BTI publications: March – mid April 2024

Collins, J., & Hackel, B. J. (2024). Sequence-activity mapping via depletion reveals striking mutational tolerance and elucidates functional motifs in Tur1a antimicrobial peptide. Protein Eng Des Sel, 37. https://doi.org/10.1093/protein/gzae006

Dogterom, M., Kamat, N. P., Jewett, M. C., & Adamala, K. P. (2024). Progress in Engineering Synthetic Cells and Cell-Free Systems. ACS Synth Biol, 13(3), 695-696. https://doi.org/10.1021/acssynbio.4c00100

Du, Z., & Behrens, S. F. (2024). Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities. PLoS One, 19(3), e0299930. https://doi.org/10.1371/journal.pone.0299930

Hajiaghabozorgi, M., Fischbach, M., Albrecht, M., Wang, W., & Myers, C. L. (2024). BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS. Nat Protoc. https://doi.org/10.1038/s41596-024-00954-8

Harcombe, W. R. (2024). Taking mechanomicrobiology from local to global. Biophys J. https://doi.org/10.1016/j.bpj.2024.03.014

Hu, X., Zhou, Y., Liu, R., Wang, J., Guo, L., Huang, X., . . . Zhou, S. (2024). Protein disulfide isomerase 1 is required for RodA assembling-based conidial hydrophobicity of. Appl Environ Microbiol, e0126023. https://doi.org/10.1128/aem.01260-23

Hying, Z. T., Miller, T. J., Loh, C. Y., & Bazurto, J. V. (2024). Glycine betaine metabolism is enabled in. Appl Environ Microbiol, e0209023. https://doi.org/10.1128/aem.02090-23

La Reau, A. J., Strom, N. B., Filvaroff, E., Mavrommatis, K., Ward, T. L., & Knights, D. (2024). Author Correction: Shallow shotgun sequencing reduces technical variation in microbiome analysis. Sci Rep, 14(1), 6116. https://doi.org/10.1038/s41598-024-56475-7

Levrier, A., Bowden, S., Nash, B., Lindner, A., & Noireaux, V. (2024a). Cell-Free Synthesis and Quantitation of Bacteriophages. Methods Mol Biol, 2760, 447-461. https://doi.org/10.1007/978-1-0716-3658-9_25

Levrier, A., Karpathakis, I., Nash, B., Bowden, S. D., Lindner, A. B., & Noireaux, V. (2024a). PHEIGES: all-cell-free phage synthesis and selection from engineered genomes. Nat Commun, 15(1), 2223. https://doi.org/10.1038/s41467-024-46585-1

Lewis, N. M., Kisgeropoulos, E. C., Lubner, C. E., & Fixen, K. R. (2024). Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe4S] Fd activity. J Inorg Biochem, 254, 112521. https://doi.org/10.1016/j.jinorgbio.2024.112521

Litsios, A., Grys, B. T., Kraus, O. Z., Friesen, H., Ross, C., Masinas, M. P. D., . . . Andrews, B. J. (2024). Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell, 187(6), 1490-1507.e1421. https://doi.org/10.1016/j.cell.2024.02.014

Liu, X., Igarashi, D., Hillmer, R. A., Stoddard, T., Lu, Y., Tsuda, K., . . . Katagiri, F. (2024). Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations. Plant Commun, 100882. https://doi.org/10.1016/j.xplc.2024.100882

Longhurst, A. D., Wang, K., Suresh, H. G., Ketavarapu, M., Ward, H. N., Jones, I. R., . . . Toczyski, D. P. (2024). The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. bioRxiv. https://doi.org/10.1101/2024.03.18.585604

Lu, M., Lin, Y. C., Kuo, H. J., Cai, W., Ye, Q., Zhao, L., & Hu, W. S. (2024). Tuning capsid formation dynamics in recombinant adeno-associated virus producing synthetic cell lines to enhance full particle productivity. Biotechnol J, 19(3), e2400051. https://doi.org/10.1002/biot.202400051

McFarlane, J. A., Garenne, D., Noireaux, V., & Bowden, S. D. (2024a). Cell-free synthesis of the Salmonella specific broad host range bacteriophage, felixO1. J Microbiol Methods, 220, 106920. https://doi.org/10.1016/j.mimet.2024.106920

Moon, S., Saboe, A., & Smanski, M. J. (2024). Using design of experiments to guide genetic optimization of engineered metabolic pathways. J Ind Microbiol Biotechnol, 51. https://doi.org/10.1093/jimb/kuae010

Rashidi, A., Ebadi, M., Rehman, T. U., Elhusseini, H., Kazadi, D., Halaweish, H., . . . Staley, C. (2024a). Long- and short-term effects of fecal microbiota transplantation on antibiotic resistance genes: results from a randomized placebo-controlled trial. Gut Microbes, 16(1), 2327442. https://doi.org/10.1080/19490976.2024.2327442

Rothschild, L. J., Averesch, N. J. H., Strychalski, E. A., Moser, F., Glass, J. I., Cruz Perez, R., . . . Adamala, K. P. (2024a). Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol. https://doi.org/10.1021/acssynbio.3c00724

Sadowsky, M. J., Matson, M., Mathai, P. P., Pho, M., Staley, C., Evert, C., . . . Khoruts, A. (2024a). Successful Treatment of Recurrent Clostridioides difficile Infection Using a Novel, Drinkable, Oral Formulation of Fecal Microbiota. Dig Dis Sci. https://doi.org/10.1007/s10620-024-08351-7

Segawa, T., Takahashi, A., Kokubun, N., & Ishii, S. (2024). Spread of antibiotic resistance genes to Antarctica by migratory birds. Sci Total Environ, 923, 171345. https://doi.org/10.1016/j.scitotenv.2024.171345

Shawver, S., Ishii, S., Strickland, M. S., & Badgley, B. (2024). Soil type and moisture content alter soil microbial responses to manure from cattle administered antibiotics. Environ Sci Pollut Res Int. https://doi.org/10.1007/s11356-024-32903-z

Sikdar, R., Beauclaire, M. V., Lima, B. P., Herzberg, M. C., & Elias, M. H. (2024). -acyl homoserine lactone signaling modulates bacterial community associated with human dental plaque. bioRxiv. https://doi.org/10.1101/2024.03.15.585217

Simpson, H. J., Andrew, C., Skrede, I., Kauserud, H., & Schilling, J. S. (2024). Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates. New Phytol. https://doi.org/10.1111/nph.19723

Sompiyachoke, K., & Elias, M. H. (2024). Engineering quorum quenching acylases with improved kinetic and biochemical properties. Protein Sci, 33(4), e4954. https://doi.org/10.1002/pro.4954

Sreekanta, S., Haaning, A., Dobbels, A., O’Neill, R., Hofstad, A., Virdi, K., . . . Lorenz, A. J. (2024). Variation in shoot architecture traits and their relationship to canopy coverage and light interception in soybean (Glycine max). BMC Plant Biol, 24(1), 194. https://doi.org/10.1186/s12870-024-04859-2

Suazo, K. F., Mishra, V., Maity, S., Auger, S. A., Justyna, K., Petre, A., . . . Distefano, M. D. (2024). Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors. bioRxiv. https://doi.org/10.1101/2024.03.03.583211

Sychla, A., Feltman, N. R., Hutchison, W. D., & Smanski, M. J. (2023). Corrigendum: Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive. Front Insect Sci, 3, 1360167. https://doi.org/10.3389/finsc.2023.1360167

Wackett, L. P. (2024). Evolutionary obstacles and not C-F bond strength make PFAS persistent. Microb Biotechnol, 17(4), e14463. https://doi.org/10.1111/1751-7915.14463

Zaret, M., Kinkel, L., Borer, E. T., & Seabloom, E. W. (2024). Plant growth-defense trade-offs are general across interactions with fungal, insect, and mammalian consumers. Ecology, e4290. https://doi.org/10.1002/ecy.4290