BIFI - - Institute for Biocomputation and Physics of Complex Systems

Biophyzza Connection 2025
2025-04-04 11:30 - 14:00 (Europe/Madrid) | 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!!!

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

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: 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: 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

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: 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

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: 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: 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: Sylvie Callegari, del Eliza Hall Institute of Medical Research, Australia
2024-09-26 12:30 - 14:30 | 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: Sara García Linares. Universidad Complutense de Madrid.
2024-06-21 12:00 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI–Talk: Sara García Linares. Universidad Complutense de Madrid.
Title: Design of nanoreactors for plastic depolymerization based on pore-forming toxins
Abstract
Petroleum-based plastics are durable and accumulate in all ecological niches. Approximately 80% of waste objects are made of macroplastics, with most ending up dumped into the oceans. PET (polyethylene terephthalate) is the primary component in many synthetic fibers and water bottles, comprising 14.4% of total plastic waste. Our work focuses on improving biotechnological processes for PET degradation by designing more efficient enzymes. To achieve this, we design biocatalytic nanopores using computational modeling, based on the homo-octamer of a sea anemone toxin that forms pores in biological membranes. These pores are assembled into nanodiscs, forming individual water-soluble particles. At a temperature of only 40 °C and neutral pH, this biocatalytic nanoreactor can degrade PET nanoparticles from plastic bottles and other commercial versions of PET used in manufacturing plastic products. The products of these reactions include soluble BHET dimer, BHET itself, and mono-(2-hydroxyethyl)-terephthalic acid (MHET). The results obtained so far constitute a proof-of-concept for building biodegradable pore-based catalytic nanoreactors that could drive new developments in nanobiotechnology. This is exemplified by efficient systems for decomposing PET at levels comparable to the best-performing known engineering PETases, and moreover, at relatively low temperatures.
References
A. Robles-Martín, R. Amigot-Sánchez, S. Roda, […], S. García-Linares*, M. Ferrer*, V. Guallar* (2023). “Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores”. Nature Catalysis 6, 1174–1185. DOI: 10.1038/s41929-023-01048-6.
FRIDAY, 21st June 2024, 12:00 h
Edificio I+D (Conference room)

BIFI TALK: Athi N Naganathan, Indian Institute of Technology Madras (IITM), Chennai, India
2024-05-24 13:00 - 15:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: Athi N Naganathan, Indian Institute of Technology Madras (IITM), Chennai, India
Title: Conformational Tuning as a Mechanism to Determine Specificity and
Promiscuity
Abstract:
Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we resolve the underlying mechanism of promiscuous binding versus partial sub-functionalization by studying paralogous Acyl-CoA Binding Proteins (ACBPs) from Plasmodium falciparum. Combining experiments and simulations on two of the paralogs, A16 and A749, we show that minor sequence differences shape nearly every conformational feature. A749 displays a heterogeneous native ensemble, weaker thermodynamic coupling, enhanced fluctuations, and a larger binding-pocket volume, compared to A16. Tryptophan probes signal a graded reduction in the sampling of substates in the holo form, hinting at conformational-selection-like mechanism of binding. They exhibit a spectrum of binding affinities to acyl-CoAs with A749, the
more promiscuous and hence the likely ancestor, binding 1000-fold stronger to Lauroyl-CoA. We thus demonstrate how minor differences in long-range coupling and dynamics contribute to the evolution of contrasting functional repertoires in paralogs.

FRIDAY, 24th May 2024, 13:00 h
Edificio I+D (Aula room)

Webinar Digital Genres and Open Science
2024-05-14 10:00 - 13:00 | Online
M José Luzón and Carmen Pérez-Llantada (Digital Science Lab
Computing and Data ScienceBIFI) cordially invite you to participate in the webinar “Digital Genres and Open Science”, which will take place on Tuesday, 14 May 2024, from 10:00 to 13:00 (Madrid time).
The webinar will consist of three sessions dedicated to the presentation of our findings on digital genres for the promotion and dissemination of science. This presentation will be followed by a multidisciplinary round table (in Spanish): Oportunidades y retos de la comunicación digital) on the opportunities and challenges of open science.
A member of BIFI (Olga Abián) and members of Fundación Ibercivis (Francisco Sanz and Daniel Lisbona) are some of the invited speakers in this round table! See the programme on our website (https://genci.unizar.es/dissemination-event/)
The webinar is aimed at linguists with an interest in digital genres and researchers who wish to disseminate their research on the web. To attend, please complete the registration form here: https://docs.google.com/forms/d/e/1FAIpQLSelvvz006mRNM9F5HRVrnL2heR9vfRsu00M8Bk70qJV4L1ZLg/viewform

BIFI TALK: Narimantas Cenas, Vilnius University of Lituania
2024-05-08 12:30 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: Narimantas Cenas, Vilnius University of Lituania
Title: Single- and two-electron reduction of nitroaromatic compounds by
flavoenzymes: mechanisms and implications for cytotoxicity
Wednesday, 8th May 2024, 12:30 h
Edificio I+D (Conference room)

Biophyzza Connection
2024-03-22 12:30 - 14:30 | Campus San Francisco de la Universidad de Zaragoza
On March 22 at 12:30 a scientific dissemination event will take place at the Agri-Food Market at the San Francisco Campus (next to the campus pond, C. Pedro Cerbuna, 12) to give visibility to the BIOPHYSICS knowledge area. This day is part of the Biophysics Week (https://www.biophysics.org/biophysics-week#/) organized annually by the Biophysical Society of the United States with events around the world.
The event will consist of two informal talks by two researchers from the Institute of Biocomputation and Physics of Complex Systems (BIFI), one on toxic proteins involved in the development of neurodegenerative diseases, given by Dr. Nunilo Cremades, and another on drug Discovery using electron microscopy, given by Dr. Javier García-Nafría. The talks will be enlivened with pizza.
Our event will be held jointly with others at different Spanish universities coordinated by the Spanish Biophysics Society (SBE, http://www.sbe.es/) in an activity called ‘The Biophyzza Connection’ with the sponsorship of Domino’s Pizza .
In addition, the event is supported by the European project ivBM-4PAP (ivBM-4PAP is a research project funded by the European Innovation Council through its Horizon Europe Pathfinder programme with grant agreement No. 101098989), whose PI is Nunilo Cremades.

Hope to see you there!!!

III Cycle of young researcher seminars: Miguel Campos
2024-02-07 10:00 - 12:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
Miguel Campos, Bioflora, Escuela Politécnica Superior, Huesca
Comparative and functional genomics: a comprehensive approach to understanding the evolution of the Brachypodium annualis complex
Wednesday, 7 th February , 10 h
Sala de conferencias. Edificio I+D, Mariano Esquillor S/N.

XI International Conference BIFI 2024. ARTIFICIAL INTELLIGENCE AT THE CROSSROADS OF INTERDISCIPLINARY SCIENCE
2024-01-17 - 2024-01-19 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España

Dr. Roch Christian Johnson, Director Médico de la Fundación Raoul Follereau y Profesor Titular de la Universidad de Abomey-Calavi, Benín.
2023-12-01 10:00 - 12:00 | Salón de actos del CIBA, Salón de actos del CIBA, Zaragoza, España
Title: Improving Buruli ulcer and leprosy control in Africa

Abstract:
Neglected Tropical Diseases (NTD) are a diverse group of communicable diseases prevalent in tropical and subtropical areas. They affect more than a billion people and cost developing economies trillions of dollars every year. The socio-economic consequences are enormous. Of the 20 NTDs, 12 are endemic in Africa. The co-endemicity of certain diseases; the similarity of the clinical signs as well as the scarcity of financial, human and temporal resources called for an integrated management of these diseases, including Buruli ulcer and leprosy. The World Health Organisation road map 2021-2030 aims to accelerate progress towards the prevention, control, elimination and eradication of the 20 NTDs. Leprosy elimination and Buruli ulcer control are among the priorities. The target of elimination of leprosy as a Public Health Problem have been achieved since 2000 at the african regional level except the Comoros. Current Buruli ulcer treatment requires 8-weeks of daily rifampicin and clarithromycin, wound care and, sometimes, tissue grafting and surgery. Several clinical trials are currently ongoing and other experimental interventions have been proposed aiming to improve Buruli ulcer treatment by shortening its duration.
Moreover, pilot integration experiences have been implemented in different countries, particularly in Benin and Ivory Coast, with success, suggesting that this strategy is effective and efficient in consolidating the achievements of the fight against these diseases.

Organizadores
Santiago Ramón García, Grupo de Genética de Micobacterias, Departamento de Microbiología Pediatría, Radiología y Salud Pública, Facultad de Medicina, Universidad de Zaragoza; Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Zaragoza.
Emma Sáez López, Grupo de Genética de Micobacterias, Departamento de Microbiología Pediatría, Radiología y Salud Pública, Facultad de Medicina, Universidad de Zaragoza.
Consorcio BLMs4BU (https://blms4bu.org/)

FRIDAY, 1st December 2023, 10:00 h
Salón de actos del CIBA

BIFI TALK: Cristina Mayor Ruiz. IRB Barcelona (Barcelona, Spain)
2023-11-24 12:00 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: CRISTINA MAYOR RUIZ
Title: Targeted protein degradation: Chasing molecular glues and coping with resistance to degraders

Abstract:
Targeted protein degradation is a pharmacological strategy based on drugs (degraders) that destroy proteins by hijacking the intracellular proteolysis machinery. This strategy has garnered significant attention in the last year owing to its potential to modulate the abundance of proteins that are difficult to target with conventional inhibitors. Degraders can be multivalent (PROTACs) or monovalent (molecular glue degraders) depending on the number of chemical warheads. Molecular glue degraders offer a promising strategy for targeting disease-relevant proteins that were previously considered “undruggable”. Mechanistically, they orchestrate direct protein-protein interactions between a target protein and an E3 ubiquitin ligase. As a result, the target protein gets ubiquitinated and then degraded by the proteasome. Despite their great therapeutic potential, the discovery of molecular glue degraders has been largely serendipitous. I will discuss our efforts to facilitate the rational development of molecular glues.
In addition, many genetic determinants governing degrader efficiency have been mapped in recent years, bringing important lessons about resistance mechanisms. Our recent chemoproteomics journey aimed at identifying strategies to overcome broad resistance to degraders will be presented.

FRIDAY, 24th November 2023, 12:00 h
Edificio I+D (Conference room)

Webinar Digital Language and Communication Training for EU Scientists
2023-11-17 11:30 - 14:00 | Online
Webinar Digital Language and Communication Training for EU Scientists, Erasmus + project funded by the European Commission (Project No. 2022-1-ES01-KA220-HED-000086749), which will take place this coming Friday, November 17 at 12.30h.
In this seminar there will be brief presentations of the consortium, its objectives and its planned activities, related to the following topics:
– Ethnographies of digital science communication practices.
– Development of digital resources for the training of researchers in professional and public communication of science.
– Piloting, validation and implementation of online training
– Development of the project’s technological infrastructure and training resources.
Please find attached th
Translated with www.DeepL.com/Translator (free version) program and some infographics about DILAN.
Registration is free and can be done at the following link. Attendance will be certified:
https://forms.gle/fPMjUQQWVDq4sGJU7

II Cycle of young researcher seminars: Pablo Valgañón
2023-11-09 10:00 - 12:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
“Procesos de reacción-difusión y estrategias de control epidémico”. PABLO VALGAÑÓN

Wednesday, 8th November, 2023
10:00-12:00 h
Salón de actos.Edificio I+D

BIFI TALK: Salvatore Adinolfi. Department of Drug Science and Technology, University of Turin, Italy
2023-10-20 12:00 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: SALVATORE ADINOLFI. Department of Drug Science and Technology, University of Turin, Italy
Title: The contradictory role of frataxin in Fe-S cluster biogenesis
Abstract:
Frataxin is a small mitochondrial protein whose limited expression impairs Fe-S cluster biogenesis and promotes iron accumulation, leading to the neurodegenerative Friedreich’s ataxia. Although frataxin role is yet to be completely unraveled, its involvement as a regulator of the desulfurase activity in the Fe-S cluster biogenesis machinery has been demonstrated for both human frataxin and its bacterial ortholog CyaY. In this frame, although the human and the bacterial proteins share high homology in their aminoacidic sequence and tridimensional structure, a dramatic discrepancy has been highlighted by in vitro studies addressing their effect on the Fe-S cluster formation machinery. In particular, while CyaY slows down the kinetics of Fe-S cluster formation on IscU, human frataxin has emerged as an activator of Fe-S cluster biogenesis. In this review it will be described all the information to better understand the evolutionary divergence of the frataxin genes.
It is difficult to clarify this apparent paradox by studying the process in vitro where the isolated proteins are in an artificial environment or in vivo under non-controlled conditions. To clarify the issue, we have used a new approach based on metabolomics to study the enzymatic reaction. We followed the enzymatic kinetics ex vivo using bacterial to investigate enzymatic kinetics of IscS and the role that frataxin plays in it. We prove that IscS is inhibited by bacterial frataxin even in this ex vivo condition. We also prove conclusively that iron acts as the effector of the reaction in prokaryotes. This study provides a new powerful tool for the study of iron sulfur cluster biogenesis.

FRIDAY, 20th October 2023, 12:00 h
Edificio I+D (Conference Room)

TALK: Prof.Derek Bowie. McGill University, Montreal, Canada
2023-10-09 12:00 - 14:30 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
Re-imagining the glutamatergic synapse: From structure-function to neurological disease
Professor Derek Bowie. Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada
Abstract:
The Bowie Lab uses a combination of techniques to study ionotropic glutamate receptors (iGluRs), GABA-A receptors and more recently, sodium and potassium channels. All ion-channel families are widespread in the vertebrate brain and fulfill many important roles in healthy individuals as well as being implicated in disease states associated with postnatal development (e.g. autism, schizophrenia), cerebral insult (e.g. stroke, epilepsy) and aging disorders (e.g. Alzheimer’s disease, Parkinsonism). We are looking at iGluRs, GABA-A receptors, Na+ and K+ channels at two inter-related levels. In molecular terms, we are examining the events that occur when each ion-channel family is activated with the aim of developing novel therapeutic compounds. At the cellular level, we are studying the role they fulfill in shaping the behaviour of neuronal circuits and how these processes may be corrected in disease states. The talk will focus on recent work from the lab on a subclass of iGluRs, called AMPA receptors.
Biosketch:
Dr. Derek Bowie is a Professor of Pharmacology & Therapeutics at McGill University and co-Director of the Cell Information Systems. The Bowie lab focuses on several major ion-channel families with a special emphasis on their role in neurodevelopmental disorders. Dr. Bowie earned his Ph.D. at the University of London after completing his undergraduate degree at Strathclyde University in Scotland. He then carried out postdoctoral training in France (Université Louis Pasteur), Switzerland (Universität Zürich) and the US (National Institutes of Health) before taking a faculty position at Emory University (Atlanta, GA, USA). He started his research program at McGill in 2002 and is currently a Full Professor. He was recently a Visiting Professor in Japan (Natl. Institutes for Physiological Sciences). He is the recipient of the Canada Research Chair award in Receptor Pharmacology and has served on numerous national and international advisory panels including IBRO. He also serves/has served on several editorial boards including the Journal of Physiology, Current Neuropharmacology, Channels, Current Opinion in Physiology and Frontiers in Neural Circuits. In 2022, he co-founded the McGill spin-off company, Nospharma, to develop and bring to market therapeutics for the treatment of rare neurological disorders.

9th October, 2023
Salón de Actos, Edificio I+D
12 h

II Cycle of young researcher seminars: Patricia Bruñen
2023-10-04 10:00 - 12:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
Design and synthesis of FMN derivatives for covalent binding to apoflavodoxin from Anabaena. PATRICIA BRUÑEN.

Wednesday, 4th October, 2023
10:00-12:00 h
Edificio I+D

BIFI TALK: Inmaculada Pérez Dorado, Instituto de Química-Física Blas Cabrera (CSIC)
2023-09-29 12:00 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
BIFI TALK: INMACULADA PÉREZ DORADO, Instituto de Química-Física Blas Cabrera (CSIC)

Title: Host-pathogen interactions in pathogenic mycobacteria. Underlying molecular mechanisms and new ways for antimicrobial development.
Abstract:
The Mycobacterium genus contains over 150 recognized species, many of which produce infectious diseases in human such as tuberculosis or leprosy, caused by Mycobacterium tuberculosis (Mtb) and Mycobacterium leprae, respectively. Human tuberculosis is one of the world’s most devastating human ID responsible of ~1.5 million deaths every year; while leprosy is an IDs associated with permanent deformation, disability and stigma, with > 200.000 new cases every year. Our group aims at using structural biology approaches to acquire a deep understanding of biological systems involved in host-pathogen interactions in pathogenic mycobacteria, as well as finding new ways for antimicrobial development. Our work mainly focuses on the study of the ESX5 secretion system and LysA mycobacteriophage-encoded endolysins. The ESX5 secretion system is a complex molecular machine, and key virulence factor essential for the viability of pathogenic mycobacteria, including Mtb. EccC5 is a large ATPase, and pivotal ESX5 component, that provides the secretion driving force via ATP hydrolysis. Our structural studies reveal the lack of ATPase activity proposed for the N-terminal DUF domain of EccC5, which is likely conserved in other ESX systems from mycobacterial and non-mycobacterial species. These results uncover key features of the ESX-dependent secretion mechanism, and it may open new ways for inhibitor development targeting the EccC5-DUF domain. Bacteriophage endolysins are peptidoglycan hydrolases targeting the bacterial surface that, when exogenously applied, can produce a rapid and specific elimination of pathogenic bacteria. In this line, DS6A-LysA and D29-LysA are complex multidomain endolysins with potential antimicrobial application against pathogenic mycobacteria. Our crystallographic studies of DS6A-LysA and D29-LysA catalytic domains uncovers important aspects of the mechanism of cell-wall binding and hydrolysis by these endolysins, knowledge that is key for their potential application as specific antimicrobials.

FRIDAY, 29 September 2023, 12:00 h
Edificio I+D

BIFI TALK: Horacio López Menéndez
2023-06-02 12:00 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
Title: Connectivity as a tool to investigate hydro-geomorphic systems: A river delta case study.
Abstract:

FRIDAY, 2nd June 2023, 12:00 h
Aula: Edificio I+D

II Cycle of young researcher seminars: Irene Oliván Muro
2023-05-10 10:00 - 12:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
“Biofilms en Anabaena sp. PCC7120: estudio de los factores que afectan a su desarrollo y regulación por proteínas FUR”. IRENE OLIVÁN MURO
Wednesday, 10th May, 2023
10:00-12:00 h
Aula del Edificio I+D

BIFI TALK: Alejandro Tejedor ( BIFI )
2023-05-05 12:00 - 14:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
Title: Connectivity as a tool to investigate hydro-geomorphic systems: A river delta case study.
Abstract:
Connectivity plays a crucial role in natural and engineered systems, driving and resulting from various processes. For example, sediment fluxes shape the landscape, creating preferential paths for water and sediment transport, ultimately leading to channelized flows that affect the system’s response to changing forcings. Research in geomorphic systems has focused on understanding the emergent connectivity structures and their impact on system dynamics. To this end, network theory provides a suitable mathematical framework for quantitatively characterizing connectivity patterns. In this presentation, I will use river deltas as a case study to demonstrate how an integrated approach, combining network theory, remote sensing, and modeling tools, can enhance our understanding of the structure and dynamics of geomorphic systems. Specifically, I will showcase how analyzing river delta channel networks can help solve the inverse problem of inferring process from form, classify and compare river deltas, and predict their dynamic response to different forcing scenarios.

FRIDAY, 5th DECEMBER 2023, 12:00
Conference room: Edificio I+D

II Cycle of young researcher seminars: Sonia Hermoso Durán
2023-03-08 10:00 - 12:00 | Edificio Institutos I+D, Mariano Esquillor, 50018 Zaragoza, Zaragoza, Zaragoza, 50018, España
“Inteligencia artificial aplicada a TLB y proteomas: mejorando la detección precoz y la vigilancia del paciente para el diagnóstico clínico”. SONIA HERMOSO DURÁN
Wednesday, 10th March, 2023
10:00-12:00 h
Aula del Edificio I+D
