Czechia

This study addresses the challenge of detecting grain spikes in images for crop yield assessment. Grain spikes are crucial but difficult to discern due to their minimal presence and similarity to surrounding leaves, posing a challenge even for advanced deep-learning networks. We enhance detection by refining the Faster R-CNN (FRCNN) architecture, simplifying feature extraction layers, and adding a global attention module. Testing on diverse European wheat varieties, including complex bushy types, our modified FRCNN (FRCNN-A) outperforms the standard model, achieving a mean Average Precision (mAP) increase from 76.0% to 81.0%. Compared to the Swin Transformer&#39;s 83.0% mAP, our model shows competitive performance. We also tested Yolov8 and Yolov4 models, achieving 0.79 and 0.78 mAP, respectively. The model was deployed on the PlantScreenTM system to extract phenotypes such as awn detection and spike count in late reproductive stage plants.


SEB Conference 2024

Enhancing Spike Detection in Greenhouse-Grown Grain Crops Using Attention-Based Deep Learning Models

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SEB Conference 2025

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.

This study addresses the challenge of detecting grain spikes in images for crop yield assessment. Grain spikes are crucial but difficult to discern due to their minimal presence and similarity to surrounding leaves, posing a challenge even for advanced deep-learning networks. We enhance detection by refining the Faster R-CNN (FRCNN) architecture, simplifying feature extraction layers, and adding a global attention module. Testing on diverse European wheat varieties, including complex bushy types, our modified FRCNN (FRCNN-A) outperforms the standard model, achieving a mean Average Precision (mAP) increase from 76.0% to 81.0%. Compared to the Swin Transformer's 83.0% mAP, our model shows competitive performance. We also tested Yolov8 and Yolov4 models, achieving 0.79 and 0.78 mAP, respectively. The model was deployed on the PlantScreenTM system to extract phenotypes such as awn detection and spike count in late reproductive stage plants.


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GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) is a histone acetyltransferase in Arabidopsis thaliana involved in numerous biological processes, including flower development. Previous studies have demonstrated GCN5's interaction with the CLAVATA (CLV) pathway, influencing gynoecium development potentially through modulating auxin and cytokinin dynamics and regulating WUSCHEL (WUS) expression. In clv1gcn5 double mutants, noticeable phenotypic alterations include reduced or absent valves, an enlarged stigma, and an elongated gynophore, indicative of disruptions in both apical-basal and mediolateral axes of the gynoecium. SPATULA (SPT), a bHLH transcription factor, is a pivotal regulator in gynoecium development. Intriguingly, this work demonstrates that SPT mutations partially alleviate clv1gcn5 phenotypes; specifically, they restore the formation of valves in the ovary. Transcriptomic analysis of gynoecium mutants, including spt, clv1, gcn5 and the various genetic combinations, reveals their significant impact on apical-basal, mediolateral, and adaxial-abaxial polarity axes. Genes such as STY1/2, PID, and TCP15 governing apical-basal polarity were misexpressed in clv1gcn5 mutants and showed either complete or partial restoration of their levels in sptclv1gcn5 gynoecia. Similarly, mediolateral genes, including CUC2, FIL, YAB3, and JAG, downregulated in clv1gcn5, were reinstated in sptclv1gcn5 mutants. Notably, adaxial-abaxial factors like REV, ATHB4, and AS1 follow a similar pattern, suggesting that GCN5, CLV1 and SPT are essential players in the proper determination of polarity axes in the Arabidopsis gynoecium.
This study unveils the intricate interplay among GCN5, CLV1, and SPT, underscoring their pivotal roles in orchestrating gene expression and polarity determination during Arabidopsis thaliana gynoecium development.

Transcription factor SPT interacts with CLAVATA signaling and GCN5 acetyltransferase to affect polarity axes in Arabidopsis thaliana gynoecium

Plasticity enables organisms to extend their tolerance limits, but the physiological basis of plastic responses is not well characterized. Here, we demonstrate that Drosophila melanogaster embryos undergo rapid thermal acclimation, on the timescale of hours, that extends their upper thermal limit. Because early development is coordinated by changes in chromatin state and gene activation, we set out to characterize the molecular basis of embryonic thermal plasticity by performing single nuclei multiome ATAC and RNA sequencing. We found coordinated changes in chromatin state and the transcriptome in response to thermal acclimation. Cool-acclimated embryos exhibited thermal compensation through increased chromatin accessibility of transcription factor binding motifs of global transcriptional activators and higher expression of genes encoding ribosomal proteins and enzymes involved in oxidative phosphorylation. Although most of these shifts were common to all cell types, many changes were cell type specific. For example, cold-acclimated embryos had higher overall gene expression in tracheal primordial cells, presumably to prepare for increased gas exchange to support a higher metabolic rate. On the other hand, we observed modestly higher expression of genes involved in cell migration and cell adhesion in warm-acclimated embryos, particularly in ventral nerve cord primordia, suggesting a potential role for locomotor and sensory development in embryonic heat tolerance. Our results indicate that thermal plasticity is largely mediated by shifts in the epigenome and transcriptome that regulate the speed of development and that may impose metabolic costs that constrain upper thermal limits.

Single nuclei multiome ATAC and RNA sequencing reveals the molecular basis of thermal acclimation in Drosophila melanogaster embryos

The evolution of the mitochondrion enabled multicellularity and diversity of life histories that necessitated not merely a large, but in many cases, a variable supply of energy. With that, individual organisms also need a means to precisely regulate energy to match life’s demands. Over the past 15 years, a growing number of researchers have delved into evaluating mitochondrial respiratory function to understand evolutionary adaption and constraints on energetic capacity. Within these data, we have seen many examples suggesting that the energetic capacity of mitochondria is not fixed within individuals and can vary with genotype, leakiness of the mitochondria’s inner membrane, and oxidative damage. Yet, these do not appear to be the only means by which animals can adjust their capacity for oxidative phosphorylation. With this presentation, I will review evidence from my lab and others suggesting that changes in mitochondrial morphology and mitochondrial dynamics (most notably fission and fusion) play an essential role in up and down-regulating oxidative phosphorylation and mitigating oxidative damage. I will propose that these processes are vital to the diversity of energetic ability observed throughout Animalia.



Remodelling the powerhouse: Mitochondria morphology and dynamics in ecological and evolutionary processes

Both adaptation and plasticity are critical for species persistence during rapid anthropogenic global change. However, we know little about how these mechanisms of resilience interact, particularly the role of epigenetic variation in long-term adaptation. We used a 25-generation selection experiment simulating future acidification, warming, and their combination to reveal how epigenetic and genetic mechanisms interact to promote resilience in a foundational copepod at the base of the marine food web. Epigenetic divergence was positively linked to gene expression divergence, indicating that epigenetic changes may facilitate phenotypic change. In contrast, genetic and epigenetic changes were negatively related, where genomic regions experiencing significant epigenetic changes had lower genetic divergence than those without. Thus, evolutionary and epigenetic changes acted in different regions of the genome during adaptation to global change conditions, due to either local inhibition of one another or distinct functional targets of selection. These results suggest that both genetic and epigenetic mechanisms underlie resilience to global change but have unique contributions.

Epigenetic and genetic mechanisms uniquely contribute to evolutionary rescue from global change

Ocean warming is one of the most pressing issues for marine species worldwide. Most marine species are ectothermic, and they rely on the conditions of the surrounding environment for appropriate development and reproduction. Thus, increasing temperatures usually lead to higher energetic requirements, and if these demands are not met, there can be cascading negative effects on key physiological processes. Further, ocean warming is also leading to the degradation of coral reef ecosystems, which is leading to a progressive simplification of tropical habitats. Despite recent advances in understanding how adaptation and plasticity (both developmental and transgenerational) can lead to compensation to environmental stressors, questions remain on the synergistic effect temperature and habitat simplification can have on marine species from both a molecular and physiological perspective. With this in mind, this seminar will focus on the molecular, behavioral and physiological responses to temperature fluctuations and habitat simplification in tropical fishes.

Transgenerational responses of marine fishes to ocean warming and habitat degradation 

Climate change is increasing the frequency and severity of heatwaves, posing a significant threat to aquatic organisms globally. During an extended heatwave, aquatic organisms, like fish, may use phenotypic plasticity to help offset the effects of increased temperatures and associated low oxygen. The ability of a population to use plasticity to cope with heatwaves could be key for predicting species responses to climate change, especially in species of conservation concern like white sturgeon. We assessed the tolerance of juvenile white sturgeon from an endangered population to heatwave conditions and the effects of heatwave acclimation on subsequent stressors. We measured both thermal and hypoxia performance paired with underlying epigenetic and transcriptional mechanisms to assess the resilience of white sturgeon to heatwaves. Sturgeon exposed to simulated heatwave conditions had increased thermal tolerance and showed complete compensation for the effects of acute hypoxia. These changes were associated with increases in mRNA levels of genes associated with thermal and hypoxic stress. Global DNA methylation was sensitive to heatwave acclimation, changing in the gill and heart over the course of the heatwave exposure. Additionally, we observed rapid changes in DNA methylation during stressor trials over the course of an hour. These data demonstrate tremendous resilience in juvenile white sturgeon to heatwaves which was associated with improved cross-tolerance and responses in epigenetic and transcriptional mechanisms.

From the epigenome to performance: heatwave resilience through impressive thermal plasticity in white sturgeon

Most studies exploring ectotherms metabolic response to warming focus on respirometric approaches, thus only reflecting individual aerobic metabolism. Here, we measured the metabolic response and lactate body content of Gammarus pulex after a shift from low (12°C) to high (22°C) temperature by coupled oxygen consumption measurements (microrespirometry) and heat production (direct microcalorimetry). Following the shift to high temperature and after an initial increase, oxygen consumption gradually decreases, getting back to the value reported at low temperature. Such phenotypic plasticity may compensate for the temperature-induced increase of metabolic rate, commonly considered as an acclimation process in ectotherms. However, the simultaneous measurements of Gammarus pulex metabolic rate by direct microcalorimetry remained stable, highlighting an uncoupling between organism heat production, reflecting total metabolic rate, and oxygen consumption. This mismatch suggests an oxygen-disconnected metabolic process, concomitant with an increase in individual lactate body content at high temperature, suggesting a shift from aerobic to anaerobic metabolism. Seven days after the shift to high temperature, the estimated proportion of anaerobic metabolic rate represents up to 50% of total metabolism. Our results indicate that the decrease in aerobic metabolism does not reflect a decrease in total metabolic rate, assimilated to metabolic acclimation, but rather a shift to anaerobic processes to sustain the temperature-induced increased in organism energetic requirements.

Metabolic acclimation: compensation or thermal stress?

Balancing the control that is possible with lab studies with the real-world applicability of field work is a challenge in all experimental work. Using the example of the relationship between temperature, metabolic potential and social behaviour in fish, I will explore ways to incorporate more field relevance into lab studies and take lab-based theory to the field. As ectotherms, temperature has been called the “master factor” for fish; playing a large role in setting metabolic potential which in turn influences many aspects of behaviour and physiology. For example, changes in temperature have the potential to shift the cost-benefit analysis fish must conduct to balance the benefits of remaining in a group with the costs of increased competition. However, when considering the complexities of the natural world this relationship becomes less straight forward.

Taking our understanding of thermal influences on social behaviour from the lab to the field

Suction-feeding is a common method for capturing prey by aquatic organisms. This method allows for the adaption of predators by enabling them to consume a wide range of prey. Suction- feeding is a complex fish-fluid interaction governed by various hydrodynamic forces: inertia, unsteady, viscous and pressure gradients that are described by the coupling between the flow physics equations (Navier-Stokes) and the dynamic behavior of the fish (motion and forces). This study focuses on estimating the pressure within the flow field surrounding the mouth of a bluegill sunfish (Lepomis macrochirus) during suction-feeding utilizing Particle Image Velocimetry (PIV). We used high-speed imaging for measurements of the fish buccal kinematics (period and amplitude). The pressure field is estimated from the velocity fields measured by PIV via the Poisson equation. The boundary conditions for the pressure field are determined from the integral momentum equation, separately, for each phase of the suction-feeding cycle. The spatial pressure distribution varied significantly as a function of phase. We explore the suction-feeding process by quantifying the pressure field that drives the flow towards the buccal cavity, where the location of a low-pressure zone varies throughout the feeding cycle.

Pressure field surrounding bluegill sunfish (Lepomis macrochirus) during suction-feeding

Cowpea is a promising crop for future Food Security in Sub-Sahra Africa (SSA) due to its nutritional value and resilience to extreme weather conditions like high temperatures and severe drought. However, projected climate changes threaten its production in SSA by exacerbating these weather conditions. While efforts have been made to improve cowpea yields by increasing the above-ground biomass, little attention has been given to enhancing its photosynthetic efficiency, which directly impacts harvest index and yield. This study investigates how heatwaves during the vegetative and reproductive stages independently affect cowpea photosynthesis and biomass using two genotypes with varying tolerance to heat. Heatwaves significantly reduced cowpea net photosynthesis and the number of grains per plant, with greater impact during the reproductive stage although the impact on photosynthesis and grain number are not directly correlated. The impact of heat on net photosynthesis could be associated with limited biochemical capacity of cowpeas during heatwave. These findings will contribute to understanding the factors of cowpea photosynthesis that need more focus for improving its photosynthetic efficiency and resilience. These insights are crucial for developing strategies to sustain cowpea productivity amidst changing climate conditions in SSA.

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Transcription factor SPT interacts with CLAVATA signaling and GCN5 acetyltransferase to affect polarity axes in Arabidopsis thaliana gynoecium

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