Student Publications

2024

Check, J., Harkness, R., Heger, L., Chilvers, M., Mahaffee, W., Sakalidis, M., Miles, T.D. 2024. It’s a trap!: An approachable guide to constructing and using rotating-arm air samplers. Plant Dis. 2. https://doi.org/10.1094/PDIS-01-24-0131-SR

JD Bibik, AE Bryson, B Hamberger (2024). Compartmentalized terpenoid production in plants using Agrobacterium-mediated transient expression. Met Mol Biol. 2760:21-34. doi: 10.1007/978-1-0716-3658-9_2.

Lotreck S, Abá KS, Lehti-Shiu MD, Seeger A, Brown BN, Ranaweera Y, Schumacher A, Ghassemi M, and Shiu S. "Plant Science Knowledge Graph Corpus: a gold standard entity and relation corpus for the molecular plant sciences." in silico Plants 6(1). doi: 10.1093/insilicoplants/diad021.

Kulke M, Kurtz E, Boren DM, Dayna M. Olson, Koenig AM, Susanne Hoffmann-Benning, Josh V. Vermaas (2024) PLAT domain protein 1 (PLAT1/PLAFP) binds to the Arabidopsis thaliana plasma membrane and inserts a lipid. Plant Science 338: 111900.

Mathieu D, AE Bryson, et al (2024). Multilevel analysis between Physcometrium patens and Mortierella explores potential long-standing interaction among land plants and fungi. Plant J. https://doi.org/10.1111/tpj.16605

Park D, Y. Al Shoffe, B.E. Algul, P. Engelgau, R.M. Beaudry, and C.B. Watkins (2024) Preharvest application of 1-methylcyclopropene and 1-aminoethoxyvinylglycine affects watercore severity and volatile profiles of ‘Fuji’ _apples stored in air and controlled atmospheres. Postharvest Biol. Technol. 211: 112840. https://doi.org/10.1016/j.postharvbio.2024.112840.

Roggenkamp EM., Check, J.C., Biswal, A.K., Floyd, C.M., Miles, L.A., Camila P. Nicolli, C.P., Shim, S., Salgado-Salazar, C., Alakonya, A., Malvick, D.K., Smith, D.L., Telenko, D.E.P., Chilvers, M.I. (2024) Development of a qPCR for species-specific detection of the tar spot pathogen Phyllachora maydis. PhytoFrontiers 4(1): 61-71.

Rosling A, Sahraei SE, Khan FK, Desirò A, Bryson A, Mondo S, Grigoriev I, Bonito G, 

Sánchez-García M (2024) Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics. https://doi.org/10.21203/rs.3.rs-3092996/v1 

Sharma N, Froehlich JF, Rillema R, Raba DA, Chambers T, Kerfeld CA, Kramer DM, Walker B, Brandizzi F (2023). Arabidopsis stromal carbonic anhydrases exhibit non‐overlapping roles in photosynthetic efficiency and development, Plant J 115(2):386-397. doi: 10.1111/tpj.16231.

Smith, K., Strand, D. D., Kramer, D. M. & Walker, B. J. (2024) The role of photorespiration in preventing feedback regulation via ATP synthase in Nicotiana tabacum. Plant, Cell & Environment, 47, 416–428. https://doi.org/10.1111/pce.14759.

Tejera-Nieves M, Seong DY, Reist L, Walker BJ (2024). The Dynamic Assimilation Technique measures photosynthetic CO2 response curves with similar fidelity as steady-state approaches in half the time. J. Exp Bot doi: 10.1093/jxb/erae057.

Thibault E, Brandizzi F (2024). Post-translational modifications: emerging directors of cell-fate decisions during endoplasmic reticulum stress in Arabidopsis thaliana, Biochem Soc Trans 52(2):831-848. doi: 10.1042/BST20231025.

2023

Amses K, Desiró A, Bryson A, Grigoriev I, Mondo S, Lipzen A, LaButti K, Riley R, Singan V, Salazar-Hamm P, King J, Ballou E, Pawlowska T, Adeleke R, Bonito G, Uehling J (2023) Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi. Fungal Genetics and Biology 169:103838. https://doi.org/10.1016/j.fgb.2023.103838.

Bibik JD, Bryson AE, Hamberger BR (2023) Compartmentalized Terpenoid Production In Plants Using Agrobacterium-mediated Transient Expression. Methods in: Synthetic Biology (second edition), Springer/Nature, Ed. Jeff Braman. Methods Mol Biol. 2024;2760:21-34. doi: 10.1007/978-1-0716-3658-9_2.

Bryson AE, ER Lanier, KH Lau, JP Hamilton, B Vaillancourt, D Mathieu, AE Yocca, GP Miller, P Edger, CR Buell, B Hamberger (2023). Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nat Comms. https://doi.org/10.1038/s41467-023-35845-1.

Chou M-Y, Andersen TB, Mechan Llontop ME, Beculheimer N, Sow A, Moreno N, Shade A, Hamberger B, Bonito G (2023) Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities. Microbiology Spectrum  11: e0133223.  https://doi.org/10.1128/spectrum.01332-23.

da Silva APG, Engelgau P, Sugimoto N, Beaudry R. (2023). Factors affecting 1-MCP release from an a-cyclodextrin encapsulant dissolved in water. Acta Horticulturae DOI: 10.17660/ActaHortic.2023.1364.11

Gregory, LM., Roze, L.V. & Walker, B.J. (2023) Increased activity of core photorespiratory enzymes and CO2 transfer conductances are associated with higher and more optimal photosynthetic rates under elevated temperatures in the extremophile Rhazya stricta. Plant, Cell & Environment, 46, 3704–3720. https://doi.org/10.1111/pce.14711

Jacobs M, Thompson S, Platts AE, Body JA, Kelsey A, Saad A, Abeli P, Teresi SJ, Schilmiller A, Beaudry R, Feldmann MJ, Knapp SJ, Song G, Miles T, and Edger PP (2023). Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry. Horticulture Research, 2023, 10: uhad169. https://doi.org/10.1093/hr/uhad169.

Jiang X, Walker B, He SY, Hu J (2023) The role of photorespiration in plant immunity. Front Plant Sci. DOI: 10.3389/fpls.2023.1125945.

Johnson LYD, Major IT, Chen Y, Yang C, Venegas-Cano LJ, Howe GA (2023) Diversification of JAZ-MYC signaling function in immune metabolism.  New Phytologist, 239:2277-2291.

Ko DK, Kim JY, Thibault EA, Brandizzi F. An IRE1-proteasome system signaling cohort controls cell fate determination in unresolved proteotoxic stress of the plant endoplasmic reticulum. Nature Plants 9: 1333-1346 (2023)

Kokarakis EJ, Rillema R, DC Ducat, JK Sakko (2023). Developing cyanobacterial quorum sensing toolkits: toward interspecies coordination in mixed autotroph/heterotroph communities, s ACS Synthetic Biology 12 (1), 265-276. 12(1):265-276. doi: 10.1021/acssynbio.2c00527

Kumar J, Gomez-Cano F, Hunt SW, Lotreck SG, Mathieu DT, Wilson ML, and Long TM (2023). Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes. CourseSource 10. DOI:10.24918/cs.2023.24.

Lanier ER, Andersen TB, Hamberger B. Plant terpene specialized metabolism: Complex networks or simple linear pathways? (2023) Plant J. doi: 10.1111/tpj.16177.

MacCready JS.*, Roggenkamp, EM.*, MacCready KG., Chilvers MI. (2023) Elucidating the obligate nature and biological capacity of an invasive fungal corn pathogen. MPMI 36(7): 411-424. Editor’s Pick.

Parks HM, Cinelli MA, Bedewitz MA, Grabar JM, Hurney SM, Walker KD, Jones AD, Barry CS (2023) Redirecting tropane alkaloid metabolism reveals pyrrolidine alkaloid diversity in Atropa belladonna. New Phytologist 237: 1810-1825 https://doi.org/10.1111/nph.18651

Solórzano JE, Issendorf SE, Drott MT., Check JC., Roggenkamp EM., Cruz CD, Kleczewski NM, Gongóra-Canul CC, Malvick DK (2023) A new and effective method to induce infection of Phyllachora maydis into corn for tar spot studies in controlled environments. Plant Methods 19, 83. 5.

Steensma AK, Shachar-Hill Y & Walker BJ (2023). The carbon-concentrating mechanism of the extremophilic red microalga Cyanidioschyzon merolae. Photosynthesis Research 156: 247-264. DOI: 10.1007/s11120-023-01000-6

Szymanski S, Longley RW, Hatlen RJ, Heger L, Sharma N, Bonito G, Miles TD (2023) The blueberry fruit mycobiome varies by tissue type and fungicide treatment. Phytobiomes Journal. 7 (2): 208-219.

Palande S, Kaste, J.A.M., Roberts, M.D., Segura Abá, K., Claucherty, C., Dacon, J., Doko, R., Jayakody, T.B., Jeffery, H.R., Kelly, N., Manousidaki, A., Parks HM, Roggenkamp EM, Schumacher, A.M., Yang, J., Percival, S., Pardo, J., Husbands, A.Y., Krishnan, A., Montgomery, B.L., Munch, E., Thompson, A.M., Rougon-Cardoso, A., Chitwood, D.H., VanBuren, R. (2023). Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS Biol 21(12): e3002397. doi: 10.1371/journal.pbio.3002397.

 

2022

Li P, Zhang Z, Tong Y, Foda BM, Day B. (2022): ILEE: Algorithms and toolbox for unguided and accurate quantitative analysis of cytoskeletal images. J Cell Biol. 222(2):e202203024. doi: 10.1083/jcb.202203024.

Edgar PP, …… Jacobs M, and 36 other co-authors (2022). There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Horticulture Research, Volume 9, 2022, uhac083, https://doi.org/10.1093/hr/uhac083.

Schenck CA, Anthony TM, Jacobs M, Jones AD, Last RL (2022). Natural variation meets synthetic biology: Promiscuous trichome-expressed acyltransferases from Nicotiana. Plant Physiology 190: 146–164. https://doi.org/10.1093/plphys/kiac192

Bird, K.A., M. Jacobs, A. Sebolt, K. Rhoades, E.I. Alger, M. Colle, M.L. Alekman, et al. "Parental Origins of the Cultivated Tetraploid Sour Cherry (Prunus Cerasus L.)." Plants, People, Planet 4, no. 5 (12 May 2022): 444-50. https://doi.org/https://doi.org/10.1002/ppp3.10267.

Bryson, A. E., E. R. Lanier, K. Lau, D. T. Mathieu, A. Yocca, G. P. Miller, P. Edger, C.R. Buell, and B. Hamberger. "Uncovering a Miltiradiene Biosynthetic Gene Cluster in the Lamiaceae Reveals a Dynamic Evolutionary Trajectory." Research Square  (18 April 2022). https://doi.org/https://doi.org/10.21203/rs.3.rs-1535494/v1.

Fiesel, P. D., H. M. Parks, R. L. Last, and C. S. Barry. "Fruity, Sticky, Stinky, Spicy, Bitter, Addictive, and Deadly: Evolutionary Signatures of Metabolic Complexity in the Solanaceae." Nat Prod Rep 39, no. 7 (Jul 20 2022): 1438-64. https://doi.org/10.1039/d2np00003b.

Kokarakis, E.J., R. Rillema, Ducat. D.C., and J.K. Sakkow. "Developing Cyanobacterial Quorum Sensing Toolkits: Towards Interspecies Coordination in Mixed Autotroph/Heterotroph Communities." bioRxiv  (21 July 2022 2022). https://doi.org/https://doi.org/10.1101/2022.07.20.500858.

Lucker, B.F., J.A. Temple, N.L. Panchy, U.F. Benning, J.D. Bibik, Neofotis. P.G., J.C. Weissman, et al. "Selection-Enriched Genomic Loci (Segl) Reveals Genetic Loci for Environmental Adaptation and Photosynthetic Productivity in Chlamydomonas Reinhardtii." Algal Research 64 (May 2022). https://doi.org/https://doi.org/10.1016/j.algal.2022.102709.

Parks, H.M., Cinelli, M.A., Bedewitz M.A., Grabar, J.M., Hurney, S.M., Walker K.D., Jones, A.D., Barry, C.S. "Redirecting tropane alkaloid metabolism reveals pyrrolidine alkaloid diversity in Atropa belladonna." New Phytologist (30 November 2022). https://doi.org/10.1111/nph.18651.

Young, D. Y., N. Pang, and Y. Shachar-Hill. "13c-Labeling Reveals How Membrane Lipid Components Contribute to Triacylglycerol Accumulation in Chlamydomonas." Plant Physiol 189, no. 3 (Jun 27 2022): 1326-44. https://doi.org/10.1093/plphys/kiac154.

 

2021

Cusack, S. A., P. Wang, S. G. Lotreck, B. M. Moore, F. Meng, J. K. Conner, P. J. Krysan, M. D. Lehti-Shiu, and S. H. Shiu. "Predictive Models of Genetic Redundancy in Arabidopsis Thaliana." Mol Biol Evol 38, no. 8 (Jul 29 2021): 3397-414. https://doi.org/10.1093/molbev/msab111.

Gregory, L. M., A. M. McClain, D. M. Kramer, J. D. Pardo, K. E. Smith, O. L. Tessmer, B. J. Walker, L. G. Ziccardi, and T. D. Sharkey. "The Triose Phosphate Utilization Limitation of Photosynthetic Rate: Out of Global Models but Important for Leaf Models." Plant Cell Environ 44, no. 10 (Oct 2021): 3223-26. https://doi.org/10.1111/pce.14153.

Li, J., J. Peng, X. Jiang, A. C. Rea, J. Peng, and J. Hu. "Deeplearnmor: A Deep-Learning Framework for Fluorescence Image-Based Classification of Organelle Morphology." Plant Physiol 186, no. 4 (Aug 3 2021): 1786-99. https://doi.org/10.1093/plphys/kiab223.

Young, D. Y., and Y. Shachar-Hill. "Large Fluxes of Fatty Acids from Membranes to Triacylglycerol and Back During N-Deprivation and Recovery in Chlamydomonas." Plant Physiol 185, no. 3 (Apr 2 2021): 796-814. https://doi.org/10.1093/plphys/kiaa071.

2020

Bryson, A. E., M. Wilson Brown, J. Mullins, W. Dong, K. Bahmani, N. Bornowski, C. Chiu, et al. "Composite Modeling of Leaf Shape Along Shoots Discriminates Vitis Species Better Than Individual Leaves." Appl Plant Sci 8, no. 12 (Dec 2020): e11404. https://doi.org/10.1002/aps3.11404.

Gomez-Cano, L., F. Gomez-Cano, F. M. Dillon, R. Alers-Velazquez, A. I. Doseff, E. Grotewold, and J. Gray. "Discovery of Modules Involved in the Biosynthesis and Regulation of Maize Phenolic Compounds." Plant Sci 291 (Feb 2020): 110364. https://doi.org/10.1016/j.plantsci.2019.110364.

Koenig, A. M., C. Benning, and S. Hoffmann-Benning. "Chapter 2 - Lipid Trafficking and Signaling in Plants." Lipid Signaling and Metabolism  (2020): 23-44. https://doi.org/https://doi.org/10.1016/B978-0-12-819404-1.00002-6.

Koenig, A. M., and S. Hoffmann-Benning. "The Interplay of Phloem-Mobile Signals in Plant Development and Stress Response." Biosci Rep 40, no. 10 (Oct 30 2020). https://doi.org/10.1042/BSR20193329.

Li, P., Y. J. Lu, H. Chen, and B. Day. "The Lifecycle of the Plant Immune System." CRC Crit Rev Plant Sci 39, no. 1 (2020): 72-100. https://doi.org/10.1080/07352689.2020.1757829.

Miller, G. P., W. W. Bhat, E. R. Lanier, S. R. Johnson, D. T. Mathieu, and B. Hamberger. "The Biosynthesis of the Anti-Microbial Diterpenoid Leubethanol in Leucophyllum Frutescens Proceeds Via an All-Cis Prenyl Intermediate." Plant J 104, no. 3 (Nov 2020): 693-705. https://doi.org/10.1111/tpj.14957.