Genomes and Genes
Affiliation: Stanford University
- Motility enhancement through surface modification is sufficient for cyanobacterial community organization during phototaxisTristan Ursell
Department of Bioengineering, Stanford University, Stanford, California, United States of America
PLoS Comput Biol 9:e1003205. 2013....
- CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulationDevaki Bhaya
Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA
Annu Rev Genet 45:273-97. 2011..Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed...
- Light matters: phototaxis and signal transduction in unicellular cyanobacteriaDevaki Bhaya
Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305, USA
Mol Microbiol 53:745-54. 2004..Furthermore, the discovery that cyclic AMP and novel gene products are necessary for phototaxis/motility suggests that there might be additional levels of communication and signal processing...
- Phototaxis and impaired motility in adenylyl cyclase and cyclase receptor protein mutants of Synechocystis sp. strain PCC 6803Devaki Bhaya
Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA
J Bacteriol 188:7306-10. 2006..We find that contrary to earlier reports, cya1 and sycrp1 mutants are motile and phototactic but are impaired in one particular phase of phototaxis in comparison with wild-type Synechocystis sp...
- Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analysesDevaki Bhaya
Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
ISME J 1:703-13. 2007....
- Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial matAnne Soisig Steunou
Department of Plant Biology, The Carnegie Institution, Stanford University, Stanford, CA, USA
ISME J 2:364-78. 2008..These results are discussed with respect to the energetics and regulation of N2 fixation in hot spring mats and factors that can markedly influence the extent of N2 fixation over the diel cycle...
- Phosphorus deprivation responses and phosphonate utilization in a thermophilic Synechococcus sp. from microbial matsMelissa M Adams
Carnegie Institution for Science, Department of Plant Biology, Stanford University, Stanford, CA 94305, USA
J Bacteriol 190:8171-84. 2008..Once acclimated, the cells grew rapidly in fresh medium with methylphosphonate as the only source of phosphorus. The possible implications of these results are discussed with respect to the ecophysiology of the microbial mats...
- Responses of a thermophilic Synechococcus isolate from the microbial mat of Octopus Spring to lightOliver Kilian
Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
Appl Environ Microbiol 73:4268-78. 2007..The results are discussed in the context of how Synechococcus OS-B' may cope with high light irradiances in the high-temperature environment of the microbial mat...
- In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial matsAnne Soisig Steunou
Department of Plant Biology, The Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 103:2398-403. 2006..In a broader context, our data suggest that there are critical regulatory switches in situ that are linked to the diel cycle and that these switches alter many metabolic processes within the microbial mat...
- A novel two domain-fusion protein in cyanobacteria with similarity to the CAB/ELIP/HLIP superfamily: evolutionary implications and regulationOliver Kilian
Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
Mol Plant 1:155-66. 2008..This additional TMH is very similar to a conserved hypothetical, single membrane-spanning polypeptide present in most cyanobacteria. The evolutionary significance of these results is discussed...
- Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial matsMaría R Gómez-García
Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
ISME J 5:141-9. 2011....
- Role of polyphosphate in thermophilic Synechococcus sp. from microbial matsMaría R Gómez-García
Carnegie Institution for Science, Department of Plant Biology, Stanford University, Stanford, California, USA
J Bacteriol 195:3309-19. 2013..We hypothesize that the opposing activities of these two enzymes allow cells to store and utilize poly P to optimize growth over a diel cycle. ..
- Whole gene amplification and protein separation from a few cellsBor han Chueh
Department of Chemistry, Stanford University, Stanford, CA 94305, USA
Anal Biochem 411:64-70. 2011..This technology opens avenues for studying protein profiles of precious environmental microbial samples and simultaneously accessing genomic information based on WGA...
- Tracking phototactic responses and modeling motility of Synechocystis sp. strain PCC6803Matthew Burriesci
Department of Plant Biology, The Carnegie Institution, 260 Panama Street, Stanford, CA 94305, United States
J Photochem Photobiol B 91:77-86. 2008..In this model, we can simulate the formation of finger-like projections that are characteristic of phototaxis...
- Multiple light inputs control phototaxis in Synechocystis sp. strain PCC6803Wing On Ng
Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305, USA
J Bacteriol 185:1599-607. 2003..These results suggest that while positive phototaxis is controlled by the red light photoreceptor TaxD1, negative phototaxis in Synechocystis sp. strain PCC6803 is mediated by one or more (as yet) unidentified blue light photoreceptors...
- Analysis of the hli gene family in marine and freshwater cyanobacteriaDevaki Bhaya
Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
FEMS Microbiol Lett 215:209-19. 2002..This information is discussed with respect to the role of hli genes in the acclimation of cyanobacteria to high light, and the possible relationships among members of this diverse gene family...
- Counting low-copy number proteins in a single cellBo Huang
Department of Chemistry, Stanford University, Stanford, CA 94305 5080, USA
Science 315:81-4. 2007..PCC 7942) and observed marked differences in the levels of specific complexes in cell populations that were grown under nitrogen-depleted conditions...
- Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR SpacersMichelle Davison
Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America
PLoS ONE 11:e0160574. 2016..Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics. ..
- Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversityMichelle Davison
Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA
Photosynth Res 126:135-46. 2015..Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations. ..
- Creation and Analysis of a Virome: Using CRISPR SpacersMichelle Davison
Department of Plant Biology, Carnegie Institution for Science, Stanford University, 260 Panama Street, Stanford, CA, 94305, USA
Methods Mol Biol 1311:307-16. 2015..This module allows for binning of contigs based on tetranucleotide frequencies, putative phage-host partner identification by CRISPR spacer matching, and identification of ORFs. ..
- Gordon research conference on the dynamics and regulation of photosynthesis: from the origin of bio-catalysis to innovative solar conversion- Govindjee
Department of Plant Biology, Department of Biochemistry, and Center of Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
Photosynth Res 127:379-89. 2016..We also provide at the end a brief report on the Gordon Research Seminar that preceded the conference. ..
- Microbial diversity. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad nicheMichael J Rosen
Applied Physics Department, Stanford University, Stanford, CA 94305, USA
Science 348:1019-23. 2015..These observations suggested a quasisexual microbial population that occupies a broad ecological niche, with selection driving frequencies of alleles rather than whole genomes. ..
- Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversionAndrew T Ulijasz
Department of Genetics and National Magnetic Resonance Facility, University of Wisconsin, Madison, WI 53706, USA
J Biol Chem 283:21251-66. 2008..We also generated a series of strongly red fluorescent derivatives of SyB-Cph1, which based on their small size and thermostability may be useful as cell biological reporters...
- 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 7942Anthony D Kappell
Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA
Arch Microbiol 186:403-13. 2006..These results point to the evolutionary conservation of the HLR1 element and its importance in NblS-mediated signaling and yield new insight into NblS-mediated control of gene expression...