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

BTI publications: February 2024

Achberger, A. M., Jones, R., Jamieson, J., Holmes, C. P., Schubotz, F., Meyer, N. R., . . . Sylvan, J. B. (2024). Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity. Nat Microbiol. https://doi.org/10.1038/s41564-024-01599-9

Allert, M., Ferretti, P., Johnson, K. E., Heisel, T., Gonia, S., Knights, D., . . . Blekhman, R. (2024). Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk. bioRxiv. https://doi.org/10.1101/2024.01.28.577594

Bisesi, A. T., Möbius, W., Nadell, C. D., Hansen, E. G., Bowden, S. D., & Harcombe, W. R. (2024a). Bacteriophage specificity is impacted by interactions between bacteria. mSystems, e0117723. https://doi.org/10.1128/msystems.01177-23

Collins, J., McConnell, A., Schmitz, Z. D., & Hackel, B. J. (2024). Sequence-function mapping of proline-rich antimicrobial peptides. bioRxiv. https://doi.org/10.1101/2024.01.28.577586

Greiss, F., Lardon, N., Schütz, L., Barak, Y., Daube, S. S., Weinhold, E., . . . Bar-Ziv, R. (2024). A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice. Nat Commun, 15(1), 883. https://doi.org/10.1038/s41467-024-45186-2

Janzen, A., Pothula, R., Sychla, A., Feltman, N. R., & Smanski, M. J. (2024). Predicting thresholds for population replacement gene drives. BMC Biol, 22(1), 40. https://doi.org/10.1186/s12915-024-01823-2

Li, J., Arnold, W. A., & Hozalski, R. M. (2024). Animal Feedlots and Domestic Wastewater Discharges are Likely Sources of. Environ Sci Technol, 58(6), 2973-2983. https://doi.org/10.1021/acs.est.3c09251

Lin, K., Chang, Y. C., Billmann, M., Ward, H. N., Le, K., Hassan, A. Z., . . . Myers, C. L. (2024). A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds. Sci Rep, 14(1), 2508. https://doi.org/10.1038/s41598-024-51735-y

Lu, M., Lee, Z., & Hu, W. S. (2024). Multi-omics kinetic analysis of recombinant adeno-associated virus production by plasmid transfection of HEK293 cells. Biotechnol Prog, e3428. https://doi.org/10.1002/btpr.3428

Mohamed, M. E., Saqr, A., Staley, C., Onyeaghala, G., Teigen, L., Dorr, C. R., . . . Jacobson, P. A. (2024). Pharmacomicrobiomics: Immunosuppressive Drugs and Microbiome Interactions in Transplantation. Transplantation. https://doi.org/10.1097/TP.0000000000004926

Oram, M. K., Baxley, R. M., Simon, E. M., Lin, K., Chang, Y. C., Wang, L., . . . Bielinsky, A. K. (2024). RNF4 prevents genomic instability caused by chronic DNA under-replication. DNA Repair (Amst), 135, 103646. https://doi.org/10.1016/j.dnarep.2024.103646

Phan, J., Macwan, S., Gralnick, J. A., & Yee, N. (2024). Extracellular organic disulfide reduction by. Microbiol Spectr, e0408123. https://doi.org/10.1128/spectrum.04081-23

Prakash, A., Rubin, N., Staley, C., Onyeaghala, G., Wen, Y. F., Shaukat, A., . . . Prizment, A. (2024). Effect of ginger supplementation on the fecal microbiome in subjects with prior colorectal adenoma. Sci Rep, 14(1), 2988. https://doi.org/10.1038/s41598-024-52658-4

Sampson, K., Sorenson, C., & Adamala, K. P. (2024). Preparing for the future of precision medicine: synthetic cell drug regulation. Synth Biol (Oxf), 9(1), ysae004. https://doi.org/10.1093/synbio/ysae004

Tassoulas, L. J., Rankin, J. A., Elias, M. H., & Wackett, L. P. (2024a). Dinickel enzyme evolved to metabolize the pharmaceutical metformin and its implications for wastewater and human microbiomes. Proc Natl Acad Sci U S A, 121(10), e2312652121. https://doi.org/10.1073/pnas.2312652121

Tassoulas, L. J., & Wackett, L. P. (2024). Insights into the action of the pharmaceutical metformin: Targeted inhibition of the gut microbial enzyme agmatinase. iScience, 27(2), 108900. https://doi.org/10.1016/j.isci.2024.108900

Travisano, M. (2024). Managing expectations. Science, 383(6684), 710. https://doi.org/10.1126/science.adn5394

Zhang, L., Wang, P., Wang, X., Zhang, Q., Wang, Y., Liu, Y., . . . Cui, X. (2024). Resource utilization of wastepaper and bentonite: Cu(II) removal in the aqueous environment. J Environ Manage, 353, 120213. https://doi.org/10.1016/j.jenvman.2024.120213

Zmuda, A. J., Kang, X., Wissbroecker, K. B., Freund Saxhaug, K., Costa, K. C., Hegeman, A. D., & Niehaus, T. D. (2024a). A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle. Nat Commun, 15(1), 846. https://doi.org/10.1038/s41467-024-45134-0

BTI publications: October – December 2023

Abdul Halim, M. F., Fonseca, D. R., Niehaus, T. D., & Costa, K. C. (2023b). Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. J Biol Chem, 105550. https://doi.org/10.1016/j.jbc.2023.105550

Adamala, K. P., Dogterom, M., Elani, Y., Schwille, P., Takinoue, M., & Tang, T. D. (2023). Present and future of synthetic cell development. Nat Rev Mol Cell Biol. https://doi.org/10.1038/s41580-023-00686-9

Baker, I. R., Matzen, S. L., Schuler, C. J., Toner, B. M., & Girguis, P. R. (2023). Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation. PNAS Nexus, 2(12), pgad421. https://doi.org/10.1093/pnasnexus/pgad421

Blanchard, P. L., Knick, B. J., Whelan, S. A., & Hackel, B. J. (2023). Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds. ACS Synth Biol, 12(12), 3608-3622. https://doi.org/10.1021/acssynbio.3c00409

Boatman, S., Kaiser, T., Nalluri-Butz, H., Khan, M. H., Dietz, M., Kohn, J., . . . Jahansouz, C. (2023). Diet-induced shifts in the gut microbiota influence anastomotic healing in a murine model of colonic surgery. Gut Microbes, 15(2), 2283147. https://doi.org/10.1080/19490976.2023.2283147

Buller, R., Lutz, S., Kazlauskas, R. J., Snajdrova, R., Moore, J. C., & Bornscheuer, U. T. (2023). From nature to industry: Harnessing enzymes for biocatalysis. Science, 382(6673), eadh8615. https://doi.org/10.1126/science.adh8615

Clare, S. J., King, R. M., Tawril, A. L., Havill, J. S., Muehlbauer, G. J., Carey, S. B., . . . Altendorf, K. R. (2023). An affordable and convenient diagnostic marker to identify male and female hop plants. G3 (Bethesda). https://doi.org/10.1093/g3journal/jkad216

Crone, K. K., Jomori, T., Miller, F. S., Gralnick, J. A., Elias, M. H., & Freeman, M. F. (2023a). RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin α-. RSC Chem Biol, 4(10), 804-816. https://doi.org/10.1039/d3cb00093a

Dietz, B. R., Olszewski, N. E., & Barney, B. M. (2023). Enhanced extracellular ammonium release in the plant endophyte. Microbiol Spectr, e0247823. https://doi.org/10.1128/spectrum.02478-23

Dodge, A. G., Thoma, C. J., O’Connor, M. R., & Wackett, L. P. (2023). Recombinant. mBio, e0278523. https://doi.org/10.1128/mbio.02785-23

Gehlbach, E. M., Robinson, A. O., Engelhart, A. E., & Adamala, K. P. (2023). Sequential gentle hydration increases encapsulation in model protocells. bioRxiv. https://doi.org/10.1101/2023.10.15.562404

Hoops, S. L., & Knights, D. (2023). LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients. Bioinformatics, 39(12). https://doi.org/10.1093/bioinformatics/btad727

Jang, J., & Ishii, S. (2023). Whole-genome sequence of. Microbiol Resour Announc, 12(12), e0080923. https://doi.org/10.1128/MRA.00809-23

Kalambokidis, M., & Travisano, M. (2023). The eco-evolutionary origins of life. Evolution. https://doi.org/10.1093/evolut/qpad195

Kalb, M. J., Grenfell, A. W., Jain, A., Fenske-Newbart, J., & Gralnick, J. A. (2023). Comparison of phage-derived recombinases for genetic manipulation of. Microbiol Spectr, 11(6), e0317623. https://doi.org/10.1128/spectrum.03176-23

Kamer, O., Rinott, E., Tsaban, G., Kaplan, A., Yaskolka Meir, A., Zelicha, H., . . . Shai, I. (2023). Successful weight regain attenuation by autologous fecal microbiota transplantation is associated with non-core gut microbiota changes during weight loss; randomized controlled trial. Gut Microbes, 15(2), 2264457. https://doi.org/10.1080/19490976.2023.2264457

Kang, J. J., Ohoka, A., & Sarkar, C. A. (2023). Designing Multivalent and Multispecific Biologics. Annu Rev Chem Biomol Eng. https://doi.org/10.1146/annurev-chembioeng-100722-112440

Lipps, S., Castell-Miller, C., Morris, C., Ishii, S., & Samac, D. (2023). Diversity of strains in the. Phytopathology. https://doi.org/10.1094/PHYTO-02-23-0059-R

Martinson, J. N. V., Chacón, J. M., Smith, B. A., Villarreal, A. R., Hunter, R. C., & Harcombe, W. R. (2023). Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities. ISME J, 17(12), 2270-2278. https://doi.org/10.1038/s41396-023-01534-6

McConnell, A., Batten, S. L., & Hackel, B. J. (2023). Determinants of Developability and Evolvability of Synthetic Miniproteins as Ligand Scaffolds. J Mol Biol, 435(24), 168339. https://doi.org/10.1016/j.jmb.2023.168339

McFarlane, J. A., Hansen, E. G., Ortega, E. C., Iskender, I., Noireaux, V., & Bowden, S. D. (2023a). A ToxIN homolog from Salmonella enterica serotype Enteritidis impairs bacteriophage infection. J Appl Microbiol, 134(12). https://doi.org/10.1093/jambio/lxad299

Park, K. H., Ordinola-Zapata, R., Noblett, W. C., Lima, B. P., & Staley, C. (2023). The effect of ultrasonic and multisonic irrigation on root canal microbial communities: An ex vivo study. Int Endod J. https://doi.org/10.1111/iej.13996

Rashidi, A., Ebadi, M., Rehman, T. U., Elhusseini, H., Kazadi, D., Halaweish, H., . . . Staley, C. (2023a). Potential of Fecal Microbiota Transplantation to Prevent Acute GVHD: Analysis from a Phase II Trial. Clin Cancer Res, 29(23), 4920-4929. https://doi.org/10.1158/1078-0432.CCR-23-2369

Reddy, S., Hu, B., & Kashani, K. (2023). Relationship between the rate of fluid resuscitation and acute kidney injury: A retrospective cohort study. Int J Crit Illn Inj Sci, 13(3), 104-110. https://doi.org/10.4103/ijciis.ijciis_7_23

Revelo, X., Fredrickson, G., Florczak, K., Barrow, F., Dietsche, K., Wang, H., . . . Ikramuddin, S. (2023). Hepatic lipid-associated macrophages mediate the beneficial effects of bariatric surgery against MASH. Res Sq. https://doi.org/10.21203/rs.3.rs-3446960/v1

Souza, V., Travisano, M., & Eguiarte, L. E. (2023). The Cuatro Ciénegas Basin. Curr Biol, 33(23), R1214-R1216. https://doi.org/10.1016/j.cub.2023.10.062

Suazo, K. F., Bělíček, J., Schey, G. L., Auger, S. A., Petre, A. M., Li, L., . . . Distefano, M. D. (2023). Thinking outside the CaaX-box: an unusual reversible prenylation on ALDH9A1. RSC Chem Biol, 4(11), 913-925. https://doi.org/10.1039/d3cb00089c

Vangay, P., Ward, T., Lucas, S., Beura, L. K., Sabas, D., Abramson, M., . . . Knights, D. (2023). Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut. Gut Microbes, 15(2), 2266627. https://doi.org/10.1080/19490976.2023.2266627

Varland, S., Silva, R. D., Kjosås, I., Faustino, A., Bogaert, A., Billmann, M., . . . Arnesen, T. (2023). N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity. Nat Commun, 14(1), 6774. https://doi.org/10.1038/s41467-023-42342-y

Wackett, L. P. (2023a). Microbial production of non-canonical amino acids: An annotated selection of World Wide Web sites relevant to the topics in microbial biotechnology. Microb Biotechnol, 16(12), 2401-2402. https://doi.org/10.1111/1751-7915.14376

Wackett, L. P. (2023b). Plasmids in environmental microbes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol Rep, 15(6), 820-821. https://doi.org/10.1111/1758-2229.13218

Wackett, L. P. (2023c). Web Alert: Fungal genomes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol, 25(10), 2054-2055. https://doi.org/10.1111/1462-2920.16067

Wackett, L. P. (2023d). Web Alert: Microbes and iodine: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol, 25(11), 2666-2667. https://doi.org/10.1111/1462-2920.16069

Wang, H., Barrow, F., Fredrickson, G., Florczak, K., Nguyen, H., Parthiban, P., . . . Revelo, X. S. (2023). Dysfunctional T Follicular Helper Cells Cause Intestinal and Hepatic Inflammation in NASH. bioRxiv. https://doi.org/10.1101/2023.06.07.544061

Zhou, Y., Bi, Z., Hamilton, M. J., Zhang, L., Su, R., Sadowsky, M. J., . . . Chen, C. (2023). -Cresol Sulfate Is a Sensitive Urinary Marker of Fecal Microbiota Transplantation and Antibiotics Treatments in Human Patients and Mouse Models. Int J Mol Sci, 24(19). https://doi.org/10.3390/ijms241914621