Institute for Bioengineering of Catalonia

PhD Discussion Sessions: Teodora Andrian and Xavier Arqué
2021-04-30 10:00 - 12:00 (Europe/Madrid)
Correlating super-resolution microscopy and transmission electron microscopy for nanoparticle characterisation
Teodora Andrian, Nanoscopy for nanomedicine group
The functionalization of nanoparticles with surface functional moieties is a key strategy to achieve bioactivity and cell targeting in nanomedicine. The interplay between size and ligand number and distribution is crucial for the formulation performance and needs to be properly characterized to understand nanoparticle structure-activity relations. However, the particle-to-particle heterogeneity poses a serious challenge due to the lack of methods able to measure both size and ligand number and distribution at the same time and at the single particle level. Here we address this issue by introducing a correlative method combining super-resolution microscopy (SRM) and transmission electron microscopy (TEM) imaging. Correlative light and electron microscopy (CLEM) techniques proved their potential in structural biology but to the best of our knowledge, they have not yet been explored for the structural characterization of nanoparticles. Here we apply our super-resCLEM method to characterize the relationship between size and ligand number, and ligand density in PLGA-PEG nanoparticles at the single particle and single-molecule level. We highlight how heterogeneity found in nanoparticle size can impact ligand distribution, and we discuss the implications on formulation performance. We show how a significant part of the nanoparticle population goes completely undetected in the single-technique analysis, demonstrating that the characterization of nanomaterials using a multiparametric correlative method outplays the information obtained compared to a one-method-at-a-time approach. Using SRM alone, we demonstrated how PEG architecture can influence ligand conjugation efficiency and accessibility. The applicability of our method spans beyond PLGA-PEG nanoparticles and holds great promise for the multiparametric analysis of several other parameters and nanomaterials.
Unraveling the fundamental aspects of enzyme-powered micromotors
Xavier Arqué, Smart Nano-Bio-Devices group
Enzyme-coated micro- and nanomotors self-propel by the biocatalytic conversion of substrates into products and show great promise as actively navigating agents in the fields of biomedicine and environmental applications. However, many of the fundamental aspects underlying enzyme-powered self-propulsion have yet to be fully understood and are crucial for their optimal implementation. Under this framework, this research is focused on elucidating and studying the intrinsic (catalytic turnover or structural flexibility) and extrinsic (bulk and local ionic media) enzymatic properties that lead to an improved active motion powered by bio-catalysis. This is enabled by exploring novel types of both i) enzymes that can act as active motion engines and ii) platforms with appealing properties to be used as chassis of enzymatic micro- and nanomotors. Overall, this work contributes to a better understanding of the mechanism of motion of enzymatic active motion, expands the current library of enzymatic engines and chassis materials available, and provides new insights into the feasibility of implementation of enzyme-powered micro- and nanomotors.
The session will be held online using the GoToMeeting Platform

PhD Thesis Defence: Martina Di Muzio
2021-05-11 10:00 - 12:00
Nanoscale dielectric mapping of biomembranes with in-liquid Scanning Dielectric Microscopy
Martina Di Muzio, Nanoscale bioelectrical characterization group
The defence will take place online, if you wish to attend to this defence, you can find the link to access here and you can find more information here
Please join the meeting few minutes before the mentioned time to avoid session interruption.
If you are joining after the mentioned time, please make sure your microphone is muted before joining the session.

PhD Thesis Defence: Harishankar Balakrishnan
2021-05-12 10:00 - 12:00
Nanoscale Tomography based in Electrostatic Force Microscopy
Harishankar Balakrishnan, Nanoscale bioelectrical characterization group
The defence will take place online, if you wish to attend to this defence, you can find the link to access here and you can find more information here
Please join the meeting few minutes before the mentioned time to avoid session interruption.
If you are joining after the mentioned time, please make sure your microphone is muted before joining the session.

Online IBEC Seminar: Mónica Marro
2021-05-14 10:00 - 12:00
A new molecular dimension: exploiting Raman spectroscopy in Biomedicine
Mónica Marro, ICFO, The Institute of Photonic Sciences

Raman spectroscopy is a promising optical technique that enables the investigation of the molecular content of biological samples in a rapid, non-invasive, label-free and multiplexed approach. In the biomedical field, it is of special interest because the device can be portable and cost-effective.
In this seminar, I will show my work exploiting Raman spectroscopy in a broad range of biomedical applications from the molecular, to cellular and tissue level. I will present how Raman spectroscopy can represent a step forward into different fields, namely: cancer diagnosis, patient stratification, and personalized medicine; neurodegeneration; and mechanobiology. I will show also optical developments that can improve Raman spectroscopy in the speed of image acquisition, like the Raman light sheet approach, or Surface Enhanced Raman spectroscopy.
Overall, I will show how Raman spectroscopy coupled with data science and developments in photonics and nano-engineering could revolutionize the biomedical field in the next years, providing new and other-wise inaccessible molecular information, and giving an unprecedented step towards a more rapid, accurate, personalized diagnosis and treatments.

Research4Talent 2021
2021-05-21 09:30 - 13:30
On Friday 21st May we’ll open our doors virtually to UNDERGRADUATE & MASTER’s students interested in a research career

The day is a chance for you to talk to our researchers and ask them questions about their day-to-day work in the lab, career paths, work-life balance, mobility etc, as well as a visit to our labs.
In 2020 IBEC signed more that 120 internship agreements for Undergraduate and Master Students with a wide range of national and international universities.
This year’s edition will be held virtually. If you are interested in IBEC’s seventh edition of reSEARCH4TALENT please stay connected, we will soon provide more info with the links to acces the event.
Visit the website here

PhD Thesis Defence: Enara Larrañaga
2021-05-25 03:00 - 17:00
Effects of substrate-derived cues in driving the self-organization of organoid-derived intestinal epithelia
Enara Larrañaga, Biomimetic systems for cell engineering
The defence will take place online, if you wish to attend to this defence, you can find the link to access here and you can find more information here

M-CELS Workshop Barcelona Satellite
2021-06-04 14:30 - 18:00
EMBL and IBEC aim to contribute to the discussion on challenges and opportunities in the expanding field of Multi-cellular engineered living systems (M-CELS).
We have organized a satellite session to the M-CELS Workshop 2021 organized by the Center for Emergent Behaviors of Integrated Cellular Systems. The session aims also to be an appetizer to the 2nd EMBL-IBEC Winter Conference on Engineering Multicellular Systems to be held on 9-11th February 2022 in Barcelona.

Multi-cellular engineered living systems are purpose-driven living systems with multiple interacting living components. They are engineered for specific goals or functions but take emergence into account during the design process, allowing the final system to emerge through natural and non-natural biological processes. M-CELS research is intended to provide a fundamental engineering understanding that enables a quantitative approach bridging between single cells and organs or organisms. The field is still developing, so M-CELS as a field of research is still rapidly expanding
Registration here

Biennal Ciutat i Ciència
2021-06-08 08:00 - 2021-06-13 17:00
Durant els dies 8 i 13 de juny tindrà lloc la segona edició de la Biennal Ciutat-Ciència de Barcelona, i l’IBEC serà un dels centres que hi contribuirà, a través dels seus experts. A més a més, aquesta Biennal culmina amb la 14ª edició de la Festa de la Ciència, amb moltes propostes per viure la ciència en primera persona.

Des de l’IBEC, diversos experts participen en les activitats programades per enguany:

Samuel Sánchez, Professor de Recerca ICREA, i líder del grup “Smart Nano-bio-devices”, paraticipa a – “Pecha Kucha express: art, ciència, tecnologia”
Nuria Montserrat, participa amb una micro-xerrada sobre “Miniòrgans humans per entendre la covid-19”
L´Anke Kleff, Senior HR Development Officer a l´IBEC, participarà en una taula rodona sobre “Expandim l´influència de la dona a la ciència”, dins d’una nova Trobada de #100tífiques

IBEC Online Seminar: Jessica Ilenburg
2021-06-18 10:00 - 12:00
Tissue Engineering in Microgravity
Jessica Ilenburg, Gravitational Biotechnologist at Yuri gravity
Tissue Engineering and regenerative medicine are two fast growing and fast moving research fields. With the invention of bioprinting and tissue chips two breakthrough innovations have been made and now research in microgravity (for example on the ISS) promises even more and faster progress. A lot of advantages, like less contact inhibition and unrestrained growth in all 3 dimensions make the cell structures grow bigger and more complex. This presentation focuses on the qualities of the unique research environment of microgravity and introduces a couple of research findings.
Jessica Ilenburg is doing her master studies in molecular biotechnology at Bielefeld University in Germany. Currently she is working at yuri GmbH as a gravitational biotechnologist focusing on Tissue Engineering, bioprinting and protein crystal growth in microgravity. Previously she has worked at the Novo Nordisk Foundation Center for Biosustainability in Copenhagen working with thermophilic organisms and isolating proteins of the butanol pathway.

PhD Thesis Defence: Xarxa Quiroga
2021-06-23 10:00 - 12:00 | Auditori Antoni Caparrós – PCB
Plasma membrane mechanosensing upon stretch-induced topography remodelling
Xarxa Quiroga, Cellular and molecular mechanobiology group.
The thesis defence takes place tomorrow at 10AM in the “Antoni Caparrós” auditorium, located at the PCB Tower D, with limited capacity.

PhD Thesis Defence: Maria Arista
2021-06-28 10:00 - 12:00
Unveiling viral structures by single-molecule localization microscopy
Maria Arista, Nanoscopy for nanomedicine group
The defence will take place online, if you wish to attend to this defence, you can find the link to access here and you can find more information here

PhD Thesis Defence: Ferran Velasco
2021-07-01 09:30 - 12:00
Carboxymethyl cellulose-based cryogels as scaffolds for pancreatic and skeletal muscle tissue engineering
Ferran Velasco, Biosensors for bioengineering group
The defence will take place online, if you wish to attend to this defence, you have to send an email to doctoratmedicina@ub.edu and you can find more information here

PhD Discussions: Ignasi Granero
2021-07-02 10:00 - 12:00
Ignasi Granero, Celular and molecular mechanobiology group
In eukaryotic cells, the cell nucleus contains the DNA and directs the reaction to important signalling cascades, both biochemical and biomechanical. At the Cellular and Molecular Mechanobiology lab we study how forces and the physical characteristics of the cell environment affect cell behaviour and homeostasis. In my case, I am interested in how the cell nucleus senses physical changes and triggers a cell response to them.
For this purpose, we have engineered a battery of fluorescent proteins, which change their location depending on the physical state of the nucleus. Higher forces in the nucleus correspond with higher nuclear accumulation of these proteins. Indicating that these proteins react to mechanical/morphological stimuli. Then, we have chosen the variant that can be used as a mechano-sensor. Currently, we are testing the sensor in single- and multi-cell approaches to understand its behaviour in different systems and the ruling principles under its functioning.
This PhD Discussion will be held online using the GoToMeeting app

Online IBEC Seminar: Xavier Fernàndez-Busquets
2021-07-09 10:00 - 12:00
Nanomalaria group: 20 years at IBEC
Xavier Fernàndez-Busques, group leader of the Nanomalaria group at IBEC
We will start by briefly looking at the origins of our group back in 2001 as part of IBEC’s embryo, the Research Center for Bioelectronics and Nanobioscience. Our current activities integrate two decades of cumulative research oriented to the development of targeted nanocarriers for parasitic diseases with focus on malaria but currently expanding to leishmaniasis.
Because eventual antimalarial nanomedicines need to be deployed in low per capita income regions, their final components must take into account this particular economic landscape. Liposomes and polymeric nanocarriers offer advantages and suffer from limitations depending on the severity of the disease in each particular clinical case. Entering erythrocytes, the host cell of Plasmodium in the blood circulation, is a challenge in itself due to their lack of endocytic processes. Antibodies, polysaccharides like heparin, synthetic polymers and DNA aptamers have been used to target and eventually penetrate red blood cells.
Finally, we have recently launched an effort to discover new antimalarial drugs that should constitute the third and final element in the design of targeted nanocarriers for malaria. The know-how acquired in the development of nanocapsules, targeting elements and drugs has the capacity of being exported to other infectious diseases. Because, no matter how cost-efficient you can make a nanomedicine, clinical trials will significantly increase its cost, we are exploring a radical alternative: designing nanocarriers to target the parasites in their arthropod vectors.
More information about Xavier’s research here
This seminar will be held using the TEAMS app

Online IBEC Seminar: Pau Gorostiza
2021-07-16 10:00 - 12:00
Electrochemically Gated Charge Transport in Redox Proteins and Photosynthetic Complexes

Pau Gorostiza, group leader of the Nanoprobes and nanoswitches group at IBEC
Interprotein electron transport is an essential process in cell respiration and photosynthesis. It takes place between redox proteins and complexes, and it displays an outstanding efficiency and environmental adaptability. Although the biochemistry of electron transport processes is well characterized, nanoscale experimental methods are needed to understand electronic pathways in these redox protein structures, both for fundamental and for technological purposes. Electrochemical scanning tunneling microscopy (ECSTM) is an excellent tool to study electronic materials and redox molecules including proteins. It offers single molecule resolution and allows working in aqueous solution, in nearly physiological conditions in the case of proteins, and under full electrochemical control. ECSTM also allows performing conductance measurements by current-potential and current-distance tunneling spectroscopy. An overview of these methods and current projects in the laboratory will be presented, with special emphasis on cytochromes of the respiratory chain and on photosystem I complexes.
More information about Pau Gorostiza’s research here
This seminar will be held using the TEAMS app

PhD Thesis Defence: Ana Candida Lopes Hortelão
2021-09-03 11:00 - 13:00
Enzyme Powered Nanomotors Towards Biomedical Applications
Ana Candida Lopes Hortelão, Smart Nano-bio-devices group
The defence will take place online, if you wish to attend to this defence you can find the link and more information here

PhD Thesis Defence: Adrianna Glinkowska
2021-09-09 11:30 - 13:30
Formulation and screening of drug nanocarriers using microfluidic technology
Adrianna Glinkowska, Nanoscopy for nanomedicine
The defence will take place online, if you wish to attend to this defence you can find the link and more information here

Online IBEC Seminar: Daniel Gonzalez-Carter
2021-09-17 10:00 - 12:00
Delivering Nanoparticles Specifically to the Brain by Generating Artificial Brain Targets
Daniel Gonzalez-Carter, Molecular Bionics group at IBEC
Achieving efficient therapy delivery to the brain is one of the most pressing medical issues today. Therapy brain delivery is severely hampered by the protective blood-brain barrier (BBB), composed of the highly impermeable endothelial cells lining the brain vasculature. To overcome the BBB, therapies may be loaded onto nanoparticles functionalized with ligands which bind to target proteins expressed at the surface of brain endothelial cells (BEC), thereby increasing brain uptake. However, such strategies have inherent brain-specificity limitations, as the target proteins are also expressed on the vasculature of other organs, resulting in increased ‘off-target’ nanoparticle accumulation.
To achieve truly selective brain targeting, our group is developing a strategy to generate artificial targets exclusively at the BBB. This is done by exploiting the low endocytic rate of BEC, a key requirement for their high impermeability, to selectively retain exogenous targets on their surface. By generating nanoparticles capable of efficiently recognizing the artificial targets, we hope to increase nanoparticle delivery exclusively to the brain with minimal ‘off-target’ nanoparticle accumulation. Furthermore, we are developing an mRNA delivery platform to continuously re-generate the artificial targets from within the BEC to allow for repeated dosing in chronic diseases like Alzheimer’s disease.

PhD Thesis Defence: Alexandre Gomila
2021-09-20 10:00 - 13:00
Development and characterization of in vivo models for photopharmacology
Alexandre Gomila, Nanoprobes and Nanoswitches
The defence will take place online, if you wish to attend to this defence you can find the link here

Online IBEC Seminar: Veronika Magdanz
2021-10-08 10:00 - 12:00
Development of biohybrid and bioinspired microrobots toward biomedical applications
Veronika Magdanz, Smart Nano-Bio-Devices
Autonomous motion and precise control on the microscale is one of the main challenges in developing non-invasive medical microrobots. In this seminar, I present my approaches of how to develop artificial, biomimetic and biohybrid microrobots. We can be inspired by nature’s solutions to achieve such propulsion on the microscale. Specifically, sperm cells offer beneficial features as components of microrobots: as propulsion sources, as templates and as cargo. By combining smart microstructures with spermatozoa, new ways to control and manipulate sperm cells emerge.
This seminar will be held using the GoToMeeting app

Online IBEC Seminar: Mohit Kumar
2021-10-15 10:00 - 12:00
Peptide based nanomaterials with life-like functions
Mohit Kumar, Molecular Bionics group at IBEC
Chemists’ curiosity to create life de novo has sought inspiration from biological systems. In nature, self-assembled nanostructures constantly form and degrade which provides unique features like on-demand function, adaptation, temporal and spatial control. Such processes are enabled by the metabolism and the ability to consume chemical energy to perform useful work. However, these features are not trivial to obtain in synthetic systems. My talk will show that now peptide based self-assembled materials can also form and degrade over time and their nanostructures and functions can be regulated in time by consuming chemical fuel. Furthermore, by using super-resolution imaging dynamic transformations in solution can be probed in real-time, in situ.
This seminar will be held using the GoToMeeting app

Hybrid IBEC Seminar: Cesar Rodriguez-Emmenegger
2021-10-22 10:00 - 12:00
Bio-inspired soft matter at the service of interactive biointerfaces and synthetic cells
Cesar Rodriguez-Emmenegger, Group Leader, DWI-Leibniz Institute for Interactive Materials
Nature achieves unmatched functionality by the self-assembly of (macro)molecular building blocks in a hierarchical manner. All information necessary for the function is encoded at the molecular level. Unraveling such blueprints serves as a powerful paradigm in the bio-inspired synthesis of materials that can seamlessly interface with living matter or perform non-natural functions. In this talk, I will present a selection of research studies from my lab addressing the overarching task of developing bio-inspired interactive materials and their application in the biomedical field. Three themes will be considered. Firstly, I will present hydrophilic arborescent polymers, a new class of quasi-dendritic macromolecules in which the topology codes for extreme flexibility and enables a myriad of multivalent interactions. Secondly, I will present highlights of the antimicrobial Kill&Repel and Adaptive hemocompatible nanocoatings and our efforts in translating them to medical devices. The last part of the talk will focus on the development of Membrane Machines, tailor-made synthetic vesicles capable of recapitulating some fundamental biological properties and performing specific tasks. We take advantage of these systems to study how biological selectivity can emerge from the lateral organization of ligand in static and dynamic systems such as the bacterial divisome. We are also developing synthetic macrophage-mimetic microrobots capable of endocytosing bacteria and viruses, including SARS-CoV-2.
This seminar will be hybrid, using the GoToMeeting app and also at the Baobab meeting room located at Tower I, 11th floor. Very few people will be able to attend this seminar in person due to the capacity of the meeting room. If you wish to attend this seminar please write an email to ibeccommunications@ibecbarcelona.eu the free spots will be assigned on a first come first served basis.. The seminar will also be available on streaming, by using the GoToMeeting app, available in this link.
More information about his research team here

PhD Thesis Defence: Ignasi Ferrer Lluís
2021-10-25 15:30 - 17:30
Novel mHealth and multimodal physiological biomarkers for non-invasive monitoring and home healthcare of obstructive sleep apnea and COPD patients with comorbidities
Ignasi Ferrer Lluís, Biomedical Signal Processing and Interpretation
he defence will take place online, using the “Google Meet” app. If you wish to attend to this defence you can find the link here

4th IBEC-ICMS Joint Symposium
2021-10-26 10:00 - 13:00
The event is in the framework of an alliance between the Institute for Bioengineering of Catalonia (IBEC) and the Institute for Complex Molecular Systems (ICMS), a research institute of the Eindhoven University of Technology (TU/e).

The event aims to identify synergies and potential for collaboration between IBEC groups and the researchers of ICMS. It is the 4th edition of a series of joint symposiums that started in Eindhoven on September 2018. During that symposium many natural connections initiated for the benefit of both our organizations. We therefore feel that there are excellent opportunities to further strengthen the ties between our institutes. Therefore, we are organizing a number of scientific exchanges and working on the identification of common research interests.
This fourth ICMS-IBEC Symposium will be a great opportunity to foster collaborations, strengthen the existing ones, and an opportunity for young researchers involved in the exchange program to present their activities in the partner organization.
The event will be held online using the Teams app. You can register here

14th IBEC Symposium - Bioengineering for Regenerative Therapies
2021-10-27 09:00 - 2021-10-28 18:30
Registration is now open for the 14th IBEC Symposium on Bioengineering for Regenerative Therapies
The 14th IBEC Symposium will focus on one of our three main areas of application of research at IBEC: Regenerative Therapies. Although this year the pandemic situation has improved, we still believe it is not safe enough to organize the symposium on-site. So, this year’s edition will be also celebrated online.
We will use the same online platform as last year, where all the talks will be streamed and posters will be available. To adapt to the online format, the Symposium will be divided into two days.
All the scientific community is invited to participate. Attendees from IBEC and abroad are welcome to present their research in their own virtual space by submitting an abstract. Moreover, some of these contributions will be selected by the scientific committee for an oral flash presentation.
This year we will evaluate your virtual space, which you will be able to personalise and upload all kinds of material (both visual and written) to show the attendees your work, if you abstract is selected. The evaluation will be carried out by a scientific committee and also by vote by the attendees, so two awards will be given.
Also, it is important that you submit your abstract and register at the same time.

Important deadlines:
Abstract submission: 15/09/2021
Notification of acceptance: 06/10/2021
Registration deadline: 26/10/2021

¡Adéntrate en la nano-escala: descubre y juega con el Microscopio de Fuerza Atómica! - Semana de la ciencia
2021-11-17 18:30 - 19:30 | Sala Félix Serratosa – PCB, c/ Baldiri i reixac 10-12, Barcelona, Spain, 08028, Spain
¡Adéntrate en la nano-escala: descubre y juega con el Microscopio de Fuerza Atómica!

Desde que en la década de los 80 se inventara el microscopio de sonda de barrido, han sido muchos y muy relevantes los descubrimientos que estas técnicas han proporcionado al conocimiento científico. Aun hoy, es un instrumento capaz de detectar fenómenos increíbles que se dan en la escala de lo muy pequeño, fenómenos que nos acercan más y más a la comprensión de este mundo sujeto a fuerzas muy distintas de lo cotidiano.
En esta charla con el investigador Rubén Millán del Instituto de Bioingeniería de Cataluña (IBEC), podréis descubrir cómo funciona un microscopio de AFM, tendréis la posibilidad de probar en vivo el juego “Catch me AFM”, y de conocer a nuestra superheroína científica IBBI.
¡No os lo podéis perder! Inscripciones aquí.

Charla divulgativa sobre la microscopia AFM en el marco de la “Setmana de la ciència 2021“

La recerca en Parkinson
2021-11-18 18:00 - 19:00 | IBEC
Vine a l’IBEC durant la Setmana de la Ciència i podràs conèixer els últims avenços sobre la recerca en Parkinson, visitar els nostres laboratoris i parlar amb els i les protagonistes d’aquesta recerca.

En el marc de la setmana de la ciència, us convidem a una jornada de portes obertes on podreu visitar els laboratoris de la Professora Sílvia Muro, investigadora ICREA a l’IBEC i responsable del projecte de recerca en Parkinson.
Més informació sobre aquesta investigació aquí

IBEC Seminar: Cristina Mayor-Ruiz
2021-11-19 10:00 - 12:00 | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
Targeted protein degradation: genetic determinants and drug discovery opportunities
Cristina Mayor-Ruiz, IRBarcelona
Targeted protein degradation is a new therapeutic modality based on drugs that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. Of particular interest are “molecular glue degraders”: compounds that can degrade otherwise unligandable proteins by orchestrating direct interactions between target and E3. However, their discovery has been serendipitous, thus hampering broad translational efforts. I will present a scalable target-agnostic strategy toward glue degrader discovery. This approach is based on differential chemical screening coupled to a multi-omics target deconvolution campaign. Collectively, our data outline a versatile and broadly applicable strategy to identify degraders and thus empower future drug discovery efforts.

This seminar will be held at Tower I, 11th floor Baobab room, there will be 30 avialable seats, the free spots will be assigned on a first come first served basis. If you wish to attend this seminar online, please write to ibeccommunications@ibecbarcelona.eu.
More information about Cristina Mayor-Ruiz’s research here
Cristina Mayor-Ruiz obtained her PhD in 2017 at the CNIO (Madrid) under the supervision of Óscar Fernández-Capetillo. There, she explored mechanisms of resistance to anticancer therapies. In 2018, she joined the group of Georg Winter at CeMM (Vienna) supported by EMBO and Marie Curie postdoctoral fellowships, where her interests focused on different aspects of chemical biology and drug screening. Since January 2021, she leads the “Targeted Protein Degradation & Drug discovery” lab at IRB Barcelona. Her research focuses on:
(1) Developing screening strategies for early drug discovery. In particular, to identify monovalent degraders and other proximity-inducing drugs with therapeutic interest.
(2) Tackling exciting biological questions that either benefit from the high kinetic resolution provided by targeted protein degradation, or that involve E3 (dys)regulation dynamics.

PhD Discussions: Yolanda Castillo and Marc Molina
2021-11-26 10:00 - 12:00
Assessment of trunk function in patients with spinal cord injury using electromyography and smartphone accelerometry
Yolanda Castillo, Biomedical Signal Processing and Interpretation
Spinal cord injury (SCI) causes motor and sensory impairment below the level of the injury, but also many other health problems. A common consequence of SCI is the lack of control over trunk muscles, leading to deficits in postural control and balance while sitting. Since trunk stability is essential to maintain upright posture and support functional movements, impaired trunk function constitutes a major cause of motor disability in SCI patients, limiting their independence and quality of life. However, trunk stability is rarely examined in studies of mobility after SCI, and one of the reasons is the lack of quantitative measures for assessing trunk function. Here we propose to record and analyze electromyographic (EMG) and smartphone accelerometric data to extract quantitative measures for the evaluation of trunk function. Our aims were: 1) to characterize muscle activity and movement patterns of trunk flexion during a reaching task in healthy subjects and patients with SCI, 2) to compare the impact of cervical and thoracic injuries in trunk function, and 3) to investigate the potentially destabilizing effects of a startling acoustic stimulus in this task. For these purposes, during a reaching movement requiring trunk flexion, we recorded the EMG activity of 8 trunk, neck, and shoulder muscles and smartphone accelerometer data from individuals with cervical SCI, thoracic SCI, and healthy control subjects. We analyzed these signals and extracted different features, including the response time until pressing a target button, EMG onset latencies and amplitudes, and trunk tilt, lateral deviation, and other movement features from accelerometry. The proposed outcome measures revealed deficits in postural control and compensatory strategies employed by SCI patients, including delayed responses and higher lateral deviations, which might have important consequences for rehabilitation. The combination of EMG and smartphone accelerometer data can help to develop more suitable methods for the assessment of trunk function in individuals with SCI, thus improving the follow-up and management of these patients.
Development of a model of “macro” substrates for the analysis of 3D chromatin structure and transcriptional profiling
Marc Molina, Cellular and Molecular Mechanobiology
Mechanically-induced changes in the genome are increasingly recognized as major drivers of cell and tissue function. However, current and past studies on this topic in vitro have often been limited by the sample size required for these genomic analyses. Here we describe the development of a polyacrylamide gel (pAAg) substrate with larger area than gels previously generated in labs worldwide. These substrates display the same tunable stiffness as their smaller counterparts and are particularly suitable to accommodate large numbers of cells. We tested the substrates to assess the effect that changes in rigidity have in the cell’s genome, both at the level of chromatin organization and transcriptional regulation. For this, two different rigidities were used (soft vs stiff) with three conditions which included: i) a control group, ii) a transiently expressing mutant of RanQ69L that prevents all nucleocytoplasmic transport and iii) a transiently expressing mutant of NES1-KASH that prevents force transmission to the nucleus. Our preliminary results suggest that cells seeded on pAAg substrates of different rigidities display differences in chromatin structure and gene expression, but more data will be necessary to further support these results. Ultimately, the aim of our project is to understand down the road how changes in rigidity affect: i) the 3D structure and interaction map of chromatin and ii) the activated or repressed transcriptional programs in soft and stiff substrates. Overall, this new model will help us to characterize how the genome is affected by rigidity both at the structural and transcriptional levels. More broadly, we expect the potential findings of this work to help the community detailing the effect of changes in tissue stiffness in the genome spatial organization.
This PhD Discussion will be hybrid. Yolanda Castillo will be doing her presentation online and Marc from the Baobab room, located in tower I floor 11. To follow the session online, find here the link, we will be using the GoToMeeting app. If you wish to attend in person, the free spots will be assigned on a first come first served basis, the capacity of the room is for 30 people.

IBEC Seminar: Rob Jelier
2021-11-30 16:00 - 17:00 | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
The effect of gene loss on adaptation | 3D cell shape analysis in embryos
Rob Jelier, CMPG – Predictive Genetics and Multicellular Systems University of Leuven
In this talk I will summarize two research projects. First, I will report on a large-scale experimental evolution study into the effect of gene deletion on adaptation. We found gene deletion can speed up adaptation. Further, tracking adaptation after the systematic perturbation of genes involved in a complex trait informs on the genetic architecture of the trait. Second, we have developed a segmentation-pipeline for membrane tagged cells from fluorescent microscopy timelapses. The pipeline uses a biophysical DEM model of cell shape to constrain the possible cell shapes. The retrieved accurate cell shapes are subsequently used for very sensitive characterization of cell shapes, for example to identify changes after perturbations.
This seminar will be held at Tower I, 11th floor Baobab room, there will be 30 avialable seats, the free spots will be assigned on a first come first served basis. If you wish to attend this seminar online, please write to ibeccommunications@ibecbarcelona.eu.
