BTI research publications: November 2024 - March 2025

March 26, 2025
  1. Almela, P., Elser, J. J., Giersch, J. J., Hotaling, S., & Hamilton, T. L. (2025). Influence of snow cover on albedo reduction by snow algae. mBio, 16(2), e0363024. https://doi.org/10.1128/mbio.03630-24
  2. Almela, P., Elser, J. J., Giersch, J. J., Hotaling, S., Rebbeck, V., & Hamilton, T. L. (2024). Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms. Environ Microbiol Rep, 16(6), e70052. https://doi.org/10.1111/1758-2229.70052
  3. Auger, S. A., Pedersen, J. S., Maity, S., Sprague-Getsy, A. M., Lorimer, E. L., Koehn, O. J.,…Distefano, M. D. (2025). An Alkyne-Containing Isoprenoid Analogue Based on a Farnesyl Diphosphate Scaffold Is a Biologically Functional Universal Probe for Proteomic Analysis. Biochemistry, 64(1), 138-155. https://doi.org/10.1021/acs.biochem.4c00558
  4. Bajaj, J. S., Fagan, A., Gavis, E. A., Sterling, R. K., Gallagher, M. L., Lee, H.,…Khoruts, A. (2025). Microbiota transplant for hepatic encephalopathy in cirrhosis: The THEMATIC trial. J Hepatol. https://doi.org/10.1016/j.jhep.2024.12.047
  5. Bosma, J. S., Latyshev, E., Ma, O. X., Hansen, E. G., Cortes-Ortega, E., Reddy, V. S.,…Bowden, S. D. (2025a). Characterization of a novel broad-host-range polyvalent Tequatrovirus bacteriophage infecting Salmonella, Shigella, and Escherichia coli. Arch Virol, 170(3), 47. https://doi.org/10.1007/s00705-025-06236-2
  6. Chowdhury, S., Westenberg, R., Wennerholm, K., Cardiff, R. A. L., Beliaev, A. S., Noireaux, V.,…Peralta-Yahya, P. (2024). Carbon Negative Synthesis of Amino Acids Using a Cell-Free-Based Biocatalyst. ACS Synth Biol, 13(12), 3961-3975. https://doi.org/10.1021/acssynbio.4c00359
  7. Cortes-Ortega, E., Hansen, E. G., Iskender, I., Farmer, M. L., Martinez-Villalobos, J. M., Vitt, J. D., & Bowden, S. D. (2024). Isolation and characterization of Salmonella enterica- and Escherichia coli-specific bacteriophages of the genus Epseptimavirus from wastewater in Minnesota. Arch Virol, 169(12), 255. https://doi.org/10.1007/s00705-024-06190-5
  8. Crone, K. K., Labonte, J. W., Elias, M. H., & Freeman, M. F. (2025a). α-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions. Protein Sci, 34(2), e70021. https://doi.org/10.1002/pro.70021
  9. Ding, L., Zamalloa, C., Lin, H., & Hu, B. (2025). Bio-electrochemically assisted sulfide, phosphorus, and nitrogen remediation in continuous anaerobic digestion of dairy manure with improved biogas production. Chemosphere, 376, 144288. https://doi.org/10.1016/j.chemosphere.2025.144288
  10. Dixon, S., Leak, L., Wang, Z., Lee, W. C., Johnson, B., Millner, A.,…Nathanson, D. (2025). A clinical drug candidate that triggers non-apoptotic cancer cell death. Res Sq. https://doi.org/10.21203/rs.3.rs-4138879/v1
  11. Flynn, C. K., Adams, J. B., Krajmalnik-Brown, R., Khoruts, A., Sadowsky, M. J., Nirmalkar, K.,…Whiteley, P. (2025). Review of Elevated Para-Cresol in Autism and Possible Impact on Symptoms. Int J Mol Sci, 26(4). https://doi.org/10.3390/ijms26041513
  12. Garcia, V. A., Sarkar, C. A., & Ogle, B. M. (2025). Syncytial therapeutics: Receptor-specific and direct-to-cytosol biologic drug delivery mediated by measles fusion complex. J Control Release, 380, 967-975. https://doi.org/10.1016/j.jconrel.2025.02.033
  13. Hansen, Z. A., Fulcher, M. R., Wornson, N., Spawn-Lee, S. A., Johnson, M., Song, Z.,…Kinkel, L. L. (2024). Soil nutrient amendment increases the potential for inter-kingdom resource competition among foliar endophytes. ISME Commun, 4(1), ycae130. https://doi.org/10.1093/ismeco/ycae130
  14. Haq, I. U., Kennedy, P., Schreiner, K. M., Agnich, J. C., & Schilling, J. S. (2024). Gene Expression by a Model Fungus in the Ascomycota Provides Insight Into the Decay of Fungal Necromass. Environ Microbiol, 26(12), e70006. https://doi.org/10.1111/1462-2920.70006
  15. Harthorn, A., Kuo, T. H., Torres, S. W., Lobb, R. R., & Hackel, B. J. (2025). Expression-Dependent Tumor Pretargeting via Engineered Avidity. Mol Pharm, 22(1), 558-572. https://doi.org/10.1021/acs.molpharmaceut.4c01177
  16. Heili, J. M., Adamala, K. P., & Engelhart, A. E. (2024). Activation of Caged Functional RNAs by An Oxidative Transformation. Chembiochem, e202401056. https://doi.org/10.1002/cbic.202401056
  17. Hirsch, W., Fischer, M., Khoruts, A., Allegretti, J. R., Kelly, C. R., & Vaughn, B. (2025). Risk Factors for Antibiotic Exposure Post-Fecal Microbiota Transplantation for Recurrent. Open Forum Infect Dis, 12(3), ofaf130. https://doi.org/10.1093/ofid/ofaf130
  18. Hoeg, A., Kuchma, N., Krane, A., Graiziger, C., Thomas, J., Kelly, C. R., & Khoruts, A. (2024). Oral Capsule FMT Combined With Bezlotoxumab Is a Successful Rescue Protocol Following Failure of FMT Alone in the Treatment of Recurrent C. difficile Infection. J Clin Gastroenterol. https://doi.org/10.1097/MCG.0000000000002108
  19. Izri, Z., & Noireaux, V. (2024). Membraneless Compartmentalization of Cell-Free Transcription-Translation by Polymer-Assisted Liquid-Liquid Phase Separation. Small, e2403243. https://doi.org/10.1002/smll.202403243
  20. Johnson, A. J., Alvear, A., Knights, D., Chow, L. S., & Bantle, A. E. (2025). A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes. Nutrients, 17(1). https://doi.org/10.3390/nu17010185
  21. Kamerlin, S. C. L., & Elias, M. H. (2025). NIH's 15% cap: a cost comparison and research outlook. EMBO Rep. https://doi.org/10.1038/s44319-025-00418-4
  22. Kolas, A., Rusman, Y., Maia, A. C. G., Williams, J., Fumuso, F. G., Cotto-Rosario, A.,…Salomon, C. E. (2025). Norditerpene natural products from subterranean fungi with anti-parasitic activity. bioRxiv. https://doi.org/10.1101/2025.01.02.631097
  23. Lane, B. R., Kuhs, M. A., Zaret, M. M., Song, Z., Borer, E. T., Seabloom, E. W.,…Kinkel, L. L. (2025). Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome. Front Plant Sci, 16, 1558191. https://doi.org/10.3389/fpls.2025.1558191
  24. Li, F., Armet, A. M., Korpela, K., Liu, J., Quevedo, R. M., Asnicar, F.,…Walter, J. (2025). Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation. Cell, 188(5), 1226-1247.e1218. https://doi.org/10.1016/j.cell.2024.12.034
  25. Li, X., Zhang, H., Hodder, T., Wang, W., Myers, C. L., Yilmaz, L. S., & Walhout, A. J. M. (2025). Systems-level design principles of metabolic rewiring in an animal. Nature. https://doi.org/10.1038/s41586-025-08636-5
  26. Lin, Y. C., Kuo, H. J., Lu, M., Mahl, T., Aslanidi, G., & Hu, W. S. (2025). A synthetic platform for developing recombinant adeno-associated virus type 8 producer cell lines. Biotechnol Prog, e70009. https://doi.org/10.1002/btpr.70009
  27. Lin, Y. C., Kuo, H. J., Lu, M., Rungkittikhun, C., & Hu, W. S. (2025). Expression of Viral DNA Polymerase in Synthetic Recombinant Adeno-Associated Virus Producer Cell Line Enhances Full Particle Productivity. Biotechnol Bioeng, 122(2), 424-434. https://doi.org/10.1002/bit.28885
  28. Longhurst, A. D., Wang, K., Suresh, H. G., Ketavarapu, M., Ward, H. N., Jones, I. R.,…Toczyski, D. P. (2025). The PRC2.1 subcomplex opposes G1 progression through regulation of CCND1 and CCND2. Elife, 13. https://doi.org/10.7554/eLife.97577
  29. McCorison, C. B., Kim, T., Donato, J. J., & LaPara, T. M. (2025). Proximity-Ligation Metagenomic Sequence Analysis Reveals That the Antibiotic Resistome Makes Significant Transitions During Municipal Wastewater Treatment. Environ Microbiol, 27(1), e70036. https://doi.org/10.1111/1462-2920.70036
  30. Nielsen, G. H., Sachs, J. N., & Hackel, B. J. (2025). Engineering Affibody Binders to Death Receptor 5 and Tumor Necrosis Factor Receptor 1 With Improved Stability. Biotechnol Bioeng. https://doi.org/10.1002/bit.28954
  31. O'Connor, M. R., Thoma, C. J., Dodge, A. G., & Wackett, L. P. (2024). Phenotypic Plasticity During Organofluorine Degradation Revealed by Adaptive Evolution. Microb Biotechnol, 17(12), e70066. https://doi.org/10.1111/1751-7915.70066
  32. Parada, Z., Hoog, T. G., Adamala, K. P., & Engelhart, A. E. (2025). Quencher-Free Fluorescence Monitoring of G-Quadruplex Folding. ACS Omega, 10(3), 3176-3181. https://doi.org/10.1021/acsomega.4c10720
  33. Reddi, S., Senyshyn, L., Ebadi, M., Podlesny, D., Minot, S. S., Gooley, T.,…Rashidi, A. (2025). Fecal microbiota transplantation to prevent acute graft-versus-host disease: pre-planned interim analysis of donor effect. Nat Commun, 16(1), 1034. https://doi.org/10.1038/s41467-025-56375-y
  34. Ricouvier, J., Mostov, P., Shabtai, O., Vonshak, O., Tayar, A., Karzbrun, E.,…Bar-Ziv, R. (2024). Large-scale-integration and collective oscillations of 2D artificial cells. Nat Commun, 15(1), 10202. https://doi.org/10.1038/s41467-024-54098-0
  35. Ritz, J. M., Khakimzhan, A., Dalluge, J. J., Noireaux, V., & Puchner, E. M. (2025). Red Light Mediated Photoconversion of Silicon Rhodamines to Oxygen Rhodamines for Single-Molecule Microscopy. J Am Chem Soc, 147(9), 7588-7596. https://doi.org/10.1021/jacs.4c16907
  36. Seelig, B., & Chen, I. A. (2025). Intellectual frameworks to understand complex biochemical systems at the origin of life. Nat Chem, 17(1), 11-19. https://doi.org/10.1038/s41557-024-01698-4
  37. Silvey, S., Patel, N., Khoruts, A., & Bajaj, J. S. (2025). Rifaximin does not increase the rate of 30-day mortality in patients with cirrhosis and daptomycin in two National US-based cohorts. Gastroenterology. https://doi.org/10.1053/j.gastro.2025.03.014
  38. Sompiyachoke, K., Bravo, J., Sikdar, R., Abdullah, J., & Elias, M. H. (2025). A Novel Screening System to Characterize and Engineer Quorum Quenching Lactonases. Biotechnol Bioeng, 122(4), 922-935. https://doi.org/10.1002/bit.28928
  39. Syal, A., Martell, M., Sikdar, R., Dietz, M., Ziegert, Z., Jahansouz, C.,…Staley, C. (2025a). Quorum quenching enzymes disrupt bacterial communication in a sex- and dose-dependent manner. Animal Model Exp Med, 8(3), 473-482. https://doi.org/10.1002/ame2.12520
  40. Torres, S. W., Lan, C., Harthorn, A., Schmitz, Z., Blanchard, P. L., Collins, J., & Hackel, B. J. (2025). Molecular Determinants of Affinity and Isoform Selectivity in Protein─Small Molecule Hybrid Inhibitors of Carbonic Anhydrase. Bioconjug Chem, 36(3), 549-562. https://doi.org/10.1021/acs.bioconjchem.5c00006
  41. Venkatachalapathy, H., Dallon, S., Yang, Z., Azarin, S. M., Sarkar, C. A., & Batchelor, E. (2025). Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate. Mol Syst Biol. https://doi.org/10.1038/s44320-025-00091-8
  42. Wackett, L. P. (2025). Confronting PFAS persistence: enzymes catalyzing C-F bond cleavage. Trends Biochem Sci, 50(1), 71-83. https://doi.org/10.1016/j.tibs.2024.11.001
  43. Wackett, L. P., & Robinson, S. L. (2024). A prescription for engineering PFAS biodegradation. Biochem J, 481(23), 1757-1770. https://doi.org/10.1042/BCJ20240283
  44. Wang, H., Feyereisen, G. W., Zhang, J., & Ishii, S. (2025). Fungal degradation of complex organic carbon supports denitrification in saturated woodchip bioreactors. Bioresour Technol, 417, 131826. https://doi.org/10.1016/j.biortech.2024.131826
  45. Xiong, E. H., Zhang, X., Robbins, N., Myers, C. L., & Cowen, L. E. (2025). Protocol to identify genes important for Candida albicans fitness in diverse environmental conditions using pooled bar-seq screening approach. STAR Protoc, 6(1), 103645. https://doi.org/10.1016/j.xpro.2025.103645
  46. Zhang, Y., Song, Z., & Schilling, J. S. (2024). Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition. Microbiologyopen, 13(6), e70007. https://doi.org/10.1002/mbo3.70007
  47. Ziegert, Z., Dietz, M., Hill, M., McBride, M., Painter, E., Elias, M. H., & Staley, C. (2024). Targeting quorum sensing for manipulation of commensal microbiota. BMC Biotechnol, 24(1), 106. https://doi.org/10.1186/s12896-024-00937-3