Research Projects

Below you will find detailed information about the various projects proposed by researchers from the BIST centres and the DCEX-UPF for the 2021/2022 academic year. MMRES students must choose one of these as their Major Project. 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.

ProjectCourseCentreResearch Group NameWebSupervisorAvailabilityDescriptionCo-supervisorTagsKeywords
IRBB-2008. Drosophila as a model in cancer biology2021-2022IRB BarcelonaDevelopment and Growth Control LaboratoryWEBSITEMarcoMilánAvailable

Cancer is a multi-hit process involving mutations in oncogenes and tumor suppressors, as well as interactions between the tumor cells and the surrounding stroma. Cancer as a disease is characterized by a series of hallmarks, which include sustained proliferative signalling, resistance to growth suppressors and to cell death, increased replicative immortality, invasiveness and metastasis, energy metabolism reprogramming, genome instability, and inflammation. We are interested in the cellular and molecular mechanisms underlying the regulation of many of these hallmarks, especially the role of Genome Instability in tumourigenesis.

The fruit fly, Drosophila, is an excellent, genetically-tractable system for modelling the development of cancer, due to the conservation of signaling pathways, cell proliferation and survival genes between fly and humans, its suitability for genetic and molecular manipulations, and its well-described developmental biology. Working with flies (an in vivo approach) allows the analysis of tumours at the cell autonomous level but also at the systemic level (relationship between tumours and the rest of the body). Drosophila is also useful to perform high-throughput screening of small molecule inhibitors that can be developed to combat human cancer.

cancer, Chromosomal Instability, Drosophila
IFAE-2019. Exploiting PAUS data with deep learning2021-2022IFAECosmologyWEBSITEMartin BørstadEriksenAvailable

PAUS is state-of-the-art ongoing galaxy survey, using a custom instrument with 40 narrow bands. This allows for high precision distance determination. These data are also expected to give novel insight into the galaxy evolution and their properties. The student will work on machine learning (ML) approaches to explore these data, focusing on the physical interpretation of the model. The student will have the chance to learn about machine learning techniques and data handling. A solid background in programming is beneficial.

distance determination, galaxy survey, Machine learning, PAU
IFAE-2018. Prediction of COVID-19 propagation and Cancer growth using Group Theory2021-2022IFAETheory DivisionWEBSITEPereMasjuanAvailable

This project shall explore the connexion between the COVID-19 propagation and the breast cancer growth based on the mathematics of group theory.
On the one hand, the propagation of the COVID-19 outbreak can be simulated based on complex dynamics’ tools such as a SEIR (Susceptible - Exposed - Infected - Recovered) model which is based on a system of coupled differential equations guiding the pandemic evolution.
While the context is crucial to understand the health data in detail, the dynamics of an averaged group of people can precisely be determined with such models as soon as the virus-dependent epidemiological parameters are known or parameterized.
On the other hand, the development of breast cancer growth, which is, the process leading the cell division, differentiation, movement, organization and death can be parameterized with the principle of minimal energy and a set of dissipative equations. Such equations can be used to explore the conditions for which cancer growth emerges from initial conditions. And again, even though the particular situation will depend on the epistemology of the given cancer, such models can provide accurate dynamics of the tissue growth in simulation.
In both scenarios, apparently disconnected, one can show that the dynamics of the process can be understood from the mathematics of Group Theory thus providing a novel synergy between both fields, an innovative perspective so far unexplored.
In this project, we pretend to establish then the bases for such an enterprise, elaborating first the dictionaries to transfer the dynamics from each field into group theory for later on exploiting what the symmetries found in such processes, which emerge from the group theory exploration, can tell us about mitigation strategies for decelerating their growth.

carcinogenesis, COVID-19, group theory
ICIQ-2003. Supramolecular sensing of relevant biomarkers for acute kidney injury2021-2022ICIQInterdisciplinar Supramolecular Chemistry GroupWEBSITEPabloBallesterAvailable

Acute Kidney Injury (AKI) is a frequent and life-threatening complication of all major surgeries. Most specialists agree that to achieve a proper early diagnosis of AKI the monitoring of two biomarkers is mandatory (creatinine - CRE and neutrophil gelatinase-associated lipocalin - NGAL). Although the current methods for CRE and NGAL detection provide reliable results, they are time-consuming and do not provide real-time measurements. A real-time monitoring of uNGAL and uCRE levels could reduce the time needed for AKI diagnosis and potentially avoid possible AKI-related irreversible damage to the patient with a minimum use of healthcare resources. Tackling this major issue, we are proposing a novel method for the simultaneous real-time detection of the two biomarkers in urine samples. Concretely, the project aims to (i) synthesize and characterize a fluorescent calix[4]pyrrole cavitand for CRE sensing, (ii) immobilize the fluorescent cavitand into a solid surface, (iii) study the binding properties of the cavitand with CRE in solution and in the solid-liquid interface in aqueous solution and in artificial urine samples. The Master candidate will have the opportunity to join Prof. Ballester group at ICIQ (Tarragona) working in the area of supramolecular sensors and perform his/her 6-month major project under optimum conditions in a modern and stimulating environment, equipped with state-of-the-art instrumentation and high-level technological resources. The candidate will experience an ambitious program based on training-through-research not only in the area of organic and physical organic chemistry but also in the field of advanced functional materials and sensor devices. Soft skills development (i.e. scientific writing and communication skills, supervision and management) will be also promoted in order to enhance the career perspectives and employability of the awarded candidate. We expect that the candidate will carry out a minor project in the area of biosensors to work on the fluorescent detection of NGAL.

Acute Kidney Injury, Calix[4]pyrrole, Creatinine, Fluorescence, Supramolecular sensor
DCEXS-2016. High-throughput analysis of hearing loss causative genes through cas13 technology2021-2022DCEXSMorphogenesis and Cell Signaling in Sensory SystemsWEBSITEBertaAlsinaAvailable

The inner ear is one of the most sophisticated sensory organs of the peripheral nervous system and is responsible for the senses of audition and balance. Sensory information is captured by the Hair Cells (HC) that transmit the information to the sensory neurons of the statoacoustic ganglion. Then, the afferent neurons connect to the brain. Mutations in genes responsible for hair cell and neuronal function cause hearing loss or vertigo. Hearing loss is the most prevalent sensory deficit in the world and approximately affects 466 million people, being 34 million children. Around 122 human genes causing non-syndromic hereditary hearing loss when mutated have been identified to date. However, the exact function of many of these genes has not been assessed carefully due to the difficulty of generating mutant animals at large scale. The CRISPR/Cas9 editing system has revolutionized the genetics field by the ability to efficiently mutate or modify any desired gene. Recently, another CRISPR derived technology has been reported in which by the use of the Cas13, a desired mRNA can be targeted and down-regulated (Kushawah et al. 2020). Our laboratory is interested in studying inner ear development, gene regulation and hearing loss using the zebrafish as a model system (see lab publications: https://www.upf.edu/web/alsina_lab/publications) and have set up many techniques for analysing gene function.
The aim of this proposal is to first, use the CRISPR/Cas13 methodology to screen for relevant genes involved in hair cell function to then generate stable mutants through CRISPR/Cas9 system. We will study hair cell differentiation markers, cell proliferation and cell death in the mutants and perform in vivo imaging of the inner ear in the mutants.
The student will learn techniques of zebrafish manipulation, mRNA injection, gene editing and life imaging.

Kushawah G et al. CRISPR-Cas13d Induces Efficient mRNA Knockdown in Animal Embryos. Dev Cell. 2020 Sep 28;54(6):805-817.e7.

CRISPR, imaging, sensory systems, zebrafish
CRG-2008. From nanoscopy observation of cell fate to tissue regeneration2021-2022CRGReprogramming and RegenerationWEBSITEMaria PiaCosmaAvailable

In our group, we are investigating the mechanisms controlling the reprogramming of somatic cells to pluripotency, and our final goal is to determine if this reprogramming contributes to tissue regeneration in higher vertebrates. In particular, we are studying how the Wnt/beta-catenin signalling pathway and cell-fusion-mediated cellular reprogramming control these processes. We tackle these questions with different approaches and through different disciplines, which range from the nanoscale level of observation of cell functions, up to the whole mouse organ.

chromatin, regeneration, reprogramming, Stem Cells, super resolution microscopy
ICFO-2011. Medical optics group IV2021-2022ICFOMedical opticsWEBSITETurgutDurduranAvailable

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-2010. Medical Optics III2021-2022ICFOMedical OpticsWEBSITETurgutDurduranAvailable

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-2009. Medical Optics II2021-2022ICFOMedical OpticsWEBSITETurgutDurduranAvailable

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-2008. Medical Optics I2021-2022ICFOMedical OpticsWEBSITETurgutDurduranAvailable

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.
The minor project will be at IFAE in design and testing of these detectors.
The expected training outcome is a trans-disciplinary experience in biomedical optics, novel detector technologies and in translational aspects of introducing new technologies to clinical use.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.
The minor project will be at IFAE in design and testing of these detectors.
The expected training outcome is a trans-disciplinary experience in biomedical optics, novel detector technologies and in translational aspects of introducing new technologies to clinical use.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.
The minor project will be at IFAE in design and testing of these detectors.
The expected training outcome is a trans-disciplinary experience in biomedical optics, novel detector technologies and in translational aspects of introducing new technologies to clinical use.

biomedical optics, biophotonics, singlephoton detectors
IBEC-2009. Smart Nano-Bio-Devices II2021-2022IBECSmart Nano-Bio-DevicesWEBSITESamuelSánchezAvailable

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 I2021-2022IBECSmart Nano-Bio-DevicesWEBSITESamuelSánchezAvailable

Active Nano-particles in nanomedicine: smart drug delivery systems
The development of active drug delivery systems will revolutionize the way we treat some diseases and reduce the side effects of extensive drug release in patients. This project aims at designing of nanoparticles and nanosystems made of organic and/or inorganic materials (e.g. polymeric nanoparticles or mesoporous nanoparticles). Those nanoparticles will become motile (named Nanobots) through the conversion of chemical energy released from catalytic reactions into kinetic energy. Nanobots will specifically transport therapeutic agents to target locations in a controllable manner using external control or internal gradients in vitro and eventually in vivo.
Nanobots will be functionalized for specific binding to target cells, and modified for triggering the release of drugs in located targets. Due to the high expectations and fast developement of this field, we aim at fundamental understanding of motion at the nanoscale, validate the nanotoxicity of nanobots and to transfer this radically new proof-of-concept to the hospital. The student will develop broad skills in a highly multidisciplinary and international group. Mainly, the synthesis of nanoparticles, bio-functionalization, cell culture, fluorescent imaging and cell internalization experiments. We seek for enthusiasts with interest in nanomaterials and drug delivery systems, specially from Chemistry, Biochemistry, Materials science, Biology, Biotechnology, Engineering background and physics.Active Nano-particles in nanomedicine: smart drug delivery systems
The development of active drug delivery systems will revolutionize the way we treat some diseases and reduce the side effects of extensive drug release in patients. This project aims at designing of nanoparticles and nanosystems made of organic and/or inorganic materials (e.g. polymeric nanoparticles or mesoporous nanoparticles). Those nanoparticles will become motile (named Nanobots) through the conversion of chemical energy released from catalytic reactions into kinetic energy. Nanobots will specifically transport therapeutic agents to target locations in a controllable manner using external control or internal gradients in vitro and eventually in vivo.
Nanobots will be functionalized for specific binding to target cells, and modified for triggering the release of drugs in located targets. Due to the high expectations and fast developement of this field, we aim at fundamental understanding of motion at the nanoscale, validate the nanotoxicity of nanobots and to transfer this radically new proof-of-concept to the hospital. The student will develop broad skills in a highly multidisciplinary and international group. Mainly, the synthesis of nanoparticles, bio-functionalization, cell culture, fluorescent imaging and cell internalization experiments. We seek for enthusiasts with interest in nanomaterials and drug delivery systems, specially from Chemistry, Biochemistry, Materials science, Biology, Biotechnology, Engineering background and physics.Active Nano-particles in nanomedicine: smart drug delivery systems
The development of active drug delivery systems will revolutionize the way we treat some diseases and reduce the side effects of extensive drug release in patients. This project aims at designing of nanoparticles and nanosystems made of organic and/or inorganic materials (e.g. polymeric nanoparticles or mesoporous nanoparticles). Those nanoparticles will become motile (named Nanobots) through the conversion of chemical energy released from catalytic reactions into kinetic energy. Nanobots will specifically transport therapeutic agents to target locations in a controllable manner using external control or internal gradients in vitro and eventually in vivo.
Nanobots will be functionalized for specific binding to target cells, and modified for triggering the release of drugs in located targets. Due to the high expectations and fast developement of this field, we aim at fundamental understanding of motion at the nanoscale, validate the nanotoxicity of nanobots and to transfer this radically new proof-of-concept to the hospital. The student will develop broad skills in a highly multidisciplinary and international group. Mainly, the synthesis of nanoparticles, bio-functionalization, cell culture, fluorescent imaging and cell internalization experiments. We seek for enthusiasts with interest in nanomaterials and drug delivery systems, specially from Chemistry, Biochemistry, Materials science, Biology, Biotechnology, Engineering background and physics.Active Nano-particles in nanomedicine: smart drug delivery systems
The development of active drug delivery systems will revolutionize the way we treat some diseases and reduce the side effects of extensive drug release in patients. This project aims at designing of nanoparticles and nanosystems made of organic and/or inorganic materials (e.g. polymeric nanoparticles or mesoporous nanoparticles). Those nanoparticles will become motile (named Nanobots) through the conversion of chemical energy released from catalytic reactions into kinetic energy. Nanobots will specifically transport therapeutic agents to target locations in a controllable manner using external control or internal gradients in vitro and eventually in vivo.
Nanobots will be functionalized for specific binding to target cells, and modified for triggering the release of drugs in located targets. Due to the high expectations and fast developement of this field, we aim at fundamental understanding of motion at the nanoscale, validate the nanotoxicity of nanobots and to transfer this radically new proof-of-concept to the hospital. The student will develop broad skills in a highly multidisciplinary and international group. Mainly, the synthesis of nanoparticles, bio-functionalization, cell culture, fluorescent imaging and cell internalization experiments. We seek for enthusiasts with interest in nanomaterials and drug delivery systems, specially from Chemistry, Biochemistry, Materials science, Biology, Biotechnology, Engineering background and physics.

Drug delivery, nanobots, nanomachines, nanoparticles, self-propulsion
ICN2-2008. Topological matter for next generation magnetic memories2021-2022ICN2Physics and Engineering of NanodevicesWEBSITESergio O.ValenzuelaAvailable

Recent years have seen an unprecedented progress in the design and engineering of artificial materials using two-dimensional (2D) and layered topological insulator systems. Such systems, dubbed van der Waal (vdW) heterostructures because of the characteristic weak interaction between its layers, comprise stacks of selected 2D crystals to achieve specific functionalities. The improvement of the quality in the atomically smooth interfaces has further shown that the aggregate band structure of the heterostructure can be fine-tuned, while properties of interest can be imprinted in the materials by means of proximity effects. This research approach has led to exciting, and sometimes unexpected, discoveries, including the observation of superconductivity in twisted bilayer graphene, the generation of spin currents with unexpected symmetries or the remarkable enhancement and tunability of the spin current generation in proximitized graphene. The Master research project will focus on the experimental study of spin current generation using topological insulators within novel van der Waals heterostructures with impact in miniaturized magnetic memories. In particular, the awardee will learn about nanofabrication and high frequency experiments to manipulate the magnetization of nanomagnets by electric means. At the intersection between material and physical sciences, the awardee will further have the opportunity to acquire fundamental knowledge in a wide range of disciplines, including nanomaterials growth, advanced characterization (e.g., x-ray diffraction, x-ray photoemission spectroscopy, electron microscopies), and magnetotransport measurements. The host is the Physics and Engineering of Nanodevices (PEN) Group at ICN2, which is widely recognized for its research on spin transport and mesoscopic quantum effects. The group currently participates in the EU Graphene Flagship and coordinates a 5M€ EU project on next generation topological devices (https://tocha-project.eu/).

layered materials, magnetic memories, magnetization dynamics, nanotechnology, Topological matter
IRBB-2007. Single-cell lineage tracing to dissect stem cell memory2021-2022IRB BarcelonaQuantitative Stem Cell DynamicsWEBSITEAlejoRodriguez-FraticelliAvailable

Our group, Quantitative Stem Cell Dynamics, applies single-cell analysis technologies to provide a more unbiased understanding of cellular physiology and disease. We combine single-cell sequencing with single-cell lineage tracing to understand how gene expression dynamics in stem cells (variation) contributes to distinct cellular functions. The Master’s thesis projects available are focused on developing new technologies for studying stem cell dynamics:
1. A method for combining the analysis of gene perturbations with lineage tracing to study the molecular machineries that regulate differentiation rates/dynamics.
2. A quantitative method for recording inflammatory perturbations that can be sequenced in typical single-cell assays

cellular heterogeneity, hematopoiesis, inflammation, regeneration, single cell analysis
IFAE-2017. The effect of the environment on the stellar mass-size relation in VIPERS galaxies2021-2022IFAECosmologyWEBSITEMalgorzataSiudekAvailable

Minor dry mergers are considered to be the very efficient process in increasing the size of the galaxies, especially of massive bulge dominated galaxies. As the probability of such mergers is different in different environments, we might expect to observe a dependence of galaxy sizes of their local environment, with galaxies in the dense environments being larger than those in less dense regions. However, the results presented in the literature so far are contradictory. Many studies have not found any correlation between the mean size and environment of galaxies. Some groups found positive correlations, some found an opposite trend. These discrepancies demonstrate that we are far from getting a clear picture of the impact of the environment on the galaxy sizes. Based on the unique spectroscopic sample of galaxies at redshift 0.5

galaxy evolution, size-mass relation, VIPERS
IFAE-2016. Environments of AGN in dwarf galaxies2021-2022IFAECosmologyWEBSITEMalgorzataSiudekAvailable

The goal of this project is to explore the relation between dwarf galaxies hosting active galactic nuclei (AGN) and their environment. The role of AGN feedback in galaxy formation and evolution is not well understood in general. While AGN are considered to be key drivers of the evolution of massive galaxies, their potentially significant role in the dwarf-galaxy the regime remains largely unexplored. There are several mechanisms thought to trigger AGN activity, some of them include environmental effects, where for example cooling gas from the cluster, cores accrete onto the central galaxies compressing and shocking gas within a galaxy and driving the gas towards the core. The shallow potential wells of dwarf galaxies leave them particularly susceptible to AGN feedback, making them ideal laboratories to study how AGN activity in the host dwarf galaxy couples with the environment. In this project, spectroscopic data comes from the VIMOS Public Extragalactic Redshift Survey (VIPERS) and different AGN selection methods are going to be utilised. Thanks to VIPERS multi-wavelength coverage and a wealth of auxiliary data, the VIPERS dataset is particularly suitable for studies of the relation of galaxy properties with the local densities.

AGN, dwarf galaxies, galaxy evolution, VIPERS
ICIQ-2002. Machine learning for electrochemical processes2021-2022ICIQTheoHetCatWEBSITENúriaLópezAvailable

The project is dedicated to leverage Machine Learning techniques to new chemical processes that can improve the design of new processes to mitigate CO2 emissions and thus climate change.

CO2 reduction, Density Functional Theory, descriptors, electrochemical interfaces, Machine learning techniques
ICIQ-2001. Design and development of tailored-made solutions for site-selective C-H functionalization reactions2021-2022ICIQPérez-Temprano groupWEBSITEMónica H.Pérez-TempranoAvailable

Without any doubts, the conversion of ubiquitous and typically inert C–H bonds into C–C and C–heteroatom bonds, considered one of the Holy Grails in Chemistry, is one of the most attractive transformations in organic synthesis. Since the second half of the 20th century, the approaches for the cleavage of “unreactive” C–H bonds have evolved from classical electrophilic or radical routes to so-called ligand-directed C–H functionalization protocols. These latter strategies have the potential of simplifying reactions by minimizing the formation of undesired by-products and/or allowing the control of site-selectivity by the use of chelating functional groups present on the reagents. These directing groups (DGs) can bind to the metal center facilitating the reactivity at a specific site on molecules that contain multitude of C–H bonds. Still now, these methodologies predominantly employ precious metals. This has implications for sustainability from both the cost and environmental perspectives.
The Pérez-Temprano group is focused on providing mechanism-driven tailored-made solutions for controlling the chemo- and regioselectivity of directed C–H activation processes catalyzed by cost-effective first-row metal-based systems. By the synergistic cooperation between organometallic and synthetic organic chemistry along with mechanistic studies, we aim to uncover the factors that determine C–H functionalization success or failure to develop more efficient and sustainable chemical transformations relevant for late-stage functionalization, key in medicinal chemistry. In this context, we seek to explore new catalytic systems based on 3d-metals, such as cobalt or manganese for promoting C–C and C–heteroatom bond-forming reactions.

C-H functionalization, catalysis, Organic Synthesis, Organometallic Chemistry, Sustainability
CRG-2007. Linking oncogenic translocations and 3D chromatin structure changes to cellular heterogeneity2021-2022CRGSingle Cell Epigenomics and Cancer DevelopmentWEBSITEReneeBeekmanAvailable

In our lab we study the early epigenetic events (= events that do not change the genetic code, but change how the code is transcribed into RNA) that contribute to tumor formation, with a major focus on tumors of the immune system known as lymphomas. Our lab can be divided into two branches: a wetlab (=labwork) and a drylab (=bioinformatics) branch. A key aspect is that these two branches are intermingled; the different team members can interact on a day-to-day basis and during weekly lab meetings.

In this combined wet- and drylab-oriented project, the student will study the role of the 3D chromatin structure in lymphoma formation: while the chromosomes are considered linear structures, they fold at the three-dimensional (3D) level in a highly organised way (Dekker et al. Nat Rev Genet 2013). This organization is needed to regulate gene expression. In lymphoma cells the 3D chromatin structure is altered in comparison to normal cells (Vilarrasa-Blasi & Soler-Vila et al. BioRxiv 2019). We aim to study how translocations (=a piece of one chromosome fuses to another chromosome) in lymphoma cells affect the 3D chromatin structure at the genome-wide level and how these changes affect single-cell gene expression and epigenetic variation in cellular pools that carry translocations. Methods used in this context comprise (i) genomic editing to generate translocations in vitro, (ii) mapping of the 3D chromatin structure (chromosome conformation capture and imaging - HiC; imaging – FISH + chromosome painting), (iii) induction of 3D chromatin interactions and study their consequences (CLOuD9; 4C; ChIP) and (iv) single-cell gene expression and chromatin accessibility analysis to study how translocations affect cellular heterogeneity (single-cell RNA-seq and ATAC-seq). The student will be exposed to these techniques and will work on the experimental and bioinformatic aspects of one of them in detail, based on personal interest.

3D chromatin structure, cancer, epigenetic heterogeneity, single-cell, translocations
CRG-2006. The functional role of 3D chromatin structure changes during early tumor formation2021-2022CRGSingle Cell Epigenomics and Cancer DevelopmentWEBSITEReneeBeekmanAvailable

In our lab we study the early epigenetic events (= events that do not change the genetic code, but change how the code is transcribed into RNA) that contribute to tumor formation, with a major focus on tumors of the immune system known as lymphomas. Our lab can be divided into two branches: a wetlab (=labwork) and a drylab (=bioinformatics) branch. A key aspect is that these two branches are intermingled; the different team members can interact on a day-to-day basis and during weekly lab meetings.

In this wetlab-oriented project, the student will study the functional role of the 3D chromatin structure in lymphoma formation: while the chromosomes are considered linear structures, they fold at the three-dimensional (3D) level in a highly organised way (Dekker et al. Nat Rev Genet 2013). This organization is needed to regulate gene expression. In lymphoma cells the 3D chromatin structure is altered in comparison to normal cells (Vilarrasa-Blasi & Soler-Vila et al. BioRxiv 2019). We aim to study how translocations (=a piece of one chromosome fuses to another chromosome) in lymphoma cells affect the genome-wide 3D chromatin structure. Furthermore, we aim to define global gene expression changes resulting from these 3D chromatin changes and their functional role in tumor development. Methods used comprise (i) genomic editing to generate translocations in vitro, (ii) 3D chromatin structure mapping (chromosome conformation capture - HiC and library preparation; imaging – FISH + chromosome painting), (iii) RNA expression analysis (RNA-seq), (iv) induction of 3D chromatin interactions and study their consequences (CLOuD9; 4C; ChIP and library preparation) and (v) studying the functional role of deregulation of genes of interest in cell line models (CRISPRa/I; cell culture). The student will be exposed to these techniques will work on one of them in detail, based on personal interest.

3D chromatin structure, cancer, cellular engineering, Epigenetics, translocations
ICFO-2007. Single-molecule microscopy tools to study membrane contact sites2021-2022ICFOSingle Molecule Biophotonics groupWEBSITEMariaGarcia-ParajoAvailable

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.

This MSc project will verse on understanding the dynamics of membrane contact sites (MCSs), in particular those that form between the endoplasmic reticulum (ER) and the Golgi complex. The Golgi complex is the central organelle responsible of protein transport to various parts of the cell and the post-translational modification of newly synthesized proteins from the ER required for their maturation. It has been recently shown that the membranes of these two organelles come to close apposition to one another forming a dynamic but highly tethered region, termed the MCS. ER-Golgi MCSs facilitate the export of proteins and lipids from the Golgi complex to the cell surface by a still unresolved mechanism. The study of MCS dynamics using conventional microscopy tools has been challenging due to their highly dynamic nature and reduced dimensions. As a result, a clear understanding of the how MCS contribute to transport carrier formation at the Golgi complex is still lacking.

The role of the MSc student will be to perform a set of innovative assays that combine different avant-garde molecular and cell biological techniques, such as the use of fluorescence complementation domains or the retention using selective hooks (RUSH)-system, with state-of-the-art microscopy and nanoscopy tools, such as STED, STORM or intracellular single particle tracking (iSPT). The data obtained will be analyzed using advanced quantitative imaging analysis to finally cast light on ER-Golgi MCS dynamics and their functional relevance for protein secretion.

Golgi complex, Membrane contact sites, Single particle tracking, super resolution microscopy, Transport carrier formation
IRBB-2006. Mutagenesis in cancer genomes2021-2022IRB BarcelonaGenome Data ScienceWEBSITEFranSupekAvailable

We are interested in using machine learning methodologies to analyze mutation patterns in cancer genomes, in order to (a) learn about mutagenesis and DNA repair mechanisms in human, and (b) predict cancer evolution such as the appearance of drug resistance mutations. The student will learn genomic data analyses methods (bioinformatics and statistical genomics), cancer biology,, applied machine learning and data visualization.

cancer, genetic disease, human genetics, Machine learning, mutations
DCEXS-2015. Nanotools for in situ structural biology and advanced light microscopy2021-2022CRGLive-cell structural biologyWEBSITEOriolGallegoAvailable

Understanding the molecular mechanisms that drive life (and those that lead to death) requires structural characterization of the protein machinery sustaining the biology of the cell. Historically, structural biology has been largely centered around in vitro approaches that can resolve protein structures at atomic resolution but that require the isolation of the proteins from their cellular context. Currently frontier in structural biology is the development of new techniques that can obtain structural measurements in vivo.
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. The aim of the project is to develop new genetically-encoded nanotools to boost the power of quantitative fluorescence microscopy. In collaboration with the group of Alex De Marco, at the Monash University (Australia), we will also asses the implementation of these new nanotools in cryo-electron tomography. Combination of both techniques in a correlative approach will allow us to resolve protein structures at atomic resolution in situ.
During the progression of the project the student will acquire a strong expertise in gene editing tools, advanced light microscopy and image analysis. Depending on the student’s skills and interest, the project could also involve in silico integration of acquired data to model 3D structures or cryo-electron tomography of large protein complexes controlling cell growth

cell growth, Cryo-Electron Tomography, Fluorescence Microscopy, gene editing, Structural biology
ICFO-2006. Live Cell Superresolution Microscopy & Embryonic Stem Cells2021-2022ICFOLive Cell Superresolution Microscopy & Embryonic Stem CellsWEBSITEStefanWieserAvailable

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.
In this highly interdisciplinary research within the BIST master program you will learn the fundamentals of live cell super resolution microscopy using structured illumination microscopy and localization microscopy. In collaborations with the lab of Verena Ruprecht (CRG) you will be trained in handling embryonic stem cells in order to prepare cells for high resolution imaging. Using the recently developed piezo driven microconfiner to compress cells and isolated nuclei you will image cortical actin/myosin and membrane constituents as well as nucleoskeleton elements at single molecule resolution. This approach will allow you to identify key control mechanisms regulating mechanosensation competence and will enable you to build quantitative and predictive models of dynamic cell transformation, migration behaviour and cell differentiation.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.
In this highly interdisciplinary research within the BIST master program you will learn the fundamentals of live cell super resolution microscopy using structured illumination microscopy and localization microscopy. In collaborations with the lab of Verena Ruprecht (CRG) you will be trained in handling embryonic stem cells in order to prepare cells for high resolution imaging. Using the recently developed piezo driven microconfiner to compress cells and isolated nuclei you will image cortical actin/myosin and membrane constituents as well as nucleoskeleton elements at single molecule resolution. This approach will allow you to identify key control mechanisms regulating mechanosensation competence and will enable you to build quantitative and predictive models of dynamic cell transformation, migration behaviour and cell differentiation.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.
In this highly interdisciplinary research within the BIST master program you will learn the fundamentals of live cell super resolution microscopy using structured illumination microscopy and localization microscopy. In collaborations with the lab of Verena Ruprecht (CRG) you will be trained in handling embryonic stem cells in order to prepare cells for high resolution imaging. Using the recently developed piezo driven microconfiner to compress cells and isolated nuclei you will image cortical actin/myosin and membrane constituents as well as nucleoskeleton elements at single molecule resolution. This approach will allow you to identify key control mechanisms regulating mechanosensation competence and will enable you to build quantitative and predictive models of dynamic cell transformation, migration behaviour and cell differentiation.

Mechanosensation, microscopy, Modeling, Stem Cells, Superresolution
ICFO-2005. Frontiers of Quantum Information Science, Quantum Simulations and Many Body Physics2021-2022ICFOQuantum Optics TheoryWEBSITEMaciejLewensteinAvailable

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
1) General mathematical theory of quantum correlations, with focus on quantumness, coherence, entanglement and non-locality of states of many body systems.
2) Relations between quantum many body phenomena (quantum phase transitions, quantum criticality, quantum localization, superconductivity, isolating states, topological order and topological phenomena.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
1) General mathematical theory of quantum correlations, with focus on quantumness, coherence, entanglement and non-locality of states of many body systems.
2) Relations between quantum many body phenomena (quantum phase transitions, quantum criticality, quantum localization, superconductivity, isolating states, topological order and topological phenomena.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
1) General mathematical theory of quantum correlations, with focus on quantumness, coherence, entanglement and non-locality of states of many body systems.
2) Relations between quantum many body phenomena (quantum phase transitions, quantum criticality, quantum localization, superconductivity, isolating states, topological order and topological phenomena.

many body physics, quantum information, quantum simulations
ICFO-2004. Hot Atoms 12021-2022ICFOAtomic Quantum OpticsWEBSITEMorganMitchellAvailable

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.
We seek to develop atomic magnetometers in several areas. Current projects in our lab include: (i) Development of microfabricated alkali vapor magnetometers, targeted at wearable magnetoencephalography (MEG) devices that localize the sources of neural currents in the brain; (ii) testing “quantum enhancement” approaches, such as polarization squeezing, that have the potential to surpass standard quantum noise limits in magnetometers; (ii) application of alkali-atom magnetometers to detect nuclear magnetism and nuclear magnetic resonance (NMR) signals in the sub-earth's field regime for spectroscopy and chemical analysis.
The student will have the opportunity to learn about cutting-edge devices in quantum sensing and magnetometry within the environment of an international research team. The project will provide a strong experimental element involving some combination of building, modifying and operating a rubidium magnetometer, to address a scientific question. The project may also require simulations of the atomic physics behaviour on a computer. The students will also develop transferable skills in programming (C/C++) data processing (python), computer-aided design and report writing.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.
We seek to develop atomic magnetometers in several areas. Current projects in our lab include: (i) Development of microfabricated alkali vapor magnetometers, targeted at wearable magnetoencephalography (MEG) devices that localize the sources of neural currents in the brain; (ii) testing “quantum enhancement” approaches, such as polarization squeezing, that have the potential to surpass standard quantum noise limits in magnetometers; (ii) application of alkali-atom magnetometers to detect nuclear magnetism and nuclear magnetic resonance (NMR) signals in the sub-earth's field regime for spectroscopy and chemical analysis.
The student will have the opportunity to learn about cutting-edge devices in quantum sensing and magnetometry within the environment of an international research team. The project will provide a strong experimental element involving some combination of building, modifying and operating a rubidium magnetometer, to address a scientific question. The project may also require simulations of the atomic physics behaviour on a computer. The students will also develop transferable skills in programming (C/C++) data processing (python), computer-aided design and report writing.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.
We seek to develop atomic magnetometers in several areas. Current projects in our lab include: (i) Development of microfabricated alkali vapor magnetometers, targeted at wearable magnetoencephalography (MEG) devices that localize the sources of neural currents in the brain; (ii) testing “quantum enhancement” approaches, such as polarization squeezing, that have the potential to surpass standard quantum noise limits in magnetometers; (ii) application of alkali-atom magnetometers to detect nuclear magnetism and nuclear magnetic resonance (NMR) signals in the sub-earth's field regime for spectroscopy and chemical analysis.
The student will have the opportunity to learn about cutting-edge devices in quantum sensing and magnetometry within the environment of an international research team. The project will provide a strong experimental element involving some combination of building, modifying and operating a rubidium magnetometer, to address a scientific question. The project may also require simulations of the atomic physics behaviour on a computer. The students will also develop transferable skills in programming (C/C++) data processing (python), computer-aided design and report writing.

Atomic sensors, Magnetic Resonance, Magnetometry, Quantum optics, Rubidium vapors
ICFO-2003. Attosecond Molecular-movies with Inner-Shell Electrons2021-2022ICFOAttoscience and Ultrafast OpticsWEBSITEJensBiegertAvailable

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.
We regularly offer projects within the various research fields and projects of our group.E.g., if you would like to discover extreme nonlinear optics and ultrafast lasers or if you are interested in attosecond dynamics, this is the place to ask! We also have several projects related to numerical simulations, electronic circuit design and data acquisition. You will join our research group and take part in the daily activities, discuss your project, research literature, propose a way to realize some tasks and present your work.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.
We regularly offer projects within the various research fields and projects of our group.E.g., if you would like to discover extreme nonlinear optics and ultrafast lasers or if you are interested in attosecond dynamics, this is the place to ask! We also have several projects related to numerical simulations, electronic circuit design and data acquisition. You will join our research group and take part in the daily activities, discuss your project, research literature, propose a way to realize some tasks and present your work.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.
We regularly offer projects within the various research fields and projects of our group.E.g., if you would like to discover extreme nonlinear optics and ultrafast lasers or if you are interested in attosecond dynamics, this is the place to ask! We also have several projects related to numerical simulations, electronic circuit design and data acquisition. You will join our research group and take part in the daily activities, discuss your project, research literature, propose a way to realize some tasks and present your work.

Attoscience, Extreme Nonlinear Optics, Ultrafast Lasers
IRBB-2005. Biomedical Genomics-Study of DNA damage and repair mechanisms2021-2022IRB BarcelonaBiomedical Genomics Group-BBGLabWEBSITENuriaLopez-BigasAvailable

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, as we have already optimized a protocol to map alkylation damage in human cell lines.
General objectives:
1. Establish alkylating, UV or crosslinking agent toxicity in selected cell lines
2. Generate nucleotide-resolution maps of DNA damage after treatment
3. Obtain mutation profiles upon DNA damage in wild type and DNA repair-mutant cells
Expected training outcomes:
1. Learn how to culture cells and perform toxicity assays
2. Functional validation of DNA damage: immunofluorescence and comet assay
3. Generate DNA repair deficient mutant cell lines by CRISPR/Cas9
4. Generate a damage library and learn how to interpret the mapping results

cancer, chemotherapy, DNA damage, DNA repair, mutational signature
DCEXS-2014. Mapping the role of enhancers in neurodevelopmental disorders2021-2022DCEXSEvolutionary Systems Biology/Functional NeurogenomicsWEBSITESandraAcostaAvailable

Many neurodevelopmental disorders are directly associated to genomic regions that have evolved fastly in our human lineage (Doan et al. 2015; Franchini and Pollard 2015). Most of the mutations identified in these regions are located in active enhancers during brain development. In the lab, we leverage the collection of human enhancers databases publicly available and generated in our lab to identify those enhancers that play a role in the human brain development and, when mutated, lead to neurodevelopmental disorders. We approach this aim from a multidisciplinary perspective incorporating functional neurogenomics based in ChIP-seq, comparative genomics and patient-derived brain organoids modified genetically. In the MSc project, the student will analyze bioinformatically the curated enhancer databases already available in the lab and select enhancers variants that subsequently will engineer in the human iPSC to model their role in human brain function.

enhancers, genomics, iPSC, neurodevelopmental disorders, organoids
IRBB-2004. The oral microbiome in health and disease2021-2022IRB BarcelonaComparative genomicsWEBSITEToniGabaldónAvailable

The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore the diversity and roles of oral microbes, even if unculturable. Recent sequencing-based studies have charted oral ecosystems and how they change due to lifestyle or disease conditions. As studies progress, there is increasing evidence of an important role of the oral microbiome in diverse health conditions, which are not limited to diseases of the oral cavity. This, in turn, opens new avenues for microbiome-based diagnostics and therapeutics that benefit from the easy accessibility of the oral cavity for microbiome monitoring and manipulation. The student will participate in the experimental procedures of several on-going project trying to understand the relationships of the oral microbiota and several diseases, including Alzheimer's disease, Down Syndrom, and Cystic Fibrosis.
The training outcomes will be: processing of oral samples to profile microbiota, isolation and characterization of microbial species, preparation of DNA and libraries for sequencing, statistical analysis and identifications of significant alterations.

disease, metagenomics, microbiology, Oral microbiome
ICN2-2007. Ultrafast Experiments on Quantum Materials2021-2022ICN2Ultrafast Dynamics in Nanoscale SystemsWEBSITEKlaas-JanTielrooijAvailable

In this project you will work with state-of-the-art ultrafast laser systems, in order to study optical, electrical and, especially, thermal phenomena in novel quantum materials. You will get hands-on experience with the fabrication of samples based on 2D materials with a thickness down to the atomic monolayer, and will learn how to study these exciting material systems with advanced optoelectronic setups with femtosecond time resolution.

2D materials, heat, optics, Ultrafast
ICN2-2006. Atomically precise graphene nanostructures for optoelectronics2021-2022ICN2Atomic Manipulation and Spectroscopy GroupWEBSITEAitorMugarzaAvailable

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.
Graphene is a gapless, diamagnetic semimetal. However, shaping graphene at the nanoscale, doping, and controlling the atomic structure of their edges can lead to magnetism, or to the induction of electronic and optical gaps. We nanostructure graphene by growing 2D nanoislands and 1D nanoribbons on metallic surfaces, and explore their singular properties. We later transfer them to insulating templates to test their applicability in electronic and optical devices.
The scientific activity of this project is related to the synthesis and characterization of graphene nanoribbons, with the main objectives being:
- Synthesis of nanoribbons with unconventional edge structure and atomically controlled dopants
- Structural, electronic and optical characterization by scanning tunnelling microscopy and spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), and Raman.
The candidate will be carrying out his own experiments in all task related to the project, always with the help of experienced senior researchers. He/she will gather experience on:
- On-surface self-assembly and chemical methods to synthesize 2D materials
- Scanning tunneling microscopy (STM)
- X-ray photoelectron techniques (XPS)
- Low-energy electron diffraction (LEED)
-Ultra-high vacuum techniques (vacuum components, evaporation of precursors, single crystal preparation…)
Recent related publications of the group:
1. Moreno, C. et al. On-surface synthesis of superlattice arrays of ultra-long graphene nanoribbons. Chem. Commun. 54, 9402–9405 (2018).
2. Moreno, C. et al. Bottom-up synthesis of multifunctional nanoporous graphene. Science (80-. ). 360, 199–203 (2018).
3. Parreiras, S. O. et al. Symmetry forbidden morphologies and domain boundaries in nanoscale graphene islands. 2D Mater. 4, 025104 (2017).
4. Garcia-Lekue, A. et al. Spin-Dependent Electron Scattering at Graphene Edges on Ni(111). Phys. Rev. Lett. 112, 066802 (2014).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.
Graphene is a gapless, diamagnetic semimetal. However, shaping graphene at the nanoscale, doping, and controlling the atomic structure of their edges can lead to magnetism, or to the induction of electronic and optical gaps. We nanostructure graphene by growing 2D nanoislands and 1D nanoribbons on metallic surfaces, and explore their singular properties. We later transfer them to insulating templates to test their applicability in electronic and optical devices.
The scientific activity of this project is related to the synthesis and characterization of graphene nanoribbons, with the main objectives being:
- Synthesis of nanoribbons with unconventional edge structure and atomically controlled dopants
- Structural, electronic and optical characterization by scanning tunnelling microscopy and spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), and Raman.
The candidate will be carrying out his own experiments in all task related to the project, always with the help of experienced senior researchers. He/she will gather experience on:
- On-surface self-assembly and chemical methods to synthesize 2D materials
- Scanning tunneling microscopy (STM)
- X-ray photoelectron techniques (XPS)
- Low-energy electron diffraction (LEED)
-Ultra-high vacuum techniques (vacuum components, evaporation of precursors, single crystal preparation…)
Recent related publications of the group:
1. Moreno, C. et al. On-surface synthesis of superlattice arrays of ultra-long graphene nanoribbons. Chem. Commun. 54, 9402–9405 (2018).
2. Moreno, C. et al. Bottom-up synthesis of multifunctional nanoporous graphene. Science (80-. ). 360, 199–203 (2018).
3. Parreiras, S. O. et al. Symmetry forbidden morphologies and domain boundaries in nanoscale graphene islands. 2D Mater. 4, 025104 (2017).
4. Garcia-Lekue, A. et al. Spin-Dependent Electron Scattering at Graphene Edges on Ni(111). Phys. Rev. Lett. 112, 066802 (2014).

atomic scale manipulation, electronic spectroscopy, graphene nanoribbons, materials synthesis, scanning probe microscopy
IBEC-2007. Improving site-specific targeting of nanomedicines for treatment of lung or brain diseases2021-2022IBECTargeted Nanotherapeutics and NanodevicesWEBSITESilviaMuroAvailable

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
CRG-2005. Reconstituting tissue self-organization and collective cell dynamics in early embryonic development via 3D synthetic culture methods2021-2022CRGCell and Tissue DynamicsWEBSITEVerenaRuprechtAvailable

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.
In this research project, we will establish synthetic 3D culture methods that enable to mimic tissue self-organization of early embryonic development in synthetic culture environments. During gastrulation, an unstructured mass of pluripotent embryonic stem cells undergoes cell fate specification and acquires a defined shape, laying the foundation for the future body plan. Morphodynamic shape formation depends on precise spatio-temporal positioning of three distinct germ layers (mesoderm, ectoderm and endoderm) that give rise to different organs of the organism. Both chemical signals (morphogens) and physical stimuli (as geometry, cell density, adhesion and cell deformation) serve as information signals to instruct cell fates and dynamic cell behaviour. Recent work from our lab has identified that mechanical tissue crowding and geometrical boundary constraints from the 3D tissue environment critically influence dynamic cell migration behaviour (Ruprecht et al., Cell 2015). These results highlight the relevance of mechanosensitive signalling pathways and cellular adaption to physical tissue parameters in early embryogenesis. In this research project, we will address how multicellular tissue dynamics and self-organization is controlled by mechanical and physical processes in early embryogenesis. We aim at identifying key molecular and cellular modules that enable cellular information processing of physical tissue parameters and how they regulate single and collective cell dynamics to build the shape of an embryo.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.
In this research project, we will establish synthetic 3D culture methods that enable to mimic tissue self-organization of early embryonic development in synthetic culture environments. During gastrulation, an unstructured mass of pluripotent embryonic stem cells undergoes cell fate specification and acquires a defined shape, laying the foundation for the future body plan. Morphodynamic shape formation depends on precise spatio-temporal positioning of three distinct germ layers (mesoderm, ectoderm and endoderm) that give rise to different organs of the organism. Both chemical signals (morphogens) and physical stimuli (as geometry, cell density, adhesion and cell deformation) serve as information signals to instruct cell fates and dynamic cell behaviour. Recent work from our lab has identified that mechanical tissue crowding and geometrical boundary constraints from the 3D tissue environment critically influence dynamic cell migration behaviour (Ruprecht et al., Cell 2015). These results highlight the relevance of mechanosensitive signalling pathways and cellular adaption to physical tissue parameters in early embryogenesis. In this research project, we will address how multicellular tissue dynamics and self-organization is controlled by mechanical and physical processes in early embryogenesis. We aim at identifying key molecular and cellular modules that enable cellular information processing of physical tissue parameters and how they regulate single and collective cell dynamics to build the shape of an embryo.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.
In this research project, we will establish synthetic 3D culture methods that enable to mimic tissue self-organization of early embryonic development in synthetic culture environments. During gastrulation, an unstructured mass of pluripotent embryonic stem cells undergoes cell fate specification and acquires a defined shape, laying the foundation for the future body plan. Morphodynamic shape formation depends on precise spatio-temporal positioning of three distinct germ layers (mesoderm, ectoderm and endoderm) that give rise to different organs of the organism. Both chemical signals (morphogens) and physical stimuli (as geometry, cell density, adhesion and cell deformation) serve as information signals to instruct cell fates and dynamic cell behaviour. Recent work from our lab has identified that mechanical tissue crowding and geometrical boundary constraints from the 3D tissue environment critically influence dynamic cell migration behaviour (Ruprecht et al., Cell 2015). These results highlight the relevance of mechanosensitive signalling pathways and cellular adaption to physical tissue parameters in early embryogenesis. In this research project, we will address how multicellular tissue dynamics and self-organization is controlled by mechanical and physical processes in early embryogenesis. We aim at identifying key molecular and cellular modules that enable cellular information processing of physical tissue parameters and how they regulate single and collective cell dynamics to build the shape of an embryo.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.
In this research project, we will establish synthetic 3D culture methods that enable to mimic tissue self-organization of early embryonic development in synthetic culture environments. During gastrulation, an unstructured mass of pluripotent embryonic stem cells undergoes cell fate specification and acquires a defined shape, laying the foundation for the future body plan. Morphodynamic shape formation depends on precise spatio-temporal positioning of three distinct germ layers (mesoderm, ectoderm and endoderm) that give rise to different organs of the organism. Both chemical signals (morphogens) and physical stimuli (as geometry, cell density, adhesion and cell deformation) serve as information signals to instruct cell fates and dynamic cell behaviour. Recent work from our lab has identified that mechanical tissue crowding and geometrical boundary constraints from the 3D tissue environment critically influence dynamic cell migration behaviour (Ruprecht et al., Cell 2015). These results highlight the relevance of mechanosensitive signalling pathways and cellular adaption to physical tissue parameters in early embryogenesis. In this research project, we will address how multicellular tissue dynamics and self-organization is controlled by mechanical and physical processes in early embryogenesis. We aim at identifying key molecular and cellular modules that enable cellular information processing of physical tissue parameters and how they regulate single and collective cell dynamics to build the shape of an embryo.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.
In this research project, we will establish synthetic 3D culture methods that enable to mimic tissue self-organization of early embryonic development in synthetic culture environments. During gastrulation, an unstructured mass of pluripotent embryonic stem cells undergoes cell fate specification and acquires a defined shape, laying the foundation for the future body plan. Morphodynamic shape formation depends on precise spatio-temporal positioning of three distinct germ layers (mesoderm, ectoderm and endoderm) that give rise to different organs of the organism. Both chemical signals (morphogens) and physical stimuli (as geometry, cell density, adhesion and cell deformation) serve as information signals to instruct cell fates and dynamic cell behaviour. Recent work from our lab has identified that mechanical tissue crowding and geometrical boundary constraints from the 3D tissue environment critically influence dynamic cell migration behaviour (Ruprecht et al., Cell 2015). These results highlight the relevance of mechanosensitive signalling pathways and cellular adaption to physical tissue parameters in early embryogenesis. In this research project, we will address how multicellular tissue dynamics and self-organization is controlled by mechanical and physical processes in early embryogenesis. We aim at identifying key molecular and cellular modules that enable cellular information processing of physical tissue parameters and how they regulate single and collective cell dynamics to build the shape of an embryo.

Biological Self-organization, biophysics, Cytoskeleton, Mechanobiology, Multicellular dynamics
CRG-2004. Epigenetic reprogramming in mammalian germ cells2021-2022CRGEpigenetic Reprogramming in Embryogenesis and the GermlineWEBSITEBernhardPayerAvailable

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.
In this project, the student would work with germ cells from mouse embryos and/or differentiated in vitro from embryonic stem cells (ESCs). The in vitro approach has the advantage of providing more material and being more amenable to perturbation. On the other hand, germ cells from embryos can provide the accurate biological context for testing the applicability of our findings from the in vitro system. Momentarily, we use this two-system strategy to elucidate the signals and mechanisms responsible for X-reactivation in mouse and human germ cells.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.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.
In this project, the student would work with germ cells from mouse embryos and/or differentiated in vitro from embryonic stem cells (ESCs). The in vitro approach has the advantage of providing more material and being more amenable to perturbation. On the other hand, germ cells from embryos can provide the accurate biological context for testing the applicability of our findings from the in vitro system. Momentarily, we use this two-system strategy to elucidate the signals and mechanisms responsible for X-reactivation in mouse and human germ cells.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.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.
In this project, the student would work with germ cells from mouse embryos and/or differentiated in vitro from embryonic stem cells (ESCs). The in vitro approach has the advantage of providing more material and being more amenable to perturbation. On the other hand, germ cells from embryos can provide the accurate biological context for testing the applicability of our findings from the in vitro system. Momentarily, we use this two-system strategy to elucidate the signals and mechanisms responsible for X-reactivation in mouse and human germ cells.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.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.
In this project, the student would work with germ cells from mouse embryos and/or differentiated in vitro from embryonic stem cells (ESCs). The in vitro approach has the advantage of providing more material and being more amenable to perturbation. On the other hand, germ cells from embryos can provide the accurate biological context for testing the applicability of our findings from the in vitro system. Momentarily, we use this two-system strategy to elucidate the signals and mechanisms responsible for X-reactivation in mouse and human germ cells.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.

Epigenetics, Germ cells, reproduction, X-chromosome reactivation
CRG-2003. X-chromosome reactivation in iPSCs and mouse embryos2021-2022CRGEpigenetic Reprogramming in Embryogenesis and the GermlineWEBSITEBernhardPayerAvailable

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.
In this project, the prospective student would study the function of candidate factors for X-chromosome reactivation in iPSCs and early mouse embryos. The project will involve iPSCs reprogramming and monitoring X-chromosome activity using an XGFP-reporter. Using knockdown and/or CRISPR deletion, the mechanism will be studied, by which the candidate acts on epigenetic reprogramming and at which stage X-reactivation is affected. The student will learn a number of methods including iPSC reprogramming, shRNA knockdown, FACS analysis, immunohistochemistry, RNA-FISH, qPCR, etc.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.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.
In this project, the prospective student would study the function of candidate factors for X-chromosome reactivation in iPSCs and early mouse embryos. The project will involve iPSCs reprogramming and monitoring X-chromosome activity using an XGFP-reporter. Using knockdown and/or CRISPR deletion, the mechanism will be studied, by which the candidate acts on epigenetic reprogramming and at which stage X-reactivation is affected. The student will learn a number of methods including iPSC reprogramming, shRNA knockdown, FACS analysis, immunohistochemistry, RNA-FISH, qPCR, etc.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.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.
In this project, the prospective student would study the function of candidate factors for X-chromosome reactivation in iPSCs and early mouse embryos. The project will involve iPSCs reprogramming and monitoring X-chromosome activity using an XGFP-reporter. Using knockdown and/or CRISPR deletion, the mechanism will be studied, by which the candidate acts on epigenetic reprogramming and at which stage X-reactivation is affected. The student will learn a number of methods including iPSC reprogramming, shRNA knockdown, FACS analysis, immunohistochemistry, RNA-FISH, qPCR, etc.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.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.
In this project, the prospective student would study the function of candidate factors for X-chromosome reactivation in iPSCs and early mouse embryos. The project will involve iPSCs reprogramming and monitoring X-chromosome activity using an XGFP-reporter. Using knockdown and/or CRISPR deletion, the mechanism will be studied, by which the candidate acts on epigenetic reprogramming and at which stage X-reactivation is affected. The student will learn a number of methods including iPSC reprogramming, shRNA knockdown, FACS analysis, immunohistochemistry, RNA-FISH, qPCR, etc.
Besides adding a piece to the X-reactivation puzzle, the student will be immersed within a young team inside a dynamic international research environment at CRG, which will help her/him to gain skills furthering his/her scientific career.

Epigenetics, iPSC-reprogramming, Pluripotency, X-chromosome reactivation
IFAE-2015. Application of machine-learning techniques to background suppression in searches for higgsino pair production with the ATLAS detector2021-2022IFAEIFAE-ATLASWEBSITEAurelioJusteAvailable

The Standard Model (SM) of particle physics provides the most accurate description currently available for the most elementary particles in nature and their interactions. However, this model comes with some inconsistencies, like the so-called “hierarchy problem”, and do not provide solutions to the dark matter problem. Extensions of the SM, such as Supersymmetry, can solve most of those issues at once by predicting new particles that have not been observed yet and that could be produced in proton collisions at the LHC. Typically, these new particles do not leave any trace in any detector and the only recognisable signature is missing energy from the total balance of the proton-proton collision. The total amount of missing energy depends, in general, on the mass of the hypothetical new particle, increasing for heavier particles and vanishing for very light ones. The SM processes that produce similar signatures to those of the new particles are called “background” and its composition also changes with the amount of missing energy in the detector. In this way, most of the background events with low missing energy, if no leptons are present in the final state, are produced purely by QCD processes where quarks and gluons are radiated, resulting in signatures with multiple jets. In this project the student will participate in a search for pair production of higgsinos (supersymmetric partner of the Higgs boson) that later decay into Higgs bosons, resulting in a final state with multiple b-jets and missing energy. The main aim of the study is to enhance the sensitivity of the analysis to light higgsinos and, to this end, machine-learning techniques will be applied in order to reject QCD multi-jet processes and increase the acceptance of supersymmetric particles.

ATLAS, CERN, detector, physics
IRBB-2003. Stress kinase signaling as target for cancer therapy2021-2022IRB BarcelonaSignaling and Cell CycleWEBSITEAngelRodriguez NebredaAvailable

An important part of the group’s work focuses on the stress-activated p38 MAPK signaling pathway, investigating the mechanisms of signal integration by this pathway and its implication in physiological and pathological processes. Our results have provided in vivo evidence for the implication of p38 MAPKs in homeostatic functions, beyond the stress response, and have illustrated how dysregulation of this pathway may contribute to cancer and other diseases. Recently, we have demonstrated important roles for p38 MAPK signaling in tumor progression as well as in the resistance to chemotherapeutic drugs using mouse models. Our work combines studies using genetically modified mice and chemical inhibitors, with experiments in cancer cell lines and biochemical approaches. An important aim of our work is the identification of therapeutic opportunities based on the modulation of p38 MAPK signaling. Ongoing projects in the group address two main topics: (1) Cancer cell homeostasis and chemoresistance mechanisms, and (2) Cross talk between cancer cells and stromal cells.

cancer cell homeostasis, chemotherapy resistance, signaling network, targeted therapy, tumor microenvironment
IFAE-2014. Search for the pair production of vector-like quarks in final states with multiple b-jets2021-2022IFAEIFAE-ATLASWEBSITEAurelioJusteAvailable

Vector-like quarks (VLQs) are predicted by many theories of physics Beyond the Standard Model (BSM) and can provide a natural solution to the hierarchy problem. The VLQs in these theories often couple preferentially to third generation quarks in the Standard Model. This research project will be based on a search for the pair production of VLQs, with subsequent decay of at least one of the VLQs to a top quark and a Higgs or Z boson. The presence of multiple jets originating from b-quarks, and of boosted heavy resonances, in the final state is a powerful discriminant against Standard Model backgrounds. Machine learning algorithms, utilising these distinguishing features, will be investigated to maximise the sensitivity of the analysis to multiple VLQ production and decay modes.

ATLAS, CERN, detector, physics
IFAE-2013. Studies of the non-linearity of the ATLAS Tile Calorimeter2021-2022IFAEIFAE-ATLASWEBSITEIlyaKorolkovAvailable

The TileCal is the central hadronic calorimeter of the ATLAS experiment at the LHC. It is designed for energy reconstruction of hadrons, jets, taus and missing transverse energy. The later is widely believed to be the likely signature of the physics beyond the SM. TileCal is a scintillator-steel sampling calorimeter. The light produced in the scintillator tiles is transmitted to the photomultiplier tubes by wavelength shifting fibres. The photo-tube response is known to be non-linear as a function of the underline anode current or as a function of the interaction rate in the detector. The exact function of the non-linearity is not known at this particular current range and was not taken into account during the LHC run-2 (2015-2018). Analytical understanding of the TileCal non-linearity will permit for slightly enhanced energy measurements in ATLAS experiment for the LHC run-3 (2022-). The goal of the project is to develop analytical expression of the TileCal photo-tubes non-linearity as a function of the LHC instantaneous interaction rate. This can be understood from an analysis of the run-2 detector calibration and collision data. Based on this analytical expression one may introduce dedicated energy corrections already for the LHC run-3 expected to start in 2022.

ATLAS, CERN, detector, physics
IFAE-2012. Studies of the Radiation2021-2022IFAEIFAE-ATLASWEBSITEIlyaKorolkovAvailable

The TileCal is the central hadronic calorimeter of the ATLAS experiment at the LHC. It is designed for energy reconstruction of hadrons, jets, taus and missing transverse energy. The later is widely believed to be the likely signature of the physics beyond the SM. TileCal is a scintillator-steel sampling calorimeter. The light produced in the scintillator tiles is transmitted to the photomultiplier tubes by wavelength shifting fibres. The optical readout components degrade with the advance of the experiment primary due to the irradiation. During the 2015-2018 LHC run-2, the most exposed tiles of the calorimeter had degraded by about 10% of their light yield. The analytical expression for the degradation function for tiles (and for tiles assembled in cells) is not trivial primarily because of the non-uniform distribution of the irradiation field across the detector volume. During the LHC run-3 and run-4 the irradiation levels in the detector may reach values several times above than the one that TileCal originally was designed for. Since the optical components of the TileCal cannot be easily replaced, the radiation hardness of the detector must be understood. The goal of the project is to develop an analytical expression of the tile (cell) degradation as a function of the irradiation in the TileCal by studying the run-2 detector calibration and collision data. Based on this analytical expression one would attempt to derive prediction for the detector degradation during the LHC run-3 (2022-) and run-4.

ATLAS, CERN, detector, physics
IFAE-2011. Machine Learning techniques in the process VBF H with the HGTD detector at the ATLAS experiment2021-2022IFAEIFAE-ATLASWEBSITEMaria PilarCasadoAvailable

The recent approval of the HGTD detector in the ATLAS collaboration makes more necessary a detailed evaluation of potential physics processes in which this detector will help to disentangle signal events from the overwhelming background in the Phase-II of the ATLAS experiment (which will start in 2026). Furthermore, Machine Learning techniques have become very relevant in many disciplines where a very efficient discrimination between two different distributions is carried out. This TFM will combine High Energy Physics techniques with modern Data Analysis tools to optimize the selection of VBF H events from other physics processes with similar topologies.

ATLAS, CERN, detector, physics
IFAE-2010. Analysis optimization for the search of new light scalar bosons using data taken by the ATLAS experiment2021-2022IFAEIFAE-ATLASWEBSITEImmaRiuAvailable

Several theoretical models predict the existence of new scalar or pseudo-scalar bosons beyond the Standard Model of physics. These would be created in top-quark decays together with a charm or up quark. A search looking for these bosons decaying into a pair of bottom quarks is currently in preparation in the mass range between 50 and 150 GeV using data from the ATLAS experiment. The final state under study includes one lepton and several jets, all of which being b-tagged apart from one. The student will work on optimizing the analysis search for the various signal hypothesis and to differentiate it against background. Data will be compared with a combination of Monte Carlo simulation samples for basic kinematical variables. A neural-network algorithm will be implemented and optimized to achieve best signal over background. The analysis will be designed in various selection regions that will need to be optimized.

ATLAS, CERN, detector, physics
IFAE-2009. Search of new charged Higgs bosons using a neural-network algorithm trained with Monte Carlo simulated samples of the ATLAS experiment2021-2022IFAEIFAE-ATLASWEBSITEImmaRiuAvailable

The ATLAS experiment is a multi-purpose experiment installed at CERN. It is the most powerful particle accelerator and collides protons against protons at 13 TeV centre-of-mass energy. After the discovery of the Higgs boson in 2012, it continues to take data and performs Standard Model physics analyses together with searches for new physics Beyond-the-Standard Model. The Two-Higgs Doublet Model is one of the simplest extensions of the Standard Model and foresees the existence of five Higgs bosons, two of which being charged. Using data taken through 2015-2018, ATLAS is searching for charged Higgs bosons decaying into a W boson and a Higgs boson, which decays into a pair of bottom quarks. The student will perform a study of how best distinguish background events from charged Higgs boson decays. A Neural-Network technique will be implemented and trained using the most up-to-date ATLAS Monte Carlo simulation samples. Its performance will be evaluated and optimized using various kinematical variables

ATLAS, CERN, detector, physics
IFAE-2008. Performance of topological trigger algorithms for few benchmark physics analyses in preparation for the new data-taking period in the ATLAS experiment at CERN2021-2022IFAEIFAE-ATLASWEBSITEImmaRiuAvailable

The high-energy physics ATLAS experiment installed at CERN has been collecting data of proton-proton collisions until end of 2018, namely the last data taking period, Run 2. It is currently in a shutdown period preparing the upcoming data taking period to start in 2021, Run 3. The preparation of the so-called topological algorithms to select events using input data from the calorimeters and from the muon system is ongoing. The student will learn about the algorithms, the software and the physics events to be selected during the data acquisition. He/she will compare the topological algorithms acceptance of Standard Model physics events or Beyond-Standard Model events using input data as was built during Run 2 or as is planned for Run 3.

ATLAS, CERN, detector, physics
DCEXS-2013. Deconstructing p53-activated DNA repair mechanisms for tumor suppression2021-2022DCEXSCancer BiologyWEBSITEAnaJanicAvailable

Cancer is a disease that affects one of three of us at some point in our lives. The tumour suppressor gene p53 is mutated in ~50% of human cancers. Many pharma and biotech companies are working towards developing drugs to activate p53 in cancers with wild-type p53, or restoring wild-type p53 function in cancers driven by mutations in p53. However, there have been many difficulties in developing such strategies, and there is still extensive morbidity and mortality associated with cancers bearing p53 mutations. Given the obstacles to developing strategies for targeting wild-type or mutant, further understanding of basic p53 biology is required for successful clinical translation. Recent studies, including ours, have challenged the previously understood model of how the p53 gene is involved in tumour suppression. This research project focuses on understanding the complexity of the p53 network in tumour suppression in different contexts. It will utilize in vitro approaches to investigate p53-dependent mechanisms in solid tumours such as lung, as well as blood cancers.
This is an exacting opportunity to join a newly established laboratory to explore molecular mechanisms of p53 tumor suppression. The role will involve the use of a wide variety of experimental techniques, including CRISPR-Cas9 gene-editing technology, cell culture and flow cytometry. Master student will be train in the laboratory for preparing CRISPR/Cas9 constructs, producing high titer lentiviral particles, flow cytometry, generating and maintaining mutant cell lines, qRT-PCR and Western blot analysis of the target genes in the panel of human and mouse cell lines.

cancer, DNA repair, p53, tumour suppression
ICFO-2002. Superconductivity in twisted bilayer graphene2021-2022ICFOQuantum NanomechanicsWEBSITEAdrianBachtoldAvailable

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.
When two graphene lattices are overlaid and tilted, they can interfere to create a moiré pattern with a long period. At a small angle of about 1.1º, it was showed that the twisted bilayer graphene stack becomes superconducting. At this “magic” angle, the energy dispersion of electrons becomes flat and the electron-electron interaction parameter becomes large. By tuning the carrier density, the twisted bilayer graphene stack becomes a Mott insulator. These properties are similar to those of cuprates and other high-temperature superconductors. Graphene has two key advantages compared to these materials. First, the band structure of monolayer graphene is simple and well understood. Second, the Fermi energy can be tuned by simply adjusting the voltage applied to the gate electrode in order to characterize the whole phase diagram of electrons. The goal of our research is to fabricate new types of electrical devices based on twisted monolayers in order to understand the physics that leads to superconductivity.

cryogenics, electrical measurements, nanofabrication, Superconductivity, twisted bilayer graphene
IRBB-2002. Drug discovery innovation for cancer treatment2021-2022IRB BarcelonaTargeted protein degradation and drug discoveryWEBSITECristinaMayor RuizAvailable

Despite tremendous progress in therapeutic drug development, more than 80% of all human proteins remain beyond the reach of inhibitor-centric traditional drug discovery, including some of the most prolific cancer targets.
Targeted protein degradation (TPD) is based on small-molecule drugs, generally called “degraders”, which induce proximity between a ubiquitin E3 ligase and a target protein of interest. As a result, the target protein is ubiquitinated and then degraded by the proteasome. Overall, the TPD technology represents a novel paradigm in drug discovery that holds the promise to eliminate otherwise undruggable proteins.
Having TPD as a foundational basis, our lab pursues highly interdisciplinary biomedical research that ranges from drug hunting to elucidation of exciting molecular biology. In brief, we develop screening strategies to find degrader compounds with therapeutic interest, and we tackle biological questions that benefit from the high kinetic resolution of TPD or that involve E3 plasticity dysregulation.
The global goal of this master project is to guide the innovation of next-generation anti-cancer therapeutics. Specifically:
1. To innovate drug screenings aiming to find degraders with therapeutic value in cancer.
2. To elucidate the mechanism of action of novel degraders and the phenotypic consequences at a single-cell level resolution.
Chemogenetics, proteomics, CRISPR screens or drug pulldowns are among the approaches that will be learnt.

CRISPR, degraders, drug discovery, screenings, Targeted protein degradation
ICFO-2001. Quantum simulation with ultracold atoms2021-2022ICFOUltracold Quantum GasesWEBSITELeticiaTarruellAvailable

In recent years ultra-cold (nanoKelvin) 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.

Our group has currently a fully operational quantum gas apparatus. There, we focus on the study of two-component potassium Bose-Einstein condensates with adjustable interactions, with two major research lines. On the one hand, we create ultra-dilute quantum liquids in Bose-Bose mixtures. These liquids are eight orders of magnitude more dilute than liquid helium, and form droplets that are self-bound in the absence of any external confinement. Their existence is a direct manifestation of quantum fluctuations in very weakly interacting systems, which makes them ideal testbeds for understanding the role of quantum correlations in quantum many-body physics [Cabrera et al., Science 359, 301-304 (2018)]. On the other hand, we generate artificial gauge fields for neutral atoms, and make them behave as if they were charged particles. We have very recently realized a vector potential that is not static, but instead displays a back-action from matter. This allows us to generate exotic chiral solitons, which only exist when moving along one direction. Our long-term goal here is to engineer various types of dynamical gauge fields in the laboratory.

In summer 2019, we started the construction of a second experimental apparatus. In this project, we aim at realizing artificial solids exploiting ultracold strontium atoms trapped in optical lattices – artificial crystals of light created by interfering laser beams – and manipulating and imaging them at the single-atom level. In the future, we will exploit this setup to both mimic strongly correlated materials (such as high-temperature superconductors and fractional quantum Hall systems), and to explore collective effects in atom-photon interactions.

We offer Master thesis projects on the two experiments. They will be focused on the design and development of a sub-system to be integrated in the experimental apparatus. For these projects, we are looking for candidates with a good background in quantum optics, atomic physics or condensed-matter physics, and a strong motivation for setting up and conducting challenging experiments in a team of three to four people. We offer training in a broad range of cutting-edge experimental techniques (from optics, electronics, ultra-high vacuum technology and computer control to quantum state engineering), as well as in theoretical atomic, quantum, statistical, and condensed matter physics.

atomic physics, Bose-Einstein condensates, Quantum gases, Quantum optics, quantum simulation
DCEXS-2012. The mysterious biology of the most abundant microbial eukaryotes in the surface oceans2021-2022DCEXSBiology and Ecology of Abundant ProtistsWEBSITEDaniel J.RichterAvailable

Which are the most abundant microbial eukaryotic species in the world’s sunlit oceans, and what roles do they play in global marine ecology? Currently, the answers to both these questions remain largely unknown. Microbial eukaryotes (also known as protists) are single-celled and colonial organisms that occupy the size range between bacteria (micrometers) and the smallest multicellular animals (millimeters), a critical position for the function of oceanic food webs. Recent seafaring expeditions, such as the Tara Oceans project, have produced DNA sequence-based catalogs of protists on a global scale. We previously analyzed Tara Oceans data to reveal that only 100 of the approximately 500,000 protist species in the surface ocean make up 50% of total protist abundance. Yet, 92 of these 100 species are unknown to science, and have not even been identified by light microscopy.

The goal of this project is to characterize the biology, interspecies interactions, and ecosystem relevance of these 92 highly abundant, ubiquitous unknown protists. We propose two research and training objectives. First, using a novel isolation approach, we will establish robust laboratory cultures and apply single-cell transcriptome sequencing to produce gene catalogs. Second, we will apply time-lapse light and fluorescence microscopy to understand their life history and behavior and to build hypotheses about their individual and community metabolic potential, followed by laboratory manipulations to test these hypotheses. Overall, we will provide the first glimpse of the morphological, life history, behavioral and transcriptional features of currently unknown globally abundant protists. Discoveries about their biology will have immediate implications for studies of the ecology and community structure of oceanic ecosystems. Finally, we anticipate that our efforts will lead to the establishment of ecologically relevant microbial eukaryotes as new model systems whose biology can be studied intensively in the laboratory.

interspecies interaction, microscopy, new species isolation, protists, single-cell transcriptomics
DCEXS-2011. Characterization of antitumor mechanisms driven by type I interferon2021-2022DCEXSGrupo de Investigación en Proteínas NFAT y Respuesta ImmunológicaWEBSITEJoseAramburuAvailable

Alterations in immune functions not only impair our organism defenses to pathogens but also underlie diseases such as cancer or neurodegenerative, cardiovascular and metabolic disorders. We focus our work on NFAT5, a transcription factor that regulates innate and adaptive immunity in different scenarios, such as inflammation, graft rejection, tumor progression and viral infection. By uncovering circuits by which immune cells tune their function in diverse scenarios, our work can guide innovative approaches that improve antitumor immunotherapy and anti-pathogen defense.

The proposed MSc research lines connect with our recent finding of a unique transcription mechanism that restrains type I interferon (IFN-I) expression to control antiviral responses while preserving hematopoietic stem cell (HSC) function (Huerga Encabo et al. 2020 J Exp Med). Recent works have established that genomic instability in tumor cells releases DNA to the cytosol, triggering IFN-I induction. This response is dually beneficial to control tumor progression as it promotes tumor cell senescence and alerts specific antitumor immunity. We will apply our experience with tumor models, lineage-specific deficient mice, and cutting edge cell and molecular biology approaches to identify new mechanisms that boost antitumor responses by enhancing IFN-I function at two levels i) improving tumor antigen presentation by dendritic cells to cytotoxic T lymphocytes and ii) promoting tumor cell senescence.

Leading recent publications:

Huerga Encabo et al., 2020 J Exp Med
Aramburu and López-Rodríguez, 2019 Frontiers Immunol
Buxadé et al., 2018 J Exp Med
Tellechea et al., 2018 J Immunol
Aramburu et al., 2014 Science Signaling
Berga-Bolaños et al., 2013 Proc Natl Acad Sci USA
Buxadé et al., 2012 J Exp Med
Ortells et al., 2012 Nucleic Acids Res.

Antitumor immune responses, gene expression
DCEXS-2010. Skin microbiome-based sensors2021-2022DCEXSTranslational Synthetic BiologyWEBSITEMarcGüellAvailable

Interested in developing novel sensing mechanisms based on natural skin bacteria? Microbes are very sophisticated molecular machines. We have developed methodologies to modify the skin microbiome in humans (Pätzold et al, Microbiome 2019). We are using the skin microbes to expand the functionalities of the host including sensing the environment or the skin status (sebum secretion, immune state). Sensed information can be registered using real time optical reporters or recorded historically on the genome using CRISPR recording.

We are offering a master thesis position to develop sensing genetic circuits to be embedded into the skin microbiome. This research is funded by a US Department of Defense grant and involves very exciting interactions with international partners. Feel free to reach me if you have any question on the project (marc.guell@upf.edu).

Our laboratory is focused on applied synthetic biology for therapeutic purposes. We have two lines of research, one in technology development for gene therapy, and one in skin microbiome engineering. We are located in the PRBB, an exciting international and cutting-edge scientific environment.

genetic circuits, sensors, skin microbiome, synthetic biology, therapy
DCEXS-2009. Precise engineering of human genomes for therapeutic applications2021-2022DCEXSTranslational Synthetic BiologyWEBSITEMarcGüellAvailable

Interested in developing a new gene writing technology? Natural gene transfer is performed by retrotransposons and retrovirus. We are combining precision of modern CRISPR systems with the efficiency of natural gene transfer mechanisms to achieve precise and efficient writing to genomes.

We are offering a master thesis position to develop this technology combining library screening with mammalian directed evolution. This research is funded by an EU H2020 project with top international partners.

Our laboratory is focused on applied synthetic biology for therapeutic purposes. We have two lines of research, one in technology development for gene therapy, and one in skin microbiome engineering. We are located in the PRBB, an exciting international and cutting-edge scientific environment.

cas9, CRISPR, gene editing, gene therapy, synthetic biology
ICN2-2005. Crossover between band and polaron-hopping in low-dimensional organic conductors2021-2022ICN2Theory & Simulation GroupWEBSITEPabloOrdejónAvailable

The goal of this project is to develop a way to understand the electronic structure of mixed-valence coordination polymers (1D-, 2D-, 3D-) using the simple but very useful Marcus-type approach based on first-principles DFT. We shall explore the conductivity of molecular or polymeric organic systems proceeding through a
small polaron hopping type mechanism. In view of the nature of the problem, i.e. the need to estimate the Marcus parabolas associated with the different oxidation states, the use of constrained DFT is needed. This technique has been recently implemented in the SIESTA code, a popular first-principles tool that is under intense development in our group at Bellaterra. The student will get familiarised with state-of-the-art computational tools to simulate the electronic properties of nanostructures, the use of supercomputing facilities, and the basic theory to describe the physics and chemistry of these organic polymers. This project is part of a collaboration with other theorists and leading experimental teams working on oxalate-type Fe(II)Fe(III) 2D networks.

computational physics/chemistry, Marcus Theory, organic conductors, polarons
IFAE-2007. Gravitational Waves detection using Deep Learning with LIGO/Virgo data2021-2022IFAEVIRGOWEBSITEMarioMartínezAvailable

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.

deep learning, Gravitational waves, VIRGO
ICN2-2004. Unconventional superconductivity in nanowires2021-2022ICN2Theory & Simulation GroupWEBSITEPabloOrdejonAvailable

Recently, superconducting nanowires seem to be the most promising candidates for topological quantum computing through Majorana fermions, which promise to yield fast, stable quantum bits. The idea of Majorana fermions hosted by superconducting nanowires is based on the Kitaev model of one-dimensional p-wave superconductors. The project would focus on more realistic generalizations of the Kitaev model including multiorbital physics together with relativistic effects from spin-orbit coupling. We will study several pairing models between the electrons in a one-dimensional chain by combining models built from first-principles with the Bogoliubov-de Gennes theory. The project will test recent implementations in the SIESTA code, a popular tool for electronic structure calculations based on Density Functional Theory that uses localised atomic orbitals to describe the electronic wavefunctions. The student will gain experience with this powerful tool for nanoscience research, the use of supercomputers, and some scripting/coding, as well as the fundamental physics, and the algorithms required to describe these exciting nanostructures.

computational physics, electronic structure, nanostructures, Superconductivity
DCEXS-2008. Zinc imbalance and cancer progression2021-2022DCEXSLaboratory of Molecular PhysiologyWEBSITERubénVicenteAvailable

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
CRG-2002. Effects of ageing on the ovarian reserve and primordial oocytes2021-2022CRGOocyte Biology and Cellular DormancyWEBSITEElvanBokeAvailable

The student will take part in an ongoing project to understand effects of ageing on oocytes, female germ cells that become eggs. The prospective student will be proficient in confocal microscopy, oocyte isolation and culture at the end of their training. Students with a strong cell biology background are encouraged to apply.

dormancy, fertility, in vitro ovarian culture, oocytes, single cell sequencing
IBEC-2006. Nanoprobes & Nanoswitches III2021-2022IBECNanoprobes & NanoswitchesWEBSITEPauGorostizaAvailable

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.
The general goal is to assess the structure, phase behavior and nanomechanical properties of model membranes, including the presence of glycosphingolipids related to specific pathologies, and associate them to their role processes at the cellular level. The student will be involved in the design and building of supported lipid membranes, and their characterization using force spectroscopy (indentation and tube-pulling) based on AFM. The student will be trained on lipid vesicles and membranes preparation, surfaces functionalization, and to work with SPMs techniques. He/she will also learn on bibliographic search, data treatment and presentation (written and oral) of the results. The student will incorporate to the Nanoprobes & Nonsnitches research group and will actively participate in the meetings and discussions. He/she will acquire basic competences related to the experimental work in a multidisciplinary lab on nanobiotechnology.

atomic force microscopy, biophysics, force spectroscopy, lipid membrane, nanomechanics
IBEC-2005. Nanoprobes & Nanoswitches II2021-2022IBECNanoprobes & NanoswitchesWEBSITEPauGorostizaAvailable

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.
Single molecule techniques can provide physical information on biological processes with molecular resolution and allow the integration of experimental set-ups that reproduce the physiological conditions. They provide information free from averaging over spatial inhomogeneities, thus revealing signatures that are normally obscured by the ensemble average in bulk experiments.
The general goal is to evaluate at the single molecule level the specific conditions that allow for an effective protein-protein ET. We use scanning probe microscopies, SPMs (scanning tunneling and atomic force microscopies and spectroscopies -STM and AFM-), to evaluate immobilized proteins under electrochemical control.
The student will perform studies at the nanoscale using SPMs to measure ET currents and interaction forces between partner proteins, under controlled environmental and biologically relevant conditions (electrochemical potential, temperature, pH, ionic environment). The student will learn to work with SPMs but also on protein immobilization protocols, surface functionalization, electrochemical studies. He/she will also learn on bibliographic search, data treatment and presentation (written and oral) of the results. The student will incorporate to the Nanoprobes & Nanoswithces research group and will actively participate in the meetings and discussions. He/she will acquire basic competences related to the experimental work in a multidisciplinary lab on nanobiotechnology.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-2004. Nanoprobes & Nanoswitches I2021-2022IBECNanoprobes & NanoswitchesWEBSITEPauGorostizaAvailable

The objective of the research line on nanoswitches is to develop molecular switches that are regulated with light in order to manipulate and functionally analyze receptors, ion channels and synaptic networks in the brain. These tools are synthetic compounds with a double functionality: They are pharmacologically active, binding specifically to certain proteins and altering their function, and they do so in a light-regulated manner that is built in the same compound usually by means of photoisomerizable azobenzene groups. Recent projects in this area include the development of light-regulated peptide inhibitors of endocytosis named TrafficLights and the synthesis of small molecule photochromic inhibitors to manipulate several G protein-coupled receptors like adenosine A2aR and metabotropic glutamate receptors mGlu5. In addition, some of these light-regulated ligands also bear an additional functionality: a reactive group for covalent conjugation to a target protein. Examples include a photochromic allosteric regulator of the G protein-couple receptor mGlu4 that binds irreversibly to this protein and allows photocontrolling its activity in a mouse model of chronic pain and a targeted covalent photoswitch of the kainate receptor-channel GluK1 that enables photosensitization of degenerated retina in a mouse model of blindness. We also demonstrated for the first time two-photon stimulation of neurons and astrocytes with azobenzene-based photoswitches.
Students can expect to learn the relevant techniques for the proposed project (from synthetic chemistry to electrophysiology and fluorescence imaging, in vitro and in vivo) and to work independently within a team of highly multidisciplinary and motivated researchers.

optogenetics, photopharmacology
IFAE-2006. A background model for the MAGIC telescopes2021-2022IFAEGamma-Ray AstronomyWEBSITECosimoNigroAvailable

Outline:
Imaging Atmospheric Cherenkov Telescopes (IACT) represent one of the main ground-based instruments for gamma-ray astronomy. Computing the flux of gamma-ray sources is typically performed with aperture photometry techniques, allowing to estimate the flux of only one source in the field of view of the telescope. Estimating the background of the telescope (constituted by cosmic rays identified as gamma rays) could allow not only to estimate the flux of many sources in the field of view, but also to consider their morphology (spatial extension). The objective of the thesis will be to build a background model for the MAGIC telescopes starting from observations devoid of strong gamma-ray signals. The background model will be then tested with recently developed open-source analysis tools for gamma-ray astronomy and the results compared with those obtained with the standard MAGIC proprietary software.

Skills that will be acquired:
The student will acquire a knowledge of the operational principle of an IACT, and will familiarise himself/herself with statistical methods for data analysis. He/she will improve his/her coding skills by using open-source analysis tools written both in C++ and python.
No previous programming knowledge is required.

background modelling, Data Analysis, gamma rays, imaging atmospheric Cherenkov telescopes
IFAE-2005. Which process explains the brightest emission of Flat Spectrum Radio Quasars?2021-2022IFAEGamma-Ray AstronomyWEBSITECosimoNigroAvailable

Active Galactic Nuclei (AGN) - galaxies hosting in their centre a supermassive black hole - are the most powerful, persistent sources in the universe. A small percentage of them presents a relativistic outflow of plasma whose electromagnetic emission spans from radio to gamma-ray energies. Flat Spectrum Radio Quasars (FSRQ) are the class of jetted AGN with the highest observed luminosity in gamma rays. Their spectrum in this wave band is commonly interpreted as due to relativistic electrons accelerated in the jet that undergo Compton scattering with photon fields generated by other AGN components (usually emitting lines or thermal spectra in the infrared or optical waveband). For FSRQ there is growing observational evidence that the actual region where the gamma-ray emission is generated resides far away from the afore mentioned target components, leading us to consider – given the absence of other targets - if gamma rays could not be generated within the jet itself, specifically by the interaction between different regions of plasma.
The objective of the thesis will be the computational implementation of a simplified model to account for the emission generated by the interaction of different jet sub-structures. This model will then be applied to observed FSRQ flux measurements.

Skills that will be acquired:
The student will acquire an introductory knowledge of active galaxies and will become familiar with radiative processes in astrophysical environments and their computational implementation. On the technical side he/she will improve his/her coding skills by working on the python code modelling AGN developed within the gamma-ray group.
No previous programming knowledge is required.
https://github.com/cosimoNigro/agnpy
https://agnpy.readthedocs.io/en/latest/

active galactic nuclei, blazars, jets, MWL astrophysics, radiative processes
IFAE-2004.Constraining the parameter space modelling the emission of jetted Active Galactic Nuclei2021-2022IFAEGamma-Ray AstronomyWEBSITECosimoNigroAvailable

Outline:
Active Galactic Nuclei (AGN) - galaxies hosting in their centre a supermassive black hole - are the most powerful, persistent sources in the universe. A small percentage of them presents a relativistic outflow of plasma whose electromagnetic emission spans from radio to gamma-ray energies. In the most commonly accepted scenario the spectrum of these sources, characterised by two distinct non-thermal components, is interpreted as a result of the radiative processes of electrons accelerated to relativistic energies. Accounting for all the physical processes generating the electromagnetic spectrum results – in the simplest scenario - in a parameter space with 7 dimensions. These large parameter spaces challenge common minimisation algorithms handling them while fitting experimental flux measurements. Nonetheless, observational features and measured quantities can be used to constraint the model parameter space. So far this has been studied only for the simplest-case scenario, namely when the highest energy component of the spectrum is generated by Compton scattering of the low-energy one. The objective of the thesis will be to reprise such studies and expand them considering more general target photon fields for the Compton scattering producing the high-energy emission.

Skills that will be acquired:
The student will acquire an introductory knowledge of active galaxies and will become familiar with radiative processes in astrophysical environments and their computational implementation. On the technical side he/she will improve his/her coding skills by working on the python code modelling AGN developed within the gamma-ray group.
No previous programming knowledge is required.
https://github.com/cosimoNigro/agnpy
https://agnpy.readthedocs.io/en/latest/

active galactic nuclei, blazars, jets, MWL astrophysics, radiative processes
IBEC-2003. Optical magnetometry for skeletal muscle biomagnetic analysis2021-2022IBECBiosensors for BioengineeringWEBSITEJavierRamon AzconAvailable

The Biosensors for Bioengineering research group develops multi-tissue organs-on-a-chip (OOC) and integrating sensing technology with tissue engineering. Within this scope, we use in situ biosensors to study insulin release under external stimuli, changes in glucose levels, and myokines secreted by skeletal muscle (multi-OOC approach)1. This project will mimic the complex native muscle structure and organization using precursor cells encapsulated in 3D scaffolds. They support the growth and differentiation of progenitor cells and provide 3D environments to cells. We have developed hybrid biomaterials with tunable mechanical and electrical properties that give structure and support to the cells, and they are biocompatible2,3. This project's framework will optimize biomaterials to improve other muscle cells' functionality, longevity, and mechanical and electrical properties. Here we partner with ICFO's Atomic Quantum Optics group to investigate myotube conductivity using exquisitely sensitive quantum devices known as optically pumped magnetometers (OPMs), which elsewhere are deployed for studies of brain and heart magnetism in vivo, i.e., magnetoencephalography and magnetocardiography4,5.

The project's main objective is to monitor myotubes' electrical conductivity and associated magnetic field response. The expectation is for OPMs to allow real-time magnetomyography in the OOC while avoiding invasive electrode placement, unlike direct conductivity measurements6. Tasks: (1) characterize the MMG signal at the myotube level, such as the orientation of the biomagnetic field relative to the cell and temporal response to a single action potential, (2) Identify and characterize responses to chemical stimuli (e.g., drugs), introduced to the OOC.

1. Ortega, M. A. et al. Muscle-on-a-chip with an on-site multiplexed biosensing system for in situ monitoring of secreted IL-6 and TNF-α. Lab Chip 19, 2568–2580 (2019).
2. García-Lizarribar, A. et al. Composite Biomaterials as Long-Lasting Scaffolds for 3D Bioprinting of Highly Aligned Muscle Tissue. Macromol. Biosci. 18, 1800167 (2018).
3. Hernández-Albors, A. et al. Microphysiological sensing platform for an in-situ detection of tissue-secreted cytokines. Biosens. Bioelectron. X 2, 100025 (2019).
4. Knappe, S., Sander, T. & Trahms, L. Optically-Pumped Magnetometers for MEG BT - Magnetoencephalography: From Signals to Dynamic Cortical Networks. in (eds. Supek, S. & Aine, C. J.) 993–999 (Springer Berlin Heidelberg, 2014). doi:10.1007/978-3-642-33045-2_49.
5. Limes, M. E. et al. Portable Magnetometry for Detection of Biomagnetism in Ambient Environments. Phys. Rev. Appl. 14, 11002 (2020).
6. Garcia, M. A. & Baffa, O. Magnetic fields from skeletal muscles: a valuable physiological measurement? Frontiers in Physiology vol. 6 228 (2015).

optically pumped magnetometer, quantum technology, skeletal muscle, tissue engineering
DCEXS-2007. Unveiling the coordination between progenitor dynamics and tissue morphogenesis during neural development2021-2022DCEXSDevelopmental NeurobiologyWEBSITECristinaPujadesAvailable

The assembly of functional neural circuits requires the specification of neuronal identities and the execution of developmental programs that establish precise neural network wiring. Our main biological interest 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.
The main goal of this proposal is to reconstruct neurogenesis and the emergence of coordinated neuronal activity in the zebrafish hindbrain by comprehensive tracking of neuronal lineages, trajectories, movements, and molecular identities. This will build up in previous knowledge and expertise from the laboratory (Voltes et al, Development 2019; Letelier et al, PNAS 2018; Dyballa et al, eLife 2017, Zecca et al, JNeurosc 2015; Calzolari et al, EMBOJ 2014). The fellow will be involved in addressing several of these questions and will take full advantage of the zebrafish experimental toolkit available in my lab: a combination of genetics, -OMICS, in vivo 4D-imaging and functional studies.This technological diversity offers the opportunity to examine directly in vivo the roles of the cell interactions, intercellular signals, and gene regulatory mechanisms proposed from molecular biology studies.

cell lineage, cell progenitors, in vivo imaging, neurogenesis, zebrafish
IFAE-2003. 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 leptons2021-2022IFAEATLASWEBSITEPilarCasadoAvailable

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
CRG-2001. Cross species genome annotation2021-2022CRGComputational Biology or RNA ProcessingWEBSITERodericGuigoAvailable

Understanding Earth’s biodiversity and responsibly administrating its resources is among the top scientific and social challenges of this century. The Earth BioGenome Project (EBP) aims to sequence, catalog and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years (http://www.pnas.org/content/115/17/4325). The outcomes of the EBP will inform a broad range of major issues facing humankind, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. It will contribute to our understanding of biology, ecology and evolution, and will facilitate advances in agriculture, medicine and in the industries based on life: it will, among others, help to discover new medicinal resources for human health, enhance control of pandemics, to identify new genetic variants for improving agriculture, and to discover novel biomaterials and new energy sources, among others.
The value of the genome sequence depends largely on the precised identification genes. The aim of the research project is to develop a gene annotation pipeline that produces high quality gene annotations that can be efficiently scaled to more than one million species. Our group has a long-standing interest in gene annotation. Roderic Guigo developed one of the first computational methods to predict genes in genomic sequences (geneid, Guigó et al, 1992), which has been widely used to annotate genomes during the past years. On the other hand, we are part of GENCODE, which aims to produce the reference annotation of the human genome. Within GENCODE we have developed experimental protocols to efficiently produced full-lengh RNA sequences.
Our pipeline will be based on identifying the genes that can be precisely predicted computationally in a given species, subtract them from RNA samples, and produced high quality RNA sequences for genes that are more difficult to annotate.

bioinforamtics, Earth BioGenome Project, gene annotation, genomics
IFAE-2002.The ESA Euclid Dark Energy Survey2021-2022IFAEEUCLIDWEBSITECristóbalPadillaAvailable

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 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 to increase the performance of the galaxies characteristics detected in the Euclid data, such is their classification, shape and distance for the observation point. We can also explore the use 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-2001. Quantum annealing with coherent superconducting qubits2021-2022IFAEQuantum Computing Technology GroupWEBSITEPolForn-DíazAvailable

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 operate the first generation of prototype quantum annealers developed at IFAE. The MsC candidate will join the team efforts in studying quantum annealing protocols that can later be implemented in the quantum annealers operated by the IFAE group.

quantum annealing, Quantum computation, superconducting qubits
IBEC-2002. Understanding Amyloid Nucleation2021-2022IBECPhase Transitions in Health and DiseaseWEBSITEBenedettaBolognesiAvailable

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 its effect on cell viability, thanks to a systematic approach that couples large scale selection assays to high-throughput DNA sequencing. As a result, we will decipher how alterations in protein sequence translate into different physical states and how those can lead to cellular toxicity and disease. The lab provides opportunities of training ranging from yeast genetics to confocal microscopy and statistical analysis of big data. After discussing with the supervisor, the student will be able to choose which skills to strengthen the most. The student will for sure receive training in performing large selection assays in S.cerevisiae as well as in mammalian cell lines. In addition the student will take part in the analysis of the sequencing data and in the biophysical validation of our findings.

Amyloid, deep sequencing, neurodegeneration, Prions
ICN2-2003. Topological structures in hybrid ferroelectric-ferromagnetic systems2021-2022ICN2Oxide NanophysicsWEBSITENeusDomingo MarimonAvailable

With the end of Moore’s law in sight, new schemes must be devised to achieve energy efficient, high density and high-speed data storage and processing. One emerging concept in today’s condensed-matter physics that may fuel next-generation information technology is topology. Topological phenomena in real space can give rise to interesting objects (for instance magnetic skyrmions), which are topologically protected, i.e. endowed with an energy barrier associated with a change in their topology class. These solitonic objects have been found mainly in magnetic materials like ferromagnets and there are very recent reports that ferroelectrics may also be able to host them. Interestingly, antiferroic orders like antiferromagnetism or antiferroelectricity would provide extra properties e.g. a faster motion or an increased robustness.
In this project the student will work on the preparation, study and characterization of topological structures in hybrid ferroelectric-magnetic/antiferromagnetic heterostructures with nanoscale dimensions looking for the coupling of ferroic and antiferroic properties and the appearance of topological structures. External stimulis such as magnetic fields and strain will be used to control and modify them. The main experimental tools to be used, in which the student will be trained are scanning probe microscopies such as Piezoresponse Force Microscopy and Magnetic Force Microscopy at room and low temperatures. Success in these endeavors will establish topological antiferroic systems as a novel versatile platform for future energy-efficient nanoelectronics.

antiferroics, atomic force microscopy, ferroelectics, ferromagnetics, nanostructures, skyrmions
ICN2-2002. Application of ferroelectric materials for H2 production2021-2022ICN2Oxide NanophysicsWEBSITENeusDomingo MarimonAvailable

Hydrogen is an essential gas and a prominent candidates as a source of energy, but economically viable and green production methods are still not available. State of the art research is looking for an innovatives routes to inexpensive, clean and sustainable hydrogen production. Our group is currently doing research to harnesses electromechanical and related phenomena at the nanoscale to overcome the limitations of existing chemical approaches for H2 production using current methods such as electrolysis or photocatalysis. We envisage the transformation of mechanical into chemical energy using piezoelectricity and flexoelectricity to create charges available for water splitting under the novel concept of piezocatalysis and flexocatalysis, using strain gradients caused by bending, and exploiting the internal electric fields of ferroelectric and polarized materials to improve the separation of charges and avoid recombination. Although ferroelectric materials (FE) are widely used in technology, fundamental research in ferroelectricity at the nanoscale is just beginning to understand the extent to which FE states are intrinsically inseparable from surface electrochemical states in polar materials. A deeper understanding, one that can define the coupling of surface electrochemistry and the mechanisms of internal and external screening of FE polarization, or the nature of charge transfer at polar interfaces, is yet to be achieved.
The general goal of the master project is to seek into energy conversion processes mediated by ferroelectricity to harvest green energies into chemical redox reactions such as photochemistry, pyrochemistry or ferrochemistry and piezochemistry, with the use of FE. We will apply these materials in hybrid electrodes for electrolysis cells, to tune oxidation and reduction reactions in piezocatalysis, seeking for more efficient production of H2. The student will be trained to use surface science techniques such as Atomic Force Microscopy and Ambient Pressure XPS and to operate electrolysis cells under different conditions to study reduction and oxidation evolution reactions.

energy harvesting, Ferrocatalysis, ferroelectrics., flexocatalysis, piezochemistry
IRBB-2001. Understanding stress adaptation2021-2022IRB BarcelonaCell Signaling groupWEBSITEEulàliade NadalAvailable

We aim to unravel how cells detect and respond to environmental changes. We focus our studies on the characterisation of stress signal transduction pathways, especially those regulated by MAP kinases of the Hog1/p38 family, also known as the stress-activated MAP kinases (SAPKs). Proper adaptation to stress involves the modulation of several basic aspects of cell biology, among them the cell cycle and gene expression. Using S. cerevisiae budding yeast as a model organism, as well as higher eukaryotic cells, we are dissecting the molecular mechanisms underlying cell response to changes in the extracellular environment and characterising the adaptive responses required for cell survival.
Research lines:
- SAPK signalling: Using quantitative data in single cells and mathematical modelling, together with mutational analyses, we study the basic signalling properties of stress-responsive MAP pathways and how to alter them.
- SAPK targets: Using proteomics, biochemistry and genetics, our main goal is to identify new targets for SAPKs and thus widen our understanding of cellular adaptation to stress. This information is expected to facilitate the characterisation of the bases of adaptation in eukaryotes.
- Cell cycle control: SAPKs act in several phases of the cell cycle to allow prompt response to extracellular stimuli and the maintenance of cell integrity. We are uncovering the mechanisms by which Hog1 and p38 SAPKs regulate the cell cycle.
- Regulation of mRNA biogenesis: SAPKs control critical steps of mRNA biogenesis and are thus key regulators of stress-responsive gene expression. Our main aim is to determine the contribution of multiple factors to overall gene expression in response to stress. We are also using genome-wide CRISPR screening to identify essential genes for stress adaptation.

Cell cycle, MAPK, Signaling, Stress, Transcripcion
DCEXS-2006. Identification of a plasma lipidomics signature underlying the beneficial health effects of tyrosol supplementation in individuals at high cardiovascular risk.2021-2022DCEXSIntegrative Pharmacology and Systems Neurosciences Research GroupWEBSITERafaelde la TorreAvailable

This project is linked to a research line whose aim is to understand the health benefits provided by dietary phenolic compounds and the use of nutraceuticals as therapeutic tools in the prevention of cardiovascular and neurodegenerative diseases. In this context, we performed a randomized, crossover, controlled nutritional intervention study in individuals at high cardiovascular risk (n=33) who received white wine, white wine plus capsules containing tyrosol (a dietary antioxidant), and water. We found that the supplementation with tyrosol promoted cardiovascular health-related benefits although further research is warranted to better understand the biological mechanisms responsible for these effects. Lipidomics is a relatively new emerging discipline with the great potential of elucidating the biochemical mechanisms underlying alterations in lipid metabolism.
The first objective of this project is to study the alterations in lipid metabolism induced by the intervention with white wine and white wine plus tyrosol. To do so, a targeted lipidomics analysis in plasma samples of participants of the previously mentioned study will be performed. The second objective of this study is to evaluate the correlation between clinical parameters of the study participants and specific lipid species in order to find biomarkers.
The student will have the possibility to actively participate in this research project, to acquire hands-on experience in an analytical laboratory, as well as to be trained on sample preparation and analysis using the state-of-the-art analytical equipment for lipidomics (liquid chromatography coupled to tandem mass spectrometry; LC-MS/MS). Additionally, the student will receive personalized training on how to integrate the results, perform statistical analysis and interpret the obtained data.

cardiovascular disease risk, dietary antioxidants, Lipidomics, nutrition., nutritional intervention studies
ICN2-2001. Advanced Electron Nanoscopy2021-2022ICN2Advanced Electron Nanoscopy (GAeN)WEBSITEJordiArbiolAvailable

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.
Our research group is closely collaborating with Microsoft on its particular approach to achieve this enormously ambitious goal, which is taking advantage of Majorana pairs as the building blocks for the generation of qubits, which are the fundamental units of information in quantum computation.
According to theory, the configuration that would suit this application the most is the interface between a semiconductor and a superconductor, and an appropriate way to build them is to arrange them in a nanowire, which creates the so-called concept of proximitized nanowires. More concretely, the semiconductor thought to present the best properties would be InSb (although different approaches are being done with InAs, too), and Al or NbTiN are usually used as the superconductor, due to their theoretical transition to topological phase under certain chemical potential and external applied magnetic field conditions. In fact, reaching the material’s topological phase is a fundamental requirement to achieve the Majorana Zero Modes (MZMs), and for them to materialize it is mandatory to create thoroughly ordered and epitaxial heterojunctions, as well as perfectly grown materials (as well as specific requirements for each of the materials implied), that avoid the disorder-based scattering that can prevent the transition or even the failure of the topological regime. As mentioned before, the major project would be devoted to the atomic resolution (S)TEM characterization and further structural and elemental analysis of these devices, as a fundamental part of the global process of optimization of the system for the best achievement of the conditions stated previously.
Incredible efforts are being made to avoid the so unwanted decoherence of the electrons and to directly apply the signatures of MZMs (basically conductance peaks) into real devices for quantum computing, as up to date, the total number and stability of the created qubits is not enough for a functional quantum processor. By the way, these qubits are based on binary gates that control the interaction between the Majorana pairs, and it is actually this interaction what can produce the quantum phenomenon based on the superposition of states. Indeed, direct observation of the theoretical properties of the MZMs is still lacking, which is really challenging but encouraging too, to be able to help to achieve this as soon as possible.
The general goal of the project would be the structural and compositional atomic scale analysis, mainly via STEM and related electron spectroscopy techniques of the primordial materials involved in the creation of the Majorana-based qubits. In this way, the initial data obtain will help to perform a structural and atomistic modelling of these nanostructures, in order to achieve a higher understanding of their nature and how the nanofabrication processes affect their integrity, obtaining a deep knowledge on their growth mechanisms and further physical properties. All the knowledge obtained will eventually give useful feedback to the device’s manufacturers that will help to create higher quality devices and more stable quantum states.

atomic models, Quantum nanomaterials, scanning transmission electron microscopy
DCEXS-2005. Targeting a nanomedicine to pancreatic tumor2021-2022DCEXSIntegrative Biomedical Materials and Nanomedicine LabWEBSITEPilarRivera GilAvailable

The student will validate in vitro (2D and 3D culture cell models) the degradation and drug release kinetics of a as-synthesized nanomedicine. The nanomedicine consist of hollow nanocapsules loaded with paclitaxel.

Nanomedicine, pancreatic cancer, targeted therapy
DCEXS-2004. Neuronal calcium intracellular signalling in Alzheimer’s disease2021-2022DCEXSMolecular PhysiologyWEBSITEFrancisco JoséMuñoz LópezAvailable

Alzheimer's disease (AD) is the most common cause of dementia affecting more than 47 million people worldwide, being a major public health problem with a high economic impact. Due to the progressive increase in life expectancy, it has been proposed that its prevalence will triple in the next 30 years.
EA is characterized by the accumulation of amyloid ß-peptide (Aß) which aggregates into ß-sheets forming neurotoxic oligomers and fibers. The fibers accumulate in the senile plaques of the cerebral parenchyma while the oligomers initiate the damage producing synaptotoxicity that will eventually produce neuronal death. Therefore the production and toxicity of Aß aggregates are determinants in the onset and progression of AD.
There are many experimental evidences that calcium dysregulation is related to the pathophysiology of the disease affecting to synaptic transmission, neuronal death and even increasing Aß production. Our group has recently screened 5,154 mutants of S. cerevisiae that overexpress Aβ, identifying a large number of genes involved in amyloid pathology. Of these we have selected 9 genes that regulate homeostasis and calcium signaling that have not been related to AD at the present time.
HYPOTHESIS: Based on previous studies by our group and other laboratories, we propose the study of the importance of calcium regulation in the pathophysiology of AD by characterizing new genes, not previously related to AD, that play key role in Aß neurotoxicity and production.
OBJECTIVES:
1. Characterization of the new molecular mechanisms mediated by calcium that affect Aß-induced toxicity. The mammalian orthologs of yeast genes that affect Aβ-induced toxicity will be studied in human neuroblastoma cells (SH-SY5Y) and in primary cultures of mouse hippocampal neurons to study their pathophysiological role in neurons. In this study we will focus on the SURF4 protein because of its possible direct relationship with the Ca2 + Store-Operated (SOC).
2. Study of the effect of calcium signaling on Aß production. Characterization of the role of SPCA1 in the production of amyloid through the study of intracellular trafficking of APP, beta- and gamma-secretases and Aß itself.

Alzheimer's Disease, Amyloid, BACE1, calcium, oxidative stress
DCEXS-2003. Structure, function and pharmacology of ion channels: relevance to neurological disorders2021-2022DCEXSLaboratory of Molecular PhysiologyWEBSITEJosé ManuelFernández FernándezAvailable

We are interested in the functional characterization of novel genetic, molecular and cellular mechanisms underlying the pathogenesis of neurological disorders, with focus on hemiplegic migraine (HM), epileptic encephalopathy and hereditary forms of ataxia. In this sense, we have identified new genetic alterations in the CACNA1A gene (coding for the pore forming alpha subunit of the high-voltage activated CaV2.1 (P/Q) calcium channel) in a clinical background of these neurological disorders. They affect not just the structure and the biophysical features of CaV2.1 channels, but also their modulation by regulatory proteins (G proteins and SNARE proteins of the vesicle docking/fusion machinery). We also study the regulation by glycosilation of the activity and membrane trafficking of CaV2.1 and mechanosensitive Piezo channels, as Phosphomannomutase Deficiency (PMM2-CDG) (the most frequent congenital disorder of N-linked glycosylation (CDG)) includes neurological alterations triggered by mild cranial trauma and shared with patients carrying CACNA1A mutations. In an international collaboration we are now developing CaV2.1 selective tool molecules capable of reversing the functional consequences of both CACNA1A human mutations linked to HM and channel hypoglycosilation, and exploring their potential to produce a treatment for these neurological pathologies and migraine in general.
For our research we employ techniques of molecular and cellular biology in combination with 3D-structural modelling, electrophysiology and calcium imaging to study the above mentioned ion channels in heterologous expression systems and neurons from wild-type and disease model knock-in mice. Similar analysis will be performed in fibroblasts of patients and healthy volunteers, and iPSC-derived neurons from those fibroblasts.

electrophysiology, Hypoglycosylation, mechanosensitive Piezo channels, Neurological disorders., neuronal voltage-gated calcium channels
DCEXS-2002. TF binding affected by methylations2021-2022CRGStructural BioinformaticsWEBSITEBaldoOlivaAvailable

CpG methylation can directly repress transcription by preventing binding of some transcription factors (TFs) to their recognition motifs1. Lea et al. developed mSTARR-seq2, a method that assesses the causal effects of DNA methylation on regulatory activity at genomic high-throughput level. Our objective is to predict the changes of TF binding caused by methylation. First, we will build a database of methylated DNA binding with known TF binding using data of Yin et al.1 and Lea et al.2. Then, we will infer the effect from the comparison of bound TF binding sites with and without methylations: using the dataset of UniBind3 and the predictions of Viestra et al.4 to select binding sites vs TFs. We will select the tracks from UCSC Genome Browser with assays of DNA methylation (i.e. Methyl-RBBS). We will compare the percentage of methylated cytosines between the binding site and any other location in the genome and split the results in three categories: 1) the ratio of methylation is lower than expected (repression); 2) the ratio of methylation is higher than expected (activation).; and 3) the methylation has no effect on TF binding. The effect of disruption (1) will be used to generate statistic potentials specific of disruption. With the new bindings (2) we will generate statistic potentials specific of methylated cytosines. Finally, we will test the capacity of predicting TF disruptions after cytosine methylation and TF-DNA new bindings with PWMs for methyl cytosines. The method will be validated using independent sets of training and validation (i.e. using data of ENCODE).

References

1 Yin, Y. et al. Science 356, doi:10.1126/science.aaj2239 (2017).
2 Lea, A. J. et al. Elife 7, doi:10.7554/eLife.37513 (2018).
3 Gheorghe, M. et al. Nucleic Acids Res 47, e21, doi:10.1093/nar/gky1210 (2019).
4 Vierstra, J. et al. Nature 583, 729-736, doi:10.1038/s41586-020-2528-x (2020).

cis-regulation, CpG methylation, Epigenetics, Transcription Factors
DCEXS-2001. Controlling the cell cycle: elaborating an integrative map of DNA synthesis regulators and tumor progression2021-2022DCEXSOxidative Stress and Cell Cycle Group (OSCCG)WEBSITEJoseAytéAvailable

We are ultimately interested in deciphering the mechanisms that control cell cycle progression. Inactivation of the Retinoblastoma protein (RB) leads to unregulated cell cycle progression promoting cell growth, genomic instability and aneuploidy, hallmarks of tumor progression. RB activity is achieved through binding the E2F family of transcription factors. It is well known that a tumor process is very complex, accumulating secondary mutations that eliminate the brakes to the cell cycle. Even though many regulators of the RB-E2F are known, an integrative view of all the regulatory events controlling the G1/S transition is required to anticipate putative interventions able to block proliferative processes.
The candidate will characterize the regulation of the yeast MBF complex (functional homolog of human RB-E2F). The regulated activity of this complex is also essential for the G1/S transition since cells with hyperactive MBF have genomic instability. The candidate will perform 2 whole-genomic screens searching for global regulators of MBF. We have developed a reporter strain in the laboratory that measures MBF activity in vivo as an YFP/RFP output, either on FACS or on an automated fluorescence microscope platform. This reporter strain will be introduced in a yeast KO deletion library. These screenings will allow the creation of a complete map with all the MBF regulators and, by extrapolation, we will establish the nodes that regulate the RB pathway.
Required student background: A high motivation towards a scientific career in projects related to basic research, which is the research that is carried out in our group, is a must. Also, a solid background in Genetics, Cell Biology and Molecular Biology is a requirement to carry out this project. Since the project includes bar-code sequencing of pools of KO strains, previous experience with ultra-sequencing will be appreciated. Similarly, previous work with yeast and/or cell cycle will be a plus.

Cell cycle, DNA damage, G1/S transition, replicative stress, transcription
IBEC-2001. Selection of DNA aptamers against Plasmodium falciparum early blood stages2021-2022IBECNanomalariaWEBSITEXavierFernàndez-BusquetsAvailable

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 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.

The Master student will work on the design of a SELEX method for the selection of DNA aptamers against early blood stages of P. falciparum, which are the main parasite forms present in the circulation. This new generation of aptamers can offer a better diagnosis alternative compared to late stages, which are sequestered on the capillary walls and therefore less abundant in blood. The techniques to be used include P. falciparum in vitro cultures, fluorescence confocal microscopy, flow cytometry, and electron microscopy. The Master work will be done at the Nanomalaria Group (https://www.fernandezbusquets.eu/), a joint unit between IBEC and the Barcelona Institute for Global Health.

aptamers, Malaria, Plasmodium falciparum, SELEX