BTI publications: September – October 2024

BTI Publications September – October 2024

Boatman, S., Khan, M. H., Ganesan, N., Nalluri-Butz, H., Kohn, J., Troester, A.,…Staley, C. (2024). Anastomotic leak occurs independently from microbiota shifts associated with surgical bowel preparation. Sci Rep, 14(1), 21711. https://doi.org/10.1038/s41598-024-72520-x

Carlson, R. P., Beck, A. E., Benitez, M. G., Harcombe, W. R., Mahadevan, R., & Gedeon, T. (2024). Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy. bioRxiv. https://doi.org/10.1101/2024.08.21.609071

Corbella, M., Bravo, J., Demkiv, A. O., Calixto, A. R., Sompiyachoke, K., Bergonzi, C.,…Kamerlin, S. C. L. (2024). Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. JACS Au, 4(9), 3519-3536. https://doi.org/10.1021/jacsau.4c00404

Fredrickson, G., Florczak, K., Barrow, F., Mahmud, S., Dietsche, K., Wang, H.,…Revelo, X. S. (2024). TREM2 macrophages mediate the beneficial effects of bariatric surgery against MASH. Hepatology. https://doi.org/10.1097/HEP.0000000000001098

Frosch, A. E. P., Musiime, V., Staley, C., Conroy, A. L., Rutebarika, D., Ategeka, G., & Cusick, S. E. (2024). Safety and efficacy of iron supplementation with 3 months of daily ferrous sulphate in children living with HIV and mild-to-moderate anaemia in Uganda: a double-blind, randomised, placebo-controlled trial. Lancet HIV, 11(11), e727-e735. https://doi.org/10.1016/S2352-3018(24)00238-8

Gonia, S., Heisel, T., Miller, N., Haapala, J., Harnack, L., Georgieff, M. K.,…Swanson, M. H. (2024). Maternal oral probiotic use is associated with decreased breastmilk inflammatory markers, infant fecal microbiome variation, and altered recognition memory responses in infants-a pilot observational study. Front Nutr, 11, 1456111. https://doi.org/10.3389/fnut.2024.1456111

Haynes, K. A., Andrews, L. B., Beisel, C. L., Chappell, J., Cuba Samaniego, C. E., Dueber, J. E.,…Young, E. (2024). Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory. ACS Synth Biol, 13(9), 2635-2642. https://doi.org/10.1021/acssynbio.4c00276

Johnson, K. E., Heisel, T., Allert, M., Fürst, A., Yerabandi, N., Knights, D.,…Blekhman, R. (2024). Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome. Cell Genom, 4(10), 100638. https://doi.org/10.1016/j.xgen.2024.100638

Lévrier, A., Capin, J., Mayonove, P., Karpathakis, I. I., Voyvodic, P., DeVisch, A.,…Bonnet, J. (2024). Split Reporters Facilitate Monitoring of Gene Expression and Peptide Production in Linear Cell-Free Transcription-Translation Systems. ACS Synth Biol, 13(10), 3119-3127. https://doi.org/10.1021/acssynbio.4c00353

Michalska-Smith, M., Schlatter, D. C., Pombubpa, N., Castle, S. C., Grandy, A. S., Borer, E. T.,…Kinkel, L. L. (2024). Plant community richness and foliar fungicides impact soil. Front Microbiol, 15, 1452534. https://doi.org/10.3389/fmicb.2024.1452534

Moutsoglou, D., Syal, A., Lopez, S., Nelson, E. C., Chen, L., Kabage, A. J.,…Staley, C. (2024a). Novel Microbial Engraftment Trajectories following Microbiota Transplantation Therapy in Ulcerative Colitis. J Crohns Colitis. https://doi.org/10.1093/ecco-jcc/jjae142

Schuweiler, D., Ordinola-Zapata, R., Dietz, M., Lima, B. P., Noblett, W. C., & Staley, C. (2024). Microbial diversity in primary endodontic infections: demographics and radiographic characteristics. Clin Oral Investig, 28(11), 591. https://doi.org/10.1007/s00784-024-05982-y

Scott, A., Khoruts, A., Freeman, M. L., Beilman, G., Ramanathan, K., Bellin, M. D., & Trikudanathan, G. (2024a). Successful Use of Fecal Microbiota Transplantation in Management of Nonobstructive Recurrent Cholangitis Following Total Pancreatectomy and Islet Autotransplant. ACG Case Rep J, 11(10), e01527. https://doi.org/10.14309/crj.0000000000001527

Sorenson, C., & Adamala, K. P. (2024). Laws of thought in living cells. Cell, 187(18), 4830-4832. https://doi.org/10.1016/j.cell.2024.08.005

Teigen, L. M., McCarter, S. J., Ziegert, Z., Staley, C., Grant, K. M., Gupta, V. K.,…Ross, O. A. (2024). Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls. Parkinsonism Relat Disord, 129, 107176. https://doi.org/10.1016/j.parkreldis.2024.107176

Vaughn, B. P., Khoruts, A., & Fischer, M. (2024). Diagnosis and Management of Clostridioides difficile in Inflammatory Bowel Disease. Am J Gastroenterol. https://doi.org/10.14309/ajg.0000000000003076

Venkatachalapathy, H., Brzakala, C., Batchelor, E., Azarin, S. M., & Sarkar, C. A. (2024). Inertial effect of cell state velocity on the quiescence-proliferation fate decision. NPJ Syst Biol Appl, 10(1), 111. https://doi.org/10.1038/s41540-024-00428-3

Wang, H., Strock, J., Ranaivoson, A., & Ishii, S. (2024). Bioremediation of nitrate in agricultural drainage ditches: Impacts of low-grade weirs on microbiomes and nitrogen cycle gene abundance. Sci Total Environ, 955, 177070. https://doi.org/10.1016/j.scitotenv.2024.177070

Wissbroecker, K. B., Zmuda, A. J., Karumanchi, H., & Niehaus, T. D. (2024). Biochemical and genomic evidence for converging metabolic routes of metformin and biguanide breakdown in environmental Pseudomonads. J Biol Chem, 107935. https://doi.org/10.1016/j.jbc.2024.107935

Zhang, R., Kang, S. Y., Gaascht, F., Peña, E. L., & Schmidt-Dannert, C. (2024). Design of a Genetically Programmable and Customizable Protein Scaffolding System for the Hierarchical Assembly of Robust, Functional Macroscale Materials. ACS Synth Biol. https://doi.org/10.1021/acssynbio.4c00587

Zhang, X., Arnold, W. A., Wright, N., Novak, P. J., & Guest, J. S. (2024). Prioritization of Early-Stage Research and Development of a Hydrogel-Encapsulated Anaerobic Technology for Distributed Treatment of High Strength Organic Wastewater. Environ Sci Technol. https://doi.org/10.1021/acs.est.4c05389

BTI publications: March – mid April 2024

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

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: January 2024

BTI Publications January 2024

Elias, M. H., Sompiyachoke, K., Fernández, F. M., & Kamerlin, S. C. L. (2024). The ineligibility barrier for international researchers in US academia. EMBO Rep. https://doi.org/10.1038/s44319-023-00053-x

Haq, I. U., Christensen, A., & Fixen, K. R. (2024). Evolution of. Appl Environ Microbiol, e0210423. https://doi.org/10.1128/aem.02104-23

Heili, J. M., Stokes, K., Gaut, N. J., Deich, C., Sharon, J., Hoog, T., . . . Adamala, K. P. (2024). Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells. Cell Syst, 15(1), 49-62.e44. https://doi.org/10.1016/j.cels.2023.12.008

Hozalski, R. M., Zhao, X., Kim, T., & LaPara, T. M. (2024a). On-site filtration of large sample volumes improves the detection of opportunistic pathogens in drinking water distribution systems. Appl Environ Microbiol, e0165823. https://doi.org/10.1128/aem.01658-23

Huang, M., Rueda-Garcia, M., Harthorn, A., Hackel, B. J., & Van Deventer, J. A. (2024). Systematic Evaluation of Protein-Small Molecule Hybrids on the Yeast Surface. ACS Chem Biol. https://doi.org/10.1021/acschembio.3c00524

Lee, K. H., Distefano, M. D., & Seelig, B. (2023a). Facile immobilization of pyridoxal 5′-phosphate using p-diazobenzoyl-derivatized Sepharose 4B. Results Chem, 6. https://doi.org/10.1016/j.rechem.2023.101044

Li, J., Wang, Y., Distefano, M. D., Wagner, C. R., & Pomerantz, W. C. K. (2024). Multivalent Fluorinated Nanorings for On-Cell. Biomacromolecules. https://doi.org/10.1021/acs.biomac.3c01391

Medina-Chávez, N. O., Torres-Cerda, A., Chacón, J. M., Harcombe, W. R., De la Torre-Zavala, S., & Travisano, M. (2023b). Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium. Front Microbiol, 14, 1276438. https://doi.org/10.3389/fmicb.2023.1276438

Phan, T., Ye, Q., Stach, C., Lin, Y. C., Cao, H., Bowen, A., . . . Hu, W. S. (2024). Synthetic Cell Lines for Inducible Packaging of Influenza A Virus. ACS Synth Biol. https://doi.org/10.1021/acssynbio.3c00526

Robinson, A. O., Lee, J., Cameron, A., Keating, C. D., & Adamala, K. P. (2024). Cell-Free Expressed Membraneless Organelles Inhibit Translation in Synthetic Cells. ACS Biomater Sci Eng. https://doi.org/10.1021/acsbiomaterials.3c01052

Schreiber, M., Wonneberger, R., Haaning, A. M., Coulter, M., Russell, J., Himmelbach, A., . . . Waugh, R. (2024). Genomic resources for a historical collection of cultivated two-row European spring barley genotypes. Sci Data, 11(1), 66. https://doi.org/10.1038/s41597-023-02850-4

BTI publications: October – December 2023

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