Meet the poster prize winners of ‘Cellular mechanisms driven by phase separation’

For many attendees of the EMBO | EMBL Symposium ‘Cellular mechanisms driven by phase separation’, it was the first in-person event after a long while. The excitement was tangible all around the Advanced Training Centre, but especially along the helices where the posters were being displayed. With 108 posters to choose from, the participants had lots of fascinating science to discover and could vote for their favorite until the third day of the event. The fourteen poster presenters who received the most votes had the chance to talk to the scientific organisers who then decided on the final poster prize winners.

Congratulations to the winners: Gea, Alberto, Tom, and Daxiao!

A conserved mechanism regulates reversible amyloids of pyruvate kinase in yeast and human cells

Presenter: Gea Cereghetti, ETH Zürich, Switzerland

Abstract

Amyloids were long viewed as irreversible, pathological aggregates, often associated with neurodegenerative diseases. However, recent insights challenge this view, providing evidence that reversible amyloids can form upon stress conditions and fulfil crucial physiological functions. Yet, the molecular mechanisms regulating functional amyloids and the differences to their pathological counterparts remain poorly understood.

Here, we investigate the conserved principles underlying amyloid reversibility by studying the essential ATP‑producing enzyme pyruvate kinase (PK) in vitro, in yeast, and in human cells. We demonstrate that PK forms stress‑dependent reversible amyloids through a pH‑sensitive amyloid core. Stress‑induced cytosolic acidification promotes PK amyloid formation via protonation of specific glutamate (in yeast) or histidine (in human) residues within the amyloid core. Upon aggregation, PK becomes inactive and is protected from stress‑induced degradation. After stress release, re‑solubilization of yeast PK is essential to restore ATP production, disassemble stress granules (SGs), and restart cell growth. Mechanistically, we demonstrate that yeats PK re‑solubilization is initiated by the glycolytic metabolite fructose‑1,6‑bisphosphate, which directly binds PK amyloids, allowing Hsp104 and Ssa2 chaperone recruitment and aggregate re‑solubilization.

In summary, our work unravels a conserved and potentially widespread molecular mechanism underlying amyloid functionality and reversibility, and highlights the important physiological implications of regulated protein aggregation.

View poster

From Surfactant to glue – how Ki-67 regulates chromosome surface properties

Presenter: Alberto Hernández Armendáriz, EMBL Heidelberg, Germany

Abstract

Compartmentalization into functional units is a key principle of cellular life. In addition to membrane‑bound organelles, eukaryotic cells utilize membrane‑less biomolecular condensates to locally concentrate proteins and nucleic acids. While we are beginning to understand how membrane‑less condensates assemble and disassemble, we know very little about the biological processes that take place at the surface of such condensates. The surface of the largest membrane‑less cellular assembly, the mitotic chromosome, is covered by the intrinsically disordered protein Ki‑67. Our previous studies have revealed that Ki‑67 has dual functionality. In early mitosis, Ki‑67 functions as a surfactant to prevent chromosomes from collapsing into a single chromatin mass, whereas it actively promotes chromosome clustering during exit from mitosis. How Ki‑67 switches between these two opposing processes – chromosome dispersal and chromosome clustering – has remained unknown. Here, we demonstrate that Ki‑67’s biophysical properties radically change during anaphase onset, when all chromosomes merge into a single cluster. Ki‑67’s amphiphilic character is lost as its molecular brush structure collapses and the soluble pool of the protein forms condensates. Our study uncovers a cell‑cycle‑regulated mechanism that controls individualization and coalescence of chromosomes during mitosis.

Due to data protection regulations, we cannot publish the poster.

Resolving molecular ageing processes of nuclear pore proteins using a microfluidic droplet assay

Presenter: Tom Scheidt, University of Mainz, Germany

Abstract

The physiological permeability barrier for molecular traffic between the nucleus and the cytosol is filled with intrinsically disorder proteins (IDPs) and assembled by the nuclear pore complex (NPC). These highly enriched disordered nuclear proteins contain domains with high amounts of phenylalanine and glycine (FG‑Nups). In order to understand the physico‑chemical properties of such molecular “gatekeeper”, we made use of a microfluidic device capable of controlled protein condensation, combined with fast and parallelised data acquisition. Our microfluidic device permits studying phase separation on the seconds time scale (due to diffusive mixing and laminar flow), coupled with rapid optical inspection of permeability barrier properties. This time resolution is challenging to achieve by conventional benchtop experiments such as coverslip assays. Our experiments show a rapid aging of FG‑Nups into different material states (liquid, gel, solid etc.) within minutes under physiologically relevant concentrations. Already early droplets show typical properties of a liquid state and resemble a barrier and cargo delivery properties found for physiological nuclear transport. This includes formation of a natural barrier for cargoes larger than ~4 nm, unless accompanied by nuclear transport receptors (NTRs). For a better understanding of the evolution of supramolecular structures as well as the mechanical properties of FG‑rich droplets, we combine our microfluidic system together with coherent anti‑Stokes Raman spectroscopy (CARS) and particle tracking microrheology (PTM). This interdisciplinary approach provides a coherent picture to explain how the balance between homo‑ and heterotypic interactions in FG/NTR mixtures modulates the phase behavior and how this relates to the permeability barrier function of the condensed liquid state. The microfluidic platform described above can work as a general tool to study LLPS of phase separating proteins, particularly those that undergo rapid maturation to gel or amyloid like states, such as e.g. FUS, Tau and alpha‑synuclein or other proteins associated to neurodegeneration.

View poster

Reconstitution of tight junction like networks via ZO1 surface condensation and local actin polymerization

Presenter: Daxiao Sun, Max Planck Institute, Germany

Abstract

Tight junctions are adhesion structures of cell-cell contact in epithelial and endothelial. Biochemical and structural analysis revealed that tight junctions are composed of densely packed proteins forming a continuous membrane associated network at sub-apical, and are involved in adhesion, barrier, polarity, development and mechanotransduction functions, although the molecular basis underlying the assembly and positioning of tight junction network is not clear. Here we combined a bottom-up reconstitution approach on SLBs and computational simulation to investigate the mechanism behind tight junction network formation. We found that tight junction scaffold protein zona occludens1 (ZO1) undergoes surface phase separation with receptor proteins on SLBs and forms membrane condensates under a physiological concentration which is far below its 3D saturation concentration. We also showed that this process depends on receptor valency, receptor density, and ZO1 concentration. With AFM, we found that ZO1 membrane condensates are 2D structures with a height of one-layer molecules. Moreover, these 2D membrane condensates are sufficient to recruit other tight junction related components, like ZO2, ZO3, afadin, cingulin and especially actin. The enrichment of actin to ZO1 membrane condensates promotes actin polymerization and actin bundle formation. ZO1 membrane condensates deform on actin bundles simultaneously, and eventually form a continuous receptor-ZO1-actin network on SLBs together. Applying computational simulation, we showed surface phase separation with the presence of specific surface binding under saturation concentration, and the dependence on receptor valency, receptor density and ZO1 bulk concentration. Thus, combining in vitro reconstitution and computational simulation, our results suggest that surface phase separation and local actin polymerization underlies tight junction network formation. And this approach and mechanism could be applied to investigate and explain other membrane associated compartments formation.

Due to data protection regulations, we cannot publish the poster.

The EMBO | EMBL Symposium ‘Cellular mechanisms driven by phase separation’ took place from 9 – 12 May 2022.

What’s new in EMBL-EBI on-demand training

What’s new for EMBL-EBI training: June 2022

At EMBL-EBI training we have a dedicated on-demand library of free to access training courses, materials, and recordings. Read on to see what each section of our 200+ strong catalogue entails.

Training materials

We’ve all had our fair share of training courses, zooms, conferences, and workshops in our careers – and can all relate to the sheer mass of materials generated in just one of these events.

EMBL-EBI logo

EMBL-EBI Training is committed to creating FAIR and shareable data through our own courses and on-demand training. We welcome you to share these already created materials so that you don’t have to spend time recreating them for yourselves.

From EMBL-EBI resource tutorials to live course slide decks – our cohesive library of training materials is ready for you to use anytime, anywhere. All we ask is you credit us when presenting them!

Themed on-demand training sets

At EMBL-EBI training, we discovered a pattern of behaviour from our on-demand audience taking multiple courses within the same topic area.

So we’ve bought together four curated sets of learning to ease the journey for you. We have more ideas in the pipeline, but if you think of a curated set of learning you’d like to see, drop us a comment below!

Webinars – join in the next series

The bioinformatics topic du jour has to be AlphaFold. We’re planning a mini webinar series on the topic, beginning on 14 June 2022 with the ‘Scope and vision of AlphaFold’.

AlphaFold protein structure prediction showing detail of chemical elements.
AlphaFold protein structure prediction showing detail of chemical elements.

Registration for the webinar series is free, but essential to secure your place. If you can’t make it live, the recordings will be made available via these same links shortly afterwards.

Envelope Icon, Transparent Envelope.PNG Images & Vector - FreeIconsPNG  To stay up to date with news from the EMBL-EBI training on-demand catalogue, create an account and opt-in to news from us.

Best poster prizes at ‘Inter-organ communication in physiology and disease’

Almost 40 posters were presented at the virtual EMBO | EMBL Symposium ‘Inter-organ communication in physiology and disease’, showcasing how studies in model organisms are revealing novel inter-organ signals that contribute to whole-organism homeostasis. There were two live poster sessions and the presenters could also be contacted via chat, message or video call throughout the conference – their work was then voted for by other attendees and speakers. We are pleased to be able to share with you the research from the three winners of the best poster prizes: congratulations to Emily, Wilson and Maxim!

1st prize: Sex and reproductive differences in gut tumours

Presenter: Emily Strachan

Due to data protection regulations, we cannot publish the poster.

2nd prize: A protective neuro-adipose tissue axis against malaria

Presenter: Temitope Wilson Ademolue

Temitope Wilson Ademolue
Temitope Wilson Ademolue, Instituto Gulbenkian de Ciência, Portugal
Abstract

Infections lead to the development of host sickness behavior. This evolutionarily conserved response includes the withdrawal of the infected host from food, known as anorexia. This behavior limits the exogenous supply of metabolic substrates; and in the absence of a countervailing metabolic response, anorexia can lead to starvation and death. We reasoned that the infected host relies on the mobilization of stored metabolic substrates to minimize the deleterious effects of anorexia. Presumably, this is required to sustain vital metabolic processes compatible with survival. Using a non lethal rodent model of malaria, we show that Plasmodium infected mice progressively developed anorexia of infection. This was coupled to a profound loss of white adipose tissue via adipose tissue triglyceride lipase (Atgl) driven lipolysis; and was associated with the mobilization of free fatty acids, induction of ketogenesis, and triglyceride synthesis. The Inhibition of adipose tissue lipolysis via Atgl deletion specifically in adipocytes increased malaria mortality. This was associated with compromised thermoregulation and the collapse of organismal energy expenditure, indicating that mobilization of fat stores via lipolysis is essential to survive Plasmodium infection. Mechanistically, malaria induced lipolysis is controlled by the central nervous system as demonstrated using chemo genetically sympathectomized mice, lacking the peripheral arm of the sympathetic nervous system. In the absence of sympathetic outflow, Plasmodium infected mice failed to mobilize adipose tissue depots and to maintain energy expenditure, succumbing to malaria. In conclusion, we show that survival from malaria relies on metabolic response and adaptation that is coordinated by the sympathetic nervous system.

View the poster

3rd prize: Skeletal muscle-derived IL-6 orchestrates physiological adaptations in the context of inflammation

Presenter: Maxim Nosenko

Maxim Nosenko, Trinity College Dublin, Ireland
Abstract

Survival during infections relies on multiple resistance and tolerance mechanisms and requires the most adaptive response being launched based on the disease setting. While many immunological pathways, distinguishing pathogen type and localization, have been discovered, less is known about the mechanisms, sensing different stages of the infection, especially transition from local to systemic disease. The latter can be life threatening in situations such as sepsis or severe COVID 19, and thus tolerance mechanisms become crucial. Inflammatory cytokines, including IL 6, are believed to govern both immune response and adaptation in the context of infection. However, the mechanisms of tolerance induction are still poorly investigated.
To address this question, we employed a mouse model of LPS induced sepsis and analysed physiological response of the animals as well as proinflammatory cytokines production. Administration of LPS resulted in fatigue, hypoglycaemia, and hypothermia, that were associated with predominant accumulation of IL 6 in the blood. To address the role of IL 6 we employed knock out mice and observed a significant suppression of fatigue, increased blood glucose level and core temperature. Surprisingly, conditional inactivation of IL 6 in myeloid cells did not affect systemic cytokine accumulation in response to LPS. We next performed screening across tissues and found only skeletal muscles showing high expression of IL 6 gene in response to LPS, independently of IL 6 production by myeloid cells. Further investigation revealed a key role of IL 6 in reprogramming of glycogen metabolism in the liver upon LPS challenge, resulting in hypoglycaemia. Recent studies indicated the positive effect of hypoglycaemia during bacterial sepsis, suggesting that IL 6 mediates adaptation to this condition.
Altogether, we hypothesize that skeletal muscles are key systemic inflammation sensing organs, responsible for accumulation of IL 6 and induction of physiological adaptations. Further investigation of the role of IL 6 in the context of local and systemic inflammation could bring novel therapeutic opportunities for induction of the tolerance in life threatening infectious diseases.

View the poster

Congratulations to all three winners!

The EMBO | EMBL Symposium ‘Inter-organ communication in physiology and disease’ took place from 21 – 23 March 2022.

Return to onsite: our first in-person meeting in 2 years

A little over 100 participants from over 20 countries attended the first on-site meeting since the COVID-19 pandemic hit Europe in March 2020. And since then, we have been preparing for this moment. We just didn’t have a clue when it would come. And the rules of the ‘game’ kept changing.

Railli Pall

Raili Pall was the conference officer for the EMBO | EMBL Symposium ‘Biological oscillators’. She was in charge of the logistical side of the meeting.

“There were many last-minute changes and cancellations due to the ongoing pandemic and travel restrictions, and we had to adjust rapidly to the changes in the programme. In addition, there was an extra layer of complexity as we had to accommodate a mix of safety protocols and added regulations.”

But then the moment was there. Nervously, we were waiting for the first bus to arrive. Checking the screens, the rooms, the badges. We have done this countless times. But this time was different, after two years of only virtual events, we were back onsite.

Having started her position in 2020, at the beginning of the COVID-19 pandemic, this was also Raili’s first on-site meeting

“I was very excited, but definitely a bit nervous before the event began. As it was the first on-site conference for many participants after more than 2 years, I wanted everything to run smoothly.”

And it did! The atmosphere was great and everyone was in high spirits. The overall feedback from all the participants and speakers was extremely positive as well. Everybody was happy to be finally back to in-person meetings. The symposium helped delegates to discuss and develop new ideas together. There was plenty of interaction and space for interesting and inspiring discussions. In addition, the programme consisted of outstanding talks by leading experts, covering a broad range of topics. The on-site poster session was highly appreciated, with a lot of lively informal chats about science.

With this event, we adapted for the first time to a new hybrid format. Apart from the 100 participants attending in person, we also had around 70 virtual participants logging on to our virtual platform. Hybrid events open up participation to a broader group of people that otherwise would not have been able to attend due to lack of resources, busy schedules or difficulties travelling across the world. But like everything new, it also brings challenges. For us, that means trying to integrate things like poster sessions and networking sessions into the virtual event. So, we accept the challenge and look forward to welcoming more scientists to our events, both onsite and virtually.

Raili: “I am looking forward to my next hybrid event to bring together scientists from across the world. Build up my knowledge organising hybrid events with new ways of interaction and exploring more opportunities to create virtual options for in-person events.”

Group photo Biological oscillators, photo by Stuart Ingham/EMBL

The EMBO|EMBL Symposium ‘Biological oscillators: design mechanism and function’ took place 6 – 9 March 2022 at EMBL Heidelberg.

Poster prize winners of ‘Biological oscillators: design, mechanism and function’

A buzzing helix at The Advanced Training Centre. Scientists holding a beer or a soft drink, pointing at the poster, discussing, laughing. It might have been a bit awkward initially, but soon enough it felt like the old days. And not only was it fun to be around peers again, but the organisers were also highly pleased with the exceptional quality of the posters.

Out of 107 onsite participants and 52 posters, four won an award for best poster by popular vote. We would like to introduce to you the winners and their research:

  1. Katharina Sonnen / Sonja Weterings, Hubrecht Institute, the Netherlands
  2. Victoria Mochulska, McGill University, Canada
  3. Laurent Jutras-Dubé, McGill University, Canada & Joshua Hawley,  the University of Manchester, UK

Signaling dynamics in the homeostasis of the small intestine

Sonja Weterings / Katharina Sonnen, Hubrecht Institute, the Netherlands

Sonja Weterings, Hubrecht Institute

Abstract:

How information is transmitted between cells to govern development and tissue homeostasis in time and space remains a central question in biology. In particular, the role of signaling dynamics in this control is still largely unknown. While signalling dynamics during embryonic development have been studied extensively, such as in the control of mesoderm segmentation, the role of signalling dynamics in adult tissue is less well
understood. In the small intestine, a network of multiple signalling pathways coordinates homeostasis of the tissue. Here, I will present our latest findings on signalling dynamics in
the small intestine.

Download poster

Modelling the entrainment response of the somite segmentation clock

Victoria Mochulska, McGill University

Victoria Mochulska, McGill University

Abstract

In this study, a coarse-graining, entrainment approach is used to gain new insights into the dynamic properties of vertebrate segmentation clock from dynamical systems perspective. We entrain the mouse segmentation clock to various periods and extract information about the dynamic phase-locking behaviour, including the range of entrainment periods, entrainment phase, and the convergence route towards the entrainment phase. Using the entrainment quantification data, we derive the segmentation clock phase response curve (PRC). The inference of the PRC reveals two properties: a highly asymmetrical, mainly negative PRC, and an adjustment of the intrinsic period during entrainment.
We next construct a minimal model of the segmentation clock. We build upon the simplest non-linear phase oscillator, the classical Radial Isochron Cycle (RIC). We perturb it into an Elliptic Radial Isochron Cycle with Acceleration or ERICA. We then use Monte Carlo optimization to find parameters best fitting the experimental PRC. The results from this
optimization put the oscillator far from the standard RIC.
From the optimized ERICA model, we derive numerically the Arnold tongues of the system and the phase/detuning curves for all entrainment parameters. We correctly capture the entrainment range and the unusual sigmoidal shape of the entrainment phase as a function
of entrainment period. Our minimal model thus captures all the essential features of the segmentation clock during entrainment and reveals its underlying dynamical properties.
Combined, this coarse-grained theoretical-experimental approach reveals how we can derive simple, essential features of a highly complex dynamical system and hereby provides precise experimental control over the pace and rhythm of the somite segmentation clock.

Download poster

Or read the publication

Dynamic switching of lateral inhibition spatial patterns

Joshua Hawley, the University of Manchester

Abstract

Notch-Delta signalling, which forms a lateral inhibition loop between cells in direct contact, typically generates a population of alternating high and low expression. However, HES5 which is a downstream target of Notch has been found to exhibit interesting non-stationary spatial patterning of similarly expressing clusters of cells in the developing neural tube (Biga
et al., 2021; Manning et al., 2019). Theses clusters organise into an average spatial repetion of higher and lower expression every 3-4 cells, and crucially do not form stationary patterns over time, instead the peaks and troughs persist for an average of 6-8 hours before switching states (high-to-low or low-to-high) (Biga et al., 2021)
Our initial investigation into how the dynamic spatial pattern might be generated started by adapting a previously parameterised single-cell HES5 model (Manning et al., 2019) to a multicellular model, whereby HES5 dynamics are coupled between cells by a lateral inhibition Hill function. With this relatively simple model, we found that intermittent
coordination of neighbouring HES5 dynamics emerges from time-delayed Notch-Delta interactions, but that this model did not explain the regular switching (every 6-8 hours) and only infrequently formed spatial patterns of 3-4 cells. We are now building on this modelling work, focussing on additional mechanisms that generate dynamic switching and longer spatial periods. Specifically, we perform explorations of gradient-induced travelling waves inspired by somitogenesis studies (Sonnen et al.,
2021) the inclusion of protrusions to extend interaction distance between cells consistent with recent reports from (Hadjivasiliou et al., 2016), as well as investigating how perturbation from altered Notch signalling, cell cycle, or cell movement may enable the regular switching
between high and low expression. Overall this work aims to understand the function of this type of dynamic patterning in the context of differentiation decisions both spatially and temporally.

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Rectified Kuramoto synchronization in an embryonic oscillator ensemble

Laurent Jutras-Dubé, McGill University, Canada

Laurent Jutras-Dubé, McGill University

Abstract

During vertebrate embryo development, presomitic mesoderm (PSM) cells tightly synchronize their genetic oscillations in time and space to form somites. To model this synchronization process, early theoretical studies, as well as recent studies combining experimental observations and numerical simulations, have used the framework of coupled
phase oscillators. To represent the coupling of these phase oscillators, most studies employ the Kuramoto model, which predicts that two coupled oscillators will reach the average phase as they synchronize, a phenomenon called phase averaging. With the aim of testing this prediction, we develop a novel experimental assay to culture mouse PSM cells that are stably oscillating for an extended period of time, with a narrow period distribution and a wide phase distribution. Our experimental evidence is in disagreement with the Kuramoto model’s phase averaging prediction. To explain the observed coupling dynamics, we devise a new synchronization model, the rectified Kuramoto model. We extract predictions from our model and verify them with our experimental assay. Thus, we propose our rectified Kuramoto model as the best current alternative to the Kuramoto model, which we falsified, at least for mouse tailbud cells.

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Biological oscillators: design, mechanism and function took place at EMBL Heidelberg from  6–9 March 2022