Institute for Bioengineering of Catalonia

IBEC Seminar: Lorenzo Albertazzi
2015-10-16 10:00 - 11:00 (Europe/Madrid)
Nanoscopy for Nanomedicine: looking at nanomaterials in action one molecule at a time
Lorenzo Albertazzi, IBEC
The use of nanomaterials for biomedical purposes such as drug or gene delivery is one of the key applications of nanotechnology. In this framework a variety of materials have been fabricated, evaluated in cells and in vivo and, in some cases, successfully translated into clinical applications. A crucial factor limiting the design of effective nanocarriers is the lack of knowledge about materials-cell interactions that severely limit the rational design of nanosized devices.
Here I’ll show how advanced optical microscopy techniques can shine a light on nanomaterials behavior in the biological environment, helping us to understand structure-activity relationships and to design improved and more effective therapeutic devices. In particular I’ll discuss the ability of super resolution microscopy to image with nanometric resolution nanomaterials interactions with target cells. The potential and the applications of the technique will be discussed, with particular emphasis on the study of self-assembled bio-inspired materials.

B·Debate: Future Tools for Biomedical Research: in vitro, in silico and in vivo disease modeling
2015-10-01 09:00 - 2015-10-02 12:30 | CosmoCaixa Barcelona, Carrer d'Isaac Newton, 08022 Barcelona, Spain
The increasing costs of biomedical research and drug discovery and the continually rising numbers of compound failures provoke an urgent need for novel tools for basic research and preclinical testing of drugs.
The cross-breeding of nanotechnologies, life and computational sciences is harnessing enabling technologies for drug discovery, development, toxicity testing and disease modeling. These advances can move in vitro cell and tissue cultures beyond the current state-of-the-art, which poorly reflect patient physiology, and create “in vivo human-like” platforms that allow cheaper and efficient drug and toxicity assays.
At the same time, important efforts are being made to create improved animal and computational models to better mimic human physiology in health and disease.
Under this framework, the B·Debate “Future Tools for Biomedical Research: In Vitro, In Silico and In Vivo Disease Modeling”, coorganized by B·Debate and IBEC, is an opportunity to debate with experts and professionals of the field to review experiences and best practices and to identify and address barriers in the development and adoption of advanced methods for disease modeling, with a potential to revolutionize preclinical research in particular, and the validation and commercialization of new therapies and diagnostics at large.
Visit the website for more details.

8th IBEC Symposium
2015-09-30 08:00 - 18:00 | AXA Auditorium, L'illa Diagonal, Av. Diagonal 547 , Barcelona, 08029
8th IBEC Symposium: Bioengineering for Regenerative Therapies
Wednesday 30th September 2015
Please save the date for the 8th IBEC Symposium on Bioengineering for Regenerative Therapies, which will take place on Wednesday 30th September 2015.
This year, the IBEC Symposium will focus on one of our three areas of applications for bioengineering, Regenerative Therapies, and will bring together high-profile international experts in our fields of expertise. It provides an open forum for interdisciplinary discussions and networking, benefitting young researchers and established scientists alike.
Confirmed speakers this year include:
Giorgio Scita, Associate Professor of General Pathology at the Department of Health Sciences, University of Milan.
Manuel Salmeron, Chair of Biomedical Engineering, University of Glasgow
Ron Mckay, Director for Basic Sciences, Lieber Institute for Brain Development, Baltimore
Josep Samitier, IBEC
Everyone is welcome to submit abstracts for the posters and flash presentations sessions by Thursday 16th July 2015. Please use this template.
We look forward to welcoming you to our symposium in September.

Useful dates:
Deadline for abstracts: 16th July 2015
Notification of acceptance: 8th September 2015
http://ibecbarcelona.eu/events/Symposium2015

8th IBEC Symposium
2015-09-30 08:00 - 18:00 | AXA Auditorium, L'illa Diagonal, Av. Diagonal 547 , Barcelona, 08029
8th IBEC Symposium: Bioengineering for Regenerative Therapies
Wednesday 30th September 2015
Please save the date for the 8th IBEC Symposium on Bioengineering for Regenerative Therapies, which will take place on Wednesday 30th September 2015.
This year, the IBEC Symposium will focus on one of our three areas of applications for bioengineering, Regenerative Therapies, and will bring together high-profile international experts in our fields of expertise. It provides an open forum for interdisciplinary discussions and networking, benefitting young researchers and established scientists alike.
Confirmed speakers this year include:
Giorgio Scita, Associate Professor of General Pathology at the Department of Health Sciences, University of Milan.
Manuel Salmeron, Chair of Biomedical Engineering, University of Glasgow
Ron Mckay, Director for Basic Sciences, Lieber Institute for Brain Development, Baltimore
Josep Samitier, IBEC
Everyone is welcome to submit abstracts for the posters and flash presentations sessions by Thursday 16th July 2015. Please use this template.
We look forward to welcoming you to our symposium in September.

Useful dates:
Deadline for abstracts: 16th July 2015
Notification of acceptance: 8th September 2015
https://ibecbarcelona.eu/events/Symposium2015

IBEC Seminar: Albert Folch
2015-09-22 00:00 - 13:00
Print-and-Play Microfluidics
Albert Folch, Associate Professor, University of Washington
Biologists and clinicians typically do not have access to microfluidic technology because they do not have the engineering expertise or equipment required to fabricate and/or operate microfluidic devices. Furthermore, the present commercialization path for microfluidic devices is usually restricted to high-volume applications in order to recover the large investment needed to develop the plastic molding processes. We are developing microfluidic devices through stereolithography, a form of 3D printing, in order to make microfluidic technology readily available via the web to biomedical scientists. Our lab presently focuses on developing 3D-printable microdevices that facilitate the advancement of basic neuroscience and translational cancer applications. The lab’s long-term mission is to make microfluidic devices as easy to use as smartphones and make them easily available to clinicians in order to enable novel cancer diagnostics and therapies.

IBEC Seminar: Marc Martí-Renom
2015-09-18 10:00 - 11:00
Structure determination of genomes and genomic domains by satisfaction of spatial restraints
Marc Martí-Renom, ICREA Research Professor / CNAG / CRG
The genome three-dimensional (3D) organization plays important, yet poorly understood roles in gene regulation. Chromosomes assume multiple distinct conformations in relation to the expression status of resident genes and undergo dramatic alterations in higher order structure through the cell cycle. Despite advances in microscopy, a general technique to determine the 3D conformation of chromatin has been lacking. We developed a new method for the determination of the 3D conformation of chromatin domains in the interphase nucleus, which combines 3C-based experiments with the computational Integrative Modeling Platform (IMP). The general approach of our method, which has been applied to study the 3D conformation of the alpha-globin domain in the human genome [1], the Caulobacter crescentus whole genome [2], and the dynamic response of Topologically Associating Domains (TADs) to hormone treatment in breast cancer cell lines [3], opens the field for comprehensive studies of the 3D conformation of chromosomal domains and contributes to a more complete characterization of genome regulation.
[1] D. Baù et al. Nat Struct Mol Biol (2011) 18:107.
[2] M.A. Umbarger, et al. Molecular Cell (2011) 44:252
[3] Le Dily, et al. Genes & Dev (2014) 28:2151

IBEC Seminar: Richard Reilly
2015-09-17 10:00 - 11:00
All a question of Timing: Sensory processing in Dystonia and Parkinson’s Disease
Professor Richard Reilly, Trinity Centre for Bioengineering · Trinity College Dublin
There are many challenges in the diagnosis and management of neurological disorders. Neural Engineering can help address some of these by the development of novel engineering, computational and experimental methods to help understand the pathogenesis of neurological disorders. This talk will detail results from recent neural engineering studies into understanding cervical dystonia and Parkinson’s disease.
While the pathogenesis of cervical dystonia remains unknown, recent animal and clinical experimental studies have indicated its probable mechanisms. Human movement involves a complex series of coordinated musculoskeletal but also neural processes. A breakdown in any of these processes can result in irregular movement. The temporal discrimination threshold is the shortest time interval at which two sensory stimuli presented sequentially are detected as asynchronous by the observer. Studies in our group and that of others have shown that abnormal temporal discrimination is a mediational endophenotype of cervical dystonia and informs new concepts of disease pathogenesis. Our hypothesis is that both abnormal temporal discrimination and cervical dystonia are due to a disorder of the midbrain network for covert attentional orienting caused by reduced gamma-aminobutyric acid inhibition, resulting from, in turn, from as yet undetermined, genetic mutations. Such disinhibition is a) subclinically manifested by abnormal temporal discrimination due to prolonged duration firing of the visual sensory neurons in the superficial laminae of the superior colliculus, b) clinically manifested by cervical dystonia due to disinhibited burst activity of the cephalomotor neurons of the intermediate and deep laminae of the superior colliculus. Abnormal temporal discrimination in unaffected first-degree relatives of patients with cervical dystonia represents a subclinical manifestation of defective gamma-aminobutyric acid activity both within the superior colliculus and from the substantia nigra pars reticulata. This talk will review some our recent experiments addressing this hypothesis.
Sensory and perceptual disturbances are common in Parkinson’s disease. Subtle deficits of the sensory system, often not detected by routine examination, occur in people with Parkinson’s disease. From simple anosmia and impaired kinesthetic perception, to more complex visual hallucinations and spatiotemporal perceptual abnormalities, altered sensory processing is found across multiple modalities. Of note, integration of multiple environmental sensory inputs is crucial for a refined but complex goal-directed motor output (e.g. locomotion through a crowded environment). There is increasing evidence that these sensory deficits contribute to the pathophysiology of some of the abnormal motor features of Parkinson’s disease. This talk will review some of our recent experiments to probe multisensory deficits in Parkinson’s disease and introduce one intervention developed around sensory and cognitive processing.

IBEC Seminar: Dr. François St. Pierre
2015-07-24 10:00 - 11:00
Imaging electrical activity in vivo with ultrafast protein sensors
Dr. François St. Pierre, Department of Neuroscience, Baylor College of Medicine /
Department of Electrical and Computer Engineering, Rice University
Imaging of rapid brain electrical activity has been on the wish list of neurobiologists for many years and has received renewed attention with the launch of the BRAIN initiative by the White House in the U.S.A. In particular, neuroscientists have long sought voltage sensors based on proteins to reveal brain activity in genetically defined neuronal circuits. I will present novel protein voltage sensors that leverage optimized parts and creative new designs to report neural activity with unprecedented temporal resolution in vitro, in brain slices and in vivo. Importantly, these synthetic sensors report neural activity at the millisecond timescale over which key information processing functions are thought to take place. I will show how these new optical tools enable us to follow neural information processing in the fly visual system with subcellular resolution. I will also present our recent success at monitoring spontaneous electrical activity in stem cell-derived cardiomyocytes.

PhD Thesis Defense: Erola Pairo
2015-07-21 11:00 - 13:00 | Sala de Graus Eduard Fontseré, Martí i Franquès, 1-11, Barcelona, 08028
“Detection of transcription factor binding sites by multivariate signal processing”

Erola Pairo, Signal and information processing for sensing systems group
Erola will be defending her PhD thesis on Tuesday 21st July at 11:00 in the Eduard Fontsere room at the Faculty of Physics.
Everybody is welcome to attend.
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If you’re an IBEC PhD student and would like to advertise your PhD defense on the IBEC calendar, please contact vleigh@ibecbarcelona.eu

PhD Thesis Defense: Carlos Ruiz
2015-07-17 15:00 - 17:00 | Aula Capella, Facultad de Ingeniería Industrial (ETSEIB), Av. Diagonal 647, Barcelona, Spain
“A computational study of intervertebral disc degeneration in relation to changes in regional tissue composition and disc nutrition”

Carlos Ruiz Wills, Biomechanics & Mechanobiology group
Carles will be defending his PhD thesis on Friday 17th July at 15:00 in the Aula Capella, Facultad de Ingeniería Industrial (ETSEIB), Av. Diagonal 647.
Everybody is welcome to attend.
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If you’re an IBEC PhD student and would like to advertise your PhD defense on the IBEC calendar, please contact vleigh@ibecbarcelona.eu

PhD Discussions Session: Verónica Hortigüela & Anna Crespo
2015-07-10 10:00 - 11:00
Developing a platform for receptor clustering studies
Verónica Hortigüela, Biomimetic systems for cell engineering group
Receptors are signaling units that usually require interactions and associations with other molecules in complexes to trigger a signaling pathway. This process is known as receptor clustering and comes typically along with a simultaneous ligand clustering underneath the cell membrane. We have developed a strategy to precisely control the ligand distribution on a substrate at the nanoscale to study in detail receptor clustering processes. Herein we present a tunable platform based on self-assembled di-block copolymers that tend to segregate into nanostructures. Di-block copolymers are confined to a thin film providing a template for ligand patterning.

Ribonucleotide Reductase anaerobic enzymes are essential for biofilm formation of Pseudomonas aeruginosa
Anna Crespo, Bacterial infections: antimicrobial therapies group
Most chronic infections in humans are caused by communities of microorganisms living in organized structures, known as biofilms. Biofilm-related infections, such as pneumonia (in patients suffering for cystic fibrosis or chronic obstructive pulmonary disease –COPD-) and catheter-associated infections, affect millions of people in the developed world.
Cell clusters in biofilms are characterized by presenting, in its extracellular polymeric matrix, gradients of oxygen, nutrients and metabolic waste products. The so-formed chemical heterogeneity (e.g., the presence of anoxic areas) leads to the appearance of different metabolic activities.
Pseudomonas aeruginosa has been used as a model bacterium for biofilm research; it causes biofilm-related chronic infections and presents high metabolic versatility, together with an extreme antibiotic resistance.
In this work we have studied P. aeruginosa, focusing in an essential enzyme for its growth, Ribonucleotide Reductase (RNR). Ribonucleotide Reductases catalyse the reduction of ribonucleotides (NTPs) to deoxyribonucleotides (dNTPs), thereby providing the building blocks for DNA synthesis. There are three different RNR classes, named class I, class II and class III, which are, respectively, oxygen-dependent, oxygen-independent and oxygen-sensitive. The last two ones, essential for anaerobic growth in Pseudomonas aeruginosa, have been proved to be necessary for biofilm formation, and therefore putative targets for new therapies against P. aeruginosa chronic infections.

IBEC Seminar: Prof. Saman K. Halgamuge
2015-07-06 15:00 - 16:00
Big Data Analytics in Metagenomics
Saman K. Halgamuge, Melbourne School of Engineering, University of Melbourne, Australia
In collaboration with researchers in Academia Sinica and Metabolomics Australia/Department of Botany at Melbourne, we have been working in two areas of Bioinformatics: Metabolomics focusing on microbes and Metagenomics focusing on plants. Profiling large sets of data resulted from technological advances in whole genome sequencing and MALDI Imaging type technologies that can reveal vital information about the environment and plants, which is our major or primary source of food on Earth. Recently we have demonstrated considerable success in using unsupervised clustering techniques to analyse genetic and metabolomic data. This includes analysis of viral quasi species, metabolomics and microbial metagenomes.
Some microbes in the environment appear to look very similar and found “living together” in communities in non-separable ways, making them harder to culture in a lab. To make matters worst, considering our belief, if it is correct at all, that we know only about up to 2% of the microbes around us. When we know only so little about the data labels, in this case, about the identity of the species. It is even more challenging to recognise patterns associated with the genomes of the quasispecies (a set of genetically related but non-identical viral mutant types, which can also be referred to as strains,) that are able to co-exist within the host. Uncovering information about quasi-species populations of microbes significantly benefits the study of disease progression, antiviral drug design, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes.

Phd Discussions Complementary Skills Session: Elisabeth Pain, Science Careers
2015-06-26 10:00 - 11:00
Planning for an Academic Career: A postdoc and beyond

Elisabeth Pain, Contributing Editor for Science Careers, Europe
Academic careers have become very competitive these days, and the career decisions you make as a Ph.D. student or postdoc may greatly influence your chances of success later on. Choosing well your first postdoc is particularly important, as you must ensure that you will be developing your skills while starting to make a name for yourself. When you should you start looking for a postdoc? What aspects should you consider? Where is the best place for you? In this session we will explore how to plan ahead and secure a successful postdoc, and how to prepare for the next steps on the career ladder.

After obtaining an engineering diploma in biotechnology from her native France, Elisabeth went to the United Kingdom to pursue her Ph.D. in immunology at the University of Bristol. Finding her calling in science journalism, she went on to obtain a postgraduate diploma in journalism studies from Cardiff University, with a bursary from the Association of British Science Writers. Since 2002, Elisabeth has been working for Science Careers, the online jobs and career guidance magazine of the journal Science – first in Cambridge as U.K. Editor and, starting in 2004, in Barcelona as Contributing Editor for Europe. Elisabeth has extensive experience covering a broad range of topics relevant to young scientists, going from job and funding opportunities in academia to alternative careers and work-life balance. Elisabeth also regularly contributes Spanish and French news stories for Science and its policy blog Science Insider.

Kids' Day
2015-06-26 09:00 - 13:30 | IBEC, Baldiri Reixac 10-12, Barcelona, 08028, Spain
On Friday, 26th June IBEC, in collaboration with IRB, will celebrate its first edition of Kids’ Day, when staff and researchers from the two institutes are invited to bring their children for a morning of science activities.
Kids’ Day is an opportunity for IBEC members to show their children their workplace, and gives them the chance to be a ‘little scientist’ for a day.
Who can participate?
To make sure that we have a manageable and safe number of kids in the lab, we have limited the number of participants to 60. Registration is on a first-come-first-served basis and priority will be given to the children of IBEC scientists and staff, and then extended to nieces and nephews until all spaces are filled.
The activities will be targeted to children between 3 and 12 years old, with the kids sorted into activity groups based on their ages. It’s recommended that kids be at least in P3 to assure that they will enjoy the whole event.
All 3-year-old kids need to be accompanied by a parent or a guardian. The other small children (4-5 years) can be accompanied by a parent only if they consider it necessary. Due to space restrictions, parents of older children do not need to be present during the activities. Volunteers will look after the kids at all times. (If you are interested in volunteering for this, please let us know at ibecevents@ibecbarcelona.eu)
http://ibecbarcelona.eu/events/Kidsday

Kids' Day
2015-06-26 09:00 - 13:30 | IBEC, Baldiri Reixac 10-12, Barcelona, 08028, Spain
On Friday, 26th June IBEC, in collaboration with IRB, will celebrate its first edition of Kids’ Day, when staff and researchers from the two institutes are invited to bring their children for a morning of science activities.
Kids’ Day is an opportunity for IBEC members to show their children their workplace, and gives them the chance to be a ‘little scientist’ for a day.
Who can participate?
To make sure that we have a manageable and safe number of kids in the lab, we have limited the number of participants to 60. Registration is on a first-come-first-served basis and priority will be given to the children of IBEC scientists and staff, and then extended to nieces and nephews until all spaces are filled.
The activities will be targeted to children between 3 and 12 years old, with the kids sorted into activity groups based on their ages. It’s recommended that kids be at least in P3 to assure that they will enjoy the whole event.
All 3-year-old kids need to be accompanied by a parent or a guardian. The other small children (4-5 years) can be accompanied by a parent only if they consider it necessary. Due to space restrictions, parents of older children do not need to be present during the activities. Volunteers will look after the kids at all times. (If you are interested in volunteering for this, please let us know at ibecevents@ibecbarcelona.eu)
https://ibecbarcelona.eu/events/Kidsday

IBEC Seminar: Matteo Palma
2015-06-19 10:00 - 11:00
Bio-inspired self-assembly for single-molecule investigations

Matteo Palma, Queen Mary University of London
One of the ultimate goals in nanotechnology is the ability to produce efficient devices based on individual molecules and nanostructures. Despite the many potential benefits envisioned for single-molecule technology (in electronics and biotechnology) the strategies employed to date suffer from various limitations. Principal among these limitations is the poor control over the molecular assembly of nanostructures and individual molecules with respect to one another, as well as their position on devices with respect to other material components.
I will first discuss techniques based on the combined use of lithographic nanopatterning and bio-molecular self-assembly to control the immobilization of biomolecules in arrayed nanodomains. I will show how this allows us to produce highly ordered, self-assembled arrangements of nano-objects, ranging from proteins to DNA nanostructures, and bio-inorganic assemblies, for a variety of (nanoscale) investigations.
I will show how by specific design of the biomolecular nanoarrays, it is possible to simultaneously monitor hundreds of protein/DNA binding events at the single-molecule level. Moreover I will discuss the use of our nanopatterned biomimetic surfaces to probe the importance of transmembrane proteins (integrins) clustering and geometric arrangement of binding sites, in the formation of cell focal adhesions
I will then highlight the broader utility of such nanopatterned surfaces for the self-organization (on surfaces) of bio-inorganic assemblies as well as DNA nanostructures and carbon nanotubes. In particular, I will discuss how the combination of high resolution patterning with end-functional chemistry enables the assembly of 1D functional nanostructures in an orderly fashion.
Finally, building on our novel bottom-up assembly strategy for the formation of (chemically and geometrically) versatile carbon nanotube (CNTs) junctions, I will present a universal approach for the generation of multifunctional nanomaterials that employ molecular building blocks assembled between DNA wrapped CNT electrodes. We will demonstrate single-molecule control in the formation of nanohybrids via the in-solution assembly of classes of molecular materials (organic, and inorganic which display promising attributes) to DNA wrapped CNTs. We believe this may be a viable avenue towards the integration of these materials in complex and functional nano-architectures.
Our findings are of general interest for the controlled assembly of a broad range of functional molecules and nanostructures, towards the fabrication of solution-processable nanoscale devices. Moreover, we believe that the knowledge developed makes a significant contribution towards the facile fabrication of nanohybrid materials for single-molecule investigations. Future technologies will require devices of this type in a variety of key areas, including biodiagnostics, ultra-high speed computation, bioelectronics, and for renewable energy applications.

IBEC Seminar: Javier G. Fernández
2015-06-16 16:00 - 17:00
Bioinspired materials

Javier G. Fernández, Assistant Professor and Founder Academic Member · Singapore University of Technology and Design
Nature is abundant with materials that possess extraordinary mechanical characteristics. New techniques in biochemistry and advances in microelectronic engineering are boosting our knowledge of biological materials, and providing tools to fabricate at the scale at which these materials are made in nature. This investigation of the structural organization of these materials leads to understanding of the principles of natural materials design that are beginning to be harnessed to fabricate biologically-inspired composites for materials engineering with tunable properties that mimic living materials, which might provide useful for environmental challenges, as well as medical applications.
