Recent publications

Spring 2024
Pardue, E. J., Sartorio, M. G., Jana, B., Scott, N. E., Beatty, W. L., Ortiz-Marquez, J. C., Van Opijnen, T., Hsu, F. F., Potter, R. F., & Feldman, M. F. (2024). Dual membrane-spanning anti-sigma factors regulate vesiculation in Bacteroides thetaiotaomicron. Proceedings of the National Academy of Sciences of the United States of America, 121(10), e2321910121. https://doi.org/10.1073/pnas.2321910121
Feng, S., McNehlan, M. E., Kinsella, R. L., Sur Chowdhury, C., Chavez, S. M., Naik, S. K., McKee, S. R., Van Winkle, J. A., Dubey, N., Samuels, A., Swain, A., Cui, X., Hendrix, S. V., Woodson, R., Kreamalmeyer, D., Smirnov, A., Artyomov, M. N., Virgin, H. W., Wang, Y. T., & Stallings, C. L. (2024). Autophagy promotes efficient T cell responses to restrict high-dose Mycobacterium tuberculosis infection in mice. Nature microbiology, 10.1038/s41564-024-01608-x. Advance online publication. https://doi.org/10.1038/s41564-024-01608-x
Tuladhar, E. T., Shrestha, S., Vernon, S., Droit, L., Mihindukulasuriya, K. A., Tamang, M., Karki, L., Ngono, A. E., Jha, B., Awal, B. K., Chalise, B. S., Jha, R., Shresta, S., Wang, D., & Manandhar, K. D. (2024). Gemykibivirus detection in acute encephalitis patients from Nepal. medRxiv : the preprint server for health sciences, 2024.02.13.24302648. https://doi.org/10.1101/2024.02.13.24302648
Rosen, A. L., Lint, M. A., Voelker, D. H., Gilbert, N. M., Tomera, C. P., Santiago-Borges, J., Wallace, M. A., Hannan, T. J., Burnham, C.-A. D., Hultgren, S. J., & Kau, A. L. (2024). Secretory leukocyte protease inhibitor protects against severe urinary tract infection in mice. mBio, 15(2), e0255423. https://doi.org/10.1128/mbio.02554-23
Zeng, Q., Antia, A., Casorla-Perez, L. A., Puray-Chavez, M., Kutluay, S. B., Ciorba, M. A., & Ding, S. (2024). Calpain-2 mediates SARS-CoV-2 entry via regulating ACE2 levels. mBio, e0228723. Advance online publication. https://doi.org/10.1128/mbio.02287-23
Li, R., Zan, Y., Wang, D., Chen, X., Wang, A., Tan, H., Zhang, G., Ding, S., Shen, C., Wu, H., & Zhu, S. (2024). A mouse model to distinguish NLRP6-mediated inflammasome-dependent and -independent functions. Proceedings of the National Academy of Sciences of the United States of America, 121(6), e2321419121. https://doi.org/10.1073/pnas.2321419121
Garay, E., Whelan, S. P. J., DuBois, R. M., O’Rourke, S. M., Salgado-Escobar, A. E., Muñoz-Medina, J. E., Arias, C. F., & López, S. (2024). Immune response to SARS-CoV-2 variants after immunization with different vaccines in Mexico. Epidemiology and infection, 152, e30. https://doi.org/10.1017/S0950268824000219
Maddirala, A. R., Tamadonfar, K., Pinkner, J. S., Sanick, D., Hultgren, S. J., & Janetka, J. W. (2024). Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections. Journal of medicinal chemistry, 10.1021/acs.jmedchem.3c02128. Advance online publication. https://doi.org/10.1021/acs.jmedchem.3c02128
Harrison, G. A., Wang, E. R., Cho, K., Mreyoud, Y., Sarkar, S., Almqvist, F., Patti, G. J., & Stallings, C. L. (2024). Inducing vulnerability to InhA inhibition restores isoniazid susceptibility in drug-resistant Mycobacterium tuberculosis. mBio, e0296823. Advance online publication. https://doi.org/10.1128/mbio.02968-23
Boodwa-Ko, D., & Doering, T. L. (2024). A Quick reCAP: Discovering Cryptococcus neoformans Capsule Mutants. Journal of fungi (Basel, Switzerland), 10(2), 114. https://doi.org/10.3390/jof10020114
Wu, M., Zheng, W., Song, X., Bao, B., Wang, Y., Ramanan, D., Yang, D., Liu, R., Macbeth, J. C., Do, E. A., Andrade, W. A., Yang, T., Cho, H. S., Gazzaniga, F. S., Ilves, M., Coronado, D., Thompson, C., Hang, S., Chiu, I. M., Moffitt, J. R., … Kasper, D. L. (2024). Gut complement induced by the microbiota combats pathogens and spares commensals. Cell, 187(4), 897–913.e18. https://doi.org/10.1016/j.cell.2023.12.036
Souza, C. E., Jacobson, N. E., An, M. A., Droit, L., Vega, A. A., Rosales, M., Mihindukulasuriya, K. A., Pastrana, K., Handley, S. A., Parkes, M., Rimmer, J., Wang, D., Dinsdale, E. A., A Edwards, R., & Segall, A. M. (2024). Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples. Microbiology resource announcements, 13(1), e0013023. https://doi.org/10.1128/mra.00130-23
Rinkenberger, N., Rosenberg, A., Radke, J. B., Bhushan, J., Tomita, T., Weiss, L. M., & Sibley, L. D. (2024). Susceptibility of Toxoplasma gondii to autophagy in human cells relies on multiple interacting parasite loci. mBio, 15(1), e0259523. https://doi.org/10.1128/mbio.02595-23
Xu, R., Beatty, W. L., Greigert, V., Witola, W. H., & Sibley, L. D. (2024). Multiple pathways for glucose phosphate transport and utilization support growth of Cryptosporidium parvum. Nature communications, 15(1), 380. https://doi.org/10.1038/s41467-024-44696-3
Whitworth, I. T., Knoener, R. A., Puray-Chavez, M., Halfmann, P., Romero, S., Baddouh, M., Scalf, M., Kawaoka, Y., Kutluay, S. B., Smith, L. M., & Sherer, N. M. (2024). Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs. Journal of proteome research, 23(1), 149–160. https://doi.org/10.1021/acs.jproteome.3c00506
Nye, T. M., Zou, Z., Obernuefemann, C. L. P., Pinkner, J. S., Lowry, E., Kleinschmidt, K., Bergeron, K., Klim, A., Dodson, K. W., Flores-Mireles, A. L., Walker, J. N., Wong, D. G., Desai, A., Caparon, M. G., & Hultgren, S. J. (2024). Microbial co-occurrences on catheters from long-term catheterized patients. Nature communications, 15(1), 61. https://doi.org/10.1038/s41467-023-44095-0
Matta, S. K., Kohio, H. P., Chandra, P., Brown, A., Doench, J. G., Philips, J. A., Ding, S., & Sibley, L. D. (2024). Genome-wide and targeted CRISPR screens identify RNF213 as a mediator of interferon gamma-dependent pathogen restriction in human cells. Proceedings of the National Academy of Sciences of the United States of America, 121(1), e2315865120. https://doi.org/10.1073/pnas.2315865120
Rinkenberger, N., Rosenberg, A., Radke, J. B., Bhushan, J., Tomita, T., Weiss, L. M., & Sibley, L. D. (2024). Susceptibility of Toxoplasma gondii to autophagy in human cells relies on multiple interacting parasite loci. mBio, 15(1), e0259523. https://doi.org/10.1128/mbio.02595-23
Greigert, V., Saraav, I., Son, J., Zhu, Y., Dayao, D., Antia, A., Tzipori, S., Witola, W. H., Stappenbeck, T. S., Ding, S., & Sibley, L. D. (2024). Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. Gut microbes, 16(1), 2297897. https://doi.org/10.1080/19490976.2023.2297897
Fall 2023
Caparon, M., Xu, W., Bradstreet, T., Zou, Z., Hickerson, S., Zhou, Y., He, H., & Edelson, B. (2023). Reprogramming Short-Chain Fatty Acid Metabolism Mitigates Tissue Damage for Streptococcus pyogenes Necrotizing Skin Infection. Research square, rs.3.rs-3689163. https://doi.org/10.21203/rs.3.rs-3689163/v1
Adams, L. J., VanBlargan, L. A., Liu, Z., Gilchuk, P., Zhao, H., Chen, R. E., Raju, S., Chong, Z., Whitener, B. M., Shrihari, S., Jethva, P. N., Gross, M. L., Crowe, J. E., Jr, Whelan, S. P. J., Diamond, M. S., & Fremont, D. H. (2023). A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell reports. Medicine, 4(12), 101305. https://doi.org/10.1016/j.xcrm.2023.101305
Achouri, E., Felt, S. A., Hackbart, M., Rivera-Espinal, N. S., & López, C. B. (2023). VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets. RNA (New York, N.Y.), 30(1), 16–25. https://doi.org/10.1261/rna.079747.123
Heeren, S., Maes, I., Sanders, M., Lye, L. F., Adaui, V., Arevalo, J., Llanos-Cuentas, A., Garcia, L., Lemey, P., Beverley, S. M., Cotton, J. A., Dujardin, J. C., & Van den Broeck, F. (2023). Diversity and dissemination of viruses in pathogenic protozoa. Nature communications, 14(1), 8343. https://doi.org/10.1038/s41467-023-44085-2
Souza, C. E., Jacobson, N. E., An, M. A., Droit, L., Vega, A. A., Rosales, M., Mihindukulasuriya, K. A., Pastrana, K., Handley, S. A., Parkes, M., Rimmer, J., Wang, D., Dinsdale, E. A., A Edwards, R., & Segall, A. M. (2024). Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples. Microbiology resource announcements, 13(1), e0013023. https://doi.org/10.1128/mra.00130-23
Castro, Í. A., Yang, Y., Gnazzo, V., Kim, D. H., Van Dyken, S. J., & López, C. B. (2023). Murine Parainfluenza Virus Persists in Lung Innate Immune Cells Sustaining Chronic Lung Pathology. bioRxiv : the preprint server for biology, 2023.11.07.566103. https://doi.org/10.1101/2023.11.07.566103
González Aparicio, L. J., Yang, Y., Hackbart, M., & López, C. B. (2023). Copy-back viral genomes induce a cellular stress response that interferes with viral protein expression without affecting antiviral immunity. PLoS biology, 21(11), e3002381. https://doi.org/10.1371/journal.pbio.3002381
Berida, T., McKee, S. R., Chatterjee, S., Manning, D. L., Li, W., Pandey, P., Tripathi, S. K., Mreyoud, Y., Smirnov, A., Doerksen, R. J., Jackson, M., Ducho, C., Stallings, C. L., & Roy, S. (2023). Discovery, Synthesis, and Optimization of 1,2,4-Triazolyl Pyridines Targeting Mycobacterium tuberculosis. ACS infectious diseases, 9(11), 2282–2298. https://doi.org/10.1021/acsinfecdis.3c00341
Hackbart, M., & López, C. B. (2023). S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections. bioRxiv : the preprint server for biology, 2023.10.31.564889. https://doi.org/10.1101/2023.10.31.564889
McGuffey, J. C., Jackson-Litteken, C. D., Di Venanzio, G., Zimmer, A. A., Lewis, J. M., Distel, J. S., Kim, K. Q., Zaher, H. S., Alfonzo, J., Scott, N. E., & Feldman, M. F. (2023). The tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection. mBio, 14(5), e0141623. https://doi.org/10.1128/mbio.01416-23
McAllaster, M. R., Bhushan, J., Balce, D. R., Orvedahl, A., Park, A., Hwang, S., Sullender, M. E., Sibley, L. D., & Virgin, H. W. (2023). Autophagy gene-dependent intracellular immunity triggered by interferon-γ. mBio, 14(6), e0233223. Advance online publication. https://doi.org/10.1128/mbio.02332-23
Agustinho, D. P., Brown, H. L., Chen, G., Gaylord, E. A., Geddes-McAlister, J., Brent, M. R., & Doering, T. L. (2023). Unbiased discovery of natural sequence variants that influence fungal virulence. Cell host & microbe, 31(11), 1910–1920.e5. https://doi.org/10.1016/j.chom.2023.10.002
Serafim, T. D., Iniguez, E., Barletta, A. B. F., Cecilio, P., Doehl, J. S. P., Short, M., Lack, J., Nair, V., Disotuar, M., Wilson, T., Coutinho-Abreu, I. V., Meneses, C., Andersen, J., Alves E Silva, T. L., Oliveira, F., Vega-Rodriguez, J., Barillas-Mury, C., Ribeiro, J. M. C., Beverley, S. M., Kamhawi, S., … Valenzuela, J. G. (2023). Leishmania genetic exchange is mediated by IgM natural antibodies. Nature, 623(7985), 149–156. https://doi.org/10.1038/s41586-023-06655-8
Rosen, A. L., Lint, M. A., Voelker, D. H., Gilbert, N. M., Tomera, C. P., Santiago-Borges, J., Wallace, M. A., Hannan, T. J., Burnham, C. D., Hultgren, S. J., & Kau, A. L. (2023). Secretory Leukocyte Protease Inhibitor Protects Against Severe Urinary Tract Infection in Mice. bioRxiv : the preprint server for biology, 2023.10.10.561753. https://doi.org/10.1101/2023.10.10.561753
Ihedioha, O. C., Sivakoses, A., Beverley, S. M., McMahon-Pratt, D., & Bothwell, A. L. M. (2023). Leishmania major-derived lipophosphoglycan influences the host’s early immune response by inducing platelet activation and DKK1 production via TLR1/2. Frontiers in immunology, 14, 1257046. https://doi.org/10.3389/fimmu.2023.1257046
Naik, S. K., McNehlan, M. E., Mreyoud, Y., Kinsella, R. L., Smirnov, A., Chowdhury, C. S., McKee, S. R., Dubey, N., Woodson, R., Kreamalmeyer, D., & Stallings, C. L. (2023). Type I IFN signaling in the absence of IRGM1 promotes M. tuberculosis replication in immune cells by suppressing T cell responses. bioRxiv : the preprint server for biology, 2023.10.03.560720. https://doi.org/10.1101/2023.10.03.560720
Berna, A. Z., Merriman, J. A., Mellett, L., Parchment, D. K., Caparon, M. G., & Odom John, A. R. (2023). Volatile profiling distinguishes Streptococcus pyogenes from other respiratory streptococcal species. mSphere, 8(5), e0019423. https://doi.org/10.1128/msphere.00194-23

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