Czechia

Transposable Elements (TEs) are the major force in genome plasticity and gene evolution, with LTR retrotransposons (LTR-TEs) constituting the most abundant class. LTR-TEs are considered autonomous when they contain the coding sequence for the translation of all factors required for their replication and transposition, and nonautonomous if they require that such factors are provided in trans. While several autonomous LTR-TEs has been found mobile in Arabidopsis thaliana epigenetic mutants or epigenetic recombinant inbreed lines (epiRILs), non-autonomous LTR-TEs ha never observed mobile in real time experiments. In this study, we observe that the LTR_gypsy transposon ATGP2N mobilises in epiRILs and transpose with high specificity into ribosomal repeats. Notably, an identical homologous region is present in the LTRs of ATGP2N and the autonomous LTR-TE, suggesting that ATGP2N hijacks ATGP2 factors for its transposition. Our studies shed light on the transpositional dynamics of nonautonomous LTR elements and contribute to expanding our knowledge of LTR transposition mechanisms.

SEB Conference 2024

Mobilisation of a nonautonomous LTR-retrotransposon in Arabidopsis thaliana.

## Welcome to 2024 Annual Conference of the North American Chapter of the Association for Computational Linguistics!
This year, the conference is in Mexico City. NAACL was actually already planned for Mexico City in 2021, but due to the pandemic the entire conference was moved online. This year, finally, we get to go! So it is my sincere pleasure to welcome you to Mexico City, whether in person or virtually. Having the conference in Mexico City is a good opportunity to emphasize that NAACL is our flagship conference for ACL members not only in North America but also in Central and South America, even though NAACL has been bearing “North” in its name. At this year’s conference, we have a theme to match, with a theme track on the Languages of Latin America to showcase the linguistic diversity of the region.
 
The opportunity to present at NAACL should not depend on a researcher’s travel budget, or their family status. This is why it is so important to make virtual participation at NAACL as good an experience as possible – but we want to also provide a good experience for in-person participants. As a community, we are still working out the best way to do that. This year at NAACL, we are trying out a big virtual poster session ahead of the conference, with the hope that this will make make for a lively and interactive experience. At the same time, we are reducing virtual oral presentations, which seem to be particularly tricky to make to work well. A big thanks to the NAACL program chairs and to Luciana Benotti for all their ideas and work to improve the virtual experience. And participants, virtual as well as in-person: Please let us know what worked for you and what didn’t, so we can continue to improve hybrid conferences. 
 
I have been lucky to work with many amazing people. Without their insight, dedication and patience, and without the many hours of work they put in, NAACL would not have been possible. A huge thank you to the program chairs Helena Gomez, Kevin Duh, and Steve Bethard – you are the best! 
 
Finally, I would like to thank all authors, invited speakers and panelists, area chairs and reviewers, the volunteers organizing and chairing sessions, and all attendees, in-person and virtual. Thank you for helping us make NAACL 2024 come to life. 
 
Welcome and hope you all enjoy the conference! 
Katrin Erk 
The University of Texas at Austin 
NAACL-2024 General Chair 
*You can read the full Welcome message in the [Conference Handbook (downloadable)](https://drive.google.com/file/d/1H1NvW0VASQjkSCYgw3mr-3l4yYDSxz6B/view?usp=sharing)*

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NAACL 2024

2024 Annual Conference of the North American Chapter of the Association for Computational Linguistics

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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.

Muscle properties such as strength and stiffness vary between species, joints, and age groups, but how these parameters interact to affect locomotor performance can be difficult to assess in complex models. To address this issue, we developed a simplified model of a single joint with two antagonistic Hill-type muscles, and varied the associated muscle parameters combinatorially over a large range. For a given parameter combination, we found optimal joint movements that minimized movement time while starting and ending at rest. The reduction of force, maximum contraction velocity and activation rate all had detrimental effects on performance, independent of other parameters. In contrast, over the large parameter space, deactivation and passive stiffness had no effect on performance on their own, but pronounced interactive effects with eachother. Increasing stiffness reduced joint movement time at fast deactivation rates, but increased movement time at low deactivation rates. This occurs because antagonist muscles resist the passive tension at rest, but are stretched eccentrically by the agonist, amplifying their active resistive force. Fast-deactivating muscles can avoid this resistive effect, allowing the passive stiffness to amplify accelerating force and enhance performance. Our results suggest that ameliorating muscle deactivation with age could be explored as a potential therapeutic target to enhance rapid motion, and that fast deactivation of muscle may be an important functional trait in animals using ballistic movements.

Interaction of muscle parameters on ballistic joint movement - implications for ageing and comparative locomotion

Competition over rare and limited resources is an important evolutionary driver of behaviour. One such resource found in nature are carrion carcasses, which the burying beetle Nicrophorus vespilloides depends on to breed. However, these carcasses are highly valuable and often bring these beetles into competition with other species, including opportunistic vertebrate scavengers. While we might predict the beetles should have some mechanism to deal with these encounters, little is known about how such interactions inform parental care decisions of N. vespilloides. Here, we test whether this includes facultative adjustments to parental care. We found that parents were slower to return to providing care when given cues that indicated vertebrate scavengers were present. Despite this, we found there was no difference in the overall amount of care parents provided, or in resulting larval fitness. Our results are consistent with previous work that shows while vertebrate competition does trigger a strong immediate response in these beetles, any long-term adjustments in parental behaviour are limited. This suggests that the selective pressure for long-term adjustments here is weak, and we find evidence that these beetles may instead rely on non-facultative behaviours such as concealing carrion to deal with asymmetric competition.

Competition with vertebrate scavengers' delays return to parental care in the burying beetle Nicrophorus vespilloides

Male crickets attract females by producing calls with their forewings. Louder calls travel further and are more effective at attracting mates. However, crickets are much smaller than the wavelength of their call, and this limits their power output. A small group called tree crickets make acoustic tools called baffles which reduce acoustic short-circuiting, a source of dipole inefficiency. Here, we ask why baffling is uncommon among crickets. We hypothesize that baffling may be rare, because like other tools they offer insufficient advantage for most species. To test this, we modelled the calling efficiencies of crickets within the full space of possible natural wing sizes and call frequencies, in multiple acoustic environments. We then generated efficiency landscapes, within which we plotted 112 cricket species across 7 phylogenetic clades. We found that all sampled crickets, in all conditions, could gain efficiency from tool use. Surprisingly, we also found that calling from the ground significantly increased efficiency, with or without a baffle, by as much as an order of magnitude. We found that the ground provides some reduction of acoustic short-circuiting but also halves the air volume within which sound is radiated. It simultaneously reflects sound upwards, allowing recapture of a significant amount of acoustic energy through constructive interference. Thus, using the ground as a reflective baffle is an effective strategy for increasing calling efficiency. Indeed, theory suggests that this increase in efficiency is accessible not just to crickets, but to all acoustically communicating animals whether they are dipole or monopole sound sources.

The Ground is Good: A Numerical Approach to Understanding Acoustic Tool Use in Crickets

Environmental variability is common in most aquatic environments, yet it has been largely stabilized in laboratory experimental physiology aimed at understanding physiological responses to environmental challenges. Climate change is expected to increase climate variability and exacerbate environmental extremes, yet we know less about the impacts of this variability on fish physiology. This information will be crucial in gauging species' vulnerability to climate change. Incorporating variability into experimental designs is challenging and leads to difficulties in interpreting data within experiments and across multiple experiments where the experimental designs can be different. In this presentation I will discuss how we have been incorporating variability into our experiments to closely match natural environments, the lessons we have learned with respect to sampling times/durations in thermally variable experiments, and the types of physiological data that we collect that can be applied to real-world scenarios. I will use examples from our published research on the physiology of wild Atlantic salmon from thermally distinct rivers in Atlantic Canada and discuss a new and on-going experimental design in our lab that focuses on incorporating both daily and seasonal environmental variability into physiological experiments in salmonids from eggs to adults.

The ups and downs of incorporating environmentally relevant variability in laboratory experiments

The Cell and Gene Therapy Catapult is one of a network of elite technology and innovation centres established by Innovate UK. Applying business-led research, Catapults help businesses transform great ideas into valuable products and services to compete in the global markets of tomorrow.
This keynote presentation will share valuable insight into sector skills challenges in one of the most novel and exciting industries, and explain how the Cell and Gene Therapy Catapult, through an ongoing effort to harness powerful collaborations, has devised and implemented a successful, award-winning training system including the Advanced Therapy Apprenticeship Community programme and an Online Training Platform to address these.


Collaboration and Training for the Future of Advanced Therapies: The Cell and Gene Therapy Catapult

The current rates of crop-yield increase are insufficient to meet the global food demands anticipated by 2050. While crop breeding has been one of the main pillars for securing yield progress in past decades, breeding programs are being confronted with new challenges due to the changing climate, particularly in areas where declining precipitation and increasing temperatures are more evident. Therefore, maximizing crop-yield potential and fortifying genetic resilience against abiotic and biotic stresses are critical to food security. High-throughput crop phenotyping is perceived as a key factor to accelerate crop genetic advance. Phenotyping not only facilitates conventional breeding, but it is necessary to fully exploit the capabilities of molecular breeding, and it can be exploited to predict breeding targets for the years ahead at the regional level through more advanced simulation models and decision support systems. In terms of phenotyping, it is necessary to determined which selection traits are relevant in each situation, and which phenotyping tools/ methods are the most suitable to assess such traits. Remote sensing methodologies are currently the most popular approaches, even when lab-based analyses are still relevant in many circumstances. On top of that, data processing and automation, together with machine learning/deep learning are contributing to a wide range of applications for phenotyping. This presentation will put emphasis on the most popular phenotyping approaches, including examples of phenotyping implementation for different traits and target environments.

Translating high-throughput phenotyping into genetic gain

Transcription factors (TF) play a pivotal role in gene regulation; however, their biophysical properties remain poorly understood. Conventional techniques have provided relatively static perspectives of their action, limiting our understanding of their rapid (millisecond scale) dynamical behavior in cellula. Fortunately, over the past decade, novel microscopy techniques have emerged, enabling us to transcend the limitations of resolution and gain a comprehensive, nanoscale view of their in vivo biodynamics directly within the nucleus. To unravel and enhance the intranuclear diffusion of transcription factors, we have integrated molecular and microscopic approaches, facilitating a dynamic representation of their activity.

Investigation of transcription factor dynamics by super-resolution microscopy

In most plants, the proportion of transcribed DNA is a small portion of the genome, and this is particularly evident for species with large genomes, e.g. hexaploid wheat (Triticum aestivum), where the 85% of the genome is composed of non-expressed repetitive DNA elements, and only about 60% of the annotated genes are expressed. Indeed, it is known that the expression of large portions of plant genomes are blocked by transcriptional gene silencing (TGS) mechanisms, controlled by epigenetic marks such as DNA methylation. In the model plant Arabidopsis thaliana, the genome wide suppression of TGS activates the expression of silenced genes and mobilises repetitive elements, generating epigenetic and genetic variation and producing new phenotypes. However, attempts to exploit this variation in crop species has been so far largely unsuccessful, mostly due to the different and more complex epigenetic regulation of larger, and often polyploid, crop genomes. Therefore, we are developing a tool to directly screen in planta for conditions able to increase epigenetic variability via the suppression of TGS. For this purpose, wheat cv. ‘Fielder’ was transformed with a reporter GUS cassette containing DNA repeats, to attract DNA methylation and establish TGS on the transgenic locus. To prove that TGS was effectively silencing the reporter gene, we exposed transgenic seedlings to Zebularine, a cytidine analog that inhibits DNA methyltransferases and suppresses TGS, resulting in an increase in GUS expression. Ongoing and future work includes the use of this reporter line to test conditions, or breeding combinations, able to affect TGS in wheat, which can generate epigenetic and genetic variation. The exploitation of such diversity in breeding programs will potentially contribute to the improvement of wheat productivity and food sustainability.

Exploitation of silenced genes for wheat breeding

Out of the tens of thousands of edible species, only 2500 species of plants underwent any human selection, and only 250 species are currently considered domesticated. Before agriculture began in the Neolithic, humans in the Fertile Crescent exploited a large diversity of plants, collecting and cultivating them, but many were abandoned. 

While the occurrence of domestication and the development of agriculture are considered a pivotal point in human history, one significant question remains. What made certain wild plants more likely to be successfully domesticated? A potential answer to this question lies in mutation rate. Domestication relies on novel phenotypes, therefore if novel phenotypes arise more quickly in some species than others, humans may favour these species, continuing to grow them, and abandoning others.

Using transcriptomic data, the rate of mutation has been estimated for crop progenitors (those that were domesticated) and never-domesticated close relatives, which could, in theory, have been domesticated. In addition, a dN/dS analysis has been carried out to investigate selection across these species. We focused on two main groups of edible plants – legumes and cereals from the Fertile Crescent – including some which were likely managed during the Neolithic and then abandoned as a crop. 

Taking this alongside other factors that could have influenced the ‘domesticability’ of some species over others, our work opens a discussion about whether certain species are predisposed to succeed under certain conditions. It therefore has implications for using neo-domestication to ensure food security and for biodiversity response in a changing climate. 


Domesticate this, not that: the implications of mutation rate and selection on present-day agriculture

P7.16 
PlantAct: plant-soil solutions for climate challenges

Catherine A. Walsh1 , Heribert Hirt2

1Lancaster University, UK, 2King Abdullah University of Sciences and Technology, Saudi Arabia

Anthropogenic greenhouse gas (GHG) emissions have meant devastating impacts for our planet with associated climate change effects reaching crisis point. The recent surpassing of a 1.5C rise in global average temperature above pre-industrial levels as set by the 2015 Paris agreement, means an urgent need for action to prevent further temperature rises causing irreversible outcomes. Currently, agriculture contributes 25% of total GHG emissions, which suggests a conversion to more sustainable practices would significantly reduce GHG outputs. Despite driving climate change, global agriculture also suffers, with increasing frequencies of drought and flooding alongside soil degradation challenging food security. PlantAct is an international, interdisciplinary think tank tackling the problem, through applying plant and soil science solutions to address the intense difficulties facing agricultural production. Furthermore, PlantAct aims to connect with a range of disciplines to deliver resilient solutions to address nitrogen use efficiency, carbon sequestration and promote plant health whilst maintaining food security. A novel, holistic approach to our food system will not only relay environmental benefits but also foster a change in attitude towards more plant based diets to improve health and well-being. In doing so, PlantAct seeks to engage students, young scientists, and the next generation to help bring around the urgent overhaul required to reduce GHG emissions within the food system while providing carbon storage solutions to support the health of our planet into the future. 


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