Research Output

Filter
Article
2020

A computational framework to explore large-scale biosynthetic diversity

Navarro-Muñoz, J. C., Selem-Mojica, N., Mullowney, M. W., Kautsar, S. A., Tryon, J. H., Parkinson, E. I., De Los Santos, E. L. C., Yeong, M., Cruz-Morales, P., Abubucker, S., Roeters, A., Lokhorst, W., Fernandez-Guerra, A., Cappelini, L. T. D., Goering, A. W., Thomson, R. J., Metcalf, W. W., Kelleher, N. L., Barona-Gomez, F. & Medema, M. H., Jan 1 2020, In : Nature chemical biology. 16, 1, p. 60-68 9 p.

Research output: Contribution to journalArticle

An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity

Athukoralage, J. S., McMahon, S. A., Zhang, C., Grüschow, S., Graham, S., Krupovic, M., Whitaker, R. J., Gloster, T. M. & White, M. F., Jan 23 2020, In : Nature. 577, 7791, p. 572-575 4 p.

Research output: Contribution to journalArticle

Assessment of microbial risks by characterization of Escherichia coli presence to analyze the public health risks from poor water quality in Nepal

Uprety, S., Dangol, B., Nakarmi, P., Dhakal, I., Sherchan, S. P., Shisler, J. L., Jutla, A., Amarasiri, M., Sano, D. & Nguyen, T. H., May 2020, In : International Journal of Hygiene and Environmental Health. 226, 113484.

Research output: Contribution to journalArticle

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis

D’alessandro-gabazza, C. N., Kobayashi, T., Yasuma, T., Toda, M., Kim, H., Fujimoto, H., Hataji, O., Takeshita, A., Nishihama, K., Okano, T., Okano, Y., Nishii, Y., Tomaru, A., Fujiwara, K., D’alessandro, V. F., Abdel-hamid, A. M., Ren, Y., Pereira, G. V., Wright, C. L., Hernandez, A. & 15 others, Fields, C. J., Yau, P. M., Wang, S., Mizoguchi, A., Fukumura, M., Ohtsuka, J., Nosaka, T., Kataoka, K., Kondoh, Y., Wu, J., Kawagishi, H., Yano, Y., Mackie, R. I., Cann, I. & Gabazza, E. C., Mar 24 2020, In : Nature Communications. 11, 1, 1539.

Research output: Contribution to journalArticle

Open Access

Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions

Weitzel, C. S., Li, L., Zhang, C., Eilts, K. K., Bretz, N. M., Gatten, A. L., Whitaker, R. J. & Martinis, S. A., Apr 3 2020, In : Journal of Biological Chemistry. 295, 14, p. 4563-4576 14 p.

Research output: Contribution to journalArticle

Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans

Nayak, D. D., Liu, A., Agrawal, N., Rodriguez-Carerro, R., Dong, S. H., Mitchell, D. A., Nair, S. K. & Metcalf, W. W., Feb 2020, In : PLoS biology. 18, 2, e3000507.

Research output: Contribution to journalArticle

Open Access

Habitat-specific effects of bark on wood decomposition: Influences of fragmentation, nitrogen concentration and microbial community composition

Jones, J. M., Heath, K. D., Ferrer, A. & Dalling, J. W., May 1 2020, In : Functional Ecology. 34, 5, p. 1123-1133 11 p.

Research output: Contribution to journalArticle

Influenza virus di particles: Defective interfering or delightfully interesting?

Alnaji, F. G. & Brooke, C. B., May 2020, In : PLoS pathogens. 16, 5, e1008436.

Research output: Contribution to journalArticle

Open Access

Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism

DeWerff, S. J., Bautista, M. A., Pauly, M., Zhang, C. & Whitaker, R. J., Apr 28 2020, In : mBio. 11, 2

Research output: Contribution to journalArticle

Open Access

Light availability and rhizobium variation interactively mediate the outcomes of legume–rhizobium symbiosis

Heath, K. D., Podowski, J. C., Heniff, S., Klinger, C. R., Burke, P. V., Weese, D. J., Yang, W. H. & Lau, J. A., Feb 1 2020, In : American journal of botany. 107, 2, p. 229-238 10 p.

Research output: Contribution to journalArticle

Open Access

Microviridin 1777: A Toxic Chymotrypsin Inhibitor Discovered by a Metabologenomic Approach

Sieber, S., Grendelmeier, S. M., Harris, L. A., Mitchell, D. A. & Gademann, K., Feb 28 2020, In : Journal of Natural Products. 83, 2, p. 438-446 9 p.

Research output: Contribution to journalArticle

Plant–environment interactions from the lens of plant stress, reproduction, and mutualisms

Baucom, R. S., Heath, K. D. & Chambers, S. M., Jan 1 2020, (Accepted/In press) In : American journal of botany.

Research output: Contribution to journalArticle

Open Access

Role of respiratory NADH oxidation in the regulation of Staphylococcus aureus virulence

Schurig-Briccio, L. A., Parraga Solorzano, P. K., Lencina, A. M., Radin, J. N., Chen, G. Y., Sauer, J. D., Kehl-Fie, T. E. & Gennis, R. B., May 6 2020, In : EMBO Reports. 21, 5, e45832.

Research output: Contribution to journalArticle

SERS Nanoprobe for Intracellular Monitoring of Viral Mutations

Dardir, K., Wang, H., Martin, B. E., Atzampou, M., Brooke, C. B. & Fabris, L., Feb 6 2020, In : Journal of Physical Chemistry C. 124, 5, p. 3211-3217 7 p.

Research output: Contribution to journalArticle

Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics

Gorin, G., Wang, M., Golding, I. & Xu, H., 2020, In : PloS one. 15, 3, e0230736.

Research output: Contribution to journalArticle

Open Access

Surface resistance to SSVs and SIRVs in pilin deletions of Sulfolobus islandicus

Rowland, E. F., Bautista, M. A., Zhang, C. & Whitaker, R. J., Apr 1 2020, In : Molecular Microbiology. 113, 4, p. 718-727 10 p.

Research output: Contribution to journalArticle

Open Access

Synergistic Combination of Oncolytic Virotherapy and Immunotherapy for Glioma

Tang, B., Guo, Z. S., Bartlett, D. L., Yan, D. Z., Schane, C. P., Thomas, D. L., Liu, J., McFadden, G., Shisler, J. L., Roy, E. J. & Roy, E. J., May 1 2020, In : Clinical Cancer Research. 26, 9, p. 2216-2230 15 p.

Research output: Contribution to journalArticle

The PATRIC Bioinformatics Resource Center: Expanding data and analysis capabilities

Davis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T., Butler, R., Butler, R. M., Chlenski, P., Conrad, N., Dickerman, A., Dietrich, E. M., Gabbard, J. L., Gerdes, S., Guard, A., Kenyon, R. W., MacHi, D., Mao, C., Murphy-Olson, D., Nguyen, M., Nordberg, E. K., Olsen, G. J. & 14 others, Olson, R. D., Overbeek, J. C., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomas, C., Vanoeffelen, M., Vonstein, V., Warren, A. S., Xia, F., Xie, D., Yoo, H. & Stevens, R., Jan 1 2020, In : Nucleic acids research. 48, D1, p. D606-D612

Research output: Contribution to journalArticle

Open Access

Thermophilic degradation of hemicellulose, a critical feedstock in the production of bioenergy and other value-added products

Cann, I., Pereira, G. V., Abdel-Hamid, M. M., Kim, H., Wefers, D., Kayang, B. B., Kanai, T., Sato, T., Bernardi, R. C., Atomi, H. & Mackie, R. I., Mar 1 2020, In : Applied and environmental microbiology. 86, 7, 2296.

Research output: Contribution to journalArticle

The structure of the periplasmic FlaG–FlaF complex and its essential role for archaellar swimming motility

Tsai, C. L., Tripp, P., Sivabalasarma, S., Zhang, C., Rodriguez-Franco, M., Wipfler, R. L., Chaudhury, P., Banerjee, A., Beeby, M., Whitaker, R. J., Tainer, J. A. & Albers, S. V., Jan 1 2020, In : Nature Microbiology. 5, 1, p. 216-225 10 p.

Research output: Contribution to journalArticle

The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice

Ridlon, J. M., Devendran, S., Alves, J. M., Doden, H., Wolf, P. G., Pereira, G. V., Ly, L., Volland, A., Takei, H., Nittono, H., Murai, T., Kurosawa, T., Chlipala, G. E., Green, S. J., Hernandez, A. G., Fields, C. J., Wright, C. L., Kakiyama, G., Cann, I., Kashyap, P. & 2 others, McCracken, V. & Gaskins, H. R., May 3 2020, In : Gut Microbes. 11, 3, p. 381-404 24 p.

Research output: Contribution to journalArticle

UV inactivation of rotavirus and tulane virus targets different components of the virions

Araud, E., Fuzawa, M., Shisler, J. L., Li, J. & Nguyen, T. H., Feb 1 2020, In : Applied and environmental microbiology. 86, 4, e02436.

Research output: Contribution to journalArticle

2019
Open Access

A novel synthesis of trans-unsaturated fatty acids by the Gram-positive commensal bacterium Enterococcus faecalis FA2-2

Kondakova, T., Kumar, S. & Cronan, J. E., Aug 2019, In : Chemistry and Physics of Lipids. 222, p. 23-35 13 p.

Research output: Contribution to journalArticle

Bacterial cyclopropane fatty acid synthase mRNA is targeted by activating and repressing small RNAs

Bianco, C. M., Fröhlich, K. S. A. & Vanderpoola, C. K., Oct 1 2019, In : Journal of bacteriology. 201, 19, e00461-19.

Research output: Contribution to journalArticle

Open Access

Biochemical characterization of the methylmercaptopropionate: Cob(I)alamin Methyltransferase from Methanosarcina acetivorans

Fu, H., Goettge, M. N. & Metcalf, W. W., Jan 1 2019, In : Journal of bacteriology. 201, 12, e00130-19.

Research output: Contribution to journalArticle

Biosynthesis and Chemical Applications of Thioamides

Mahanta, N., Szantai-Kis, D. M., Petersson, E. J. & Mitchell, D. A., Jan 1 2019, In : ACS chemical biology.

Research output: Contribution to journalArticle

Cell structure changes in the hyperthermophilic crenarchaeon Sulfolobus islandicus lacking the S-layer

Zhang, C., Wipfler, R. L., Li, Y., Wang, Z., Hallett, E. N. & Whitaker, R. J., Jul 1 2019, In : mBio. 10, 4, e01589-19.

Research output: Contribution to journalArticle

Open Access

Combined genomic, transcriptomic, proteomic, and physiological characterization of the growth of Pecoramyces sp. F1 in Monoculture and Co-culture with a Syntrophic Methanogen

Li, Y., Li, Y., Jin, W., Sharpton, T. J., Mackie, R. I., Cann, I., Cheng, Y. & Zhu, W., Jan 1 2019, In : Frontiers in Microbiology. 10, MAR, 435.

Research output: Contribution to journalArticle

Open Access

Comparative genome analysis of an extensively drug-resistant isolate of avian sequence type 167 Escherichia coli strain sanji with novel in silico serotype O89b:H9

Zeng, X., Chi, X., Ho, B. T., Moon, D., Lambert, C., Hall, R. J., Baybayan, P., Wang, S., Wilson, B. A. & Ho, M., Jan 2019, In : mSystems. 4, 1, e0024218.

Research output: Contribution to journalArticle

Open Access

Correction Factors for δ18O-Derived Global Sea Surface Temperature Reconstructions From Diagenetically Altered Intervals of Coral Skeletal Density Banding

Sivaguru, M., Fouke, K. W., Todorov, L., Kingsford, M. J., Fouke, K. E., Trop, J. M. & Fouke, B. W., Jun 18 2019, In : Frontiers in Marine Science. 6, JUN, 306.

Research output: Contribution to journalArticle

Open Access
Open Access

Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS

Bobrovskyy, M., Azam, M. S., Frandsen, J. K., Zhang, J., Poddar, A., Ma, X., Henkin, T. M., Ha, T. & Vanderpool, C. K., Oct 1 2019, In : Molecular Microbiology. 112, 4, p. 1199-1218 20 p.

Research output: Contribution to journalArticle

Disruption of glycolysis by nutritional immunity activates a two-component system that coordinates a metabolic and antihost response by staphylococcus aureus

Párraga Solórzano, P. K., Yao, J., Rock, C. O. & Kehl-Fiea, T. E., Jan 1 2019, In : mBio. 10, 4, e01321-19.

Research output: Contribution to journalArticle

Open Access

Diverse hydrogen production and consumption pathways influence methane production in ruminants

Greening, C., Geier, R., Wang, C., Woods, L. C., Morales, S. E., McDonald, M. J., Rushton-Green, R., Morgan, X. C., Koike, S., Leahy, S. C., Kelly, W. J., Cann, I., Attwood, G. T., Cook, G. M. & Mackie, R. I., Oct 1 2019, In : ISME Journal. 13, 10, p. 2617-2632 16 p.

Research output: Contribution to journalArticle

Open Access

Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus

Pauly, M. D., Bautista, M. A., Black, J. A. & Whitaker, R. J., May 13 2019, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 374, 1772, 20180093.

Research output: Contribution to journalArticle

Open Access

Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes

Thibault, D., Jensen, P. A., Wood, S., Qabar, C., Clark, S., Shainheit, M. G., Isberg, R. R. & van Opijnen, T., Dec 1 2019, In : Nature communications. 10, 1, 5729.

Research output: Contribution to journalArticle

Open Access

Enterococcus faecalis encodes an atypical auxiliary acyl carrier protein required for efficient regulation of fatty acid synthesis by exogenous fatty acids

Zhu, L., Zou, Q., Cao, X. & Cronan, J. E., May 1 2019, In : mBio. 10, 3, e00577-19.

Research output: Contribution to journalArticle

Open Access

Environment-Friendly Antibiofouling Superhydrophobic Coatings

Razavi, S. M. R., Oh, J., Haasch, R. T., Kim, K., Masoomi, M., Bagheri, R., Slauch, J. M. & Miljkovic, N., Sep 3 2019, In : ACS Sustainable Chemistry and Engineering. 7, 17, p. 14509-14520 12 p.

Research output: Contribution to journalArticle

Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin

Dicaprio, A. J., Firouzbakht, A., Hudson, G. A. & Mitchell, D. A., Jan 9 2019, In : Journal of the American Chemical Society. 141, 1, p. 290-297 8 p.

Research output: Contribution to journalArticle

Escherichia coli vectors having stringently repressible replication origins allow a streamlining of Crispr/Cas9 gene editing

Srinivas, S., Hu, Z. & Cronan, J. E., May 2019, In : Plasmid. 103, p. 53-62 10 p.

Research output: Contribution to journalArticle

Fosmidomycin biosynthesis diverges from related phosphonate natural products

Parkinson, E. I., Erb, A., Eliot, A. C., Ju, K. S. & Metcalf, W. W., Nov 1 2019, In : Nature chemical biology. 15, 11, p. 1049-1056 8 p.

Research output: Contribution to journalArticle

Free Chlorine Disinfection Mechanisms of Rotaviruses and Human Norovirus Surrogate Tulane Virus Attached to Fresh Produce Surfaces

Fuzawa, M., Araud, E., Li, J., Shisler, J. L. & Nguyen, T. H., Oct 15 2019, In : Environmental Science and Technology. 53, 20, p. 11999-12006 8 p.

Research output: Contribution to journalArticle

GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean

Zeng, Z., Liu, X. L., Farley, K. R., Wei, J. H., Metcalf, W. W., Summons, R. E. & Welander, P. V., Nov 5 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 45, p. 22505-22511 7 p.

Research output: Contribution to journalArticle

Open Access

Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Mohamed, E. T., Mundhada, H., Landberg, J., Cann, I., MacKie, R. I., Nielsen, A. T., Herrgård, M. J. & Feist, A. M., Jun 29 2019, In : Microbial cell factories. 18, 1, 116.

Research output: Contribution to journalArticle

Open Access