BTI publications: June – August 2024

Alejo, J. L., Girodat, D., Hammerling, M. J., Willi, J. A., Jewett, M. C., Engelhart, A. E., & Adamala, K. P. (2024). Alternate conformational trajectories in ribosome translocation. PLoS Comput Biol, 20(8), e1012319. https://doi.org/10.1371/journal.pcbi.1012319

Barney, B. M. (2024). Azotobacter vinelandii. Trends Microbiol. https://doi.org/10.1016/j.tim.2024.07.006

Barney, B. M., & Dietz, B. R. (2024). Precision control of ammonium release in Azotobacter vinelandii. Microb Biotechnol, 17(7), e14523. https://doi.org/10.1111/1751-7915.14523

Belofsky, G., Cruz, C., Schultz, T., Zapata, M., Wilcox, D., Wasmund, B.,…Spiegel, P. C. (2024). Antimicrobial isoflavans and other metabolites of Dalea nana. Phytochemistry, 226, 114224. https://doi.org/10.1016/j.phytochem.2024.114224

Bruger, E. L., Hying, Z. T., Singla, D., Márquez Reyes, N. L., Pandey, S. K., Patel, J. S., & Bazurto, J. V. (2024). Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in. Appl Environ Microbiol, 90(7), e0031024. https://doi.org/10.1128/aem.00310-24

Camur, B. B., Mancipe, N. C., & Barney, B. M. (2024). A polyethylene surrogate for microbial community enrichment and characterization. Environ Microbiol, 26(6), e16658. https://doi.org/10.1111/1462-2920.16658

de Souza Heidel, B. L., Benson, J., O’Keane, S., Dodge, A. G., Wackett, L. P., & Aksan, A. (2024a). A Model for Mechanical Stress Limited Bacterial Growth and Resporulation in Confinement. ACS Appl Mater Interfaces, 16(32), 41800-41809. https://doi.org/10.1021/acsami.4c04354

Dietz, B. R., Nelson, T. J., Olszewski, N. E., & Barney, B. M. (2024). A deoxyviolacein-based transposon insertion vector for pigmented tracer studies. Microbiologyopen, 13(4), e1425. https://doi.org/10.1002/mbo3.1425

Dorner, M., & Behrens, S. (2024). Biochar as ammonia exchange biofilm carrier for enhanced aerobic nitrification in activated sludge. Bioresour Technol, 131374. https://doi.org/10.1016/j.biortech.2024.131374

Fair, H., Hamilton, T. L., Smiley, P. C., & Liu, Q. (2024). Determinants of microbial community structure in supraglacial pool sediments of monsoonal Tibetan Plateau. Microbiol Spectr, 12(9), e0075424. https://doi.org/10.1128/spectrum.00754-24

Grettenberger, C. L., Abou-Shanab, R., & Hamilton, T. L. (2024). Limiting factors in the operation of photosystems I and II in cyanobacteria. Microb Biotechnol, 17(8), e14519. https://doi.org/10.1111/1751-7915.14519

Hsu, D., Flynn, J. R., Schuler, C. J., Santelli, C. M., Toner, B. M., Bond, D. R., & Gralnick, J. A. (2024a). Isolation and genomic analysis of “. Appl Environ Microbiol, 90(8), e0004424. https://doi.org/10.1128/aem.00044-24

Hu, B., Cui, Y., Lee, J. J., Ma, J. X., & Duerfeldt, A. S. (2024). Design and Assessment of First-Generation Heterobifunctional PPARα/STING Modulators. ACS Med Chem Lett, 15(8), 1279-1286. https://doi.org/10.1021/acsmedchemlett.4c00153

Johnson, K. E., Hernandez-Alvarado, N., Blackstad, M., Heisel, T., Allert, M., Fields, D. A.,…Blekhman, R. (2024). Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth. Nat Commun, 15(1), 6216. https://doi.org/10.1038/s41467-024-50282-4

Khakimzhan, A., Izri, Z., Thompson, S., Dmytrenko, O., Fischer, P., Beisel, C., & Noireaux, V. (2024). Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol, 7(1), 1005. https://doi.org/10.1038/s42003-024-06690-9

Kumar, V., Johnson, B. P., Mandal, P. S., Sheffield, D. R., Dimas, D. A., Das, R.,…Singh, S. (2024). The utility of Streptococcus mutans undecaprenol kinase for the chemoenzymatic synthesis of diverse non-natural isoprenoids. Bioorg Chem, 151, 107707. https://doi.org/10.1016/j.bioorg.2024.107707

Lemke, K. A., Sarkar, C. A., & Azarin, S. M. (2024). Rapid retinoic acid-induced trophoblast cell model from human induced pluripotent stem cells. Sci Rep, 14(1), 18204. https://doi.org/10.1038/s41598-024-68952-0

Li, X., Wang, J., Li, J., Zhou, Y., Huang, X., Guo, L.,…Zhou, S. (2024). Exploring genetic codon expansion for unnatural amino acid incorporation in filamentous fungus Aspergillus nidulans. J Biotechnol, 393, 91-99. https://doi.org/10.1016/j.jbiotec.2024.07.018

Lin, Y. C., Lu, M., Cai, W., & Hu, W. S. (2024). Comparative transcriptomic and proteomic kinetic analysis of adeno-associated virus production systems. Appl Microbiol Biotechnol, 108(1), 385. https://doi.org/10.1007/s00253-024-13203-5

Liu, Y., Li, Y., Shao, C., Wang, P., Wang, X., & Li, R. (2024). Curcumin-based residue-free and reusable photodynamic inactivation system for liquid foods and its application in freshly squeezed orange juice. Food Chem, 458, 140316. https://doi.org/10.1016/j.foodchem.2024.140316

Lopez-Morales, J., Vanella, R., Appelt, E. A., Whillock, S., Paulk, A. M., Shusta, E. V.,…Nash, M. A. (2023). Protein Engineering and High-Throughput Screening by Yeast Surface Display: Survey of Current Methods. Small Sci, 3(12). https://doi.org/10.1002/smsc.202300095

Lu, Y. A., McCann, M. G., Hu, W. S., & Zhang, Q. (2024). Multi-cell-line learning for the data-driven construction of mechanistic metabolic models. Biotechnol Bioeng, 121(9), 2833-2847. https://doi.org/10.1002/bit.28757

Mandarino Alves, A., Lecchi, C., Lopez, S., Stornetta, A., Mathai, P. P., Villalta, P. W.,…Khoruts, A. (2024). Dysfunctional mucus structure in cystic fibrosis increases vulnerability to colibactin-mediated DNA adducts in the colon mucosa. Gut Microbes, 16(1), 2387877. https://doi.org/10.1080/19490976.2024.2387877

Mohamed, M. E., Saqr, A., Al-Kofahi, M., Onyeaghala, G., Remmel, R. P., Staley, C.,…Jacobson, P. A. (2024). Limited Sampling Strategies Fail to Accurately Predict Mycophenolic Acid Area Under the Curve in Kidney Transplant Recipients and the Impact of Enterohepatic Recirculation. Ther Drug Monit. https://doi.org/10.1097/FTD.0000000000001248

Nielsen, G. H., Schmitz, Z. D., & Hackel, B. J. (2024). Sequence-developability mapping of affibody and fibronectin paratopes via library-scale variant characterization. Protein Eng Des Sel, 37. https://doi.org/10.1093/protein/gzae010

Onyeaghala, G. C., Sharma, S., Oyenuga, M., Staley, C. M., Milne, G. L., Demmer, R. T.,…Prizment, A. E. (2024). The Effects of Aspirin Intervention on Inflammation-Associated Lingual Bacteria: A Pilot Study from a Randomized Clinical Trial. Microorganisms, 12(8). https://doi.org/10.3390/microorganisms12081609

Sharma, S., Prizment, A., Nelson, H., Zhang, L., Staley, C., Poynter, J. N.,…Thyagarajan, B. (2024). Association between Accelerated Biological Aging, Diet, and Gut Microbiome. Microorganisms, 12(8). https://doi.org/10.3390/microorganisms12081719

Vivek, S., Shen, Y. S., Guan, W., Onyeaghala, G., Oyenuga, M., Staley, C.,…Thyagarajan, B. (2024). Association between Circulating T Cells and the Gut Microbiome in Healthy Individuals: Findings from a Pilot Study. Int J Mol Sci, 25(13). https://doi.org/10.3390/ijms25136831

Wang, P., Driscoll, W. W., & Travisano, M. (2024a). Genomic sequencing reveals convergent adaptation during experimental evolution in two budding yeast species. Commun Biol, 7(1), 825. https://doi.org/10.1038/s42003-024-06485-y

Xiao, Y. X., Lee, S. Y., Aguilera-Uribe, M., Samson, R., Au, A., Khanna, Y.,…Moffat, J. (2024). The TSC22D, WNK, and NRBP gene families exhibit functional buffering and evolved with Metazoa for cell volume regulation. Cell Rep, 43(7), 114417. https://doi.org/10.1016/j.celrep.2024.114417

Xiong, E. H., Zhang, X., Yan, H., Ward, H. N., Lin, Z. Y., Wong, C. J.,…Cowen, L. E. (2024). Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions. Cell Rep, 43(8), 114601. https://doi.org/10.1016/j.celrep.2024.114601

Xu, F., Thoma, C. J., Zhao, W., Zhu, Y., Men, Y., & Wackett, L. P. (2024). Dual feedback inhibition of ATP-dependent caffeate activation economizes ATP in caffeate-dependent electron bifurcation. Appl Environ Microbiol, e0060224. https://doi.org/10.1128/aem.00602-24

Yu, Y., Xu, F., Zhao, W., Thoma, C., Che, S., Richman, J. E.,…Men, Y. (2024). Electron bifurcation and fluoride efflux systems implicated in defluorination of perfluorinated unsaturated carboxylic acids by. Sci Adv, 10(29), eado2957. https://doi.org/10.1126/sciadv.ado2957

Zinselmeier, M. H., Casas-Mollano, J. A., Cors, J., Sychla, A., Heinsch, S. C., Voytas, D. F., & Smanski, M. J. (2024). Optimized dCas9 programmable transcriptional activators for plants. Plant Biotechnol J. https://doi.org/10.1111/pbi.14441

Zinßmeister, D., Leibovitch, M., Natan, E., Turjeman, S., Koren, O., Travisano, M.,…Baselga-Cervera, B. (2024). Detecting life by behavior, the overlooked sensitivity of behavioral assays. Sci Rep, 14(1), 18904. https://doi.org/10.1038/s41598-024-69942-y

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

A new perspective on research

A new perspective on research

A new perspective on research

Liangning Lu reflects on experiences and insights from BTI and University of Tokyo research exchange program.

By Lance Janssen

As part of an ongoing academic exchange program, colleagues from the BioTechnology Institute at the University of Minnesota and the University of Tokyo have worked together to further their research and teaching efforts since 2017. In addition to sharing research as well as hosting symposia, the exchange also brings the opportunity for graduate students to do research and train at each others’ institutions. Liangning Lu, a graduate student at the University of Tokyo, is a participant in the exchange program, conducting research with Dr. Satoshi Ishii at the U of M. We recently caught up with Lu to hear more about her time in the Twin Cities. 

What are you currently working on?
In Dr. Ishii’s lab, my current focus is on applying molecular biology techniques to better understand the mechanisms of two important steps in denitrification. I am particularly fascinated by the study of denitrifying microorganisms because N2O, as a greenhouse gas, poses a threat to the environment, and these emissions mostly originate from soil microorganisms.  

What interested you in coming to the University of Minnesota to do research?
Choosing the University of Minnesota for my research was driven by its outstanding reputation in the field of soil agronomy. The collaborative and innovative environment here aligns perfectly with my research interests. Additionally, the well-established experimental fields and faculty resources available at the University further informed my decision.

What part of your experience has stood out the most? What’s been the most challenging?
The most standout aspect of my experience has been the application of micro-sensor technology for simultaneous measurement of N2O and O2. This technique ingeniously achieves a simple and high-throughput detection of N2O. On the flip side, one of the most challenging aspects has been applying molecular biology principles to disrupt genes in microorganisms. This process involves many meticulous steps, and the need for precision in each step has given me a profound appreciation for rigorous scientific inquiry.  

What about this experience do you think is unique for visiting researchers?
What makes this experience unique for visiting scholars is that this academic visit not only facilitated meaningful academic exchange and provided me with a wealth of knowledge, but also included extensive cultural interactions. It provided me with a more comprehensive understanding of the open and egalitarian academic atmosphere in the United States, which greatly enhanced the richness of my research journey.