Jenn Brophy

All Publications

• Getting to the root of the pattern. Science (New York, N.Y.) Kozaeva, E., Brophy, J. A. 2025; 390 (6768): 24-25

  Abstract

  Root barriers and metabolite leakage shape microbial colonization of plants.

  View details for DOI 10.1126/science.aeb6058

  View details for PubMedID 41037628

• Focus Issue Editorial: Numeracy, Realism and Relevance in Plant Science. Plant physiology Brophy, J. A., Lin, Y. R., Shanks, J. V., Smith, A. G., Williams, M., Hanson, A. D. 2025

  View details for DOI 10.1093/plphys/kiaf295

  View details for PubMedID 40605771

• SeedSeg: image-based transgenic seed counting for segregation analysis of T-DNA loci. Plant methods Hernández, S., Zhong, V., Brophy, J. A. 2025; 21 (1): 87

  Abstract

  Transgenic plants are essential for both basic and applied plant biology. Recently, fluorescent and colorimetric markers were developed to enable nondestructive identification of transformed seeds and accelerate the generation of transgenic plant lines. Yet, transformation often results in the integration of multiple copies of transgenes in the plant genome. Multiple transgene copies can lead to transgene silencing and complicate the analysis of transgenic plants by requiring researcher to track multiple T-DNA loci in future generations. Thus, to simplify analysis of transgenic lines, plant researchers typically screen transformed plants for lines where the T-DNA inserted in a single locus - an analysis that involves laborious manual counting of fluorescent and non-fluorescent seeds for screenable markers.To expedite T-DNA segregation analysis, we developed SeedSeg, an image analysis tool that uses a segmentation algorithm to count the number of transformed and wild-type seeds in an image. SeedSeg runs a chi-squared test to determine the number of T-DNA loci. Parameters can be adjusted to optimize for different brightness intensities and seed sizes.By automating the seed counting process, SeedSeg reduces the manual labor associated with identifying transgenic lines containing a single T-DNA locus. SeedSeg is adaptable to different seed sizes and visual transgene markers, making it a versatile tool for accelerating plant research.

  View details for DOI 10.1186/s13007-025-01406-4

  View details for PubMedID 40551218

  View details for PubMedCentralID PMC12186423

• Roots of synthetic ecology: microbes that foster plant resilience in the changing climate. Current opinion in biotechnology Kozaeva, E., Eida, A. A., Gunady, E. F., Dangl, J. L., Conway, J. M., Brophy, J. A. 2024; 88: 103172

  Abstract

  Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.

  View details for DOI 10.1016/j.copbio.2024.103172

  View details for PubMedID 39029405

• Policy makers, genetic engineers, and an engaged public can work together to create climate-resilient plants. PLoS biology Archibald, B. N., Zhong, V., Brophy, J. A. 2023; 21 (7): e3002208

  Abstract

  As climate change affects weather patterns and soil health, agricultural productivity could decrease substantially. Synthetic biology can be used to enhance climate resilience in plants and create the next generation of crops, if the public will accept it.

  View details for DOI 10.1371/journal.pbio.3002208

  View details for PubMedID 37440471

• Forging a path toward a more sustainable laboratory. Trends in biochemical sciences Leak, L. B., Tamborski, J., Commissaris, A., Brophy, J. A. 2023; 48 (1): 5-8

  Abstract

  Scientific discovery has advanced human society in countless ways, but research requires the expenditure of energy and resources. This Scientific Life article details one laboratory's efforts to reduce the environmental impact of wet-lab research and provides a series of resources to improve lab sustainability.

  View details for DOI 10.1016/j.tibs.2022.09.001

  View details for PubMedID 36563657

• Transcriptional and post-transcriptional controls for tuning gene expression in plants. Current opinion in plant biology Zhong, V., Archibald, B. N., Brophy, J. A. 2022; 71: 102315

  Abstract

  Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability to precisely control gene expression in plants is still limited. Here, we review transcription and translation in the model plants Arabidopsis thaliana and Nicotiana benthamiana with an eye toward control points that may be used to predictably modify gene expression. We highlight differences in gene expression requirements between these plants and other species, and discuss the ways in which our understanding of gene expression has been used to engineer plants. This review is intended to serve as a resource for plant scientists looking to achieve precise control over gene expression.

  View details for DOI 10.1016/j.pbi.2022.102315

  View details for PubMedID 36462457

• Synthetic genetic circuits as a means of reprogramming plant roots. Science (New York, N.Y.) Brophy, J. A., Magallon, K. J., Duan, L., Zhong, V., Ramachandran, P., Kniazev, K., Dinneny, J. R. 2022; 377 (6607): 747-751

  Abstract

  The shape of a plant's root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.

  View details for DOI 10.1126/science.abo4326

  View details for PubMedID 35951698

• First Plant Cell Atlas symposium report PLANT DIRECT Rice, S. L., Lazarus, E., Anderton, C., Birnbaum, K., Brophy, J., Cole, B., Dickel, D., Ehrhardt, D., Fahlgren, N., Frank, M., Haswell, E., Huang, S., Leiboff, S., Libault, M., Otegui, M. S., Provart, N., Uhrig, R., Rhee, S. Y., Plant Cell Atlas Consortium 2022; 6 (6)

  View details for DOI 10.1002/pld3.406

  View details for Web of Science ID 000807524600001

• Toward synthetic plant development. Plant physiology Brophy, J. A. 1800

  Abstract

  The ability to engineer plant form will enable the production of novel agricultural products designed to tolerate extreme stresses, boost yield, reduce waste, and improve manufacturing practices. While historically, plants were altered through breeding to change their size or shape, advances in our understanding of plant development and our ability to genetically engineer complex eukaryotes are leading to the direct engineering of plant structure. In this review, I highlight the central role of auxin in plant development and the synthetic biology approaches that could be used to turn auxin-response regulators into powerful tools for modifying plant form. I hypothesize that recoded, gain-of-function auxin response proteins combined with synthetic regulation could be used to override endogenous auxin signaling and control plant structure. I also argue that auxin-response regulators are key to engineering development in non-model plants and that single cell-omics techniques will be essential for characterizing and modifying auxin response in these plants. Collectively, advances in synthetic biology, single cell -omics, and our understanding of the molecular mechanisms underpinning development have set the stage for a new era in the engineering of plant structure.

  View details for DOI 10.1093/plphys/kiab568

  View details for PubMedID 34904660

• Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nature communications Cuevas-Velazquez, C. L., Vellosillo, T., Guadalupe, K., Schmidt, H. B., Yu, F., Moses, D., Brophy, J. A., Cosio-Acosta, D., Das, A., Wang, L., Jones, A. M., Covarrubias, A. A., Sukenik, S., Dinneny, J. R. 2021; 12 (1): 5438

  Abstract

  Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.

  View details for DOI 10.1038/s41467-021-25736-8

  View details for PubMedID 34521831

• Vision, challenges and opportunities for a Plant Cell Atlas. eLife Plant Cell Atlas Consortium, Jha, S. G., Borowsky, A. T., Cole, B. J., Fahlgren, N., Farmer, A., Huang, S. C., Karia, P., Libault, M., Provart, N. J., Rice, S. L., Saura-Sanchez, M., Agarwal, P., Ahkami, A. H., Anderton, C. R., Briggs, S. P., Brophy, J. A., Denolf, P., Di Costanzo, L. F., Exposito-Alonso, M., Giacomello, S., Gomez-Cano, F., Kaufmann, K., Ko, D. K., Kumar, S., Malkovskiy, A. V., Nakayama, N., Obata, T., Otegui, M. S., Palfalvi, G., Quezada-Rodriguez, E. H., Singh, R., Uhrig, R. G., Waese, J., Van Wijk, K., Wright, R. C., Ehrhardt, D. W., Birnbaum, K. D., Rhee, S. Y., Ahmed, J., Alaba, O., Ameen, G., Arora, V., Arteaga-Vazquez, M. A., Arun, A., Bailey-Serres, J., Bartley, L. E., Bassel, G. W., Bergmann, D. C., Bertolini, E., Bhati, K. K., Blanco-Tourinan, N., Briggs, S. P., Brumos, J., Buer, B., Burlaocot, A., Cervantes-Perez, S. A., Chen, S., Contreras-Moreira, B., Corpas, F. J., Cruz-Ramirez, A., Cuevas-Velazquez, C. L., Cuperus, J. T., David, L. I., de Folter, S., Denolf, P. H., Ding, P., Dwyer, W. P., Evans, M. M., George, N., Handakumbura, P. P., Harrison, M. J., Haswell, E. S., Herath, V., Jiao, Y., Jinkerson, R. E., John, U., Joshi, S., Joshi, A., Joubert, L., Katam, R., Kaur, H., Kazachkova, Y., Raju, S. K., Khan, M. A., Khangura, R., Kumar, A., Kumar, A., Kumar, P., Kumar, P., Lavania, D., Lew, T. T., Lewsey, M. G., Lin, C., Liu, D., Liu, L., Liu, T., Lokdarshi, A., My Luong, A., Macaulay, I. C., Mahmud, S., Mahonen, A. P., Malukani, K. K., Marand, A. P., Martin, C. A., McWhite, C. D., Mehta, D., Martin, M. M., Mortimer, J. C., Nikolov, L. A., Nobori, T., Nolan, T. M., Ogden, A. J., Otegui, M. S., Ott, M., Palma, J. M., Paul, P., Rehman, A. U., Romera-Branchat, M., Romero, L. C., Roth, R., Sah, S. K., Shahan, R., Solanki, S., Song, B., Sozzani, R., Stacey, G., Stepanova, A. N., Taylor, N. L., Tello-Ruiz, M. K., Tran, T. M., Tripathi, R. K., Vadde, B. V., Varga, T., Vidovic, M., Walley, J. W., Wang, Z., Weizbauer, R. A., Whelan, J., Wijeratne, A. J., Xiang, T., Xu, S., Yadegari, R., Yu, H., Yuan, H. Y., Zanini, F., Zhao, F., Zhu, J., Zhuang, X. 2021; 10

  Abstract

  With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

  View details for DOI 10.7554/eLife.66877

  View details for PubMedID 34491200

• Understanding and engineering plant form SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY Brophy, J. A. N., LaRue, T., Dinneny, J. R. 2018; 79: 68–77

  View details for DOI 10.1016/j.semcdb.2017.08.051

  View details for Web of Science ID 000433227500008

• Understanding and engineering plant form. Seminars in cell & developmental biology Brophy, J. A., LaRue, T. n., Dinneny, J. R. 2017

  Abstract

  A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.

  View details for PubMedID 28864344