed. De Bruijn, Wiley/Blackwell PDF

Bhaya, D, Levy, D., Requeijo, T.  (2006) Group Dynamics of Phototaxis: Interacting Stochastic Many-Particles Systems and their Continuum Limit, in S. Benzoni-Gavage and D. Serre (Eds.), Hyperbolic Problems: Theory, Numerics, Applications'', Proceedings of the Eleventh International Conference on Hyperbolic Problems, Lyon,  Springer-Verlag, Berlin, pp.145--159. PDF

Bhaya, D., R. Schwarz and A. R. Grossman (2000)  “Molecular responses to environmental stresses” in “Ecology of Cyanobacteria: Their diversity in time and space” Ed. B. A. Whitton and M. Potts, Kluwer Academic Publishers Ltd. pp 397-442

Grossman, A. R., R. Schwarz, D. Bhaya and N. Dolganov (1998) Phycobilisome degradation and responses of cyanobacteria to nutrient limitation and high light. Proceedings of the XI th International Congress on Photosynthesis. Eds. G. Gareb and J. Pusztai, Kluwer Academic Publishers Ltd

Grossman. A.R., D. Bhaya and J.L. Collier (1994) Specific and general responses of cyanobacteria to macronutrient deprivation. In Cellular and Molecular Biology of Phosphate and Phosphorylated Compounds in Microorganisms. Eds. Torriani-Gorini, Yagil and Silver, ASM Press, Washington DC, USA.  pp. 112-118

Bhaya, D., and P.A. Castelfranco (1986) Synthesis of chlorophyll and assembly of chlorophyll protein complexes in developing plastids. In  Chloroplast Development. Ed. G. Akoyunoglou.