Czechia

Ensuring food security for an ever-growing global population while adapting to climate change is the main challenge for agriculture in the 21st century. The gene discovery pipeline BREEDIT, combines multiplex genome editing with crossing schemes to improve complex traits such as yield and drought tolerance. During the presentation, I will explain different use cases of the BREEDIT technology, while I will also highlight how it brings together genomics, transcriptomics, phenotyping and machine learning.

SEB Conference Prague 2024

Multiplex genome editing strategies to assess the combinatorial potential of yield contributing alleles in maize

maize

phenotyping

genomics

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.

In fishes, the fish pseudobranch is the paired, small hemibranchs of mandibular arch-derived gill tissue. Each pseudobranch receives oxygenated arterial blood and the efferent blood travels to the eyes. In the Nile tilapia (Oreochromis niloticus), the pseudobranch is fully embedded without any freely exposed gill filaments to the water which precludes the typical gill function of gas exchange. The pseudobranch parenchyma cells are rich in mitochondria and have a tubular system similar to gill ionocytes indicating a high metabolic capacity. Despite being identified over 200 years ago, the pseudobranch has remained enigmatic. One hypothesis regarding its function is that it acidifies the blood to aid in oxygen unloading (Root shift) to aid eye oxygen delivery; however, supporting physiological data is lacking. In the present study we used RNAseq to characterize the gene repertoire of the pseudobranch by contrasting expression with gill tissue. We identified 2621 higher and 2502 lower expressed genes (|FC| > 2 p<0.05; PBr:Gill). This notably included higher pseudobranch expression of genes involved in the pentose phosphate shunt, and lactate metabolism as well as ion transport gene isoform differences (eg Na+/K+-ATPase α1a is higher in gill and α1b in pseudobranch). Transporters involved in Na+ uptake (nhe2, ncc2) were higher in gill too. However, the nhe5 was very highly expressed in pseudobranch and using immunohistochemistry Nhe5 was localized to the pillar cells (specialized endothelial cells) of the pseudobranch but not the gills. Together, these results suggest that in tilapia the pseudobranch may be involved in blood acidification.

Elucidating the function of the enigmatic fish pseudobranch using transcriptomics. Novel expression of the Na+/H+-exchanger 5.

In the context of fast-paced global changes, understanding the adaptive potential of organisms to stressors is paramount. This study investigates whether prior stress can alter an individual’s response to mutagens. We hypothesised that this would increase mutation rates, providing scope for rapid adaptation. To explore this, we exposed zebrafish (Danio rerio) embryos to heat stress (up to 32°C) prior to a UVB/UVA damage/repair assay. To account for the complex social propagation of stress in natural environments, we also exposed embryos to social metabolites from stressed conspecifics, in isolation and in combination to heat stress, prior to the UV assay. Our findings reveal a surprising hormetic effect of heat stress that protected and/or rescued embryos from UV damage by activating cellular stress pathways and DNA repair mechanisms. This protective effect improved their overall fitness as the embryos presented less mutations, less defects and performed better in behavioural assays. Whilst not supporting our initial hypothesis, this suggests the potential adaptive significance of stress preconditioning, at least at sublethal levels of stress history. However, when heat stress was coupled with social metabolites, further activation of stress molecular pathways prevented the heat hormetic effect, in turn increasing mutation rates and declining larval performance, emphasising the importance of considering social contexts in stress response studies. Our results demonstrate the complexity of stress responses and the need to consider cross-protective mechanisms but also social stress propagation in predicting the adaptive potential of aquatic animals to global changes.

Heat to the rescue… unless you're in a group! Social context in zebrafish embryos prevents heat hormetic effect against mutagens


Allometry describes how the characteristics of living organisms change with body size. Although a decline in fish size is acknowledged as one of the widespread responses to global warming, relatively few studies have investigated the allometry of thermal limits, and even fewer have attempted to quantify the cardiorespiratory responses that may underlie any size-dependent thermal tolerance.

We measured the allometry of arterial and venous oxygen tension (PaO2 and PvO2) of 65 rainbow trout ranging from 200 to 3800 g across stepwise, acute temperature increases (18, 21.5, and 25°C) and under both normoxia and hyperoxia (150% O2). Additionally, we measured the aerobic metabolic rates of 130 rainbow trout ranging from 10 to 350 g under similar temperature and oxygen regimes.

While PaO2 did not scale with body mass throughout the temperature ramp, oxygen supplementation via hyperoxia lifted overall arterial oxygen tension. Aligning with previous work on salmonids, PvO2 declined with increasing fish size in normoxia, suggesting the potential for cardiac impairments in large individuals. While the mass-dependent decline in PvO2 was attenuated in hyperoxia, thermal limitations were observed without clear correlation to oxygen supply capacity. These findings have implications for the global discussion around climate warming and fish oxygen limitations and highlight the need for a better empirical understanding of size-dependent thermal tolerance.

The allometry of vascular oxygen supply during an acute thermal challenge in rainbow trout

Florida Bay’s shallow seagrass beds experience daily diurnal fluctuations in environmental oxygen, leading to hypoxic episodes (PO2 < 2 mg∙L-1, 4.6 kPa) that have increased in recent decades. To survive, the native Gulf toadfish can employ a suite of adaptive cardiorespiratory and metabolic adjustments. Previous work has demonstrated that toadfish reduce heart rate (HF) and increase ventilatory amplitude during moderate hypoxia (PO2 ~2-4 kPa for 20 min). Toadfish also have a regulation index of 0.5, suggesting that they use strategies other than maintaining oxygen consumption to tolerate hypoxia. The objective of this study was to characterize the acute response of Gulf toadfish to severe hypoxia (< 2 kPa). We hypothesized that Gulf toadfish would respond to severe hypoxia by reducing energy expenditure while switching to anaerobic metabolism. Cannulated adult toadfish (0.062 kg ± 0.003; n=29) were exposed to either control conditions (normoxia for 4 h) or hypoxia (PO2 ~ 0.44 kPa for 3 h followed by 1 h recovery). Cardiovascular and ventilatory parameters were monitored and blood samples were taken from both groups at t = 0, 1.5, and 4 h, and analyzed for pH, glucose, lactate, and other endpoints. Hypoxia-exposed fish experienced a ~72% decrease in HF and a ~25% decrease in VF during hypoxia exposure. Moreover, plasma glucose concentrations increased 5-fold, and plasma lactate concentrations increased 10-fold while pH decreased by 2.7% during hypoxia exposure. Our findings support our hypothesis that toadfish survive hypoxia by reducing energy expenditure and switching to anaerobic metabolism.

The key mechanisms associated with the survival of Gulf toadfish, Opsanus beta, when in severe hypoxia

The body muscles of fish are separated into segments by connective tissue sheets (myosepta) folded into a W-shape of slopes and cones. The biomechanical function of this complex shape is a long-standing question. Current hypotheses link myosepta shape to the magnitude of lateral bending during swimming, with morphological studies focusing on changes in myosepta shape across the mid- and caudal-regions of the body. We know little about how myosepta may contribute to dorsal bending during feeding, and comparative studies of myosepta morphology have been limited by the difficulty of visualising and measuring myosepta shape in 3D. How does myosepta shape vary from head to tail, and among species with differing dorsal bending during feeding? We used contrast-enhanced magnetic resonance imaging (MRI) to visualize cranial, dorsal (epaxial) myosepta in 7 fish species including different body shapes and feeding behaviours. We observed a surprising diversity of shapes across species. The more cranial myosepta of frogfish (Antennarius sp.), anglerfish (Chaenophryne draco), Cape dory (Zeus capensis), and pufferfish (Canthogaster punctissima) were relatively planar and cone-less myosepta, and bisected by a horizontal connective tissue sheet (except in pufferfish). More caudal myosepta in these species and all myosepta in trout (Oncorhynchus mykiss) and killifish (Fundulus parvipinnis) were more typically W-shaped. These results demonstrate myosepta shape can vary substantially across the spine and among species. We hypothesize that planar, cone-less myosepta may allow relatively large, local dorsal bending of the vertebral column. More data are needed to untangle the impact of functional and phylogeny on myosepta shape.

Unexpected diversity in the 3D shape of myosepta in fish body muscles

In nearshore environments, exposure of marine invertebrates to low pH/low dissolved oxygen (DO) conditions fluctuate over diel timescales. It is unclear how contrasting diel variability along coastal upwelling regions can determine distinct spatial patterns in the exposure of marine populations to such extreme conditions on a daily basis, e.g. ‘upwelling center’ vs. ‘upwelling shadows’. Here, we investigate the interactive effect of diel pH and DO fluctuations on the metabolic performance of different populations of the kelp crab Taliepus dentatus during upwelling and downwelling events. We deployed DO and pH sensors in two different environmentally-contrasting coastal sites in Chile; and then the diurnal cycles of DO and pH were replicated at our laboratory under common-garden conditions. Estimates of metabolic rate and respiratory quotient (RQ) were determined along other biochemical analyses (Hemolymph pH, glucose and lactate). Oceanographic data showed clear diel fluctuations in DO/pH during downwelling, while during upwelling, DO daily cycle was maintained although with extreme hypoxia at night, and the pH diel cycle was decoupled, exposing organisms to quasi-permanent low pH conditions. When mimicking such fluctuations at the Lab, we observed that metabolism was depressed upon low pH/low DO at night. Moreover, upwelling cycle had significant impact on metabolic rates, which was depressed during upwelling. Individuals collected from the active upwelling site showed an increase in hemolymph pH and lactate content in comparison to those from the upwelling shadow, especially during low pH/low DO conditions, suggesting this boosted acid-base balance is one of the compensatory mechanisms for local adaptation.

Decoupling in oxygen and pH fluctuations drive contrasting physiological responses in kelp crabs across an environmental mosaic in a coastal upwelling system

This talk will cover my development as a “scholar of teaching and learning”, specifically focusing on my interest in the nexus between teaching and research in Higher Education. 
 
There is plenty of rhetoric about the links between discipline research and teaching/learning, but despite the apparent trend towards research-oriented curricula, there are a number of documented challenges to ensuring meaningful links between these twin missions of higher education.  This talk will explore the mutual benefits of linking teaching and research, introducing an adapted framework that articulates how research can be incorporated into the teaching curriculum, and then exploring how a research-mindset can be employed to improve educational offerings. I’ll describe the barriers and opportunities I have encountered, focusing on the practical steps that all educators can take to enhance their teaching practice and contribute to the Scholarship of Teaching and Learning.


My SoTL journey- a personal perspective

A limitation of genomic prediction models is that they do not readily incorporate or take into account genotype by environment effects, which decrease the prediction accuracy of genomic selection (GS) across different growing conditions. In a large collaborative project with commercial breeding companies, we tested whether GS prediction accuracy could be improved by taking into account the environmental influence on phenotype by incorporating a large number of phenomic markers using high-throughput field phenotyping methods. To assess the effectiveness of the approach on a scale approximating that of a practical breeding programme, 44 winter wheat elite populations comprising 2,994 lines were grown on two sites contrasting in soil type over two years. Remote sensing data were collected from multi- and hyperspectral cameras mounted on drones and piloted aircraft, and were combined with ground-based visual crop assessment scores and ultra-local spatial variations in soil physical properties. The predictive power for grain yield was tested with or without incorporating genome-wide marker data sets. Models using phenomic traits alone had a greater predictive value (R2 = 0.39–0.47) than genomic data (approximately R2 = 0.1). The average improvement in predictive power by combining trait and marker data was 6%–12% over the best phenomic-only model, and performed best when data from one full location was used to predict the yield on an entire second location. The results suggest that genetic gain can be increased by utilising phenomic data, perhaps most efficiently at early stages of the breeding cycle.

Phenomic and genomic prediction of yield in winter wheat

Reproductive ageing is intrinsically linked with the interactions
between the germline and the soma, where germline maintenance
appears to come at the cost of somatic ageing. Signalling pathways
determine the level of cellular and genome maintenance in
the germline and the soma. Because germline maintenance is
predicted to be costly, the allocation to germline maintenance
may vary throughout an organism’s life resulting from the putative
trade-off between somatic maintenance, offspring number and
offspring quality through the production of high-quality gametes
carrying healthy genomes. Males appear to be particularly
vulnerable to sub-optimal germline maintenance and germline
ageing as spermatogenesis continues throughout life and involves
continuous mitotic and meiotic divisions for tissue proliferation.
We tested the germline-soma interactions in male zebrafish
Danio rerio using knockdown and knockout to generate germlinefree
fish and compare somatic responses to genotoxic stress in
germline-free and germline-carrying males. We also performed
mutation accumulation experiments using the nematode
Caenorhabditis remanei to assess germline mutation rates as an
indicator of germline maintenance in young, peak reproductionaged
and old worms. All our experiments hint at a tight regulation
and interaction between germline and soma and I will discuss our
results in the light of the expensive germline hypothesis and its role
in reproductive ageing.

The role of germline-soma interactions in reproductive ageing

Metabolic rate represents an organism’s cost of living, as it sets its demands for food and oxygen from the environment. Yet, within species, an approximately 2-fold variation in metabolic rate exists among comparable individuals, so that one individual can have twice the metabolic rate of another of the same age, size, and sex. In addition to this variation in metabolic rate at a given size, variation also exists among individuals in how steeply metabolic rate changes (scales) with body size, but the causes and consequences of individual variation in metabolic rate and its scaling relationship with body size are poorly understood. Using examples from my work on fish, I will here discuss how and why there is variation in metabolic rate and its scaling, and what it means for our understanding of the physiology, ecology, and life-history of animals.

Multiplex genome editing strategies to assess the combinatorial potential of yield contributing alleles in maize

Downloads

Next from SEB Conference Prague 2024

Elucidating the function of the enigmatic fish pseudobranch using transcriptomics. Novel expression of the Na+/H+-exchanger 5.

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Multiplex genome editing strategies to assess the combinatorial potential of yield contributing alleles in maize

.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

Elucidating the function of the enigmatic fish pseudobranch using transcriptomics. Novel expression of the Na+/H+-exchanger 5.

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Downloads