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.

BTI members connect with colleagues in Japan

BTI members connect with colleagues in Japan

BTI members connect with colleagues in Japan

BioTechnology Institute members travel to the University of Tokyo to strengthen research ties.

By Lance Janssen

Despite hours-long flights and an ocean of separation, researchers from the BioTechnology Institute (BTI) and the University of Tokyo have close connections. This past November, eight BTI faculty members traveled to Japan for a shared research symposium as a continued piece of an academic exchange program launched between the two institutions in 2017. With common research focus areas in areas like ​​microbial engineering, synthetic biology, protein design and environmental engineering, as well as opportunities to build connections and train students, the initiative aims to offer opportunities that will advance research and educational efforts for both BTI and the University of Tokyo.

“Our hope is that we can build collaborations with researchers that have shared interest areas and complementary scientific skills and expertise,” says Jeff Gralnick, a professor in the Department of Plant and Microbial Biology and a BTI member. “By establishing a student and postdoc exchange program, we also hope to provide important learning experiences for our trainees.”

Gralnick attended this year’s symposium along with Alptekin Aksan from the College of Science and Engineering, Christine Salomon from the College of Pharmacy and Medical School, as well as Michael Freeman, Kate Adamala, Michael Travisano and Claudia Schmidt-Dannert from the College of Biological Sciences. The symposium not only offered researchers the chance to share some of their research endeavors in Minnesota, but also build closer connections with their Tokyo counterparts. 

“The University of Tokyo is the premier research institution in Japan – with excellent research groups that conduct complementary research to BTI faculty,” says Schmidt-Dannert, head of BTI and a professor in the Department of Biochemistry, Molecular Biology and Biophysics. “Through this symposium we were able to learn first-hand about specific research conducted at the University of Tokyo through lectures, visits to labs and meetings with students, researchers and faculty – both in a formal but also more informal setting – and get insights into the academic environment and culture in Japan.”

Over the course of their visit, the BTI team took part in the symposium, as well as tours to the Mt. Fuji area, a formal banquet with colleagues and a visit to the National Institute of Genetics. These experiences offered researchers the chance to not only learn about research and visit a new city, but also future research opportunities for years to come.

“I think all of us identified areas of overlap for research collaboration,” says Schmidt-Dannert. “Some concrete connections have already been made that will result in material exchange and hosting of students and postdocs. We will use all of the knowledge and experience gathered to identify and apply for joint funding opportunities and develop a program that will allow for an exchange of graduate students and potentially postdocs between BTI and University of Tokyo labs.” 

Symposium presentations

Structural and metabolic insights in RiPP peptide backbone α-N- methylation.
Michael Freeman (University of Minnesota)

Natural product discovery for biocontrol and infectious disease treatment.
Christine Salomon (University of Minnesota)

Molecular Plant-Microbe interactions along the parasitic-mutualistic continuum.
Ke Hirumai (University of Tokyo)

Life but not alive: bioengineering with synthetic cells.
Kate Adamala (University of Minnesota)

Leveraging biological self-organization for the design of functional materials.
Claudia Schmidt-Dannert (University of Minnesota)

Molecular mechanisms of morphological development in the rare actinomycete Actinoplanes missouriensis.
Yasuo Ohnishi (University of Tokyo)

Extracellular electron transfer in Bacteria.
Jeffrey Gralnick (University of Minnesota)

Bioremediation of nitrate pollution in agricultural subsurface drainage.
Satoshi Ishii (University of Minnesota)

Plasmid business: effects to host cell physiology and fate in nature.
Hideaki Nojiri (University of Tokyo)

Active biomaterials for biotechnology applications.
Alptekin Aksan AKSAN (University of Minnesota)

Exploring microbial solutions using Experimental Evolution.
Michael Travisano (University of Minnesota)

Bioinformatics for revealing rules behind microbial genome evolution.
Wataru Iwasaki (University of Tokyo)