Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on 1xed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, acquisition settings even on non plant samples. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface (https://github.com/hci-unihd/plant-seg).

Timely perception of adverse environmental changes is critical for survival. Dynamic changes in gases are important cues for plants to sense environmental perturbations, such as submergence. In Arabidopsis thaliana , changes in oxygen and nitric oxide (NO) control the stability of ERFVII transcription factors. ERFVII proteolysis is regulated by the N-degron pathway and mediates adaptation to flooding-induced hypoxia. However, how plants detect and transduce early submergence signals remains elusive. Here we show that plants can rapidly detect submergence through passive ethylene entrapment and use this signal to pre-adapt to impending hypoxia. Ethylene can enhance ERFVII stability prior to hypoxia by increasing the NO-scavenger PHYTOGLOBIN1. This ethylene-mediated NO depletion and consequent ERFVII accumulation pre-adapts plants to survive subsequent hypoxia. Our results reveal the biological link between three gaseous signals for the regulation of flooding survival and identifies key regulatory targets for early stress perception that could be pivotal for developing flood-tolerant crops.

25 Timely perception of adverse environmental changes is critical for survival. Dynamic 26 changes in gases are important cues for plants to sense environmental perturbations, such 27 as submergence. In Arabidopsis thaliana, changes in oxygen and nitric oxide (NO) control 28 the stability of ERFVII transcription factors. ERFVII proteolysis is regulated by the N-29 degron pathway and mediates adaptation to flooding-induced hypoxia. However, how 30 plants detect and transduce early submergence signals remains elusive. Here we show that 31 plants can rapidly detect submergence through passive ethylene entrapment and use this 32 signal to pre-adapt to impending hypoxia. Ethylene can enhance ERFVII stability prior to 33 hypoxia by increasing the NO-scavenger PHYTOGLOBIN1. This ethylene-mediated NO 34 depletion and consequent ERFVII accumulation pre-adapts plants to survive subsequent 35 hypoxia. Our results reveal the biological link between three gaseous signals for the 36 regulation of flooding survival and identifies novel regulatory targets for early stress 37 perception that could be pivotal for developing flood-tolerant crops. 38 39 42 cellular oxygen (O 2 ) deprivation (hypoxia) and survival strongly depends on molecular responses 43 that enhance hypoxia tolerance 2,3 . In submerged plant tissues the limited gas diffusion causes 44 passive ethylene accumulation. This rapid ethylene build-up can occur prior to the onset of 45 severe hypoxia, making it a timely and reliable signal for submergence 4,5 . In several plant 46 species, ethylene regulates adaptive responses to flooding involving morphological and 47anatomical modifications that prevent hypoxia 5 . Surprisingly, ethylene has so far not been 48 linked to metabolic responses that reduce hypoxia damage. In addition, how plants detect and 49 transduce early submergence signals to enhance survival remains elusive. 50 Here we show that plants can quickly detect submergence using passive ethylene accumulation 51 and integrate this signal to acclimate to subsequent hypoxia. This ethylene-mediated hypoxia 52 acclimation is dependent on enhanced ERFVII stability prior to hypoxia. We show that ethylene 53 limits ERFVII proteolysis under normoxic conditions by increasing the NO-scavenger 54 3 PHYTOGLOBIN1. Our results reveal a molecular mechanism that plants use to integrate early 55 stress signals to pre-adapt to forthcoming severe stress. 57 Results 58Early ethylene signalling enhances hypoxia acclimation 59 To unravel the spatial and temporal dynamics of ethylene signalling upon plant submergence, we 60 monitored the nuclear accumulation of ETHYLENE INSENSITIVE 3 (EIN3) 6-9 , an essential 61 transcription factor for mediating ethylene responses. We show, through an increase in EIN3- 62GFP fluorescence signal, that ethylene is rapidly perceived (within 1-2 h) in Arabidopsis 63 thaliana (hereafter Arabidopsis) root tips upon submergence (Supplementary Figure 1a-c). An 64 ethylene or submergence pre-treatment of only 4 hours was sufficient to increase root m...

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Orchard, S. et al. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42, D358-363,

SummaryThe control of cell position and division act in concert to dictate multicellular organization in tissues and organs. How these processes shape global order and molecular movement across organs is an outstanding problem in biology. Using live 3D imaging and computational analyses, we extracted networks capturing cellular connectivity dynamics across the Arabidopsis shoot apical meristem (SAM) and topologically analyzed the local and global properties of cellular architecture. Locally generated cell division rules lead to the emergence of global tissue-scale organization of the SAM, facilitating robust global communication. Cells that lie upon more shorter paths have an increased propensity to divide, with division plane placement acting to limit the number of shortest paths their daughter cells lie upon. Cell shape heterogeneity and global cellular organization requires KATANIN, providing a multiscale link between cell geometry, mechanical cell-cell interactions, and global tissue order.

Variability is observed in biology across multiple scales, ranging from populations, individuals, and cells to the molecular components within cells. This review explores the sources and roles of this variability across these scales, focusing on seeds. From a biological perspective, the role and the impact this variability has on seed behaviour and adaptation to the environment is discussed. The consequences of seed variability on agricultural production systems, which demand uniformity, are also examined. We suggest that by understanding the basis and underlying mechanisms of variability in seeds, strategies to increase seed population uniformity can be developed, leading to enhanced agricultural production across variable climatic conditions.

The relationship between expression of a negative regulator of GA signal transduction (RGL2) belonging to the DELLA gene family and repression of Arabidopsis seed germination has been studied (Lee S, Cheng H, King KE, Wang W, He Y, Hussain A, Lo J, Harberd NP, Peng J [2002] Genes and Development 16: 646-658). There is one DELLA gene (LeGAI) present in tomato (Lycopersicon esculentum Mill.), which is expressed in both vegetative and reproductive tissues. During germination of wildtype tomato seed, there was no decline in the expression of LeGAI in either the embryo or the endosperm. Rather, LeGAI transcripts increased in these tissues following imbibition and remained high during and following germination. A similar increase in LeGAI transcripts occurred in the endosperm and embryo of GA-treated gib-1 mutant seed during and following germination. Likewise in soybean (Glycine max) seed, there was no decline in the expression of two DELLA genes in the radicle before or after germination. Upon reexamination of RGL2 in Arabidopsis seeds, a decline in its expression was noted but only after radicle emergence, i.e. after germination had been completed. Taken together, these data are consistent with GA-induced down-regulation of DELLA genes not being a prerequisite for germination of tomato, soybean, and Arabidopsis seeds.