Czechia

&quot;Green Intelligence: Harnessing Machine Learning and Data Topology for Plant Science&quot; explores the transformative potential of integrating machine learning and data topology in plant science research. Focusing on the model plant Arabidopsis thaliana, this presentation delves into advanced computer vision tasks such as image segmentation, object detection, image prediction, and evaluation. By employing these cutting-edge technologies, we aim to discover intricate patterns within botanical data, facilitating a deeper understanding of plant growth, development, and behavior. Our findings highlight the efficacy of these methodologies in enhancing the precision and efficiency of plant research, paving the way for innovative applications in agriculture and biotechnology.

SEB Conference 2024

The Digital Greenhouse: Harnessing AI for Advanced Plant Growth Monitoring and Prediction

data topology

plant phenotyping

machine learning

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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.

"Green Intelligence: Harnessing Machine Learning and Data Topology for Plant Science" explores the transformative potential of integrating machine learning and data topology in plant science research. Focusing on the model plant Arabidopsis thaliana, this presentation delves into advanced computer vision tasks such as image segmentation, object detection, image prediction, and evaluation. By employing these cutting-edge technologies, we aim to discover intricate patterns within botanical data, facilitating a deeper understanding of plant growth, development, and behavior. Our findings highlight the efficacy of these methodologies in enhancing the precision and efficiency of plant research, paving the way for innovative applications in agriculture and biotechnology.

technical paper

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The arrival of next-generation nucleotide sequencing techniques more than a decade ago promised transformative change in comparative physiology by providing unprecedented insights into animal function. Sequenced, and well-annotated genomes have enabled physiologists to identify candidate genes and proteins involved in physiological adaptations through genome-wide associated studies, targeted and non-targeted transcriptomics, proteomics, and other ‘omics’ approaches. I will share how our work utilizing the genome of the extremely anoxia-tolerant Western painted turtle has elucidated the mechanisms underlying the adaptations of heart and brain to cold temperatures and anoxia and the interactive effects of development. I will also share some of the shortcomings of these approaches that we have discovered, and how their insight into the physiological function of turtles has been limited.

How 'omics' does and does not help us understand the mechanisms of anoxia tolerance in turtles

Crucian carp (Carassius carassius) overwinter in ice-covered lakes and can survive anoxia for several months at low temperatures. The physiological adaptations allowing this survival are well understood at the whole-organism level, but we know less about the molecular machinery coordinating this adaptation to anoxia and reoxygenation and the possible involvement of epigenetic mechanisms. Due to the profound impact of DNA methylation on regulating gene expression, by directly influencing the accessibility of transcription factors and other regulatory proteins to the DNA, it acts as a switch mechanism and makes investigating it particularly interesting. Past RNA sequencing experiments to analyze the whole brain transcriptome have revealed that many genes are expressed differently in response to anoxia. We suspect that some of these changes in gene transcription during anoxia may be influenced by DNA methylation. Utilizing the next-generation Whole Genome Bisulfite Sequencing (WGBS) method combined with RNA sequencing, we investigated the altered gene activity-environment interaction, providing comprehensive, high-resolution, and quantitative methylation data. Our goal was to determine if genes that are differentially regulated during anoxic conditions are under epigenetic regulation by identifying a correlation between the DNA methylation loci on cytosines and differential RNA expression on the transcriptional level during and after anoxia exposure in the brain. The obtained data elucidates the role of DNA methylation in regulating the response to anoxia and guides us toward uncovering potentially novel molecular players in anoxia tolerance.

DNA methylation alterations during anoxia and re-oxygenation in crucian carp brain

The impacts of warming and hypoxia on aerobic metabolism and respiratory capacity are thought to mediate the susceptibility of marine organisms to these stressors and broadly shape marine biogeographic distributions. However, how evolutionary adaptation and physiological trade-offs affect these traits under multiple stressor conditions remains unclear. Using intertidal sculpins (Actinopterygii: Cottidae), we studied how adaptation to the temperature- and oxygen-variable intertidal has shaped the temperature sensitivity of hypoxic respiratory capacity. Based on the acute temperature sensitivity of the critical oxygen tension for standard metabolic rate (Pcrit), we found that tidepool-specializing species maintain greater capacity for oxygen uptake (i.e., lower Pcrit) in warm, hypoxic water compared to subtidal species. To determine whether improved respiratory capacity in hot, hypoxic water comes with an osmoregulatory performance penalty, we measured diffusive water flux (DWF), an index of water permeability and a key component of osmoregulation, in the tidepool-specialist Oligocottus maculosus. We found that O. maculosus suppressed DWF in hypoxia but this suppression was lost during combined exposure to hypoxia and high temperature. Together these results suggest increased hypoxic respiratory capacity improves metabolic performance under combined warming and hypoxia, but physiological trade-offs between respiration and osmoregulation could reduce the marginal value of increased respiratory capacity under complex variation in temperature and oxygen conditions.

Integrative aspects of respiratory and metabolic performance in fish under dynamic temperature and oxygen conditions: insights from intertidal fishes

As climate change accelerates, increasing air temperature average and variability pose substantial thermal challenges to animals. While plasticity in thermoregulatory traits could potentially attenuate this impact, whether thermal acclimatisation can occur quickly enough to track weather variability in hot climates is unknown in any endotherm, and sex differences have never been tested. We investigated acclimatisation responsiveness of male and female wild zebra finches to short-term (<2 weeks) summer temperature fluctuations in the Australian desert. Hotter weather before respirometry trials triggered a typical acclimatisation response. However, acclimatisation occurred remarkably rapidly: metabolic rate responded within just one day, while body temperature (Tb) and evaporative cooling capacity (EHL/MHP) were best predicted by weather on the trial day; whereas evaporative water loss responded more slowly (1 week). Nonetheless, rapid acclimatisation only occurred in males; and females had higher Tb and lower evaporative cooling capacity than males, potentially increasing hyperthermia risk. Furthermore, acclimatisation did not translate into greater acute heat tolerance (i.e. ability to tolerate chamber temperature =46°C). Our results therefore reveal surprisingly rapid acclimatisation, and even anticipatory adjustments to heat. However, with no changes in acute heat tolerance, nor in females, phenotypic flexibility may provide only limited buffering against the detrimental impact of heatwaves.

Thermal acclimatisation to heatwaves is rapid but sex-specific in wild zebra finches

Climate change and eutrophication increase the frequency and duration of heat waves (HWs) along with diurnal oxygen and pH fluctuations (FH) in coastal ecosystems. Mussels (Mytilus edulis) are marine ecosystem engineers commonly exposed to temperature, pH and oxygen fluctuations and an excellent model species for investigating the cumulative effects of these stressors on survival and physiological performance of keystone benthic organisms. Here, we evaluated whether a 3-week exposure to FH would alter mussels’ responses to a HW scenario. 
We examined the physiological responses including respiration (RR), clearance (CR) and nitrogen excretion (ER) rates, and byssus production, as well as biochemical indicators of energy status and oxidative stress in the gills of mussels exposed to well-oxygenated or FH conditions before and after 24h, 1 and 2 weeks of HW (1826°C). 
ER and RR increased transiently during the HW, and FH exposure prevented the return to baseline (ER) or slight decrease (RR) observed after 2w HW in normoxia. A parallel increase of the protein concentrations between 24h and 1w HW indicate that protein turnover is linked to the thermal acclimation. Decrease in the lipid peroxidation levels was found after 1w HW, indicating adjustments of redox balance after prolonged warming, although FH altered the antioxidant upregulation pattern. Mussels CR decreased, but cellular energy status remained stable during HW.
These results highlight that FH acclimation affects the physiological responses of M. edulis to HW and could reduce mussels’ resilience to the intense scenarios predicted for future Baltic Sea coasts.

Does fluctuating hypoxia and hypercapnia interact with the response of the bivalve Mytilus edulis to a heat wave scenario ?

Climate change is causing rapid warming of Arctic regions threatening the ecosystem and their species such as the polar cod (Boreogadus saida). Polar cod is considered the most abundant forage fish species linking lower and higher trophic levels in the Arctic food web. In particular, the thermal tolerance of sensitive life stages, such as reproducing adults, is important for an assessment of biodiversity changes in the context of global warming. Here, a non-invasive experimental approach using magnetic resonance imaging (MRI) is presented to investigate the physiological performance of reproducing male, female and non-reproducing polar cod during acute warming. Inside the MRI scanner, 0°C pre-acclimated polar cod were exposed to a temperature ramp from 0°C to 8.5°C at a rate of 1.5 °C every two hours. A set of physiological performance parameters of the cardio-vascular system and energy status were continuously determined during the temperature ramp. In particular, flow-weighted MRI techniques were used to quantify blood flow in the head and in the abdomen, respectively, and the ventilation rate was assessed using CINE MRI. The energy status was determined by in vivo 31P-NMR spectroscopy. A preliminary data analysis showed a similar blood flow at the control temperature of 0°C for all three animal groups, whereas blood flow increased remarkably in the head of reproducing males during warming, which was more pronounced in comparison to non-reproducing individuals. These initial results could indicate a higher energy requirement of the reproducing males, leading to a higher sensitivity to future warming conditions.

Physiological response to acute warming of reproducing male and female polar cod (Boreogadus saida) using MRI

Mechanisms of climate warming impacts on fish

Diverse scientific teams do more productive and high-impact science. Here we present student and staff ethnicity and disability data from the UK Higher Education Statistics Authority (HESA) for subdisicplines within biology. We identify significant underrepresentation of Black, Asian and disabled staff at senior academic levels, and a disproportionate loss of ethnic minority and disabled talent in the academic pipeline. We explore reasons that might underpin this from curriculum design to lack of role models to discrimiation and exclusionary practice. We offer recommendations for action, providing practical suggestions for how our disciplines can become less exclusionary and more welcoming to all students.

Ethnic Diversity and Disability in UK Bioscience: Structural Biases and Recommendations for Action

A growing number of studies have employed genomic analysis with next-generation sequencing technologies to differentiate genome-wide variations between treatment and control samples. However, instances in which biological samples contain genetic sequences from multiple organisms, such as those from plant grafting experiments or to distinguish pathogen gene expression within a host, pose challenges related to correct mapping across multiple reference genomes. Mapping algorithms are designed to find the most suitable alignment in the provided reference. Therefore, when multiple references are involved, the independent mapping approach of the same sample on separated genomes is not an efficient solution to correctly map RNA reads to the genome of origin. Here, we introduce a pipeline integrated into a Bioconductor/R package, mobileRNA, which performs simultaneous alignment of mRNA or small RNA sequencing reads using two independent reference genomes. Using real and simulated datasets, we show that mobileRNA can place reads to their genomic origin more accurately than previous approaches. The results demonstrated that the mobileRNA method retrieved results with less data noise; however, the similarity of the two genomes used as references plays the main role in the expected confidence in the discrimination of the placed reads across the two genomes. Downstream, our studies are utilising mobileRNA to investigate the changes in crop productivity between eggplant and tomato heterografts by integrating phenotypic, physiologic, and genomic data. Here we observed that a rootstock can affect the scion’s physiology and horticultural traits, and we have identified potential mobile RNAs associated with the observed alteration.

mobileRNA: A new tool for efficient analysis of RNA expression in multiple genomes

Exploring barley mutant and germplasm collections for plant architecture genes and alleles
Presenting author: Laura Rossini, University of Milan, Department of Agricultural and Environmental Sciences (DiSAA), Via Celoria 2, 20133 Milan, Italy
Laura.rossini@unimi.it 
Plant architecture traits play a fundamental role in plant fitness and adaptation. Breeders leverage variation in architectural features to select crops with improved performance under changing environments and agricultural practices. As a Neolithic founder crop now cultivated for different end uses across a wide ecogeographical range from Boreal regions to Tibet and sub-desertic areas in Africa, barley exhibits striking adaptability and genetic diversity. Further expanding barley germplasm diversity and taking advantage of its diploid genome, extensive mutant collections have been obtained through large scale mutagenesis programmes, establishing barley as a model for genetics and genomics of the Triticeae tribe. Research in our group builds upon these resources to identify and characterize genes and alleles shaping plant architecture traits, such as branching, culm morphology, leaf size and angle. In this talk I will illustrate current progress through selected case studies.

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How 'omics' does and does not help us understand the mechanisms of anoxia tolerance in turtles

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AI-based metabolome predictions to study complex plant traits

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