BIFI TALK: Sylvie Callegari, del Eliza Hall Institute of Medical Research, Australia
2024-09-26 12:30 - 14:30 (Europe/Madrid) | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALKS: Sylvie Callegari, del Eliza Hall Institute of Medical Research, Australia
Title: Activating PINK1 to treat Parkinson’s disease
Abstract
PINK1, a protein linked to Parkinson’s disease, is a ubiquitin kinase that accumulates on the outer membrane of damaged mitochondria. Upon accumulation, PINK1 becomes activated and phosphorylates ubiquitin, generating a unique phospho-ubiquitin signal that triggers mitophagy to remove damaged mitochondria. Enhancing PINK1 activation is a promising strategy for boosting mitochondrial turnover in Parkinson’s patients. Using Cryo-EM, we recently elucidated the activation mechanism of PINK1 and used our structural platform to study PINK1 activator compounds, overturning previous assumptions about their mechanism of action. Another therapeutic approach to target PINK1 is to enhance it’s stabilisation on the outer mitochondrial membrane, but despite decades of research into PINK1 function, the mechanism of PINK1 stabilisation has remained elusive. Using single particle cryo-EM, we determine the structure of stabilised human PINK1 on the Translocase of the Outer Membrane (TOM) to a resolution of 2.8 Å. This uncovers an unusual arrangement of the TOM complex and challenges previous models on the mode of ubiquitin phosphorylation by PINK1. Understanding the mechanisms of PINK1 stabilisation and activation opens up new therapeutic possibilities for using PINK1 to promote the turnover of damaged mitochondria in Parkinson’s disease patients.
Thursday, 26th September 2024, 12:30 h
Edificio I+D (Conference room)

BIFI TALK: José Manuel Martín García, Instituto Blas Cabrera, CSIC, Madrid
2024-09-27 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: José Manuel Martín García, del Instituto Blas Cabrera, CSIC, Madrid
Title: Time-resolved structural studies with serial crystallography: A new frontier in biomedical research.
Abstract
Structural biology, especially X-ray crystallography, has significantly advanced our understanding of diseases by revealing the 3D structures of proteins. However, traditional X-ray crystallography encounters challenges, such as difficulties in obtaining suitable protein crystals and studying protein dynamics. X-ray free-electron lasers (XFELs) have transformed this field with their bright and brief X-ray pulses, allowing for high-resolution structures of radiation-sensitive and hard-to-crystallize proteins. With XFELs, structural biology is also shifting its focus from determining static structures to exploring the dynamic aspects of protein function. A key tool for investigating these dynamics is mix-and-inject time-resolved crystallography (MISC), which has emerged as a transformative approach in drug discovery, offering unprecedented insights into the dynamic processes of protein function. Traditional X-ray crystallography provides static snapshots of protein structures, which, while valuable, do not capture the full complexity of molecular interactions and conformational changes critical to drug efficacy. MISC, leveraging the capabilities of XFELs and advanced synchrotron sources, allows researchers to observe proteins in action at atomic resolution and in real-time. This technique employs ultra-fast, intense X-ray pulses to trigger and capture transient states and intermediates in biochemical reactions, providing a dynamic view of protein-ligand interactions, enzyme mechanisms, and conformational changes. These insights are crucial for the rational design of drugs with improved specificity and efficacy. In this seminar, I will introduce MISC at XFEL and synchrotron facilities, as well as present some of the most recent results we have obtained in my group by applying this powerful technology to several biomedical research projects.
FRIDAY, 27th September 2024, 12:30 h
Edificio I+D (Conference room)

BIFI TALK: David Fernández-Antorán. Gurdon Institute, Cambrigde and ARAID-IIS Aragón
2024-10-18 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: David Fernández-Antorán. Gurdon Institute, Cambrigde and ARAID-IIS Aragón
Title: Epithelioids: Long-term and self-maintained primary 3D cultures to study tissue behaviour in vitro
Abstract
This talk will introduce “Epithelioids,” a novel 3D primary epithelial culture system that enables the long-term, self-sustaining growth of tissues derived from both normal and tumour samples. Epithelioids maintain the proliferation, differentiation, and structural integrity of adult epithelial tissues, faithfully replicating the complex interactions between different cell types, including the immune system. With their high genomic stability, Epithelioids are particularly suited for studying long-term tissue responses to clinical treatments and environmental factors. This system offers a powerful tool for investigating tumour-normal tissue interactions and is ideal for research into stem cell dynamics and cancer biology, including tumour responses to radio and chemotherapies.
FRIDAY, 18th October 2024, 12:30 h
Edificio I+D (Conference room)

BIFI TALK: Ariadna Pié Porta, Department of Chemical and Biochemical Engineering, Technical University of Denmark
2024-11-22 12:30 - 14:00 | Salón de Grados, Facultad de Ciencias
BIFI TALK: Ariadna Pié Porta, Department of Chemical and Biochemical Engineering, Technical University of Denmark
Title:Oxidases and their Michaels Constant for Oxygen: Relevance and Measurement
Abstract
Medicine has benefited from the great features of enzymes for many years. During the past decades, the interest in the application of enzymes as (bio)catalysts to produce a wide range of valuable compounds has increased. In particular, oxidative reactions are crucial in many synthetic processes for the production of a wide range of chemicals. Oxidative biocatalysis has a number of pros and cons regarding the need of a constant supply of oxygen, which affect kinetics and stability. Often, oxidative biocatalytic processes tend to become oxygen limited. Not only oxygen is a rather hydrophobic molecule (the maximum concentration of oxygen dissolved in water in equilibrium with air is 250 µM), but also industrially-relevant enzymes tend to have a rather high Michaelis constant for oxygen (KMO). This is, considering oxygen a secondary substrate in the reaction, enzymes reach only low reaction rates even at the maximum concentration of dissolved oxygen in the media. On one hand, oxygen limitation reduces the rate of the reaction in an industrial perspective, and on the other hand, prevents scientists from measuring and calculating the correct and absolute KM for any oxygen-related enzyme that does not reach its maximum rate of reaction. To address this issue, we present the Tube-in-Tube Reactor Setup1. The Tube-in-Tube Reactor Setup is a novel tool that allows the saturation of virtually any enzyme with oxygen in order to determine its absolute KMO.
References: Ringborg, R. H.; Toftgaard Pedersen, A.; Woodley, J. M. Automated Determination of Oxygen-Dependent Enzyme Kinetics in a Tube-in-Tube Flow Reactor. ChemCatChem 2017, 9 (17), 3285–3288. https://doi.org/10.1002/cctc.201700811.
FRIDAY, 22 November 2024, 12:30 h
Sala de grados Grados de la Facultad de Ciencias (edificio A)

BIFI TALK: Francisco Ciruela, Universidad de Barcelona e Institut d’Investigació Biomèdica de Bellvitge
2024-11-29 12:30 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: Francisco Ciruela, Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain.
Neuropharmacology and Pain Group, Neuroscience Program, Institut d’Investigació Biomèdica de Bellvitge, IDIBELL, 08907 L’Hospitalet de Llobregat, Spain.
Title: Adenosine receptor heteromers: biasing antipsychotics
Abstract
The striatal dopamine D2 receptor (D2R) is generally accepted to be involved in positive symptoms of schizophrenia and is a main target for clinically used antipsychotic drugs (APDs). In fact, D2R is highly expressed in the striatum, where they form heteromers with the adenosine A2A receptor
(A2AR). Changes in the density of A2AR-D2R heteromers have been reported in postmortem tissuefrom patients with schizophrenia,1 but the degree to which A2AR are involved in schizophrenia and the effect on antipsychotic drugs is unknown. Therefore, we first assessed the impact of A2AR expression on psychotic-like behaviour and dopaminergic transmission in mice. Interestingly, mice lacking A2AR showed behavioural alterations related to cognitive impairment, anxiety, and anhedonia. In addition, these animals have altered sensorimotor gating. These behavioural alterations are compatible with a psychotic-like phenotype. Importantly, while total adenosine levels in the striatum of the A2AR -/- mouse are increased, total dopamine was unaltered. However, alterations in dopamine release were observed in the open field arena in the A2AR -/- mouse. Next, we examine the effect of exposure of different prototypical APDs on A2AR-D2R heteromerization in mammalian cells using a NanoBiT assay. Interestingly, clozapine, but not haloperidol or aripiprazole, was associated with a significant decrease in A2AR-D2R heteromerization after 2 h of treatment. Computational binding models of these compounds revealed distinctive molecular signatures that explain their different influence on heteromerization. The bulky tricyclic moiety of clozapine displaces TM 5 of D2R, inducing a clash with A2AR, while the extended binding mode of haloperidol and aripiprazole stabilizes a specific conformation of the second extracellular loop of D2R that improves the interaction with A2AR.2 Finally, we evaluated the heteromerization capacity of the genetic variants of the D2R gene associated with schizophrenia.3 While the ICL2-based D2R schizophrenia associated genetic variants did not affect receptor’s heteromerization with A2AR, the R150H located at the TM4 stabilizes the D2R-A2AR heteromer. Interestingly, aripiprazole showed reduced efficacy in stabilizing D2R-A2AR heteromers containing the genetic variant D2R-R150H, compared to haloperidol, suggesting a differential impact of D2R schizophrenia associated genetic variants in antipsychotic treatments. Overall, there exists a clinical need for the development of mechanistically novel and more efficacious APDs, thus understanding the impact of D2R-A2AR heteromer formation on D2R downstream signalling will certainly contribute to the development of such novel APDs.

References
1. Valle-León, M. et al. Decreased striatal adenosine A2A-dopamine D2 receptor heteromerization in schizophrenia. Neuropsychopharmacology 46, 665–672 (2021).
2. Valle-León, M. et al. Unique effect of clozapine on adenosine A2A-dopamine D2 receptor heteromerization. Biomed Pharmacother 160, (2023).
3. Valle-León, M. et al. Insights of schizophrenia-associated dopamine D2 receptor variants: eƯects on antipsychotic-mediated modulation of receptor heteromerization. Transl Psychiatry In preparation,(2024).

FRIDAY, 29 November 2024, 12:30 h
AULA del edificio I+D

XII National Conference BIFI 2025
2025-01-15 08:00 - 2025-01-17 21:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
XII Congreso Nacional BIFI 2025
The XII National Conference BIFI 2025, hosted by the Institute for Bio-computation and Physics of Complex Systems of the University of Zaragoza, provides a unique occasion for participants to share their latest findings across the Institute’s diverse research fields: from Physics and Computation to Bio-Physics, Bio-Chemistry, and Cell and Molecular Biology.
On this occasion, the conference will be held at the institute premises in the I+D building of Campus Río Ebro, in the University of Zaragoza, from January 15th to January 17th 2025.
As in previous editions of the BIFI National Conferences, we regard this meeting as an important occasion to strengthen our collaborations, foster new connections, and collectively advance our research. All BIFI members, especially those in the early stages of their careers, are strongly encouraged to participate and send their contributions.
More information https://bifi25.bifi.es/
MAIN TRACKS:

Biochemistry, Molecular and Cellular Biology
Physics
Biophysics
Computation

IMPORTANT DATES
Dates of the Conference: January 15th – January 17th, 2025.
Registration deadline: December 13th, 2024.
Abstract submission deadline: December 13th, 2024.
VENUE
Conference Room, Edificio I+D, Campus Río Ebro.
SPONSORS

BIFI TALK: Giovanni Catania. UCM, Madrid
2025-02-06 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
Title:Challenges and advances in the training of Energy-Based Models: theoretical insights on non-equilibrium sampling and overfitting
Abstract
In the context of unsupervised learning and generative models in artificial intelligence, energy-based models (EBMs) provide a simple way to describe arbitrary complex datasets, by encoding their empirical distribution into a Boltzmann probability law with a given energy function. EBMs can be used to generate new data statistically equivalent to the training set, and to extract microscopic information, i.e. effective interactions among data components. In this talk, I will review the basic foundations of EBMs from a statistical physics point of view, highlighting their connection with maximum-entropy models. I will then focus on typical challenges/issues related to the training, which is usually performed through an iterative maximum-likelihood procedure. The first problem is related to the sampling protocol, which is required to estimate one of the terms appearing in the log-likelihood’s gradient: in this context, I will discuss a recent work that theoretically describes recent proposed training strategies based on non-persistent short Markov Chain MonteCarlo (MCMC) runs as an efficient way to generate good-quality samples. The second part focuses on the impact of finite amount of data in the model’s reconstruction, a problem related to the concept of overfitting in machine learning: I will discuss recent theoretical results that analyze the training dynamics of simple EBMs (focusing on the Gaussian model), and show how i) overfitting emerges from an interplay of different learning timescales associated to different principal components of the data and ii) how different data-correction protocols can be used to mitigate the impact of overfitting for EBMs that employ low-order sufficient statistics of the data.

Thursday, 6 February 2025, 12:30 h
Conference Room. Edificio I+D

BIFI-TALK: James Krieger. CNB-CSIC, Madrid
2025-02-11 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI-TALK: James Krieger. CNB-CSIC, Madrid
Title: A Perspective on CryoEM, Heterogeneity and Dynamics
Abstract
Proteins are dynamic objects that change their shape (conformation) and move around and interact with other molecules (composition) to carry out functions. Cryogenic electron microscopy (CryoEM) is a valuable technique for capturing the resulting heterogeneity, thanks to many developments in hardware and software.
Nevertheless, understanding dynamics and function from CryoEM is still a challenge. The last few years has seen a second revolution in image processing to handle heterogeneity in new ways, driven by developments in machine learning.Many new approaches have been tried, giving the field much to think about.
I will reflect on the challenges of analysing CryoEM images and the successes and limitations achieved with new heterogeneity methods, focusing on two methods developed in our lab: Zernike3D and HetSIREN.
I will give examples based on synthetic data, widely used public data sets and specific systems that we have studied, particularly the coronavirus Spike protein.
Thursday, 11 February 2025, 12:30 h
Conference Room. Edificio I+D

BIFI TALK: Angel Perez Lara, Universidad de Granada
2025-02-21 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: Ángel Pérez Lara, Universidad de Granada
Title: Molecular mechanism of neurotransmitter release machinery
Abstract
Transmission of information between neurons relies on the neurotransmitter release from synaptic vesicles into the synaptic cleft upon the influx of Ca2+, a process known as synaptic exocytosis. Synaptic exocytosis is mediated by the SNARE proteins syntaxin 1 (syx-1A), synaptobrevin-2 (syb-2), and SNAP-25, which form the core of the supramolecular fusion machinery. However, SNARE proteins require additional regulatory proteins to control the early steps of their assembly, such as Munc-18 and Munc-13, and proteins that are specialized for fast, calcium-dependent synaptic exocytosis, such as synaptotagmin and complexin. Additionally, after exocytosis, the SNARE complex needs to be disassembled by the NSF/a-SNAP complex to recycle the individual SNARE proteins for another round of neurotransmitter release.
Understanding the molecular mechanisms underlying synaptic vesicle exocytosis and recycling is a central goal of molecular neuroscience. Despite major efforts by many laboratories, we have still no coherent picture of the sequence of the protein associations and dissociations, and the related conformational changes. Our lab aims to characterize the sequence of protein associations and dissociations of the assembly and disassembly of the SNARE complex -the choreography-, and its regulation, providing an in-depth understanding of the synaptic vesicle exocytosis.
Friday, 21 February 2025, 12:30 h
Conference Room. Edificio I+D

BIFI-TALK: Xavier de la Cruz Monserrat. Vall d'Hebron Institute of Research, Barcelona
2025-03-14 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI-TALK: Xavier de la Cruz Monserrat. Vall d’Hebron Institute of Research, Barcelona
Title: Cracking the Hereditary Disease Code: Revisiting Predictive Properties with a Probabilistic Touch
Abstract
As genomic sequencing becomes widespread in clinical settings, in silico pathogenicity predictions are increasingly vital for precision medicine. However, despite advances in machine learning-based classifiers, existing approaches are reaching a performance plateau while still facing interpretation challenges. In response, a paradigm shift has emerged in recent years, moving from binary classification toward modeling the quantitative impact of genetic variants.
Our work in this area has shown good performance, as demonstrated by our contributions to the CAGI5 and CAGI6 challenges, yet there is still room for improvement. In this talk, I will focus on a key aspect of pathogenicity prediction: the extraction of new discriminant features from traditional predictive properties, using a simple probabilistic framework. In particular, I will share insights from our approach and present preliminary results that highlight its potential impact on predictive models.
Friday, 14 February 2025, 12:30 h
Conference Room. Edificio I+D

Biophyzza Connection 2025
2025-04-04 11:30 - 14:00 | Campus San Francisco de la Universidad de Zaragoza
On the 4th of April, 2025, from 12 to 2 pm, there will be a Scientific Dissemination Day in the Agroalimentary Market of the San Francisco Campus (next to the Campus Pond, C. Pedro Cerbuna, 12), in order to make the field of BIOPHYSICS more visible. There will be a tent where two informative talks on biophysics will be held and free pizza will be provided by Domino’s Pizza. The speakers are two eminent researchers: Jesús Gómez-Gardeñes (BIFI-UZ) and Inmacula Yruela (Experimental Station Aula Dei – CSIC). You can see the poster on the link.
This event is part of Biophysics Week (https://www.biophysics.org/biophysics-week#/), which organises activities in this field all over the world. In Spain, the Biophysics Society of Spain coordinates the Biophyzza Connection event, which has been held simultaneously in many Spanish cities for the last two years and is sponsored by Dominos pizza.
This will be the second edition in Zaragoza and, like the previous one, is being promoted by BIFI researcher Nunilo Cremades Casasín.
Last year we were the second country in the world with the most biophysics activities! And this year it can’t be less.
We are waiting for you on the 4th April in the tent of the Agrifood Market of the San Francisco Campus!
Hope to see you there!!!
