Czechia

Plant stress phenotyping based on image-analysis techniques can facilitate targeted interventions and optimize management practices. However, considering abiotic stresses – especially under the influence of climate changes – various technical challenges still need to be overcome, and there is a need to identify functional traits that can be used as markers to monitor plants health status accurately and rapidly. This study aimed to develop a machine learning model able to detect salt stress status in Phaseolus vulgaris, by combining image-based approaches and minimal morpho-physiological/biochemical analyses. Therefore, a flexible pipeline was created, starting with the data acquisition and analysis (feature extraction) followed by the feature selection phase, which involved statistical approaches such as principal component analysis and correlation analysis. Finally, two predictive models based on decision trees were developed to detect stress presence (2-class model) and intensity (3-class model). Specific biochemical parameters and image-analysis-derived traits, like malondialdehyde content, chroma difference and chroma ratio indexes, resulted as key features in categorizing both non-stressed and stressed plants (model’s precision: 0.91) as well as stress intensity (model’s precision: 0.84). These results highlighted the potential of machine learning techniques and automated image-based analysis in plant science. In the future, the models’ reliability and accuracy will be improved by adjusting the pipeline to different plant growth stages and specific leaf characteristics, and testing the model across different plant species and abiotic stresses (e.g. drought, temperature).

SEB Conference Prague 2024

Enhancing plant stress phenotyping with machine learning: a novel approach for salt stress detection in Phaseolus vulgaris

phaseolus vulgaris

salt stress

phenotyping

machine learning

technical paper

If you see this page it means you are not logged in or registered.

If you  feel like you see this message by mistake please make sure you are logged in with the email you registered with.

If you are not registered yet you can do so [**here**](https://www.sebiology.org/events/seb-conference-prague-2024/registration2024.html). 

Please login or register

SEB’s Annual Conference is celebrated for creating the perfect composition of research, new discoveries and collaborative connections. Be creative and innovative by exchanging ideas and knowledge with masters of biology from all over the world.

How steeply metabolic rate scales with body mass has been investigated and debated for a century; however, little is known about scaling within the same individuals as they grow, let alone how environmental variability affects such ontogenetic scaling relationships. We quantified the ontogenetic (within-individual) scaling of metabolic and growth rates of juvenile rainbow trout (Oncorhynchus mykiss) at 10°C after different early-life temperature treatments: (1) 10°C throughout the experiment; (2) 14°C as eggs, then 10°C from hatching onwards; and (3) 10°C as eggs, then 14°C from hatching to completion of the yolk-sac stage, then back to 10°C (10°C being the optimal temperature and 14°C simulating an early-life warm-spell). The steepness (scaling exponent) of both metabolic and growth rate scaling varied significantly but modestly among individuals. No difference was found in the scaling of standard metabolic rate (SMR) between treatments, but maximum metabolic rate (MMR) and aerobic scope (AS) scaled shallower in the 14°C-yolk group, whereas growth rate scaled steeper in the 14°C-egg group. This shows that a warm-spell can have lasting and negative carryover effects on juvenile aerobic performance (MMR and AS) if warming occurs in the yolk-sac stage, and induce compensatory growth if warming occurs in the egg stage. Correlations between metabolic and growth scaling exponents for individual fish further indicated that compensatory growth did not come at the expense of an elevated SMR but traded off with MMR and AS. The specific ontogenetic timing of temperature variability thus affects ontogenetic scaling of metabolic and growth rates differently and independently.

Early-life temperature variability has life-stage-specific effects on later-life ontogenetic scaling of fish metabolic and growth rates

Birds can adaptively regulate body mass in response to the cost-benefit trade-off between risks of starvation and predation. Despite this, little is known about how birds actually monitor, detect, and interpret their body mass and the mechanisms employed to regulate or adjust body mass to match their current ecological conditions. Using zebra finches, we experimentally increased perceived mass via attachment of weighted backpacks and provided the birds with either ad libitum standard mixed-seed diet or supplementary high-fat to investigate (a) how birds assess their own body mass and (b) the mechanisms birds employ to adjust mass. In both experiments, independent of diet treatment, birds with backpacks rapidly lost mass and reduced overall activity, time spent in active behaviors and food intake. We found no evidence that mass loss was due to stress associated with backpack attachment - there was no difference in plasma corticosterone concentrations directly after rapid mass loss. We found evidence that birds likely interpret body mass via a physical mechanosensory pathway rather than a physiological pathway - rapid loss of mass was not linked to changes in plasma metabolites (glycerol or triglyceride concentrations). Our results suggest that the process of energy balance and mass regulation can involve a greater array of mechanisms than simply matching energy in (food consumed) to energy out. Zebra finches are able to force a negative energy balance through other, unidentified, mechanisms, even while maintaining high-fat dietary intake and reducing overall activity.

The enviable ability of zebra finches to get slim, even when eating a tasty high-fat diet

SETBP1 haploinsufficiency disorder (SETBP1-HD) is a rare human genetic disorder (currently only 131 known cases) that affects development —particularly neurodevelopment. Individuals carry a hemizygous deletion or LoF in the SETBP1 region, which results in insufficient production of SET binding protein 1. Typically, SET binding protein 1 alters histone methylation to regulate the expression of target genes. When SETBP1 expression is low, key developmental genes are underexpressed, leading to developmental delay phenotypes. Symptoms include childhood hypotonia, motor development delay, intellectual and learning disabilities, anxiety, autism spectrum disorder, and attention-deficit/hyperactivity disorder. The aim of this study is to establish whether zebrafish represent a useful biomedical model for SETBP1-HD. Specifically, we deleted a single copy of SETBP1 via CRISPR transgenesis to investigate whether zebrafish SETBP1 hemizygosity induces the behavioral syndromes characteristic of human patients. Social and cognitive behaviours were assessed through larval behavioural assays; including thigmotaxis, startle response, and light dark response. A zebrafish model of SETBP1-HD will increase pathophysiological understanding of the disease and help to determine the molecular underpinnings of disease-linked variants, including Schinzel-Giedion syndrome and leukemia. Zebrafish represent a great model for high-throughput drug screening, which means that our transgenic SETBP1-HD lines may aid in the screening and development of potential SETBP1-HD therapies.

Modelling SETBP1 Haploinsufficiency Disorder (SETBP1-HD) in Zebrafish (Danio rerio)

In recent years, the COVID-19 virus pandemic has threatened public health globally. In several nations, the pandemic's aftermath is still affecting the human population. Numerous mutant strains of SARS CoV-2 spreading caused several waves of infection. These variants were linked to high infectivity or high mortality. But in the face of such assaults, human immune system developed a defence mechanism of its own against the infection to deal with cytokine storm, antibody neutralization escape and multiple organ failure. In order to boost the defence mechanism and SARS CoV-2 broadly being a respiratory disorder was targeted with multiple remedial strategies procured from traditional knowledge of medicinal plants. A survey was conducted to surmise the usage of such medicinal plants with therapeutic properties during the pandemic in a random population in West Bengal, India. Our data demonstrates the most often utilized raw traditional medicines. To deal with clinical manifestations associated with SARS CoV-2 (such as cough and cold) and boosting immunity, Tulsi (Ocimum tenuiflorum) was the most widely used plant which is easy to manage in kitchen gardens and have a high growth rate on the Indian subcontinent. This survey-based study is done to correlate with the efficacy of Tulsi in combating infectious diseases from common cough and cold to COVID-19. Regulated long-term use of these medicinal plants will also help avoid a number of prevalent illnesses and be advantageous for household healthcare. 


Immune Boosting Against SARS CoV-2 Infection: An Approach to Traditional Medicine

Climate change is impacting temperatures globally, altering the frequency, intensity, and extent of extreme events such as heatwaves and droughts. This modification poses a challenge to biodiversity worldwide and presents a particular threat to tropical biota, which already reside close to their thermal maxima. Fish play a crucial role in the diet of the Amazon, particularly for traditional communities that rely on them as their primary protein source. The Amazon boasts the largest diversity of freshwater fish globally, each exhibiting numerous physiological and behavioural adaptations to thrive in the warm and often hypoxic waters of the Amazon. Comprehending how rising temperatures affect Amazonian fish species is essential for policymakers tasked with crafting strategies to safeguard the bio and sociodiversity of the Amazon. Faced with increasing temperatures, fish respond by adjusting their physiology and behaviour until they reach their thermal limit. Traditional thermal tolerance tests conventionally use the loss of equilibrium as the final endpoint for determining thermal limits. However, well before this loss of equilibrium, fish undergo physiological and behavioural adjustments to cope with the changing conditions. Monitoring behavioural changes during critical thermal tolerance tests provides insights into how fish utilise physiological and behavioural adaptations in this progressively warmer environment. We will elucidate behavioural changes observed during thermal tolerance tests of various Amazonian species and explore their connection to physiological adaptations to the Amazonian environment. Additionally, we will consider how these changes can serve as early warning signs of thermal vulnerability for fish species.

Dealing with changes in an extreme world: how is living in tropical waters?

Enhancing fertilizer use efficiency is a key aspect in attaining sustainable agriculture objectives, aiming to curtail costs, mitigate greenhouse gas emissions, and alleviate pollution stemming from nutrient runoff. While extensive research has delved into fertilizer utilization in cereal crops, understanding the broader monocot plant community could unveil novel insights. In this study, we investigated nitrogen uptake efficiency across three species—Anthurium andreanum, Epipremnum aureum, and Philodendron scandens—belonging to the Araceae family. Like maize, these species are characterized by root development from both subterranean and aerial tissues. Employing 15N-labeled sources of nitrate, ammonium, and glycine, we assessed nitrogen uptake capacity in both aerial and soil-originating roots, juxtaposed with similar investigations conducted on maize brace roots from field-grown plants. Intriguingly, our findings revealed a positive correlation between nitrogen uptake capacity and root thickness across all species. Notably, nitrate exhibited the strongest correlation with root thickness, succeeded by ammonium, while glycine uptake displayed variable patterns among species. Further examination of species-specific traits encompassing growth form, anatomy, and physiological attributes elucidates finer nuances in nitrogen uptake dynamics. Unravelling these parallels and distinctions among diverse species not only informs translational advancements in crop breeding but also underscores opportunities for enhancing urban greenspaces.

Inside out or outside in? Using aroid indoor plants and field grown maize to gain translational insights about nitrogen uptake patterns.

As Journal of Experimental Botany (JXB) editors, we often receive manuscripts focusing on phenotyping drought tolerance and plant responses to water deficit. Despite extensive research identifying multiple drought tolerance genes in recent decades, practical field application remains limited. We have observed that the quality of research in this field frequently suffers from flawed experimental designs, inconsistent terminology, overinterpretation of data, or unrealistic lab-to-field extrapolations. To tackle these challenges, the JXB editorial board established a working group to guide better experiment design, data interpretation, and result reporting, focusing on experiments performed in supposedly ‘controlled conditions’. Our recommendations include:
• Establishing clear, testable hypotheses and objectives moving away from vague goals like "improving drought tolerance".
• Utilizing precise, consensus-driven terminology to clearly communicate objectives and hypotheses. 
• Designing experiments that adequately account for the complexities of genotype-environment (GxE) interactions, by including sufficient biological replicates and conducting multiple experiments as well as measuring soil, plant and environmental parameters in parallel to monitor complex cross-interactions. 
• Considering the impact of whole-plant transpiration on soil-moisture and stress levels, stemming from interactions with pot sizes and soil-substrate, and acknowledging that plant responses to drought depend on, and also affect, their developmental stage.
These guidelines aim to enhance research quality, contributing vital knowledge to combat the growing threat of drought to agriculture.


Guidelines for designing and interpreting drought experiments in controlled conditions 

The General Control Non–derepressible 5 (GCN5) protein is a histone acetyltransferase that acetylates Lys residues in the N-terminal tail of the core histone H3. GCN5 interacts with the Alteration / Deficiency in Activation 2b (ADA2b), which enhances its ability to acetylate histones. These two proteins regulate multiple developmental processes, including reproductive fitness, in Arabidopsis thaliana. This study demonstrates that GCN5 and ADA2b affect anther dehiscence and pollen tube growth. Anthers of ada2b-1 do not release their pollen, leading to seed absence, while gcn5-1 partially releases its pollen and carries an overall reduced seed set inside a smaller silique. Anther indehiscence is supported by RNA-sequencing data, which revealed that both mutants exhibit down-regulation of genes implicated in their anther development. When gcn5-1 pollen was used to fertilise emasculated Ws-2 flowers, the resulting siliques had a wild-type phenotype with a complete seed set, indicative of proper pollen tube growth. The transcriptomic analysis also showed that ada2b-1 inflorescences, contrary to gcn5-1, exhibit down-regulation of pollen tube growth-related genes, including transcription factors. Therefore, GCN5 and ADA2b are positive regulators of anther and pollen development and are essential contributors to the reproductive success of Arabidopsis thaliana.

This work is supported by the Hellenic Foundation for Research and Innovation (HFRI) Grant Number 73333. PI Konstantinos Vlachonasios

GCN5 and ADA2b regulate pollen development and function in Arabidopsis thaliana.

After recovery from stress by pests and diseases, plants maintain an elevated state of defence. This induced resistance (IR) is often based on defence priming, which enables a faster and stronger immune response upon recurrent exposure to the same type of attacker. We study the epigenetic basis of this form of immune memory. We have recently shown that exposure of seedlings to herbivory induces long-lasting DNA de-methylation at transposable elements (TEs), which prime genomically distant defence genes. Although more variable in intensity, immune memory can partially be transmitted to the offspring of stressed plants. This heritable IR is proportional to the stress encountered in previous generations and involves the DNA demethylase ROS1. To advance our understanding of how DNA demethylation controls immune memory, we are following artificial strategies to manipulate the plant methylome. Using epigenetic recombinant inbred lines (epiRILs), which share the same genetic (wild-type) background but vary in heritable DNA methylation of TE-rich regions, we have previously identified epialleles that prime defence gene expression and provide high levels of disease resistance without negative effects on plant growth. To translate this form of epigenetic disease resistance to crops, we are currently developing a new method to introduce dosed amounts of ROS1-dependent DNA hypo-methylation into plant genomes. This tool will not only allow us to induce long-lasting resistance against pests and diseases, but also explore the epigenetic mechanisms by which plants establish, maintain and reset immune memory.



Primed plants do not forget: epigenetic drivers of immune memory

The development of multicellular organisms requires the integration of signals controlling and coordinating cell fates. This process relies on numerous regulatory events that impact both chromatin structure and transcription. Chromatin undergoes global modifications at specific times and within specific cell subsets to dictate distinct cellular programs. However, the mechanisms by which chromatin is modulated during development remains highly elusive.
Plants are ideal models for investigating cell-specific chromatin remodelling. Plant cells do not move, and their plastic development is the result of an exquisite interaction between environmental and intrinsic signals. How does this signal crosstalk guide chromatin orchestration?
Our findings, derived from the study of flowering time in Arabidopsis may bring some answers. One key function of the plant hormone Brassinosteroids is to regulate the vegetative to reproductive fate transition of the cells in flower primordium. BR signalling acts through inactivation of GSK3 kinases responsible for the modulation of other protein’s activity. Interestingly, in contrast to other hormones, BR do not undergo long distant transport. We discovered that the BR dependent GSK3s bind and phosphorylate a central component of chromatin machinery involved in establishing and maintaining transcriptional programs. This finding may help explaining how chromatin is orchestrated in specific cells to guide cell fate transitions. 


Enhancing plant stress phenotyping with machine learning: a novel approach for salt stress detection in Phaseolus vulgaris

Downloads

Next from SEB Conference Prague 2024

Early-life temperature variability has life-stage-specific effects on later-life ontogenetic scaling of fish metabolic and growth rates

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Enhancing plant stress phenotyping with machine learning: a novel approach for salt stress detection in Phaseolus vulgaris

.css-70qvj9{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-align-items:center;-webkit-box-align:center;-ms-flex-align:center;align-items:center;}Downloads

Next from SEB Conference Prague 2024

Early-life temperature variability has life-stage-specific effects on later-life ontogenetic scaling of fish metabolic and growth rates

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Downloads