Institute for Bioengineering of Catalonia

PhD Discussions Sessions: Anna Vila and Alexandre Gomila
2018-10-26 10:00 - 11:00 (Europe/Madrid) | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
Engineering of 3D Small Intestinal Mucosa Models
Anna Vila, Biomimetic Systems for Cell Engineering
Hydrogels have been used as a scaffold for engineering tissue-like structures due to their biocompatibility and properties similar to the extracellular matrix. There are two main types of hydrogels (i) natural hydrogels, such as gelatin, which are biodegradable and present cell adhesion motifs and (ii) synthetic hydrogels, such as poly(ethylene glycol) diacrylate (PEGDA), which are non-biodegradable and can withstand long-term cell cultures but do not have bioadhesion sequences [El-Sherbiny M.I. et al., 2013]. Both types of hydrogels present complementary benefits.
For this reason, we fabricated a hydrogel co-polymer composed of gelatin methacrylate (GelMA) co-polymerized with PEGDA [Hutson. B.C. et al., 2011]. We employed a single-step, moldless, UV-photolithography-based fabrication technique [Castaño A. et al., submitted] to fabricate scaffolds mimicking the 3D architecture of the small intestinal mucosa. Using this approach, we obtained hydrogel co-polymers with finger-like microstructures, with the roundness and dimensions found in the villi of the native tissue. Mechanical and physicochemical properties such as an approach of the Young’s modulus, degradation rate and swelling ratio of the hydrogels have been characterized. Adding PEGDA to the GelMA hydrogels have provided hydrogels with lower degradation and higher Young’s modulus, which ca be easily tuned by changing the composition of GelMA and PEGDA polymers. Furthermore, we have demonstrated that our scaffolds support the growth and differentiation of intestinal epithelial Caco-2 cells up to 21 days, obtaining a matured epithelial monolayer with effective tissue barrier properties.
Additionally, we increased the complexity of our model of the small intestinal mucosa by incorporating an additional cell compartment to mimic the stroma of the in vivo tissue. To do that, we embedded 3T3-NIH fibroblasts in our scaffolds during the photopolymerization procedure. Then, we cultured Caco-2 cells on top of the 3T3-NIH fibroblast-laden hydrogels up to 21 days. Our preliminary results showed that the co-culture of Caco-2 cells with 3T3-NIH fibroblasts favours the epithelial cell growth and improves their barrier function. Taking all together, we have generated an intestinal mucosa model that allows for the co-culture of different intestinal cell types distributed in compartments, mimicking the spatial-physiological features of the small intestinal mucosa. We believe our model better recapitulates cell-cell crosstalk and cell-matrix interactions found in vivo, being an improved alternative for the cell-base in vitro assays.

In vivo photomodulation of GABA and Glycine receptor channels
Alexandre Gomila, Nanoprobes and Nanoswitches
Neuronal networks are highly complex interactions, which determine even the finest behaviour. The major inhibitory pathways in the central nervous system (CNS) act through chloride ion flux, which are mostly driven by fast-acting ionotropic GABAA and Glycine receptors (GlyR). All of them share structural similarities and belong to pentameric ligand-gated ion channels of the Cys-loop family. Photoswitchable molecules have become a powerful tool in any applied field of bioscience, and are broadly used in biomedical research due to their capacity for enlightening biological aspects from their very basics, such as molecular level, up to entire neuronal networks.
Photopharmacology has proven to be advantageous for spatial and temporal control of biological processes without interfering the system natural dynamics and outcomes. Physiology can be tuned with photomimetic ligands and naturally occurring complex network responses can be segmented into light dependent activities discerning relevant data from a vast matrix of results. As these new tools are broadly used for biomedical purposes and most of them focused towards medical applications, an interpretative analytical platform is needed to screen and identify potential photoswitchable molecules.
Zebrafish (Danio rerio) larvae constitute an excellent animal model for studying and screening photoswitchable molecules in vivo. Zebrafish present a transparent body during larval stages, and therefore are capable of receiving specific and determined light applications. From the 19th hour post fertilisation they acquire behavioural traits, from spontaneous twisting movements to full swimming capacities, which are easily traceable and measurable. The use of up to 96 animals simultaneously allows a parallel high throughput data recovery system to analyse high complexity movements and behaviours, all of it with the use of photopharmacology. Here, we aimed at introducing an effective and reliable methodology for high throughput screening of photoswitchable compounds, including photopharmacological derivatives or peptidoswitches, for any in vivo possible target, from specific neuronal correlated diseases up to possible toxicological outcomes. We focused on the study of the main inhibitory neuronal pathways and their locomotion outcomes on a reliable and comparable animal model.
Hence, several photoswitchable compounds with a common benzodiazepine core and an azobenzene photoswitchable moiety were tested. A first light dependent activity ratio was applied in order to discern the most promising candidates. We identified the UR-DW290 molecule as a light dependent trigger of activity in larvae zebrafish. Larvae zebrafish treated with UR-DW290 maintained higher activity in terms of swimming distance (mm) during the relaxation period and UV-Blue light cycles in comparison to controls. Whole-cell recordings of GABAA and glycine mediated currents by URDW290 showed a potentiating of inhibition when irradiated with ultraviolet light in comparison to visible light illumination.
We propose the combination of high through-put screening and optopharmacology tools for the study and characterisation of zebrafish larvae behaviour focusing on their swimming activity. We identified a first photoswitchable molecule for glycine receptor modulation in vitro and in vivo, UR-DW290, which increases basal activity in zebrafish larvae. This increase is tuneable with UV and Blue light illumniation.

IBEC-IRB Barcelona joint seminar: Guillaume Salbreux, Francis Crick Institute
2018-10-30 09:30 - 10:30 | Sala Félix Serratossa, Parc Científic de Barcelona, Barcelona, Spain
Physics of epithelial flows and folds
Guillaume Salbreux, Theoretical Physics of Biology Laboratory, The Francis Crick Institute, London
The shape of a biological tissue is determined by mechanical stresses acting within the tissue cells. During embryonic morphogenesis, forces generated in the actomyosin cytoskeleton in the cell of epithelia result in cell deformation, cell rearrangements, and 3D bending of the epithelium. To understand tissue morphogenesis, force generation at the cellular scale must be related to flows and deformation occurring at the tissue scale. Here I will discuss how this relation can be captured by a 3D vertex model or by a continuum theory of active surfaces to understand epithelial fold formation during embryonic development. Using this framework, one finds that two different mechanisms, basal relaxation and lateral constriction, can account for fold formation in the Drosophila wing disc. I will also discuss how planar tissue flows are related to cell shape changes and cell division, and show how the growth of the Drosophila histoblast nests can be decomposed into basic cellular events.

II International Symposium on Photopharmacology (ISPP2018)
2018-11-01 08:00 - 2018-11-02 17:00
II International Symposium on Photopharmacology (ISPP2018) – Innovative therapeutics using light
The world’s leading researchers and experts in the field will meet at the second international photopharmacology symposium in Vic on 1 and 2 November.
The convention is being organised jointly by the University of Vic – Central University of Catalonia (UVic-UCC), the Bioengineering Institute of Catalonia (IBEC) and the Institute for Advanced Chemistry of Catalonia – Spanish National Research Council (IQAC-CSIC). More than 120 people, the vast majority of whom come from countries other than Spain, will be attending the event, which will take place in the Torre dels Frares building at the UVic.
The symposium will include around twenty lectures, three blocks of short presentations and two poster sessions. The speakers include Ben Feringa, of the University of Groningen (Netherlands), who was awarded the Nobel Prize in Chemistry in 2016 for the design and synthesis of molecular machines – an award he shared with Jean-Pierre Sauvage and Fraser Stoddart. Among others, the scheduled lectures include those by Edith C. Glazer of the University of Kentucky, who is working on the development of complex metals such as possible photoactive drugs, and by Austria’s Dirk Trauner of the University of New York, focusing on the application of photopharmacology in neurobiology. One of the main achievements of his team, working with Richard Kramer and Ehud Isacoff, has been to restore sight in blind animals, using drugs that respond to visible light as molecular prostheses.
Information: http://events.ibecbarcelona.eu/ispp2018/

What is photopharmacology?
Photopharmacology is based on administering photosensitive compounds as drugs, which are only activated and take effect in combination with light. This specific characteristic provides a high level of control over the administration of medications and therapies, since it means that the specific point of the body where it is applied and the duration of the application can be decided. This precision and location means that as a technique, photopharmacological treatments are not invasive, and can achieve optimum results with minimal secondary effects.
Although its history dates back to the 1960s, photopharmacology has primarily developed over the last ten years. During this period, a significant critical mass of researchers has been created in research centres and universities around the world that focus on the field from various perspectives. It is a multifaceted science, which includes biology, pharmacology, physics, chemistry, engineering and medicine. Its applications are also extremely wide-ranging: it may be therapeutically useful in a wide variety of medical fields, within which neurosciences and cardiology are particularly important. Some applications that are being studied could also provide substantial improvements in pathologies such as diabetes and chronic pain. Photopharmacology can also be used as a research tool, and can be combined with other technologies, such as materials nanotechnology.

II International Symposium on Photopharmacology (ISPP2018)
2018-11-01 08:00 - 2018-11-02 17:00
Innovative therapeutics using light
Photopharmacology is an emerging branch of science based in the administration of a photosensitive compound in combination with illumination to provide a high degree of local and temporal control of compound activity, which makes it useful both for therapeutic applications and as a research tool.
In the last 10 years photopharmacology, a polyhedric science involving biology, pharmacology, chemistry, physics, engineering and medicine, has flourished and achieved a critical mass of researchers and resourceful methods in chemistry and optics, raising hopes for clinical trials of the most advanced compounds.
The First International Symposium on Photopharmacology took place at the University Medical Center Groningen on February 16th, 2017. Topics covered in this First Symposium ranged from photochemistry and organic synthesis to vision restoration and brain research.
Information: http://events.ibecbarcelona.eu/ispp2018/

I'll Push You
2018-11-08 17:00 - 19:00 | Auditori Antoni Caparrós, PCB, Tower D, c/Baldiri Reixac 4-8, Barcelona, Spain
Take a break to enjoy a movie and help accelerate research into muscular dystrophy!
IBEC, in collaboration with the PCB, is organizing a special screening of
“I’ll Push You”
This inspiring feature-length documentary follows Justin Skeesuck and Patrick Gray, the first people to complete the Camino de Santiago in a wheelchair.
Entrance is free, although donations to the Faster Future campaign will be gladly accepted! Feel free to invite your friends and family.
Thursday 8th November, 5:00 pm · Auditorium Antoni Caparrós, PCB
In English with Spanish subtitles
Register here: https://i-ll-push-you.eventbrite.com

IBEC Seminar: new junior group leader Benedetta Bolognesi
2018-11-09 10:00 - 11:00 | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
Title TBC
Benedetta Bolognesi, IBEC
Coming soon

Workshop organized with Mind the Byte
2018-11-09 12:00 - 14:00 | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
Computational chemistry in drug discovery: the SME perspective
Business Development Director Mariona Esquerdo and Product Manager Fernando Martín, Mind the Byte
Mind the Byte is a bioinformatics company specializing in the development of new technologies applied to drug discovery. As a SME (small/medium-sized enterprise) we focus our resources in the research and development of new technologies, applying cutting-edge methods in artificial intelligence and cloud computing, providing to our clients with the best resources for the success of their projects. In this workshop we will present the company, how computational chemistry can help the drug discovery process and how we have made accessible our technology through our platform.
They have been invited by Giulia Fornabaio of IBEC’s PhD Committee, which will provide a pica-pica after the event.

PhD Thesis Defence: Joan Martí Muñoz
2018-11-14 12:00 - 14:00 | Sala d’Actes de la Facultat de Matemàtica i Estadística (FME), C. Pau Gargallo, 5, Barcelona, 08028
Chemical design and validation of Ca 2+ -releasing platforms to promote vascularization in tissue regeneration
Joan Martí Muñoz, Biomaterials for Regenerative Therapies group
Joan will be defending his PhD thesis on Wednesday 14th November at 12:00 in the Sala d’Actes of the UPC’s Facultat de Matemàtiques i Estadística, Campus Diagonal Sud, Carrer de Pau Gargallo.
Everybody is welcome to attend.
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If you’re an IBEC PhD student and would like to advertise your PhD defence on the IBEC calendar, please contact vleigh@ibecbarcelona.eu

Learning to write clearly, the ‘how’ of good scientific writing
2018-11-15 | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
This workshop aims to help participants improve their writing skills through awareness of the elements of clear writing. Participants will learn linguistic tools to transmit scientific messages.
Dates:
15th November, from 10 to 18 pm. In person class sessions = 8 hours. One whole day.
Target group:
PhD students and post-docs
Trainer:
Dr. Susan Frekko

IBEC Seminar: Benedetta Bolognesi
2018-11-16 10:00 - 11:00 | IBEC, floor 11, Tower I, Baldiri Reixac 4-8, 08028 Barcelona, Spain
The mutational landscape of a prion-like domain
Benedetta Bolognesi, IBEC
At least 70 human RNA-binding proteins (RBPs) contain a prion-like domain (PrLD). PrLDs are low complexity domains which resemble in composition the infectious yeast prions. Mutations in PrLDs are associated to the onset of many neurodegenerative conditions, such as Amyotrophic Lateral Sclerosis (ALS). PrLDs are able to populate multiple physical states: diffuse, liquid de-mixed, insoluble amyloid. Pathological mutations affect these equilibria in ways we cannot yet fully understand, or predict. The TAR DNA binding protein TDP-43 contains a 140 aa long PrLD and forms cytoplasmic aggregates in most cases of ALS. We use deep mutational scanning to understand how sequence determines the toxicity of TDP-43 in a yeast model. I will present the first “genotype-to-phenotype” map of TDP-43 where we quantify the effect of all possible amino acid substitutions in the PrLD on cellular fitness. While allowing us to understand the impact of mutations within low-complexity regions, these data provide the basis to understand by which mechanism protein inclusions drive pathogenesis.

nanoBio&Med2018
2018-11-20 08:00 - 2018-11-22 17:00 | Auditori Antoni Caparrós, PCB, Tower D, c/Baldiri Reixac 4-8, Barcelona, Spain
The nanoBio&Med2018 International Conference (www.nanobiomedconf.com) will take place in Barcelona (Spain): November 20-22, 2018. This event is going to present again the most recent international developments in the field of Nanobiotechnology and Nanomedicine and will provide a platform for multidisciplinary communication, new cooperations and projects to participants from both science and industry.
An industrial forum will also be organized to promote constructive dialogue between business and public leaders and put specific emphasis on the technologies and applications in the nanoBioMed sector.
The call for abstracts is currently open (deadline: October 01, 2018) and abstracts can be submitted online through the website.
Deadlines
Abstract Submission (Oral request): October 01, 2018
Student Grant (Travel bursary) Request: October 01, 2018
Author Submission Acceptance Notification: October 05, 2018
Student Grant Notification: October 05, 2018
Early Bird Registration Fee: October 12, 2018
Abstract Submission (Poster request): October 26, 2018
Early Bird Registration Fee (Exhibitors): October 07, 2018
The conference will offer during this week an impressive list of Invited & Keynote speakers.
Keynote/Invited speakers already confirmed (20 as of 13/08/2018):
– Lorenzo Albertazzi (Institute for Bioengineering of Catalonia (IBEC), Spain)
– Giuseppe Battaglia (University College London, UK)
– Ofra Benny (The Hebrew University of Jerusalem, Israel)
– Gianaurelio Cuniberti (TU Dresden, Germany)
– Cecile Delacour (Institut Néel (CNRS), France)
– Carlos Fito-López (ITENE, Spain)
– Meytal Landau (Technion, Israel)
– Jesus M de la Fuente (ICMA, CSIC/ UNIZAR / CIBER-BBN, Spain)
– Xing Ma (Harbin Institute of Technology (Shenzhen), China )
– Veronika Magdanz (TU Dresden, Germany )
– Shlomo Magdassi (The Hebrew University of Jerusalem, Israel)
– Cécilia Ménard-Moyon (CNRS, France)
– Salvador Pané i Vidal (ETH Zurich, Switzerland)
– Danny Porath (The Hebrew University of Jerusalem, Israel)
– Samuel Sánchez (IBEC, Spain)
– Ronit Satchi-Fainaro (Tel Aviv University, Israel)
– Avi Schroeder (Technion, Israel)
– Philip Tinnefeld (LMU München, Germany)
– Thomas Velten (Fraunhofer IBMT, Germany)
– María J. Vicent (Príncipe Felipe Research Center, Spain)
Further speakers will be announced the upcoming weeks
Several opportunities to exhibit are also available.
