CEMi Publications

Articles listed below derive from interdisciplinary research projects supported by the CEMI (listed here), and are posted on an on-going basis.  Other publications involving Caltech microbiology can be found on individual web pages of the CEMI faculty.

Subramanian, Poorna and Pirbadian, Sahand and El-Naggar, Mohamed Y. and Jensen, Grant J. (2017) The ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryo-tomography. . (Submitted) http://resolver.caltech.edu/CaltechAUTHORS:20170619-134442390

Niesen, Michiel J. M. and Marshall, Stephen S. and Miller, Thomas F., III and Clemons, William M., Jr. (2017)Improving membrane protein expression by optimizing integration efficiency. Journal of Biological Chemistry . ISSN 0021-9258. (In Press) http://resolver.caltech.edu/CaltechAUTHORS:20170925-084831113

Piraner, Dan I. and Farhadi, Arash and Davis, Hunter C. and Wu, Di and Maresca, David and Szablowski, Jerzy O. and Shapiro, Mikhail G. (2017) Going Deeper: Biomolecular Tools for Acoustic and Magnetic Imaging and Control of Cellular Function. Biochemistry, 56 (39). pp. 5202-5209. ISSN 0006-2960.http://resolver.caltech.edu/CaltechAUTHORS:20170814-132937862

Oikonomou, Catherine M. and Jensen, Grant J. (2017) Cellular Electron Cryotomography: Toward Structural Biology In Situ. Annual Review of Biochemistry, 86 . pp. 873-896. ISSN 0066-4154. http://resolver.caltech.edu/CaltechAUTHORS:20170421-082204689

Bedbrook, Claire N. and Rice, Austin J. and Yang, Kevin K. and Ding, Xiaozhe and Chen, Siyuan and LeProust, Emily M. and Gradinaru, Viviana and Arnold, Frances H. (2017) Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins. Proceedings of the National Academy of Sciences of the United States of America, 114 (13). E2624-E2633. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:20170310-130542741

Herwig, Lukas and Rice, Austin J. and Bedbrook, Claire N. and Zhang, Ruijie K. and Lignell, Antti and Cahn, Jackson K. B. and Renata, Hans and Dodani, Sheel C. and Cho, Inha and Cai, Long and Gradinaru, Vivianaand Arnold, Frances H. (2017) Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore. Cell Chemical Biology, 24 (3). pp. 415-425. ISSN 2451-9456. PMCID PMC5357175.http://resolver.caltech.edu/CaltechAUTHORS:20170307-082231020

Rittle, Jonathan and Peters, Jonas C. (2017) N-H Bond Dissociation Enthalpies and Facile H-atom Transfers for Early Intermediates of Fe-N_2 and Fe-CN Reductions. Journal of the American Chemical Society, 139 (8). pp. 3161-3170. ISSN 0002-7863. http://resolver.caltech.edu/CaltechAUTHORS:20170201-092020177

Glenn, Weslee S. and Stone, Shannon E. and Ho, Samuel H. and Sweredoski, Michael J. and Moradian, Annie and Hess, Sonja and Bailey-Serres, Julia and Tirrell, David A. (2017) BONCAT enables time-resolved analysis of protein synthesis in native plant tissue. Plant Physiology . ISSN 0032-0889. (In Press)http://resolver.caltech.edu/CaltechAUTHORS:20170123-111643957

Stone, Shannon E. and Glenn, Weslee S. and Hamblin, Graham D. and Tirrell, David A. (2017) Cell-selective proteomics for biological discovery. Current Opinion in Chemical Biology, 36 . pp. 50-57. ISSN 1367-5931. PMCID PMC5337159. http://resolver.caltech.edu/CaltechAUTHORS:20170117-150138453

Maker, Allison and Hemp, James and Pace, Laura A. and Ward, Lewis M. and Fischer, Woodward W. (2017) Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the Bacilli Class of Firmicutes. Genome Announcements, 5 (3). Art. No. e00380-16. ISSN 2169-8287. PMCID PMC5255923. http://resolver.caltech.edu/CaltechAUTHORS:20170130-083631885

Shih, P. M. and Hemp, J. and Ward, L. M. et al. (2017) Crown group Oxyphotobacteria postdate the rise of oxygen. Geobiology, 15 (1). pp. 19-29. ISSN 1472-4677.http://resolver.caltech.edu/CaltechAUTHORS:20160718-081438054

Ho, Samuel H. and Tirrell, David A. (2016) Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells. Journal of the American Chemical Society, 138 (46). pp. 15098-15101. ISSN 0002-7863. http://resolver.caltech.edu/CaltechAUTHORS:20161116-100355067

Skennerton, Connor T. and Haroon, Mohamed F. and Briegel, Ariane and Shi, Jian and Jensen, Grant J. and Tyson, Gene W. and Orphan, Victoria J. (2016) Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps. ISME Journal, 10 (11). pp. 2679-2692. ISSN 1751-7362. PMCID PMC5113845. http://resolver.caltech.edu/CaltechAUTHORS:20160418-080655842

Hemp, James and Lücker, Sebastian and Schott, Joachim and Pace, Laura A. and Johnson, Jena E. and Schink, Bernhard and Daims, Holger and Fischer, Woodward W. (2016) Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification. ISME Journal, 10 (11). pp. 2669-2678. ISSN 1751-7362. http://resolver.caltech.edu/CaltechAUTHORS:20160425-075949394

Davis, Hunter C. and Ramesh, Pradeep and Bhatnagar, Aadyot and Lee-Gosselin, Audrey and Barry, John F. and Glenn, David R. and Walsworth, Ronald L. and Shapiro, Mikhail G. (2016) Mapping the Microscale Origins of MRI Contrast with Subcellular NV Diamond Magnetometry. . (Submitted) http://resolver.caltech.edu/CaltechAUTHORS:20161205-095517669

DePas, William H. and Starwalt-Lee, Ruth and Van Sambeek, Lindsey and Kumar, Sripriya Ravindra and Gradinaru, Viviana and Newman, Dianne K. (2016) Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling. mBio, 7 (5). e00796-16. ISSN 2150-7511. PMCID PMC5040109. http://resolver.caltech.edu/CaltechAUTHORS:20160927-144217261

Marshall, Stephen S. and Niesen, Michiel J. M. and Müller, Axel et al. (2016) A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency. Cell Reports, 16 (8). pp. 2169-2177. ISSN 2211-1247. PMCID PMC5001948.http://resolver.caltech.edu/CaltechAUTHORS:20160816-075308782

Fischer, Woodward W. and Hemp, James and Johnson, Jena E. (2016) Evolution of Oxygenic Photosynthesis. Annual Review of Earth and Planetary Sciences, 44 . pp. 647-683. ISSN 0084-6597. http://resolver.caltech.edu/CaltechAUTHORS:20160531-083106180

Xiao, Cheng and Cho, Jounhong Ryan and Zhou, Chunyi and Treweek, Jennifer B. and Chan, Ken and McKinney, Sheri L. and Yang, Bin and Gradinaru, Viviana (2016) Cholinergic Mesopontine Signals Govern Locomotion and Reward through Dissociable Midbrain Pathways. Neuron, 90 (2). pp. 333-347. ISSN 0896-6273. PMCID PMC4840478. http://resolver.caltech.edu/CaltechAUTHORS:20160420-090626768

Oikonomou, Catherine M. and Jensen, Grant J. (2016) A new view into prokaryotic cell biology from electron cryotomography. Nature Reviews Microbiology, 14 (4). pp. 205-220. ISSN 1740-1526. http://resolver.caltech.edu/CaltechAUTHORS:20160307-090319472

Rittle, Jonathan and Peters, Jonas C. (2016) An Fe-N_2 Complex That Generates Hydrazine and Ammonia via Fe═NNH_2: Demonstrating a Hybrid Distal-to-Alternating Pathway for N_2 Reduction. Journal of the American Chemical Society, 138 (12). pp. 4243-4248. ISSN 0002-7863. PMCID PMC5065353. http://resolver.caltech.edu/CaltechAUTHORS:20160328-143527690

Ward, Lewis M. and Kirschvink, Joseph L. and Fischer, Woodward W. (2016) Timescales of Oxygenation Following the Evolution of Oxygenic Photosynthesis. Origins of life and evolution of the biosphere, 46 (1). pp. 51-65. ISSN 0169-6149. http://resolver.caltech.edu/CaltechAUTHORS:20150825-080916332

Spatzal, Thomas and Perez, Kathryn A. and Howard, James B. and Rees, Douglas C. (2015) Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor. eLife, 4 . Art. No. e11620. ISSN 2050-084X. PMCID PMC4755756.http://resolver.caltech.edu/CaltechAUTHORS:20151221-153134644

Hemp, James and Ward, Lewis M. and Pace, Laura A. and Fischer, Woodward W. (2015) Draft Genome Sequence of Ardenticatena maritime 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia. Genome Announcements, 3 (6). Art. No. e01347-15. ISSN 2169-8287. PMCID PMC4653789. http://resolver.caltech.edu/CaltechAUTHORS:20151221-091145750

Hemp, James and Ward, Lewis M. and Pace, Laura A. and Fischer, Woodward W. (2015) Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae. Genome Announcements, 3 (6). Art. No. e01357-15. ISSN 2169-8287. PMCID PMC4653796. http://resolver.caltech.edu/CaltechAUTHORS:20151221-084436954

Hemp, James and Ward, Lewis M. and Pace, Laura A. and Fischer, Woodward W. (2015) Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae. Genome Announcements, 3 (6). Art. No. e01353-15. ISSN 2169-8287. PMCID PMC4653791. http://resolver.caltech.edu/CaltechAUTHORS:20151221-090203951

Pace, Laura A. and Hemp, James and Ward, Lewis M. and Fischer, Woodward W. (2015) Draft Genome of Thermanaerothrix daxensis GNS-1, a Thermophilic Facultative Anaerobe from the Chloroflexi Class Anaerolineae. Genome Announcements, 3 (6). Art. No. e01354-15. ISSN 2169-8287. PMCID PMC4653792. http://resolver.caltech.edu/CaltechAUTHORS:20151221-085728522

Ward, Lewis M. and Hemp, James and Pace, Laura A. and Fischer, Woodward W. (2015) Draft Genome Sequence of Herpetosiphon geysericola GC-42, a Nonphototrophic Member of the Chloroflexi Class Chloroflexia. Genome Announcements, 3 (6). Art. No. e01352-15. ISSN 2169-8287. PMCID PMC4653791. http://resolver.caltech.edu/CaltechAUTHORS:20151221-090706555

Ward, Lewis M. and Hemp, James and Pace, Laura A. and Fischer, Woodward W. (2015) Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae. Genome Announcements, 3 (6). Art. No. e01356-15. ISSN 2169-8287. PMCID PMC4653795. http://resolver.caltech.edu/CaltechAUTHORS:20151221-084953964

Fischer, Woodward W. and Hemp, James and Johnson, Jena E. (2015) Manganese and the Evolution of Photosynthesis. Origins of Life and Evolution of Biospheres, 45 (3). pp. 351-357. ISSN 0169-6149. http://resolver.caltech.edu/CaltechAUTHORS:20150602-140446953

Rasmussen, Tim and Rasmussen, Akiko and Singh, Shivani and Galbiati, Heloisa and Edwards, Michelle D. and Miller, Samantha and Booth, Ian R. (2015) Properties of the Mechanosensitive Channel MscS Pore Revealed by Tryptophan Scanning Mutagenesis. Biochemistry, 54 (29). pp. 4519-4530. ISSN 0006-2960. PMCID PMC4519979. http://resolver.caltech.edu/CaltechAUTHORS:20150827-104629563

Anderson, John S. and Cutsail, George E., III and Rittle, Jonathan and Connor, Bridget A. and Gunderson, William A. and Zhang, Limei and Hoffman, Brian M. and Peters, Jonas C. (2015) Characterization of an Fe≡N−NH_2 Intermediate Relevant to Catalytic N_2 Reduction to NH_3. Journal of the American Chemical Society, 137 (24). pp. 7803-7809. ISSN 0002-7863. PMCID PMC4603982.http://resolver.caltech.edu/CaltechAUTHORS:20150708-084228936

Yano, Jessica M. and Yu, Kristie and Donaldson, Gregory P. et al. (2015) Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis. Cell, 161 (2). pp. 264-276. ISSN 0092-8674. PMCID PMC4393509.http://resolver.caltech.edu/CaltechAUTHORS:20150409-093248232

Booth, Ian R. and Miller, Samantha and Müller, Axel and Lehtovirta-Morley, Laura (2015) The evolution of bacterial mechanosensitive channels. Cell Calcium, 57 (3). pp. 140-150. ISSN 0143-4160.http://resolver.caltech.edu/CaltechAUTHORS:20150121-095159810

Zhang, Li-Mei and Morrison, Christine N. and Kaiser, Jens T. and Rees, Douglas C. (2015) Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein. Acta Crystallographica Section D: Biological Crystallography, 71 (2). pp. 274-282. ISSN 0907-4449. PMCID PMC4321486. http://resolver.caltech.edu/CaltechAUTHORS:20150310-101137660

Grodick, Michael A. and Muren, Natalie B. and Barton, Jacqueline K. (2015)DNA Charge Transport within the Cell. Biochemistry, 54 (4). pp. 962-973. ISSN 0006-2960. PMCID PMC4587570.http://resolver.caltech.edu/CaltechAUTHORS:20150202-150621170

Spatzal, Thomas and Perez, Kathryn A. and Einsle, Oliver and Howard, James B. and Rees, Douglas C. (2014)Ligand binding to the FeMo-cofactor: Structures of CO-bound and reactivated nitrogenase. Science, 345 (6204). pp. 1620-1623. ISSN 0036-8075. PMCID PMC4205161.http://resolver.caltech.edu/CaltechAUTHORS:20140721-203544454

Grodick, Michael A. and Segal, Helen M. and Zwang, Theodore J. and Barton, Jacqueline K. (2014) DNA-Mediated Signaling by Proteins with 4Fe−4S Clusters Is Necessary for Genomic Integrity. Journal of the American Chemical Society, 136 (17). pp. 6470-6478. ISSN 0002-7863. PMCID PMC4017601. http://resolver.caltech.edu/CaltechAUTHORS:20140422-093606577

Booth, Ian R. (2014) Bacterial mechanosensitive channels: progress towards an understanding of their roles in cell physiology. Current Opinion in Microbiology, 18 . pp. 16-22. ISSN 1369-5274. PMCID PMC4005912. http://resolver.caltech.edu/CaltechAUTHORS:20140403-100546813

Lucey, Kaitlyn S. and Leadbetter, Jared R. (2014) Catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes in the “anaerobic” termite gut spirochete Treponema primitia. Molecular Ecology, 23 (6). pp. 1531-1543. ISSN 0962-1083. http://resolver.caltech.edu/CaltechAUTHORS:20131204-090224188

Pilhofer, Martin and Aistleitner, Karin and Ladinsky, Mark S. and König, Lena and Horn, Matthias and Jensen, Grant J. (2014) Architecture and host interface of environmental chlamydiae revealed by electron cryotomography. Environmental Microbiology, 16 (2). pp. 417-429. ISSN 1462-2912. PMCID PMC4949044.http://resolver.caltech.edu/CaltechAUTHORS:20140318-101020463

Shikuma, Nicholas J. and Pilhofer, Martin and Weiss, Gregor L. and Hadfield, Michael G. and Jensen, Grant J.and Newman, Dianne K. (2014) Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail–Like Structures. Science, 343 (6170). pp. 529-533. ISSN 0036-8075. PMCID PMC4949041.http://resolver.caltech.edu/CaltechAUTHORS:20140113-134430398

Olovnikov, Ivan and Le Thomas, Adrien and Aravin, Alexei A. (2014) A Framework for piRNA Cluster Manipulation. In: PIWI-Interacting RNAs: Methods and Protocols. Methods in Molecular Biology. No.1093. Humana Press , New York, NY, pp. 47-58. ISBN 978-1-62703-693-1.http://resolver.caltech.edu/CaltechAUTHORS:20131112-093205322

Pilhofer, Martin and Aistleitner, Karin and Biboy, Jacob and Gray, Joe and Kuru, Erkin and Hall, Edward and Brun, Yves V.and VanNieuwenhze, Michael S. and Vollmer, Waldemar and Horn, Matthias and Jensen, Grant J. (2013) Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ. Nature Communications, 4 (12). Art. No. 2856. ISSN 2041-1723. http://resolver.caltech.edu/CaltechAUTHORS:20140204-110344222

Matson, Eric G. and Rosenthal, Adam Z. and Zhang , Xinning and Leadbetter, Jared R. (2013) Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia. mBio, 4 (6). Art. No. e00869-13. ISSN 2150-7511. PMCID PMC3892789. http://resolver.caltech.edu/CaltechAUTHORS:20140123-094750237

Tocheva, Elitza I. and Dekas, Anne E. and McGlynn, Shawn E. and Morris, Dylan and Orphan, Victoria J. and Jensen, Grant J. (2013) Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema longum. Journal of Bacteriology, 195 (17). pp. 3940-3946. ISSN 0021-9193. PMCID PMC3754598.http://resolver.caltech.edu/CaltechAUTHORS:20130909-141442695

Rosenthal, Adam Z. and Zhang, Xinning and Lucey, Kaitlyn S. and Ottesen, Elizabeth A. and Trivedi, Vikas and Choi, Harry M. T. and Pierce, Niles A. and Leadbetter, Jared R. (2013) Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. Proceedings of the National Academy of Sciences of the United States of America, 110 (40). pp. 16163-16168. ISSN 0027-8424. PMCID PMC3791709. http://resolver.caltech.edu/CaltechAUTHORS:20130930-102728287

Olovnikov, Ivan and Chan, Ken and Sachidanandam, Ravi and Newman, Diane K. and Aravin, Alexei A. (2013)Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA. Molecular Cell, 51 (5). pp. 594-605. ISSN 1097-2765. PMCID PMC3809076. http://resolver.caltech.edu/CaltechAUTHORS:20140220-100231898