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AI-summarized plant biology research papers from bioRxiv

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Latest 122 Papers

Synthetic pectin-cellulose nanofiber capsule provides minimal model capturing mechanics of a regenerating plant cell wall

Authors: Grandjean, C., Shanker, R., Pfaff, S. A., Mao, A., Chan, J., Asnacios, S., Asnacios, A., Zhang, S., Cosgrove, D. J., Coen, E., Svagan, A. J., Durand-Smet, P.

Date: 2025-10-07 · Version: 1
DOI: 10.1101/2025.10.07.680914

Category: Plant Biology

Model Organism: General

AI Summary

Researchers constructed a minimal synthetic spherical shell composed of pectin and cellulose and compared its mechanical behavior to that of primary cell walls regenerated on plant protoplasts. Parallel‑plate compression tests revealed a similar thickness‑dependent increase in stiffness for both systems, indicating that these two components are sufficient to confer key viscoelastic properties. The synthetic analogue thus provides a controllable platform to dissect the mechanical contributions of individual wall components.

synthetic cell wall primary cell wall pectin cellulose wall stiffness

EPP1 couples receptor activation to cytoplasmic signaling in root nodule symbiosis

Authors: Noergaard, M., Abel, N., Birkeskov, E., Landry, D., Stougaard, J., Andersen, K. R.

Date: 2025-10-01 · Version: 1
DOI: 10.1101/2025.09.29.679184

Category: Plant Biology

Model Organism: General

AI Summary

The study identifies Early Phosphorylated Protein 1 (EPP1) as a pivotal cytoplasmic mediator that links the SYMRK receptor to downstream symbiotic signaling, with phosphorylation of a key serine residue being both necessary and sufficient for nodule formation. Structural and functional analyses confirm the SYMRK‑EPP1 complex, and engineered synthetic interaction of these proteins can induce nodule organogenesis without bacterial presence.

EPP1 SYMRK receptor symbiotic signaling root nodule development synthetic engineering

Glycan recognition by a plant sentinel immune receptor

Authors: Jimenez-Sandoval, P., Broyart, C., Kentish, O., Lee, H. K., Culjak, K., Osswald, U., Aitouguinane, M., Tettamanti, E., Schmidli, M., Zhang, L., Roussin-Leveillee, C., Berlanga, D. J., Martin-Dacal, M., Torres, M. A., Kumar, V., Fernandez-Calvo, P., Jimenez-Gomez, J. M., Macho, A. M., Pfrengle, F., Jorda, L., Molina, A., Santiago, J.

Date: 2025-09-30 · Version: 1
DOI: 10.1101/2025.09.28.679030

Category: Plant Biology

Model Organism: General

AI Summary

The study elucidates the structure of the plant receptor IGP1 in both apo and cellotriose‑bound states, showing that prearranged Leucine‑Rich Repeat‑malectin interactions create a highly specific sugar‑binding pocket that discriminates cellulose‑derived oligosaccharides. By directly sensing cell wall‑derived DAMPs, IGP1 functions as a sentinel linking wall degradation to rapid immune activation.

cell wall DAMPs cellotriose LRR-malectin receptor IGP1 plant innate immunity

Techniques and challenges in studying photosynthetic diversity in freshwater aquatic vascular plants

Authors: Loew-Mendelson, E., Wickell, D., Mrozinski, C., Doan, E., Hupp, J., Vath, R. L., Yuan, L., Heyduk, K.

Date: 2025-09-26 · Version: 1
DOI: 10.1101/2025.09.24.677520

Category: Plant Biology

Model Organism: General

AI Summary

The abstract reviews and evaluates current methods for detecting carbon concentrating mechanisms (CCMs) in aquatic plants, highlighting the limitations of terrestrial‑derived physiological and isotopic techniques in submerged environments. It proposes a targeted molecular assay of phosphoenolpyruvate carboxylase (PEPC) expression as a sensitive approach to better characterize photosynthetic diversity across aquatic species.

aquatic plants carbon concentrating mechanisms photosynthetic diversity methodological challenges phosphoenolpyruvate carboxylase

Progressive oxygenation of developing leaves directs morphogenesis

Authors: Panicucci, G., Shukla, V., Voloboeva, V., Jo, L., van Kollenburg, K., Buti, S., Dalle Carbonare, L., Licausi, F., Weits, D. A.

Date: 2025-09-21 · Version: 1
DOI: 10.1101/2025.09.21.677629

Category: Plant Biology

Model Organism: General

AI Summary

The study demonstrates that developing leaves create a spatiotemporal oxygen gradient that is sensed by the PLANT CYSTEINE OXIDASE branch of the N‑degron pathway, linking local hypoxia to restricted cell expansion and later oxygenation to specialized cell fate acquisition. This reveals oxygen as a positional cue that guides leaf morphogenesis, suggesting that manipulation of oxygen gradients could direct plant form and function.

oxygen gradient PLANT CYSTEINE OXIDASE N-degron pathway leaf morphogenesis hypoxia signaling

Fun-Sized Library Prep: Miniaturization is a valid method for per-sample cost reduction in targeted sequencing of angiosperm DNA

Authors: Bullock, M. R., Fokar, M., Creek, R. D., Stevens, E. A., Johnson, M. G.

Date: 2025-09-20 · Version: 1
DOI: 10.1101/2025.09.17.676862

Category: Plant Biology

Model Organism: General

AI Summary

The study evaluated low‑volume library preparation (0.1X vs 0.5X reaction volumes) for targeted Angiosperms353 sequencing across 768 angiosperm samples, including fresh and herbarium material. Miniaturizing reactions to 0.1X significantly cut costs while delivering comparable sequencing quality, insert size, and read mapping performance. The approach enables cost‑effective population‑level genomics using herbarium collections.

population genomics targeted sequencing library miniaturization herbarium DNA cost reduction

Antimycin A, but not antimycin A3 or myxothiazol, directly suppresses photosystem II activity

Authors: Imaizumi, K., Ifuku, K.

Date: 2025-09-16 · Version: 1
DOI: 10.1101/2025.09.11.675326

Category: Plant Biology

Model Organism: General

AI Summary

The authors examined the direct effects of antimycin A (AA), its analogue AA3, and myxothiazol on photosystem II (PSII) activity and linear electron transport using isolated plant PSII complexes and thylakoid membranes. They found that AA, but not AA3 or myxothiazol, suppresses PSII activity in a batch‑dependent manner, leading them to recommend AA3 for specific inhibition of cyclic electron flow and myxothiazol for complex III inhibition.

Antimycin A Antimycin A3 myxothiazol photosystem II cyclic electron flow

The 'Iceberg region of the Grapevine leafroll-associated virus 3 replicase polyprotein contains signals for mitochondrial targeting and outer membrane association

Authors: Fust, C., Li, C., Meng, B.

Date: 2025-09-07 · Version: 1
DOI: 10.1101/2025.09.05.674466

Category: Plant Biology

Model Organism: General

AI Summary

The study identifies an amphipathic helix and a downstream transmembrane domain within the GLRaV3 replicase polyprotein (PP1a) that direct its targeting and anchoring to the outer mitochondrial membrane, facilitating viral replication complex formation. Using EGFP-tagged truncations, confocal microscopy, mutagenesis, mitochondrial fractionation, and Western blotting, the authors map the mitochondrial targeting signal and propose a dodecameric oligomeric structure that may gate VRCs.

GLRaV3 viral replication complexes outer mitochondrial membrane amphipathic helix replicase polyprotein

Qualifying the effectiveness of Cannabis smoke filtration via Bong water using GC-MS and risk assessment of inhaling smoke compounds

Authors: Kiatchaipipat, S., Vimolmangkang, S., Jinta, P., Khasitanon, P.

Date: 2025-09-05 · Version: 1
DOI: 10.1101/2025.09.01.673549

Category: Plant Biology

Model Organism: General

AI Summary

The manuscript has been withdrawn due to potential bureaucratic conflicts concerning the research location and author affiliations, and the authors request that it not be cited.

withdrawal bureaucracy non-citable

What Large Language Models Know About Plant Molecular Biology

Authors: Fernandez Burda, M., Ferrero, L., Gaggion, N., Fonouni-Farde, C., Iglesias, M. J., Fragkostefanakis, S., Tonelli, M. L., Zanetti, M. E., Krapp, A., Mencia, R., Romani, F., Muschietti, J. P., Mansilla, N., Casal, J., Pagnussat, L. A., Ballare, C. L., Mammarella, M. F., Blanco, F. A., Roy, S., Maroniche, G. A., Rivarola, M., Fiol, D. F., Cubas, P., Dezar, C., Casati, P., Ibanez, F., Fernanda, d. C.-N., Staiger, D., Fusari, C. M., Auge, G., Arana, M. V., Parmar, R., Zhang, W., Mathur, S., Verslues, P. E. V., Manavella, P. A., Mateos, J. L., Bouche, N., Lucero, L. E., Drincovich, M. F., Traubenik,

Date: 2025-09-04 · Version: 1
DOI: 10.1101/2025.08.31.672925

Category: Plant Biology

Model Organism: General

AI Summary

The authors introduce MO_SCPLOWOC_SCPLOWBO_SCPLOWIC_SCPLOWPO_SCPLOWLANTC_SCPLOW, a benchmark consisting of 565 expert‑curated and 1,075 synthetic multiple‑choice questions to evaluate large language models (LLMs) in plant molecular biology. Benchmarking seven chat‑based LLMs showed high multiple‑choice accuracy (>75%) but revealed systematic biases, factual errors, hallucinations, and a performance link to citation frequency of source literature.

large language models plant molecular biology benchmark dataset multiple-choice evaluation model bias and hallucination
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