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: 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: June – September 2023

BTI publications: June – September 2023

Publications by BTI faculty

Bohn, B., Chalupova, M., Staley, C., Holtan, S., Maakaron, J., Bachanova, V., & El Jurdi, N. (2023). Temporal variation in oral microbiome composition of patients undergoing autologous hematopoietic cell transplantation with keratinocyte growth factor. BMC Microbiol, 23(1), 258. https://doi.org/10.1186/s12866-023-03000-x

Cai, Z., Donahue, N., Jones, K. C., McNeill, K., Manaia, C., Novak, P. J., & Vikesland, P. J. (2023). Best Papers from 2022 published in the. Environ Sci Process Impacts, 25(7), 1141-1143. https://doi.org/10.1039/d3em90018e

Chang, Y. C., Lin, K., Baxley, R. M., Durrett, W., Wang, L., Stojkova, O., . . . Bielinsky, A. K. (2023). RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication. Open Biol, 13(8), 230068. https://doi.org/10.1098/rsob.230068

Chowdhury, S., Kennedy, J. J., Ivey, R. G., Murillo, O. D., Hosseini, N., Song, X., . . . Paulovich, A. G. (2023). Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell, 186(16), 3476-3498.e3435. https://doi.org/10.1016/j.cell.2023.07.004

Costa, K. C., & Whitman, W. B. (2023). Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism. J Bacteriol, 205(8), e0011523. https://doi.org/10.1128/jb.00115-23

El Jurdi, N., Holtan, S. G., Hoeschen, A., Velguth, J., Hillmann, B., Betts, B. C., . . . Shields-Cutler, R. (2023). Pre-transplant and longitudinal changes in faecal microbiome characteristics are associated with subsequent development of chronic graft-versus-host disease. Br J Haematol. https://doi.org/10.1111/bjh.19016

Golinski, A. W., Schmitz, Z. D., Nielsen, G. H., Johnson, B., Saha, D., Appiah, S., . . . Martiniani, S. (2023). Predicting and Interpreting Protein Developability Via Transfer of Convolutional Sequence Representation. ACS Synth Biol, 12(9), 2600-2615. https://doi.org/10.1021/acssynbio.3c00196

Gralnick, J. A., & Bond, D. R. (2023). Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest. Annu Rev Microbiol, 77, 517-539. https://doi.org/10.1146/annurev-micro-032221-023725

Hassan, A. Z., Ward, H. N., Rahman, M., Billmann, M., Lee, Y., & Myers, C. L. (2023). Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens. Mol Syst Biol, e11657. https://doi.org/10.15252/msb.202311657

Hill, E. R., Chun, C. L., Hamilton, K., & Ishii, S. (2023). High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers. ACS ES T Water, 3(8), 2647-2658. https://doi.org/10.1021/acsestwater.3c00169

Hu, L. S., D’Angelo, F., Weiskittel, T. M., Caruso, F. P., Fortin Ensign, S. P., Blomquist, M. R., . . . Tran, N. L. (2023). Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures. Nat Commun, 14(1), 6066. https://doi.org/10.1038/s41467-023-41559-1

Huang, S., Bergonzi, C., Smith, S., Hicks, R. E., & Elias, M. H. (2023). Field testing of an enzymatic quorum quencher coating additive to reduce biocorrosion of steel. Microbiol Spectr, e0517822. https://doi.org/10.1128/spectrum.05178-22

Justyna, K., Das, R., Lorimer, E. L., Hu, J., Pedersen, J. S., Sprague-Getsy, A. M., . . . Distefano, M. D. (2023). Synthesis, Enzymatic Peptide Incorporation, and Applications of Diazirine-Containing Isoprenoid Diphosphate Analogues. Org Lett, 25(36), 6767-6772. https://doi.org/10.1021/acs.orglett.3c02736

Kalambokidis, M., & Travisano, M. (2023). Multispecies interactions shape the transition to multicellularity. Proc Biol Sci, 290(2007), 20231055. https://doi.org/10.1098/rspb.2023.1055

Kong, W., Qiu, L., Ishii, S., Jia, X., Su, F., Song, Y., . . . Wei, X. (2023). Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems. ISME Commun, 3(1), 81. https://doi.org/10.1038/s43705-023-00286-w

Lane, B. R., Anderson, H. M., Dicko, A. H., Fulcher, M. R., & Kinkel, L. L. (2023). Temporal variability in nutrient use among Streptomyces suggests dynamic niche partitioning. Environ Microbiol. https://doi.org/10.1111/1462-2920.16498

Li, J., Arnold, W. A., & Hozalski, R. M. (2023). Spatiotemporal Variability in. Environ Sci Technol, 57(37), 13959-13969. https://doi.org/10.1021/acs.est.3c01767

Lu, M., Lee, Z., Lin, Y. C., Irfanullah, I., Cai, W., & Hu, W. S. (2023). Enhancing the production of recombinant adeno-associated virus in synthetic cell lines through systematic characterization. Biotechnol Bioeng. https://doi.org/10.1002/bit.28562

McConnell, A., & Hackel, B. J. (2023). Protein engineering via sequence-performance mapping. Cell Syst, 14(8), 656-666. https://doi.org/10.1016/j.cels.2023.06.009

Miley, K., Meyer-Kalos, P., Ma, S., Bond, D. J., Kummerfeld, E., & Vinogradov, S. (2023). Causal pathways to social and occupational functioning in the first episode of schizophrenia: uncovering unmet treatment needs. Psychol Med, 53(5), 2041-2049. https://doi.org/10.1017/S0033291721003780

Morra, A., Schreurs, M. A. C., Andrulis, I. L., Anton-Culver, H., Augustinsson, A., Beckmann, M. W., . . . Investigators, k. (2023). Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer-specific survival. Cancer Med, 12(15), 16142-16162. https://doi.org/10.1002/cam4.6272

Ndinga-Muniania, C., Wornson, N., Fulcher, M. R., Borer, E. T., Seabloom, E. W., Kinkel, L., & May, G. (2023). Cryptic functional diversity within a grass mycobiome. PLoS One, 18(7), e0287990. https://doi.org/10.1371/journal.pone.0287990

Qualls, D. A., Lambert, N., Caimi, P. F., Merrill, M. H., Pullarkat, P., Godby, R. C., . . . Salles, G. A. (2023). Tafasitamab and lenalidomide in large B cell lymphoma: real-world outcomes in a multicenter retrospective study. Blood. https://doi.org/10.1182/blood.2023021274

Sakai, A., Jonker, A. J., Nelissen, F. H. T., Kalb, E. M., van Sluijs, B., Heus, H. A., . . . Huck, W. T. S. (2023). Cell-Free Expression System Derived from a Near-Minimal Synthetic Bacterium. ACS Synth Biol, 12(6), 1616-1623. https://doi.org/10.1021/acssynbio.3c00114

Seabloom, E. W., Caldeira, M. C., Davies, K. F., Kinkel, L., Knops, J. M. H., Komatsu, K. J., . . . Borer, E. T. (2023). Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores. Nat Commun, 14(1), 3516. https://doi.org/10.1038/s41467-023-39179-w

van Hees, D., Hanneman, C., Paradis, S., Camara, A. G., Matsumoto, M., Hamilton, T., . . . Kodner, R. B. (2023). Patchy and Pink: Dynamics of a Chlainomonas sp. (Chlamydomonadales, Chlorophyta) algal bloom on Bagley Lake, North Cascades, WA. FEMS Microbiol Ecol. https://doi.org/10.1093/femsec/fiad106

Vitt, J. D., Hansen, E. G., Garg, R., & Bowden, S. D. (2023). Bacteria intrinsic to Medicago sativa (alfalfa) reduce Salmonella enterica growth in planta. J Appl Microbiol, 134(9). https://doi.org/10.1093/jambio/lxad204

Wackett, L. P. (2023a). A microbial evolutionary approach for a sustainable future. Microb Biotechnol, 16(10), 1895-1899. https://doi.org/10.1111/1751-7915.14331

Wackett, L. P. (2023b). Acid stress in microbes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol Rep, 15(4), 335-336. https://doi.org/10.1111/1758-2229.13185

Wackett, L. P. (2023c). Cyanobacterial algal blooms: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol, 25(7), 1375-1376. https://doi.org/10.1111/1462-2920.16061

Wackett, L. P. (2023d). Microbes at low substrate concentrations: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol, 25(6), 1218-1219. https://doi.org/10.1111/1462-2920.16059

Wackett, L. P. (2023e). Web alert: Fabrication with microbial spores: An annotated selection of World Wide Web sites relevant to the topics in Microbial Biotechnology. Microb Biotechnol, 16(10), 2007-2008. https://doi.org/10.1111/1751-7915.14345

Wackett, L. P. (2023f). Web Alert: Solvent stress on environmental microbes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology. Environ Microbiol, 25(8), 1563-1564. https://doi.org/10.1111/1462-2920.16063

Wackett, L. P. (2023g). Web alert: Two-phase biocatalysis. Microb Biotechnol, 16(8), 1702. https://doi.org/10.1111/1751-7915.14314

Wackett, L. P., & McKnight. (2023). Web alert: Microbial biofilm catalysis. Microb Biotechnol, 16(7), 1577-1578. https://doi.org/10.1111/1751-7915.14299

Wang, H., Feyereisen, G. W., Wang, P., Rosen, C., Sadowsky, M. J., & Ishii, S. (2023). Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes. Microbiol Spectr, e0405322. https://doi.org/10.1128/spectrum.04053-22

Wang, Q. Q., Sun, M., Tang, T., Lai, D. H., Liu, J., Maity, S., . . . Long, S. (2023). Functional screening reveals. mBio, 14(4), e0130923. https://doi.org/10.1128/mbio.01309-23

Wang, Z., Ishii, S., & Novak, P. J. (2023). Quantification of depth-dependent microbial growth in encapsulated systems. Microb Biotechnol. https://doi.org/10.1111/1751-7915.14341

Worner, K., Liu, Q., Maschhoff, K. R., & Hu, W. (2023). Identification of RNA-binding proteins’ direct effects on gene expression via the degradation tag system. RNA, 29(10), 1453-1457. https://doi.org/10.1261/rna.079669.123

Zhang, Q., Xuan, Q., Wang, C., Shi, C., Wang, X., Ma, T., . . . Chen, C. (2023). Bioengineered “Molecular Glue”-Mediated Tumor-Specific Cascade Nanoreactors with Self-Destruction Ability for Enhanced Precise Starvation/Chemosynergistic Tumor Therapy. ACS Appl Mater Interfaces, 15(35), 41271-41286. https://doi.org/10.1021/acsami.3c06871

Zhang, W., Dong, H., Wang, X., Zhang, L., Chen, C., & Wang, P. (2023). Engineered. ACS Appl Mater Interfaces. https://doi.org/10.1021/acsami.3c09123

Zhu, B., Du, Z., Dai, Y., Kitaguchi, T., Behrens, S., & Seelig, B. (2023). Nanodroplet-Based Reagent Delivery into Water-in-Fluorinated-Oil Droplets. Biosensors (Basel), 13(8). https://doi.org/10.3390/bios13080768

Zlotorzynska, M., Chea, N., Eure, T., Alkis Ramirez, R., Blazek, G. T., Czaja, C. A., . . . Grigg, C. T. (2023). Residential social vulnerability among healthcare personnel with and without severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in Five US states, May-December 2020. Infect Control Hosp Epidemiol, 1-7. https://doi.org/10.1017/ice.2023.131

Schedule

Schedule


Friday May 5, 2023

(One day symposium)

McNamara Alumni Center
University of Minnesota
Minneapolis, MN USA.

Map & Directions

 Symposium Time Table

 

9:00-9:15

 

Opening Messages

  • Professor Romas Kazlauskas  (UMN)
  • Professor Ismail (PPIC)
  • President Amano (Video message: Amano Enzyme Japan)

9:15-9:45

9:45-10:15

10:15-10:45

10:45-11:15

Presentation 1

Presentation 2

Presentation 3

Presentation 4

11:15-12:00 Panel discussion
12:00-13:30

Lunch
Poster session

13:30-14:00

14:00-14:30

14:30-15:00

Presentation 5

Presentation 6

Presentation 7

15:00-15:20 Coffee Break

15:20-15:50

15:50-16:20

16:20-16:50

Presentation 8

Presentation 9

Presentation 10

16:50-16:55

 

Messages from Dr. Shotaro Yamaguchi (Amano Enzyme Japan)
17:00-18:30 Cocktail hour

 

Presenters

Romas Kazlauskas

Romas Kazlauskas, Ph.D.

Professor, Biochemistry, Molecular Biology & Biophysics
Biotechnology Institute
University of Minnesota
rjk@umn.edu

Romas Kazlauskas studied chemistry at the Massachusetts Institute of Technology (Ph.D.) and Harvard University (postdoc with George Whitesides). He worked at General Electric Company (1985-88) and McGill University, Montreal, Canada (1988-2003) and is currently a professor in Biochemistry, Molecular Biology and Biophysics at the University of Minnesota. He has been a visiting professor in Germany, Sweden and South Korea. He is an expert in protein engineering of enzymes for biocatalysis and the author of a forthcoming textbook on protein engineering (www.betterenzyme.com).

 Research Interests

  • Engineering new catalytic activity in enzymes
  • Rational design of enzyme properties
  • Enzyme applications to support sustainability
Shotaro Yamaguchi

Shotaro Yamaguchi, PhD.

CTO, Managing Director of Innovation
Amano Enzyme Inc.
shotaro_yamaguchi@amano-enzyme.com

Shotaro Yamaguchi joined Amano in 1984 after receiving a master’s degree in food engineering from the Graduate School of Agriculture, Kyoto University. Since then, he has been engaged in industrial enzymology, fungal genetic engineering, microbial fermentation, and food and medical enzyme applications. He received Ph.D. degree from Kyoto University on lipase in 1991 and spent three years at the Institute of Food Research (UK) from 1999 to 2001. He discovered a novel protein-modifying enzyme, protein glutaminase.

He received the following awards: Encouragement Award from Brewing Society of Japan (2003) and Technology Award from Japan Society for Bioscience, Biotechnology, and Agrochemistry (2010). He is an active Editor for Applied Microbiology and Biotechnology, Headquarters Officer/Auditor for Japan Society for Bioscience, Biotechnology, and Agrochemistry, and Representative for The Society for Biotechnology, Japan.

Todd Hester

Todd Hyster, Ph.D.

Associate Professor
Department of Chemistry and Chemical Biology
Cornell University
 

Prof. Todd Hyster is an Associate Professor of Chemistry and Chemical Biology at Cornell University. He received his B.S. in Chemistry from the University of Minnesota. He did his Ph.D. studies with Tomislav Rovis at Colorado State University. As part of his Ph.D., he was a Marie Curie Fellow with Thomas Ward at the University of Basel. He was an NIH Postdoctoral Fellow with Prof. Frances Arnold at Caltech. He started his independent career at Princeton University in 2015. His group has developed new methods in photoenzymatic catalysis.

Research Interests
  • Photoenzymatic Catalysis
  • Enzyme engineering via directed evolution
  • Selective organic synthesis

Photoenzymatic Catalysis – Using Light to Reveal New Enzyme Functions
Todd K. Hyster

Enzymes are exquisite catalysts for chemical synthesis, capable of providing unparalleled levels of chemo-, regio-, diastereo- and enantioselectivity. Unfortunately, biocatalysts are often limited to the reactivity patterns found in nature. In this talk, I will share my groups efforts to use light to expand the reactivity profile of enzymes. In our studies, we have exploited the photoexcited state of common biological cofactors, such as NADH and FMN to facilitate electron transfer to substrates bound within enzyme active sites. In other studies, we found that enzymes will electronically activate bound substrates for electron transfer. In the presence of common photoredox catalysts, this activation can be used to direct radical formation to enzyme active sites. Using these approaches, we can develop biocatalysts to solve long-standing selectivity challenges in chemical synthesis.

    Stefan Lutz

    Stefan Lutz, Ph.D.

    Sr VP Research
    Codexis Inc.
    stefan.lutz@codexis.com

    Stefan received a B.Sc. in chemistry/chemical engineering from the Zurich University of Applied Sciences, an M.Sc. in Biotechnology from the University of Teesside and a Ph.D. in chemistry from the University of Florida. He was a postdoctoral fellow at Pennsylvania State University. He joined Codexis in 2020 as the Senior Vice President of Research to lead the company’s research team advancing the technology platform, as well as the discovery and engineering of novel enzymes. Prior to his arrival in Redwood City, he was a Professor and Chair of the Chemistry Department at Emory University, having joined the university in 2002 and ascending to Chemistry Department Chair in 2014. Stefan is interested in advanced technologies for creating new, innovative, and economically-sustainable enzyme solutions to benefit society, industry, and the planet.

    Research Interests

    • Advanced technologies for enzyme design and engineering
    • Engineered enzyme applications
    • Biocatalysis

    Engineering Enzyme Products
    Stefan Lutz

    Codexis’ CodeEvolver® directed evolution technology has been applied to improve enzymes for specific functions for well over a decade. Advances in high-throughput gene & protein synthesis (build) and biochemical screening (test) in combination with advanced data analytics (learn) and computational design tools have, and continue to, enable the optimization and drive increasing complexity in developing novel biocatalysts for sustainable manufacturing, the life sciences, and the discovery and optimization of biologics.

    Tomoko Matsuda, Ph.D.

    Associate Professor
    Department of Life Science and Technology
    Tokyo Institute of Technology
    tmatsuda@bio.titech.ac.jp

    Tomoko Matsuda received a doctoral degree in science from Kyoto University (2000). Her doctoral thesis is about the biocatalytic asymmetric reduction of ketone for organic synthesis. She has been engaged in research on biocatalysis since then. She was appointed as an assistant professor at Ryukoku University in Japan (1999-2004) and began the study for biocatalysis using pressurized carbon dioxide. She was appointed as an associate professor in 2004 at the Tokyo Institute of Technology in Japan. She published over 130 scientific articles and received the following awards; the Taisho Pharmaceutical Research Planning Award from the Society of Synthetic Organic Chemistry, Japan (2001), the Morita Scientific Research Encouragement Award from the Japanese Association of University Women (2006), the Shiseido Woman Researcher Science Grant from Shiseido (2011), the Takeda International Contribution Award from Takeda Rika Kogyo (2018).

    Research Interests

    • Utilization of pressurized CO2 for biocatalysis
    • Green chemistry using biocatalysis

    Utilization of Carbon Dioxide as Solvent and Substrate for Biocatalysis
    Tomoko Matsuda

    As carbon dioxide (CO2) is an abundant carbon source and is causing global warming, developments in its utilization methods have been awaited. Therefore, pressurized CO2such as supercritical CO2 has been applied as a solvent for organic synthesis to develop efficient reactions replacing ordinary organic solvents derived from fossil fuel. However, the application of pressurized CO2 to biocatalysis has been limited. Therefore, we have been studying on utilization of CO2 as a solvent for lipase-catalyzed transesterification reactions and as a substrate for biocatalytic carboxylation reactions.

    Supercritical and liquid CO2 has been used for lipase-catalyzed transesterifications to replace conventional organic solvents. In this study, CO2-expanded liquids, liquids expanded by dissolving pressurized CO2, were utilized since they can be achieved at a lower pressure than supercritical and liquid CO2. Then, we found that for lipase-catalyzed transesterifications of bulky substrates, such as 1-(1-adamantyl)ethanol, o-substituted 1-phenylethanol analogs, and substituted 1-tetralol analogs, the conversions were higher for the reaction in CO2-expanded liquids than those in the corresponding liquids without CO2 (Figure 1).

    Matsuda Figure 1

    Figure 1 Solvent engineering using CO2 for lipase-catalyzed transesterifications

    On the other hand, a two-layer solvent system consisting of an aqueous buffer and the carbon dioxide layer was utilized for the carboxylation reactions since carboxylation enzymes are not stable in pressurized CO2 without bulk water. Catalyzed by enzymes from a thermophilic microorganism, Thermoplasma acidophilum isocitrate dehydrogenase (TaIDH) and T. acidophilum glucose dehydrogenase (TaGDH), the reductive carboxylation reactions have been successfully conducted using CO2 as a substrate (Figure 2). These enzymes were also co-immobilized to achieve higher stabilities and activities by forming an enzyme-inorganic hybrid nanocrystal.

    Matsuda Figure 2

    Figure 2 Utilization of CO2v as a substrate of biocatalytic carboxylation

    Anne Meyer

    Anne Meyer, Ph.D.

    Anne S. Meyer is Professor of Enzyme Technology, Head of the Protein Chemistry & Enzyme Technology Section at Dept. of Biotechnology and Biomedicine, Technical University of Denmark. The Section comprises 8 professor research groups, in total ~75 persons, incl. ~20 PhD students. She is group leader of Enzyme Technology in the Section.

     
    Research interests:

    • Applied enzyme technology, incl. enzyme enzymatic biorefining of biomass, agro-industrial side streams, starch, pectin, and seaweeds for production of bioactives and functional food compounds.
    • Enzymatic synthesis of human milk oligosaccharides.
    • Enzymatic degradation of plastic, and enzymatic conversion of CO2.
    • Bioinformatics, enzyme characterization, assays, kinetics, and carbohydrate chemistry

    New food processes and ingredients via targeted enzyme catalysis
    Anne S. Meyer, Technical University of Denmark, Denmark

    One of the major challenges confronting the modern food supply chain is providing safe, nutritious, and preferably functionally healthy food to an expanding global population while utilizing resources sensibly and protecting the environment and the climate. Many agro-industrial co-processing streams are rich in complex plant fibers that should not go to waste, as they may be a valuable source of beneficial, ‘prebiotic’ dietary fibers or a feedstock for functional ingredients production. Corn bran, a residue from large scale corn starch processing, is for example rich in highly substituted feruloylated glucurono-arabinoxylan, and even includes diferuloyl cross links, and is considered recalcitrant to enzymatic modification. We recently discovered a bacterial endo-xylanase (GH30 from Dickeya chrysantemi) that attacks complex corn arabinoxylan to enable gentle solubilization of substituted glucurono-arabinoxylan oligomers1. The recent news is that the GH30-solubilized corn arabinoxylan molecules modulate the human gut microbiota during simulated colon fermentation in vitro, paving the way for using corn bran streams as a resource to generate new soluble prebiotics2. Human milk oligosaccharides (HMOs) are unique, beneficial oligosaccharides in human breast milk. Enzymatic synthesis of HMOs is attractive to create new additives for infant formula and other products. Several glycoside hydrolases can catalyze transglycosylation (incl. transfucosylation) for precise enzymatic synthesis of nature-identical HMO products3. To attain high yields, we are using different types of protein engineering approaches to modify the enzyme to catalyze relevant transglycosylations at high yield4. Citrus-pectin residues have turned out to hold fucosylated xyloglucan that can serve as a source of fucose for enzymatic production of fucosylated HMOs via targeted enzymatic transfucosylation5. Seaweeds, i.e. marine macroalgae, have for decades been a source of food hydrocolloids. As the demand for hydrocolloids keep increasing, kelp seaweeds are now cultivated in the Northern hemisphere and new enzymes are being discovered for enzymatic refining options for kelp biorefining beyond extraction of hydrocolloids. One line of our research relates to enzymatic modification of alginate from kelp6, another concerns enzymatic extraction and modification of fucoidan for medical uses7,8,9. Lastly, we have recently introduced  new microbial 4-alpha-glucanotransferases to modify starch functionality10.

     

    1. Munk et al., 2020. ACS Sust Chem Eng 8 (22), 8164-8174.
    2. Lin et al. 2023. J Agric Food Chem 71, 385-3897
    3. Zeuner and Meyer 2020. Carb Res 493, 108029.
    4. Zeuner et al. 2020 J of Fungi 6(4), 295-313
    5. Nielsen et al. 2022. Carb Res. 519, 198627
    6. Pilgaard et al. 2021. J of Fungi 7, 80-95.
    7. Nguyen et al. 2020. Marine Drugs 18(6), 296-313
    8. Trang et al. 2022. Frontiers Plant Sci 13, 823668
    9. Ohmes et al. 2020 Marine Drugs 18, 481-418
    10. Christensen et al. 2023. Intl J Biol Macromol 224, 105-114.

     

    Jun Ogawa, Ph.D.

    Professor
    Division of Applied Life Sciences,
    Graduate School of Agriculture,
    Kyoto University
    ogawa.jun.8a@kyoto-u.ac.jp

    Jun Ogawa studied applied microbiology and completed his doctorate in 1995 at Kyoto University and became an assistant professor at the same university. He was a visiting researcher at French National Institute for Agricultural Research (INRA) (2006-2007) and has appointed as a full professor of the current position in 2009. He has published over 270 papers in applied microbiology such as bioprocess development, microbial metabolism analysis, etc. He was awarded “Agrochemistry Award for the Encouragement of Young Scientists” by Japan Society for Bioscience, Biotechnology, and Agrochemistry (2006), “Oleoscience Award” by the Japan Oil Chemists’ Society (2015 and 2020), “Society Award of Japanese Association for Food Immunology” (2018), “Ching Hou Biotechnology Award” (2020) and “Fellow” (2021) by American Oil Chemists’ Society, and “Chevreul Medal” by the French association for the study of lipids (2021).

    Research Interests

    • Microbial physiology
    • Fermentation technology
    • Enzyme technology
    • Metabolic engineering
    • Microbial consortia studies

     
    From function to genes, enzymes, and communities; creating novel biotechnology tools
    Jun Ogawa

    Information obtained through detail analysis of microbial function leads to finding of unexpected enzymes, metabolisms, and communities useful for bioprocess design. The screening of the novel biotechnological tools required analysis of unrevealed function with difficulties in establishing the methods, however, recent omics technologies make easier to identify the novel genes, enzymes, and communities, expanding their bioprocess application. Here, examples of bioprocess development by applying unique tools found through functional analysis of microbial metabolisms are introduced.

    1)  Novel amino acid metabolism involving hydroxylase- and dehydrogenase- catalyzing reactions was found. The hydroxylase library expanded through genomic information analysis and coupled with related enzymes made possible the production of various chiral hydroxy amino acids and chiral amino acid sulfoxides1,2.

    2)  Novel fatty acid reducing metabolism, polyunsaturated fatty acid (PUFA) saturation metabolism, was found in gut microorganisms. The metabolism involving four enzymes of hydratase, dehydrogenase, isomerase, and reductase was applied to the production of various hydroxy, oxo, and enone fatty acids with unique physiological activity useful for health3. Novel desaturases involved in PUFA biosynthesis4, and cyclooxygenase5 and P450 monooxygenase6 generating PUFA-derivatives were found and applied to the production of physiologically active PUFA derivatives.

    3)  Novel nucleosidases acting on 2’-O-methylribonucleosides were found and their ribosyl transferring activity was applied for the production of 2’-O-methylribonucleosides7. A novel enzyme, allantoinase, in the purine degradation metabolism was found to useful for the production of chiral amides via prochiral cyclic imide hydrolysis8. The reversible reactions involved in nucleoside degradation metabolism were applied to produce deoxyribonucleosides9.

    4)  Phytochemicals in foods and medicines are changed into bioactive molecules by gut microbial metabolism. The analysis of gut microbial metabolism of phytochemicals such as glucosinolates10, ellagic acid11, baicalin12, and astragaloside IV13 resulted in finding of novel enzymes. Besides, novel aglycon-glycosylating enzymes were found in microorganisms and applied to enhance the applicability of phytochemicals14,15.

    5)  Nitrifying bacteria play an important role in generating nitrate for crop cultivations. Organic nitrogen compounds are converted to nitrate through ammonification and nitrification. Understanding the interactions of the nitrifying microbial consortia is important for controlling the mineralization of organic nitrogen compounds. We established a controllable model consortium for ammonification and nitrification under organic conditions using a co-culture of only three strains selected through metagenomic analysis16,17. 

    References

    1. Hibi, M. et al. Appl Microbiol Biotechnol, 97, 2467-2472 (2013))
    2. Hibi, M. et al. Commun Biol, 4:16 (2021).)
    3. Kishino, S. et al. Proc Natl Acad Sci USA, 110, 17808-17813 (2013))
    4. Mo, B. K. H. et al. Biosci Biotechnol Biochem, 85, 1252–1265 (2021))
    5. Mohd Fazli, F. A. et al. Biosci Biotechnol Biochem, 83, 774-780 (2019))
    6. Saika, A. et al. FASEB Bioadv, 2, 59-71 (2020))
    7. Mitsukawa, Y. et al. J Biosci Bioeng, 125, 38-45 (2017))
    8. Nojiri, M. et al. Appl Microbiol Biotechnol, 99, 9961-9969 (2015))
    9. Horinouchi, N. et al. Microbial Cell Factories, 11, 82, (2012))
    10. Watanabe, H. et al. Sci Rep, 11, 23715, (2021))
    11. Watanabe, H. et al. J Biosci Bioeng, 129, 552-557 (2020))
    12. Sakurama, H. et al. Appl Microbiol Biotechnol, 98, 4021-4032 (2014))
    13. Takeuchi, D. M. et al. Biosci Biotechnol Biochem, 86(10) 1467–1475 (2022))
    14. Suzuki, T. et al. Biocatal Agric Biotechnol, 30, 101837 (2020))
    15. Kimoto, S. et al. J Biosci Bioeng, 134, 213-219 (2022))
    16. Saijai, S. et al. Biosci Biotechnol Biochem, 80, 2247-2254 (2016))
    17. Meeboon, J. et al. Sci Rep, 12, 7968 (2022)

    Mission Statement

    Mission Statement

    Our Mission

    The BioTechnology Institute (BTI) provides advanced research, training, and industry interaction in biological process technology, a major area of biotechnology research. The Institute is the central University of Minnesota vehicle for coordinated research in the biological, chemical, and engineering aspects of biotechnology and home to the MnDRIVE Environment Initiative 

    BTI’s Mission

    (1) Advance and support cross-disciplinary research and innovation at the forefront of biotechnology, (2) Support workforce and professional skills training in biotechnology, (3) Facilitate and develop industry relations in biotechnology, (4) Serve as a central biotechnology resource on campus and (5) Provide biomanufacturing expertise and services to the University, Minnesota, and industry through its BioResource Center (BRC).

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    (1) bringing together life-science and engineering faculty, researchers, postdocs, and students with shared research interests in biotechnology-related disciplines and
    (2) providing administrative support and resources for scientific exchange, networking, collaborative research, and professional skills development and training of its community members.

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    BTIs goals are:

    I. To be a major driver for the creation of a sustainable bioeconomy in MN by promoting and prioritizing cutting-edge fundamental and applied research towards the development of crucial enabling biotechnologies and synthetic biology approaches. BTI drives advances in a broad array of applications, including:

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    (1) offering up-to-date biotechnology training, professional skills development, and industrial networking
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