Below you will find detailed information about the various projects proposed by researchers from the BIST centres and the DCEX-UPF. MMRES students must choose one of these as their Major Project. Projects available for the 2021/2022 academic year will be published when the new call opens (December 2020). During the call period, as students are admitted, their selected projects become assigned and are no longer available in later calls. Once the programme has started, each student will decide on their Minor Project together with their research supervisor.
For more information about the duration and content of the major and minor projects, see the syllabus.
|Project||Course||Centre||Research Group Name||Web||Supervisor||Availability||Description||Co-supervisor||Tags||Keywords|
|IRBB-2007. Biomedical Genomics||2020-2021||IRB Barcelona||Biomedical Genomics Group||WEBSITE||Nuria||Lopez-Bigas||Assigned|
In addition to contributing to finding drivers of cancer and precision medicine, our group is focused on understanding mutational processes by analysing tumour genomes. By studying the observed pattern of somatic mutations across genomic regions, we are able to explore the basic cell mechanisms that produce them. The interplay between these mechanisms, such as internal and external insults that damage DNA, chromosomal replication, transcription, and DNA repair mechanisms, leads to mutational processes that give rise to heterogeneous patterns of somatic mutations across the genome. Our efforts are now focused on generating nucleotide-resolution genome-wide maps of DNA damage and repair upon exposure to chemotherapeutic agents.
|cancer, chemotherapy, DNA damage, DNA repair, mutational signature|
|IRBB-2006. Signalling and Cell Cycle||2020-2021||IRB Barcelona||Signalling and Cell Cycle||WEBSITE||Angel||Rodriguez Nebreda||Assigned|
The group is interested in how cells interpret different signals to elaborate the appropriate responses. An important part of the work focuses on the p38 MAPK signalling pathway, and our group has made major contributions to understanding the mechanisms of signal integration by this pathway. We have also provided in vivo evidence for the implication of p38 MAPKs in homeostatic functions, beyond the stress response, and have shown how dysregulation of this pathway may contribute to cancer and other diseases. Recently, we have demonstrated important roles for p38 MAPK signalling in tumour initiation and progression as well as in the resistance to chemotherapeutic drugs using both genetic mouse models and patient-derived xenografts. Our work combines genetically modified mice, which allow the inactivation of p38 MAPK signalling in a regulated and tissue-specific manner, with the use of chemical inhibitors, studies in cancer cell lines and biochemical approaches. Overall, an important aim of our work is the identification of therapeutic opportunities based on the modulation of p38 MAPK signalling.
|cancer cell homeostasis, chemotherapy resistance, MAP kinase, signalling network, targeted therapy, tumour microenvironment|
|IRBB-2004. Cell Division Laboratory||2020-2021||IRB Barcelona||Cell Division Laboratory||WEBSITE||Cayetano||González||Assigned|
We model cancer in flies to understand the cellular changes that drive malignant growth and to identify conserved mechanisms that might be relevant for human cancer therapy (Nat Rev Cancer, 2013). Over the last years we have made a number of significant contributions to this field. We have found that neuroblasts can originate tumours if the process of self-renewing asymmetric division is disrupted (Nat Genet, 2005). We have discovered that brain tumours that originate in l(3)mbt mutants larvae are characterized by the ectopic expression of “Cancer Testis”/“Germ Line” antigens and showed for the first time that some of those genes are essential for tumour growth (Science, 2010; Open Biol Roy Soc, 2017). Recently we have revealed that l(3)mbt mutant brain tumours are strongly dimorphic, being more aggressive in males than in females. This tendency is in line with what is known for a wide range of human cancer types, for which the striking male predominance remains unexplained. We have found out that Drosophila experimental models of malignant growth may serve to investigate the cell biological axes that control sex-linked tumour dimorphism. We have identified potential regulators of sex-linked tumour dimorphism and showed that these genes may serve as targets to suppress sex-linked malignant traits (Science Advances, 2019). We have also described a method to assay the tumorigenic potential of Drosophila mutant tissues (Nat Protoc, 2015).
|cancer testis antigens, cancer therapy, Drosophila, malignant growth, sex-linked tumour dimorphism|
|IRBB-2003. Understanding stress adaptation from yeast to mammalian cells||2020-2021||IRB Barcelona||Cell Signaling||WEBSITE||Eulàlia||de Nadal||Assigned|
The main focus of our group is to understand how cells detect and respond to environmental changes. We have focused our studies on the characterization of the stress signal transduction pathways, especially those controlled by MAP kinases of the Hog1/p38 family, also known as the stress-activated MAP kinases (SAPK). Using S. cerevisiae budding yeast as a model organism, as well as mammalian cells, we study the molecular mechanisms required to respond to changes in the extracellular environment and which are the adaptive responses required for cell survival. Our main research lines are:
|cell cycle regulation, SAPK, Signalling, single cell analysis, Stress adaptation, transcriptional regulation|
|IRBB-2001. Development and Growth Control Laboratory||2020-2021||IRB Barcelona||Development and Growth Control Laboratory||WEBSITE||Marco||Milán||Available|
Chromosomal Instability (CIN), defined as an increased rate of changes in chromosome structure and number, is a feature of most, if not all, solid tumours. Our lab has recently developed an epithelial model of CIN in Drosophila where the relevant cell populations and pertinent cell interactions involved in the response of an epithelial tissue to CIN have been identified and where the molecular mechanisms driving emerging, tumour-like, cellular behaviours have started to be elucidated. In this model of CIN, cross-feeding interactions between two well defined populations, highly aneuploid cells and proliferating cells, increase each other size and contribute to the unlimited growth potential of CIN tumours. CIN-induced aneuploidy promotes a cell autonomous epithelial to mesenchymal (EMT)-like cell fate transition associated with a highly invasive behaviour and the entry into a senescence-like state. This senescence-like state is characterized by a cell cycle arrest in G2 and a well-defined senescence associated secretory phenotype (SASP) that includes mitogenic molecules inducing tumour-like overgrowths, and systemic hormones promoting tumour malignancy, as revealed by chronic blockade of developmental timing, cachexia and eventual animal lethality. The active invasive behaviour of highly aneuploid cells is characterized by the expression of Matrix Metalloproteinases (MMPs) and the production of dynamic actin-rich cellular protrusions and membrane blebs.
|Chromosomal Instability, Drosophila as a model in Cancer, EMT, Senescence|
|IFAE-2010. The ESA Euclid Dark Energy Survey||2020-2021||IFAE||EUCLID||WEBSITE||Cristóbal||Padilla||Available|
Euclid is a mission for the European Space Agency (ESA) Cosmic Vision (CV) 2015-25 programme to explore how the Universe evolved over the past 10 billion years to address questions related to fundamental physics and cosmology on the nature and properties of dark energy, dark matter and gravity, as well as on the physics of the early universe and the initial conditions which seed the formation of cosmic structure. The satellite is expected to be launched in the first half of 2022 by a Soyuz ST-2.1B rocket and then travel to the L2 Sun-Earth Lagrangian point for a six years mission. To accomplish its goals, Euclid will carry out a wide survey of 15,000 deg2 of the sky free of contamination by light from the Milky Way and the Solar System and a 40 deg2 deep survey to measure the high-redshift universe. The complete survey represents hundreds of thousands of images and several tens of Petabytes of data. With these images Euclid will probe the expansion history of the Universe and the evolution of cosmic structures by measuring the modification of shapes of galaxies induced by gravitational lensing effects of dark matter and the 3-dimension distribution of structures from spectroscopic redshifts of galaxies and clusters of galaxies. In this project, we will use machine learning techniques such as Convolutional Neural Networks to identify the galaxies and improve de-blending algorithms the Euclid simulated images and/or Generative-Adversarial Networks to make fast simulations of images and Cosmologies. This work will serve to prepare the scientific analysis tools and be ready when Euclid produces its first images after lunch.
|Cosmology, Dark Energy, ESA, galaxies, Image Processing, Machine learning, Neural Networks, Space, Universe Evolution|
|IFAE-2009. Gravitational Waves detection using Deep Learning with LIGO/Virgo data||2020-2021||IFAE||VIRGO||WEBSITE||Mario||Martínez||Available|
The discovery of gravitational waves (GWs) by the LIGO/Virgo interferometers has opened a complete new field for testing fundamental physics and cosmology. Events are interpreted as originated from the coalescence of binary systems made of black holes and/or neutron stars. The detail study of such events provides a unique opportunity to perform stringent tests of general relativity, the potential identification of primordial black holes as candidates for dark matter, and the study of the early universe via GW signals from inflation. In addition, in the case of neutron star events, the combination with electro-magnetic signals from identified galaxies provides a new an independent measurement of the expansion rate of the universe. The detection of GWs relies on the pattern recognition of the GW signal embedded in the data, which makes it an ideal environment for the adoption of an artificial intelligent approach. In this master thesis, a project is proposed for using state-of-the-art machine learning techniques, in the form of convoluted neutral networks, for the identification of events in the LIGO/Virgo data streams. The project involves the design, training and optimization of neural networks to discriminate background events from GW signals, using massive simulated signal templates and the full LIGO/Virgo dataset. The work will be developed within the framework of the LIGO/Virgo experiments and in contact with high-performance computing centers.
|IFAE-2008. The PAU Survey: the potential of narrow-band observations for revealing the true panoply of different galaxy types||2020-2021||IFAE||Cosmology||WEBSITE||Malgorzata||Siudek||Available|
Machine learning techniques will be crucial for the analysis of galaxy populations in the impending era of big data in astronomy. The student will be able to learn about machine-learning, including developing galaxy classification schemes using (un)supervised clustering algorithms. These deep state-of-the-art methods will be applied to the PAU Survey (PAUS), an innovative photometric survey with 40 narrow bands at the William Herschel Telescope. This multi-filter data has the potential to conduct novel galaxy evolution studies allowing for a detailed description of different galaxy types and their properties. Machine learning tools can efficiently extract relevant information from very large and complex datasets such as PAU. In the era of large deep surveys, they are the optimal approach compared to standard methods or color-color diagrams. A solid background in programming is beneficial.
|galaxies, Machine learning|
|IFAE-2007. Avalanche Photodiodes for Medical Diffuse Optics||2020-2021||IFAE||Instrumentation||WEBSITE||Sebastian||Grinstein||Available|
Medical diffuse optical methods utilize near-infrared light to probe into the tissues and obtain information about its absorbers and scatterers. The diffuse light carries information about the movement of red cells which can be used to measure blood flow. In this relatively new technique a laser shines light into the subject tissue and an extremely sensitive detector extracts the signal to obtain the desired measurements. However, to date, these systems are limited by the sensor technology, they are not cost-effective, they are bulky for wearable implementations and they cannot easily be scaled up.
|Avalanche photo-diodes, biophotonics, CMOS sensors|
|IFAE-2006. Fractal dynamics and cancer growth||2020-2021||IFAE||Theory Division||WEBSITE||Rafel||Escribano||Available|
The dynamics of fractal and chaotic structures in nature follow the principle of minimal energy. Guided by such principle, together with a set of dissipative equations, and the notion of attractor, we shall consider the epistemology of the origin of cancer. Under certain boundary conditions, we propose to study how the pre-cancerous niche develops inspired by the chaotic evolution of dissipative systems with inhomogeneities. The tools of analytic mechanics may spell out a sequence of steps, one or more of which could be interdicted to prevent the progression of cancer.
|carcinogenesis, Chaotic systems, fractal structures, inhomogeneities, metastasis|
|IFAE-2005. Large-scale correlations and cancer cell metastasis||2020-2021||IFAE||Theory Division||WEBSITE||Rafel||Escribano||Assigned|
The study of the behavior of large and complex stochastic systems can be undertaken using the mean field theory within statistical mechanics. In this context the interaction of all the other elements into one singular individual is approximated by an averaged effect. As soon as large-scale correlations appear, specially between spatially separated fluctuating and frozen regions, the system may develop critical points and the theory becomes inhomogeneous. Boundary conditions and critical phenomena are important elements to understand the system growth and evolution.
|inhomogeneities, large-scale correlations, metastasis, Statistical mechanics|
|IFAE-2004. Quantum annealing with coherent superconducting qubits||2020-2021||IFAE||Quantic||WEBSITE||Pol||Forn||Available|
Quantum annealing is a technique developed to perform adiabatic quantum computing in a real, open quantum system. The computation typically involves evolving the Hamiltonian of the system from an initial trivial scenario towards a more complex final one. The final state of the system can be mapped to the value of a given cost function. The final Hamiltonian of the system is built in such a way that its lowest energy eigenvalue corresponds to the minimum of the cost function, thereby obtaining the solution to a certain optimization problem codified in the values of the cost function. This type of quantum algorithm is very versatile and does not require quantum error correction. A quantum annealer is thus considered an analogic quantum computer with a big potential to display a quantum speedup in the not-so-distant future. Superconducting quantum bits are ideal candidates to be building blocks of quantum annealers. The tunability of their parameters, the flexibility to scale up to large-sized systems combined with their long coherence times, make superconducting qubits a suitable choice to embed adiabatic quantum computing protocols. The IFAE group on Quantum Computing Technology started to operate in 2019 with the goal to develop a quantum annealing prototype using superconducting qubits as its core technology. This project will focus on joining the efforts to build the first generation of prototype quantum annealers consisting of two superconducting flux qubits coupled through an rf-SQUID coupler. The MsC candidate will join the team efforts in circuit design, device characterization and measurements. The main goal is to obtain evidence of quantum annealing performed with two superconducting flux qubits with a long coherence time.
|quantum annealing, Quantum computation, superconducting qubits|
|IFAE-2003. Commissioning of the first Large-Size Telescope of the Cherenkov Telescope Array||2020-2021||IFAE||Gamma rays||WEBSITE||Oscar||Blanch||Available|
The Cherenkov Telescope Array (CTA, https://www.ctaobservatory.org) is the next generation ground-based observatory for gamma-ray astronomy at very-high energies (from 20 GeV to > 100 TeV). The gamma-ray astrophysics group at IFAE has played a leading role in the construction of the first of the four large-size telescopes of CTA-North observatory, dubbed LST-1, which was inaugurated on October 10th 2018 at the Roque de los Muchachos in the island of La Palma (https://phys.org/news/201810-telescope-cherenkov-array-sitedebut.html). LST-1 is equipped with a 23-m diameter dish, and is the most advanced telescope of its kind worldwide. The telescope is currently in its commissioning phase, which is expected to extend until mid-2020. The goal of this master thesis project is to contribute to the analysis of the first scientific observations of the LST-1 telescope, particularly those of known bright gamma-ray sources, with the purpose of fully characterizing the instrument’s performance. We are searching for a student with good programming skills, preferentially with some experience in the use of Python.
|Cherenkov Telescope Array, Gamma ray, physics|
|IFAE-2002. Impact of high-granularity timing detectors in the search for the Standard Model Higgs boson produced in the vector boson fusion process and decaying into a pair of tau leptons||2020-2021||IFAE||IFAE-ATLAS||WEBSITE||M. Pilar||Casado||Available|
The ATLAS experiment will start a phase with high intensity data collection in 2025. The amount of recorded data will be increased by a factor 10. Specialized detectors will be placed to cope with the new conditions, specially to handle the overlap of different events in the same beam-crossing, pile-up. The high granularity timing detector (HGTD) will be one of these detectors, located at ±3.5m from the interaction point, with inner radius 12 cm and outer radius 64 cm. HGTD will provide timing measurements of charged particles from the interaction cross and will help in jet algorithms, particle reconstruction and in b-tagging. Furthermore, the impact of HGTD is currently being evaluated in physics analyses where the presence of jets is important in the forward region, as Higgs produced in vector boson fusion with taus in the final state. The student will implement the analysis for a pair of taus produced in the above process decaying into a lepton and a hadron. The analysis will be cross-checked with on-going Run 2 studies. Finally, the effect of HGTD will be assessed and the results will be part of an ATLAS publication covering VBF H -> tau tau with taus decaying to all possible topologies.
|ATLAS, CERN, detector, Higgs, physics|
|IFAE-2001. Enhanced ATLAS Level-1 trigger capabilities with Artificial-Intelligence regression on Field-Programmable Gate Array architecture.||2020-2021||IFAE||IFAE-ATLAS||WEBSITE||Imma||Riu||Available|
The ATLAS trigger system is a crucial component of the experiment. It is responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions at the Large Hadron Collider (LHC). The Level-1 (L1) trigger is the first rate-reducing step in the ATLAS trigger system with an output rate of up to 100 kHz and decision latency of less than 2.5 microseconds. In the L1 system, an important role is played by the Level-1 Topological Processor (L1Topo). It selects interesting events by applying kinematic and angular requirements on electromagnetic clusters, hadronic jets, muons and total energy reconstructed in the ATLAS apparatus. This results in a significantly improved background event rejection rate and improved acceptance of physics signal events. During the current LHC shutdown, upgraded L1Topo modules are being installed benefiting from a larger processing power available for the implemented algorithms. They exploit the latest generation of the Xilinx Ultrascale+ FPGA, XCVU9P-2FLGA2577E, characterized by large input bandwidth, up to ~3Tb/s per module, and large processing power. The objective of this research project is to improve the event reconstruction at L1 by using state-of-the-art Artificial Intelligence (AI) algorithms to solve regression tasks; the event properties are inferred by training a suitable AI model on bitwise data representing the recorded event in the ATLAS detector prior to the high-level reconstruction. The AI model will use the L1Topo capability for fast evaluations in a single FPGA operation by means of look-up tables.
|ATLAS, detector, Hadron collider, physics|
|ICN2-2005. New Transfection Agents And Nanoparticle-Antioxidant Adjuvants For Inflammatory Related Diseases||2020-2021||ICN2||Inorganic Nanoparticles Group||WEBSITE||Victor||Puntes||Available|
Inorganic nanoparticles (NPs) are emerging as potential probes in next-generation biomedical applications. Among them, cerium oxide nanoparticles (CeONPs) has emerged as a fascinating and lucrative material in biological fields such as bioanalysis, biomedicine, drug delivery, and bioscaffolding. CeONPs have received much attention because of their excellent catalytic activities, which are derived from quick and expedient mutation of the oxidation state between Ce4+ and Ce3+. The cerium atom has the ability to easily and drastically adjust its electronic configuration to best fit its immediate environment. Being a mature engineered nanoparticle with various industrial applications, CeONP was recently found to have multi-enzyme, including superoxide oxidase, catalase and oxidase, mimetic properties that produce various biological effects, such as being potentially antioxidant towards almost all noxious intracellular reactive oxygen species.
|biomedicine, catalysis, CeO nanoparticles, inflammation, nanoenzimes|
|ICN2-2004. Nanoremediation: Emerging-Micropollutants And Nanopharmaceuticals||2020-2021||ICN2||Inorganic Nanoparticles Group||WEBSITE||Victor||Puntes||Available|
The development of functional colloidal inorganic NCs has increased exponentially offering a “toolbox” ready to be used in a wide range of applications, such as environmental remediation. One important group of compounds and personal care products which are regarded as a rising environmental problem, is pharmaceutical pollutants, which persistence to processes of human metabolism is very high. The development of advanced oxidation process (AOPs) represents a hopeful and effective way for the degradation of pharmaceuticals. Among them, catalysis and photocatalysis using inorganic NCs as an advanced oxidation technique has been a focus of research during the last two decades aiming at improving its performance, robustness and recyclability.
|catalysis, Inorganic nanocrystals, nanoremediation, pharmaceutical pollutants, wet-chemistry synthesis|
|ICN2-2003. Complex Inorganic Nanocrystals For Artificial Photosynthesis, Biogas Production And Fuel Cells||2020-2021||ICN2||Inorganic Nanoparticles Group||WEBSITE||Victor||Puntes||Available|
Energy availability is one of the most important problems facing our civilization. Consequently, a major challenge in 21st century is the development of renewable carbon-neutral sources. In this context, the main idea of the research project is to address the long-term challenge of identifying, designing and producing a new generation of complex NCs that integrate dissimilar materials in a unique multicomponent heterostructured system with controlled architecture and advanced functionality. _x000D_
|artificial photosynthesis, biogas, catalytic performance, fuel cells, Inorganic nanocrystals|
|ICN2-2002. Atomically precise graphene nanostructures for optoelectronics||2020-2021||ICN2||Atomic Manipulation and Spectroscopy Group||WEBSITE||Aitor||Mugarza||Available|
Our group aims to understand and manipulate electronic, magnetic and optical phenomena at the atomic scale, with the final goal of searching for new ways to sense, and to store and process information. The project proposed here focuses on developing methods to tailor graphene’s properties by nanostructuration.
|atomic scale manipulation, electronic spectroscopy, graphene nanoribbons, materials synthesis, scanning probe microscopy|
|ICN2-2001. Advanced Electron Nanoscopy||2020-2021||ICN2||Advanced Electron Nanoscopy (GAeN)||WEBSITE||Jordi||Arbiol||Assigned|
Quantum technology is supposed to be the biggest revolution that has to happen on the next few years, implying a wide range of fields such as computational and health sciences, energy applications and even the generation of extra-secure communications and encrypting. It will come to stay and deeply change everyone’s life. This project aims to focus on the materials science that is behind quantum computation. However, multiple approaches that compete with each other, (as are carried and sponsored by the main computation companies, i.e. Microsoft, Google, IBM, Intel) are being pursued in order to reach the final common goal of the process, which is the fabrication of a fully functional and commercial quantum computer.
|atomic models, Quantum nanomaterials, scanning transmission electron microscopy|
|ICIQ-2002. Nanomaterials for energy applications||2020-2021||ICIQ||Photoactive Materials||WEBSITE||Emilio||Palomares||Assigned|
The group's research is focussed in photoactive materials for energy and biosensing applications. Currently the projects where the applicant can work will be perovskite solar cells or biosensing for infectious diseases. The applicant will learn how to prepare and characterize materials with optical and electrical properties. Moreover, the applicant will prepare and measure devices. The applicant will benefit of an outstanding multidisciplinary environment with chemists, physicists, biologists and electronic engineers.
|biosensing, perovskite, quantum dots, solar cells|
|ICIQ-2001. Machine Learning Techniques in Electro-Catalysis||2020-2021||ICIQ||Theoretical Heterogeneous Catalysis||WEBSITE||Núria||López||Assigned|
The project will be devoted to explore several different types of machine learning techniques to materials that can be employed as electrocatalysts to reuse CO2 and thus mitigate climate change.
|CO2 reduction, Density Functional Theory, energy, Machine learning, Programming|
|ICFO-2016. Single photons from two-dimensional materials||2020-2021||ICFO||Quantum Nano-optoelectronics||WEBSITE||Frank||Koppens||Available|
Very exciting quantum optical properties of materials that are only one atom thick have been discovered only during the last few years. These so-called two-dimensional materials showed, surprisingly, emission of light photon-by-photon, instead of a continuous photon stream. This single photon emission has so far not been fully controlled.
|2D materials, quantum emitters|
|ICFO-2015. Hyperfocusing infrared light for sensitive photodetection||2020-2021||ICFO||Quantum Nano-optoelectronics||WEBSITE||Frank||Koppens||Available|
Graphene based photodetectors have been proposed as an alternative of current technologies due to its broad band absorption properties ranging from visible to terahertz range, low electronic heat capacity and its hot electron cooling time in the picosecond timescale , which enables graphene as an interesting platform for ultrafast photodetection. In this work, propose to combine graphene pn junctions photodetectors [2, 3] with metallic nanostructures that serve as launchers-guiders for hyperbolic phonon polaritons to achieve hyperfocusing of the incident mid-infrared light and to boost light-matter interactions. We will use 2D materials that present long lifetimes polaritons, such as hBN and MoO3 .
|2D materials, graphene, Nanophotonics, photodetection|
|ICFO-2014. Cavity quantum electrodynamics||2020-2021||ICFO||Quantum Nano-optoelectronics||WEBSITE||Frank||Koppens||Available|
This project will explore the extreme limits of light-matter interactions. We exploit the ability to confine light to subwavelength cavities able to confine light to extremely subwavelength volumes on the order of just a nanometer. This unprecedented degree of confinement, as we have demonstrated very recently, gives rise to very high fields and dramatically enhanced coupling between the cavity modes and nearby quantum entities. The goal of this research project will be to investigate the resultant quantum behaviors enabled by these cavities with spectrally resolved optical measurements. The objective is to touch upon the unexplored physics of the ultra-strong coupling between light and matter. The master's student will acquire optical measurement and nanofabrication skills, working on cutting edge experimental research.
|Nanophotonics, Polaritons, QED, ultra strong coupling|
|ICFO-2013. Frontiers of Quantum Information Science, Quantum Simulations and Many Body Physics||2020-2021||ICFO||Quantum Optics Theory||WEBSITE||Maciej||Lewenstein||Assigned|
The MSc student will join one of the running research projects in the ICFO-QOT. The concrete choice will depend on the current efforts in the group (that change adjusting to scientific needs), student’s preferences and preparation, availability of supervisor/co-supervisor and resources for a specific theme. At this stage ICFO-QOT can absorb one MSc student in this area. QOT-ICFO studies and develops in particular
|many body physics, quantum information, quantum simulations|
|ICFO-2012. Real time 3D video tracking of nanoparticle motion confined in an optical trap||2020-2021||ICFO||Neurophotonic & Mechanical Systems Biology||WEBSITE||Michael||Krieg||Available|
The group recently set up an optical trapping platform for mechanical manipulation of nanoparticles in aqueous solutions. In order to infer and measure forces in this configuration, tracking of the particles with angstrom accuracy is of utmost importance. During this project, the successful applicant will work with experienced users to implement a camera-based video tracking of xyz motion of nanoparticles, with the aim to perform real-time force and displacement measurements on immobilized biomolecules and cells. During the master thesis, the applicant will learn the essentials of optical trapping and LabView programming. Opportunities to collaborate with other BIST centres (IBEC, CRG) are available. A strong computational background and basic knowledge in instrument automation is a plus.
|Mechanobiology, Neuroscience, optical tweezer, video tracking|
|ICFO-2011. Attosecond Molecular-movies with Inner-Shell Electrons||2020-2021||ICFO||Attoscience and Ultrafast Optics||WEBSITE||Jens||Biegert||Available|
The aim of our research is the development of tools and establishment of methodologies for investigation of the ultrafast events that are caused by electrons inside atoms, molecules, solids and biological matter. The power of attoscience and ultrafast optics lies in the incredible time resolution that gives access to observing the triggering events that are caused by electronic rearrangement and ultimately lead, at hugely varying temporal scales, to molecular dissociation, chemical reactions, excitonic energy transfer or even biological function.
|Attoscience, Extreme Nonlinear Optics, Ultrafast Lasers|
|ICFO-2010. Single-molecule microscopy tools to study intra-Golgi membrane traffic||2020-2021||ICFO||Single Molecule Biophotonics||WEBSITE||Maria||Garcia-Parajo||Available|
We are an interdisciplinary group studying intracellular membrane morphology and dynamics, with a special focus on understanding the secretory pathway. We combine advanced microscopy techniques (single-molecule fluorescence and super-resolution nanoscopy), molecular and cell biology tools, with theoretical biophysics approaches to tackle highly controversial or still mysterious fundamental topics in cell biology with a clear pathophysiological relevance.
|Cargo wave synchronization, Intra-Golgi transport, Single particle tracking, super resolution microscopy|
|ICFO-2009. Quantum simulation with ultracold atoms||2020-2021||ICFO||Ultracold Quantum Gases||WEBSITE||Leticia||Tarruell||Available|
In recent years ultra-cold atomic gases have emerged as a novel platform for the study of quantum many-body systems. Exploiting these gases, it is possible to synthesize quantum matter of highly controllable properties (interactions, dimensionality, potential landscape, etc.) in table-top experiments. In our group, we use them to explore experimentally collective phenomena originally studied in condensed-matter physics, such as superfluidity, superconductivity, magnetism, or topological order.
|atomic physics, Quantum gases, Quantum optics, quantum simulation|
|ICFO-2008. Hot Atoms 1||2020-2021||ICFO||Atomic Quantum Optics||WEBSITE||Morgan||Mitchell||Available|
Our group studies the interactions between light and the quantized electronic states of atoms. Ground electronic states of alkali atoms in the gas phase, in particular, can be extremely sensitive to magnetic fields. Using knowledge of the atomic physics, we investigate how these systems can be used as “magnetometers” to detect and measure weak magnetic fields, yielding a noise floor as low as 10^(-15) tesla. The term “weak” is relative to both present technological limits and fundamental quantum limits of existing magnetic sensors.
|Atomic sensors, Magnetic Resonance, Magnetometry, Quantum optics, Rubidium vapors|
|ICFO-2007. Engineering superconductivity in twisted bilayer graphene.||2020-2021||ICFO||Bachtold group||WEBSITE||Adrian||Bachtold||Available|
Two-dimensional (2D) monolayers have generated a huge research interest in the past years. The discovery of graphene was awarded with the 2010 Nobel Prize in physics. Very recently, it was realised that twisted bilayer graphene represents a promising platform for understanding the elusive properties of unconventional superconductivity. Better understanding high-temperature superconductors may allow physicists to reach superconductivity at room temperature. This would likely have an enormous impact on our society, since it could dramatically reduce energy consumption in many devices and electricity distribution. Here, we propose to explore new types of twisted bilayer graphene devices in order to understand how superconductivity emerges from the strong correlation between electrons.
|cryogenics, electrical measurements, nanofabrication, Superconductivity, twisted bilayer graphene|
|ICFO-2006. All-optical interrogation of synaptic transmission in C elegans||2020-2021||ICFO||Neurphotonics and Mechanical Systems Biology||WEBSITE||Michael||Krieg||Assigned|
Proper localization and activity of synaptic proteins is critical for neuronal communication and synaptic transmission. Mutations in the transmission machinery responsible for various congenital diseases, including ALS and neuropsychological disorders. Here we propose to use C elegans as a model system to understand how mechanical properties of neurons influence synaptic transmission at the neuromuscular junction (NMJ). We specifically ask the question whether or not structural components of the synaptic cytoskeleton, such as microtubules and the actin/spectrin cytoskeleton are involved in signal transmission. To understand this problem, we will take advantage of an all-optical interrogation, in which we selectively activate motorneurons optogenetically using novel light-gated ion channels, while reading out muscle activation by genetically encoded reporters for voltage and calcium activity. We will first record muscle signals after a careful titration of a controlled number of photons and later repeat these measurement in animals forced into given body postures. Once we charazterized the dose-response curve, we will expand these analyses into specific disease models of muscular dystrophies of synaptic transmission mutants hypothesized to involve changes in the synaptic cytoskeleton.
|Calcium Imaging, Neuroscience, optogenetics, Photonics, Synaptic Transmission|
|ICFO-2005. Medical optics group IV||2020-2021||ICFO||Medical Optics||WEBSITE||Turgut||Durduran||Available|
Diffuse optical instrumentation for translational and clinical biomedical research: develop state-of-the-art biomedical instrumentation for translational and clinical research. These range from portable, hybrid systems that combine diffuse correlation spectroscopy (DCS) with near-infrared diffuse optical spectroscopy (NIRS-DOS) to laser speckle based animal images. We have industrial, biomedical and clinical relationships that drive the specifications of these systems.
|Biomedical diffuse correlation spectroscopy|
|ICFO-2004. Medical Optics III||2020-2021||ICFO||Medical Optics||WEBSITE||Turgut||Durduran||Available|
Validation and testing of compact components for diffuse correlation spectroscopy analysis and define the healthy variation.
|biomedical optics, diffuse optics, medical devices, Neuro-monitoring|
|ICFO-2003. Medical Optics II||2020-2021||ICFO||Medical Optics||WEBSITE||Turgut||Durduran||Available|
How does the cerebrovascular reactivity vary over days and weeks? Non-invasive, longitudinal diffuse optical neuro-monitors based on diffuse correlation spectroscopy and near-infrared spectroscopy allow us to study this topic and relate to our findings on pathological conditions (ischemic stroke, traumatic brain injury, carotid stenosis and chronic sleep apnea). This project will study this aspect by measuring healthy volunteers and carry out diffuse optical data analysis, biostatistical analysis and define the healthy variation.
|biomedical optics, diffuse optics, laser speckles, neuroimaging|
|ICFO-2002. Medical Optics I||2020-2021||ICFO||Medical Optics||WEBSITE||Turgut||Durduran||Available|
ICFO-Medical Optics group developed techniques based on near-infrared diffuse optics that are being translated to the clinics to measure tissue physiology in neuro-critical care and in oncology. These devices deliver laser light and detect the diffuse photons in order to calculate the laser speckle statistics. These statistics are then analysed by a physical model of photon propagation in tissues to quantify parameters such as microvascular blood flow. In this project, we will test next generation single-photon counting avalanche photo-diodes developed in collaboration with IFAE as highly-sensitive fast detectors. If successful, these detectors will pave the way to next generation novel systems.
|biomedical optics, biophotonics, singlephoton detectors|
|ICFO-2001. Live Cell Superresolution Microscopy & Embryonic Stem Cells||2020-2021||ICFO||Live Cell Superresolution Microscopy & Embryonic Stem Cells||WEBSITE||Stefan||Wieser||Available|
Our team works at the interface of physics and biology. We are developing live cell super-resolution imaging techniques for 3D imaging of whole cell dynamics. We mainly focus onto the behaviour of early embryonic stem cells (ES cells) and immune cells under physical force to understand the fine-tuned mechanisms providing tissue homeostasis, normal development and cell differentiation under complex environmental conditions. One objective is to unravel the mechanosensation of the nucleus which has recently been realized as a mechanosensation platform regulating transcription and cell differentiation. The second objective is to unravel the actomyosin-plasma membrane contribution in compression induced cell transformation and migration competence. Our recent work highlighted profound changes in cortical actin network organization and myosin II-mediated cellular contractility under compression that triggered rapid changes in cell morphology and migration competence (Ruprecht et al, CELL 2015). To gain a mechanistic understanding of these processes we apply advanced imaging techniques – with a focus on sophisticated structured Illumination technologies - and data analysis tools that allow for integrating molecular dynamics with largescale cell behaviour.
|Mechanosensation, microscopy, Modeling, Stem Cells, Superresolution|
|IBEC-2015. Developing organ-on-a-chips for the study of diabetes type II||2020-2021||IBEC||Biosensors for Bioengineering (B4b)||WEBSITE||Javier||Ramón Azcón||Assigned|
Biosensors for Bioengineering group (B4b) is a multidisciplinary research group, led by Prof. Javier Ramon, focused in the development of Organs-on-a-Chip. One of our lines of research aims to engineer a new in vitro model to mimic the insulin-mediated skeletal muscle glucose metabolism. To this aim, muscle tissues and pancreatic islets will be engineered and combined in a multi-organ-on-a-chip approach to study the insulin secretion of pancreatic islets and the glucose-induced contraction of muscle tissues. In a multidisciplinary approach, we will make use of micro- and nanoscale fabrication technologies developed by our research group and will integrate novel biosensing technology to monitor metabolic processes relevant in diabetes. Engineered tissues will benefit from novel scaffolds and will be integrated with bioreactors, an electrical stimulator and biosensors to detect the glucose consumption, myokine secretion from skeletal muscle cells, insulin production and effects of some target drugs for T2D treatment on both tissues.
|3D-Bioprinting, biomaterials, biosensors, Organs-on-a-Chip, tissue engineering|
|IBEC-2014. Nanoscopy for Nanomedicine||2020-2021||IBEC||Nanoscopy for Nanomedicine||WEBSITE||Lorenzo||Albertazzi||Available|
Nanoscopy for Nanomedicine group uses super resolution microscopy (SRM) to track nanomaterials with therapeutic potential in the biological environment and to visualize the interactions with blood components, immune system and target cells. The understanding of materials-cell interactions is the key towards the development of novel nanotechnology-based therapies for treatment of cancer and infectious diseases.
|Drug delivery, Nanomedicine, Nanoscopy, super resolution microscopy|
|IBEC-2013. Deep Mutagenesis of Prion-Like Domains||2020-2021||IBEC||Protein Phase Transitions in Health and Disease||WEBSITE||Benedetta||Bolognesi||Available|
Many proteins implicated in neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease and Amyotrophic Lateral Sclerosis (ALS), contain Prion-like domains. Prion-like domains are intrinsically disordered regions that can drive proteins to populate multiple physical states in the cytoplasm: diffuse, liquid de-mixed, solid aggregate. Pathological mutations affect these equilibria in ways we cannot yet understand or predict. In this project we will use deep mutagenesis to quantify the effects of all possible mutations in a prion-like domain implicated in ALS. For thousands of protein variants we will measure how mutations affect both the physical state acquired by the protein and
|Deep mutagenesis, Intrinsic Disorder, Liquid Phase Separation, Prions, Protein Aggregation|
|IBEC-2012. Bacterial infections: antimicrobial therapies II||2020-2021||IBEC||Bacterial infections: antimicrobial therapies||WEBSITE||Eduard||Torrents||Assigned|
Control of chronic lung infections and clearance of well-formed biofilms remain tedious and extremely difficult to treat, with only a few therapeutic options nowadays available in clinics. This difficulty in treating infections has become an alarming problem with a global impact currently affecting hundreds of millions of children and adults worldwide. Additionally, and aggravating the problem, most of the biofilm-related infections are caused by multispecies biofilms.
|antibiotic multiresistant, antimicrobials, biofilm, infectious diseases, nanoparticles|
|IBEC-2011. Bacterial infections: antimicrobial therapies I||2020-2021||IBEC||Bacterial infections: antimicrobial therapies||WEBSITE||Eduard||Torrents||Assigned|
Infectious diseases are the leading cause of death worldwide. Disease-causing bacteria that resist antibiotic treatment are now widespread in every part of the world and have reached "alarming levels" in many areas as stated by the World Health Organization. "The problem is so serious that it threatens the achievements of modern medicine," entering to A post-antibiotic era in which common infections and minor injuries can kill. Nowadays, bacterial biofilm-based infections have emerged as a significant public health concern.
|antibiotic multiresistant, antimicrobials, bacterial genetics, biofilm, infectious diseases|
|IBEC-2010. Selection of DNA aptamers against Plasmodium falciparum early blood stages||2020-2021||IBEC||Nanomalaria||WEBSITE||Xavier||Fernàndez-Busquets||Available|
The World Health Organization Global Technical Strategy for Malaria 2016-2030 lists the universal access to malaria diagnosis as an essential part of the strategic framework that should eventually lead to eradicating the disease, since knowing parasitemia and parasite species is crucial in order to select the most appropriate drug treatment. Currently, national malaria programs rely on light microscopy and rapid diagnostic tests, which are not sensitive enough to detect low parasite density infections (sub-microscopic malaria in which patients are usually asymptomatic) that are crucial in the transmission dynamics. Molecular techniques can detect sub-microscopic malaria, but are inadequate for massive use because of elevated costs or need for highly trained staff. Therefore, new diagnostic methods are needed in order to advance towards malaria eradication. Antibody production often involves the use of laboratory animals and is time-consuming and costly, especially when the target is Plasmodium, whose variable antigen expression complicates the development of long-lived biomarkers. To circumvent these obstacles we are applying in our group the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method to the rapid identification of DNA aptamers against late stages of Plasmodium falciparum-infected red blood cells, to be used in future diagnosis devices.
|aptamers, Malaria, Plasmodium falciparum, SELEX|
|IBEC-2009. Smart Nano-Bio-Devices II||2020-2021||IBEC||Smart Nano-Bio-Devices||WEBSITE||Samuel||Sánchez||Available|
IBEC's Smart Nano-Bio-Devices group focuses in the minituarization and design of new bio-devices and advanced materials that bridge the gap between chemistry, biology, material science and physics, which can have relevant applications in the robotics, biomedical or environmental fields. The group has wide experience in the design and fabrication of smart nano- and micro-motors and actuators and also investigates the integration of artificial microstructures with living cells and biomaterials (hybrid bio-robots) based on 3D bioprinted skeletal muscle tissue. The project consists on the fabrication (using state-of-the-art 3D bioprinters) of hybrid bio-robotic devices or Bio-Bots, that can act as walkers or swimmers, combining artificial components (hydrogels, smart polymers, magnets, nanoparticles) and biological moieties (skeletal muscle tissue). Depending on the background and skills of the student, the individual objectives can be: i) synthetizing and characterizing new combinations of (nano-structured) materials (either artificial polymers or hydrogels for cell encapsulation), their 3D-printability, their biocompatibility and effects on cell differentiation and maturation; ii) further studying capabilities of hybrid bio-bots, such as adaptability, self-healing or response to external stimuli; iii) using optogenetics techniques to stimulate skeletal muscle cells with blue light and studying their controllability, local stimulation or differences with respect to electrical stimulation. The student will join a highly multidisciplinary team and project, and thus will learn techniques ranging from cell culture and tissue engineering to material science, chemistry, physics and engineering. Students from all sorts of background (material science, biomedical engineering, physics, biology, chemistry…) with multidisciplinary interests are welcome.
|3D-Bioprinting, Bio-Hybrid Robotic Systems, Engineered Skeletal Muscle Actuators, Nano-structured Biomaterials|
|IBEC-2008. Smart Nano-Bio-Devices I||2020-2021||IBEC||Smart Nano-Bio-Devices||WEBSITE||Samuel||Sánchez||Available|
Active Nano-particles in nanomedicine: smart drug delivery systems
|Drug delivery, nanobots, nanomachines, nanoparticles, self-propulsion|
|IBEC-2007. Integrative Cell and Tissue Dynamics||2020-2021||IBEC||Integrative Cell and Tissue Dynamics||WEBSITE||Xavier||Trepat||Available|
We aim at understanding how physical forces and molecular control modules cooperate to drive biological function. We develop new technologies to map and perturb the main physical properties that determine how cells and tissues grow, move, invade and remodel. By combining this physical information with systematic molecular perturbations and computational models we explore the principles that govern the interplay between chemical and physical cues in living tissues. We study how these principles are regulated in physiology and development, and how they are derailed in cancer and aging. Our group is composed of physicists, engineers, biologists and biochemists.
|cancer, epithelium, Mechanobiology, microscopy, organoid|
|IBEC-2006. Equivalence of chemical measurement methods||2020-2021||IBEC||Signal and Information Processing for Sensing Systems||WEBSITE||Santiago||Marco||Available|
In the development of new sensors and instruments it is important to compare their performance against gold reference techniques. This requires the comparison of the measurement accuracy provided by their respective calibration models. This comparison is carried out with statistical techniques. There are several methodologies to determine the equivalence of measurement methods. The student will survey the state of the art and implement those methodogies in Python/R/matlab and apply those to a practical problem. These techniques are essential for the standardization of novel measurement methods in areas such as clinical chemistry or environmental monitoring.
|Calibration, Programming, Regression, Standardization, Statistics|
|IBEC-2005. Development of computational Solutions for Ion Mobility Spectrometry Data Analysis||2020-2021||IBEC||Signal and Information Processing for Sensing Systems||WEBSITE||Santiago||Marco||Available|
In the group we develop full computational workflows for the analysis of metabolomics data based on NMR, GC-MS or LC-MS techniques. Gas Chromatography-Ion Mobility Spectrometry is a novel technique for the analysis of the volatile fraction of the metabolome. Based on previous research at the group, the main aim is to produce an R-package that integrates basic GC-IMS signal processing. The student will get training in signal processing in the R technology and in the development of software packages.
|Data Analysis, Metabolomics, R language, Signal Processing|
|IBEC-2004. Improving site-specific targeting of nanomedicines for treatment of lung or brain diseases||2020-2021||IBEC||Targeted Nanotherapeutics and Nanodevices||WEBSITE||Silvia||Muro||Available|
Novel drug nanocarriers improve the solubility, biodistribution, and overall performance and safety of therapeutic agents. Their functionalization with targeting moieties enables site-specific drug delivery to selected cells. Although this paradigm is easily achieved in cell mono-culture models, in vivo specificity of targeted vehicles remains a challenge. The complexity of the physiological environment within the body and its diversity in cellular phenotypes contribute to this. The project will focus on examining specific targeting of nanocarriers in complex and physiologically relevant co-culture models, providing guidance for future design of nanomedicines. This will be examined for one of two relevant organs: (1) the brain, a part of the central nervous system very difficult to reach from the circulation due to the blood-brain barrier, vs. (2) the lung, a peripheral organ which receives full cardiac output after i.v. injection. Different diseases affecting each organ require targeting drugs to particular cell types, but not all, for which the project will broadly help design more precise systems for efficiency and safe treatment. Three aims will be encompassed, including (a) biological characterization a new co-culture cell model, (b) synthesis and characterization of targeted nanocarriers, and (c) examination of the specific interaction of said nanocarriers with said co-culture models vs. more classical systems. Techniques to be used include solvent-evaporation methods for polymer nanoparticle synthesis, dynamic light scattering, electrophoretic mobility and electron microscopy for nanoparticle size/shape and surface charge, human cell culture and fluorescence microscopy to visualize nanoparticle-cell interactions, and image analysis algorithms for semiquantitative measurements. Additional experiences to be gained include training on research safety and ethical conduct, participation in the process of designing, executing, recording and reporting of research, oral and written communication skills, authorship if publishable results are used for conference presentations or article submissions, and overall participation in a stimulating, interdisciplinary and innovative research program.
|brain disease, Drug delivery, lung disease, multicellular models, nanocarriers, site-specific targeting|
|IBEC-2003. Nanoprobes & Nanoswitches III||2020-2021||IBEC||Nanoprobes & Nanoswitches||WEBSITE||Pau||Gorostiza||Available|
Cell processes like endocytosis, membrane resealing, signaling and transcription, involve conformational changes which depend on the chemical composition and the physicochemical properties of the lipid membrane. These properties are directly related to the lateral packing and interactions at the molecular level, that govern the membrane structure and segregation into nano (or micro) domains. The better understanding of the mechanical role of the lipids in cell membrane force-triggered and sensing mechanisms has recently become the focus of attention. The local and dynamic nature of such cell processes requires observations at high spatial resolution. Atomic force microscopy (AFM) is widely used to study the mechanical properties of supported lipid bilayers (SLBs). We investigate the physicochemical and structural properties of lipid membranes combining AFM and force spectroscopy (AFM-FS) under environmentally controlled conditions. We use simplified model membranes including several lipid representatives of mammalian or bacterial cells. We also study the mechanical properties of lipid membranes from nanovesicles with technological applications, like drug delivery.
|atomic force microscopy, biophysics, force spectroscopy, lipid membrane, nanomechanics|
|IBEC-2002. Nanoprobes & Nanoswitches II||2020-2021||IBEC||Nanoprobes & Nanoswitches||WEBSITE||Pau||Gorostiza||Available|
Protein mediated electron transfer (ET) is essential in many biological processes, like cellular respiration or photosynthesis. The exceptional efficacy of these processes is based on the maximization of donor/acceptor coupling and the optimization of the reorganization energy.
|electron transport, interactions, Proteins, scanning probe microscopies, single molecule|
|IBEC-2001. Nanoprobes & Nanoswitches I||2020-2021||IBEC||Nanoprobes & Nanoswitches||WEBSITE||Pau||Gorostiza||Available|
One of the group’s research lines is focused on developing nanoscale tools to study biological systems. These tools include instrumentation based on proximity probes, such as electrochemical tunneling microscopy and spectroscopy (ECSTM, ECTS), atomic force microscopy (ECAFM) and single molecule force spectroscopy (SMFS) that we apply to investigate electron transfer in metal oxides and individual redox proteins. These studies are relevant to the development of biosensors and molecular electronics devices. Recent advances include the following projects: methods for nanoscale conductance imaging under electrochemical control, measurement of the nanomechanical stability and electron transfer distance decay constants of individual redox proteins. Based on our development of nanoscale field-effect transistors using redox proteins, we have recently published a method to measure conductance switching in proteins “wired” between two electrodes and their current-voltage characteristics.
|electrochemistry, optogenetics, photopharmacology, photosynthetic complexes, redox proteins|
|CRG-2007. Dynamics of Living Systems||2020-2021||CRG||Dynamics of Living Systems||WEBSITE||Nicholas||Stroustrup||Available|
Our research group seeks to link the macroscopic symptoms of aging to their molecular origins. In aging, a variety of mechanisms contribute at short, medium, and longtime scales. Furthermore, aging appears to involve a substantial degree of random chance. To tackle this complexity, we incorporate techniques from a wide range of fields-- molecular genetics, reliability engineering, bioinformatics, statistical physics, survival analysis, high-throughput imaging, and stochastic modelling. Focusing on C.elegans as a model system, we seek to develop experimental and computational methods in parallel to help us characterize where, when, and why aging occurs, and how we might effectively intervene in its progression.
|aging, microscopy, stochastic processes|
|CRG-2006. Epigenetic reprogramming in mammalian germ cells||2020-2021||CRG||Epigenetic Reprogramming in Embryogenesis and the Germline||WEBSITE||Bernhard||Payer||Assigned|
In our lab, we are studying how epigenetic information is erased during mammalian development. In particular, we study epigenetic reprogramming of the X-chromosome in mouse embryos, induced pluripotent stem cell (iPSC) and in the germ cell lineage in vivo and in vitro. Using a multidisciplinary approach, we want to gain insight into how epigenetic reprogramming is linked to its biological context, with long-term implications for regenerative and reproductive medicine.
|Epigenetics, Germ cells, reproduction, X-chromosome reactivation|
|CRG-2005. X-chromosome reactivation in iPSCs and mouse embryos||2020-2021||CRG||Epigenetic Reprogramming in Embryogenesis and the Germline||WEBSITE||Bernhard||Payer||Assigned|
In our lab, we are studying how epigenetic information is erased during mammalian development. In particular, we study epigenetic reprogramming of the X-chromosome in mouse embryos, induced pluripotent stem cell (iPSC) and in the germ cell lineage in vivo and in vitro. Using a multidisciplinary approach, we want to gain insight into how epigenetic reprogramming is linked to its biological context, with long-term implications for regenerative and reproductive medicine.
|Epigenetics, iPSC-reprogramming, Pluripotency, X-chromosome reactivation|
|CRG-2004. Understanding the molecular basis for bidirectional neuronal mRNA transport||2020-2021||CRG||Cytoskeleton dependent RNA localisation mechanisms||WEBSITE||Sebastian||Maurer||Available|
The Maurer Lab wants to understand the biochemical processes that drive the generation of neuronal mRNA distributions. Thousands of mRNAs are transported into axons and dendrites and their local translation at the right location is important for neuron development, polarization and synaptic plasticity which underlies long-term memory formation. How motor proteins such as kinesins and dynein recognise their mRNA cargo and transport them to their destination is not understood. The Maurer lab develops new single-molecule assays in microfluidic chambers to assemble neuronal mRNA transport complexes from purified components. Through this approach, the Maurer Lab recently revealed the essential building blocks of a minimal mammalian mRNA transport system and their function (Baumann et al. bioRxiv, 2019). To further understand which different mRNA transport pathways exist, the Maurer Lab develops new high-throughput (HT) protein-protein and protein-RNA interaction assays (Yang et al. Nature Communications, 2018).
|auxin-induced degrons, live cell imaging, Neuronal mRNA localisation, photo-inactivation, protein and RNA biochemistry|
|CRG-2003. Understanding the molecular basis of neuronal 3’UTR length-dependent mRNA sorting||2020-2021||CRG||Cytoskeleton dependent RNA localisation mechanisms||WEBSITE||Sebastian||Maurer||Available|
The Maurer Lab wants to understand the biochemical processes that drive the generation of neuronal mRNA distributions. Thousands of mRNAs are transported into axons and dendrites and their local translation at the right location is important for neuron development, polarization and synaptic plasticity which underlies long-term memory formation. How motor proteins such as kinesins and dynein recognise their mRNA cargo and transport them to their destination is not understood. The Maurer lab develops new single-molecule assays in microfluidic chambers to assemble neuronal mRNA transport complexes from purified components. Through this approach, the Maurer Lab recently revealed the essential building blocks of a minimal mammalian mRNA transport system and their function (Baumann et al. bioRxiv, 2019). To further understand which different mRNA transport pathways exist, the Maurer Lab develops new high-throughput protein-protein and protein-RNA interaction assays (Yang et al. Nature Communications, 2018).
|biophysics, motor proteins, Neuronal mRNA localisation, RNA binding proteins, single-molecule microscopy|
|CRG-2002. Trans-generational epigenetic influences on mutation outcome||2020-2021||CRG||Genetic Systems||WEBSITE||Ben||Lehner||Assigned|
Many detrimental mutations only cause disease in a subset of their carriers, a phenomenon known as incomplete penetrance. Further, individuals often display variable expressivity of a disease, ranging from mild to severe health impairments. Animal studies show that incomplete penetrance and variable expressivity are still present in the absence of environmental or genetic variation, with inter-individual variation in gene expression during development able to predict to some extent whether an individual is affected or not by an inherited mutation [1, 2]. We hypothesized that an additional influence on mutation penetrance and expressivity might be the environment or physiological state of an individual’s parents or even previous generations. To test this hypothesis, we have established an automated screening platform to quantify how environmental perturbations in previous generations influence the outcome of inherited mutations in C. elegans. We identified several environmental factors that altered mutation outcome in subsequent generations that were never directly exposed to the environmental challenge. Your master thesis project will investigate possible molecular mechanisms underlying the multi-generation memory of environmental perturbations. To this end, you will use transgenic C. elegans lines, time-lapse microscopy, protein biochemistry, as well as genetic techniques.
|C. elegans, epigenetic inheritance|
|CRG-2001. Reconstituting tissue self-organization and collective cell dynamics in early embryonic development via 3D synthetic culture methods||2020-2021||CRG||Cell and Tissue Dynamics||WEBSITE||Verena||Ruprecht||Available|
The Ruprecht lab studies multi-scale dynamics of cell and tissue organization in early embryogenesis. We have a key focus on understanding biological self-organization, cell and tissue shape formation and dynamic cell behaviour in 3D tissues. Our lab follows a highly interdisciplinary approach combining molecular and cell biological tools with advanced biophysical methods and quantitative live cell imaging approaches.
|Biological Self-organization, biophysics, Cytoskeleton, Mechanobiology, Multicellular dynamics|
|DCEXS-2011. Cancer Biology||2020-2021||DCEXS-UPF||Cancer Biology||WEBSITE||Ana||Janic||Assigned|
The tumour suppressor gene p53 is mutated in half of the human cancers. Given the difficulties in developing strategies for targeting wild-type or mutant p53, further understanding of its basic biology is required for successful clinical translation. The present project focuses on understanding the complexity of the p53 network in tumour suppression in different contexts, in order to determine which p53 downstream function should be targeted for treatment of different tumour types, without targeting p53 itself. The successful candidate will be involved in the use of a wide variety of experimental techniques, including mouse models of cancer, tissue/tumour pathology, CRISPR-Cas9 gene-editing technology, next-generation sequencing, molecular biology, cell culture and flow cytometry.
|cancer, DNA damage, p53, tumour suppression|
|DCEXS-2010. Engineering Intracellular Nanotools To Image Protein Structures In Vivo: Resolving The Mechanism Of Exocytosis||2020-2021||DCEXS-UPF||Live-cell Structural Biology||WEBSITE||Oriol||Gallego||Available|
Our group develops new methods of fluorescence microscopy that allow the study of macromolecular complexes directly in living cells beyond the limits of current approaches.
|cell growth, genetic engineering, light microscopy, molecular mechanisms|
|DCEXS-2009. Monitoring oxidative stress in living cells – use of genetically encoded reporters to determine H2O2 levels linked to signalling and disease||2020-2021||DCEXS-UPF||Oxidative Stress and Cell Cycle Group||WEBSITE||Elena||Hidalgo||Available|
General objectives: Intracellular peroxides are important drivers of both toxicity and signalling events. Several genetically encoded fluorescent probes have been developed to monitor H2O2 fluctuations in response to endogenous and exogenous oxidant sources. We have recently developed a new reporter, based on the fission yeast H2O2 sensor Tpx1 fused to a redox sensitive GFP, which is more sensitive to peroxide fluctuations that any other reporter characterized so far. We aim at comparing its behaviour in response to genetic and environmental interventions. The candidate will characterize the regulation of our H2O2 reporter in different S. pombe backgrounds and in different biological situations, such as during chronological aging or cell cycle progression, to assess the role of moderate intracellular H2O2 fluctuations as drivers of these processes. Furthermore, an unprecedented experiment in the redox field will be to use our fluorescent reporter in different biological models (ranging from bacteria to human cells), to compare intracellular H2O2 levels using the same protein sensor.
|aging, H2O2, Redox biology, yeast|
|DCEXS-2008. In vivo mapping of the neuronal circuity related to vestibular and auditory sensory function||2020-2021||DCEXS-UPF||Morphogenesis and Cell Signaling Sensory Systems||WEBSITE||Berta||Alsina||Available|
The inner ear capturing auditory and balance information though specialized hair cells transmits the sensory information to the brain through bipolar neurons. We have investigated though high-resolution imaging and genetic perturbations the development of the sensory neurons of the inner ear in zebrafish (Hoijman et al. 2017 eLife, Taberner et al. biorxiv). This information is currently also being mapped with spatial transcriptomic data to discriminate between different neuronal subtypes. However, it remains unexplored how different stimuli activate specific neurons of the ganglion and how neuronal activity is mapped into the brain. Neuronal activity can be monitored in vivo by the use of GCAMP, a genetically encoded calcium sensor. The project aims at imaging at high spatial and temporal resolution the patterns of neuronal activity in the statoacoustic ganglion and the hindbrain when specific neurons are activated or specific stimuli are presented to the zebrafish. For this aim, the student will use a transgenic line expressing GCAMP5G in neurons, will learn how to image neuronal activity in vivo and will collaborate with a laboratory with expertise in photochemically activation of neuronal receptors. Moreover, analysis of behaviour will also be assessed when specific populations of neurons are activated in order to integrate neuronal circuit maps with behaviour output. We aim for a student highly motivated in neurobiology, imaging and circuitry to undertake this challenging project.
|in vivo imaging, neural activity, optogenetics, zebrafish|
|DCEXS-2007. Hypoglycosylation Of Voltage-Gated And Mechanosensitive Ion Channels: New Pathological Mechanisms And Therapeutic Targets For Neurological Disorders In Phosphomannomutase 2 Deficiency (PMM2-CDG)||2020-2021||DCEXS-UPF||Laboratory of Molecular Physiology||WEBSITE||José Manuel||Fernández Fernández||Available|
Phosphomannomutase Deficiency (PMM2-CDG) is the most frequent congenital disorder of N-linked glycosylation (CDG). PMM2-CDG symptoms include severe neurological alterations. Progressive atrophy of the cerebellum is usually found in all PMM2-CDG patients, leading to the ataxia cerebellar syndrome. Also, the stroke-like episode (SLE) is one of the unpredictable and serious neurological complications occurring in PMM2-CDG. Mechanisms underlying both SLE and cerebellar syndrome in PMM2-CDG are unknown and there are no guidelines for their prevention, detection and treatment. We have recently identified the neuronal voltage-gated Ca2+ channel CaV2.1 as a potential target of glycosylation defect in the Central Nervous System of PMM2-CDG patients, and an important contributor to SLEs and cerebellar syndrome in PMM2-CDG. Besides, we found that mild cranial trauma is a potential SLE trigger in PMM2-CDG patients. In this respect, mechanosensitive Piezo channels have been suggested to underlie the transduction of different mechanical forces into a variety of neurological responses in the brain._x000D_
|electrophysiology, Hypoglycosylation, mechanosensitive Piezo channels, neuronal voltage-gated calcium channels, Phosphomannomutase Deficiency (PMM2-CDG)|
|DCEXS-2006. Integrative Biomedical Materials and Nanomedicine Lab||2020-2021||DCEXS-UPF||Integrative Biomedical Materials and Nanomedicine Lab||WEBSITE||Pilar||Rivera Gil||Available|
Our research lies at the crossroads between nanoscience and biomedicine, the field of nanobiomecine. We convert basic research findings on nanobiotechnology into new approaches addressing biomedical challenges. We fabricate multifunctional biomaterials by integrating selected building-blocks into one single system depending on the application's requirements and considering the biophysicochemical properties of the nanomaterial. We target independently two areas: diagnostics and therapeutics of diseases but also simultaneously by creating a theranostic tool towards a more personalized medicinal approach of diseases. We focus on understanding and engineering the nanomaterial-biological system interface. We use state of the art material and biological/molecular characterization methods to find predictive patterns of cellular outcomes after exposure to nanomaterials for translational medicine.
|Controlled release, Nanomaterials, Nanomedicine, Optical biosensing, Theranostics|
|DCEXS-2005. Zinc imbalance and cancer progression||2020-2021||DCEXS-UPF||Laboratory of Molecular Physiology-Biophysics of the immune system||WEBSITE||Rubén||Vicente García||Assigned|
The human body contains 2–3 g of zinc. In the cell, aside from being a structural component of many proteins, zinc plays a role as a second messenger regulating different signalling cascades involved in proliferation, migration and differentiation. Several transporters (Zip and ZnT family) and zinc binding proteins work in a coordinated way to tightly regulate cytosolic zinc concentrations. Zinc dysregulation has been described in several kinds of cancers affecting both, the patient zinc serum levels and tumour zinc content. The expression of certain zinc transporters has been correlated with the stage, progression of tumours and acquisition of pro-metastatic features. However, the underlying mechanisms behind zinc imbalance and cancer progression are not fully understood. The project is based on a multidisciplinary approach combining molecular biology, biophysics and nanotechnology. The students will acquire skills in different techniques of all these different disciplines.
|cancer, metastasis, transporter, zinc|
|DCEXS-2004. Molecular Physiology Laboratory||2020-2021||DCEXS-UPF||Molecular Physiology Laboratory||WEBSITE||Francisco José||Muñoz||Available|
1. Group: Dr. Francisco J. Muñoz (University lecturer; Pubs: 64; Total Citations: 2244; h-index: 25) is focused on the study of the production, aggregation and cytotoxicity of amyloid ß-peptide (Aß) in Alzheimer’s disease (AD) and its regulation by oxidative stress and nitric oxide.
|aging, Alzheimer's Disease, Amyloid, GM1, hippocampal neurons|
|DCEXS-2003. Uncovering the clonal dynamics of the hindbrain: balancing proliferation and differentiation||2020-2021||DCEXS-UPF||Development of the Vertebrate Central Nervous System||WEBSITE||Cristina||Pujades||Available|
Our main goal is to understand how spatiotemporally coordinated cell progenitor specification and differentiation occurs alongside morphogenesis to construct the functional brain. Thus, we need to blend the information provided by morphogenesis and tissue growth studies -balancing progenitors vs. differentiated cells-, with the reconstruction of cell lineages, with the demand to incorporate the time as a crucial factor. We make use of the zebrafish embryo because it allows to combine high-resolution in vivo imaging with the genome-editing technology. We take advantage of complementary approaches such as 4D-imaging, functional perturbations, clonal growth studies and transcriptomics in order to fill the void between gene regulatory networks and tissue architecture. The specific objective of the project is to uncover the clonal growth dynamics of the hindbrain in order to understand how cell proliferation and cell differentiation are balanced. For this we will life-monitor the whole embryonic hindbrain upon time and compare the growth of specific progenitor cell populations with the overall growth, using genetic clonal experiments combined with a Machine Learning platform for their analysis. These results will provide us insights into the mechanisms of segregation of progenitors within the hindbrain and how brain morphogenesis and growth are coordinated. To explore how different groups of progenitors contribute to the growth of the hindbrain, zebrafish transgenic embryos will be used allowing for fluorescent lifemonitoring clonal growth. To get insight into the growth of the tissue and the specific progenitor cell populations we will assess: i) clonal growth, and ii) morphological spatial variability of the clones. Clone tracking will allow deciphering modes of clonal behaviour (symmetric vs. asymmetric divisions). We will develop a Machine Learning approach for cell motion pattern recognition and allocation, since an automatised, accurate segmentation and tracking framework will represent an improvement to identify distinct modes of growth and movement patterns. The student will learn the experimental skills for 4D-imaging and cell-tracking, and the computational tools to extract biological insights from big-data analyses.
|4Dimaging, brain morphogenesis|
|DCEXS-2002. Dynamical Systems Biology||2020-2021||DCEXS-UPF||Dynamical Systems Biology||WEBSITE||Jordi||Garcia-Ojalvo||Assigned|
The Dynamical Systems Biology laboratory of the Universitat Pompeu Fabra studies the dynamics of living systems, from unicellular organisms to human beings. The lab uses dynamical phenomena to identify the molecular mechanisms of a large variety of biological processes including cellular decision-making, spatial self-organization and tissue homeostasis. We use experimental biochemical and electrophysiological data to constrain computational models of living systems, and thereby unravel the underlying molecular circuitry of physiological processes. Using a combination of theoretical modelling and experimental tools including time-lapse fluorescence microscopy and microfluidics, we investigate dynamical phenomena such as pulses and oscillations, and study how multiple instances of these processes coexist inside cells and tissues in a coordinated way. At a larger level of organization, we use conductance-based neural models to explain the emergence of collective rhythms in cortical networks, and mesoscopic neural-mass models to link the structural properties of brain networks with their function.
|biophysics, complexity, nonlinear dynamics, quantitative biology, statistical physics|
|DCEXS-2001. Translational Synthetic Biology||2020-2021||DCEXS-UPF||Translational Synthetic Biolo||WEBSITE||Marc||Güell||Assigned|
Our group aims to leverage synthetic biology and gene editing to generate technologies with therapeutic potential. Our ability to modify genomes has profoundly affected how we perform scientific research, and future therapies. Emergent consequences of reinventing biology have already started to reach society. For example, engineered human immune T cells (CAR-T) cure cancers with outstanding performance, or ‘ex vivo’ applied gene editing technologies have successfully cured severe genetic diseases such as ‘bubble boys’ or sickle cell disease. Biological technology will have a growing influence in our lives. We have lines of research in developing precise tools for applied gene editing technologies and in skin microbiome based therapeutics.
|CRISPR, gene therapy, genetic engineering, microbiome, synthetic biology|