Microarray data: Response of Prochlorococcus to varying CO2:O2 ratios
Published:
Bagby and Chisholm (2015) data
Posts by Collection
portfolio
Research compendium: Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon
Published:
Bagby et al. (2016) data and code
publications
Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria
Published in Current Biology, 2008
Auxiliary metabolic genes in cyanophage exploit a non-host-derived mechanism of pigment biosynthesis. Enzymology, metagenomics, qRT-PCR.
Recommended citation: TD Dammeyer, SC Bagby, MB Sullivan, SW Chisholm, and N Frankenbert-Dinkel. (2008). "Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria." Curr Biol 18(6):442.
Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport
Published in Journal of Molecular Biology, 2009
A previously unrecognized component of bacterial microcompartments shows potential for dynamic gating. Bioinformatics, x-ray crystallography, expression analysis.
Recommended citation: M Klein, P Zwart, SC Bagby, F Cai, SW Chisholm, S Heinhorst, G Cannon, and CA Kerfeld (2009). "Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport." J Mol Biol 392(2):319.
Crystal structure of the catalytic core of an RNA-polymerase ribozyme
Published in Science, 2009
An RNA enzyme evolved from random sequence relies on familiar Mg2+-dependent chemistry to catalyze phosphodiester bond formation. X-ray crystallography, enzymology, structural biochemistry.
Recommended citation: DM Shechner, SC Bagby, R Grant, Y Koldobskaya, J Piccirilli, and DP Bartel (2009). "Crystal structure of the catalytic core of an RNA-polymerase ribozyme." Science 326:1271.
A class I ligase ribozyme with reduced Mg2+ dependence: selection, sequence analysis, and tertiary-structure mapping
Published in RNA, 2009
A ribozyme selected for rapid catalysis shows changes to a network of structural interactions that contribute to metal-binding. In vitro evolution, statistics, structural biochemistry.
Recommended citation: SC Bagby,1 NH Bergman,1 DM Shechner, C Yen, and DP Bartel (2009). "A class I ligase ribozyme with reduced Mg2+ dependence: selection, sequence analysis, and tertiary-structure mapping." RNA 15:2129. (1joint first authors)
Asphalt volcanoes as a potential source of methane to late Pleistocene coastal waters
Published in Nature Geoscience, 2010
A newly discovered cluster of extinct asphalt volcanoes on the Santa Barbara Basin seafloor may explain historical methane anomalies. Submarine exploration, hydrocarbon geochemistry, paleoclimate.
Recommended citation: DL Valentine, CM Reddy, C Farwell, TM Hill, O Pizarro, DR Yoerger, R Camilli, RK Nelson, E Peacock, SC Bagby, BA Clark, CN Roman, and M Soloway. (2010). "Asphalt volcanoes as a potential source of methane to late Pleistocene coastal waters." Nature Geosci 3:345.
Conformational changes in IgE contribute to its uniquely slow dissociation rate from receptor FcεRI
Published in Nature Structural & Molecular Biology, 2011
Entropy drives the high-affinity receptor interaction underlying asthma and allergy. X-ray crystallography, surface plasmon resonance, thermodynamics.
Recommended citation: MD Holdom, AM Davies, JE Nettleship, SC Bagby, B Dhaliwal, E Girardi, J Hunt, HJ Gould, AJ Beavil, JM McDonnell, RJ Owens, and BJ Sutton (2011). "Conformational changes in IgE contribute to its uniquely slow dissociation rate from receptor FcεRI." Nature Struct Mol Biol 18:571.
Fallout plume of submerged oil from Deepwater Horizon
Published in Proceedings of the National Academy of Sciences, 2014
Spill response teams found, and then lost, a plume of oil that had been trapped ~1 km deep in the Gulf of Mexico. We found its 3200-km2 contamination footprint on the seafloor. Hydrocarbon geochemistry, statistics, GIS.
Recommended citation: DL Valentine, GB Fisher, SC Bagby, RK Nelson, CM Reddy, SP Sylva, and MA Woo (2014). "A fallout plume of submerged oil from Deepwater Horizon." PNAS 111:15906.
Targeted diversity generation by intraterrestrial archaea and archaeal viruses
Published in Nature Communications, 2015
A genomic cassette with more diversity-generating potential than the vertebrate immune system is active in archaea and archaeal viruses, not just in bacteria and bacteriophage. Metagenomics, single-cell genomics, evolution.
Recommended citation: BG Paul, SC Bagby, E Czornyj, D Arambula, S Handa, A Sczyrba, P Ghosh, JF Miller, and DL Valentine (2015). "Targeted diversity generation by intraterrestrial archaea and archaeal viruses." Nature Comm 6:6585. DOI: 10.1038/ncomms7585.
Response of Prochlorococcus to varying CO2:O2 ratios
Published in The ISME Journal, 2015
Minimal marine phototrophs use oxygen reduction as a safety valve when CO2 limitation makes ordinary light levels stressful. Growth curves, flow cytometry, transcriptomics.
Recommended citation: SC Bagby and SW Chisholm. (2015). "Response of Prochlorococcus to varying CO2:O2 ratios." ISME J 9(10):2232.
The Tao of open science for ecology
Published in Ecosphere, 2015
Ecologists need to change the way we do our work, to make open, reproducible research the norm. Opinion.
Recommended citation: SE Hampton, SS Anderson, SC Bagby, C Gries, X Han, EM Hart, MB Jones, WC Lenhardt, A MacDonald, WK Michener, J Mudge, A Pourmokhtarian, M Schildhauer, KH Woo, and N Zimmerman (2014). "The Tao of open science for ecology." Ecosphere 6:art120. DOI: 10.1890/ ES14-00402.1.
Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon
Published in Proceedings of the National Academy of Sciences, 2016
A novel chemical fingerprint identifies sediment samples contaminated with oil from Deepwater Horizon, and the loss rates of 125 hydrocarbon analytes in these samples show that contamination level strongly influences chemical structure-based trends in biodegradation kinetics. Hydrocarbon geochemistry, statistics, more statistics.
Recommended citation: SC Bagby, CM Reddy, C Aeppli, GB Fisher, and DL Valentine. (2016). "Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon." PNAS 114(1):E9. DOI: 10.1073/pnas.1610110114.
Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep
Published in Frontiers in Microbiology, 2017
Microbial mats from a shallow hydrocarbon seep field are among the most diverse communities yet characterized, with multiple avenues of primary production. Stable isotope probing, metagenomics, lipid analysis.
Recommended citation: BG Paul, H Ding, SC Bagby, MY Kellermann, MC Redmond, GL Andersen, and DL Valentine. (2017). "Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep." Front Microbiol 8:186. DOI: 10.3389/fmicb.2017.00186.
talks
Talk 1 on Relevant Topic in Your Field
Published in UC San Francisco, Department of Testing, 2012
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Tutorial 1 on Relevant Topic in Your Field
Published in UC-Berkeley Institute for Testing Science, 2013
Talk 2 on Relevant Topic in Your Field
Published in London School of Testing, 2014
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published in Testing Institute of America 2014 Annual Conference, 2014
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 2
Published in University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.
BIOL 303: From Black Box to Toolbox: How molecular biology moves forward
Published in CWRU Department of Biology, 2017