Czechia

The Northern shrimp (Pandalus borealis) is an ecologically and socio-economically important species in the North Atlantic, yet several of its different populations are collapsing due in part to global change drivers. Here, we aimed to elucidate the molecular mechanisms underlying shrimp responses to combined ocean warming (OW) and acidification (OA). Specifically, we profiled the phospholipidome of the abdominal muscle of female shrimp from four origins in the Northwest Atlantic, subjected to an orthogonal design of temperature (2, 6, or 10 °C) and pH (pH 7.75 or 7.40) scenarios. A suite of multivariate analyses revealed a complex interplay between shrimp origin and exposure to combined OW and OA, with OW primarily driving the phospholipidomic response, particularly at 10 °C. Warming to 10 °C altered phospholipids related to membrane thickness and lateral diffusion, and upregulated sphingomyelins. Notably, OA caused subtler effects, dependent on shrimp origin. Specimens from the Gulf of St. Lawrence showed an interactive effect of OW and OA, whilst those from the coasts of Newfoundland and Nova Scotia were not impacted by OA. Our finding has direct implications for prioritising conservation efforts on shrimp populations featuring a higher sensitivity to multiple stressors. Overall, our findings highlight the power of comparative omics to reveal different levels of intraspecific plasticity in the molecular response of marine organisms to future oceanic conditions. Our results will be refined by integrating multiomics and physiological traits within a multilayer framework to gain a comprehensive understanding of the response to global change drivers.

SEB Conference 2024

Molecular Responses of the Northern shrimp facing combined Ocean Warming and Acidification across the Northwest Atlantic Reveal Intraspecific Plasticity

intraspecific plasticity

local adaptation

long-term acclimatisation

cellular physiology

comparative lipidomics

ocean warming

ocean acidification

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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.

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

In recent years, an important decline of honey bee populations is observed, in part due to environmental variations caused by climate change. Particularly, increased temperatures during winter and spring bring forth new challenges, as the transition from winter to summer is crucial for the colony's survival. We have recently demonstrated that honey bee mitochondria undergo drastic changes between the winter and summer seasons, which is attributed to their different roles within the hive. Specifically, winter bees have lower CI-linked respiration but increased mtG3PDH- and CII-linked respiration. However we do not know whether and how this affects ATP and reactive oxygen species (ROS) production. Further, the regulation mechanisms behind this drastic change in phenotype is unknown. In this study, we investigated the seasonal differences in mitochondrial oxygen consumption, ATP production, and site-specific ROS production in honey bees (Apis mellifera). We also evaluated supercomplex assembly to determine if this could explain the changes observed in the mitochondrial parameters measured. Our results demonstrate that even though CI-linked respiration is diminished in winter bees, ATP production by CI is increased, suggesting that CI is more efficient in winter. Differences were also detected in terms of ROS production, with summer bees producing less ROS than all other season. In terms of supercomplex assembly, we are currently performing the analyses, which has never been done in honey bees, and will be included in this talk. We hypothesize that supercomplex assembly could shed light on the results described above, explaining the contrasting mitochondrial phenotypes observed between seasons.

Seasonal effect on metabolism and mitochondrial supercomplex assembly in honey bees (Apis mellifera)

The severity and frequency of marine heatwaves (MHWs) have increased dramatically across the globe, particularly in the last decade. In ectotherms like fishes, temperature directly influences oxygen transport, leading to changes in oxygen consumption (i.e., metabolic rates). The effects of temperature on metabolism have consequences for organismal function, including swimming performance. Performance is expected to decline as metabolic demands accumulate at temperatures beyond a fish’s optimum, though declines may be mitigated through various means, including plastic responses. Rapid changes in temperature, exemplified through MHWs, may outpace an individual’s acclimation capacity, leaving them more vulnerable to detrimental thermal effects.
We investigated how heatwave exposure (i.e., +2°C and +4°C above normal summer temperature) over a five-day period affects the metabolic rate and swimming performance of a common nearshore marine fish species, the shiner perch (Cymatogaster aggregata), on San Juan Island, Washington. Using a swim tunnel respirometer, we measured standard and maximum metabolic rate (SMR and MMR, respectively), as well as critical swimming speed (Ucrit) and optimal swimming speed (Uopt). SMR was highest with moderate heatwave exposure (+2°C), while MMR was highly variable within treatments and increased slightly at the highest treatment temperature (+4°C). Ucrit did not vary across temperatures, but Uopt did decline with increasing temperatures. These findings provide insight into how this species may respond to future projected marine heatwaves, and also highlight the need for further studies focusing on metabolic performance across a range of relevant temperatures and acclimation periods.


Effects of heatwave exposure on the metabolism and swimming performance of a nearshore marine fish, Cymatogaster aggregata

Productive marine coastal ecosystems such as coral reefs, seagrass meadows, kelp forests and mangroves are characterised by circadian fluctuations of oxygen controlled by temperature and the cycle of photosynthesis and respiration of the primary producers. Marine species living in such productive coastal habitats have therefore evolved in highly dynamic diel and seasonally fluctuating environments. Consequently, studies strictly based on rigorous laboratory conditions may not capture, or test, the real effect of environmental fluctuations on the thermal tolerance of marine species, which is directly linked with environmental oxygen availability. In this study we selected three areas, across a large latitudinal scale, with different levels of temperature and oxygen fluctuations and predictability. By incorporating lab experiments with ecologically relevant oxygen levels recorded from the field, we hypothesized that the degree of the diel environmental fluctuations in the coastal areas can explain the thermal response of marine species. To test this hypothesis, we measured the thermal tolerance of 17 marine ectotherm animal species from the three different locations, from tropical to warm and cold temperate environment. Our results showed that higher predictability of oxygen and temperature fluctuation increases the magnitude of species’ thermal tolerance compared to those in less predictable environments. We advocate that ecologically relevant environmental oxygen fluctuation needs to be considered when measuring and forecasting the response of marine animals to global warming and it provides a new background to assess aquatic communities’ thermal tolerance.

Accounting for ecologically relevant oxygen fluctuation explains thermal tolerance plasticity in marine species

Functional trade-offs impose important constraints on the biomechanics of musculo-skeletal systems. In songbirds, for example, a force-velocity trade-off has been described in singing, showing that hard-biting birds sing at lower syllable rates. However, we do not yet know whether and how this also affects their feeding kinematics. Many songbirds are granivorous, i.e., rely on seeds as their major food source. Thus, we analysed seed processing in two granivorous species, canaries (bite force ≈3 N) and Java finches (bite force ≈10 N), using X-ray Reconstruction of Moving Morphology (XROMM). We show that canaries move their beaks at a ≈23% higher angular velocity and at a ≈31% higher frequency compared to Java finches. Furthermore, canaries use a wider range of motion in both the upper and lower beak during seed processing. Last, we show that these differences in beak biomechanics are also associated with differences in seed processing strategies in the tested species: Java finches crack the seeds more easily than canaries, but they often crush the inner kernel and consequently drop parts of it. Canaries, however, are able to remove the shell without crushing the seed and swallow the kernel in whole. This suggests that a force-accuracy trade-off might be at play in the beak's fine motor control. Our results indicate that a combination of trade-offs (force-velocity, force-frequency, and force-accuracy) has an impact on the feeding biomechanics of granivorous songbirds and hence may play an important role in the adaptation to specific seed types.

Biting fast or biting hard? Comparative XROMM analysis reveals functional trade-offs in beak movements of feeding songbirds.

Plant formin proteins belong to a large family of eukaryotic cytoskeleton regulators. The role of formin in cellular processes and actin regulation has been studied in the Arabidopsis root. The plamsmodesmata localised formins has shown influence on the symplastic transport by affecting the callose and actin. An extensive comparison among mutants and effects of cytoskeletal drugs on symplastic transport have been performed using DRONPa technique. Formins also studied to affect the lateral root formation.

Characterizing the role of plant class I formins in symplastic transport

Developing an inclusive, diverse, and cutting-edge curriculum is high on the priority list for universities. However, to undertake this it requires time and energy, something that as educators we are often lacking - regardless of our drive. Working in partnership with students provides unique opportunities to enable content development. Through student-staff partnerships, students are often best placed to provide insights into their own learning, by having autonomy over content through ownership of novel ideas and approaches that are relevant to today’s needs. This partnership also provides a platform for students to build confidence in their abilities and the education system that they are a part of to provide a more inclusive environment. Staff on a learning and teaching track gain valuable opportunities for scholarship from these partnerships and it can also spread the time constraints.
As with any opportunity we need to balance the scales. It takes time to find students that are able to balance this extra workload with their studies and have the maturity to see beyond their own needs. After leading on student-staff partnerships, I am aware of the differing outcomes which can arise, and these are often down to the individual team, where resources are limited and tightly time-bound. When it works it provides an insightful curriculum. When it doesn’t then the shift of workflow falls to us. I will provide some insights into student-staff partnerships and highlight the benefits and areas to be wary of before jumping in. 


Student-Staff Partnerships the way forward for an inclusive curriculum-Some insights before jumping in

"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.

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

Autochthonous ecotypes are plant genetic resources characterized by high genetic variability, tolerance to environmental stress conditions, the presence of specialized metabolites (terpenoids, flavonoids, and alkaloids), and health-promoting compounds. However, autochthonous ecotypes are gravely threatened by extinction, mainly because of their replacement by commercial varieties. To preserve autochthonous ecotypes and their diversity, as well as to make them an ideal alternative for commercial varieties, it is very important to identify their unique characteristics. The present study aimed to provide a global view of the metabolite diversity of three autochthonous lentil ecotypes from different villages of the Molise region (Italy): Capracotta, CA; Rionero Sannitico, RS; and Agnone, A; and one ecotype from the Umbria region (Italy): Castelluccio di Norcia, CS. Untargeted metabolomics, performed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), allowed the detection of 663 differentially accumulated metabolites (DAMs), which were assigned to 13 metabolic categories using MS libraries (e.g., the GNPS Public Spectral Library) and a molecular network approach. Major classes included flavonoids (90–13.6%), amino acids and derivatives (70–10.5%), and cinnamic acids (55–8.3%). According to the PCA and PLS-DA score plots, the metabolite compositions of autochthonous ecotypes differed significantly from each other. These results have been confirmed by heatmap, allowing the selection of ecotype-specific metabolic features. The enrichment analysis is in progress to assess the presence of enriched metabolic categories for each ecotype, and the antibacterial, antiproliferative, and antioxidative activity of lentil extracts was also evaluated according to the differential metabolic profiles characterizing each ecotype.

METABOLOMIC CHARACTERIZATION OF AUTOCHTHONOUS LENTIL ECOTYPES

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.

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