Arguments for and against self and non-self root recognition in plants

Root–root interaction research gained more and more attention over the past few years. Roots are pivotal for plant survival because they ensure uptake of water and nutrients. Therefore, detection of adjacent roots might lead to competitive advantages. Several lines of experimental evidence suggest that roots have ways to discriminate non-related roots, kin, and—importantly—that they can sense self/non-self roots to avoid intra-plant competition. In this mini-review, the existence of self/non-self recognition in plant roots will be discussed and the current knowledge on the mechanisms that could be involved will be summarized. Although the process of identity recognition is still not completely understood, interesting data are available and emerging new technologies will certainly aid to better understand this research field that can have an important biological, ecological, and agricultural impact

Rapid toxicity assessment of six antifouling booster biocides using a microplate-based chlorophyll fluorescence in Undaria pinnatifida gametophytes

Biocides of antifouling agents can cause problems in marine ecosystems by damaging to non-target algal species. Aquatic bioassays are important means of assessing the quality of water containing mixtures of contaminants and of providing a safety standard for water management in an ecological context. In this study, a rapid, sensitive and inexpensive test method was developed using free-living male and female gametophytes of the brown macroalga Undaria pinnatifida. A conventional fluorometer was employed to evaluate the acute (48 h) toxic effects of six antifouling biocides: 4,5-Dichloro-2-octyl-isothiazolone (DCOIT), diuron, irgarol, medetomidine, tolylfluanid, zinc pyrithione (ZnPT). The decreasing toxicity in male and female gametophytes as estimated by EC50 (effective concentration at which 50% inhibition occurs) values was: diuron (0.037 and 0.128 mg l(-1), respectively) > irgarol (0.096 and 0.172 mg l(-1), respectively) > tolylfluanid (0.238 and 1.028 mg l(-1), respectively) > DCOIT (1.015 and 0.890 mg l(-1), respectively) > medetomidine (12.032 and 12.763 mg l(-1), respectively). For ZnPT, 50% fluorescence inhibition of U. pinnatifida gametophytes occurred at concentrations above 0.4 mg l(-1). The Undaria method is rapid, simple, practical, and cost-effective for the detection of photosynthesis-inhibiting biocides, thus making a useful tool for testing the toxicity of antifouling agents in marine environments

Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data

Even though deep neural networks (DNNs) achieve state-of-the-art results for a number of problems involving genomic data, getting DNNs to explain their decision-making process has been a major challenge due to their black-box nature. One way to get DNNs to explain their reasoning for prediction is via attribution methods which are assumed to highlight the parts of the input that contribute to the prediction the most. Given the existence of numerous attribution methods and a lack of quantitative results on the fidelity of those methods, selection of an attribution method for sequence-based tasks has been mostly done qualitatively. In this work, we take a step towards identifying the most faithful attribution method by proposing a computational approach that utilizes point mutations. Providing quantitative results on seven popular attribution methods, we find Layerwise Relevance Propagation (LRP) to be the most appropriate one for translation initiation, with LRP identifying two important biological features for translation: the integrity of Kozak sequence as well as the detrimental effects of premature stop codons.Comment: Accepted for publication at the 36th Conference on Neural Information Processing Systems (NeurIPS 2022), Workshop on Learning Meaningful Representations of Life (LMRL

Strigolactones as an auxiliary hormonal defence mechanism against leafy gall syndrome in Arabidopsis thaliana

Leafy gall syndrome is the consequence of modified plant development in response to a mixture of cytokinins secreted by the biotrophic actinomycete Rhodococcus fascians. The similarity of the induced symptoms with the phenotype of plant mutants defective in strigolactone biosynthesis and signalling prompted an evaluation of the involvement of strigolactones in this pathology. All tested strigolactone-related Arabidopsis thallana mutants were hypersensitive to R. fascians. Moreover, treatment with the synthetic strigolactone mixture GR24 and with the carotenoid cleavage dioxygenase inhibitor D2 illustrated that strigolactones acted as antagonistic compounds that restricted the morphogenic activity of R. fascians. Transcript profiling of the MORE ILLARY GROWTH1 (M 1), M, M 3, M, 4, and BRANCHED1 (BRC1) genes in the wild-type Columbia-0 accession and in different mutant backgrounds revealed that upregulation of strigolactone biosynthesis genes was triggered indirectly by the bacterial cytokinins via host-derived auxin and led to the activation of BRC1 expression, inhibiting the outgrowth of the newly developing shoots, a typical hallmark of leafy gall syndrome. Taken together, these data support the emerging insight that balances are critical for optimal leafy gall development: the long-lasting biotrophic interaction is possible only because the host activates a set of countermeasures including the strigolactone response in reaction to bacterial cytokinins to constrain the activity of R. fascians

Pathogenicity strategies in the gall-forming bacterium Rhodococcus fascians

C

Strigolactones spatially influence lateral root development through the cytokinin signaling network

Strigolactones are important rhizosphere signals that act as phytohormones and have multiple functions, including modulation of lateral root (LR) development. Here, we show that treatment with the strigolactone analog GR24 did not affect LR initiation, but negatively influenced LR priming and emergence, the latter especially near the root-shoot junction. The cytokinin module ARABIDOPSIS HISTIDINE KINASE3 (AHK3)/ARABIDOPSIS RESPONSE REGULATOR1 (ARR1)/ARR12 was found to interact with the GR24-dependent reduction in LR development, because mutants in this pathway rendered LR development insensitive to GR24. Additionally, pharmacological analyses, mutant analyses, and gene expression analyses indicated that the affected polar auxin transport stream in mutants of the AHK3/ARR1/ARR12 module could be the underlying cause. Altogether, the data reveal that the GR24 effect on LR development depends on the hormonal landscape that results from the intimate connection with auxins and cytokinins, two main players in LR development

Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Background: Rice (Oryza sativa) is one of the most important model crops in plant research. Despite its considerable advantages, (phenotypic) bioassays for rice are not as well developed as for Arabidopsis thaliana. Here, we present a phenotype-based screening method to study shoot-related parameters of rice seedlings via an automated computer analysis. Results: The phenotype-based screening method was validated by testing several compounds in pharmacological experiments that interfered with hormone homeostasis, confirming that the assay was consistent with regard to the anticipated plant growth regulation and revealing the robustness of the set-up in terms of reproducibility. Moreover, abiotic stress tests using NaCl and DCMU, an electron transport blocker during the light dependent reactions of photosynthesis, confirmed the validity of the new method for a wide range of applications. Next, this method was used to screen the impact of semi-purified fractions of marine invertebrates on the initial stages of rice seedling growth. Certain fractions clearly stimulated growth, whereas others inhibited it, especially in the root, illustrating the possible applications of this novel, robust, and fast phenotype-based screening method for rice. Conclusions: The validated phenotype-based and cost-efficient screening method allows a quick and proper analysis of shoot growth and requires only small volumes of compounds and media. As a result, this method could potentially be used for a whole range of applications, ranging from discovery of novel biostimulants, plant growth regulators, and plant growth-promoting bacteria to analysis of CRISPR knockouts, molecular plant breeding, genome-wide association, and phytotoxicity studies. The assay system described here can contribute to a better understanding of plant development in general

RENEB intercomparison exercises analyzing micronuclei (Cytokinesis-block Micronucleus Assay)

Purpose: In the framework of the ‘Realizing the European Network of Biodosimetry’ (RENEB) project, two intercomparison exercises were conducted to assess the suitability of an optimized version of the cytokinesis-block micronucleus assay, and to evaluate the capacity of a large laboratory network performing biodosimetry for radiation emergency triages. Twelve European institutions participated in the first exercise, and four non-RENEB labs were added in the second one. Materials and methods: Irradiated blood samples were shipped to participating labs, whose task was to culture these samples and provide a blind dose estimate. Micronucleus analysis was performed by automated, semi-automated and manual procedures. Results: The dose estimates provided by network laboratories were in good agreement with true administered doses. The most accurate estimates were reported for low dose points (≤ 0.94 Gy). For higher dose points (≥ 2.7 Gy) a larger variation in estimates was observed, though in the second exercise the number of acceptable estimates increased satisfactorily. Higher accuracy was achieved with the semi-automated method. Conclusion: The results of the two exercises performed by our network demonstrate that the micronucleus assay is a useful tool for large-scale radiation emergencies, and can be successfully implemented within a large network of laboratories.VII Programa Marco de Investigación y Desarrollo (VIIPM) de la Unión Europea. nº 295513University Development Cooperation "VLIR Own Initiative Programme" enetre Bélgica and Sudáfrica. ZEIN2011PR38

Unraveling the MAX2 protein network in Arabidopsis thaliana : identification of the protein phosphatase PAPP5 as a novel MAX2 interactor

The F-box protein MORE AXILLARY GROWTH 2 (MAX2) is a central component in the signaling cascade of strigolactones (SLs) as well as of the smoke-derived karrikins (KARs) and the so far unknown endogenous KAI2 ligand (KL). The two groups of molecules are involved in overlapping and unique developmental processes, and signal-specific outcomes are attributed to perception by the paralogous α/β-hydrolases DWARF14 (D14) for SL and KARRIKIN INSENSITIVE 2/HYPOSENSITIVE TO LIGHT (KAI2/HTL) for KAR/KL. In addition, depending on which receptor is activated, specific members of the SUPPRESSOR OF MAX2 1 (SMAX1)-LIKE (SMXL) family control KAR/KL and SL responses. As proteins that function in the same signal transduction pathway often occur in large protein complexes, we aimed at discovering new players of the MAX2, D14, and KAI2 protein network by tandem affinity purification in Arabidopsis cell cultures. When using MAX2 as a bait, various proteins were copurified, among which were general components of the Skp1-Cullin-F-box complex and members of the CONSTITUTIVE PHOTOMORPHOGENIC 9 signalosome. Here, we report the identification of a novel interactor of MAX2, a type 5 serine/threonine protein phosphatase, designated PHYTOCHROME-ASSOCIATED PROTEIN PHOSPHATASE 5 (PAPP5). Quantitative affinity purification pointed at PAPP5 as being more present in KAI2 rather than in D14 protein complexes. In agreement, mutant analysis suggests that PAPP5 modulates KAR/KL-dependent seed germination under suboptimal conditions and seedling development. In addition, a phosphopeptide enrichment experiment revealed that PAPP5 might dephosphorylate MAX2 in vivo independently of the synthetic SL analog, rac-GR24. Together, by analyzing the protein complexes to which MAX2, D14, and KAI2 belong, we revealed a new MAX2 interactor, PAPP5, that might act through dephosphorylation of MAX2 to control mainly KAR/KL-related phenotypes and, hence, provide another link with the light pathway

Reappraisal of the toxicity test method using the green alga Ulva pertusa Kjellman (Chlorophyta),

This study was aimed to develop an objective way of quantifying the reproductive status of the green macroalga, Ulva pertusa using a vital stain and programmed automated analysis (by Image J program). The EC50 values (with 95% CI), the concentrations of toxicants inducing a reduction of 50% in sporulation after 96 h exposure, from the newly developed method were similar to those obtained by the conventional method: 0.651 (0.598-0.705) mg l(-1) for Cd, 0.144 (0.110-0.162) mg l(-1) for Cu, 0.180 (0.165-0.195) mg l(-1) for atrazine, 0.076 (0.049-0.094) mg l(-1) for diuron and 30.6 (26.5-34.4) ml l(-1) for DMSO, respectively. When the EC50 values from this study were compared to that those from literatures, the sensitivity for some toxicants was similar or higher than that of U. fasciata (1.930 mg l(-1) for germination for Cd), U. armoricana (0.250 mg l(-1) for Fv/Fm for Cu), U. reticulata (0.126-1.585 mg l(-1) for growth for Cu), and U. intestinalis (0.650 mg l(-1) for Fv/Fm for atrazine). The subjective views of the experimental performers can be eliminated using the newly developed method. The Ulva method gave consistent responses to Cu and Cd of internationally allowable ranges for effluents, implying that the method is a useful tool for monitoring industrial wastewaters containing these metals